From chiaracaronna at hotmail.com  Thu Feb  1 11:46:26 2007
From: chiaracaronna at hotmail.com (Chiara Caronna)
Date: Thu, 01 Feb 2007 16:46:26 +0000
Subject: [SciPy-user] error importing scipy
Message-ID: <BAY114-F38BCD4C2A77E4E1C22C5A7A1A40@phx.gbl>

Hello,
since a couple of days I got an error when I try to run "from scipy import 
*"
here is the error message....


" Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File "/usr/local/lib/python2.4/site-packages/scipy/linalg/__init__.py", 
line 8, in ?
    from basic import *
  File "/usr/local/lib/python2.4/site-packages/scipy/linalg/basic.py", line 
227, in ?
    import decomp
  File "/usr/local/lib/python2.4/site-packages/scipy/linalg/decomp.py", line 
21, in ?
    from blas import get_blas_funcs
  File "/usr/local/lib/python2.4/site-packages/scipy/linalg/blas.py", line 
14, in ?
    from scipy.linalg import fblas
ImportError: /usr/local/lib/python2.4/site-packages/scipy/linalg/fblas.so: 
undefined symbol: srotmg_"

does anyone have a clue?!

thanks,
Chiara

_________________________________________________________________
Express yourself instantly with MSN Messenger! Download today it's FREE! 
http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/



From robert.kern at gmail.com  Thu Feb  1 11:56:14 2007
From: robert.kern at gmail.com (Robert Kern)
Date: Thu, 01 Feb 2007 10:56:14 -0600
Subject: [SciPy-user] error importing scipy
In-Reply-To: <BAY114-F38BCD4C2A77E4E1C22C5A7A1A40@phx.gbl>
References: <BAY114-F38BCD4C2A77E4E1C22C5A7A1A40@phx.gbl>
Message-ID: <45C21BAE.7040004@gmail.com>

Chiara Caronna wrote:
> Hello,
> since a couple of days I got an error when I try to run "from scipy import 
> *"
> here is the error message....
> 
> 
> " Traceback (most recent call last):
>   File "<stdin>", line 1, in ?
>   File "/usr/local/lib/python2.4/site-packages/scipy/linalg/__init__.py", 
> line 8, in ?
>     from basic import *
>   File "/usr/local/lib/python2.4/site-packages/scipy/linalg/basic.py", line 
> 227, in ?
>     import decomp
>   File "/usr/local/lib/python2.4/site-packages/scipy/linalg/decomp.py", line 
> 21, in ?
>     from blas import get_blas_funcs
>   File "/usr/local/lib/python2.4/site-packages/scipy/linalg/blas.py", line 
> 14, in ?
>     from scipy.linalg import fblas
> ImportError: /usr/local/lib/python2.4/site-packages/scipy/linalg/fblas.so: 
> undefined symbol: srotmg_"
> 
> does anyone have a clue?!

Your scipy was not linked to a BLAS library correctly. What BLAS library were
you trying to link against? Where are its files located on your system? Did you
use a site.cfg file to configure scipy? Can you show us the output of

  $ cd ~/src/scipy  # or whatever
  $ python setup.py configure

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
 that is made terrible by our own mad attempt to interpret it as though it had
 an underlying truth."
  -- Umberto Eco


From chiaracaronna at hotmail.com  Thu Feb  1 12:31:44 2007
From: chiaracaronna at hotmail.com (Chiara Caronna)
Date: Thu, 01 Feb 2007 17:31:44 +0000
Subject: [SciPy-user] error importing scipy
In-Reply-To: <45C21BAE.7040004@gmail.com>
Message-ID: <BAY114-F304391A8D4D1F1BED62200A1A40@phx.gbl>




>From: Robert Kern <robert.kern at gmail.com>
>Reply-To: SciPy Users List <scipy-user at scipy.org>
>To: SciPy Users List <scipy-user at scipy.org>
>Subject: Re: [SciPy-user] error importing scipy
>Date: Thu, 01 Feb 2007 10:56:14 -0600
>
>Chiara Caronna wrote:
> > Hello,
> > since a couple of days I got an error when I try to run "from scipy 
>import
> > *"
> > here is the error message....
> >
> >
> > " Traceback (most recent call last):
> >   File "<stdin>", line 1, in ?
> >   File 
>"/usr/local/lib/python2.4/site-packages/scipy/linalg/__init__.py",
> > line 8, in ?
> >     from basic import *
> >   File "/usr/local/lib/python2.4/site-packages/scipy/linalg/basic.py", 
>line
> > 227, in ?
> >     import decomp
> >   File "/usr/local/lib/python2.4/site-packages/scipy/linalg/decomp.py", 
>line
> > 21, in ?
> >     from blas import get_blas_funcs
> >   File "/usr/local/lib/python2.4/site-packages/scipy/linalg/blas.py", 
>line
> > 14, in ?
> >     from scipy.linalg import fblas
> > ImportError: 
>/usr/local/lib/python2.4/site-packages/scipy/linalg/fblas.so:
> > undefined symbol: srotmg_"
> >
> > does anyone have a clue?!
>
>Your scipy was not linked to a BLAS library correctly. What BLAS library 
>were
>you trying to link against?

'_' ... I have never tried to do that... at least I am not aware of...


Where are its files located on your system?

I don't know it, how can I find that out?

>Did you use a site.cfg file to configure scipy?

I am not sure I understood the question... I download the file 
scipy-0.5.2.tar.gz, extracted it and followed the instructions... so I guess 
the answer is "no, I didn't"


Can you show us the output of
>
>   $ cd ~/src/scipy  # or whatever
>   $ python setup.py configure


I did this:

cd /usr/local/lib/python2.4/site-packages/scipy
python setup.py configure

here is the output:





non-existing path in 'cluster': 'src/vq_wrap.cpp'
Appending scipy.cluster configuration to scipy
Ignoring attempt to set 'name' (from 'scipy' to 'scipy.cluster')
mkl_info:
  libraries mkl,vml,guide not found in /usr/local/lib
  libraries mkl,vml,guide not found in /usr/lib
  NOT AVAILABLE

fftw3_info:
  libraries fftw3 not found in /usr/local/lib
  libraries fftw3 not found in /usr/lib
  fftw3 not found
  NOT AVAILABLE

fftw2_info:
  libraries rfftw,fftw not found in /usr/local/lib
  libraries rfftw,fftw not found in /usr/lib
  fftw2 not found
  NOT AVAILABLE

dfftw_info:
  libraries drfftw,dfftw not found in /usr/local/lib
  libraries drfftw,dfftw not found in /usr/lib
  dfftw not found
  NOT AVAILABLE

djbfft_info:
  NOT AVAILABLE

could not resolve pattern in 'fftpack': 'dfftpack/*.f'
non-existing path in 'fftpack': 'fftpack.pyf'
non-existing path in 'fftpack': 'src/zfft.c'
non-existing path in 'fftpack': 'src/drfft.c'
non-existing path in 'fftpack': 'src/zrfft.c'
non-existing path in 'fftpack': 'src/zfftnd.c'
non-existing path in 'fftpack': 'convolve.pyf'
non-existing path in 'fftpack': 'src/convolve.c'
Appending scipy.fftpack configuration to scipy
Ignoring attempt to set 'name' (from 'scipy' to 'scipy.fftpack')
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
Setting PTATLAS=ATLAS
Setting PTATLAS=ATLAS
  FOUND:
    libraries = ['lapack', 'blas']
    library_dirs = ['/usr/lib']
    language = c

Could not locate executable gfortran
Could not locate executable f95
customize GnuFCompiler
invalid command 'configure'
Could not locate executable ifort
Could not locate executable ifc
Could not locate executable ifort
Could not locate executable efort
Could not locate executable efc
Could not locate executable ifort
Could not locate executable efort
Could not locate executable efc
customize IntelFCompiler
invalid command 'configure'
customize LaheyFCompiler
invalid command 'configure'
customize PGroupFCompiler
invalid command 'configure'
customize AbsoftFCompiler
invalid command 'configure'
customize NAGFCompiler
invalid command 'configure'
customize VastFCompiler
invalid command 'configure'
customize CompaqFCompiler
invalid command 'configure'
customize IntelItaniumFCompiler
invalid command 'configure'
customize IntelEM64TFCompiler
invalid command 'configure'
customize Gnu95FCompiler
invalid command 'configure'
customize G95FCompiler
invalid command 'configure'
customize GnuFCompiler
invalid command 'configure'
customize Gnu95FCompiler
invalid command 'configure'
customize GnuFCompiler
customize GnuFCompiler using config
  FOUND:
    libraries = ['lapack', 'blas']
    library_dirs = ['/usr/lib']
    language = c
    define_macros = [('ATLAS_INFO', '"\\"?.?.?\\""')]

could not resolve pattern in 'integrate': 'linpack_lite/*.f'
could not resolve pattern in 'integrate': 'mach/*.f'
could not resolve pattern in 'integrate': 'quadpack/*.f'
could not resolve pattern in 'integrate': 'odepack/*.f'
non-existing path in 'integrate': '_quadpackmodule.c'
non-existing path in 'integrate': '_odepackmodule.c'
non-existing path in 'integrate': 'vode.pyf'
Appending scipy.integrate configuration to scipy
Ignoring attempt to set 'name' (from 'scipy' to 'scipy.integrate')
could not resolve pattern in 'interpolate': 'fitpack/*.f'
non-existing path in 'interpolate': '_fitpackmodule.c'
non-existing path in 'interpolate': 'fitpack.pyf'
Appending scipy.interpolate configuration to scipy
Ignoring attempt to set 'name' (from 'scipy' to 'scipy.interpolate')
non-existing path in 'io': 'numpyiomodule.c'
Appending scipy.io configuration to scipy
Ignoring attempt to set 'name' (from 'scipy' to 'scipy.io')
ATLAS version ?.?.?
non-existing path in 'lib/blas': 'fblas.pyf.src'
non-existing path in 'lib/blas': 'fblaswrap.f.src'
could not resolve pattern in 'lib/blas': 'fblas_l?.pyf.src'
non-existing path in 'lib/blas': 'cblas.pyf.src'
could not resolve pattern in 'lib/blas': 'cblas_l?.pyf.src'
Appending scipy.lib.blas configuration to scipy.lib
Ignoring attempt to set 'name' (from 'scipy.lib' to 'scipy.lib.blas')
lapack_opt_info:
lapack_mkl_info:
  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_atlas not found in /usr/lib
numpy.distutils.system_info.atlas_threads_info
Setting PTATLAS=ATLAS
Setting PTATLAS=ATLAS
  FOUND:
    libraries = ['lapack', 'lapack', 'blas']
    library_dirs = ['/usr/lib']
    language = f77

customize GnuFCompiler
invalid command 'configure'
customize IntelFCompiler
invalid command 'configure'
customize LaheyFCompiler
invalid command 'configure'
customize PGroupFCompiler
invalid command 'configure'
customize AbsoftFCompiler
invalid command 'configure'
customize NAGFCompiler
invalid command 'configure'
customize VastFCompiler
invalid command 'configure'
customize CompaqFCompiler
invalid command 'configure'
customize IntelItaniumFCompiler
invalid command 'configure'
customize IntelEM64TFCompiler
invalid command 'configure'
customize Gnu95FCompiler
invalid command 'configure'
customize G95FCompiler
invalid command 'configure'
customize GnuFCompiler
invalid command 'configure'
customize Gnu95FCompiler
invalid command 'configure'
customize GnuFCompiler
customize GnuFCompiler using config
  FOUND:
    libraries = ['lapack', 'lapack', 'blas']
    library_dirs = ['/usr/lib']
    language = f77
    define_macros = [('ATLAS_INFO', '"\\"?.?.?\\""')]

ATLAS version ?.?.?
non-existing path in 'lib/lapack': 'flapack.pyf.src'
could not resolve pattern in 'lib/lapack': 'flapack_*.pyf.src'
non-existing path in 'lib/lapack': 'clapack.pyf.src'
non-existing path in 'lib/lapack': 'calc_lwork.f'
non-existing path in 'lib/lapack': 'atlas_version.c'
Appending scipy.lib.lapack configuration to scipy.lib
Ignoring attempt to set 'name' (from 'scipy.lib' to 'scipy.lib.lapack')
Appending scipy.lib configuration to scipy
Ignoring attempt to set 'name' (from 'scipy' to 'scipy.lib')
ATLAS version ?.?.?
non-existing path in 'linalg': 'src/fblaswrap.f'
non-existing path in 'linalg': 'generic_fblas.pyf'
non-existing path in 'linalg': 'generic_fblas1.pyf'
non-existing path in 'linalg': 'generic_fblas2.pyf'
non-existing path in 'linalg': 'generic_fblas3.pyf'
non-existing path in 'linalg': 'generic_cblas.pyf'
non-existing path in 'linalg': 'generic_cblas1.pyf'
non-existing path in 'linalg': 'generic_flapack.pyf'
non-existing path in 'linalg': 'flapack_user_routines.pyf'
non-existing path in 'linalg': 'generic_clapack.pyf'
non-existing path in 'linalg': 'src/det.f'
non-existing path in 'linalg': 'src/lu.f'
non-existing path in 'linalg': 'src/calc_lwork.f'
non-existing path in 'linalg': 'atlas_version.c'
non-existing path in 'linalg': 'iterative/STOPTEST2.f.src'
non-existing path in 'linalg': 'iterative/getbreak.f.src'
non-existing path in 'linalg': 'iterative/BiCGREVCOM.f.src'
non-existing path in 'linalg': 'iterative/BiCGSTABREVCOM.f.src'
non-existing path in 'linalg': 'iterative/CGREVCOM.f.src'
non-existing path in 'linalg': 'iterative/CGSREVCOM.f.src'
non-existing path in 'linalg': 'iterative/GMRESREVCOM.f.src'
non-existing path in 'linalg': 'iterative/QMRREVCOM.f.src'
non-existing path in 'linalg': 'iterative/_iterative.pyf.src'
Appending scipy.linalg configuration to scipy
Ignoring attempt to set 'name' (from 'scipy' to 'scipy.linalg')
could not resolve pattern in 'linsolve': 'SuperLU/SRC/*.c'
non-existing path in 'linsolve': '_zsuperlumodule.c'
non-existing path in 'linsolve': '_superlu_utils.c'
non-existing path in 'linsolve': '_superluobject.c'
non-existing path in 'linsolve': '_dsuperlumodule.c'
non-existing path in 'linsolve': '_superlu_utils.c'
non-existing path in 'linsolve': '_superluobject.c'
non-existing path in 'linsolve': '_csuperlumodule.c'
non-existing path in 'linsolve': '_superlu_utils.c'
non-existing path in 'linsolve': '_superluobject.c'
non-existing path in 'linsolve': '_ssuperlumodule.c'
non-existing path in 'linsolve': '_superlu_utils.c'
non-existing path in 'linsolve': '_superluobject.c'
umfpack_info:
  libraries umfpack not found in /usr/local/lib
  libraries umfpack not found in /usr/lib
/usr/local/lib/python2.4/site-packages/numpy/distutils/system_info.py:401: 
UserWarning:
    UMFPACK sparse solver (http://www.cise.ufl.edu/research/sparse/umfpack/)
    not found. Directories to search for the libraries can be specified in 
the
    numpy/distutils/site.cfg file (section [umfpack]) or by setting
    the UMFPACK environment variable.
  warnings.warn(self.notfounderror.__doc__)
  NOT AVAILABLE

non-existing path in 'linsolve/umfpack': 'umfpack.i'
non-existing path in 'linsolve/umfpack': 'umfpack.i'
Appending scipy.linsolve.umfpack configuration to scipy.linsolve
Ignoring attempt to set 'name' (from 'scipy.linsolve' to 
'scipy.linsolve.umfpack')
Appending scipy.linsolve configuration to scipy
Ignoring attempt to set 'name' (from 'scipy' to 'scipy.linsolve')
non-existing path in 'maxentropy': 'doc'
Appending scipy.maxentropy configuration to scipy
Ignoring attempt to set 'name' (from 'scipy' to 'scipy.maxentropy')
Appending scipy.misc configuration to scipy
Ignoring attempt to set 'name' (from 'scipy' to 'scipy.misc')
non-existing path in 'odr': 'odrpack/d_odr.f'
non-existing path in 'odr': 'odrpack/d_mprec.f'
non-existing path in 'odr': 'odrpack/dlunoc.f'
non-existing path in 'odr': 'odrpack/d_lpk.f'
non-existing path in 'odr': '__odrpack.c'
Appending scipy.odr configuration to scipy
Ignoring attempt to set 'name' (from 'scipy' to 'scipy.odr')
could not resolve pattern in 'optimize': 'minpack/*f'
non-existing path in 'optimize': '_minpackmodule.c'
could not resolve pattern in 'optimize': 'Zeros/*.c'
non-existing path in 'optimize': 'zeros.c'
non-existing path in 'optimize': 'lbfgsb/lbfgsb.pyf'
non-existing path in 'optimize': 'lbfgsb/routines.f'
non-existing path in 'optimize': 'tnc/moduleTNC.c'
non-existing path in 'optimize': 'tnc/tnc.c'
non-existing path in 'optimize': 'cobyla/cobyla.pyf'
non-existing path in 'optimize': 'cobyla/cobyla2.f'
non-existing path in 'optimize': 'cobyla/trstlp.f'
non-existing path in 'optimize': 'minpack2/minpack2.pyf'
non-existing path in 'optimize': 'minpack2/dcsrch.f'
non-existing path in 'optimize': 'minpack2/dcstep.f'
Appending scipy.optimize configuration to scipy
Ignoring attempt to set 'name' (from 'scipy' to 'scipy.optimize')
Appending scipy.sandbox configuration to scipy
Ignoring attempt to set 'name' (from 'scipy' to 'scipy.sandbox')
non-existing path in 'signal': 'sigtoolsmodule.c'
non-existing path in 'signal': 'firfilter.c'
non-existing path in 'signal': 'medianfilter.c'
non-existing path in 'signal': 'sigtools.h'
non-existing path in 'signal': 'splinemodule.c'
non-existing path in 'signal': 'S_bspline_util.c'
non-existing path in 'signal': 'D_bspline_util.c'
non-existing path in 'signal': 'C_bspline_util.c'
non-existing path in 'signal': 'Z_bspline_util.c'
non-existing path in 'signal': 'bspline_util.c'
Appending scipy.signal configuration to scipy
Ignoring attempt to set 'name' (from 'scipy' to 'scipy.signal')
non-existing path in 'sparse': 'sparsetools/spblas.f.src'
non-existing path in 'sparse': 'sparsetools/spconv.f.src'
non-existing path in 'sparse': 'sparsetools/sparsetools.pyf.src'
Appending scipy.sparse configuration to scipy
Ignoring attempt to set 'name' (from 'scipy' to 'scipy.sparse')
could not resolve pattern in 'special': 'c_misc/*.c'
could not resolve pattern in 'special': 'cephes/*.c'
could not resolve pattern in 'special': 'mach/*.f'
could not resolve pattern in 'special': 'amos/*.f'
could not resolve pattern in 'special': 'toms/*.f'
could not resolve pattern in 'special': 'cdflib/*.f'
could not resolve pattern in 'special': 'specfun/*.f'
non-existing path in 'special': '_cephesmodule.c'
non-existing path in 'special': 'amos_wrappers.c'
non-existing path in 'special': 'specfun_wrappers.c'
non-existing path in 'special': 'toms_wrappers.c'
non-existing path in 'special': 'cdf_wrappers.c'
non-existing path in 'special': 'ufunc_extras.c'
non-existing path in 'special': 'specfun.pyf'
Appending scipy.special configuration to scipy
Ignoring attempt to set 'name' (from 'scipy' to 'scipy.special')
could not resolve pattern in 'stats': 'statlib/*.f'
non-existing path in 'stats': 'statlib.pyf'
non-existing path in 'stats': 'futil.f'
non-existing path in 'stats': 'mvn.pyf'
non-existing path in 'stats': 'mvndst.f'
Appending scipy.stats configuration to scipy
Ignoring attempt to set 'name' (from 'scipy' to 'scipy.stats')
non-existing path in 'ndimage': 'src/nd_image.c'
non-existing path in 'ndimage': 'src/ni_filters.c'
non-existing path in 'ndimage': 'src/ni_fourier.c'
non-existing path in 'ndimage': 'src/ni_interpolation.c'
non-existing path in 'ndimage': 'src/ni_measure.c'
non-existing path in 'ndimage': 'src/ni_morphology.c'
non-existing path in 'ndimage': 'src/ni_support.c'
non-existing path in 'ndimage': 'src'
Appending scipy.ndimage configuration to scipy
Ignoring attempt to set 'name' (from 'scipy' to 'scipy.ndimage')
Warning: Assuming default configuration 
(stsci/convolve/{setup_convolve,setup}.py was not
found)
Traceback (most recent call last):
  File "setup.py", line 31, in ?
    setup(**configuration(top_path='').todict())
  File "setup.py", line 23, in configuration
    config.add_subpackage('stsci')
  File 
"/usr/local/lib/python2.4/site-packages/numpy/distutils/misc_util.py", line 
765, in add_subpackage
    caller_level = 2)
  File 
"/usr/local/lib/python2.4/site-packages/numpy/distutils/misc_util.py", line 
748, in get_subpackage
    caller_level = caller_level + 1)
  File 
"/usr/local/lib/python2.4/site-packages/numpy/distutils/misc_util.py", line 
695, in _get_configuration_from_setup_py
    config = setup_module.configuration(*args)
  File "/usr/local/lib/python2.4/site-packages/scipy/stsci/setup.py", line 
5, in configuration
    config.add_subpackage('convolve')
  File 
"/usr/local/lib/python2.4/site-packages/numpy/distutils/misc_util.py", line 
765, in add_subpackage
    caller_level = 2)
  File 
"/usr/local/lib/python2.4/site-packages/numpy/distutils/misc_util.py", line 
741, in get_subpackage
    caller_level = caller_level+1)
  File 
"/usr/local/lib/python2.4/site-packages/numpy/distutils/misc_util.py", line 
541, in __init__
    raise ValueError("%r is not a directory" % (package_path,))
ValueError: 'stsci/convolve' is not a directory







>
>--
>Robert Kern
>
>"I have come to believe that the whole world is an enigma, a harmless 
>enigma
>  that is made terrible by our own mad attempt to interpret it as though it 
>had
>  an underlying truth."
>   -- Umberto Eco
>_______________________________________________
>SciPy-user mailing list
>SciPy-user at scipy.org
>http://projects.scipy.org/mailman/listinfo/scipy-user

_________________________________________________________________
Don't just search. Find. Check out the new MSN Search! 
http://search.msn.com/



From robert.kern at gmail.com  Thu Feb  1 12:41:46 2007
From: robert.kern at gmail.com (Robert Kern)
Date: Thu, 01 Feb 2007 11:41:46 -0600
Subject: [SciPy-user] error importing scipy
In-Reply-To: <BAY114-F304391A8D4D1F1BED62200A1A40@phx.gbl>
References: <BAY114-F304391A8D4D1F1BED62200A1A40@phx.gbl>
Message-ID: <45C2265A.4040101@gmail.com>

Chiara Caronna wrote:
>> From: Robert Kern <robert.kern at gmail.com>

>> Your scipy was not linked to a BLAS library correctly. What BLAS library 
>> were
>> you trying to link against?
> 
> '_' ... I have never tried to do that... at least I am not aware of...

Okay, what kind of system are you on? If Linux, what distribution? What LAPACK
and BLAS packages do you have installed?

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
 that is made terrible by our own mad attempt to interpret it as though it had
 an underlying truth."
  -- Umberto Eco


From chiaracaronna at hotmail.com  Thu Feb  1 12:49:34 2007
From: chiaracaronna at hotmail.com (Chiara Caronna)
Date: Thu, 01 Feb 2007 17:49:34 +0000
Subject: [SciPy-user] error importing scipy
In-Reply-To: <45C2265A.4040101@gmail.com>
Message-ID: <BAY114-F8FDBCF6BEA946A7FAE203A1A40@phx.gbl>




>From: Robert Kern <robert.kern at gmail.com>
>Reply-To: SciPy Users List <scipy-user at scipy.org>
>To: SciPy Users List <scipy-user at scipy.org>
>Subject: Re: [SciPy-user] error importing scipy
>Date: Thu, 01 Feb 2007 11:41:46 -0600
>
>Chiara Caronna wrote:
> >> From: Robert Kern <robert.kern at gmail.com>
>
> >> Your scipy was not linked to a BLAS library correctly. What BLAS 
>library
> >> were
> >> you trying to link against?
> >
> > '_' ... I have never tried to do that... at least I am not aware of...
>
>Okay, what kind of system are you on? If Linux, what distribution?

I have Linux, Suse 8.4 (quite old, I know, but I can't change it, it's my 
office pc...)

>What LAPACK and BLAS packages do you have installed?
I have never installed them... how can I check which I have?



>
>--
>Robert Kern
>
>"I have come to believe that the whole world is an enigma, a harmless 
>enigma
>  that is made terrible by our own mad attempt to interpret it as though it 
>had
>  an underlying truth."
>   -- Umberto Eco
>_______________________________________________
>SciPy-user mailing list
>SciPy-user at scipy.org
>http://projects.scipy.org/mailman/listinfo/scipy-user

_________________________________________________________________
Express yourself instantly with MSN Messenger! Download today it's FREE! 
http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/



From rowen at cesmail.net  Thu Feb  1 13:21:58 2007
From: rowen at cesmail.net (Russell E. Owen)
Date: Thu, 01 Feb 2007 10:21:58 -0800
Subject: [SciPy-user] What it the best way to install on a Mac?
References: <723eb6930701310617v42a4a098s5582ef6dff01e8d4@mail.gmail.com>
	<45C0C5F5.2000100@unc.edu>
	<db6b5ecc0701310947o3d9e8912lc72fd2fa300854be@mail.gmail.com>
	<20070131223800.GA20121@avicenna.cc.columbia.edu>
Message-ID: <rowen-9290F6.10215801022007@sea.gmane.org>

In article <20070131223800.GA20121 at avicenna.cc.columbia.edu>,
 Lev Givon <lev at columbia.edu> wrote:

> ...It might be desirable to encourage a matplotlib person to add some
> information regarding the installation of that package, as I suspect
> that many folks in need of installation wisdom think in terms of the
> tetrad ipython/numpy/scipy/matplotlib.

My instructions for building a universal matplotlib for MacOS X from 
source are here (google for "build matplotlib for mac"):
http://www.astro.washington.edu/owen/BuildingMatplotlibForMac.html

I would be happy to move this to a wiki if anyone can suggest an 
appropriate one.

Having good instructions for building complex packages like matplotlib 
is very important. It should be kept current and readily available. That 
said, building matplotlib is tricky enough that few users will want to 
bother. And they shouldn't have to. Most people will be much happier 
with downloadable packages.

-- Russell



From pgreisen at gmail.com  Thu Feb  1 14:12:11 2007
From: pgreisen at gmail.com (Per Jr. Greisen)
Date: Thu, 1 Feb 2007 20:12:11 +0100
Subject: [SciPy-user] error importing scipy
In-Reply-To: <BAY114-F8FDBCF6BEA946A7FAE203A1A40@phx.gbl>
References: <45C2265A.4040101@gmail.com>
	<BAY114-F8FDBCF6BEA946A7FAE203A1A40@phx.gbl>
Message-ID: <e016526e0702011112s10c1b378w33086d41b23ff0f9@mail.gmail.com>

Hi,

Maybe this work . on suse machines there should be a yast to configure new
programs. From yast it should be possible to get BLAS and LAPACK libraries

(regarding suse 8.4 maybe you should try to upgrade it)

On 2/1/07, Chiara Caronna <chiaracaronna at hotmail.com> wrote:
>
>
>
>
> >From: Robert Kern <robert.kern at gmail.com>
> >Reply-To: SciPy Users List <scipy-user at scipy.org>
> >To: SciPy Users List <scipy-user at scipy.org>
> >Subject: Re: [SciPy-user] error importing scipy
> >Date: Thu, 01 Feb 2007 11:41:46 -0600
> >
> >Chiara Caronna wrote:
> > >> From: Robert Kern <robert.kern at gmail.com>
> >
> > >> Your scipy was not linked to a BLAS library correctly. What BLAS
> >library
> > >> were
> > >> you trying to link against?
> > >
> > > '_' ... I have never tried to do that... at least I am not aware of...
> >
> >Okay, what kind of system are you on? If Linux, what distribution?
>
> I have Linux, Suse 8.4 (quite old, I know, but I can't change it, it's my
> office pc...)
>
> >What LAPACK and BLAS packages do you have installed?
> I have never installed them... how can I check which I have?
>
>
>
> >
> >--
> >Robert Kern
> >
> >"I have come to believe that the whole world is an enigma, a harmless
> >enigma
> >  that is made terrible by our own mad attempt to interpret it as though
> it
> >had
> >  an underlying truth."
> >   -- Umberto Eco
> >_______________________________________________
> >SciPy-user mailing list
> >SciPy-user at scipy.org
> >http://projects.scipy.org/mailman/listinfo/scipy-user
>
> _________________________________________________________________
> Express yourself instantly with MSN Messenger! Download today it's FREE!
> http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
>
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user
>



-- 
Best regards
Per Jr. Greisen

"If you make something idiot-proof, the universe creates a better idiot."
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20070201/e7b2971b/attachment.html>

From robert.kern at gmail.com  Thu Feb  1 14:53:07 2007
From: robert.kern at gmail.com (Robert Kern)
Date: Thu, 01 Feb 2007 13:53:07 -0600
Subject: [SciPy-user] error importing scipy
In-Reply-To: <BAY114-F8FDBCF6BEA946A7FAE203A1A40@phx.gbl>
References: <BAY114-F8FDBCF6BEA946A7FAE203A1A40@phx.gbl>
Message-ID: <45C24523.8090706@gmail.com>

Chiara Caronna wrote:
>> From: Robert Kern <robert.kern at gmail.com>
>> Reply-To: SciPy Users List <scipy-user at scipy.org>
>> To: SciPy Users List <scipy-user at scipy.org>
>> Subject: Re: [SciPy-user] error importing scipy
>> Date: Thu, 01 Feb 2007 11:41:46 -0600
>>
>> Chiara Caronna wrote:
>>>> From: Robert Kern <robert.kern at gmail.com>
>>>> Your scipy was not linked to a BLAS library correctly. What BLAS 
>> library
>>>> were
>>>> you trying to link against?
>>> '_' ... I have never tried to do that... at least I am not aware of...
>> Okay, what kind of system are you on? If Linux, what distribution?
> 
> I have Linux, Suse 8.4 (quite old, I know, but I can't change it, it's my 
> office pc...)
> 
>> What LAPACK and BLAS packages do you have installed?
> I have never installed them... how can I check which I have?

Apparently you have since the configuration process has found some such
libraries in /usr/lib/. That means that they were most likely installed from
SuSE packages. You might need to talk to the person that administers your
computer to find out what packages they installed.

SuSE has often been problematic, especially with regards to its LAPACK and BLAS
libraries. I'm afraid that I don't know much of the details, like which versions
of which specific packages are known to work. Other people with SuSE experience
will have to chime in here.

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
 that is made terrible by our own mad attempt to interpret it as though it had
 an underlying truth."
  -- Umberto Eco


From anand at soe.ucsc.edu  Thu Feb  1 14:56:28 2007
From: anand at soe.ucsc.edu (Anand Patil)
Date: Thu, 01 Feb 2007 11:56:28 -0800
Subject: [SciPy-user] numpy installer not finding ATLAS in spite of correct
 environment variable
Message-ID: <45C245EC.7080305@cse.ucsc.edu>

Hi all,

I'm trying to install numpy on a machine in which 
/usr/local/atlas/lib/Linux_HAMMER64SSE2_4 contains:

libatlas.a  libcblas.a  liblapack.a  libptcblas.a  libtstatlas.a  
Makefile  Make.inc

I've set the relevant environment variables as follows:

setenv ATLAS /usr/local/atlas/lib/Linux_HAMMER64SSE2_4/
setenv BLAS /usr/local/atlas/lib/Linux_HAMMER64SSE2_4/
setenv LAPACK /usr/local/atlas/lib/Linux_HAMMER64SSE2_4/
setenv BLAS_SRC /usr/local/atlas/src/blas
setenv LAPACK_SRC /usr/local/atlas/src/lapack

However, numpy's installer does this:

atlas_blas_threads_info:
Setting PTATLAS=ATLAS
  libraries lapack,blas not found in 
/usr/local/atlas/lib/Linux_HAMMER64SSE2_4/
  libraries lapack,blas not found in /usr/local/lib
  libraries lapack,blas not found in /usr/lib/sse2
  libraries lapack,blas not found in /usr/lib
  NOT AVAILABLE

atlas_blas_info:
  libraries lapack,blas not found in 
/usr/local/atlas/lib/Linux_HAMMER64SSE2_4/
  libraries lapack,blas not found in /usr/local/lib
  libraries lapack,blas not found in /usr/lib/sse2
  libraries lapack,blas not found in /usr/lib
  NOT AVAILABLE

/projects/mangellab/anand/numpy-1.0.1/numpy/distutils/system_info.py:1301: 
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/atlas/lib/Linux_HAMMER64SSE2_4/
  libraries blas not found in /usr/local/lib
  libraries blas not found in /usr/lib
  NOT AVAILABLE

/projects/mangellab/anand/numpy-1.0.1/numpy/distutils/system_info.py:1310: 
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

/projects/mangellab/anand/numpy-1.0.1/numpy/distutils/system_info.py:1313: 
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

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/atlas/lib/Linux_HAMMER64SSE2_4/
  libraries lapack_atlas not found in 
/usr/local/atlas/lib/Linux_HAMMER64SSE2_4/
  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/sse2
  libraries lapack_atlas not found in /usr/lib/sse2
  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/atlas/lib/Linux_HAMMER64SSE2_4/
  libraries lapack_atlas not found in 
/usr/local/atlas/lib/Linux_HAMMER64SSE2_4/
  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/sse2
  libraries lapack_atlas not found in /usr/lib/sse2
  libraries lapack,blas not found in /usr/lib
  libraries lapack_atlas not found in /usr/lib
numpy.distutils.system_info.atlas_info
  NOT AVAILABLE

/projects/mangellab/anand/numpy-1.0.1/numpy/distutils/system_info.py:1210: 
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:
  FOUND:
    libraries = ['lapack']
    library_dirs = ['/usr/local/atlas/lib/Linux_HAMMER64SSE2_4/']
    language = f77

/projects/mangellab/anand/numpy-1.0.1/numpy/distutils/system_info.py:1234: 
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__)
/projects/mangellab/anand/numpy-1.0.1/numpy/distutils/system_info.py:1237: 
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

Then, even though it apparently found lapack, it builds lapack_lite:

gcc: numpy/linalg/dlamch.c
gcc: numpy/linalg/lapack_litemodule.c
gcc: numpy/linalg/zlapack_lite.c
gcc: numpy/linalg/dlapack_lite.c
gcc: numpy/linalg/blas_lite.c
gcc: numpy/linalg/f2c_lite.c

What am I doing wrong?

Thanks much,
Anand


From robert.kern at gmail.com  Thu Feb  1 14:59:36 2007
From: robert.kern at gmail.com (Robert Kern)
Date: Thu, 01 Feb 2007 13:59:36 -0600
Subject: [SciPy-user] numpy installer not finding ATLAS in spite of
 correct environment variable
In-Reply-To: <45C245EC.7080305@cse.ucsc.edu>
References: <45C245EC.7080305@cse.ucsc.edu>
Message-ID: <45C246A8.8050707@gmail.com>

Anand Patil wrote:
> Hi all,
> 
> I'm trying to install numpy on a machine in which 
> /usr/local/atlas/lib/Linux_HAMMER64SSE2_4 contains:
> 
> libatlas.a  libcblas.a  liblapack.a  libptcblas.a  libtstatlas.a  
> Makefile  Make.inc

You are missing libf77blas.a which should have the FORTRAN-compatible symbols
that numpy.linalg uses. Make sure that the ATLAS configuration process
recognizes your FORTRAN compiler (probably g77). Then it should build that library.

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
 that is made terrible by our own mad attempt to interpret it as though it had
 an underlying truth."
  -- Umberto Eco


From chiaracaronna at hotmail.com  Thu Feb  1 15:07:48 2007
From: chiaracaronna at hotmail.com (Chiara Caronna)
Date: Thu, 01 Feb 2007 20:07:48 +0000
Subject: [SciPy-user] error importing scipy
In-Reply-To: <45C24523.8090706@gmail.com>
Message-ID: <BAY114-F36ADF2D4B48EB8E4A5300EA1A40@phx.gbl>


Ok, thank you anyway fro your time!

>From: Robert Kern <robert.kern at gmail.com>
>Reply-To: SciPy Users List <scipy-user at scipy.org>
>To: SciPy Users List <scipy-user at scipy.org>
>Subject: Re: [SciPy-user] error importing scipy
>Date: Thu, 01 Feb 2007 13:53:07 -0600
>
>Chiara Caronna wrote:
> >> From: Robert Kern <robert.kern at gmail.com>
> >> Reply-To: SciPy Users List <scipy-user at scipy.org>
> >> To: SciPy Users List <scipy-user at scipy.org>
> >> Subject: Re: [SciPy-user] error importing scipy
> >> Date: Thu, 01 Feb 2007 11:41:46 -0600
> >>
> >> Chiara Caronna wrote:
> >>>> From: Robert Kern <robert.kern at gmail.com>
> >>>> Your scipy was not linked to a BLAS library correctly. What BLAS
> >> library
> >>>> were
> >>>> you trying to link against?
> >>> '_' ... I have never tried to do that... at least I am not aware of...
> >> Okay, what kind of system are you on? If Linux, what distribution?
> >
> > I have Linux, Suse 8.4 (quite old, I know, but I can't change it, it's 
>my
> > office pc...)
> >
> >> What LAPACK and BLAS packages do you have installed?
> > I have never installed them... how can I check which I have?
>
>Apparently you have since the configuration process has found some such
>libraries in /usr/lib/. That means that they were most likely installed 
>from
>SuSE packages. You might need to talk to the person that administers your
>computer to find out what packages they installed.
>
>SuSE has often been problematic, especially with regards to its LAPACK and 
>BLAS
>libraries. I'm afraid that I don't know much of the details, like which 
>versions
>of which specific packages are known to work. Other people with SuSE 
>experience
>will have to chime in here.
>
>--
>Robert Kern
>
>"I have come to believe that the whole world is an enigma, a harmless 
>enigma
>  that is made terrible by our own mad attempt to interpret it as though it 
>had
>  an underlying truth."
>   -- Umberto Eco
>_______________________________________________
>SciPy-user mailing list
>SciPy-user at scipy.org
>http://projects.scipy.org/mailman/listinfo/scipy-user

_________________________________________________________________
Don't just search. Find. Check out the new MSN Search! 
http://search.msn.click-url.com/go/onm00200636ave/direct/01/



From suhlhorn at gmail.com  Thu Feb  1 15:33:41 2007
From: suhlhorn at gmail.com (Stephen Uhlhorn)
Date: Thu, 1 Feb 2007 15:33:41 -0500
Subject: [SciPy-user] NameError on scipy import
Message-ID: <47edc1a0702011233j5e280f52i40ac4237aca764c8@mail.gmail.com>

I built numpy/scipy on my OS X 10.4 machine following the instructions
at the scipy.org page.

I installed ActiveState python 2.4 and had no build errors thru the
entire process including numpy 1.0.1 and scipy 0.5.2. The post-install
numpy test passed without error, but importing scipy gave this error:

>>> import scipy
Traceback (most recent call last):
 File "<stdin>", line 1, in ?
 File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/__init__.py",
line 33, in ?
   del lib
NameError: name 'lib' is not defined

Should I update to the latest svn version? Any suggestions?
Thanks-
-stephen


From robert.kern at gmail.com  Thu Feb  1 15:41:20 2007
From: robert.kern at gmail.com (Robert Kern)
Date: Thu, 01 Feb 2007 14:41:20 -0600
Subject: [SciPy-user] NameError on scipy import
In-Reply-To: <47edc1a0702011233j5e280f52i40ac4237aca764c8@mail.gmail.com>
References: <47edc1a0702011233j5e280f52i40ac4237aca764c8@mail.gmail.com>
Message-ID: <45C25070.2010004@gmail.com>

Stephen Uhlhorn wrote:
> I built numpy/scipy on my OS X 10.4 machine following the instructions
> at the scipy.org page.
> 
> I installed ActiveState python 2.4 and had no build errors thru the
> entire process including numpy 1.0.1 and scipy 0.5.2. The post-install
> numpy test passed without error, but importing scipy gave this error:
> 
>>>> import scipy
> Traceback (most recent call last):
>  File "<stdin>", line 1, in ?
>  File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/__init__.py",
> line 33, in ?
>    del lib
> NameError: name 'lib' is not defined
> 
> Should I update to the latest svn version? Any suggestions?

Double-check that the scipy that is trying to be imported is the same as the one
you thought you installed. There is no line "del lib" in scipy 0.5.2's __init__.py.

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
 that is made terrible by our own mad attempt to interpret it as though it had
 an underlying truth."
  -- Umberto Eco


From eike.welk at gmx.net  Thu Feb  1 15:46:51 2007
From: eike.welk at gmx.net (Eike Welk)
Date: Thu, 01 Feb 2007 21:46:51 +0100
Subject: [SciPy-user] error importing scipy
In-Reply-To: <45C24523.8090706@gmail.com>
References: <BAY114-F8FDBCF6BEA946A7FAE203A1A40@phx.gbl>
	<45C24523.8090706@gmail.com>
Message-ID: <200702012146.52456.eike.welk@gmx.net>

On Thursday 01 February 2007 20:53, Robert Kern wrote:
> SuSE has often been problematic, especially with regards to its
> LAPACK and BLAS libraries. I'm afraid that I don't know much of the
> details, like which versions of which specific packages are known
> to work. Other people with SuSE experience will have to chime in
> here.

Yes, Suse ship broken packages, also for Suse 10.2. I use comunity 
contributed packages from:
http://repos.opensuse.org/science/

But these are not helpfull for Chiara because the are none for Suse  
8.4.

So, is there a way to compile NumPy and SciPy without using BLAS and 
LAPACK at all?


Regards, Eike.



From suhlhorn at gmail.com  Thu Feb  1 15:54:13 2007
From: suhlhorn at gmail.com (Stephen Uhlhorn)
Date: Thu, 1 Feb 2007 15:54:13 -0500
Subject: [SciPy-user] NameError on scipy import
In-Reply-To: <45C25070.2010004@gmail.com>
References: <47edc1a0702011233j5e280f52i40ac4237aca764c8@mail.gmail.com>
	<45C25070.2010004@gmail.com>
Message-ID: <47edc1a0702011254y5b60c32cw4b460c05fa2616c6@mail.gmail.com>

I do have another installation via fink... many problems.

How do I find out which scipy my python is importing?

On 2/1/07, Robert Kern <robert.kern at gmail.com> wrote:
> Stephen Uhlhorn wrote:
> > I built numpy/scipy on my OS X 10.4 machine following the instructions
> > at the scipy.org page.
> >
> > I installed ActiveState python 2.4 and had no build errors thru the
> > entire process including numpy 1.0.1 and scipy 0.5.2. The post-install
> > numpy test passed without error, but importing scipy gave this error:
> >
> >>>> import scipy
> > Traceback (most recent call last):
> >  File "<stdin>", line 1, in ?
> >  File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/__init__.py",
> > line 33, in ?
> >    del lib
> > NameError: name 'lib' is not defined
> >
> > Should I update to the latest svn version? Any suggestions?
>
> Double-check that the scipy that is trying to be imported is the same as the one
> you thought you installed. There is no line "del lib" in scipy 0.5.2's __init__.py.
>
> --
> Robert Kern
>
> "I have come to believe that the whole world is an enigma, a harmless enigma
>  that is made terrible by our own mad attempt to interpret it as though it had
>  an underlying truth."
>   -- Umberto Eco
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user
>


From robert.kern at gmail.com  Thu Feb  1 15:56:55 2007
From: robert.kern at gmail.com (Robert Kern)
Date: Thu, 01 Feb 2007 14:56:55 -0600
Subject: [SciPy-user] NameError on scipy import
In-Reply-To: <47edc1a0702011254y5b60c32cw4b460c05fa2616c6@mail.gmail.com>
References: <47edc1a0702011233j5e280f52i40ac4237aca764c8@mail.gmail.com>	<45C25070.2010004@gmail.com>
	<47edc1a0702011254y5b60c32cw4b460c05fa2616c6@mail.gmail.com>
Message-ID: <45C25417.5010000@gmail.com>

Stephen Uhlhorn wrote:
> I do have another installation via fink... many problems.
> 
> How do I find out which scipy my python is importing?

The traceback showed you the filename:

/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/__init__.py

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
 that is made terrible by our own mad attempt to interpret it as though it had
 an underlying truth."
  -- Umberto Eco


From robert.kern at gmail.com  Thu Feb  1 15:58:20 2007
From: robert.kern at gmail.com (Robert Kern)
Date: Thu, 01 Feb 2007 14:58:20 -0600
Subject: [SciPy-user] error importing scipy
In-Reply-To: <200702012146.52456.eike.welk@gmx.net>
References: <BAY114-F8FDBCF6BEA946A7FAE203A1A40@phx.gbl>	<45C24523.8090706@gmail.com>
	<200702012146.52456.eike.welk@gmx.net>
Message-ID: <45C2546C.5020208@gmail.com>

Eike Welk wrote:
> So, is there a way to compile NumPy and SciPy without using BLAS and 
> LAPACK at all?

Depends on what you mean by that. Strictly speaking, no; at least parts of BLAS
and LAPACK must be used somewhere along the line. numpy includes implementations
for the parts it needs if an already installed BLAS and LAPACK cannot be found.
However, you can build BLAS and LAPACK yourself relatively easily if you don't
care about optimization.

http://www.scipy.org/Installing_SciPy/BuildingGeneral#head-e618da78f29d5a85f680cc47e574a84951c8dffb

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
 that is made terrible by our own mad attempt to interpret it as though it had
 an underlying truth."
  -- Umberto Eco


From suhlhorn at gmail.com  Thu Feb  1 16:09:52 2007
From: suhlhorn at gmail.com (Stephen Uhlhorn)
Date: Thu, 1 Feb 2007 16:09:52 -0500
Subject: [SciPy-user] NameError on scipy import
In-Reply-To: <45C25417.5010000@gmail.com>
References: <47edc1a0702011233j5e280f52i40ac4237aca764c8@mail.gmail.com>
	<45C25070.2010004@gmail.com>
	<47edc1a0702011254y5b60c32cw4b460c05fa2616c6@mail.gmail.com>
	<45C25417.5010000@gmail.com>
Message-ID: <47edc1a0702011309w3179bc43j6b9b86e1dd11782@mail.gmail.com>

The one in the path below is definitely the version I built. My
working numpy is installed under the same tree. The other (fink)
version is under /sw/lib/python/site-packages and I changed my path so
that the python called is completely outside the fink tree.

Should I update scipy via svn?

On 2/1/07, Robert Kern <robert.kern at gmail.com> wrote:
> Stephen Uhlhorn wrote:
> > I do have another installation via fink... many problems.
> >
> > How do I find out which scipy my python is importing?
>
> The traceback showed you the filename:
>
> /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/__init__.py
>
> --
> Robert Kern


From robert.kern at gmail.com  Thu Feb  1 16:13:41 2007
From: robert.kern at gmail.com (Robert Kern)
Date: Thu, 01 Feb 2007 15:13:41 -0600
Subject: [SciPy-user] NameError on scipy import
In-Reply-To: <47edc1a0702011309w3179bc43j6b9b86e1dd11782@mail.gmail.com>
References: <47edc1a0702011233j5e280f52i40ac4237aca764c8@mail.gmail.com>	<45C25070.2010004@gmail.com>	<47edc1a0702011254y5b60c32cw4b460c05fa2616c6@mail.gmail.com>	<45C25417.5010000@gmail.com>
	<47edc1a0702011309w3179bc43j6b9b86e1dd11782@mail.gmail.com>
Message-ID: <45C25805.1030003@gmail.com>

Stephen Uhlhorn wrote:
> The one in the path below is definitely the version I built. My
> working numpy is installed under the same tree. The other (fink)
> version is under /sw/lib/python/site-packages and I changed my path so
> that the python called is completely outside the fink tree.
> 
> Should I update scipy via svn?

I would double-check that the file

/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/__init__.py

is the same as from the source that you built. That file in the
scipy-0.5.2.tar.gz that I just downloaded does not have the line that is causing
the error. Most likely, you should delete the directory

/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/

and re-install from the source that you have (provided that it does not also
have the erroneous "del lib" line).

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
 that is made terrible by our own mad attempt to interpret it as though it had
 an underlying truth."
  -- Umberto Eco


From suhlhorn at gmail.com  Thu Feb  1 16:13:37 2007
From: suhlhorn at gmail.com (Stephen Uhlhorn)
Date: Thu, 1 Feb 2007 16:13:37 -0500
Subject: [SciPy-user] NameError on scipy import
In-Reply-To: <45C25070.2010004@gmail.com>
References: <47edc1a0702011233j5e280f52i40ac4237aca764c8@mail.gmail.com>
	<45C25070.2010004@gmail.com>
Message-ID: <47edc1a0702011313v6c359d5aude097f23389758a0@mail.gmail.com>

I just checked the file and 'del lib' is in  __init__.py  My scipy is
from the 0.5.2 tarball.

On 2/1/07, Robert Kern <robert.kern at gmail.com> wrote:

> Double-check that the scipy that is trying to be imported is the same as the one
> you thought you installed. There is no line "del lib" in scipy 0.5.2's __init__.py.
>
> --
> Robert Kern
>


From robert.kern at gmail.com  Thu Feb  1 16:17:07 2007
From: robert.kern at gmail.com (Robert Kern)
Date: Thu, 01 Feb 2007 15:17:07 -0600
Subject: [SciPy-user] NameError on scipy import
In-Reply-To: <47edc1a0702011313v6c359d5aude097f23389758a0@mail.gmail.com>
References: <47edc1a0702011233j5e280f52i40ac4237aca764c8@mail.gmail.com>	<45C25070.2010004@gmail.com>
	<47edc1a0702011313v6c359d5aude097f23389758a0@mail.gmail.com>
Message-ID: <45C258D3.2030907@gmail.com>

Stephen Uhlhorn wrote:
> I just checked the file and 'del lib' is in  __init__.py  My scipy is
> from the 0.5.2 tarball.

But is that line in the __init__.py that resides in the tarball that you have
rather than the one that is installed? It does not exist in the tarball that I
just downloaded.

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
 that is made terrible by our own mad attempt to interpret it as though it had
 an underlying truth."
  -- Umberto Eco


From eike.welk at gmx.net  Thu Feb  1 16:23:47 2007
From: eike.welk at gmx.net (Eike Welk)
Date: Thu, 01 Feb 2007 22:23:47 +0100
Subject: [SciPy-user] error importing scipy
In-Reply-To: <45C2546C.5020208@gmail.com>
References: <BAY114-F8FDBCF6BEA946A7FAE203A1A40@phx.gbl>
	<200702012146.52456.eike.welk@gmx.net> <45C2546C.5020208@gmail.com>
Message-ID: <200702012223.47275.eike.welk@gmx.net>

Thank you!

Eike.



From suhlhorn at gmail.com  Thu Feb  1 18:11:49 2007
From: suhlhorn at gmail.com (Stephen Uhlhorn)
Date: Thu, 1 Feb 2007 18:11:49 -0500
Subject: [SciPy-user] NameError on scipy import
In-Reply-To: <45C258D3.2030907@gmail.com>
References: <47edc1a0702011233j5e280f52i40ac4237aca764c8@mail.gmail.com>
	<45C25070.2010004@gmail.com>
	<47edc1a0702011313v6c359d5aude097f23389758a0@mail.gmail.com>
	<45C258D3.2030907@gmail.com>
Message-ID: <47edc1a0702011511g290bb0dk1a1f95506a605fc9@mail.gmail.com>

Strange... I cleaned out my build directory and the scipy site-package
dir to make sure the files matched up... now it won't compile:

/usr/bin/ld: can't locate file for: -lcc_dynamic
collect2: ld returned 1 exit status
/usr/bin/ld: can't locate file for: -lcc_dynamic
collect2: ld returned 1 exit status
error: Command "/usr/local/bin/g77 -g -Wall -undefined dynamic_lookup
-bundle build/temp.darwin-8.8.
0-Power_Macintosh-2.4/build/src.darwin-8.8.0-Power_Macintosh-2.4/Lib/fftpack/_fftpackmodule.o
build/
temp.darwin-8.8.0-Power_Macintosh-2.4/Lib/fftpack/src/zfft.o
build/temp.darwin-8.8.0-Power_Macintosh
-2.4/Lib/fftpack/src/drfft.o
build/temp.darwin-8.8.0-Power_Macintosh-2.4/Lib/fftpack/src/zrfft.o
bui
ld/temp.darwin-8.8.0-Power_Macintosh-2.4/Lib/fftpack/src/zfftnd.o
build/temp.darwin-8.8.0-Power_Maci
ntosh-2.4/build/src.darwin-8.8.0-Power_Macintosh-2.4/fortranobject.o
-L/usr/local/lib -L/usr/local/l
ib/gcc/powerpc-apple-darwin7.9.0/3.4.4
-Lbuild/temp.darwin-8.8.0-Power_Macintosh-2.4 -ldfftpack -lff
tw3 -lg2c -lcc_dynamic -o
build/lib.darwin-8.8.0-Power_Macintosh-2.4/scipy/fftpack/_fftpack.so
-lSys
temStubs" failed with exit status 1

I tried making the changes to Lib/fftpack.setup.py according to the
instructions, but no go... any ideas?

-stephen

On 2/1/07, Robert Kern <robert.kern at gmail.com> wrote:
> Stephen Uhlhorn wrote:
> > I just checked the file and 'del lib' is in  __init__.py  My scipy is
> > from the 0.5.2 tarball.
>
> But is that line in the __init__.py that resides in the tarball that you have
> rather than the one that is installed? It does not exist in the tarball that I
> just downloaded.
>
> --
> Robert Kern


From robert.kern at gmail.com  Thu Feb  1 18:18:44 2007
From: robert.kern at gmail.com (Robert Kern)
Date: Thu, 01 Feb 2007 17:18:44 -0600
Subject: [SciPy-user] NameError on scipy import
In-Reply-To: <47edc1a0702011511g290bb0dk1a1f95506a605fc9@mail.gmail.com>
References: <47edc1a0702011233j5e280f52i40ac4237aca764c8@mail.gmail.com>	<45C25070.2010004@gmail.com>	<47edc1a0702011313v6c359d5aude097f23389758a0@mail.gmail.com>	<45C258D3.2030907@gmail.com>
	<47edc1a0702011511g290bb0dk1a1f95506a605fc9@mail.gmail.com>
Message-ID: <45C27554.4020408@gmail.com>

Stephen Uhlhorn wrote:
> Strange... I cleaned out my build directory and the scipy site-package
> dir to make sure the files matched up... now it won't compile:
> 
> /usr/bin/ld: can't locate file for: -lcc_dynamic
> collect2: ld returned 1 exit status
> /usr/bin/ld: can't locate file for: -lcc_dynamic
> collect2: ld returned 1 exit status
> error: Command "/usr/local/bin/g77 -g -Wall -undefined dynamic_lookup
> -bundle build/temp.darwin-8.8.
> 0-Power_Macintosh-2.4/build/src.darwin-8.8.0-Power_Macintosh-2.4/Lib/fftpack/_fftpackmodule.o
> build/

You will need to use gfortran for a Universal build of Python on Tiger. g77 does
not build Universal binaries. See the instructions I give here:

http://projects.scipy.org/pipermail/numpy-discussion/2007-January/025368.html

> temp.darwin-8.8.0-Power_Macintosh-2.4/Lib/fftpack/src/zfft.o
> build/temp.darwin-8.8.0-Power_Macintosh
> -2.4/Lib/fftpack/src/drfft.o
> build/temp.darwin-8.8.0-Power_Macintosh-2.4/Lib/fftpack/src/zrfft.o
> bui
> ld/temp.darwin-8.8.0-Power_Macintosh-2.4/Lib/fftpack/src/zfftnd.o
> build/temp.darwin-8.8.0-Power_Maci
> ntosh-2.4/build/src.darwin-8.8.0-Power_Macintosh-2.4/fortranobject.o
> -L/usr/local/lib -L/usr/local/l
> ib/gcc/powerpc-apple-darwin7.9.0/3.4.4
> -Lbuild/temp.darwin-8.8.0-Power_Macintosh-2.4 -ldfftpack -lff
> tw3 -lg2c -lcc_dynamic -o
> build/lib.darwin-8.8.0-Power_Macintosh-2.4/scipy/fftpack/_fftpack.so
> -lSys
> temStubs" failed with exit status 1
> 
> I tried making the changes to Lib/fftpack.setup.py according to the
> instructions, but no go... any ideas?

What instructions? (This has nothing to do with your problem, but I am unaware
of instructions which tell you to modify Lib/fftpack/setup.py and would like to
nail down any false information).

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
 that is made terrible by our own mad attempt to interpret it as though it had
 an underlying truth."
  -- Umberto Eco


From suhlhorn at gmail.com  Thu Feb  1 18:30:58 2007
From: suhlhorn at gmail.com (Stephen Uhlhorn)
Date: Thu, 1 Feb 2007 18:30:58 -0500
Subject: [SciPy-user] NameError on scipy import
In-Reply-To: <45C27554.4020408@gmail.com>
References: <47edc1a0702011233j5e280f52i40ac4237aca764c8@mail.gmail.com>
	<45C25070.2010004@gmail.com>
	<47edc1a0702011313v6c359d5aude097f23389758a0@mail.gmail.com>
	<45C258D3.2030907@gmail.com>
	<47edc1a0702011511g290bb0dk1a1f95506a605fc9@mail.gmail.com>
	<45C27554.4020408@gmail.com>
Message-ID: <47edc1a0702011530m832edc4s942de3367f5e507a@mail.gmail.com>

> What instructions? (This has nothing to do with your problem, but I am unaware
> of instructions which tell you to modify Lib/fftpack/setup.py and would like to
> nail down any false information).

Just followed the advice from here:

http://www.scipy.org/Installing_SciPy/Mac_OS_X#head-bf65e6cbe5d205c7e8fd574139a9e4db7b3d12e3

Perhaps its oudated?


From robert.kern at gmail.com  Thu Feb  1 18:40:12 2007
From: robert.kern at gmail.com (Robert Kern)
Date: Thu, 01 Feb 2007 17:40:12 -0600
Subject: [SciPy-user] NameError on scipy import
In-Reply-To: <47edc1a0702011530m832edc4s942de3367f5e507a@mail.gmail.com>
References: <47edc1a0702011233j5e280f52i40ac4237aca764c8@mail.gmail.com>	<45C25070.2010004@gmail.com>	<47edc1a0702011313v6c359d5aude097f23389758a0@mail.gmail.com>	<45C258D3.2030907@gmail.com>	<47edc1a0702011511g290bb0dk1a1f95506a605fc9@mail.gmail.com>	<45C27554.4020408@gmail.com>
	<47edc1a0702011530m832edc4s942de3367f5e507a@mail.gmail.com>
Message-ID: <45C27A5C.5010801@gmail.com>

Stephen Uhlhorn wrote:
>> What instructions? (This has nothing to do with your problem, but I am unaware
>> of instructions which tell you to modify Lib/fftpack/setup.py and would like to
>> nail down any false information).
> 
> Just followed the advice from here:
> 
> http://www.scipy.org/Installing_SciPy/Mac_OS_X#head-bf65e6cbe5d205c7e8fd574139a9e4db7b3d12e3
> 
> Perhaps its oudated?

Yes, apparently.

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
 that is made terrible by our own mad attempt to interpret it as though it had
 an underlying truth."
  -- Umberto Eco


From aisaac at american.edu  Thu Feb  1 22:23:27 2007
From: aisaac at american.edu (Alan G Isaac)
Date: Thu, 1 Feb 2007 22:23:27 -0500
Subject: [SciPy-user] Release 0.6.1 of pyaudio, renamed pyaudiolab
In-Reply-To: <45C0A076.2090805@ar.media.kyoto-u.ac.jp>
References: <45C0A076.2090805@ar.media.kyoto-u.ac.jp>
Message-ID: <Mahogany-0.67.0-1096-20070201-222327.00@american.edu>

On Wed, 31 Jan 2007, David Cournapeau apparently wrote: 
> With pyaudiolab, you should be able to read and write most 
> common audio files from and to numpy arrays. The 
> underlying IO operations are done using libsndfile from 
> Erik Castro Lopo (http://www.mega-nerd.com/libsndfile/) 

I think it is worth mentioning (on this list) that 
pyaudiolab uses the SciPy license and libsndfile is LGPL.

Cheers,
Alan Isaac






From david at ar.media.kyoto-u.ac.jp  Thu Feb  1 22:50:42 2007
From: david at ar.media.kyoto-u.ac.jp (David Cournapeau)
Date: Fri, 02 Feb 2007 12:50:42 +0900
Subject: [SciPy-user] Release 0.6.1 of pyaudio, renamed pyaudiolab
In-Reply-To: <Mahogany-0.67.0-1096-20070201-222327.00@american.edu>
References: <45C0A076.2090805@ar.media.kyoto-u.ac.jp>
	<Mahogany-0.67.0-1096-20070201-222327.00@american.edu>
Message-ID: <45C2B512.9070003@ar.media.kyoto-u.ac.jp>

Alan G Isaac wrote:
> On Wed, 31 Jan 2007, David Cournapeau apparently wrote: 
>> With pyaudiolab, you should be able to read and write most 
>> common audio files from and to numpy arrays. The 
>> underlying IO operations are done using libsndfile from 
>> Erik Castro Lopo (http://www.mega-nerd.com/libsndfile/) 
>
> I think it is worth mentioning (on this list) that 
> pyaudiolab uses the SciPy license and libsndfile is LGPL.
Indeed, I forgot to mention this fact in the announcement. It is 
mentioned somewhere in the source, but it should be done better. It is 
the only reason that pyaudiolab is not part of scipy.

Your post made me realize that I actually didn't look at how applying 
the license correctly, which is not good at all (that's the first 
project I started from scratch). I will change that.

David


From nwagner at iam.uni-stuttgart.de  Fri Feb  2 02:45:02 2007
From: nwagner at iam.uni-stuttgart.de (Nils Wagner)
Date: Fri, 02 Feb 2007 08:45:02 +0100
Subject: [SciPy-user] asanyarray
Message-ID: <45C2EBFE.3060902@iam.uni-stuttgart.de>

Hi,

I am confused about the behaviour of asanyarray

Python 2.4.1 (#1, Oct 13 2006, 16:51:58)
[GCC 4.0.2 20050901 (prerelease) (SUSE Linux)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from scipy import *
>>> A = io.mmread('mhd416a.mtx.gz')
>>> A
<416x416 sparse matrix of type '<type 'numpy.float64'>'
        with 8562 stored elements in COOrdinate format>
>>> shape(A)
(416, 416)
>>> A=asanyarray(A)
>>> A
array(<416x416 sparse matrix of type '<type 'numpy.float64'>'
        with 8562 stored elements in COOrdinate format>, dtype=object)
>>> shape(A)
()
 
Help on function asanyarray in module numpy.core.numeric:

asanyarray(a, dtype=None, order=None)
    Returns a as an array, but will pass subclasses through.

Why is the shape altered by asanyarray ?

Nils




From robert.kern at gmail.com  Fri Feb  2 02:56:39 2007
From: robert.kern at gmail.com (Robert Kern)
Date: Fri, 02 Feb 2007 01:56:39 -0600
Subject: [SciPy-user] asanyarray
In-Reply-To: <45C2EBFE.3060902@iam.uni-stuttgart.de>
References: <45C2EBFE.3060902@iam.uni-stuttgart.de>
Message-ID: <45C2EEB7.9010305@gmail.com>

Nils Wagner wrote:
> Hi,
> 
> I am confused about the behaviour of asanyarray
> 
> Python 2.4.1 (#1, Oct 13 2006, 16:51:58)
> [GCC 4.0.2 20050901 (prerelease) (SUSE Linux)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
>>>> from scipy import *
>>>> A = io.mmread('mhd416a.mtx.gz')
>>>> A
> <416x416 sparse matrix of type '<type 'numpy.float64'>'
>         with 8562 stored elements in COOrdinate format>
>>>> shape(A)
> (416, 416)
>>>> A=asanyarray(A)
>>>> A
> array(<416x416 sparse matrix of type '<type 'numpy.float64'>'
>         with 8562 stored elements in COOrdinate format>, dtype=object)
>>>> shape(A)
> ()
>  
> Help on function asanyarray in module numpy.core.numeric:
> 
> asanyarray(a, dtype=None, order=None)
>     Returns a as an array, but will pass subclasses through.
> 
> Why is the shape altered by asanyarray ?

Because sparse arrays are not instances of a subclass of numpy.ndarray. Thus,
asanyarray(A) is interpreted as a 0-dim object array.

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
 that is made terrible by our own mad attempt to interpret it as though it had
 an underlying truth."
  -- Umberto Eco


From chiaracaronna at hotmail.com  Fri Feb  2 03:14:15 2007
From: chiaracaronna at hotmail.com (Chiara Caronna)
Date: Fri, 02 Feb 2007 08:14:15 +0000
Subject: [SciPy-user] error importing scipy
In-Reply-To: <e016526e0702011112s10c1b378w33086d41b23ff0f9@mail.gmail.com>
Message-ID: <BAY114-F22DF08E2E0593E8AADB0CCA19B0@phx.gbl>




>From: "Per Jr. Greisen" <pgreisen at gmail.com>
>Reply-To: SciPy Users List <scipy-user at scipy.org>
>To: "SciPy Users List" <scipy-user at scipy.org>
>Subject: Re: [SciPy-user] error importing scipy
>Date: Thu, 1 Feb 2007 20:12:11 +0100
>
>Hi,
>
>Maybe this work . on suse machines there should be a yast to configure new
>programs. From yast it should be possible to get BLAS and LAPACK libraries

Hi, I checked that out, and apparently blas and lapack are already 
installed...
?
>
>(regarding suse 8.4 maybe you should try to upgrade it)

(I really would like, but I can't...)
>
>On 2/1/07, Chiara Caronna <chiaracaronna at hotmail.com> wrote:
>>
>>
>>
>>
>> >From: Robert Kern <robert.kern at gmail.com>
>> >Reply-To: SciPy Users List <scipy-user at scipy.org>
>> >To: SciPy Users List <scipy-user at scipy.org>
>> >Subject: Re: [SciPy-user] error importing scipy
>> >Date: Thu, 01 Feb 2007 11:41:46 -0600
>> >
>> >Chiara Caronna wrote:
>> > >> From: Robert Kern <robert.kern at gmail.com>
>> >
>> > >> Your scipy was not linked to a BLAS library correctly. What BLAS
>> >library
>> > >> were
>> > >> you trying to link against?
>> > >
>> > > '_' ... I have never tried to do that... at least I am not aware 
>>of...
>> >
>> >Okay, what kind of system are you on? If Linux, what distribution?
>>
>>I have Linux, Suse 8.4 (quite old, I know, but I can't change it, it's my
>>office pc...)
>>
>> >What LAPACK and BLAS packages do you have installed?
>>I have never installed them... how can I check which I have?
>>
>>
>>
>> >
>> >--
>> >Robert Kern
>> >
>> >"I have come to believe that the whole world is an enigma, a harmless
>> >enigma
>> >  that is made terrible by our own mad attempt to interpret it as though
>>it
>> >had
>> >  an underlying truth."
>> >   -- Umberto Eco
>> >_______________________________________________
>> >SciPy-user mailing list
>> >SciPy-user at scipy.org
>> >http://projects.scipy.org/mailman/listinfo/scipy-user
>>
>>_________________________________________________________________
>>Express yourself instantly with MSN Messenger! Download today it's FREE!
>>http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
>>
>>_______________________________________________
>>SciPy-user mailing list
>>SciPy-user at scipy.org
>>http://projects.scipy.org/mailman/listinfo/scipy-user
>>
>
>
>
>--
>Best regards
>Per Jr. Greisen
>
>"If you make something idiot-proof, the universe creates a better idiot."


>_______________________________________________
>SciPy-user mailing list
>SciPy-user at scipy.org
>http://projects.scipy.org/mailman/listinfo/scipy-user

_________________________________________________________________
Express yourself instantly with MSN Messenger! Download today it's FREE! 
http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/



From nwagner at iam.uni-stuttgart.de  Fri Feb  2 03:22:26 2007
From: nwagner at iam.uni-stuttgart.de (Nils Wagner)
Date: Fri, 02 Feb 2007 09:22:26 +0100
Subject: [SciPy-user] arpack.speigs.ARPACK_gen_eigs
Message-ID: <45C2F4C2.5090307@iam.uni-stuttgart.de>

Hi,

The shift must be real in arpack.speigs.ARPACK_gen_eigs.
For what reason ?

How can I compute the eigenvalues enclosed by the green circle ?
 
Nils


-------------- next part --------------
A non-text attachment was scrubbed...
Name: arpack.png
Type: image/png
Size: 26196 bytes
Desc: not available
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20070202/76703a4d/attachment.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: test_ARPACK_gen_eigs.py
Type: text/x-python
Size: 883 bytes
Desc: not available
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20070202/76703a4d/attachment.py>

From nwagner at iam.uni-stuttgart.de  Fri Feb  2 03:27:24 2007
From: nwagner at iam.uni-stuttgart.de (Nils Wagner)
Date: Fri, 02 Feb 2007 09:27:24 +0100
Subject: [SciPy-user] error importing scipy
In-Reply-To: <BAY114-F22DF08E2E0593E8AADB0CCA19B0@phx.gbl>
References: <BAY114-F22DF08E2E0593E8AADB0CCA19B0@phx.gbl>
Message-ID: <45C2F5EC.8030501@iam.uni-stuttgart.de>

Chiara Caronna wrote:
>
>   
>> From: "Per Jr. Greisen" <pgreisen at gmail.com>
>> Reply-To: SciPy Users List <scipy-user at scipy.org>
>> To: "SciPy Users List" <scipy-user at scipy.org>
>> Subject: Re: [SciPy-user] error importing scipy
>> Date: Thu, 1 Feb 2007 20:12:11 +0100
>>
>> Hi,
>>
>> Maybe this work . on suse machines there should be a yast to configure new
>> programs. From yast it should be possible to get BLAS and LAPACK libraries
>>     
>
> Hi, I checked that out, and apparently blas and lapack are already 
> installed...
> ?
>   
The problem is that the libraries shipped by SUSE are incomplete !
Please remove the rpm's and compile BLAS and LAPACK from scratch.

http://www.scipy.org/Installing_SciPy/BuildingGeneral?highlight=%28%28----%28-%2A%29%28%5Cr%29%3F%5Cn%29%28.%2A%29CategoryInstallation%5Cb%29#head-e618da78f29d5a85f680cc47e574a84951c8dffb

Nils

>> (regarding suse 8.4 maybe you should try to upgrade it)
>>     
>
> (I really would like, but I can't...)
>   
>> On 2/1/07, Chiara Caronna <chiaracaronna at hotmail.com> wrote:
>>     
>>>
>>>
>>>       
>>>> From: Robert Kern <robert.kern at gmail.com>
>>>> Reply-To: SciPy Users List <scipy-user at scipy.org>
>>>> To: SciPy Users List <scipy-user at scipy.org>
>>>> Subject: Re: [SciPy-user] error importing scipy
>>>> Date: Thu, 01 Feb 2007 11:41:46 -0600
>>>>
>>>> Chiara Caronna wrote:
>>>>         
>>>>>> From: Robert Kern <robert.kern at gmail.com>
>>>>>>             
>>>>>> Your scipy was not linked to a BLAS library correctly. What BLAS
>>>>>>             
>>>> library
>>>>         
>>>>>> were
>>>>>> you trying to link against?
>>>>>>             
>>>>> '_' ... I have never tried to do that... at least I am not aware 
>>>>>           
>>> of...
>>>       
>>>> Okay, what kind of system are you on? If Linux, what distribution?
>>>>         
>>> I have Linux, Suse 8.4 (quite old, I know, but I can't change it, it's my
>>> office pc...)
>>>
>>>       
>>>> What LAPACK and BLAS packages do you have installed?
>>>>         
>>> I have never installed them... how can I check which I have?
>>>
>>>
>>>
>>>       
>>>> --
>>>> Robert Kern
>>>>
>>>> "I have come to believe that the whole world is an enigma, a harmless
>>>> enigma
>>>>  that is made terrible by our own mad attempt to interpret it as though
>>>>         
>>> it
>>>       
>>>> had
>>>>  an underlying truth."
>>>>   -- Umberto Eco
>>>> _______________________________________________
>>>> SciPy-user mailing list
>>>> SciPy-user at scipy.org
>>>> http://projects.scipy.org/mailman/listinfo/scipy-user
>>>>         
>>> _________________________________________________________________
>>> Express yourself instantly with MSN Messenger! Download today it's FREE!
>>> http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
>>>
>>> _______________________________________________
>>> SciPy-user mailing list
>>> SciPy-user at scipy.org
>>> http://projects.scipy.org/mailman/listinfo/scipy-user
>>>
>>>       
>>
>> --
>> Best regards
>> Per Jr. Greisen
>>
>> "If you make something idiot-proof, the universe creates a better idiot."
>>     
>
>
>   
>> _______________________________________________
>> SciPy-user mailing list
>> SciPy-user at scipy.org
>> http://projects.scipy.org/mailman/listinfo/scipy-user
>>     
>
> _________________________________________________________________
> Express yourself instantly with MSN Messenger! Download today it's FREE! 
> http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
>
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user
>   
 


From suhlhorn at gmail.com  Fri Feb  2 13:57:24 2007
From: suhlhorn at gmail.com (Stephen Uhlhorn)
Date: Fri, 2 Feb 2007 13:57:24 -0500
Subject: [SciPy-user] NameError on scipy import
In-Reply-To: <45C27554.4020408@gmail.com>
References: <47edc1a0702011233j5e280f52i40ac4237aca764c8@mail.gmail.com>
	<45C25070.2010004@gmail.com>
	<47edc1a0702011313v6c359d5aude097f23389758a0@mail.gmail.com>
	<45C258D3.2030907@gmail.com>
	<47edc1a0702011511g290bb0dk1a1f95506a605fc9@mail.gmail.com>
	<45C27554.4020408@gmail.com>
Message-ID: <47edc1a0702021057g64013cb1nccac4a250e474ae2@mail.gmail.com>

I followed your directions below up to the point of installing
matplotlib (my real purpose). After getting numpy/scipy built
correctly (now they are), can I use the matplotlib binary .egg
installation with the wxpython library?

-stephen

On 2/1/07, Robert Kern <robert.kern at gmail.com> wrote:

> You will need to use gfortran for a Universal build of Python on Tiger. g77 does
> not build Universal binaries. See the instructions I give here:
>
> http://projects.scipy.org/pipermail/numpy-discussion/2007-January/025368.html


From robert.kern at gmail.com  Fri Feb  2 14:25:43 2007
From: robert.kern at gmail.com (Robert Kern)
Date: Fri, 02 Feb 2007 13:25:43 -0600
Subject: [SciPy-user] NameError on scipy import
In-Reply-To: <47edc1a0702021057g64013cb1nccac4a250e474ae2@mail.gmail.com>
References: <47edc1a0702011233j5e280f52i40ac4237aca764c8@mail.gmail.com>	<45C25070.2010004@gmail.com>	<47edc1a0702011313v6c359d5aude097f23389758a0@mail.gmail.com>	<45C258D3.2030907@gmail.com>	<47edc1a0702011511g290bb0dk1a1f95506a605fc9@mail.gmail.com>	<45C27554.4020408@gmail.com>
	<47edc1a0702021057g64013cb1nccac4a250e474ae2@mail.gmail.com>
Message-ID: <45C39037.5040303@gmail.com>

Stephen Uhlhorn wrote:
> I followed your directions below up to the point of installing
> matplotlib (my real purpose). After getting numpy/scipy built
> correctly (now they are), can I use the matplotlib binary .egg
> installation with the wxpython library?

I don't know. I don't pay attention to the matplotlib binary releases. Try it
and see. If it doesn't work, then an egg is easy enough to uninstall.

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
 that is made terrible by our own mad attempt to interpret it as though it had
 an underlying truth."
  -- Umberto Eco


From griffitts_lists at comcast.net  Sat Feb  3 17:11:08 2007
From: griffitts_lists at comcast.net (Jonathan Griffitts)
Date: Sat, 3 Feb 2007 15:11:08 -0700
Subject: [SciPy-user] Windows binary 0.5.2 requires SSE2
Message-ID: <OwABvSK8hQxFFA0a@griffitts.org>

Hi!

I have installed SciPy 0.5.2 for Python 2.5 on several Windows
computers, using the precompiled binary scipy-0.5.2.win32-py2.5.exe.
This works fine on some, but on others it crashes Python with an Illegal
Instruction exception.  The crash is easy to find by running the test()
suite or by attempting to make any use of scipy.integrate.quad.

Digging into it, I see that the exception comes from _quadpack.pyd, and
it dies at a MOVSD instruction.  I believe MOVSD is an SSE2 instruction
that is only implemented on the more recent CPUs from both Intel and
AMD.

Has anyone out there compiled win32 binaries for Python 2.5 and older
CPUs without SSE2?  If so, could I beg for a copy?  If not, I'll dig
into getting set up to compile SciPy myself.

                        Thanks,
-- 
                        Jonathan Griffitts
AnyWare Engineering                             Boulder, CO, USA



From hasslerjc at comcast.net  Sat Feb  3 17:47:04 2007
From: hasslerjc at comcast.net (John Hassler)
Date: Sat, 03 Feb 2007 17:47:04 -0500
Subject: [SciPy-user] Windows binary 0.5.2 requires SSE2
In-Reply-To: <OwABvSK8hQxFFA0a@griffitts.org>
References: <OwABvSK8hQxFFA0a@griffitts.org>
Message-ID: <45C510E8.3060602@comcast.net>

An HTML attachment was scrubbed...
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20070203/c46d40d5/attachment.html>

From v-nijs at kellogg.northwestern.edu  Sun Feb  4 18:06:29 2007
From: v-nijs at kellogg.northwestern.edu (Vincent Nijs)
Date: Sun, 04 Feb 2007 17:06:29 -0600
Subject: [SciPy-user] QME-Dev wxSciPY workbench 0.0.9.24 released -
 updated and corrected for Python 2.4
In-Reply-To: <20070128135932.6628.qmail@web27407.mail.ukl.yahoo.com>
Message-ID: <C1EBC315.4826%v-nijs@kellogg.northwestern.edu>

Has anyone been able to run workbench on a mac, os x 10.4 ppc, Python 2.4,
wxPython 2.8. When I try to run it, it seems to start but then quits before
anything appears on screen without any error messages.

Vincent


On 1/28/07 7:59 AM, "Robert VERGNES" <robert.vergnes at yahoo.fr> wrote:

> Version Alpha 0.0.9.2.4 updated today.
> 
> New ZIP file for download.
> 
> Correction made to the plotting/Graph issue with Python 2.4
> + Example files added for review of workbench.
> 
> https://sourceforge.net/project/showfiles.php?group_id=181979
> 
> Note: wxPython 2.8 is still necessary to run the wrokbench.
> 
>  
> 
>  D?couvrez une nouvelle fa?on d'obtenir des r?ponses ? toutes vos questions !
> Profitez des connaissances, des opinions et des exp?riences des internautes
> sur Yahoo! Questions/R?ponses
> <http://fr.rd.yahoo.com/evt=42054/*http://fr.answers.yahoo.com> .
> 
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20070204/73a9ae22/attachment.html>

From edschofield at gmail.com  Sun Feb  4 19:40:15 2007
From: edschofield at gmail.com (Ed Schofield)
Date: Mon, 5 Feb 2007 01:40:15 +0100
Subject: [SciPy-user] RHEL 4 SciPy Install Failure
In-Reply-To: <eooohd$mbu$1@sea.gmane.org>
References: <eooohd$mbu$1@sea.gmane.org>
Message-ID: <1b5a37350702041640r23d5be9enbd498f6bda97e923@mail.gmail.com>

On 1/18/07, Chad Kidder <cckidder at gmail.com> wrote:
>
> I was trying to install SciPy today after a successful numpy install and
> it went
> well until it got to the fortran compilation of dfftpack.  Below is an
> exerpt of
> the error.  Anyone know what's going on?


We've improved the CPU detection code in NumPy SVN so SciPy compiles on
Core2 CPUs. If you want a simple patch to get it working, without moving to
NumPy SVN, apply this:

http://projects.scipy.org/scipy/numpy/changeset/3538

-- Ed
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20070205/62038ed6/attachment.html>

From gael.varoquaux at normalesup.org  Mon Feb  5 02:00:19 2007
From: gael.varoquaux at normalesup.org (Gael Varoquaux)
Date: Mon, 5 Feb 2007 08:00:19 +0100
Subject: [SciPy-user] Getting started wiki page
In-Reply-To: <45AD641F.3080406@ru.nl>
References: <20070111225611.GD4479@clipper.ens.fr> <45AD641F.3080406@ru.nl>
Message-ID: <20070205070019.GB9953@clipper.ens.fr>

Hi Stef,

Sorry for taking so long to answer your mail, I am a bit overwhelmed
currently.

On Wed, Jan 17, 2007 at 12:47:43AM +0100, Stef Mientki wrote:
>    apparently not everybody is allowed to edit the pages,

Just create an account and log in.

>    I saw yesterday the lecture of Eric Jones, Travis Oliphant,
>    despite the not-overwhelming image quality, I think it's real information
>    for newbies.
>    And if the lecture is too long, at least the handouts are great !!

The lecture is pretty good as it presents python first and numpy/scipy
afterward. It is quite outdated, though (reference to numeric and to
another plotting library than matplotlib) so I am not to keen on linking
it from the "Getting_Started" page, as it might confuse beginners.

The goal of the "Getting_Started" page is not to provide a tutorial, but
to proivde links to the minimal amount of reading needed to start hacking
in python, and to provide info that is not in tutorials (like wha modules
to use, for instance).

>    Another interesting point for newbies, might be an overview of
>    variable types, what's the difference between list and tupple ? I
>    have put my personal notes on my website, maybe it's worth to
>    include something like this

I think this should go in a mini python tutorial, just like the first
part of Travis and Eric's talk. If you want to create a page on the scipy
wiki that is a mini python tutorial and add this data to it, I think it
would be great. Such a page, combined with Dave Kuhlman's course, would
be great to get people started.

Regards,

Ga?l



From chiaracaronna at hotmail.com  Mon Feb  5 10:38:13 2007
From: chiaracaronna at hotmail.com (Chiara Caronna)
Date: Mon, 05 Feb 2007 15:38:13 +0000
Subject: [SciPy-user] newbie: easy question (I hope)
In-Reply-To: <45C2F5EC.8030501@iam.uni-stuttgart.de>
Message-ID: <BAY114-F38A5D3E801C1C6C5F221C4A1980@phx.gbl>

Hi,
I have an old code, where I used numarray, and there is this command:
where c is a 1d array

c= unpack(format, string)
ccdimage=N.array(c,shape=[nrows,ncol])

if I use array from numpy I got this error:

"shape is an invalid keyword argument for this function"
I need to transform c in an array of shape [nrows,ncol], how can I do it 
with numpy?

_________________________________________________________________
Don't just search. Find. Check out the new MSN Search! 
http://search.msn.com/



From gael.varoquaux at normalesup.org  Mon Feb  5 11:54:16 2007
From: gael.varoquaux at normalesup.org (Gael Varoquaux)
Date: Mon, 5 Feb 2007 17:54:16 +0100
Subject: [SciPy-user] newbie: easy question (I hope)
In-Reply-To: <BAY114-F38A5D3E801C1C6C5F221C4A1980@phx.gbl>
References: <45C2F5EC.8030501@iam.uni-stuttgart.de>
	<BAY114-F38A5D3E801C1C6C5F221C4A1980@phx.gbl>
Message-ID: <20070205165415.GE17139@clipper.ens.fr>

On Mon, Feb 05, 2007 at 03:38:13PM +0000, Chiara Caronna wrote:
> I have an old code, where I used numarray, and there is this command:
> where c is a 1d array

> c= unpack(format, string)
> ccdimage=N.array(c,shape=[nrows,ncol])

> if I use array from numpy I got this error:

> "shape is an invalid keyword argument for this function"
> I need to transform c in an array of shape [nrows,ncol], how can I do it 
> with numpy?

c is an array, right, not, a list.

Then you can do something like

c = unpack(format, string)
ccdimage = N.reshape(c, (nrows, nol)) 

If c is a list you can convert it to a 1D array using N.array(c).

HTH,

Ga?l


From chiaracaronna at hotmail.com  Mon Feb  5 11:55:35 2007
From: chiaracaronna at hotmail.com (Chiara Caronna)
Date: Mon, 05 Feb 2007 16:55:35 +0000
Subject: [SciPy-user] newbie: easy question (I hope)
In-Reply-To: <20070205165415.GE17139@clipper.ens.fr>
Message-ID: <BAY114-F285A0307F1CB2EA09F4119A1980@phx.gbl>

it works, thank you!
Chiara


>From: Gael Varoquaux <gael.varoquaux at normalesup.org>
>Reply-To: SciPy Users List <scipy-user at scipy.org>
>To: SciPy Users List <scipy-user at scipy.org>
>Subject: Re: [SciPy-user] newbie: easy question (I hope)
>Date: Mon, 5 Feb 2007 17:54:16 +0100
>
>On Mon, Feb 05, 2007 at 03:38:13PM +0000, Chiara Caronna wrote:
> > I have an old code, where I used numarray, and there is this command:
> > where c is a 1d array
>
> > c= unpack(format, string)
> > ccdimage=N.array(c,shape=[nrows,ncol])
>
> > if I use array from numpy I got this error:
>
> > "shape is an invalid keyword argument for this function"
> > I need to transform c in an array of shape [nrows,ncol], how can I do it
> > with numpy?
>
>c is an array, right, not, a list.
>
>Then you can do something like
>
>c = unpack(format, string)
>ccdimage = N.reshape(c, (nrows, nol))
>
>If c is a list you can convert it to a 1D array using N.array(c).
>
>HTH,
>
>Ga?l
>_______________________________________________
>SciPy-user mailing list
>SciPy-user at scipy.org
>http://projects.scipy.org/mailman/listinfo/scipy-user

_________________________________________________________________
Express yourself instantly with MSN Messenger! Download today it's FREE! 
http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/



From oliphant at ee.byu.edu  Mon Feb  5 14:20:59 2007
From: oliphant at ee.byu.edu (Travis Oliphant)
Date: Mon, 05 Feb 2007 12:20:59 -0700
Subject: [SciPy-user] newbie: easy question (I hope)
In-Reply-To: <BAY114-F38A5D3E801C1C6C5F221C4A1980@phx.gbl>
References: <BAY114-F38A5D3E801C1C6C5F221C4A1980@phx.gbl>
Message-ID: <45C7839B.7080904@ee.byu.edu>

Chiara Caronna wrote:

>Hi,
>I have an old code, where I used numarray, and there is this command:
>where c is a 1d array
>
>c= unpack(format, string)
>ccdimage=N.array(c,shape=[nrows,ncol])
>
>if I use array from numpy I got this error:
>
>"shape is an invalid keyword argument for this function"
>I need to transform c in an array of shape [nrows,ncol], how can I do it 
>with numpy?
>  
>
What exactly are you asking?

If you want to use numarray-compatibile syntax then use the 
numpy.numarray module like this

import numpy.numarray as N

This is a compatibility-layer and is not recommended except for porting 
older code.

Otherwise you change the shape of an array using the reshape method or 
setting the shape attribute of an ndarray.

-Travis



From chiaracaronna at hotmail.com  Mon Feb  5 14:25:49 2007
From: chiaracaronna at hotmail.com (Chiara Caronna)
Date: Mon, 05 Feb 2007 19:25:49 +0000
Subject: [SciPy-user] newbie: easy question (I hope)
In-Reply-To: <45C7839B.7080904@ee.byu.edu>
Message-ID: <BAY114-F266108E3CE770367150949A1980@phx.gbl>




>From: Travis Oliphant <oliphant at ee.byu.edu>
>Reply-To: SciPy Users List <scipy-user at scipy.org>
>To: SciPy Users List <scipy-user at scipy.org>
>Subject: Re: [SciPy-user] newbie: easy question (I hope)
>Date: Mon, 05 Feb 2007 12:20:59 -0700
>
>Chiara Caronna wrote:
>
> >Hi,
> >I have an old code, where I used numarray, and there is this command:
> >where c is a 1d array
> >
> >c= unpack(format, string)
> >ccdimage=N.array(c,shape=[nrows,ncol])
> >
> >if I use array from numpy I got this error:
> >
> >"shape is an invalid keyword argument for this function"
> >I need to transform c in an array of shape [nrows,ncol], how can I do it
> >with numpy?
> >
> >
>What exactly are you asking?
>
>If you want to use numarray-compatibile syntax then use the
>numpy.numarray module like this
>
>import numpy.numarray as N
>
>This is a compatibility-layer and is not recommended except for porting
>older code.
>
>Otherwise you change the shape of an array using the reshape method or
>setting the shape attribute of an ndarray.
>

Actually I wanted to remove all the numarray syntax from my code... they are 
not so much and I prefer to have a "cleaner" code.
I used the reshape method, thanks

Chiara

>-Travis
>
>_______________________________________________
>SciPy-user mailing list
>SciPy-user at scipy.org
>http://projects.scipy.org/mailman/listinfo/scipy-user

_________________________________________________________________
Express yourself instantly with MSN Messenger! Download today it's FREE! 
http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/



From ewald.zietsman at gmail.com  Tue Feb  6 03:02:26 2007
From: ewald.zietsman at gmail.com (Ewald Zietsman)
Date: Tue, 6 Feb 2007 10:02:26 +0200
Subject: [SciPy-user] scipy.optimize.leastsq error estimates
Message-ID: <be152e7d0702060002q4966192bl75f72b8aed12437f@mail.gmail.com>

Hi all,

I want to fit a sinusoid of the form A*cos(2*pi*f*t) + B*sin(2*pi*f*t) to
irregularly spaced data so that I can get a wave of the  form C*cos(2*pi*f*t
+ phi) where C**2 = A**2 + B**2 and phi = arctan(-B/A). I have implemented
this using the leastsq function but, I'd would like to also know the
variances ( or standard errors ) of A,B and f. Is there a way I can get the
variance-covariance matrix out from leastsq? or at least get a good estimate
of the standard errors of my unknowns?

-Ewald Zietsman
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20070206/a8719bcf/attachment.html>

From ckkart at hoc.net  Tue Feb  6 03:06:50 2007
From: ckkart at hoc.net (Christian Kristukat)
Date: Tue, 06 Feb 2007 17:06:50 +0900
Subject: [SciPy-user] scipy.optimize.leastsq error estimates
In-Reply-To: <be152e7d0702060002q4966192bl75f72b8aed12437f@mail.gmail.com>
References: <be152e7d0702060002q4966192bl75f72b8aed12437f@mail.gmail.com>
Message-ID: <45C8371A.9040608@hoc.net>

Ewald Zietsman wrote:
> Hi all,
> 
> I want to fit a sinusoid of the form A*cos(2*pi*f*t) + B*sin(2*pi*f*t)
> to irregularly spaced data so that I can get a wave of the  form
> C*cos(2*pi*f*t + phi) where C**2 = A**2 + B**2 and phi = arctan(-B/A). I
> have implemented this using the leastsq function but, I'd would like to
> also know the variances ( or standard errors ) of A,B and f. Is there a
> way I can get the variance-covariance matrix out from leastsq? or at
> least get a good estimate of the standard errors of my unknowns?

When setting full_output=True leastsq will return the covraiance matrix:

      cov_x -- uses the fjac and ipvt optional outputs to construct an
               estimate of the covariance matrix of the solution.
               None if a singular matrix encountered (indicates
               infinite covariance in some direction).

However I recommend using scipy.sandbox.odr instead which returns confidence
intervals for all parameters.

Christian


From nwagner at iam.uni-stuttgart.de  Tue Feb  6 03:14:08 2007
From: nwagner at iam.uni-stuttgart.de (Nils Wagner)
Date: Tue, 06 Feb 2007 09:14:08 +0100
Subject: [SciPy-user] scipy.optimize.leastsq error estimates
In-Reply-To: <45C8371A.9040608@hoc.net>
References: <be152e7d0702060002q4966192bl75f72b8aed12437f@mail.gmail.com>
	<45C8371A.9040608@hoc.net>
Message-ID: <45C838D0.6060404@iam.uni-stuttgart.de>

Christian Kristukat wrote:
> Ewald Zietsman wrote:
>   
>> Hi all,
>>
>> I want to fit a sinusoid of the form A*cos(2*pi*f*t) + B*sin(2*pi*f*t)
>> to irregularly spaced data so that I can get a wave of the  form
>> C*cos(2*pi*f*t + phi) where C**2 = A**2 + B**2 and phi = arctan(-B/A). I
>> have implemented this using the leastsq function but, I'd would like to
>> also know the variances ( or standard errors ) of A,B and f. Is there a
>> way I can get the variance-covariance matrix out from leastsq? or at
>> least get a good estimate of the standard errors of my unknowns?
>>     
>
> When setting full_output=True leastsq will return the covraiance matrix:
>
>       cov_x -- uses the fjac and ipvt optional outputs to construct an
>                estimate of the covariance matrix of the solution.
>                None if a singular matrix encountered (indicates
>                infinite covariance in some direction).
>
> However I recommend using scipy.sandbox.odr instead which returns confidence
> intervals for all parameters.
>
> Christian
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user
>   
 
AFAIK odr is directly available through scipy.odr.
So I guess the odr directory in the sandbox is obsolete. Is that correct ?

Nils



From ckkart at hoc.net  Tue Feb  6 03:37:46 2007
From: ckkart at hoc.net (Christian Kristukat)
Date: Tue, 06 Feb 2007 17:37:46 +0900
Subject: [SciPy-user] scipy.optimize.leastsq error estimates
In-Reply-To: <45C838D0.6060404@iam.uni-stuttgart.de>
References: <be152e7d0702060002q4966192bl75f72b8aed12437f@mail.gmail.com>	<45C8371A.9040608@hoc.net>
	<45C838D0.6060404@iam.uni-stuttgart.de>
Message-ID: <45C83E5A.90101@hoc.net>

Nils Wagner wrote:
>  
> AFAIK odr is directly available through scipy.odr.
> So I guess the odr directory in the sandbox is obsolete. Is that correct ?
> 

At least not in scipy 0.5.2.dev2299. Might be differnt in svn.

Christian


From nwagner at iam.uni-stuttgart.de  Tue Feb  6 03:47:00 2007
From: nwagner at iam.uni-stuttgart.de (Nils Wagner)
Date: Tue, 06 Feb 2007 09:47:00 +0100
Subject: [SciPy-user] scipy.optimize.leastsq error estimates
In-Reply-To: <45C83E5A.90101@hoc.net>
References: <be152e7d0702060002q4966192bl75f72b8aed12437f@mail.gmail.com>	<45C8371A.9040608@hoc.net>	<45C838D0.6060404@iam.uni-stuttgart.de>
	<45C83E5A.90101@hoc.net>
Message-ID: <45C84084.9080305@iam.uni-stuttgart.de>

Christian Kristukat wrote:
> Nils Wagner wrote:
>   
>>  
>> AFAIK odr is directly available through scipy.odr.
>> So I guess the odr directory in the sandbox is obsolete. Is that correct ?
>>
>>     
>
> At least not in scipy 0.5.2.dev2299. Might be differnt in svn.
>
> Christian
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user
>   
I am using

>>> scipy.__version__
'0.5.3.dev2667'


Nils



From robert.kern at gmail.com  Tue Feb  6 04:47:17 2007
From: robert.kern at gmail.com (Robert Kern)
Date: Tue, 06 Feb 2007 03:47:17 -0600
Subject: [SciPy-user] scipy.optimize.leastsq error estimates
In-Reply-To: <45C838D0.6060404@iam.uni-stuttgart.de>
References: <be152e7d0702060002q4966192bl75f72b8aed12437f@mail.gmail.com>	<45C8371A.9040608@hoc.net>
	<45C838D0.6060404@iam.uni-stuttgart.de>
Message-ID: <45C84EA5.8080307@gmail.com>

Nils Wagner wrote:

> AFAIK odr is directly available through scipy.odr.
> So I guess the odr directory in the sandbox is obsolete. Is that correct ?

There is no more odr/ directory in the sandbox since it got moved into the main
package.

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
 that is made terrible by our own mad attempt to interpret it as though it had
 an underlying truth."
  -- Umberto Eco


From joshuafr at gmail.com  Tue Feb  6 05:42:09 2007
From: joshuafr at gmail.com (Joshua Petterson)
Date: Tue, 6 Feb 2007 11:42:09 +0100
Subject: [SciPy-user] errors with scipy.stats
Message-ID: <e59181230702060242k4ecb2f55ode945a7d11d7cbd0@mail.gmail.com>

Hi,
I'm going into trouble with scipy.stats, does someone can explain me that?:
#############################
|datas|[135]>import scipy.stats

|datas|[136]>a.dtype
   Out [136]:dtype('float64')

|datas|[137]>a.fill_value()
   Out [137]:-9.9999999999999995e-21

|datas|[138]>a.shape
   Out [138]:(744,)

|datas|[144]>a.max()
   Out [144]:36.0

|datas|[146]>a.min()
   Out [146]:0.0

|datas|[147]>a.mean()
   Out [147]:array(3.20519835841)

|datas|[148]>stats.mean(a)
   Out [148]:1750.47849462

|datas|[152]>his = stats.histogram2(a, [0,10,20,30,40,50])

|datas|[153]>his
   Out [153]:array([692,  27,  10,   2,   0,  13])
#########################
then mean and histogram2 give wrong results!

Thanks for your help!
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20070206/83f26be0/attachment.html>

From v-nijs at kellogg.northwestern.edu  Tue Feb  6 13:00:29 2007
From: v-nijs at kellogg.northwestern.edu (Vincent Nijs)
Date: Tue, 06 Feb 2007 12:00:29 -0600
Subject: [SciPy-user] Installing umfpack on mac?
In-Reply-To: <e59181230702060242k4ecb2f55ode945a7d11d7cbd0@mail.gmail.com>
Message-ID: <C1EE1E5D.4877%v-nijs@kellogg.northwestern.edu>

Are there any installation instructions for installing umfpack on mac? I
tried install suitesparse via macports but this seems to be broken.

Vincent




-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20070206/544cf4ea/attachment.html>

From robert.kern at gmail.com  Tue Feb  6 13:24:46 2007
From: robert.kern at gmail.com (Robert Kern)
Date: Tue, 06 Feb 2007 12:24:46 -0600
Subject: [SciPy-user] errors with scipy.stats
In-Reply-To: <e59181230702060242k4ecb2f55ode945a7d11d7cbd0@mail.gmail.com>
References: <e59181230702060242k4ecb2f55ode945a7d11d7cbd0@mail.gmail.com>
Message-ID: <45C8C7EE.8010401@gmail.com>

Joshua Petterson wrote:
> Hi,
> I'm going into trouble with scipy.stats, does someone can explain me that?:
> #############################
> |datas|[135]>import scipy.stats
> 
> |datas|[136]>a.dtype
>    Out [136]:dtype('float64')
> 
> |datas|[137]>a.fill_value()
>    Out [137]:-9.9999999999999995e-21

This appears like a is a masked array, correct? Not all of the functions in
scipy.stats support masked arrays. The methods on masked arrays do support
masked arrays, of course.

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
 that is made terrible by our own mad attempt to interpret it as though it had
 an underlying truth."
  -- Umberto Eco


From pgmdevlist at gmail.com  Tue Feb  6 13:32:20 2007
From: pgmdevlist at gmail.com (Pierre GM)
Date: Tue, 6 Feb 2007 13:32:20 -0500
Subject: [SciPy-user] errors with scipy.stats
In-Reply-To: <45C8C7EE.8010401@gmail.com>
References: <e59181230702060242k4ecb2f55ode945a7d11d7cbd0@mail.gmail.com>
	<45C8C7EE.8010401@gmail.com>
Message-ID: <200702061332.20674.pgmdevlist@gmail.com>

On Tuesday 06 February 2007 13:24:46 Robert Kern wrote:

> This appears like a is a masked array, correct? Not all of the functions in
> scipy.stats support masked arrays. The methods on masked arrays do support
> masked arrays, of course.

If the data is 1D or can be ravelled safely, you can try to compress it before 
applying stats methods. At least you get rid of your masked data...


From david.warde.farley at utoronto.ca  Tue Feb  6 16:37:18 2007
From: david.warde.farley at utoronto.ca (David Warde-Farley)
Date: Tue, 6 Feb 2007 16:37:18 -0500
Subject: [SciPy-user] find(M) equivalent for sparse matrices?
Message-ID: <B769C3E8-1BFA-4AE5-8F03-B93B4BB8C14C@utoronto.ca>

Hi there,

I'm porting some Matlab code to Numpy and having some trouble.  
Basically, in the matlab code we have a line that does a find() on a  
sparse matrix and grabs out the rows, columns and values of the non- 
zero element positions. It then modifies each element in a manner  
dependent on its row and column, and then stores all the elements  
back into their original spots.

I can't figure out a way to do this, as comparisons don't  seem to be  
implemented for the sparse matrix classes. I suppose I should mention  
I'm using Python 2.4, scipy 0.5.1, numpy 1.0.

Anyone got an idea of how to do this?

By the way, what I'm doing can be expressed as left and right  
multiplying it by a (the same on both sides) diagonal matrix, but  
this appears to take a lot longer than it should when I write it that  
way (with the diagonal stored as a sparse).

David


From emsellem at obs.univ-lyon1.fr  Wed Feb  7 08:07:34 2007
From: emsellem at obs.univ-lyon1.fr (Eric Emsellem)
Date: Wed, 07 Feb 2007 14:07:34 +0100
Subject: [SciPy-user] back with a problem in scipy installation...
In-Reply-To: <45BF808B.1090807@gmail.com>
References: 45B46D75.5030300@obs.univ-lyon1.fr	<45B4883A.2050606@obs.univ-lyon1.fr>
	<45B4F692.6080904@gmail.com> <45BF6B41.304@obs.univ-lyon1.fr>
	<45BF808B.1090807@gmail.com>
Message-ID: <45C9CF16.1060607@obs.univ-lyon1.fr>

An HTML attachment was scrubbed...
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20070207/d03326de/attachment.html>

From sgarcia at olfac.univ-lyon1.fr  Wed Feb  7 08:49:17 2007
From: sgarcia at olfac.univ-lyon1.fr (Samuel GARCIA)
Date: Wed, 07 Feb 2007 14:49:17 +0100
Subject: [SciPy-user] FFT speed ?
Message-ID: <45C9D8DD.9040101@olfac.univ-lyon1.fr>

Hello list,

I have a problem with fft speed.
could someone try this :

from scipy import *
import time

a = rand((186888));t1=time.time();fft(a);t2=time.time();t2-t1

# for me about 0.67791390419006348 s. on centrino 1.6GHz

a = rand((186890));t1=time.time();fft(a);t2=time.time();t2-t1

# for me about 1.622053861618042 s. on centrino 1.6GHz

a = rand((186889));t1=time.time();fft(a);t2=time.time();t2-t1

# the computation is infinit !!!! (no time to wait)


Question : why is there a problem specialy for that size (186889) of fft ?
It is not the only size with that problem.


Thank

Sam


-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Samuel Garcia
Universite Claude Bernard LYON 1
CNRS - UMR5020, Laboratoire des Neurosciences et Systemes Sensoriels
50, avenue Tony Garnier
69366 LYON Cedex 07
FRANCE
T?l : 04 37 28 74 64
Fax : 04 37 28 76 01
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~



From nwagner at iam.uni-stuttgart.de  Wed Feb  7 08:59:00 2007
From: nwagner at iam.uni-stuttgart.de (Nils Wagner)
Date: Wed, 07 Feb 2007 14:59:00 +0100
Subject: [SciPy-user] FFT speed ?
In-Reply-To: <45C9D8DD.9040101@olfac.univ-lyon1.fr>
References: <45C9D8DD.9040101@olfac.univ-lyon1.fr>
Message-ID: <45C9DB24.6080805@iam.uni-stuttgart.de>

Samuel GARCIA wrote:
> Hello list,
>
> I have a problem with fft speed.
> could someone try this :
>
> from scipy import *
> import time
>
> a = rand((186888));t1=time.time();fft(a);t2=time.time();t2-t1
>
> # for me about 0.67791390419006348 s. on centrino 1.6GHz
>
> a = rand((186890));t1=time.time();fft(a);t2=time.time();t2-t1
>
> # for me about 1.622053861618042 s. on centrino 1.6GHz
>
> a = rand((186889));t1=time.time();fft(a);t2=time.time();t2-t1
>
> # the computation is infinit !!!! (no time to wait)
>
>
> Question : why is there a problem specialy for that size (186889) of fft ?
> It is not the only size with that problem.
>
>
> Thank
>
> Sam
>
>
>   
What you can find with help (fft) is ...

"This is most efficient for n a power of two"

Nils


 



From ckkart at hoc.net  Wed Feb  7 09:02:23 2007
From: ckkart at hoc.net (Christian Kristukat)
Date: Wed, 07 Feb 2007 23:02:23 +0900
Subject: [SciPy-user] FFT speed ?
In-Reply-To: <45C9D8DD.9040101@olfac.univ-lyon1.fr>
References: <45C9D8DD.9040101@olfac.univ-lyon1.fr>
Message-ID: <45C9DBEF.8090205@hoc.net>

Samuel GARCIA wrote:
> Hello list,
> 
> I have a problem with fft speed.
> could someone try this :
> 
> from scipy import *
> import time
> 
> a = rand((186888));t1=time.time();fft(a);t2=time.time();t2-t1
> 
> # for me about 0.67791390419006348 s. on centrino 1.6GHz
> 
> a = rand((186890));t1=time.time();fft(a);t2=time.time();t2-t1
> 
> # for me about 1.622053861618042 s. on centrino 1.6GHz
> 
> a = rand((186889));t1=time.time();fft(a);t2=time.time();t2-t1
> 
> # the computation is infinit !!!! (no time to wait)
> 
> 
> Question : why is there a problem specialy for that size (186889) of fft ?
> It is not the only size with that problem.

I guess this is due to the design of fft which is made for input lengths of
2**x. If you try e.g. 262144=2**18 which is even larger than 186889 you'll see
that it's pretty fast.

Christian



From sgarcia at olfac.univ-lyon1.fr  Wed Feb  7 09:04:07 2007
From: sgarcia at olfac.univ-lyon1.fr (Samuel GARCIA)
Date: Wed, 07 Feb 2007 15:04:07 +0100
Subject: [SciPy-user] FFT speed ?
In-Reply-To: <45C9DB24.6080805@iam.uni-stuttgart.de>
References: <45C9D8DD.9040101@olfac.univ-lyon1.fr>
	<45C9DB24.6080805@iam.uni-stuttgart.de>
Message-ID: <45C9DC57.6030603@olfac.univ-lyon1.fr>

Yes I know this.
But 186888 186889 and 186890 are not power of 2 and the computation time
is very very different just for a difference of size of only one point.
What is the reason ?
And how to deal with that ? (I realy need to compute fft with a random
nomber of point)


Nils Wagner wrote:
> Samuel GARCIA wrote:
>   
>> Hello list,
>>
>> I have a problem with fft speed.
>> could someone try this :
>>
>> from scipy import *
>> import time
>>
>> a = rand((186888));t1=time.time();fft(a);t2=time.time();t2-t1
>>
>> # for me about 0.67791390419006348 s. on centrino 1.6GHz
>>
>> a = rand((186890));t1=time.time();fft(a);t2=time.time();t2-t1
>>
>> # for me about 1.622053861618042 s. on centrino 1.6GHz
>>
>> a = rand((186889));t1=time.time();fft(a);t2=time.time();t2-t1
>>
>> # the computation is infinit !!!! (no time to wait)
>>
>>
>> Question : why is there a problem specialy for that size (186889) of fft ?
>> It is not the only size with that problem.
>>
>>
>> Thank
>>
>> Sam
>>
>>
>>   
>>     
> What you can find with help (fft) is ...
>
> "This is most efficient for n a power of two"
>
> Nils
>
>
>  
>
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user
>   

-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Samuel Garcia
Universite Claude Bernard LYON 1
CNRS - UMR5020, Laboratoire des Neurosciences et Systemes Sensoriels
50, avenue Tony Garnier
69366 LYON Cedex 07
FRANCE
T?l : 04 37 28 74 64
Fax : 04 37 28 76 01
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20070207/b543e3bd/attachment.html>

From sgarcia at olfac.univ-lyon1.fr  Wed Feb  7 09:07:48 2007
From: sgarcia at olfac.univ-lyon1.fr (Samuel GARCIA)
Date: Wed, 07 Feb 2007 15:07:48 +0100
Subject: [SciPy-user] FFT speed ?
In-Reply-To: <45C9DBEF.8090205@hoc.net>
References: <45C9D8DD.9040101@olfac.univ-lyon1.fr> <45C9DBEF.8090205@hoc.net>
Message-ID: <45C9DD34.1060807@olfac.univ-lyon1.fr>

Yes it is pretty fast.
The difference of time is not a problem for the end user (between 0.2
and 1 s).
But specialy the value of 186889 is really a problem, the computation is
infinit.
Did you try tis value especialy ?




Christian Kristukat wrote:
> Samuel GARCIA wrote:
>   
>> Hello list,
>>
>> I have a problem with fft speed.
>> could someone try this :
>>
>> from scipy import *
>> import time
>>
>> a = rand((186888));t1=time.time();fft(a);t2=time.time();t2-t1
>>
>> # for me about 0.67791390419006348 s. on centrino 1.6GHz
>>
>> a = rand((186890));t1=time.time();fft(a);t2=time.time();t2-t1
>>
>> # for me about 1.622053861618042 s. on centrino 1.6GHz
>>
>> a = rand((186889));t1=time.time();fft(a);t2=time.time();t2-t1
>>
>> # the computation is infinit !!!! (no time to wait)
>>
>>
>> Question : why is there a problem specialy for that size (186889) of fft ?
>> It is not the only size with that problem.
>>     
>
> I guess this is due to the design of fft which is made for input lengths of
> 2**x. If you try e.g. 262144=2**18 which is even larger than 186889 you'll see
> that it's pretty fast.
>
> Christian
>
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user
>   

-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Samuel Garcia
Universite Claude Bernard LYON 1
CNRS - UMR5020, Laboratoire des Neurosciences et Systemes Sensoriels
50, avenue Tony Garnier
69366 LYON Cedex 07
FRANCE
T?l : 04 37 28 74 64
Fax : 04 37 28 76 01
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20070207/c043b3d0/attachment.html>

From nwagner at iam.uni-stuttgart.de  Wed Feb  7 09:13:05 2007
From: nwagner at iam.uni-stuttgart.de (Nils Wagner)
Date: Wed, 07 Feb 2007 15:13:05 +0100
Subject: [SciPy-user] FFT speed ?
In-Reply-To: <45C9DD34.1060807@olfac.univ-lyon1.fr>
References: <45C9D8DD.9040101@olfac.univ-lyon1.fr> <45C9DBEF.8090205@hoc.net>
	<45C9DD34.1060807@olfac.univ-lyon1.fr>
Message-ID: <45C9DE71.1070302@iam.uni-stuttgart.de>

Samuel GARCIA wrote:
> Yes it is pretty fast.
> The difference of time is not a problem for the end user (between 0.2
> and 1 s).
> But specialy the value of 186889 is really a problem, the computation
> is infinit.
> Did you try tis value especialy ?
>
You may try

a = rand((186889))
t1=time.time()
fft(a,pow(2,18))
t2=time.time()
print t2-t1
 
Nils



From sgarcia at olfac.univ-lyon1.fr  Wed Feb  7 09:18:19 2007
From: sgarcia at olfac.univ-lyon1.fr (Samuel GARCIA)
Date: Wed, 07 Feb 2007 15:18:19 +0100
Subject: [SciPy-user] FFT speed ?
In-Reply-To: <45C9DE71.1070302@iam.uni-stuttgart.de>
References: <45C9D8DD.9040101@olfac.univ-lyon1.fr>
	<45C9DBEF.8090205@hoc.net>	<45C9DD34.1060807@olfac.univ-lyon1.fr>
	<45C9DE71.1070302@iam.uni-stuttgart.de>
Message-ID: <45C9DFAB.2050303@olfac.univ-lyon1.fr>

yes I was thinking of doing something like that but
fft(a,pow(2,18)).shape is of course 262144 (2**18)
and when I use ifft after that The length of my signal have changed I
have an interpolated signal ... new problem for me ...



Nils Wagner wrote:
> Samuel GARCIA wrote:
>   
>> Yes it is pretty fast.
>> The difference of time is not a problem for the end user (between 0.2
>> and 1 s).
>> But specialy the value of 186889 is really a problem, the computation
>> is infinit.
>> Did you try tis value especialy ?
>>
>>     
> You may try
>
> a = rand((186889))
> t1=time.time()
> fft(a,pow(2,18))
> t2=time.time()
> print t2-t1
>  
> Nils
>
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user
>   

-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Samuel Garcia
Universite Claude Bernard LYON 1
CNRS - UMR5020, Laboratoire des Neurosciences et Systemes Sensoriels
50, avenue Tony Garnier
69366 LYON Cedex 07
FRANCE
T?l : 04 37 28 74 64
Fax : 04 37 28 76 01
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20070207/751b8992/attachment.html>

From stefan at sun.ac.za  Wed Feb  7 09:39:21 2007
From: stefan at sun.ac.za (Stefan van der Walt)
Date: Wed, 7 Feb 2007 16:39:21 +0200
Subject: [SciPy-user] FFT speed ?
In-Reply-To: <45C9DFAB.2050303@olfac.univ-lyon1.fr>
References: <45C9D8DD.9040101@olfac.univ-lyon1.fr> <45C9DBEF.8090205@hoc.net>
	<45C9DD34.1060807@olfac.univ-lyon1.fr>
	<45C9DE71.1070302@iam.uni-stuttgart.de>
	<45C9DFAB.2050303@olfac.univ-lyon1.fr>
Message-ID: <20070207143921.GE6274@mentat.za.net>

On Wed, Feb 07, 2007 at 03:18:19PM +0100, Samuel GARCIA wrote:
> yes I was thinking of doing something like that but
> fft(a,pow(2,18)).shape is of course 262144 (2**18)
> and when I use ifft after that The length of my signal have changed I have an
> interpolated signal ... new problem for me ...

An interpolated signal?

In [19]: N.real(N.fft.ifft(N.fft.fft(N.arange(11),16)))
Out[19]: 
array([  0.,   1.,   2.,   3.,   4.,   5.,   6.,   7.,   8.,   9.,  10.,
        -0.,   0.,   0.,   0.,   0.])

Padding in the Fourier-domain, on the other hand:

In [20]: N.real(N.fft.ifft(N.fft.fft(N.arange(11)),16))
Out[20]: 
array([ 0.        ,  2.10035464,  3.04455839,  1.35780382,  3.23688237,
        3.12291155,  2.35790278,  4.12133152,  3.4375    ,  3.29213721,
        5.00323313,  3.69035768,  4.32561763,  5.98165513,  3.3443057 ,
        6.58344845])


Cheers
St?fan


From paul.ray at nrl.navy.mil  Wed Feb  7 09:42:46 2007
From: paul.ray at nrl.navy.mil (Paul Ray)
Date: Wed, 7 Feb 2007 09:42:46 -0500
Subject: [SciPy-user] SciPy-user Digest, Vol 42, Issue 10
In-Reply-To: <mailman.4914.1170857052.8339.scipy-user@scipy.org>
References: <mailman.4914.1170857052.8339.scipy-user@scipy.org>
Message-ID: <15276EE7-5A45-4D31-82DB-C4FF4D634F2A@nrl.navy.mil>


On Feb 7, 2007, at 9:04 AM, scipy-user-request at scipy.org wrote:

> I have a problem with fft speed.

The speed of most FFT algorithms depends greatly on the largest prime  
factor of N.

Here are the factors of your example numbers:
 >factor 186888
186888: 2 2 2 3 13 599

 >factor 186890
186890: 2 5 11 1699

 >factor 186889
186889: 186889

Note that 186889 is prime!  This is the worst case situation!   
Numbers which are powers of 2 can be FFT'ed in order N*Log_2(N) time,  
while prime numbers take order N**2 time.  This is what you are seeing.
You might do a survey of FFT algorithms to see which ones perform  
best on prime Ns.  Many you will find, work ONLY on power of 2 Ns!
You should make sure that your SciPy is using FFTW3 for the FFT  
engine for sure, since I think it does about as well as possible on  
prime Ns.  You can read about FFTW at http://fftw.org

I rarely use FFT in SciPy/NumPy since there are many confusing  
statements in the instructions about FFTW2/FFTW3 support which don't  
make sense.  The API changed from FFTW2 to FFTW3 and it is really  
important to get this right. I think FFTW2 support should be removed  
and someone should do a check to make sure the FFTW3 support is  
implemented correctly.


Cheers,

-- Paul



From sgarcia at olfac.univ-lyon1.fr  Wed Feb  7 10:05:18 2007
From: sgarcia at olfac.univ-lyon1.fr (Samuel GARCIA)
Date: Wed, 07 Feb 2007 16:05:18 +0100
Subject: [SciPy-user] FFT speed ?
In-Reply-To: <20070207143921.GE6274@mentat.za.net>
References: <45C9D8DD.9040101@olfac.univ-lyon1.fr>
	<45C9DBEF.8090205@hoc.net>	<45C9DD34.1060807@olfac.univ-lyon1.fr>	<45C9DE71.1070302@iam.uni-stuttgart.de>	<45C9DFAB.2050303@olfac.univ-lyon1.fr>
	<20070207143921.GE6274@mentat.za.net>
Message-ID: <45C9EAAE.9010308@olfac.univ-lyon1.fr>

Ok sorry.
I answered without trying !
Thank a lot.
I will solve that way.

Sam


Stefan van der Walt wrote:
> On Wed, Feb 07, 2007 at 03:18:19PM +0100, Samuel GARCIA wrote:
>   
>> yes I was thinking of doing something like that but
>> fft(a,pow(2,18)).shape is of course 262144 (2**18)
>> and when I use ifft after that The length of my signal have changed I have an
>> interpolated signal ... new problem for me ...
>>     
>
> An interpolated signal?
>
> In [19]: N.real(N.fft.ifft(N.fft.fft(N.arange(11),16)))
> Out[19]: 
> array([  0.,   1.,   2.,   3.,   4.,   5.,   6.,   7.,   8.,   9.,  10.,
>         -0.,   0.,   0.,   0.,   0.])
>
> Padding in the Fourier-domain, on the other hand:
>
> In [20]: N.real(N.fft.ifft(N.fft.fft(N.arange(11)),16))
> Out[20]: 
> array([ 0.        ,  2.10035464,  3.04455839,  1.35780382,  3.23688237,
>         3.12291155,  2.35790278,  4.12133152,  3.4375    ,  3.29213721,
>         5.00323313,  3.69035768,  4.32561763,  5.98165513,  3.3443057 ,
>         6.58344845])
>
>
> Cheers
> St?fan
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user
>   

-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Samuel Garcia
Universite Claude Bernard LYON 1
CNRS - UMR5020, Laboratoire des Neurosciences et Systemes Sensoriels
50, avenue Tony Garnier
69366 LYON Cedex 07
FRANCE
T?l : 04 37 28 74 64
Fax : 04 37 28 76 01
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20070207/4278b361/attachment.html>

From emsellem at obs.univ-lyon1.fr  Wed Feb  7 10:20:29 2007
From: emsellem at obs.univ-lyon1.fr (Eric Emsellem)
Date: Wed, 07 Feb 2007 16:20:29 +0100
Subject: [SciPy-user] back with a problem in scipy installation...
Message-ID: <45C9EE3D.1020907@obs.univ-lyon1.fr>

Hi again (sorry for the second post: the first one was scrubbed),


I now went through a full install of atlas, lapack, blas, numpy, scipy
again.
I still have some failure in scipy (none in numpy except for the umfpack
which I haven't installed) you can find below.
I also include the explicit site.cfg that I had to twiggle in order for
scipy to find atlas (no Environment variable or other way did the work
for some reason): it looks weird if I compare it to "advised" site.cfg
but this is the only option that recognised atlas properly.

any help is welcome as always.
thanks again
Eric
=======================
below is a summary of:

1/ the failure in scipy
2/ my site.cfg used for building numpy and scipy

***************************************************************************************************
******** Output of scipy.test() = (starting with some failure due to the
lack of umfpack and then..):
....................
Warning: FAILURE importing tests for <module
'scipy.linsolve.umfpack.umfpack' from '...y/linsolve/umfpack/umfpack.pyc'>
/usr/local/lib/python2.4/site-packages/scipy/linsolve/umfpack/tests/test_umfpack.py:17:
AttributeError: 'module' object has no attribute 'umfpack' (in ?)
................................
Found 4 tests for scipy.io.recaster
Warning: FAILURE importing tests for <module 'scipy.linsolve.umfpack'
from '.../linsolve/umfpack/__init__.pyc'>
/usr/local/lib/python2.4/site-packages/scipy/linsolve/umfpack/tests/test_umfpack.py:17:
AttributeError: 'module' object has no attribute 'umfpack' (in ?)
...................
..zswap:n=4
..zswap:n=3
..................Residual: 1.05006950608e-07
.........................................................................................
======================================================================
FAIL: check_syevr (scipy.lib.tests.test_lapack.test_flapack_float)
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/usr/local/lib/python2.4/site-packages/scipy/lib/lapack/tests/esv_tests.py",
line 41, in check_syevr
    assert_array_almost_equal(w,exact_w)
  File "/usr/local/lib/python2.4/site-packages/numpy/testing/utils.py",
line 230, in assert_array_almost_equal
    header='Arrays are not almost equal')
  File "/usr/local/lib/python2.4/site-packages/numpy/testing/utils.py",
line 215, in assert_array_compare
    assert cond, msg
AssertionError:
Arrays are not almost equal

(mismatch 33.3333333333%)
 x: array([-0.66992444,  0.48769444,  9.18222618], dtype=float32)
 y: array([-0.66992434,  0.48769389,  9.18223045])

======================================================================
FAIL: check_syevr_irange (scipy.lib.tests.test_lapack.test_flapack_float)
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/usr/local/lib/python2.4/site-packages/scipy/lib/lapack/tests/esv_tests.py",
line 66, in check_syevr_irange
    assert_array_almost_equal(w,exact_w[rslice])
  File "/usr/local/lib/python2.4/site-packages/numpy/testing/utils.py",
line 230, in assert_array_almost_equal
    header='Arrays are not almost equal')
  File "/usr/local/lib/python2.4/site-packages/numpy/testing/utils.py",
line 215, in assert_array_compare
    assert cond, msg
AssertionError:
Arrays are not almost equal

(mismatch 33.3333333333%)
 x: array([-0.66992444,  0.48769444,  9.18222618], dtype=float32)
 y: array([-0.66992434,  0.48769389,  9.18223045])

----------------------------------------------------------------------
Ran 1619 tests in 5.764s

FAILED (failures=2)

***************************************************************************************************
******** My site.cfg used for both numpy and scipy
******** it finds atlas, but that's all. If I uncomment the lines on
lapack_opt and blas_opt, it finds the

[DEFAULT]
library_dirs = /usr/local/lib/atlas
include_dirs = /usr/local/lib/atlas
[atlas]
library_dirs = /usr/local/lib/atlas
atlas_libs = lapack, f77blas, cblas, atlas
# [blas_opt]
# library_dirs = /usr/local/lib/atlas
# blas_libs = fblas, f77blas, cblas
# [lapack_opt]
# library_dirs = /usr/local/lib/atlas
# lapack_libs = lapack
[blas]
library_dirs = /usr/local/lib/atlas
libraries = f77blas, cblas, atlas
#
[lapack]
library_dirs = /usr/local/lib/atlas
libraries = lapack, f77blas, cblas, atlas
[fftw]
libraries = fftw3

-- 
====================================================================
Eric Emsellem                             emsellem at obs.univ-lyon1.fr
                           Centre de Recherche Astrophysique de Lyon
9 av. Charles-Andre                        tel: +33 (0)4 78 86 83 84
69561 Saint-Genis Laval Cedex              fax: +33 (0)4 78 86 83 86
France                    http://www-obs.univ-lyon1.fr/eric.emsellem
====================================================================


From edschofield at gmail.com  Wed Feb  7 10:53:35 2007
From: edschofield at gmail.com (Ed Schofield)
Date: Wed, 7 Feb 2007 16:53:35 +0100
Subject: [SciPy-user] build issue on 64-bit Intel Core2 Duo
In-Reply-To: <200701311116.22016.sransom@nrao.edu>
References: <1170227383.12321.11.camel@nadav.envision.co.il>
	<200701311116.22016.sransom@nrao.edu>
Message-ID: <1b5a37350702070753q6e47ad86l9446192288fed75e@mail.gmail.com>

On Wednesday 31 January 2007 02:09, Nadav Horesh wrote:
> >python numpy/distutils/cpuinfo.py:
> >
> >CPU information: getNCPUs=4 has_mmx has_sse has_sse2 is_64bit
> > is_Intel is_XEON is_Xeon is_i686
>
> Well,
>  Crossing our systems' info it looks to me that the best and straight
> forward way to identify Intel's imitation to amd64 arch is:
>
> def _is_Nocona(self):
>      return self.is_64bit() and self.is_Intel() and self.is_i686()
>
> Did not test it but it fits and looks logical.
>
>   Nadav.

On 1/31/07, Scott Ransom <sransom at nrao.edu> wrote:
>
> This works for me on a 64-bit Debian Core2 Duo system.
>
> eiger:~$ uname -a
> Linux eiger 2.6.18-3-amd64 #1 SMP Sun Dec 10 19:57:44 CET 2006 x86_64
> GNU/Linux
>
> eiger:~$ python cpuinfo.py
> CPU information: getNCPUs=2 has_mmx has_sse has_sse2 is_64bit is_Intel
> is_Nocona is_i686


I can also confirm that this works for Core2. I've checked it in to SVN
without the redundant is_Intel() check. I've also added a separate entry for
Core2 processors, which will be supported with an explicit -march flag in
GCC 4.3.

-- Ed
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20070207/7957996b/attachment.html>

From sransom at nrao.edu  Wed Feb  7 11:12:36 2007
From: sransom at nrao.edu (Scott Ransom)
Date: Wed, 7 Feb 2007 11:12:36 -0500
Subject: [SciPy-user] FFT speed ?
In-Reply-To: <20070207143921.GE6274@mentat.za.net>
References: <45C9D8DD.9040101@olfac.univ-lyon1.fr> <45C9DBEF.8090205@hoc.net>
	<45C9DD34.1060807@olfac.univ-lyon1.fr>
	<45C9DE71.1070302@iam.uni-stuttgart.de>
	<45C9DFAB.2050303@olfac.univ-lyon1.fr>
	<20070207143921.GE6274@mentat.za.net>
Message-ID: <20070207161236.GB19902@ssh.cv.nrao.edu>

On Wed, Feb 07, 2007 at 04:39:21PM +0200, Stefan van der Walt wrote:
> On Wed, Feb 07, 2007 at 03:18:19PM +0100, Samuel GARCIA wrote:
> > yes I was thinking of doing something like that but
> > fft(a,pow(2,18)).shape is of course 262144 (2**18)
> > and when I use ifft after that The length of my signal have changed I have an
> > interpolated signal ... new problem for me ...
> 
> An interpolated signal?

Padding a time series gives you an interpolated (actually, the
term often used is "oversampled" Fourier spectrum).

Scott

> In [19]: N.real(N.fft.ifft(N.fft.fft(N.arange(11),16)))
> Out[19]: 
> array([  0.,   1.,   2.,   3.,   4.,   5.,   6.,   7.,   8.,   9.,  10.,
>         -0.,   0.,   0.,   0.,   0.])
> 
> Padding in the Fourier-domain, on the other hand:
> 
> In [20]: N.real(N.fft.ifft(N.fft.fft(N.arange(11)),16))
> Out[20]: 
> array([ 0.        ,  2.10035464,  3.04455839,  1.35780382,  3.23688237,
>         3.12291155,  2.35790278,  4.12133152,  3.4375    ,  3.29213721,
>         5.00323313,  3.69035768,  4.32561763,  5.98165513,  3.3443057 ,
>         6.58344845])
> 
> 
> Cheers
> St?fan
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user

-- 
-- 
Scott M. Ransom            Address:  NRAO
Phone:  (434) 296-0320               520 Edgemont Rd.
email:  sransom at nrao.edu             Charlottesville, VA 22903 USA
GPG Fingerprint: 06A9 9553 78BE 16DB 407B  FFCA 9BFA B6FF FFD3 2989


From cimrman3 at ntc.zcu.cz  Wed Feb  7 11:44:18 2007
From: cimrman3 at ntc.zcu.cz (Robert Cimrman)
Date: Wed, 07 Feb 2007 17:44:18 +0100
Subject: [SciPy-user] Installing umfpack on mac?
In-Reply-To: <C1EE1E5D.4877%v-nijs@kellogg.northwestern.edu>
References: <C1EE1E5D.4877%v-nijs@kellogg.northwestern.edu>
Message-ID: <45CA01E2.70200@ntc.zcu.cz>

Vincent Nijs wrote:
> Are there any installation instructions for installing umfpack on mac? I
> tried install suitesparse via macports but this seems to be broken.

Try checking UMFPACK/Doc/UserGuide.pdf, but there are only generic
Unix/Windows instructions, IMHO.

r.


From peridot.faceted at gmail.com  Wed Feb  7 12:13:12 2007
From: peridot.faceted at gmail.com (Anne Archibald)
Date: Wed, 7 Feb 2007 12:13:12 -0500
Subject: [SciPy-user] FFT speed ?
In-Reply-To: <45C9DC57.6030603@olfac.univ-lyon1.fr>
References: <45C9D8DD.9040101@olfac.univ-lyon1.fr>
	<45C9DB24.6080805@iam.uni-stuttgart.de>
	<45C9DC57.6030603@olfac.univ-lyon1.fr>
Message-ID: <ce557a360702070913o19167dfbx8da82564bc163bee@mail.gmail.com>

On 07/02/07, Samuel GARCIA <sgarcia at olfac.univ-lyon1.fr> wrote:
>
>  Yes I know this.
>  But 186888 186889 and 186890 are not power of 2 and the computation time is
> very very different just for a difference of size of only one point.
>  What is the reason ?
>  And how to deal with that ? (I realy need to compute fft with a random
> nomber of point)

Many problems can be solved by padding. But once in a while one comes
up which needs a particular number of points, and it's not always a
power of two.

Can FFTW (or any of the FFT packages numpy/scipy can use) compute an
FFT of size 186889 in a reasonable time? I know there are algorithms
for large prime factors, and for small prime factors, and that you can
combine the two (though perhaps primes of moderate size are a
problem).

Anne M. Archibald


From peridot.faceted at gmail.com  Wed Feb  7 12:20:13 2007
From: peridot.faceted at gmail.com (Anne Archibald)
Date: Wed, 7 Feb 2007 12:20:13 -0500
Subject: [SciPy-user] SciPy-user Digest, Vol 42, Issue 10
In-Reply-To: <15276EE7-5A45-4D31-82DB-C4FF4D634F2A@nrl.navy.mil>
References: <mailman.4914.1170857052.8339.scipy-user@scipy.org>
	<15276EE7-5A45-4D31-82DB-C4FF4D634F2A@nrl.navy.mil>
Message-ID: <ce557a360702070920u67456335h80d328645a5b8280@mail.gmail.com>

On 07/02/07, Paul Ray <paul.ray at nrl.navy.mil> wrote:
>
> On Feb 7, 2007, at 9:04 AM, scipy-user-request at scipy.org wrote:
>
> > I have a problem with fft speed.
>
> The speed of most FFT algorithms depends greatly on the largest prime
> factor of N.
>
> Here are the factors of your example numbers:
>  >factor 186888
> 186888: 2 2 2 3 13 599
>
>  >factor 186890
> 186890: 2 5 11 1699
>
>  >factor 186889
> 186889: 186889
>
> Note that 186889 is prime!  This is the worst case situation!
> Numbers which are powers of 2 can be FFT'ed in order N*Log_2(N) time,
> while prime numbers take order N**2 time.  This is what you are seeing.
> You might do a survey of FFT algorithms to see which ones perform
> best on prime Ns.  Many you will find, work ONLY on power of 2 Ns!
> You should make sure that your SciPy is using FFTW3 for the FFT
> engine for sure, since I think it does about as well as possible on
> prime Ns.  You can read about FFTW at http://fftw.org

There are at least two algorithms to efficiently compute prime-length
FFTs (Rader's conversion and the chirp-z transform).

How does one determine which FFT package one is actually using? (I
normally use the scipy and numpy that are packaged in ubuntu edgy, but
even if you compile it yourself it may not be obvious whether it found
the packages you have installed.)

Anne M. Archibald


From stefan at sun.ac.za  Wed Feb  7 12:34:32 2007
From: stefan at sun.ac.za (Stefan van der Walt)
Date: Wed, 7 Feb 2007 19:34:32 +0200
Subject: [SciPy-user] SciPy-user Digest, Vol 42, Issue 10
In-Reply-To: <ce557a360702070920u67456335h80d328645a5b8280@mail.gmail.com>
References: <mailman.4914.1170857052.8339.scipy-user@scipy.org>
	<15276EE7-5A45-4D31-82DB-C4FF4D634F2A@nrl.navy.mil>
	<ce557a360702070920u67456335h80d328645a5b8280@mail.gmail.com>
Message-ID: <20070207173432.GG6274@mentat.za.net>

On Wed, Feb 07, 2007 at 12:20:13PM -0500, Anne Archibald wrote:
> On 07/02/07, Paul Ray <paul.ray at nrl.navy.mil> wrote:
> >
> > On Feb 7, 2007, at 9:04 AM, scipy-user-request at scipy.org wrote:
> >
> > > I have a problem with fft speed.
> >
> > The speed of most FFT algorithms depends greatly on the largest prime
> > factor of N.
> >
> > Here are the factors of your example numbers:
> >  >factor 186888
> > 186888: 2 2 2 3 13 599
> >
> >  >factor 186890
> > 186890: 2 5 11 1699
> >
> >  >factor 186889
> > 186889: 186889
> >
> > Note that 186889 is prime!  This is the worst case situation!
> > Numbers which are powers of 2 can be FFT'ed in order N*Log_2(N) time,
> > while prime numbers take order N**2 time.  This is what you are seeing.
> > You might do a survey of FFT algorithms to see which ones perform
> > best on prime Ns.  Many you will find, work ONLY on power of 2 Ns!
> > You should make sure that your SciPy is using FFTW3 for the FFT
> > engine for sure, since I think it does about as well as possible on
> > prime Ns.  You can read about FFTW at http://fftw.org
> 
> There are at least two algorithms to efficiently compute prime-length
> FFTs (Rader's conversion and the chirp-z transform).

Here is a rough implementation (I don't guarantee anything).

Cheers
St?fan
-------------- next part --------------
A non-text attachment was scrubbed...
Name: chirpz.py
Type: text/x-python
Size: 1135 bytes
Desc: not available
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20070207/73ba32a7/attachment.py>

From sransom at nrao.edu  Wed Feb  7 12:35:43 2007
From: sransom at nrao.edu (Scott Ransom)
Date: Wed, 7 Feb 2007 12:35:43 -0500
Subject: [SciPy-user] FFT speed ?
In-Reply-To: <ce557a360702070913o19167dfbx8da82564bc163bee@mail.gmail.com>
References: <45C9D8DD.9040101@olfac.univ-lyon1.fr>
	<45C9DB24.6080805@iam.uni-stuttgart.de>
	<45C9DC57.6030603@olfac.univ-lyon1.fr>
	<ce557a360702070913o19167dfbx8da82564bc163bee@mail.gmail.com>
Message-ID: <20070207173543.GA19870@ssh.cv.nrao.edu>

On Wed, Feb 07, 2007 at 12:13:12PM -0500, Anne Archibald wrote:
> On 07/02/07, Samuel GARCIA <sgarcia at olfac.univ-lyon1.fr> wrote:
> >
> >  Yes I know this.
> >  But 186888 186889 and 186890 are not power of 2 and the computation time is
> > very very different just for a difference of size of only one point.
> >  What is the reason ?
> >  And how to deal with that ? (I realy need to compute fft with a random
> > nomber of point)
> 
> Many problems can be solved by padding. But once in a while one comes
> up which needs a particular number of points, and it's not always a
> power of two.
> 
> Can FFTW (or any of the FFT packages numpy/scipy can use) compute an
> FFT of size 186889 in a reasonable time? I know there are algorithms
> for large prime factors, and for small prime factors, and that you can
> combine the two (though perhaps primes of moderate size are a
> problem).

I know that FFTW uses O(NlogN) algorithms for any N, even large
prime factors.  It is quite likely that for large prime N, FFTPACK
(which is what numpy uses) goes to a standard DFT algorithm
(O(N^2)).  

One important thing to remember is that the constant in front of
the NlogN is highly dependent on the algorithm.  That is why even
though FFTW v3 uses NlogN algorithms for all N, some N (like
powers of 2 and those composed of only small prime factors) are
_much_ faster than those for other N.  But the bottom line is that
no matter what the constant, for large N, O(NlogN) is _much_ faster
than O(N^2).

Scott

-- 
Scott M. Ransom            Address:  NRAO
Phone:  (434) 296-0320               520 Edgemont Rd.
email:  sransom at nrao.edu             Charlottesville, VA 22903 USA
GPG Fingerprint: 06A9 9553 78BE 16DB 407B  FFCA 9BFA B6FF FFD3 2989


From griffitts_lists at comcast.net  Wed Feb  7 14:00:50 2007
From: griffitts_lists at comcast.net (Jonathan Griffitts)
Date: Wed, 7 Feb 2007 12:00:50 -0700
Subject: [SciPy-user] Windows binary 0.5.2 requires SSE2
In-Reply-To: <45C510E8.3060602@comcast.net>
References: <OwABvSK8hQxFFA0a@griffitts.org> <45C510E8.3060602@comcast.net>
Message-ID: <Rg0Gr3BiHiyFFAPJ@griffitts.org>

In message <45C510E8.3060602 at comcast.net>, John Hassler
<hasslerjc at comcast.net> wrote
>Jonathan Griffitts wrote:
>  Hi!
>  I have installed SciPy 0.5.2 for Python 2.5 on several Windows
>  computers, using the precompiled binary scipy-0.5.2.win32-py2.5.exe.
>  This works fine on some, but on others it crashes Python with an
>  Illegal
>  Instruction exception.? The crash is easy to find by running the
>  test()
>  suite or by attempting to make any use of scipy.integrate.quad.
>  Digging into it, I see that the exception comes from _quadpack.pyd,
>  and
>  it dies at a MOVSD instruction.? I believe MOVSD is an SSE2
>  instruction
>  that is only implemented on the more recent CPUs from both Intel and
>  AMD.
>
>It's a problem with the Athlon.? It also happened with a previous
>version of SciPy this summer.?

This is not just an Athlon issue.  It also fails on a Pentium 3
processor.

To reiterate, this binary (scipy-0.5.2.win32-py2.5) uses SSE2
instructions, which are available only on the newer CPUs from both AMD
and Intel.

-- 
                        Jonathan Griffitts
AnyWare Engineering                             Boulder, CO, USA



From peridot.faceted at gmail.com  Wed Feb  7 14:15:23 2007
From: peridot.faceted at gmail.com (Anne Archibald)
Date: Wed, 7 Feb 2007 14:15:23 -0500
Subject: [SciPy-user] FFT speed ?
In-Reply-To: <20070207173543.GA19870@ssh.cv.nrao.edu>
References: <45C9D8DD.9040101@olfac.univ-lyon1.fr>
	<45C9DB24.6080805@iam.uni-stuttgart.de>
	<45C9DC57.6030603@olfac.univ-lyon1.fr>
	<ce557a360702070913o19167dfbx8da82564bc163bee@mail.gmail.com>
	<20070207173543.GA19870@ssh.cv.nrao.edu>
Message-ID: <ce557a360702071115w47b53aa8l28c9fafa5b000d73@mail.gmail.com>

On 07/02/07, Scott Ransom <sransom at nrao.edu> wrote:
> On Wed, Feb 07, 2007 at 12:13:12PM -0500, Anne Archibald wrote:

> > Can FFTW (or any of the FFT packages numpy/scipy can use) compute an
> > FFT of size 186889 in a reasonable time? I know there are algorithms
> > for large prime factors, and for small prime factors, and that you can
> > combine the two (though perhaps primes of moderate size are a
> > problem).
>
> I know that FFTW uses O(NlogN) algorithms for any N, even large
> prime factors.  It is quite likely that for large prime N, FFTPACK
> (which is what numpy uses) goes to a standard DFT algorithm
> (O(N^2)).

Indeed, for numbers in the vicinity of 10000, some take 500 times as
long as others (on my machine), so I suspect that it is falling back
to a DFT.

> One important thing to remember is that the constant in front of
> the NlogN is highly dependent on the algorithm.  That is why even
> though FFTW v3 uses NlogN algorithms for all N, some N (like
> powers of 2 and those composed of only small prime factors) are
> _much_ faster than those for other N.  But the bottom line is that
> no matter what the constant, for large N, O(NlogN) is _much_ faster
> than O(N^2).

Of course. But when you say the constant varies, do you mean by a
factor of ten? a hundred? a thousand?

On my machine, scipy.show_config reports that it can find FFTW2 but
not FFTW3; does that mean it is actually *using* FFTW2? How does one
tell?

Does scipy provide any access to the special features of FFTW's
interface? (wisdom, for efficiently computing many FFTs on the same
array, for example)

Anne M. Archibald


From rowen at cesmail.net  Wed Feb  7 14:27:35 2007
From: rowen at cesmail.net (Russell E. Owen)
Date: Wed, 07 Feb 2007 11:27:35 -0800
Subject: [SciPy-user] Hints for easy install of scipy on RHEL 4?
Message-ID: <rowen-D78C9A.11273507022007@sea.gmane.org>

We installed scipy on RHEL 4 using the "built in" blas/lapack. Much of 
it works but some components that we need fail, apparently because 
RedHat's blas/lapack is incomplete.

So...can anyone point me to an existing RPM of a complete blas/lapack 
(or a complete Atlas) that we can just use? Google showed lots of RPMs 
but they didn't appear to be for RedHat Enterprise Linux and I'm not 
unix-savvy enough to know what alternatives we can get away with.

-- Russell



From pebarrett at gmail.com  Wed Feb  7 14:56:26 2007
From: pebarrett at gmail.com (Paul Barrett)
Date: Wed, 7 Feb 2007 14:56:26 -0500
Subject: [SciPy-user] Hints for easy install of scipy on RHEL 4?
In-Reply-To: <rowen-D78C9A.11273507022007@sea.gmane.org>
References: <rowen-D78C9A.11273507022007@sea.gmane.org>
Message-ID: <40e64fa20702071156s20437821m3a2336b3a3a2719c@mail.gmail.com>

Russell,

Is RHEL 4 necessary?  I had the same problems building scipy, so I
decided to save myself some grief.  I installed FC 6 instead, while I
wait for RHEL 5. If you have to have RHEL as opposed to FC, then I
suggest you upgrade to RHEL 5beta2, which is based on FC 6/7.

Just my $.02 worth.

 -- Paul


On 2/7/07, Russell E. Owen <rowen at cesmail.net> wrote:
> We installed scipy on RHEL 4 using the "built in" blas/lapack. Much of
> it works but some components that we need fail, apparently because
> RedHat's blas/lapack is incomplete.
>
> So...can anyone point me to an existing RPM of a complete blas/lapack
> (or a complete Atlas) that we can just use? Google showed lots of RPMs
> but they didn't appear to be for RedHat Enterprise Linux and I'm not
> unix-savvy enough to know what alternatives we can get away with.
>
> -- Russell
>
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user
>


From a.h.jaffe at gmail.com  Wed Feb  7 15:48:06 2007
From: a.h.jaffe at gmail.com (Andrew Jaffe)
Date: Wed, 07 Feb 2007 20:48:06 +0000
Subject: [SciPy-user] FFT speed ?
In-Reply-To: <20070207173543.GA19870@ssh.cv.nrao.edu>
References: <45C9D8DD.9040101@olfac.univ-lyon1.fr>	<45C9DB24.6080805@iam.uni-stuttgart.de>	<45C9DC57.6030603@olfac.univ-lyon1.fr>	<ce557a360702070913o19167dfbx8da82564bc163bee@mail.gmail.com>
	<20070207173543.GA19870@ssh.cv.nrao.edu>
Message-ID: <eqddu6$sjs$1@sea.gmane.org>

Scott Ransom wrote:
> On Wed, Feb 07, 2007 at 12:13:12PM -0500, Anne Archibald wrote:
>> On 07/02/07, Samuel GARCIA <sgarcia at olfac.univ-lyon1.fr> wrote:
>>>  Yes I know this.
>>>  But 186888 186889 and 186890 are not power of 2 and the computation time is
>>> very very different just for a difference of size of only one point.
>>>  What is the reason ?
>>>  And how to deal with that ? (I realy need to compute fft with a random
>>> nomber of point)


It's probably worth pointing out that 186889 is, in fact, prime, which 
is certainly the worst case for any algorithm.

Andrew



From david at ar.media.kyoto-u.ac.jp  Wed Feb  7 19:12:14 2007
From: david at ar.media.kyoto-u.ac.jp (David Cournapeau)
Date: Thu, 08 Feb 2007 09:12:14 +0900
Subject: [SciPy-user] FFT speed ?
In-Reply-To: <eqddu6$sjs$1@sea.gmane.org>
References: <45C9D8DD.9040101@olfac.univ-lyon1.fr>	<45C9DB24.6080805@iam.uni-stuttgart.de>	<45C9DC57.6030603@olfac.univ-lyon1.fr>	<ce557a360702070913o19167dfbx8da82564bc163bee@mail.gmail.com>	<20070207173543.GA19870@ssh.cv.nrao.edu>
	<eqddu6$sjs$1@sea.gmane.org>
Message-ID: <45CA6ADE.3060400@ar.media.kyoto-u.ac.jp>

Andrew Jaffe wrote:
> Scott Ransom wrote:
>> On Wed, Feb 07, 2007 at 12:13:12PM -0500, Anne Archibald wrote:
>>> On 07/02/07, Samuel GARCIA <sgarcia at olfac.univ-lyon1.fr> wrote:
>>>>  Yes I know this.
>>>>  But 186888 186889 and 186890 are not power of 2 and the computation time is
>>>> very very different just for a difference of size of only one point.
>>>>  What is the reason ?
>>>>  And how to deal with that ? (I realy need to compute fft with a random
>>>> nomber of point)
>
>
> It's probably worth pointing out that 186889 is, in fact, prime, which 
> is certainly the worst case for any algorithm.
Indeed, this is an important point. There are several things to check, 
and there are some problems with FFT as implemented now in numpy/scipy 
when used with fftw (it is suboptimal by several factors).

    - First, is the numpy/scipy installed fft really using fftw ?
    - Also, if fftw is used, it is important to remember that the first 
time you are using a certain size, fftw has to compute a plan, which may 
take time.

    I tested on my machine (Pentium 4, 3.2 Ghz) fftw (in C) for the 
given size, each result being the best shot on 100 iterations (source 
attached):

testing cached for size 186888
computing plan...done !
         cycle is 1.357218e+10, 1.357218e+08 per execution on average, 
min is 1.323569e+08
testing cached for size 186889
computing plan...done !
         cycle is 6.188211e+10, 6.188211e+08 per execution on average, 
min is 6.016043e+08
testing cached for size 186890
computing plan...done !
         cycle is 1.623674e+10, 1.623674e+08 per execution on average, 
min is 1.595604e+08
testing cached for size 131072
computing plan...done !
         cycle is 1.730136e+10, 1.730136e+08 per execution on average, 
min is 1.682170e+08
testing cached for size 262144
computing plan...done !
         cycle is 3.018974e+10, 3.018974e+08 per execution on average, 
min is 2.978997e+08

cycle being the number of CPU cycles taken by the 100 iterations. The 
fact that 2 ** 17 is slower than 186888 is weird, though. May be due to 
some weird cache effects, I don't know.

For reference, on my laptop (pentium M, thus much better memory 
performances and FPU performances overall):

testing cached for size 186888
computing plan...done !
         cycle is 1.152835e+10, 1.152835e+08 per execution on average, 
min is 1.070749e+08
testing cached for size 186889
computing plan...done !
         cycle is 3.845418e+10, 3.845418e+08 per execution on average, 
min is 3.654266e+08
testing cached for size 186890
computing plan...done !
         cycle is 1.389736e+10, 1.389736e+08 per execution on average, 
min is 1.314722e+08
testing cached for size 131072
computing plan...done !
         cycle is 5.142997e+09, 5.142997e+07 per execution on average, 
min is 4.860954e+07
testing cached for size 262144
computing plan...done !
         cycle is 1.347407e+10, 1.347407e+08 per execution on average, 
min is 1.287470e+08

Which is more logical... This once again shows how bad a Pentium 4 is 
for FPU performances on a per cycle point of view :)
   
For speed issues, 0 padding is the easiest solution I can think of,

David
-------------- next part --------------
A non-text attachment was scrubbed...
Name: test.c
Type: text/x-csrc
Size: 2684 bytes
Desc: not available
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20070208/100ef389/attachment.c>

From david at ar.media.kyoto-u.ac.jp  Wed Feb  7 20:18:58 2007
From: david at ar.media.kyoto-u.ac.jp (David Cournapeau)
Date: Thu, 08 Feb 2007 10:18:58 +0900
Subject: [SciPy-user] FFT speed ?
In-Reply-To: <45CA6ADE.3060400@ar.media.kyoto-u.ac.jp>
References: <45C9D8DD.9040101@olfac.univ-lyon1.fr>	<45C9DB24.6080805@iam.uni-stuttgart.de>	<45C9DC57.6030603@olfac.univ-lyon1.fr>	<ce557a360702070913o19167dfbx8da82564bc163bee@mail.gmail.com>	<20070207173543.GA19870@ssh.cv.nrao.edu>	<eqddu6$sjs$1@sea.gmane.org>
	<45CA6ADE.3060400@ar.media.kyoto-u.ac.jp>
Message-ID: <45CA7A82.40507@ar.media.kyoto-u.ac.jp>

David Cournapeau wrote:
> Andrew Jaffe wrote:
>>
>>
>> It's probably worth pointing out that 186889 is, in fact, prime, 
>> which is certainly the worst case for any algorithm.
I went a bit further to see why it stuck on 186889. First, it only 
happens with numpy.fft.fft, not with scipy.fftpack. So fftw has nothing 
to do with it.

It seems like the fft used in numpy is really slow for prime number (eg 
N^2, which becomes quite big when your number is 186889...). One thing 
which could be done at least is to enable SIGINT to be sent to the 
function to abort it (It takes around 15 minutes to complete on my 
workstsation).

I guess the question is: is there any other implementation of fft usable 
for prime number in numpy ?

David


From sgarcia at olfac.univ-lyon1.fr  Thu Feb  8 04:06:07 2007
From: sgarcia at olfac.univ-lyon1.fr (Samuel GARCIA)
Date: Thu, 08 Feb 2007 10:06:07 +0100
Subject: [SciPy-user] FFT speed ?
In-Reply-To: <20070207161236.GB19902@ssh.cv.nrao.edu>
References: <45C9D8DD.9040101@olfac.univ-lyon1.fr>
	<45C9DBEF.8090205@hoc.net>	<45C9DD34.1060807@olfac.univ-lyon1.fr>	<45C9DE71.1070302@iam.uni-stuttgart.de>	<45C9DFAB.2050303@olfac.univ-lyon1.fr>	<20070207143921.GE6274@mentat.za.net>
	<20070207161236.GB19902@ssh.cv.nrao.edu>
Message-ID: <45CAE7FF.30406@olfac.univ-lyon1.fr>

Thanks all,
for fast and efficient answers.
Zeros padding was really my solution.

Sam


Scott Ransom wrote:
> On Wed, Feb 07, 2007 at 04:39:21PM +0200, Stefan van der Walt wrote:
>   
>> On Wed, Feb 07, 2007 at 03:18:19PM +0100, Samuel GARCIA wrote:
>>     
>>> yes I was thinking of doing something like that but
>>> fft(a,pow(2,18)).shape is of course 262144 (2**18)
>>> and when I use ifft after that The length of my signal have changed I have an
>>> interpolated signal ... new problem for me ...
>>>       
>> An interpolated signal?
>>     
>
> Padding a time series gives you an interpolated (actually, the
> term often used is "oversampled" Fourier spectrum).
>
> Scott
>
>   
>> In [19]: N.real(N.fft.ifft(N.fft.fft(N.arange(11),16)))
>> Out[19]: 
>> array([  0.,   1.,   2.,   3.,   4.,   5.,   6.,   7.,   8.,   9.,  10.,
>>         -0.,   0.,   0.,   0.,   0.])
>>
>> Padding in the Fourier-domain, on the other hand:
>>
>> In [20]: N.real(N.fft.ifft(N.fft.fft(N.arange(11)),16))
>> Out[20]: 
>> array([ 0.        ,  2.10035464,  3.04455839,  1.35780382,  3.23688237,
>>         3.12291155,  2.35790278,  4.12133152,  3.4375    ,  3.29213721,
>>         5.00323313,  3.69035768,  4.32561763,  5.98165513,  3.3443057 ,
>>         6.58344845])
>>
>>
>> Cheers
>> St?fan
>> _______________________________________________
>> SciPy-user mailing list
>> SciPy-user at scipy.org
>> http://projects.scipy.org/mailman/listinfo/scipy-user
>>     
>
>   

-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Samuel Garcia
Universite Claude Bernard LYON 1
CNRS - UMR5020, Laboratoire des Neurosciences et Systemes Sensoriels
50, avenue Tony Garnier
69366 LYON Cedex 07
FRANCE
T?l : 04 37 28 74 64
Fax : 04 37 28 76 01
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20070208/0898fd2e/attachment.html>

From edschofield at gmail.com  Thu Feb  8 05:38:41 2007
From: edschofield at gmail.com (Ed Schofield)
Date: Thu, 8 Feb 2007 11:38:41 +0100
Subject: [SciPy-user] Windows binary 0.5.2 requires SSE2
In-Reply-To: <Rg0Gr3BiHiyFFAPJ@griffitts.org>
References: <OwABvSK8hQxFFA0a@griffitts.org> <45C510E8.3060602@comcast.net>
	<Rg0Gr3BiHiyFFAPJ@griffitts.org>
Message-ID: <1b5a37350702080238q6ab7b505r21940797f3bb006d@mail.gmail.com>

On 2/7/07, Jonathan Griffitts <griffitts_lists at comcast.net> wrote:
>
> In message <45C510E8.3060602 at comcast.net>, John Hassler
> <hasslerjc at comcast.net> wrote
> >Jonathan Griffitts wrote:
> >  Hi!
> >  I have installed SciPy 0.5.2 for Python 2.5 on several Windows
> >  computers, using the precompiled binary scipy-0.5.2.win32-py2.5.exe.
> >  This works fine on some, but on others it crashes Python with an
> >  Illegal
> >  Instruction exception. The crash is easy to find by running the
> >  test()
> >  suite or by attempting to make any use of scipy.integrate.quad.
> >  Digging into it, I see that the exception comes from _quadpack.pyd,
> >  and
> >  it dies at a MOVSD instruction. I believe MOVSD is an SSE2
> >  instruction
> >  that is only implemented on the more recent CPUs from both Intel and
> >  AMD.
> >
> >It's a problem with the Athlon. It also happened with a previous
> >version of SciPy this summer.
>
> This is not just an Athlon issue.  It also fails on a Pentium 3
> processor.
>
> To reiterate, this binary (scipy-0.5.2.win32-py2.5) uses SSE2
> instructions, which are available only on the newer CPUs from both AMD
> and Intel.


Thanks for the info. We linked the 0.5.0 and (I think) 0.4.9 Win32 binaries
to the ATLAS library labelled "ATLAS-P2" that doesn't require SSE2
instructions. Sorry that we've reverted to the SSE2 builds in the the last
release or two. Rebuilding takes time, and it may be more productive for us
to wait for the next release, when we'll try to get it right. Meanwhile I've
changed the release notes on the SourceForge page to reflect the SSE2
requirement. I'll also explain the situation on the SciPy.org Download page
(as soon as I can log in ;) ...

-- Ed
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20070208/6bc11e80/attachment.html>

From pecontal at obs.univ-lyon1.fr  Thu Feb  8 11:42:57 2007
From: pecontal at obs.univ-lyon1.fr (Emmanuel Pecontal)
Date: Thu, 8 Feb 2007 17:42:57 +0100
Subject: [SciPy-user] scipy print using ipython
Message-ID: <200702081742.57873.pecontal@obs.univ-lyon1.fr>

Hello,

I am using the fmin_l_bfgs_b function in scipy. This function has a parameter
for controling the iteration printing during the minimization. In fact the printing
is done by the fortran routine via a command like:
write (6,1002) iter,f,sbgnrm
which is a print on the screen. 
For some reason I don't understand, when I use the routine in ipython, the print
is done only by bunch of lines every few minutes... just like if it was bufferized 
before printing. Does someone knows the reason of this beheviour? is it a python, 
ipython or scipy problem?

Cheers
Emmanuel
-- 
Emmanuel P?contal

CRAL - Observatoire de Lyon
9, Av. Charles Andre
F-69561 Saint Genis Laval Cedex

tel (33) (0)4.78.86.83.76 - fax (33) (0)4.78.86.83.86

email : pecontal at obs.univ-lyon1.fr
~

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20070208/f3a377a8/attachment.html>

From robert.vergnes at yahoo.fr  Thu Feb  8 12:21:05 2007
From: robert.vergnes at yahoo.fr (Robert VERGNES)
Date: Thu, 8 Feb 2007 18:21:05 +0100 (CET)
Subject: [SciPy-user] RE : Re: QME-Dev wxSciPY workbench 0.0.9.24 released -
	updated and corrected for Python 2.4
In-Reply-To: <C1EBC315.4826%v-nijs@kellogg.northwestern.edu>
Message-ID: <20070208172105.4581.qmail@web27402.mail.ukl.yahoo.com>

For ppc , i don't know. never try and i don't have a ppc. i can try on mac osXx86 only... next week I will make a test.

Vincent Nijs <v-nijs at kellogg.northwestern.edu> a ?crit :  Has anyone been able to run workbench on a mac, os x 10.4 ppc, Python 2.4, wxPython 2.8. When I try to run it, it seems to start but then quits before anything appears on screen without any error messages. 

Vincent


On 1/28/07 7:59 AM, "Robert VERGNES" <robert.vergnes at yahoo.fr> wrote:

  Version Alpha 0.0.9.2.4 updated today.

New ZIP file for download.

Correction made to the plotting/Graph issue with Python 2.4
+ Example files added for review of workbench.

https://sourceforge.net/project/showfiles.php?group_id=181979

Note: wxPython 2.8 is still necessary to run the wrokbench.

 
  
---------------------------------
  D?couvrez une nouvelle fa?on d'obtenir des r?ponses ? toutes vos questions ! Profitez des connaissances, des opinions et des exp?riences des internautes sur Yahoo! Questions/R?ponses <http://fr.rd.yahoo.com/evt=42054/*http://fr.answers.yahoo.com> .
  
---------------------------------
  _______________________________________________
SciPy-user mailing list
SciPy-user at scipy.org
http://projects.scipy.org/mailman/listinfo/scipy-user_______________________________________________
SciPy-user mailing list
SciPy-user at scipy.org
http://projects.scipy.org/mailman/listinfo/scipy-user


 		
---------------------------------
 D?couvrez une nouvelle fa?on d'obtenir des r?ponses ? toutes vos questions ! Profitez des connaissances, des opinions et des exp?riences des internautes sur Yahoo! Questions/R?ponses.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20070208/cdd2b1e7/attachment.html>

From rowen at cesmail.net  Fri Feb  9 15:45:23 2007
From: rowen at cesmail.net (Russell E. Owen)
Date: Fri, 09 Feb 2007 12:45:23 -0800
Subject: [SciPy-user] Hints for easy install of scipy on RHEL 4?
References: <rowen-D78C9A.11273507022007@sea.gmane.org>
	<40e64fa20702071156s20437821m3a2336b3a3a2719c@mail.gmail.com>
Message-ID: <rowen-E863E6.12452309022007@sea.gmane.org>

In article 
<40e64fa20702071156s20437821m3a2336b3a3a2719c at mail.gmail.com>,
 "Paul Barrett" <pebarrett at gmail.com> wrote:

(in response to my question about how to most easily obtain a 
scipy-friendly blas/lapack for RHEL 4, because the one that comes with 
RHEL 4 is not)

> Is RHEL 4 necessary?  I had the same problems building scipy, so I
> decided to save myself some grief.  I installed FC 6 instead, while I
> wait for RHEL 5. If you have to have RHEL as opposed to FC, then I
> suggest you upgrade to RHEL 5beta2, which is based on FC 6/7.

That is very interesting. So if we can hold off for RHEL 5 then the 
problem magically goes away? I'll see if we can do that.

(This is for a large department's worth of linux boxes. I don't manage 
them, but do have permission to install software in a space for shared 
software. Thus I typically can't install RPMs and can only advise when 
it comes to OS versions.)

Regards,

-- Russell



From Glen.Mabey at swri.org  Fri Feb  9 15:57:14 2007
From: Glen.Mabey at swri.org (Glen W. Mabey)
Date: Fri, 9 Feb 2007 14:57:14 -0600
Subject: [SciPy-user] parallel usage of fftw
Message-ID: <20070209205714.GK16082@swri16wm.electro.swri.edu>

Hello,

I've read at

http://www.fftw.org/fftw3_doc/Usage-of-Multi_002dthreaded-FFTW.html#Usage-of-Multi_002dthreaded-FFTW

that getting fftw to use multiple threads to speed up performance on SMP
machines is quite easy to initiate.

Has anyone used tried this?  

I haven't ever used fftw without scipy, but if there were some way to
easily implement a python interface such that fftw_init_threads(),
fftw_plan_with_nthreads(), and fftw_cleanup_threads() could be called,
it would be really cool.

I'm having a bit of a time trying to figure out how fftpack is married
to fftw ... maybe I should just try calling those functions with ctypes?

Any input would be greatly appreciated.

Thanks,
Glen



From krlong at sandia.gov  Fri Feb  9 16:22:01 2007
From: krlong at sandia.gov (Kevin Long)
Date: Fri, 9 Feb 2007 15:22:01 -0600
Subject: [SciPy-user] problem with _num.seterr when importing scipy
Message-ID: <200702091522.01125.krlong@sandia.gov>


Hello,

I'm getting an error message about "_num.seterr" when importing scipy. 
Output is below. 

<diogenes:/home/krlong> python
Python 2.4.4 (#1, Feb  9 2007, 14:45:36)
[GCC 3.4.6] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import scipy
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File "/usr/local/lib/python2.4/site-packages/scipy/__init__.py", line 37, 
in ?
    _num.seterr(all='ignore')
TypeError: seterr() got an unexpected keyword argument 'all'
>>>        

I've googled the error message, but found no other reports of it. 
To get past this problem, I commented out line 37 in __init.py__ and pressed 
bravely (or foolishly) onwards. Things seem to work OK after that, but 
I'm nervous about commenting something out of your code.

This is on SuSE 10.1, but I'm not using the versions of python, gcc, blas, or 
lapack that were bundled with the system. The python version is 2.4.4. Lapack 
is the distribution from netlib. The BLAS is the version shipped with 
netlib's lapack, with srotmg.f, srotm.f, drotm.f,  and drotmg.f added (from 
netlib's blas.tar.gz) to provide the complete BLAS needed by scipy. 
Everything was built with gcc 3.4.6. 

Any ideas?

Thank you,

Kevin Long


--
-----------------------------------------------------------------------------
        Dr. Kevin Long
        Computational Science and Mathematics Research Department 
        Sandia National Laboratories          

        MS 9217                               krlong at sandia.gov
        Livermore, CA 94551                   (925)-294-4910
-----------------------------------------------------------------------------


From robert.kern at gmail.com  Fri Feb  9 16:24:14 2007
From: robert.kern at gmail.com (Robert Kern)
Date: Fri, 09 Feb 2007 13:24:14 -0800
Subject: [SciPy-user] problem with _num.seterr when importing scipy
In-Reply-To: <200702091522.01125.krlong@sandia.gov>
References: <200702091522.01125.krlong@sandia.gov>
Message-ID: <45CCE67E.1090508@gmail.com>

Kevin Long wrote:
> Hello,
> 
> I'm getting an error message about "_num.seterr" when importing scipy. 
> Output is below. 
> 
> <diogenes:/home/krlong> python
> Python 2.4.4 (#1, Feb  9 2007, 14:45:36)
> [GCC 3.4.6] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
>>>> import scipy
> Traceback (most recent call last):
>   File "<stdin>", line 1, in ?
>   File "/usr/local/lib/python2.4/site-packages/scipy/__init__.py", line 37, 
> in ?
>     _num.seterr(all='ignore')
> TypeError: seterr() got an unexpected keyword argument 'all'
>>>>        

What versions of numpy and scipy do you have installed? E.g.:

>>> import numpy
>>> print numpy.__version__
1.0.2.dev3521
>>> import scipy
>>> print scipy.__version__
0.5.3.dev2620

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
 that is made terrible by our own mad attempt to interpret it as though it had
 an underlying truth."
  -- Umberto Eco


From krlong at sandia.gov  Fri Feb  9 16:31:11 2007
From: krlong at sandia.gov (Kevin Long)
Date: Fri, 9 Feb 2007 15:31:11 -0600
Subject: [SciPy-user] problem with _num.seterr when importing scipy
In-Reply-To: <45CCE67E.1090508@gmail.com>
References: <200702091522.01125.krlong@sandia.gov> <45CCE67E.1090508@gmail.com>
Message-ID: <200702091531.11770.krlong@sandia.gov>


Hi Robert,

Numpy 1.0b5 and scipy 0.5.2.

- kevin

On Friday 09 February 2007 15:24, Robert Kern wrote:
> Kevin Long wrote:
> > Hello,
> >
> > I'm getting an error message about "_num.seterr" when importing scipy.
> > Output is below.
> >
> > <diogenes:/home/krlong> python
> > Python 2.4.4 (#1, Feb  9 2007, 14:45:36)
> > [GCC 3.4.6] on linux2
> > Type "help", "copyright", "credits" or "license" for more information.
> >
> >>>> import scipy
> >
> > Traceback (most recent call last):
> >   File "<stdin>", line 1, in ?
> >   File "/usr/local/lib/python2.4/site-packages/scipy/__init__.py", line
> > 37, in ?
> >     _num.seterr(all='ignore')
> > TypeError: seterr() got an unexpected keyword argument 'all'
>
> What versions of numpy and scipy do you have installed? E.g.:
> >>> import numpy
> >>> print numpy.__version__
>
> 1.0.2.dev3521
>
> >>> import scipy
> >>> print scipy.__version__
>
> 0.5.3.dev2620


From anand at soe.ucsc.edu  Fri Feb  9 17:12:34 2007
From: anand at soe.ucsc.edu (Anand Patil)
Date: Fri, 09 Feb 2007 14:12:34 -0800
Subject: [SciPy-user] Vectorization question
Message-ID: <45CCF1D2.1050404@cse.ucsc.edu>

Hi all,

I want to make array A from array B like so:

A[t, j, k] = \sum_i B[t, j, i] B[t, i, k]

That is, for each t

A[t,] = dot(B[t,], B[t,])

There's no loopless way to do this in numpy, right?

Thanks much,
Anand


From oliphant at ee.byu.edu  Fri Feb  9 17:20:22 2007
From: oliphant at ee.byu.edu (Travis Oliphant)
Date: Fri, 09 Feb 2007 15:20:22 -0700
Subject: [SciPy-user] Vectorization question
In-Reply-To: <45CCF1D2.1050404@cse.ucsc.edu>
References: <45CCF1D2.1050404@cse.ucsc.edu>
Message-ID: <45CCF3A6.3010402@ee.byu.edu>

Anand Patil wrote:

>Hi all,
>
>I want to make array A from array B like so:
>
>A[t, j, k] = \sum_i B[t, j, i] B[t, i, k]
>
>That is, for each t
>
>A[t,] = dot(B[t,], B[t,])
>
>There's no loopless way to do this in numpy, right?
>  
>
You should be able to do this just using

A = dot(B,B)

Because the dot function returns the sum of products over the last 
dimension of the first argument and the second-to-last dimension of the 
second argument.

-Travis



From jbattat at cfa.harvard.edu  Fri Feb  9 17:44:56 2007
From: jbattat at cfa.harvard.edu (James Battat)
Date: Fri, 9 Feb 2007 17:44:56 -0500 (EST)
Subject: [SciPy-user] new behaviour of c_[] in scipy 0.5.2
Message-ID: <Pine.SOL.4.58.0702091738260.8803@cfa0.cfa.harvard.edu>

Hi,

In the past:
  (scipy 0.4.8, numpy 0.9.6)

>>> print scipy.c_[1,2,3]
[1,2,3]

but now:
 (scipy 0.5.2, numpy 1.0.1)

>>> print scipy.c_[1,2,3]
[[1,2,3]]

A nested array!  This breaks my old code because:

>>> array = scipy.c_[1,2,3]
>>> print array[1]
IndexError: index is out of bounds

Is the current behaviour expected?

Thanks for your help,
James






**************************
Harvard University
Dept. of Astronomy
60 Garden Street
MS-10
Cambridge, MA 02138
phone 617.496.0742
lab   617.495.3267
email jbattat at cfa.harvard.edu
**************************



From brad.malone at gmail.com  Fri Feb  9 17:57:29 2007
From: brad.malone at gmail.com (Brad Malone)
Date: Fri, 9 Feb 2007 14:57:29 -0800
Subject: [SciPy-user] Error on trying to install SciPy
Message-ID: <bf16929a0702091457g247c5c58k255c9211f590fa88@mail.gmail.com>

Hi everyone, sorry to be a bother but I'm getting really frustrated with
trying to install SciPy.  When I build or install this is what it tells me
before it exits.  Anyone have a clue why this would be?  I REALLY appreciate
any help.

IPO link: can not find "("
ifort: error: problem during multi-file optimization compilation (code 1)
error: Command "/auto/opt/intel/fc/9.0/bin/ifort -shared -nofor_main -tpp6
-xM -arch SSE
build/temp.linux-i686-2.4/build/src.linux-i686-2.4
/Lib/fftpack/_fftpackmodule.o
build/temp.linux-i686-2.4/Lib/fftpack/src/zfft.o
build/temp.linux-i686-2.4/Lib/fftpack/src/drfft.o
build/temp.linux-i686-2.4/Lib/fftpack/src/zrfft.o
build/temp.linux-i686-2.4/Lib/fftpack/src/zfftnd.o
build/temp.linux-i686-2.4/build/src.linux-i686-2.4/fortranobject.o
-L/opt/lib -Lbuild/temp.linux-i686-2.4 -ldfftpack -lrfftw -lfftw -o
build/lib.linux-i686-2.4/scipy/fftpack/_fftpack.so" failed with exit
status 1

Best,
Brad
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20070209/ec902fb1/attachment.html>

From anand at soe.ucsc.edu  Fri Feb  9 21:00:03 2007
From: anand at soe.ucsc.edu (Anand Patil)
Date: Fri, 09 Feb 2007 18:00:03 -0800
Subject: [SciPy-user] Vectorization question
Message-ID: <45CD2723.5040201@cse.ucsc.edu>

>Anand Patil wrote:

>>/Hi all,
/>>/
/>>/I want to make array A from array B like so:
/>>/
/>>/A[t, j, k] = \sum_i B[t, j, i] B[t, i, k]
/>>/
/>>/That is, for each t
/>>/
/>>/A[t,] = dot(B[t,], B[t,])
/>>/
/>>/There's no loopless way to do this in numpy, right?
/>>/  
/>>/
/>You should be able to do this just using
>
>A = dot(B,B)
>
>Because the dot function returns the sum of products over the last 
>dimension of the first argument and the second-to-last dimension of the 
>second argument.
>
>-Travis


The output array I'm looking for is rank-3, but as I understand them dot and tensordot can only ever return even-rank arrays:

In [1]: from numpy import zeros, dot

In [2]: B=zeros((4,3,3))

In [3]: dot(B,B).shape
Out[3]: (4, 3, 4, 3)

In [4]: 

Thanks,
Anand



From pebarrett at gmail.com  Sat Feb 10 07:42:03 2007
From: pebarrett at gmail.com (Paul Barrett)
Date: Sat, 10 Feb 2007 07:42:03 -0500
Subject: [SciPy-user] Hints for easy install of scipy on RHEL 4?
In-Reply-To: <rowen-E863E6.12452309022007@sea.gmane.org>
References: <rowen-D78C9A.11273507022007@sea.gmane.org>
	<40e64fa20702071156s20437821m3a2336b3a3a2719c@mail.gmail.com>
	<rowen-E863E6.12452309022007@sea.gmane.org>
Message-ID: <40e64fa20702100442p747cc1c0k355a145d383d5b8e@mail.gmail.com>

On 2/9/07, Russell E. Owen <rowen at cesmail.net> wrote:
> In article
> <40e64fa20702071156s20437821m3a2336b3a3a2719c at mail.gmail.com>,
>  "Paul Barrett" <pebarrett at gmail.com> wrote:
>
> (in response to my question about how to most easily obtain a
> scipy-friendly blas/lapack for RHEL 4, because the one that comes with
> RHEL 4 is not)
>
> > Is RHEL 4 necessary?  I had the same problems building scipy, so I
> > decided to save myself some grief.  I installed FC 6 instead, while I
> > wait for RHEL 5. If you have to have RHEL as opposed to FC, then I
> > suggest you upgrade to RHEL 5beta2, which is based on FC 6/7.
>
> That is very interesting. So if we can hold off for RHEL 5 then the
> problem magically goes away? I'll see if we can do that.
>
> (This is for a large department's worth of linux boxes. I don't manage
> them, but do have permission to install software in a space for shared
> software. Thus I typically can't install RPMs and can only advise when
> it comes to OS versions.)

Yes, we are in the same situation. We are beginning to investigate
RHEL 5b2 now, which is available for download. RHEL 5 final was
suppose to be available at the beginning of the year, but they are
apparently putting some final touches on the smartcard and
virtualization software, which many enterprises need.  Given how
stable FC 6 has been, I sure RHEL 5b2 is fine if you do not need these
features.

 -- Paul


From gnata at obs.univ-lyon1.fr  Sat Feb 10 11:51:10 2007
From: gnata at obs.univ-lyon1.fr (Xavier Gnata)
Date: Sat, 10 Feb 2007 17:51:10 +0100
Subject: [SciPy-user] scipy print using ipython
In-Reply-To: <200702081742.57873.pecontal@obs.univ-lyon1.fr>
References: <200702081742.57873.pecontal@obs.univ-lyon1.fr>
Message-ID: <45CDF7FE.2090801@obs.univ-lyon1.fr>

Hello,

On my box I cannot reproduce this behavior with the following code:
x0 = rand(100000)
xopt = fmin_l_bfgs_b(rosen, x0, fprime=rosen_der,iprint=1)

Cheers,
Xavier
ps : iprime = "any positive value" works also well on my box.

> Hello,
>
> I am using the fmin_l_bfgs_b function in scipy. This function has a
> parameter
>
> for controling the iteration printing during the minimization. In fact
> the printing
>
> is done by the fortran routine via a command like:
>
> write (6,1002) iter,f,sbgnrm
>
> which is a print on the screen.
>
> For some reason I don't understand, when I use the routine in ipython,
> the print
>
> is done only by bunch of lines every few minutes... just like if it
> was bufferized
>
> before printing. Does someone knows the reason of this beheviour? is
> it a python,
>
> ipython or scipy problem?
>
> Cheers
>
> Emmanuel
>
> -- 
>
> Emmanuel P?contal
>
> CRAL - Observatoire de Lyon
>
> 9, Av. Charles Andre
>
> F-69561 Saint Genis Laval Cedex
>
> tel (33) (0)4.78.86.83.76 - fax (33) (0)4.78.86.83.86
>
> email : pecontal at obs.univ-lyon1.fr
>
> ~
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user
>   


-- 
############################################
Xavier Gnata
CRAL - Observatoire de Lyon
9, avenue Charles Andr?
69561 Saint Genis Laval cedex
Phone: +33 4 78 86 85 28
Fax: +33 4 78 86 83 86
E-mail: gnata at obs.univ-lyon1.fr
############################################ 



From strang at nmr.mgh.harvard.edu  Sat Feb 10 19:47:00 2007
From: strang at nmr.mgh.harvard.edu (Gary Strangman)
Date: Sat, 10 Feb 2007 19:47:00 -0500 (EST)
Subject: [SciPy-user] Hilbert-Huang?
Message-ID: <Pine.LNX.4.62.0702101941280.30008@gate.nmr.mgh.harvard.edu>


Hi all,

Does anyone know of (or have) a python implementation of the Hilbert-Huang 
transform out there somewhere? Numpy, Numeric, numarray, scipy, doesn't 
matter to me. 'fraid my searches have come up empty ...

-best
Gary


From robert.kern at gmail.com  Sat Feb 10 21:26:48 2007
From: robert.kern at gmail.com (Robert Kern)
Date: Sat, 10 Feb 2007 20:26:48 -0600
Subject: [SciPy-user] Hilbert-Huang?
In-Reply-To: <Pine.LNX.4.62.0702101941280.30008@gate.nmr.mgh.harvard.edu>
References: <Pine.LNX.4.62.0702101941280.30008@gate.nmr.mgh.harvard.edu>
Message-ID: <45CE7EE8.708@gmail.com>

Gary Strangman wrote:
> Hi all,
> 
> Does anyone know of (or have) a python implementation of the Hilbert-Huang 
> transform out there somewhere? Numpy, Numeric, numarray, scipy, doesn't 
> matter to me. 'fraid my searches have come up empty ...

As it appears to be patented, you probably won't find one.

  http://techtransfer.gsfc.nasa.gov/HHT/#patents

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
 that is made terrible by our own mad attempt to interpret it as though it had
 an underlying truth."
  -- Umberto Eco


From zunzun at zunzun.com  Sun Feb 11 07:15:51 2007
From: zunzun at zunzun.com (zunzun at zunzun.com)
Date: Sun, 11 Feb 2007 07:15:51 -0500
Subject: [SciPy-user] Hilbert-Huang?
In-Reply-To: <45CE7EE8.708@gmail.com>
References: <Pine.LNX.4.62.0702101941280.30008@gate.nmr.mgh.harvard.edu>
	<45CE7EE8.708@gmail.com>
Message-ID: <20070211121551.GA10312@zunzun.com>




From topengineer at gmail.com  Sun Feb 11 10:01:51 2007
From: topengineer at gmail.com (Hui Chang Moon)
Date: Mon, 12 Feb 2007 00:01:51 +0900
Subject: [SciPy-user] Doesn't Scipy have the Fermi-Dirac distribution?
Message-ID: <296323b50702110701k110cd1f9k10fa49576cda83b1@mail.gmail.com>

I am a graduate school student.
Nowadays I'm writing a semiconductor simulation code with numpy and scipy.
In my field, the Fermi-Dirac distribution function is frequently used.
I hope to know if the scipy has the Fermi-Dirac distribution function or
not.

Have a nice day~! ^o^
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20070212/36444ee6/attachment.html>

From strang at nmr.mgh.harvard.edu  Sun Feb 11 10:16:03 2007
From: strang at nmr.mgh.harvard.edu (Gary Strangman)
Date: Sun, 11 Feb 2007 10:16:03 -0500 (EST)
Subject: [SciPy-user] Hilbert-Huang?
In-Reply-To: <45CE7EE8.708@gmail.com>
References: <Pine.LNX.4.62.0702101941280.30008@gate.nmr.mgh.harvard.edu>
	<45CE7EE8.708@gmail.com>
Message-ID: <Pine.LNX.4.62.0702111010160.10925@gate.nmr.mgh.harvard.edu>


Yeah, I figured HHT was unavailable, but thought I'd ask anyway.

Anyone know of a python version of (the related and I believe not 
patented) empirical mode decomposition?

Gary

On Sat, 10 Feb 2007, Robert Kern wrote:

> Gary Strangman wrote:
>> Hi all,
>>
>> Does anyone know of (or have) a python implementation of the Hilbert-Huang
>> transform out there somewhere? Numpy, Numeric, numarray, scipy, doesn't
>> matter to me. 'fraid my searches have come up empty ...
>
> As it appears to be patented, you probably won't find one.
>
>  http://techtransfer.gsfc.nasa.gov/HHT/#patents
>
>


From lev at columbia.edu  Sun Feb 11 15:13:08 2007
From: lev at columbia.edu (Lev Givon)
Date: Sun, 11 Feb 2007 15:13:08 -0500
Subject: [SciPy-user] Doesn't Scipy have the Fermi-Dirac distribution?
In-Reply-To: <296323b50702110701k110cd1f9k10fa49576cda83b1@mail.gmail.com>
References: <296323b50702110701k110cd1f9k10fa49576cda83b1@mail.gmail.com>
Message-ID: <20070211201308.GH2273@avicenna.cc.columbia.edu>

Received from Hui Chang Moon on Sun, Feb 11, 2007 at 10:01:51AM EST:
> I am a graduate school student.
> Nowadays I'm writing a semiconductor simulation code with numpy and scipy.
> In my field, the Fermi-Dirac distribution function is frequently used.
> I hope to know if the scipy has the Fermi-Dirac distribution function or
> not.
> 
> Have a nice day~! ^o^

As of version 0.5.2, I don't believe so. 

It is worth noting that one can create a random variable with the
Fermi-Dirac distribution as its PDF by extending the
scipy.stats.rv_continuous class as described in
$PYTHONHOME/site-packages/scipy/stats/distribution.py

							L.G.


From sinclaird at ukzn.ac.za  Mon Feb 12 01:02:17 2007
From: sinclaird at ukzn.ac.za (Scott Sinclair)
Date: Mon, 12 Feb 2007 08:02:17 +0200
Subject: [SciPy-user] Hilbert-Huang?
In-Reply-To: <Pine.LNX.4.62.0702111010160.10925@gate.nmr.mgh.harvard.edu>
References: <Pine.LNX.4.62.0702101941280.30008@gate.nmr.mgh.harvard.edu>
	<45CE7EE8.708@gmail.com>
	<Pine.LNX.4.62.0702111010160.10925@gate.nmr.mgh.harvard.edu>
Message-ID: <45D01EC8.F934.009F.0@ukzn.ac.za>

>>> Gary Strangman <strang at nmr.mgh.harvard.edu> 2/11/2007 17:16 >>>
Anyone know of a python version of (the related and I believe not 
patented) empirical mode decomposition?
>>>
 
No Python implementation (to my knowledge) but you can find a MATLAB
implementation here 
 
http://perso.ens-lyon.fr/patrick.flandrin/emd.html 
 
It shouldn't be too hard to translate, the algorithm is pretty simple.
 
Cheers,
Scott

Please find our Email Disclaimer here: http://www.ukzn.ac.za/disclaimer/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20070212/68b89f4b/attachment.html>

From oliphant at ee.byu.edu  Mon Feb 12 12:09:43 2007
From: oliphant at ee.byu.edu (Travis Oliphant)
Date: Mon, 12 Feb 2007 10:09:43 -0700
Subject: [SciPy-user] Vectorization question
In-Reply-To: <45CD2723.5040201@cse.ucsc.edu>
References: <45CD2723.5040201@cse.ucsc.edu>
Message-ID: <45D09F57.5080104@ee.byu.edu>

Anand Patil wrote:

>>Anand Patil wrote:
>>    
>>
>
>  
>
>>>/Hi all,
>>>      
>>>
>/>>/
>/>>/I want to make array A from array B like so:
>/>>/
>/>>/A[t, j, k] = \sum_i B[t, j, i] B[t, i, k]
>/>>/
>/>>/That is, for each t
>/>>/
>/>>/A[t,] = dot(B[t,], B[t,])
>/>>/
>/>>/There's no loopless way to do this in numpy, right?
>/>>/  
>/>>/
>/>You should be able to do this just using
>  
>
>>A = dot(B,B)
>>
>>Because the dot function returns the sum of products over the last 
>>dimension of the first argument and the second-to-last dimension of the 
>>second argument.
>>
>>-Travis
>>    
>>
>
>
>The output array I'm looking for is rank-3, but as I understand them dot and tensordot can only ever return even-rank arrays:
>
>  
>
I see the difference now.  Yes, you are right, you are wanting to do a 
sum of products without an outer-product.  You would have to extract the 
"diagonal" of the result.

-Travis



From zunzun at zunzun.com  Tue Feb 13 03:09:16 2007
From: zunzun at zunzun.com (zunzun at zunzun.com)
Date: Tue, 13 Feb 2007 03:09:16 -0500
Subject: [SciPy-user] Fit statistics for sum of squared relative error
Message-ID: <20070213080915.GA5684@zunzun.com>

I've been doing fits to lowest sum of squared relative
error for a while now.  These are useful when a data
set exhibits increasing heteroscedasticity as the
values of the independent variable increase, i.e.,
data scatter proportional to distance along the x axis.

You can test this at http://zunzun.com by selecting a 
fitting target of "Lowest sum of squared relative errors"
when fitting, and this is also in the Python Equations
package at http://sf.net/ptojects/pythonequations.


Having investigated fit statistics for some time now,
it seems *everything* is geared toward absolute error,
with not the slightest drop that I can find regarding
relative error.  These statistics are needed when
performing SSQREL rather than SSQABS fitting.

Can I safely use existing routines for covariance
matrices and parameter standard errors simply by
substituting dy(relative)/dx and relative error
whenever dy(absolute)/dx and absolute error are
used?  I apologize, but this is over my head and
I would like to report the fit statistics properly.

     James Phillips
     http;//zunzun.com


P.S. I don't yet have much in the way of fit statistics
on the web site, this is what I'm currently working on.
I found much of what I need in the BSD-style licensed MPFIT.py
at http://cars9.uchicago.edu/software/python/mpfit.html
written by Mark Rivers.


From nwagner at iam.uni-stuttgart.de  Tue Feb 13 05:14:14 2007
From: nwagner at iam.uni-stuttgart.de (Nils Wagner)
Date: Tue, 13 Feb 2007 11:14:14 +0100
Subject: [SciPy-user] Mittag-Leffler function
Message-ID: <45D18F76.7080108@iam.uni-stuttgart.de>

Hi,

has someone implemented the Mittag-Leffler function with the aid of scipy ?
A Matlab code is available here
http://www.mathworks.com/matlabcentral/fileexchange/loadFile.do?objectId=8738&objectType=FILE

Nils

References:
http://mathworld.wolfram.com/Mittag-LefflerFunction.html
http://en.wikipedia.org/wiki/Mittag-Leffler_function

 



From ryanlists at gmail.com  Tue Feb 13 14:57:46 2007
From: ryanlists at gmail.com (Ryan Krauss)
Date: Tue, 13 Feb 2007 13:57:46 -0600
Subject: [SciPy-user] problem with signal.residue
Message-ID: <c5b438120702131157h6ddd045et78436b452397095c@mail.gmail.com>

I think I have found a small bug in signal.residue and may have found
a simple solution.  The problem seems to come from polydiv requiring
that the numerator polynomial be of degree at most 1 less than the
denominator.  If I have a denominator of s^2+3*s+2, the numerator must
have an s coefficient (even if that coefficient is 0) for
signal.residue to work:

In [75]: a
Out[75]: array([1, 3, 2])

In [76]: signal.residue([1],a)
---------------------------------------------------------------------------
exceptions.ValueError                                Traceback (most recent cal
 last)

C:\Python24\<ipython console>

C:\Python24\Lib\site-packages\scipy\signal\signaltools.py in residue(b, a, tol,
rtype)
   1054
   1055     b,a = map(asarray,(b,a))
-> 1056     k,b = polydiv(b,a)
   1057     p = roots(a)
   1058     r = p*0.0

C:\Python24\Lib\site-packages\numpy\lib\polynomial.py in polydiv(u, v)
    399     n = len(v) - 1
    400     scale = 1. / v[0]
--> 401     q = NX.zeros((m-n+1,), float)
    402     r = u.copy()
    403     for k in range(0, m-n+1):

ValueError: negative dimensions are not allowed

In [77]: signal.residue([0,1],a)
Out[77]:
(array([ 1.+0.j, -1.+0.j]),
 array([-1.+0.j, -2.+0.j]),
  array([], dtype=float64))


I think the simple solution is to replace line 1056 with these four lines:
    if len(b)<len(a):
        k=[]
    else:
        k,b = polydiv(b,a)

where the last line above is the old line 1056.  Basically, specify
that there is no k term if the len of b is less than the len of a.

Is this too simple?  What do I do to actually submit this if it is the
right solution?

Ryan


From akumar at iitm.ac.in  Tue Feb 13 20:06:07 2007
From: akumar at iitm.ac.in (Kumar Appaiah)
Date: Wed, 14 Feb 2007 06:36:07 +0530
Subject: [SciPy-user] problem with signal.residue
In-Reply-To: <c5b438120702131157h6ddd045et78436b452397095c@mail.gmail.com>
References: <c5b438120702131157h6ddd045et78436b452397095c@mail.gmail.com>
Message-ID: <20070214010607.GA5728@localhost>

On Tue, Feb 13, 2007 at 01:57:46PM -0600, Ryan Krauss wrote:
> I think I have found a small bug in signal.residue and may have found
> a simple solution.  The problem seems to come from polydiv requiring
> that the numerator polynomial be of degree at most 1 less than the
> denominator.  If I have a denominator of s^2+3*s+2, the numerator must
> have an s coefficient (even if that coefficient is 0) for
> signal.residue to work:
> 
> In [75]: a
> Out[75]: array([1, 3, 2])
> 
> In [76]: signal.residue([1],a)
> ---------------------------------------------------------------------------
> exceptions.ValueError                                Traceback (most recent cal
>  last)
[snip]
> In [77]: signal.residue([0,1],a)
> Out[77]:
> (array([ 1.+0.j, -1.+0.j]),
>  array([-1.+0.j, -2.+0.j]),
>   array([], dtype=float64))
> 
> 
> I think the simple solution is to replace line 1056 with these four lines:
>     if len(b)<len(a):
>         k=[]
>     else:
>         k,b = polydiv(b,a)
> 
> where the last line above is the old line 1056.  Basically, specify
> that there is no k term if the len of b is less than the len of a.
> 
> Is this too simple?  What do I do to actually submit this if it is the
> right solution?

I think you are right. This seems to be a bug.
Please register and open a ticket at
http://projects.scipy.org/scipy/scipy and state the problem and the
specified solution.

Thanks.

Kumar
-- 
Kumar Appaiah,
462, Jamuna Hostel,
Indian Institute of Technology Madras,
Chennai - 600 036



From nwagner at iam.uni-stuttgart.de  Wed Feb 14 03:02:34 2007
From: nwagner at iam.uni-stuttgart.de (Nils Wagner)
Date: Wed, 14 Feb 2007 09:02:34 +0100
Subject: [SciPy-user] Array manipulation
Message-ID: <45D2C21A.3040809@iam.uni-stuttgart.de>

Hi,

I would like to remove the i-th column and row from a two-dimensional
array A. The remaining array
should be kept and stored in B

A = random.rand(n,n)

This task is very easy if i is the first or last row/column. In that
case one can use

B = A[1:,1:]

or

B=A[:-1,:-1]

But, what is the best way to get B  if  0 < i < n-1 ?

Nils

 


From joris at ster.kuleuven.ac.be  Wed Feb 14 03:34:40 2007
From: joris at ster.kuleuven.ac.be (joris at ster.kuleuven.ac.be)
Date: Wed, 14 Feb 2007 09:34:40 +0100
Subject: [SciPy-user] Array manipulation
Message-ID: <1171442080.45d2c9a00bd8a@webmail.ster.kuleuven.be>

Hi Nils,

It's not a one-liner, but it may serve you:


In [40]: n = 4
In [41]: i = 2
In [42]:
In [42]: A = arange(n*n).reshape(n,n)
In [43]: A
Out[43]:
array([[ 0,  1,  2,  3],
       [ 4,  5,  6,  7],
       [ 8,  9, 10, 11],
       [12, 13, 14, 15]])
In [44]: I = range(n)
In [45]: I.remove(i)
In [46]: B = A[ix_(I,I)]
In [47]: B
Out[47]:
array([[ 0,  1,  3],
       [ 4,  5,  7],
       [12, 13, 15]])


Cheers,
Joris




On Wednesday 14 February 2007 09:02, Nils Wagner wrote:
>Hi,
>
>I would like to remove the i-th column and row from a two-dimensional
>array A. The remaining array
>should be kept and stored in B
>
>A = random.rand(n,n)
>
>This task is very easy if i is the first or last row/column. In that
>case one can use
>
>B = A[1:,1:]
>
>or
>
>B=A[:-1,:-1]
>
>But, what is the best way to get B  if  0 < i < n-1 ?
>
>Nils



Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm



From stefan at sun.ac.za  Wed Feb 14 04:03:53 2007
From: stefan at sun.ac.za (Stefan van der Walt)
Date: Wed, 14 Feb 2007 11:03:53 +0200
Subject: [SciPy-user] Array manipulation
In-Reply-To: <45D2C21A.3040809@iam.uni-stuttgart.de>
References: <45D2C21A.3040809@iam.uni-stuttgart.de>
Message-ID: <20070214090353.GV6150@mentat.za.net>

On Wed, Feb 14, 2007 at 09:02:34AM +0100, Nils Wagner wrote:
> Hi,
> 
> I would like to remove the i-th column and row from a two-dimensional
> array A. The remaining array
> should be kept and stored in B
> 
> A = random.rand(n,n)
> 
> This task is very easy if i is the first or last row/column. In that
> case one can use
> 
> B = A[1:,1:]
> 
> or
> 
> B=A[:-1,:-1]
> 
> But, what is the best way to get B  if  0 < i < n-1 ?

numpy.delete(x, i, 1)

Cheers
St?fan


From nwagner at iam.uni-stuttgart.de  Wed Feb 14 05:13:01 2007
From: nwagner at iam.uni-stuttgart.de (Nils Wagner)
Date: Wed, 14 Feb 2007 11:13:01 +0100
Subject: [SciPy-user] Array manipulation
In-Reply-To: <20070214090353.GV6150@mentat.za.net>
References: <45D2C21A.3040809@iam.uni-stuttgart.de>
	<20070214090353.GV6150@mentat.za.net>
Message-ID: <45D2E0AD.7050409@iam.uni-stuttgart.de>

Stefan van der Walt wrote:
> On Wed, Feb 14, 2007 at 09:02:34AM +0100, Nils Wagner wrote:
>   
>> Hi,
>>
>> I would like to remove the i-th column and row from a two-dimensional
>> array A. The remaining array
>> should be kept and stored in B
>>
>> A = random.rand(n,n)
>>
>> This task is very easy if i is the first or last row/column. In that
>> case one can use
>>
>> B = A[1:,1:]
>>
>> or
>>
>> B=A[:-1,:-1]
>>
>> But, what is the best way to get B  if  0 < i < n-1 ?
>>     
>
> numpy.delete(x, i, 1)
>
> Cheers
> St?fan
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user
>   
 Hi Joris and Stefan,

Thank you for your replies. It's nice to see that there are different
ways to realize this task.

BTW, "insert" is missing in http://www.scipy.org/Numpy_Example_List.
I forgot my password to access the wiki page. Joris, please can you
add an example for insert. I saw that you have just edited that page.

Thanks in advance.


Cheers
                  Nils



From chiaracaronna at hotmail.com  Wed Feb 14 05:22:15 2007
From: chiaracaronna at hotmail.com (Chiara Caronna)
Date: Wed, 14 Feb 2007 10:22:15 +0000
Subject: [SciPy-user] scipy.optimize.leastsq error estimates
In-Reply-To: <45C84EA5.8080307@gmail.com>
Message-ID: <BAY114-F254E0BCC45C7696A7A24BDA1970@phx.gbl>

Hi,
I am also interested in having errors from the fit, and I tried to import 
the module scipy.odr as you said, but I got this errors:

File "/usr/local/lib/python2.4/site-packages/scipy/odr/__init__.py", line 
49, in ?
    import odrpack
  File "/usr/local/lib/python2.4/site-packages/scipy/odr/odrpack.py", line 
103, in ?
    from scipy.sandbox.odr import __odrpack
ImportError: No module named odr


And the same is if I try to import  sandbox.odr

import scipy.sandbox.odr

Traceback (most recent call last):
  File "<stdin>", line 1, in ?
ImportError: No module named odr

Where am I wrong?
Thank you,
Chiara





>From: Robert Kern <robert.kern at gmail.com>
>Reply-To: SciPy Users List <scipy-user at scipy.org>
>To: SciPy Users List <scipy-user at scipy.org>
>Subject: Re: [SciPy-user] scipy.optimize.leastsq error estimates
>Date: Tue, 06 Feb 2007 03:47:17 -0600
>
>Nils Wagner wrote:
>
> > AFAIK odr is directly available through scipy.odr.
> > So I guess the odr directory in the sandbox is obsolete. Is that correct 
>?
>
>There is no more odr/ directory in the sandbox since it got moved into the 
>main
>package.
>
>--
>Robert Kern
>
>"I have come to believe that the whole world is an enigma, a harmless 
>enigma
>  that is made terrible by our own mad attempt to interpret it as though it 
>had
>  an underlying truth."
>   -- Umberto Eco
>_______________________________________________
>SciPy-user mailing list
>SciPy-user at scipy.org
>http://projects.scipy.org/mailman/listinfo/scipy-user

_________________________________________________________________
Express yourself instantly with MSN Messenger! Download today it's FREE! 
http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/



From nwagner at iam.uni-stuttgart.de  Wed Feb 14 05:24:56 2007
From: nwagner at iam.uni-stuttgart.de (Nils Wagner)
Date: Wed, 14 Feb 2007 11:24:56 +0100
Subject: [SciPy-user] scipy.optimize.leastsq error estimates
In-Reply-To: <BAY114-F254E0BCC45C7696A7A24BDA1970@phx.gbl>
References: <BAY114-F254E0BCC45C7696A7A24BDA1970@phx.gbl>
Message-ID: <45D2E378.5070401@iam.uni-stuttgart.de>

Chiara Caronna wrote:
> Hi,
> I am also interested in having errors from the fit, and I tried to import 
> the module scipy.odr as you said, but I got this errors:
>
> File "/usr/local/lib/python2.4/site-packages/scipy/odr/__init__.py", line 
> 49, in ?
>     import odrpack
>   File "/usr/local/lib/python2.4/site-packages/scipy/odr/odrpack.py", line 
> 103, in ?
>     from scipy.sandbox.odr import __odrpack
> ImportError: No module named odr
>
>
> And the same is if I try to import  sandbox.odr
>
> import scipy.sandbox.odr
>
> Traceback (most recent call last):
>   File "<stdin>", line 1, in ?
> ImportError: No module named odr
>
> Where am I wrong?
> Thank you,
> Chiara
>
>
>
>
>
>   
>> From: Robert Kern <robert.kern at gmail.com>
>> Reply-To: SciPy Users List <scipy-user at scipy.org>
>> To: SciPy Users List <scipy-user at scipy.org>
>> Subject: Re: [SciPy-user] scipy.optimize.leastsq error estimates
>> Date: Tue, 06 Feb 2007 03:47:17 -0600
>>
>> Nils Wagner wrote:
>>
>>     
>>> AFAIK odr is directly available through scipy.odr.
>>> So I guess the odr directory in the sandbox is obsolete. Is that correct 
>>>       
>> ?
>>
>> There is no more odr/ directory in the sandbox since it got moved into the 
>> main
>> package.
>>
>> --
>> Robert Kern
>>
>> "I have come to believe that the whole world is an enigma, a harmless 
>> enigma
>>  that is made terrible by our own mad attempt to interpret it as though it 
>> had
>>  an underlying truth."
>>   -- Umberto Eco
>> _______________________________________________
>> SciPy-user mailing list
>> SciPy-user at scipy.org
>> http://projects.scipy.org/mailman/listinfo/scipy-user
>>     
>
> _________________________________________________________________
> Express yourself instantly with MSN Messenger! Download today it's FREE! 
> http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
>
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user
>   
odr is in the main tree.

Python 2.4 (#1, Oct 13 2006, 16:43:49)
[GCC 3.3.5 20050117 (prerelease) (SUSE Linux)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import scipy
>>> scipy.__version__
'0.5.3.dev2704'
>>> import scipy.odr

works fine for me.

Nils


 



From joris at ster.kuleuven.ac.be  Wed Feb 14 05:36:55 2007
From: joris at ster.kuleuven.ac.be (joris at ster.kuleuven.ac.be)
Date: Wed, 14 Feb 2007 11:36:55 +0100
Subject: [SciPy-user] Array manipulation
Message-ID: <1171449415.45d2e64700ec8@webmail.ster.kuleuven.be>



On Wednesday 14 February 2007 11:13, Nils Wagner wrote:

>BTW, "insert" is missing in http://www.scipy.org/Numpy_Example_List.
>I forgot my password to access the wiki page. Joris, please can you
>add an example for insert. I saw that you have just edited that page.

Done.

Ciao,
Joris


Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm



From nwagner at iam.uni-stuttgart.de  Wed Feb 14 05:48:01 2007
From: nwagner at iam.uni-stuttgart.de (Nils Wagner)
Date: Wed, 14 Feb 2007 11:48:01 +0100
Subject: [SciPy-user] Experiences with LAPACK3.1 and scipy
Message-ID: <45D2E8E1.4000305@iam.uni-stuttgart.de>

Hi all,

has someone tested LAPACK3.1 in connection with scipy ?
I am curious about it.

Version 3.1 has many improvements
http://www.netlib.org/lapack/lapack-3.1.0.changes

I am mainly interested in the new MRRR and the Hessenberg QR algorithm
with the small bulge multi-shift QR algorithm together with aggressive
early deflation. Are there wrappers for these routines ?


Nils



From chiaracaronna at hotmail.com  Wed Feb 14 07:30:24 2007
From: chiaracaronna at hotmail.com (Chiara Caronna)
Date: Wed, 14 Feb 2007 12:30:24 +0000
Subject: [SciPy-user] scipy.optimize.leastsq error estimates
In-Reply-To: <45D2E378.5070401@iam.uni-stuttgart.de>
Message-ID: <BAY114-F344AEF3E809CF3849016DCA1970@phx.gbl>

ok I have scipy 0.5.2... I guess this is the problem...
How can I get the 0.5.3 version, It seems that 0.5.2 is the last version 
available on scipy.org...

>From: Nils Wagner <nwagner at iam.uni-stuttgart.de>
>Reply-To: SciPy Users List <scipy-user at scipy.org>
>To: SciPy Users List <scipy-user at scipy.org>
>Subject: Re: [SciPy-user] scipy.optimize.leastsq error estimates
>Date: Wed, 14 Feb 2007 11:24:56 +0100
>
>Chiara Caronna wrote:
> > Hi,
> > I am also interested in having errors from the fit, and I tried to 
>import
> > the module scipy.odr as you said, but I got this errors:
> >
> > File "/usr/local/lib/python2.4/site-packages/scipy/odr/__init__.py", 
>line
> > 49, in ?
> >     import odrpack
> >   File "/usr/local/lib/python2.4/site-packages/scipy/odr/odrpack.py", 
>line
> > 103, in ?
> >     from scipy.sandbox.odr import __odrpack
> > ImportError: No module named odr
> >
> >
> > And the same is if I try to import  sandbox.odr
> >
> > import scipy.sandbox.odr
> >
> > Traceback (most recent call last):
> >   File "<stdin>", line 1, in ?
> > ImportError: No module named odr
> >
> > Where am I wrong?
> > Thank you,
> > Chiara
> >
> >
> >
> >
> >
> >
> >> From: Robert Kern <robert.kern at gmail.com>
> >> Reply-To: SciPy Users List <scipy-user at scipy.org>
> >> To: SciPy Users List <scipy-user at scipy.org>
> >> Subject: Re: [SciPy-user] scipy.optimize.leastsq error estimates
> >> Date: Tue, 06 Feb 2007 03:47:17 -0600
> >>
> >> Nils Wagner wrote:
> >>
> >>
> >>> AFAIK odr is directly available through scipy.odr.
> >>> So I guess the odr directory in the sandbox is obsolete. Is that 
>correct
> >>>
> >> ?
> >>
> >> There is no more odr/ directory in the sandbox since it got moved into 
>the
> >> main
> >> package.
> >>
> >> --
> >> Robert Kern
> >>
> >> "I have come to believe that the whole world is an enigma, a harmless
> >> enigma
> >>  that is made terrible by our own mad attempt to interpret it as though 
>it
> >> had
> >>  an underlying truth."
> >>   -- Umberto Eco
> >> _______________________________________________
> >> SciPy-user mailing list
> >> SciPy-user at scipy.org
> >> http://projects.scipy.org/mailman/listinfo/scipy-user
> >>
> >
> > _________________________________________________________________
> > Express yourself instantly with MSN Messenger! Download today it's FREE!
> > http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
> >
> > _______________________________________________
> > SciPy-user mailing list
> > SciPy-user at scipy.org
> > http://projects.scipy.org/mailman/listinfo/scipy-user
> >
>odr is in the main tree.
>
>Python 2.4 (#1, Oct 13 2006, 16:43:49)
>[GCC 3.3.5 20050117 (prerelease) (SUSE Linux)] on linux2
>Type "help", "copyright", "credits" or "license" for more information.
> >>> import scipy
> >>> scipy.__version__
>'0.5.3.dev2704'
> >>> import scipy.odr
>
>works fine for me.
>
>Nils
>
>
>
>
>_______________________________________________
>SciPy-user mailing list
>SciPy-user at scipy.org
>http://projects.scipy.org/mailman/listinfo/scipy-user

_________________________________________________________________
Express yourself instantly with MSN Messenger! Download today it's FREE! 
http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/



From ckkart at hoc.net  Wed Feb 14 07:37:49 2007
From: ckkart at hoc.net (Christian Kristukat)
Date: Wed, 14 Feb 2007 21:37:49 +0900
Subject: [SciPy-user] scipy.optimize.leastsq error estimates
In-Reply-To: <BAY114-F344AEF3E809CF3849016DCA1970@phx.gbl>
References: <BAY114-F344AEF3E809CF3849016DCA1970@phx.gbl>
Message-ID: <45D3029D.5060808@hoc.net>

Chiara Caronna wrote:
> ok I have scipy 0.5.2... I guess this is the problem...
> How can I get the 0.5.3 version, It seems that 0.5.2 is the last version 
> available on scipy.org...

I guess Nils is using the svn version. So make a checkout as described here
http://www.scipy.org/Download
and edit the file Lib/sandbox/setup.py to make sure that the odr module will be
built.

Christian



From nwagner at iam.uni-stuttgart.de  Wed Feb 14 07:40:58 2007
From: nwagner at iam.uni-stuttgart.de (Nils Wagner)
Date: Wed, 14 Feb 2007 13:40:58 +0100
Subject: [SciPy-user] scipy.optimize.leastsq error estimates
In-Reply-To: <BAY114-F344AEF3E809CF3849016DCA1970@phx.gbl>
References: <BAY114-F344AEF3E809CF3849016DCA1970@phx.gbl>
Message-ID: <45D3035A.3040700@iam.uni-stuttgart.de>

Chiara Caronna wrote:
> ok I have scipy 0.5.2... I guess this is the problem...
> How can I get the 0.5.3 version, It seems that 0.5.2 is the last version 
> available on scipy.org...
>
>   
You can get the latest version via

svn co http://svn.scipy.org/svn/scipy/trunk scipy

If you use 0.5.2

look into the directory scipy/Lib/sandbox
and create a file called enabled_packages.txt which should contain

odr

in the first line (a new line for each package)
Afterwards you have to reinstall scipy. Assuming that 0.5.2 has odr in
the sandbox
you can import odr from the sandbox afterwards.
If you use the svn version you can import odr from the main tree.

import scipy.odr

Anyway there is an open ticket wrt odr
http://projects.scipy.org/scipy/scipy/ticket/357

Nils


>> From: Nils Wagner <nwagner at iam.uni-stuttgart.de>
>> Reply-To: SciPy Users List <scipy-user at scipy.org>
>> To: SciPy Users List <scipy-user at scipy.org>
>> Subject: Re: [SciPy-user] scipy.optimize.leastsq error estimates
>> Date: Wed, 14 Feb 2007 11:24:56 +0100
>>
>> Chiara Caronna wrote:
>>     
>>> Hi,
>>> I am also interested in having errors from the fit, and I tried to 
>>>       
>> import
>>     
>>> the module scipy.odr as you said, but I got this errors:
>>>
>>> File "/usr/local/lib/python2.4/site-packages/scipy/odr/__init__.py", 
>>>       
>> line
>>     
>>> 49, in ?
>>>     import odrpack
>>>   File "/usr/local/lib/python2.4/site-packages/scipy/odr/odrpack.py", 
>>>       
>> line
>>     
>>> 103, in ?
>>>     from scipy.sandbox.odr import __odrpack
>>> ImportError: No module named odr
>>>
>>>
>>> And the same is if I try to import  sandbox.odr
>>>
>>> import scipy.sandbox.odr
>>>
>>> Traceback (most recent call last):
>>>   File "<stdin>", line 1, in ?
>>> ImportError: No module named odr
>>>
>>> Where am I wrong?
>>> Thank you,
>>> Chiara
>>>
>>>
>>>
>>>
>>>
>>>
>>>       
>>>> From: Robert Kern <robert.kern at gmail.com>
>>>> Reply-To: SciPy Users List <scipy-user at scipy.org>
>>>> To: SciPy Users List <scipy-user at scipy.org>
>>>> Subject: Re: [SciPy-user] scipy.optimize.leastsq error estimates
>>>> Date: Tue, 06 Feb 2007 03:47:17 -0600
>>>>
>>>> Nils Wagner wrote:
>>>>
>>>>
>>>>         
>>>>> AFAIK odr is directly available through scipy.odr.
>>>>> So I guess the odr directory in the sandbox is obsolete. Is that 
>>>>>           
>> correct
>>     
>>>> ?
>>>>
>>>> There is no more odr/ directory in the sandbox since it got moved into 
>>>>         
>> the
>>     
>>>> main
>>>> package.
>>>>
>>>> --
>>>> Robert Kern
>>>>
>>>> "I have come to believe that the whole world is an enigma, a harmless
>>>> enigma
>>>>  that is made terrible by our own mad attempt to interpret it as though 
>>>>         
>> it
>>     
>>>> had
>>>>  an underlying truth."
>>>>   -- Umberto Eco
>>>> _______________________________________________
>>>> SciPy-user mailing list
>>>> SciPy-user at scipy.org
>>>> http://projects.scipy.org/mailman/listinfo/scipy-user
>>>>
>>>>         
>>> _________________________________________________________________
>>> Express yourself instantly with MSN Messenger! Download today it's FREE!
>>> http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
>>>
>>> _______________________________________________
>>> SciPy-user mailing list
>>> SciPy-user at scipy.org
>>> http://projects.scipy.org/mailman/listinfo/scipy-user
>>>
>>>       
>> odr is in the main tree.
>>
>> Python 2.4 (#1, Oct 13 2006, 16:43:49)
>> [GCC 3.3.5 20050117 (prerelease) (SUSE Linux)] on linux2
>> Type "help", "copyright", "credits" or "license" for more information.
>>     
>>>>> import scipy
>>>>> scipy.__version__
>>>>>           
>> '0.5.3.dev2704'
>>     
>>>>> import scipy.odr
>>>>>           
>> works fine for me.
>>
>> Nils
>>
>>
>>
>>
>> _______________________________________________
>> SciPy-user mailing list
>> SciPy-user at scipy.org
>> http://projects.scipy.org/mailman/listinfo/scipy-user
>>     
>
> _________________________________________________________________
> Express yourself instantly with MSN Messenger! Download today it's FREE! 
> http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
>
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user
>   
 


From nwagner at iam.uni-stuttgart.de  Wed Feb 14 07:53:58 2007
From: nwagner at iam.uni-stuttgart.de (Nils Wagner)
Date: Wed, 14 Feb 2007 13:53:58 +0100
Subject: [SciPy-user] Wriitng a list to an ascii file
Message-ID: <45D30666.9000603@iam.uni-stuttgart.de>

Hi,

I have a list

>>> data[0]
[1, 3.98, 3.131435898787629, 146.25144654434166]
>>> data[1]
[2, 4.0014113157358633, -0.23777483140261779, 169.32304332115922]
>>> data[2]
[3, 4.0000070483264265, -0.0011815833829018629, 167.64445564164987]
>>> data[3]
[4, 4.0000000001757536, -2.946728727692971e-08, 167.63609488306861]

where the first entry is an integer and the remaining entries are floats.

How can I write this list to an ascii file without destroying the
integer type of the first entry?

Nils
 
io.write_array() yields

1.000000000000000e+00 3.980000000000000e+00 3.131435898787629e+00
1.462514465443417e+02
2.000000000000000e+00 4.001411315735863e+00 -2.377748314026178e-01
1.693230433211592e+02
3.000000000000000e+00 4.000007048326427e+00 -1.181583382901863e-03
1.676444556416499e+02
4.000000000000000e+00 4.000000000175754e+00 -2.946728727692971e-08
1.676360948830686e+02

but I would prefer

1 3.980000000000000e+00 3.131435898787629e+00 1.462514465443417e+02
2 4.001411315735863e+00 -2.377748314026178e-01 1.693230433211592e+02
3 4.000007048326427e+00 -1.181583382901863e-03 1.676444556416499e+02
4 4.000000000175754e+00 -2.946728727692971e-08 1.676360948830686e+02

 


From chiaracaronna at hotmail.com  Wed Feb 14 07:54:30 2007
From: chiaracaronna at hotmail.com (Chiara Caronna)
Date: Wed, 14 Feb 2007 12:54:30 +0000
Subject: [SciPy-user] scipy.optimize.leastsq error estimates
In-Reply-To: <45D3035A.3040700@iam.uni-stuttgart.de>
Message-ID: <BAY114-F60C9F859ACC196B74CDDAA1970@phx.gbl>




>If you use 0.5.2
>
>look into the directory scipy/Lib/sandbox
>and create a file called enabled_packages.txt which should contain
>
>odr
>
>in the first line (a new line for each package)

I did what you said, but when reinstalling scipy I got this error:

  File "Lib/sandbox/setup.py", line 22, in configuration
    config.add_subpackage(p)
  File 
"/usr/local/lib/python2.4/site-packages/numpy/distutils/misc_util.py", line 
765, in add_subpackage
    caller_level = 2)
  File 
"/usr/local/lib/python2.4/site-packages/numpy/distutils/misc_util.py", line 
741, in get_subpackage
    caller_level = caller_level+1)
  File 
"/usr/local/lib/python2.4/site-packages/numpy/distutils/misc_util.py", line 
541, in __init__
    raise ValueError("%r is not a directory" % (package_path,))
ValueError: 'Lib/sandbox/odr' is not a directory




>Afterwards you have to reinstall scipy. Assuming that 0.5.2 has odr in
>the sandbox
>you can import odr from the sandbox afterwards.
>If you use the svn version you can import odr from the main tree.
>
>import scipy.odr
>
>Anyway there is an open ticket wrt odr
>http://projects.scipy.org/scipy/scipy/ticket/357
>
>Nils
>
>
> >> From: Nils Wagner <nwagner at iam.uni-stuttgart.de>
> >> Reply-To: SciPy Users List <scipy-user at scipy.org>
> >> To: SciPy Users List <scipy-user at scipy.org>
> >> Subject: Re: [SciPy-user] scipy.optimize.leastsq error estimates
> >> Date: Wed, 14 Feb 2007 11:24:56 +0100
> >>
> >> Chiara Caronna wrote:
> >>
> >>> Hi,
> >>> I am also interested in having errors from the fit, and I tried to
> >>>
> >> import
> >>
> >>> the module scipy.odr as you said, but I got this errors:
> >>>
> >>> File "/usr/local/lib/python2.4/site-packages/scipy/odr/__init__.py",
> >>>
> >> line
> >>
> >>> 49, in ?
> >>>     import odrpack
> >>>   File "/usr/local/lib/python2.4/site-packages/scipy/odr/odrpack.py",
> >>>
> >> line
> >>
> >>> 103, in ?
> >>>     from scipy.sandbox.odr import __odrpack
> >>> ImportError: No module named odr
> >>>
> >>>
> >>> And the same is if I try to import  sandbox.odr
> >>>
> >>> import scipy.sandbox.odr
> >>>
> >>> Traceback (most recent call last):
> >>>   File "<stdin>", line 1, in ?
> >>> ImportError: No module named odr
> >>>
> >>> Where am I wrong?
> >>> Thank you,
> >>> Chiara
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>> From: Robert Kern <robert.kern at gmail.com>
> >>>> Reply-To: SciPy Users List <scipy-user at scipy.org>
> >>>> To: SciPy Users List <scipy-user at scipy.org>
> >>>> Subject: Re: [SciPy-user] scipy.optimize.leastsq error estimates
> >>>> Date: Tue, 06 Feb 2007 03:47:17 -0600
> >>>>
> >>>> Nils Wagner wrote:
> >>>>
> >>>>
> >>>>
> >>>>> AFAIK odr is directly available through scipy.odr.
> >>>>> So I guess the odr directory in the sandbox is obsolete. Is that
> >>>>>
> >> correct
> >>
> >>>> ?
> >>>>
> >>>> There is no more odr/ directory in the sandbox since it got moved 
>into
> >>>>
> >> the
> >>
> >>>> main
> >>>> package.
> >>>>
> >>>> --
> >>>> Robert Kern
> >>>>
> >>>> "I have come to believe that the whole world is an enigma, a harmless
> >>>> enigma
> >>>>  that is made terrible by our own mad attempt to interpret it as 
>though
> >>>>
> >> it
> >>
> >>>> had
> >>>>  an underlying truth."
> >>>>   -- Umberto Eco
> >>>> _______________________________________________
> >>>> SciPy-user mailing list
> >>>> SciPy-user at scipy.org
> >>>> http://projects.scipy.org/mailman/listinfo/scipy-user
> >>>>
> >>>>
> >>> _________________________________________________________________
> >>> Express yourself instantly with MSN Messenger! Download today it's 
>FREE!
> >>> http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
> >>>
> >>> _______________________________________________
> >>> SciPy-user mailing list
> >>> SciPy-user at scipy.org
> >>> http://projects.scipy.org/mailman/listinfo/scipy-user
> >>>
> >>>
> >> odr is in the main tree.
> >>
> >> Python 2.4 (#1, Oct 13 2006, 16:43:49)
> >> [GCC 3.3.5 20050117 (prerelease) (SUSE Linux)] on linux2
> >> Type "help", "copyright", "credits" or "license" for more information.
> >>
> >>>>> import scipy
> >>>>> scipy.__version__
> >>>>>
> >> '0.5.3.dev2704'
> >>
> >>>>> import scipy.odr
> >>>>>
> >> works fine for me.
> >>
> >> Nils
> >>
> >>
> >>
> >>
> >> _______________________________________________
> >> SciPy-user mailing list
> >> SciPy-user at scipy.org
> >> http://projects.scipy.org/mailman/listinfo/scipy-user
> >>
> >
> > _________________________________________________________________
> > Express yourself instantly with MSN Messenger! Download today it's FREE!
> > http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
> >
> > _______________________________________________
> > SciPy-user mailing list
> > SciPy-user at scipy.org
> > http://projects.scipy.org/mailman/listinfo/scipy-user
> >
>
>_______________________________________________
>SciPy-user mailing list
>SciPy-user at scipy.org
>http://projects.scipy.org/mailman/listinfo/scipy-user

_________________________________________________________________
Express yourself instantly with MSN Messenger! Download today it's FREE! 
http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/



From nwagner at iam.uni-stuttgart.de  Wed Feb 14 08:01:19 2007
From: nwagner at iam.uni-stuttgart.de (Nils Wagner)
Date: Wed, 14 Feb 2007 14:01:19 +0100
Subject: [SciPy-user] scipy.optimize.leastsq error estimates
In-Reply-To: <BAY114-F60C9F859ACC196B74CDDAA1970@phx.gbl>
References: <BAY114-F60C9F859ACC196B74CDDAA1970@phx.gbl>
Message-ID: <45D3081F.9090708@iam.uni-stuttgart.de>

Chiara Caronna wrote:
>
>   
>> If you use 0.5.2
>>
>> look into the directory scipy/Lib/sandbox
>> and create a file called enabled_packages.txt which should contain
>>
>> odr
>>
>> in the first line (a new line for each package)
>>     
>
> I did what you said, but when reinstalling scipy I got this error:
>
>   File "Lib/sandbox/setup.py", line 22, in configuration
>     config.add_subpackage(p)
>   File 
> "/usr/local/lib/python2.4/site-packages/numpy/distutils/misc_util.py", line 
> 765, in add_subpackage
>     caller_level = 2)
>   File 
> "/usr/local/lib/python2.4/site-packages/numpy/distutils/misc_util.py", line 
> 741, in get_subpackage
>     caller_level = caller_level+1)
>   File 
> "/usr/local/lib/python2.4/site-packages/numpy/distutils/misc_util.py", line 
> 541, in __init__
>     raise ValueError("%r is not a directory" % (package_path,))
> ValueError: 'Lib/sandbox/odr' is not a directory
>
>
>   
 
What is the output of ls -l  in your sandbox directory
I have
Lib/sandbox> ls -l
 total 17
drwxr-xr-x   5 root root  272 2006-09-03 11:30 ann
drwxr-xr-x   6 root root  376 2006-11-21 08:45 arpack
drwxr-xr-x   4 root root  184 2006-11-06 08:48 arraysetops
drwxr-xr-x   3 root root  232 2006-06-27 08:32 buildgrid
drwxr-xr-x   5 root root  344 2006-12-15 15:35 cdavid
drwxr-xr-x   3 root root  192 2006-06-22 09:18 constants
drwxr-xr-x   3 root root  248 2006-03-15 08:29 cow
drwxr-xr-x   4 root root  544 2006-10-02 08:19 delaunay
-rw-r--r--   1 root root   40 2007-02-08 13:11 enabled_packages.txt
drwxr-xr-x   5 root root  272 2006-03-15 08:29 exmplpackage
drwxr-xr-x   6 root root  280 2006-04-24 08:41 fdfpack
drwxr-xr-x   3 root root  600 2006-09-03 11:30 ga
drwxr-xr-x   3 root root  360 2006-09-03 11:30 gplt
drwxr-xr-x   3 root root  352 2006-09-03 11:30 image
-rw-r--r--   1 root root    0 2006-02-28 08:50 __init__.py
drwxr-xr-x   4 root root  520 2007-02-12 08:33 maskedarray
drwxr-xr-x   6 root root  688 2007-02-12 08:33 models
drwxr-xr-x   5 root root  232 2006-11-23 08:29 montecarlo
drwxr-xr-x   3 root root  320 2006-07-10 08:09 netcdf
drwxr-xr-x   4 root root  264 2007-01-11 10:57 newoptimize
drwxr-xr-x   4 root root  432 2006-11-17 09:02 numexpr
drwxr-xr-x   3 root root   72 2006-10-05 08:30 oliphant
drwxr-xr-x   3 root root  456 2006-09-03 11:30 plt
drwxr-xr-x   6 root root  904 2006-12-07 09:05 pyem
drwxr-xr-x  13 root root  592 2006-08-16 16:21 pysparse
drwxr-xr-x   4 root root  232 2007-02-08 13:11 rbf
drwxr-xr-x   3 root root  184 2006-09-03 11:30 rkern
-rw-r--r--   1 root root 2732 2007-02-08 13:07 setup.py
-rw-r--r--   1 root root 1028 2007-02-08 13:11 setup.pyc
drwxr-xr-x   5 root root  360 2007-02-09 08:42 spline
drwxr-xr-x   3 root root  192 2006-10-10 08:22 stats
drwxr-xr-x   5 root root  464 2006-09-11 08:44 svm
drwxr-xr-x   9 root root  576 2007-02-13 08:27 timeseries
drwxr-xr-x   3 root root   72 2006-12-07 08:52 wavelet
drwxr-xr-x   6 root root 1864 2007-01-23 08:35 xplt

Note that I am using the svn version. So odr is not present in the sandbox.
How about 0.5.2 ?
Do you have a directory odr in the sandbox ?

Nils




From pgreisen at gmail.com  Wed Feb 14 08:04:33 2007
From: pgreisen at gmail.com (Per Jr. Greisen)
Date: Wed, 14 Feb 2007 14:04:33 +0100
Subject: [SciPy-user] Wriitng a list to an ascii file
In-Reply-To: <45D30666.9000603@iam.uni-stuttgart.de>
References: <45D30666.9000603@iam.uni-stuttgart.de>
Message-ID: <e016526e0702140504v14e4a61dk6f8634096ec563c1@mail.gmail.com>

why dont you split the data between integer and floats ?

On 2/14/07, Nils Wagner <nwagner at iam.uni-stuttgart.de> wrote:
>
> Hi,
>
> I have a list
>
> >>> data[0]
> [1, 3.98, 3.131435898787629, 146.25144654434166]
> >>> data[1]
> [2, 4.0014113157358633, -0.23777483140261779, 169.32304332115922]
> >>> data[2]
> [3, 4.0000070483264265, -0.0011815833829018629, 167.64445564164987]
> >>> data[3]
> [4, 4.0000000001757536, -2.946728727692971e-08, 167.63609488306861]
>
> where the first entry is an integer and the remaining entries are floats.
>
> How can I write this list to an ascii file without destroying the
> integer type of the first entry?
>
> Nils
>
> io.write_array() yields
>
> 1.000000000000000e+00 3.980000000000000e+00 3.131435898787629e+00
> 1.462514465443417e+02
> 2.000000000000000e+00 4.001411315735863e+00 -2.377748314026178e-01
> 1.693230433211592e+02
> 3.000000000000000e+00 4.000007048326427e+00 -1.181583382901863e-03
> 1.676444556416499e+02
> 4.000000000000000e+00 4.000000000175754e+00 -2.946728727692971e-08
> 1.676360948830686e+02
>
> but I would prefer
>
> 1 3.980000000000000e+00 3.131435898787629e+00 1.462514465443417e+02
> 2 4.001411315735863e+00 -2.377748314026178e-01 1.693230433211592e+02
> 3 4.000007048326427e+00 -1.181583382901863e-03 1.676444556416499e+02
> 4 4.000000000175754e+00 -2.946728727692971e-08 1.676360948830686e+02
>
>
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user
>



-- 
Best regards
Per Jr. Greisen

"If you make something idiot-proof, the universe creates a better idiot."
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20070214/71a1632d/attachment.html>

From chiaracaronna at hotmail.com  Wed Feb 14 08:09:13 2007
From: chiaracaronna at hotmail.com (Chiara Caronna)
Date: Wed, 14 Feb 2007 13:09:13 +0000
Subject: [SciPy-user] scipy.optimize.leastsq error estimates
In-Reply-To: <45D3081F.9090708@iam.uni-stuttgart.de>
Message-ID: <BAY114-F3621EA49F2C0F49A7BE118A1970@phx.gbl>

Ah. No, there is not an odr directory... :(

Here is the output:


drwxr-xr-x   28 root     root         4096 2007-02-14 13:46 .
drwxr-xr-x   22 root     root         4096 2007-01-17 09:37 ..
-rw-r--r--    1 500      1000            0 2006-01-05 04:35 __init__.py
drwxr-xr-x    4 root     root         4096 2006-12-08 05:05 ann
drwxr-xr-x    4 root     root         4096 2006-12-08 05:05 arpack
drwxr-xr-x    3 root     root         4096 2006-12-08 05:05 arraysetops
drwxr-xr-x    2 root     root         4096 2006-12-08 05:05 buildgrid
drwxr-xr-x    2 root     root         4096 2006-12-08 05:05 constants
drwxr-xr-x    2 root     root         4096 2006-12-08 05:05 cow
drwxr-xr-x    3 root     root         4096 2006-12-08 05:05 delaunay
-rw-r--r--    1 root     root            4 2007-02-14 13:46 
enabled_packages.txt
drwxr-xr-x    4 root     root         4096 2006-12-08 05:05 exmplpackage
drwxr-xr-x    5 root     root         4096 2006-12-08 05:05 fdfpack
drwxr-xr-x    2 root     root         4096 2006-12-08 05:05 ga
drwxr-xr-x    2 root     root         4096 2006-12-08 05:05 gplt
drwxr-xr-x    2 root     root         4096 2006-12-08 05:05 image
drwxr-xr-x    5 root     root         4096 2006-12-08 05:05 models
drwxr-xr-x    4 root     root         4096 2006-12-08 05:05 montecarlo
drwxr-xr-x    2 root     root         4096 2006-12-08 05:05 netcdf
drwxr-xr-x    2 root     root         4096 2006-12-08 05:05 newoptimize
drwxr-xr-x    3 root     root         4096 2006-12-08 05:05 numexpr
drwxr-xr-x    2 root     root         4096 2006-12-08 05:05 plt
drwxr-xr-x    5 root     root         4096 2006-12-08 05:05 pyem
drwxr-xr-x   12 root     root         4096 2006-12-08 05:05 pysparse
drwxr-xr-x    2 root     root         4096 2006-12-08 05:05 rkern
-rw-r--r--    1 500      1000         2656 2006-12-02 04:24 setup.py
-rw-r--r--    1 root     root         1028 2007-01-17 09:37 setup.pyc
drwxr-xr-x    4 root     root         4096 2006-12-08 05:05 spline
drwxr-xr-x    2 root     root         4096 2006-12-08 05:05 stats
drwxr-xr-x    4 root     root         4096 2006-12-08 05:05 svm
drwxr-xr-x    3 root     root         4096 2006-12-08 05:05 umfpack
drwxr-xr-x    5 root     root         4096 2006-12-08 05:05 xplt


>From: Nils Wagner <nwagner at iam.uni-stuttgart.de>
>Reply-To: SciPy Users List <scipy-user at scipy.org>
>To: SciPy Users List <scipy-user at scipy.org>
>Subject: Re: [SciPy-user] scipy.optimize.leastsq error estimates
>Date: Wed, 14 Feb 2007 14:01:19 +0100
>
>Chiara Caronna wrote:
> >
> >
> >> If you use 0.5.2
> >>
> >> look into the directory scipy/Lib/sandbox
> >> and create a file called enabled_packages.txt which should contain
> >>
> >> odr
> >>
> >> in the first line (a new line for each package)
> >>
> >
> > I did what you said, but when reinstalling scipy I got this error:
> >
> >   File "Lib/sandbox/setup.py", line 22, in configuration
> >     config.add_subpackage(p)
> >   File
> > "/usr/local/lib/python2.4/site-packages/numpy/distutils/misc_util.py", 
>line
> > 765, in add_subpackage
> >     caller_level = 2)
> >   File
> > "/usr/local/lib/python2.4/site-packages/numpy/distutils/misc_util.py", 
>line
> > 741, in get_subpackage
> >     caller_level = caller_level+1)
> >   File
> > "/usr/local/lib/python2.4/site-packages/numpy/distutils/misc_util.py", 
>line
> > 541, in __init__
> >     raise ValueError("%r is not a directory" % (package_path,))
> > ValueError: 'Lib/sandbox/odr' is not a directory
> >
> >
> >
>
>What is the output of ls -l  in your sandbox directory
>I have
>Lib/sandbox> ls -l
>  total 17
>drwxr-xr-x   5 root root  272 2006-09-03 11:30 ann
>drwxr-xr-x   6 root root  376 2006-11-21 08:45 arpack
>drwxr-xr-x   4 root root  184 2006-11-06 08:48 arraysetops
>drwxr-xr-x   3 root root  232 2006-06-27 08:32 buildgrid
>drwxr-xr-x   5 root root  344 2006-12-15 15:35 cdavid
>drwxr-xr-x   3 root root  192 2006-06-22 09:18 constants
>drwxr-xr-x   3 root root  248 2006-03-15 08:29 cow
>drwxr-xr-x   4 root root  544 2006-10-02 08:19 delaunay
>-rw-r--r--   1 root root   40 2007-02-08 13:11 enabled_packages.txt
>drwxr-xr-x   5 root root  272 2006-03-15 08:29 exmplpackage
>drwxr-xr-x   6 root root  280 2006-04-24 08:41 fdfpack
>drwxr-xr-x   3 root root  600 2006-09-03 11:30 ga
>drwxr-xr-x   3 root root  360 2006-09-03 11:30 gplt
>drwxr-xr-x   3 root root  352 2006-09-03 11:30 image
>-rw-r--r--   1 root root    0 2006-02-28 08:50 __init__.py
>drwxr-xr-x   4 root root  520 2007-02-12 08:33 maskedarray
>drwxr-xr-x   6 root root  688 2007-02-12 08:33 models
>drwxr-xr-x   5 root root  232 2006-11-23 08:29 montecarlo
>drwxr-xr-x   3 root root  320 2006-07-10 08:09 netcdf
>drwxr-xr-x   4 root root  264 2007-01-11 10:57 newoptimize
>drwxr-xr-x   4 root root  432 2006-11-17 09:02 numexpr
>drwxr-xr-x   3 root root   72 2006-10-05 08:30 oliphant
>drwxr-xr-x   3 root root  456 2006-09-03 11:30 plt
>drwxr-xr-x   6 root root  904 2006-12-07 09:05 pyem
>drwxr-xr-x  13 root root  592 2006-08-16 16:21 pysparse
>drwxr-xr-x   4 root root  232 2007-02-08 13:11 rbf
>drwxr-xr-x   3 root root  184 2006-09-03 11:30 rkern
>-rw-r--r--   1 root root 2732 2007-02-08 13:07 setup.py
>-rw-r--r--   1 root root 1028 2007-02-08 13:11 setup.pyc
>drwxr-xr-x   5 root root  360 2007-02-09 08:42 spline
>drwxr-xr-x   3 root root  192 2006-10-10 08:22 stats
>drwxr-xr-x   5 root root  464 2006-09-11 08:44 svm
>drwxr-xr-x   9 root root  576 2007-02-13 08:27 timeseries
>drwxr-xr-x   3 root root   72 2006-12-07 08:52 wavelet
>drwxr-xr-x   6 root root 1864 2007-01-23 08:35 xplt
>
>Note that I am using the svn version. So odr is not present in the sandbox.
>How about 0.5.2 ?
>Do you have a directory odr in the sandbox ?
>
>Nils
>
>
>_______________________________________________
>SciPy-user mailing list
>SciPy-user at scipy.org
>http://projects.scipy.org/mailman/listinfo/scipy-user

_________________________________________________________________
FREE pop-up blocking with the new MSN Toolbar - get it now! 
http://toolbar.msn.click-url.com/go/onm00200415ave/direct/01/



From nwagner at iam.uni-stuttgart.de  Wed Feb 14 08:13:38 2007
From: nwagner at iam.uni-stuttgart.de (Nils Wagner)
Date: Wed, 14 Feb 2007 14:13:38 +0100
Subject: [SciPy-user] scipy.optimize.leastsq error estimates
In-Reply-To: <BAY114-F3621EA49F2C0F49A7BE118A1970@phx.gbl>
References: <BAY114-F3621EA49F2C0F49A7BE118A1970@phx.gbl>
Message-ID: <45D30B02.10208@iam.uni-stuttgart.de>

Chiara Caronna wrote:
> Ah. No, there is not an odr directory... :(
>
> Here is the output:
>
>
> drwxr-xr-x   28 root     root         4096 2007-02-14 13:46 .
> drwxr-xr-x   22 root     root         4096 2007-01-17 09:37 ..
> -rw-r--r--    1 500      1000            0 2006-01-05 04:35 __init__.py
> drwxr-xr-x    4 root     root         4096 2006-12-08 05:05 ann
> drwxr-xr-x    4 root     root         4096 2006-12-08 05:05 arpack
> drwxr-xr-x    3 root     root         4096 2006-12-08 05:05 arraysetops
> drwxr-xr-x    2 root     root         4096 2006-12-08 05:05 buildgrid
> drwxr-xr-x    2 root     root         4096 2006-12-08 05:05 constants
> drwxr-xr-x    2 root     root         4096 2006-12-08 05:05 cow
> drwxr-xr-x    3 root     root         4096 2006-12-08 05:05 delaunay
> -rw-r--r--    1 root     root            4 2007-02-14 13:46 
> enabled_packages.txt
> drwxr-xr-x    4 root     root         4096 2006-12-08 05:05 exmplpackage
> drwxr-xr-x    5 root     root         4096 2006-12-08 05:05 fdfpack
> drwxr-xr-x    2 root     root         4096 2006-12-08 05:05 ga
> drwxr-xr-x    2 root     root         4096 2006-12-08 05:05 gplt
> drwxr-xr-x    2 root     root         4096 2006-12-08 05:05 image
> drwxr-xr-x    5 root     root         4096 2006-12-08 05:05 models
> drwxr-xr-x    4 root     root         4096 2006-12-08 05:05 montecarlo
> drwxr-xr-x    2 root     root         4096 2006-12-08 05:05 netcdf
> drwxr-xr-x    2 root     root         4096 2006-12-08 05:05 newoptimize
> drwxr-xr-x    3 root     root         4096 2006-12-08 05:05 numexpr
> drwxr-xr-x    2 root     root         4096 2006-12-08 05:05 plt
> drwxr-xr-x    5 root     root         4096 2006-12-08 05:05 pyem
> drwxr-xr-x   12 root     root         4096 2006-12-08 05:05 pysparse
> drwxr-xr-x    2 root     root         4096 2006-12-08 05:05 rkern
> -rw-r--r--    1 500      1000         2656 2006-12-02 04:24 setup.py
> -rw-r--r--    1 root     root         1028 2007-01-17 09:37 setup.pyc
> drwxr-xr-x    4 root     root         4096 2006-12-08 05:05 spline
> drwxr-xr-x    2 root     root         4096 2006-12-08 05:05 stats
> drwxr-xr-x    4 root     root         4096 2006-12-08 05:05 svm
> drwxr-xr-x    3 root     root         4096 2006-12-08 05:05 umfpack
> drwxr-xr-x    5 root     root         4096 2006-12-08 05:05 xplt
>
>
>   
>> From: Nils Wagner <nwagner at iam.uni-stuttgart.de>
>> Reply-To: SciPy Users List <scipy-user at scipy.org>
>> To: SciPy Users List <scipy-user at scipy.org>
>> Subject: Re: [SciPy-user] scipy.optimize.leastsq error estimates
>> Date: Wed, 14 Feb 2007 14:01:19 +0100
>>
>> Chiara Caronna wrote:
>>     
>>>       
>>>> If you use 0.5.2
>>>>
>>>> look into the directory scipy/Lib/sandbox
>>>> and create a file called enabled_packages.txt which should contain
>>>>
>>>> odr
>>>>
>>>> in the first line (a new line for each package)
>>>>
>>>>         
>>> I did what you said, but when reinstalling scipy I got this error:
>>>
>>>   File "Lib/sandbox/setup.py", line 22, in configuration
>>>     config.add_subpackage(p)
>>>   File
>>> "/usr/local/lib/python2.4/site-packages/numpy/distutils/misc_util.py", 
>>>       
>> line
>>     
>>> 765, in add_subpackage
>>>     caller_level = 2)
>>>   File
>>> "/usr/local/lib/python2.4/site-packages/numpy/distutils/misc_util.py", 
>>>       
>> line
>>     
>>> 741, in get_subpackage
>>>     caller_level = caller_level+1)
>>>   File
>>> "/usr/local/lib/python2.4/site-packages/numpy/distutils/misc_util.py", 
>>>       
>> line
>>     
>>> 541, in __init__
>>>     raise ValueError("%r is not a directory" % (package_path,))
>>> ValueError: 'Lib/sandbox/odr' is not a directory
>>>
>>>
>>>
>>>       
>> What is the output of ls -l  in your sandbox directory
>> I have
>> Lib/sandbox> ls -l
>>  total 17
>> drwxr-xr-x   5 root root  272 2006-09-03 11:30 ann
>> drwxr-xr-x   6 root root  376 2006-11-21 08:45 arpack
>> drwxr-xr-x   4 root root  184 2006-11-06 08:48 arraysetops
>> drwxr-xr-x   3 root root  232 2006-06-27 08:32 buildgrid
>> drwxr-xr-x   5 root root  344 2006-12-15 15:35 cdavid
>> drwxr-xr-x   3 root root  192 2006-06-22 09:18 constants
>> drwxr-xr-x   3 root root  248 2006-03-15 08:29 cow
>> drwxr-xr-x   4 root root  544 2006-10-02 08:19 delaunay
>> -rw-r--r--   1 root root   40 2007-02-08 13:11 enabled_packages.txt
>> drwxr-xr-x   5 root root  272 2006-03-15 08:29 exmplpackage
>> drwxr-xr-x   6 root root  280 2006-04-24 08:41 fdfpack
>> drwxr-xr-x   3 root root  600 2006-09-03 11:30 ga
>> drwxr-xr-x   3 root root  360 2006-09-03 11:30 gplt
>> drwxr-xr-x   3 root root  352 2006-09-03 11:30 image
>> -rw-r--r--   1 root root    0 2006-02-28 08:50 __init__.py
>> drwxr-xr-x   4 root root  520 2007-02-12 08:33 maskedarray
>> drwxr-xr-x   6 root root  688 2007-02-12 08:33 models
>> drwxr-xr-x   5 root root  232 2006-11-23 08:29 montecarlo
>> drwxr-xr-x   3 root root  320 2006-07-10 08:09 netcdf
>> drwxr-xr-x   4 root root  264 2007-01-11 10:57 newoptimize
>> drwxr-xr-x   4 root root  432 2006-11-17 09:02 numexpr
>> drwxr-xr-x   3 root root   72 2006-10-05 08:30 oliphant
>> drwxr-xr-x   3 root root  456 2006-09-03 11:30 plt
>> drwxr-xr-x   6 root root  904 2006-12-07 09:05 pyem
>> drwxr-xr-x  13 root root  592 2006-08-16 16:21 pysparse
>> drwxr-xr-x   4 root root  232 2007-02-08 13:11 rbf
>> drwxr-xr-x   3 root root  184 2006-09-03 11:30 rkern
>> -rw-r--r--   1 root root 2732 2007-02-08 13:07 setup.py
>> -rw-r--r--   1 root root 1028 2007-02-08 13:11 setup.pyc
>> drwxr-xr-x   5 root root  360 2007-02-09 08:42 spline
>> drwxr-xr-x   3 root root  192 2006-10-10 08:22 stats
>> drwxr-xr-x   5 root root  464 2006-09-11 08:44 svm
>> drwxr-xr-x   9 root root  576 2007-02-13 08:27 timeseries
>> drwxr-xr-x   3 root root   72 2006-12-07 08:52 wavelet
>> drwxr-xr-x   6 root root 1864 2007-01-23 08:35 xplt
>>
>> Note that I am using the svn version. So odr is not present in the sandbox.
>> How about 0.5.2 ?
>> Do you have a directory odr in the sandbox ?
>>
>> Nils
>>
>>
>> _______________________________________________
>> SciPy-user mailing list
>> SciPy-user at scipy.org
>> http://projects.scipy.org/mailman/listinfo/scipy-user
>>     
>
> _________________________________________________________________
> FREE pop-up blocking with the new MSN Toolbar - get it now! 
> http://toolbar.msn.click-url.com/go/onm00200415ave/direct/01/
>
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user
>   
And in scipy/Lib ? I have

 drwxr-xr-x   6 root root  280 2007-01-24 13:58 cluster
drwxr-xr-x   7 root root  536 2007-01-11 09:16 fftpack
drwxr-xr-x   2 root root   80 2006-03-20 11:42 image
-rw-r--r--   1 root root 2356 2007-01-11 09:16 __init__.py
drwxr-xr-x   8 root root  656 2007-02-12 09:54 integrate
drwxr-xr-x   5 root root  456 2007-02-12 09:54 interpolate
drwxr-xr-x   6 root root  672 2007-02-12 09:54 io
drwxr-xr-x   5 root root  232 2007-01-11 09:16 lib
drwxr-xr-x   6 root root 1024 2007-01-25 09:35 linalg
drwxr-xr-x   5 root root  552 2007-01-25 09:35 linsolve
drwxr-xr-x   2 root root   80 2006-01-19 10:27 maxent
drwxr-xr-x   5 root root  296 2007-01-11 09:16 maxentropy
drwxr-xr-x   3 root root  392 2007-01-11 09:16 misc
drwxr-xr-x   2 root root   80 2006-01-19 10:27 montecarlo
drwxr-xr-x   5 root root  456 2007-02-12 09:54 ndimage
drwxr-xr-x   2 root root   80 2006-03-17 10:51 nd_image
drwxr-xr-x   5 root root  360 2007-01-24 14:00 odr
drwxr-xr-x  10 root root  712 2007-01-29 10:06 optimize
drwxr-xr-x  35 root root 1032 2007-02-12 09:54 sandbox
-rw-r--r--   1 root root  679 2005-12-01 10:57 scipy_version.pyc
-rw-r--r--   1 root root 1126 2006-11-28 16:59 setup.py
-rw-r--r--   1 root root 1141 2006-11-28 17:02 setup.pyc
drwxr-xr-x   5 root root  744 2007-01-30 15:29 signal
drwxr-xr-x   5 root root  272 2007-01-15 09:33 sparse
drwxr-xr-x  12 root root 1056 2007-01-26 11:21 special
drwxr-xr-x   5 root root  568 2007-01-11 09:16 stats
drwxr-xr-x   5 root root  208 2006-08-04 09:02 stsci
drwxr-xr-x   3 root root  232 2006-10-02 08:38 tests
-rw-r--r--   1 root root  485 2006-12-08 09:21 version.py
-rw-r--r--   1 root root  580 2006-12-08 09:23 version.pyc
drwxr-xr-x   8 root root 1272 2007-01-22 09:42 weave

Also look into your setup.py file in scipy/Lib

def configuration(parent_package='',top_path=None):
    from numpy.distutils.misc_util import Configuration
    config = Configuration('scipy',parent_package,top_path)
    config.add_subpackage('cluster')
    config.add_subpackage('fftpack')
    config.add_subpackage('integrate')
    config.add_subpackage('interpolate')
    config.add_subpackage('io')
    config.add_subpackage('lib')
    config.add_subpackage('linalg')
    config.add_subpackage('linsolve')
    config.add_subpackage('maxentropy')
    config.add_subpackage('misc')
    config.add_subpackage('odr')   #  This should be enabled !!
    config.add_subpackage('optimize')
    config.add_subpackage('sandbox')
    config.add_subpackage('signal')
    config.add_subpackage('sparse')
    config.add_subpackage('special')
    config.add_subpackage('stats')
    #config.add_subpackage('ndimage')
    config.add_subpackage('stsci')
    config.add_subpackage('weave')
    config.make_svn_version_py()  # installs __svn_version__.py
    config.make_config_py()
    return config

if __name__ == '__main__':
    from numpy.distutils.core import setup
    setup(**configuration(top_path='').todict())

Nils



From chiaracaronna at hotmail.com  Wed Feb 14 08:19:49 2007
From: chiaracaronna at hotmail.com (Chiara Caronna)
Date: Wed, 14 Feb 2007 13:19:49 +0000
Subject: [SciPy-user] scipy.optimize.leastsq error estimates
In-Reply-To: <45D30B02.10208@iam.uni-stuttgart.de>
Message-ID: <BAY114-F26F4F5992A325534DB813FA1970@phx.gbl>

Ok, I have an odr directory in Lib/scipy and the file setup.py looks ok:

def configuration(parent_package='',top_path=None):
    from numpy.distutils.misc_util import Configuration
    config = Configuration('scipy',parent_package,top_path)
    config.add_subpackage('cluster')
    config.add_subpackage('fftpack')
    config.add_subpackage('integrate')
    config.add_subpackage('interpolate')
    config.add_subpackage('io')
    config.add_subpackage('lib')
    config.add_subpackage('linalg')
    config.add_subpackage('linsolve')
    config.add_subpackage('maxentropy')
    config.add_subpackage('misc')
    config.add_subpackage('odr')
    config.add_subpackage('optimize')
    config.add_subpackage('sandbox')
    config.add_subpackage('signal')
    config.add_subpackage('sparse')
    config.add_subpackage('special')
    config.add_subpackage('stats')
    config.add_subpackage('ndimage')
    config.add_subpackage('stsci')
    config.add_subpackage('weave')
    config.make_svn_version_py()  # installs __svn_version__.py
    config.make_config_py()
    return config

if __name__ == '__main__':
    from numpy.distutils.core import setup
    setup(**configuration(top_path='').todict())

so.... why it doesn't work?!

>From: Nils Wagner <nwagner at iam.uni-stuttgart.de>
>Reply-To: SciPy Users List <scipy-user at scipy.org>
>To: SciPy Users List <scipy-user at scipy.org>
>Subject: Re: [SciPy-user] scipy.optimize.leastsq error estimates
>Date: Wed, 14 Feb 2007 14:13:38 +0100
>
>Chiara Caronna wrote:
> > Ah. No, there is not an odr directory... :(
> >
> > Here is the output:
> >
> >
> > drwxr-xr-x   28 root     root         4096 2007-02-14 13:46 .
> > drwxr-xr-x   22 root     root         4096 2007-01-17 09:37 ..
> > -rw-r--r--    1 500      1000            0 2006-01-05 04:35 __init__.py
> > drwxr-xr-x    4 root     root         4096 2006-12-08 05:05 ann
> > drwxr-xr-x    4 root     root         4096 2006-12-08 05:05 arpack
> > drwxr-xr-x    3 root     root         4096 2006-12-08 05:05 arraysetops
> > drwxr-xr-x    2 root     root         4096 2006-12-08 05:05 buildgrid
> > drwxr-xr-x    2 root     root         4096 2006-12-08 05:05 constants
> > drwxr-xr-x    2 root     root         4096 2006-12-08 05:05 cow
> > drwxr-xr-x    3 root     root         4096 2006-12-08 05:05 delaunay
> > -rw-r--r--    1 root     root            4 2007-02-14 13:46
> > enabled_packages.txt
> > drwxr-xr-x    4 root     root         4096 2006-12-08 05:05 exmplpackage
> > drwxr-xr-x    5 root     root         4096 2006-12-08 05:05 fdfpack
> > drwxr-xr-x    2 root     root         4096 2006-12-08 05:05 ga
> > drwxr-xr-x    2 root     root         4096 2006-12-08 05:05 gplt
> > drwxr-xr-x    2 root     root         4096 2006-12-08 05:05 image
> > drwxr-xr-x    5 root     root         4096 2006-12-08 05:05 models
> > drwxr-xr-x    4 root     root         4096 2006-12-08 05:05 montecarlo
> > drwxr-xr-x    2 root     root         4096 2006-12-08 05:05 netcdf
> > drwxr-xr-x    2 root     root         4096 2006-12-08 05:05 newoptimize
> > drwxr-xr-x    3 root     root         4096 2006-12-08 05:05 numexpr
> > drwxr-xr-x    2 root     root         4096 2006-12-08 05:05 plt
> > drwxr-xr-x    5 root     root         4096 2006-12-08 05:05 pyem
> > drwxr-xr-x   12 root     root         4096 2006-12-08 05:05 pysparse
> > drwxr-xr-x    2 root     root         4096 2006-12-08 05:05 rkern
> > -rw-r--r--    1 500      1000         2656 2006-12-02 04:24 setup.py
> > -rw-r--r--    1 root     root         1028 2007-01-17 09:37 setup.pyc
> > drwxr-xr-x    4 root     root         4096 2006-12-08 05:05 spline
> > drwxr-xr-x    2 root     root         4096 2006-12-08 05:05 stats
> > drwxr-xr-x    4 root     root         4096 2006-12-08 05:05 svm
> > drwxr-xr-x    3 root     root         4096 2006-12-08 05:05 umfpack
> > drwxr-xr-x    5 root     root         4096 2006-12-08 05:05 xplt
> >
> >
> >
> >> From: Nils Wagner <nwagner at iam.uni-stuttgart.de>
> >> Reply-To: SciPy Users List <scipy-user at scipy.org>
> >> To: SciPy Users List <scipy-user at scipy.org>
> >> Subject: Re: [SciPy-user] scipy.optimize.leastsq error estimates
> >> Date: Wed, 14 Feb 2007 14:01:19 +0100
> >>
> >> Chiara Caronna wrote:
> >>
> >>>
> >>>> If you use 0.5.2
> >>>>
> >>>> look into the directory scipy/Lib/sandbox
> >>>> and create a file called enabled_packages.txt which should contain
> >>>>
> >>>> odr
> >>>>
> >>>> in the first line (a new line for each package)
> >>>>
> >>>>
> >>> I did what you said, but when reinstalling scipy I got this error:
> >>>
> >>>   File "Lib/sandbox/setup.py", line 22, in configuration
> >>>     config.add_subpackage(p)
> >>>   File
> >>> "/usr/local/lib/python2.4/site-packages/numpy/distutils/misc_util.py",
> >>>
> >> line
> >>
> >>> 765, in add_subpackage
> >>>     caller_level = 2)
> >>>   File
> >>> "/usr/local/lib/python2.4/site-packages/numpy/distutils/misc_util.py",
> >>>
> >> line
> >>
> >>> 741, in get_subpackage
> >>>     caller_level = caller_level+1)
> >>>   File
> >>> "/usr/local/lib/python2.4/site-packages/numpy/distutils/misc_util.py",
> >>>
> >> line
> >>
> >>> 541, in __init__
> >>>     raise ValueError("%r is not a directory" % (package_path,))
> >>> ValueError: 'Lib/sandbox/odr' is not a directory
> >>>
> >>>
> >>>
> >>>
> >> What is the output of ls -l  in your sandbox directory
> >> I have
> >> Lib/sandbox> ls -l
> >>  total 17
> >> drwxr-xr-x   5 root root  272 2006-09-03 11:30 ann
> >> drwxr-xr-x   6 root root  376 2006-11-21 08:45 arpack
> >> drwxr-xr-x   4 root root  184 2006-11-06 08:48 arraysetops
> >> drwxr-xr-x   3 root root  232 2006-06-27 08:32 buildgrid
> >> drwxr-xr-x   5 root root  344 2006-12-15 15:35 cdavid
> >> drwxr-xr-x   3 root root  192 2006-06-22 09:18 constants
> >> drwxr-xr-x   3 root root  248 2006-03-15 08:29 cow
> >> drwxr-xr-x   4 root root  544 2006-10-02 08:19 delaunay
> >> -rw-r--r--   1 root root   40 2007-02-08 13:11 enabled_packages.txt
> >> drwxr-xr-x   5 root root  272 2006-03-15 08:29 exmplpackage
> >> drwxr-xr-x   6 root root  280 2006-04-24 08:41 fdfpack
> >> drwxr-xr-x   3 root root  600 2006-09-03 11:30 ga
> >> drwxr-xr-x   3 root root  360 2006-09-03 11:30 gplt
> >> drwxr-xr-x   3 root root  352 2006-09-03 11:30 image
> >> -rw-r--r--   1 root root    0 2006-02-28 08:50 __init__.py
> >> drwxr-xr-x   4 root root  520 2007-02-12 08:33 maskedarray
> >> drwxr-xr-x   6 root root  688 2007-02-12 08:33 models
> >> drwxr-xr-x   5 root root  232 2006-11-23 08:29 montecarlo
> >> drwxr-xr-x   3 root root  320 2006-07-10 08:09 netcdf
> >> drwxr-xr-x   4 root root  264 2007-01-11 10:57 newoptimize
> >> drwxr-xr-x   4 root root  432 2006-11-17 09:02 numexpr
> >> drwxr-xr-x   3 root root   72 2006-10-05 08:30 oliphant
> >> drwxr-xr-x   3 root root  456 2006-09-03 11:30 plt
> >> drwxr-xr-x   6 root root  904 2006-12-07 09:05 pyem
> >> drwxr-xr-x  13 root root  592 2006-08-16 16:21 pysparse
> >> drwxr-xr-x   4 root root  232 2007-02-08 13:11 rbf
> >> drwxr-xr-x   3 root root  184 2006-09-03 11:30 rkern
> >> -rw-r--r--   1 root root 2732 2007-02-08 13:07 setup.py
> >> -rw-r--r--   1 root root 1028 2007-02-08 13:11 setup.pyc
> >> drwxr-xr-x   5 root root  360 2007-02-09 08:42 spline
> >> drwxr-xr-x   3 root root  192 2006-10-10 08:22 stats
> >> drwxr-xr-x   5 root root  464 2006-09-11 08:44 svm
> >> drwxr-xr-x   9 root root  576 2007-02-13 08:27 timeseries
> >> drwxr-xr-x   3 root root   72 2006-12-07 08:52 wavelet
> >> drwxr-xr-x   6 root root 1864 2007-01-23 08:35 xplt
> >>
> >> Note that I am using the svn version. So odr is not present in the 
>sandbox.
> >> How about 0.5.2 ?
> >> Do you have a directory odr in the sandbox ?
> >>
> >> Nils
> >>
> >>
> >> _______________________________________________
> >> SciPy-user mailing list
> >> SciPy-user at scipy.org
> >> http://projects.scipy.org/mailman/listinfo/scipy-user
> >>
> >
> > _________________________________________________________________
> > FREE pop-up blocking with the new MSN Toolbar - get it now!
> > http://toolbar.msn.click-url.com/go/onm00200415ave/direct/01/
> >
> > _______________________________________________
> > SciPy-user mailing list
> > SciPy-user at scipy.org
> > http://projects.scipy.org/mailman/listinfo/scipy-user
> >
>And in scipy/Lib ? I have
>
>  drwxr-xr-x   6 root root  280 2007-01-24 13:58 cluster
>drwxr-xr-x   7 root root  536 2007-01-11 09:16 fftpack
>drwxr-xr-x   2 root root   80 2006-03-20 11:42 image
>-rw-r--r--   1 root root 2356 2007-01-11 09:16 __init__.py
>drwxr-xr-x   8 root root  656 2007-02-12 09:54 integrate
>drwxr-xr-x   5 root root  456 2007-02-12 09:54 interpolate
>drwxr-xr-x   6 root root  672 2007-02-12 09:54 io
>drwxr-xr-x   5 root root  232 2007-01-11 09:16 lib
>drwxr-xr-x   6 root root 1024 2007-01-25 09:35 linalg
>drwxr-xr-x   5 root root  552 2007-01-25 09:35 linsolve
>drwxr-xr-x   2 root root   80 2006-01-19 10:27 maxent
>drwxr-xr-x   5 root root  296 2007-01-11 09:16 maxentropy
>drwxr-xr-x   3 root root  392 2007-01-11 09:16 misc
>drwxr-xr-x   2 root root   80 2006-01-19 10:27 montecarlo
>drwxr-xr-x   5 root root  456 2007-02-12 09:54 ndimage
>drwxr-xr-x   2 root root   80 2006-03-17 10:51 nd_image
>drwxr-xr-x   5 root root  360 2007-01-24 14:00 odr
>drwxr-xr-x  10 root root  712 2007-01-29 10:06 optimize
>drwxr-xr-x  35 root root 1032 2007-02-12 09:54 sandbox
>-rw-r--r--   1 root root  679 2005-12-01 10:57 scipy_version.pyc
>-rw-r--r--   1 root root 1126 2006-11-28 16:59 setup.py
>-rw-r--r--   1 root root 1141 2006-11-28 17:02 setup.pyc
>drwxr-xr-x   5 root root  744 2007-01-30 15:29 signal
>drwxr-xr-x   5 root root  272 2007-01-15 09:33 sparse
>drwxr-xr-x  12 root root 1056 2007-01-26 11:21 special
>drwxr-xr-x   5 root root  568 2007-01-11 09:16 stats
>drwxr-xr-x   5 root root  208 2006-08-04 09:02 stsci
>drwxr-xr-x   3 root root  232 2006-10-02 08:38 tests
>-rw-r--r--   1 root root  485 2006-12-08 09:21 version.py
>-rw-r--r--   1 root root  580 2006-12-08 09:23 version.pyc
>drwxr-xr-x   8 root root 1272 2007-01-22 09:42 weave
>
>Also look into your setup.py file in scipy/Lib
>
>def configuration(parent_package='',top_path=None):
>     from numpy.distutils.misc_util import Configuration
>     config = Configuration('scipy',parent_package,top_path)
>     config.add_subpackage('cluster')
>     config.add_subpackage('fftpack')
>     config.add_subpackage('integrate')
>     config.add_subpackage('interpolate')
>     config.add_subpackage('io')
>     config.add_subpackage('lib')
>     config.add_subpackage('linalg')
>     config.add_subpackage('linsolve')
>     config.add_subpackage('maxentropy')
>     config.add_subpackage('misc')
>     config.add_subpackage('odr')   #  This should be enabled !!
>     config.add_subpackage('optimize')
>     config.add_subpackage('sandbox')
>     config.add_subpackage('signal')
>     config.add_subpackage('sparse')
>     config.add_subpackage('special')
>     config.add_subpackage('stats')
>     #config.add_subpackage('ndimage')
>     config.add_subpackage('stsci')
>     config.add_subpackage('weave')
>     config.make_svn_version_py()  # installs __svn_version__.py
>     config.make_config_py()
>     return config
>
>if __name__ == '__main__':
>     from numpy.distutils.core import setup
>     setup(**configuration(top_path='').todict())
>
>Nils
>
>_______________________________________________
>SciPy-user mailing list
>SciPy-user at scipy.org
>http://projects.scipy.org/mailman/listinfo/scipy-user

_________________________________________________________________
Express yourself instantly with MSN Messenger! Download today it's FREE! 
http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/



From nwagner at iam.uni-stuttgart.de  Wed Feb 14 08:27:30 2007
From: nwagner at iam.uni-stuttgart.de (Nils Wagner)
Date: Wed, 14 Feb 2007 14:27:30 +0100
Subject: [SciPy-user] scipy.optimize.leastsq error estimates
In-Reply-To: <BAY114-F26F4F5992A325534DB813FA1970@phx.gbl>
References: <BAY114-F26F4F5992A325534DB813FA1970@phx.gbl>
Message-ID: <45D30E42.2040408@iam.uni-stuttgart.de>

Chiara Caronna wrote:
> Ok, I have an odr directory in Lib/scipy and the file setup.py looks ok:
>
> def configuration(parent_package='',top_path=None):
>     from numpy.distutils.misc_util import Configuration
>     config = Configuration('scipy',parent_package,top_path)
>     config.add_subpackage('cluster')
>     config.add_subpackage('fftpack')
>     config.add_subpackage('integrate')
>     config.add_subpackage('interpolate')
>     config.add_subpackage('io')
>     config.add_subpackage('lib')
>     config.add_subpackage('linalg')
>     config.add_subpackage('linsolve')
>     config.add_subpackage('maxentropy')
>     config.add_subpackage('misc')
>     config.add_subpackage('odr')
>     config.add_subpackage('optimize')
>     config.add_subpackage('sandbox')
>     config.add_subpackage('signal')
>     config.add_subpackage('sparse')
>     config.add_subpackage('special')
>     config.add_subpackage('stats')
>     config.add_subpackage('ndimage')
>     config.add_subpackage('stsci')
>     config.add_subpackage('weave')
>     config.make_svn_version_py()  # installs __svn_version__.py
>     config.make_config_py()
>     return config
>
> if __name__ == '__main__':
>     from numpy.distutils.core import setup
>     setup(**configuration(top_path='').todict())
>
> so.... why it doesn't work?!
>
>   
 
Sorry I am running out of ideas ?
It works for me

Python 2.4.1 (#1, Oct 13 2006, 16:51:58)
[GCC 4.0.2 20050901 (prerelease) (SUSE Linux)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import scipy.odr
>>> import scipy
>>> scipy.__version__
'0.5.3.dev2707'

Nils



From chiaracaronna at hotmail.com  Wed Feb 14 08:34:51 2007
From: chiaracaronna at hotmail.com (Chiara Caronna)
Date: Wed, 14 Feb 2007 13:34:51 +0000
Subject: [SciPy-user] scipy.optimize.leastsq error estimates
In-Reply-To: <45D30E42.2040408@iam.uni-stuttgart.de>
Message-ID: <BAY114-F13F6C4B4206A6AE5D08F92A1970@phx.gbl>

Ok, the error I got is this:

>>>import scipy.odr
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File "/usr/local/lib/python2.4/site-packages/scipy/odr/__init__.py", line 
49, in
?
    import odrpack
  File "/usr/local/lib/python2.4/site-packages/scipy/odr/odrpack.py", line 
103, in
?
    from scipy.sandbox.odr import __odrpack
ImportError: No module named odr

can you check you file : 
"/usr/local/lib/python2.4/site-packages/scipy/odr/odrpack.py" at  line 103? 
I think the problem is that it tries to import something from 
scipy.sandbox.odr that doesn't exist...


>From: Nils Wagner <nwagner at iam.uni-stuttgart.de>
>Reply-To: SciPy Users List <scipy-user at scipy.org>
>To: SciPy Users List <scipy-user at scipy.org>
>Subject: Re: [SciPy-user] scipy.optimize.leastsq error estimates
>Date: Wed, 14 Feb 2007 14:27:30 +0100
>
>Chiara Caronna wrote:
> > Ok, I have an odr directory in Lib/scipy and the file setup.py looks ok:
> >
> > def configuration(parent_package='',top_path=None):
> >     from numpy.distutils.misc_util import Configuration
> >     config = Configuration('scipy',parent_package,top_path)
> >     config.add_subpackage('cluster')
> >     config.add_subpackage('fftpack')
> >     config.add_subpackage('integrate')
> >     config.add_subpackage('interpolate')
> >     config.add_subpackage('io')
> >     config.add_subpackage('lib')
> >     config.add_subpackage('linalg')
> >     config.add_subpackage('linsolve')
> >     config.add_subpackage('maxentropy')
> >     config.add_subpackage('misc')
> >     config.add_subpackage('odr')
> >     config.add_subpackage('optimize')
> >     config.add_subpackage('sandbox')
> >     config.add_subpackage('signal')
> >     config.add_subpackage('sparse')
> >     config.add_subpackage('special')
> >     config.add_subpackage('stats')
> >     config.add_subpackage('ndimage')
> >     config.add_subpackage('stsci')
> >     config.add_subpackage('weave')
> >     config.make_svn_version_py()  # installs __svn_version__.py
> >     config.make_config_py()
> >     return config
> >
> > if __name__ == '__main__':
> >     from numpy.distutils.core import setup
> >     setup(**configuration(top_path='').todict())
> >
> > so.... why it doesn't work?!
> >
> >
>
>Sorry I am running out of ideas ?
>It works for me
>
>Python 2.4.1 (#1, Oct 13 2006, 16:51:58)
>[GCC 4.0.2 20050901 (prerelease) (SUSE Linux)] on linux2
>Type "help", "copyright", "credits" or "license" for more information.
> >>> import scipy.odr
> >>> import scipy
> >>> scipy.__version__
>'0.5.3.dev2707'
>
>Nils
>
>_______________________________________________
>SciPy-user mailing list
>SciPy-user at scipy.org
>http://projects.scipy.org/mailman/listinfo/scipy-user

_________________________________________________________________
Express yourself instantly with MSN Messenger! Download today it's FREE! 
http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/



From nwagner at iam.uni-stuttgart.de  Wed Feb 14 08:42:51 2007
From: nwagner at iam.uni-stuttgart.de (Nils Wagner)
Date: Wed, 14 Feb 2007 14:42:51 +0100
Subject: [SciPy-user] scipy.optimize.leastsq error estimates
In-Reply-To: <BAY114-F13F6C4B4206A6AE5D08F92A1970@phx.gbl>
References: <BAY114-F13F6C4B4206A6AE5D08F92A1970@phx.gbl>
Message-ID: <45D311DB.2040903@iam.uni-stuttgart.de>

Chiara Caronna wrote:
> Ok, the error I got is this:
>
>   
>>>> import scipy.odr
>>>>         
> Traceback (most recent call last):
>   File "<stdin>", line 1, in ?
>   File "/usr/local/lib/python2.4/site-packages/scipy/odr/__init__.py", line 
> 49, in
> ?
>     import odrpack
>   File "/usr/local/lib/python2.4/site-packages/scipy/odr/odrpack.py", line 
> 103, in
> ?
>     from scipy.sandbox.odr import __odrpack
> ImportError: No module named odr
>
> can you check you file : 
> "/usr/local/lib/python2.4/site-packages/scipy/odr/odrpack.py" at  line 103? 
> I think the problem is that it tries to import something from 
> scipy.sandbox.odr that doesn't exist...
>
>
>   
I have

from scipy.odr import __odrpack
What is the output of

scipy.__version__

on your machine ?

I suggest to remove the build directory and scipy below site-packages with

rm -rf build
rm -rf scipy

Afterwards reinstall everything from scratch with

python setput.py install

HTH

Nils




From chiaracaronna at hotmail.com  Wed Feb 14 08:48:16 2007
From: chiaracaronna at hotmail.com (Chiara Caronna)
Date: Wed, 14 Feb 2007 13:48:16 +0000
Subject: [SciPy-user] scipy.optimize.leastsq error estimates
In-Reply-To: <45D311DB.2040903@iam.uni-stuttgart.de>
Message-ID: <BAY114-F3FC013910DE9AF5DF0CBAA1970@phx.gbl>




>From: Nils Wagner <nwagner at iam.uni-stuttgart.de>
>Reply-To: SciPy Users List <scipy-user at scipy.org>
>To: SciPy Users List <scipy-user at scipy.org>
>Subject: Re: [SciPy-user] scipy.optimize.leastsq error estimates
>Date: Wed, 14 Feb 2007 14:42:51 +0100
>
>Chiara Caronna wrote:
> > Ok, the error I got is this:
> >
> >
> >>>> import scipy.odr
> >>>>
> > Traceback (most recent call last):
> >   File "<stdin>", line 1, in ?
> >   File "/usr/local/lib/python2.4/site-packages/scipy/odr/__init__.py", 
>line
> > 49, in
> > ?
> >     import odrpack
> >   File "/usr/local/lib/python2.4/site-packages/scipy/odr/odrpack.py", 
>line
> > 103, in
> > ?
> >     from scipy.sandbox.odr import __odrpack
> > ImportError: No module named odr
> >
> > can you check you file :
> > "/usr/local/lib/python2.4/site-packages/scipy/odr/odrpack.py" at  line 
>103?
> > I think the problem is that it tries to import something from
> > scipy.sandbox.odr that doesn't exist...
> >
> >
> >
>I have
>from scipy.odr import __odrpack
>

I changed my "from scipy.sandbox.odr import __odrpack" into  "from scipy.odr 
import __odrpack" and now it works... I'll see if this works fine now, other 
wise I'll try to reinstall everything. Thank's a lot for  your help!

Chiara
>What is the output of
>
>scipy.__version__
>
>on your machine ?
>
>I suggest to remove the build directory and scipy below site-packages with
>
>rm -rf build
>rm -rf scipy
>
>Afterwards reinstall everything from scratch with
>
>python setput.py install
>
>HTH
>
>Nils
>
>
>_______________________________________________
>SciPy-user mailing list
>SciPy-user at scipy.org
>http://projects.scipy.org/mailman/listinfo/scipy-user

_________________________________________________________________
FREE pop-up blocking with the new MSN Toolbar - get it now! 
http://toolbar.msn.click-url.com/go/onm00200415ave/direct/01/



From nwagner at iam.uni-stuttgart.de  Wed Feb 14 08:58:14 2007
From: nwagner at iam.uni-stuttgart.de (Nils Wagner)
Date: Wed, 14 Feb 2007 14:58:14 +0100
Subject: [SciPy-user] scipy.optimize.leastsq error estimates
In-Reply-To: <BAY114-F3FC013910DE9AF5DF0CBAA1970@phx.gbl>
References: <BAY114-F3FC013910DE9AF5DF0CBAA1970@phx.gbl>
Message-ID: <45D31576.2060100@iam.uni-stuttgart.de>

 
>
> I changed my "from scipy.sandbox.odr import __odrpack" into  "from scipy.odr 
> import __odrpack" and now it works... I'll see if this works fine now, other 
> wise I'll try to reinstall everything. Thank's a lot for  your help!
>
>   
 You're welcome !

Nils



From lorenzo.isella at gmail.com  Wed Feb 14 10:47:58 2007
From: lorenzo.isella at gmail.com (Lorenzo Isella)
Date: Wed, 14 Feb 2007 16:47:58 +0100
Subject: [SciPy-user] Newbie Question about Scipy
Message-ID: <a2b3004b0702140747y2b829d19y406439b926f0b24@mail.gmail.com>

Dear All,
I am pretty new to Python, but it has such a good reputation that I
decided to give it a try.
I am slightly puzzled about the syntax modulename.function.
I am going through the SciPy tutorial by Oliphant (btw, is there
anywhere online a free updated version of a document of this kind?).
To use SciPy I normally do the following:

~$ ipython
Python 2.4.4 (#2, Jan 13 2007, 17:50:26)
Type "copyright", "credits" or "license" for more information.

IPython 0.7.3 -- An enhanced Interactive Python.
?       -> Introduction to IPython's features.
%magic  -> Information about IPython's 'magic' % functions.
help    -> Python's own help system.
object? -> Details about 'object'. ?object also works, ?? prints more.

In [1]: from scipy import *

However, statements like the ones in the guide:

In [12]: from integrate import quad
---------------------------------------------------------------------------
exceptions.ImportError                               Traceback (most
recent call last)

/home/iselllo/<ipython console>

ImportError: No module named integrate

do not work.
So I have to use: scipy.integrate. Similarly, the function gamma is
not recognized, but special.gamma is.
How is this chosen by the system? Then: once I have import everything
from scipy, is importing explicitly the gamma function a necessity at
all?
****************************************************************************
On a more general ground, how does Python compare with e.g. MatLab or
Octave for scientific computing? Which are the advantages and
drawbacks (sorry if this is not the right forum).
Kind Regards

Lorenzo


From akumar at iitm.ac.in  Wed Feb 14 11:16:08 2007
From: akumar at iitm.ac.in (Kumar Appaiah)
Date: Wed, 14 Feb 2007 21:46:08 +0530
Subject: [SciPy-user] Newbie Question about Scipy
In-Reply-To: <a2b3004b0702140747y2b829d19y406439b926f0b24@mail.gmail.com>
References: <a2b3004b0702140747y2b829d19y406439b926f0b24@mail.gmail.com>
Message-ID: <20070214161608.GA12622@localhost>

On Wed, Feb 14, 2007 at 04:47:58PM +0100, Lorenzo Isella wrote:
> However, statements like the ones in the guide:
> 
> In [12]: from integrate import quad
> ---------------------------------------------------------------------------
> exceptions.ImportError                               Traceback (most
> recent call last)
> 
> /home/iselllo/<ipython console>
> 
> ImportError: No module named integrate
> 
> do not work.
> So I have to use: scipy.integrate. Similarly, the function gamma is
> not recognized, but special.gamma is.

How about

from scipy.integrate import quad
from scipy.special import gamma

That works. But most of us non-experts don't bother importing things
in bits and pieces, so I somehow am used to special.<func>,
signal.<func> etc. But of course, it does make a difference if you
have to use the function over and over again.

And here's another cheap Python trick:

<trick>
import scipy

g = scipy.special.gamma
print g == scipy.special.gamma # should be True
print g(0.5) # prints sqrt(pi)
</trick>

So, g is special.gamma.

HTH.

Kumar

-- 
Kumar Appaiah,
462, Jamuna Hostel,
Indian Institute of Technology Madras,
Chennai - 600 036



From ryanlists at gmail.com  Wed Feb 14 11:07:32 2007
From: ryanlists at gmail.com (Ryan Krauss)
Date: Wed, 14 Feb 2007 10:07:32 -0600
Subject: [SciPy-user] Newbie Question about Scipy
In-Reply-To: <a2b3004b0702140747y2b829d19y406439b926f0b24@mail.gmail.com>
References: <a2b3004b0702140747y2b829d19y406439b926f0b24@mail.gmail.com>
Message-ID: <c5b438120702140807j17d6fff1q8ae9cd0626d45c3f@mail.gmail.com>

Hey Lorenzo,

Your question has to do with a feature of Python called namespaces.
This can be a little vague and weird to the newcomer, but it is a
great strength of Python.  It is also very necessary because there are
so many people writing so many modules for Python.  Namespaces allow
two different modules to have functions with the same name without
conflicting with one another.  So, if module1 and module2 both have
functions called sqrt, module1.sqrt and module2.sqrt can be two
different functions.  Using from module1 import * will load that
module's sqrt into the global namespace.  This may seem weird, but
trust me, it is a good thing.  If you googled for "python namespaces"
you might get a better explanation.  There is an in-depth discussion
of the concept in the book "Learning Python" by Mark Lutz - most
libraries should have it.

The question about how python (or better
scipy/numpy/matplotlib/ipython) compares with Matlab or Octave will
start a war if asked in the wrong places.  Most people on this list
will tell you stories similar to mine: I switched from Matlab to
Python midway through my Ph.D. work and it was one of the best
decisions I ever made.  I find writing Python code so much faster and
easier that I enjoy it quite a bit.  I think the only risk is that if
you are closely attached to some Matlab toolbox that doesn't yet exist
in Python/Scipy and friends, you will need to go through the learning
process of writing some things yourself.  Fortunately, Python and the
number of existing modules make this process not so bad.

Ryan

On 2/14/07, Lorenzo Isella <lorenzo.isella at gmail.com> wrote:
> Dear All,
> I am pretty new to Python, but it has such a good reputation that I
> decided to give it a try.
> I am slightly puzzled about the syntax modulename.function.
> I am going through the SciPy tutorial by Oliphant (btw, is there
> anywhere online a free updated version of a document of this kind?).
> To use SciPy I normally do the following:
>
> ~$ ipython
> Python 2.4.4 (#2, Jan 13 2007, 17:50:26)
> Type "copyright", "credits" or "license" for more information.
>
> IPython 0.7.3 -- An enhanced Interactive Python.
> ?       -> Introduction to IPython's features.
> %magic  -> Information about IPython's 'magic' % functions.
> help    -> Python's own help system.
> object? -> Details about 'object'. ?object also works, ?? prints more.
>
> In [1]: from scipy import *
>
> However, statements like the ones in the guide:
>
> In [12]: from integrate import quad
> ---------------------------------------------------------------------------
> exceptions.ImportError                               Traceback (most
> recent call last)
>
> /home/iselllo/<ipython console>
>
> ImportError: No module named integrate
>
> do not work.
> So I have to use: scipy.integrate. Similarly, the function gamma is
> not recognized, but special.gamma is.
> How is this chosen by the system? Then: once I have import everything
> from scipy, is importing explicitly the gamma function a necessity at
> all?
> ****************************************************************************
> On a more general ground, how does Python compare with e.g. MatLab or
> Octave for scientific computing? Which are the advantages and
> drawbacks (sorry if this is not the right forum).
> Kind Regards
>
> Lorenzo
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user
>


From bryanv at enthought.com  Wed Feb 14 11:11:50 2007
From: bryanv at enthought.com (Bryan Van de Ven)
Date: Wed, 14 Feb 2007 10:11:50 -0600
Subject: [SciPy-user] Newbie Question about Scipy
In-Reply-To: <a2b3004b0702140747y2b829d19y406439b926f0b24@mail.gmail.com>
References: <a2b3004b0702140747y2b829d19y406439b926f0b24@mail.gmail.com>
Message-ID: <45D334C6.9060305@enthought.com>

Lorenzo,

Here is some python documentation about modules and submodules with some 
examples:

http://docs.python.org/tut/node8.html#SECTION008400000000000000000

"from scipy import *" imports the integrate module, which means you can 
use "integrate.quad(...)" If you just want to be able to do "quad(...)" 
then you need either "from scipy.integrate import quad" or "from 
scipy.integrate import *"

As for python vs Matlab, I will mention one area of comparison that I am 
most familiar with. If you have any need for building out an interactive 
GUI data analysis tool, even an extremely modest one, python is a clear 
win. Python has available Chaco2, Matplotlib and VTK/TVTK (and others) 
for displaying 2D and 3D data, and then your choice of toolkits, WX, 
GTK, Qt (and others), for building GUI applications large or small. By 
contrast, building even the simplest of interactive GUI applications in 
Matlab is a nightmare.


Lorenzo Isella wrote:
> Dear All,
> I am pretty new to Python, but it has such a good reputation that I
> decided to give it a try.
> I am slightly puzzled about the syntax modulename.function.
> I am going through the SciPy tutorial by Oliphant (btw, is there
> anywhere online a free updated version of a document of this kind?).
> To use SciPy I normally do the following:
> 
> ~$ ipython
> Python 2.4.4 (#2, Jan 13 2007, 17:50:26)
> Type "copyright", "credits" or "license" for more information.
> 
> IPython 0.7.3 -- An enhanced Interactive Python.
> ?       -> Introduction to IPython's features.
> %magic  -> Information about IPython's 'magic' % functions.
> help    -> Python's own help system.
> object? -> Details about 'object'. ?object also works, ?? prints more.
> 
> In [1]: from scipy import *
> 
> However, statements like the ones in the guide:
> 
> In [12]: from integrate import quad
> ---------------------------------------------------------------------------
> exceptions.ImportError                               Traceback (most
> recent call last)
> 
> /home/iselllo/<ipython console>
> 
> ImportError: No module named integrate
> 
> do not work.
> So I have to use: scipy.integrate. Similarly, the function gamma is
> not recognized, but special.gamma is.
> How is this chosen by the system? Then: once I have import everything
> from scipy, is importing explicitly the gamma function a necessity at
> all?
> ****************************************************************************
> On a more general ground, how does Python compare with e.g. MatLab or
> Octave for scientific computing? Which are the advantages and
> drawbacks (sorry if this is not the right forum).
> Kind Regards
> 
> Lorenzo
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user
> 



From sgarcia at olfac.univ-lyon1.fr  Wed Feb 14 12:10:03 2007
From: sgarcia at olfac.univ-lyon1.fr (Samuel GARCIA)
Date: Wed, 14 Feb 2007 18:10:03 +0100
Subject: [SciPy-user] str(numpy.inf)
Message-ID: <45D3426B.1050600@olfac.univ-lyon1.fr>

Hi list,

I have this problem
str(numpy.inf) under linux give 'inf'
str(numpy.inf) under win32 give '1.#INF'

It is a problem for me because with a GUI in LineEdit, for example, the
end user who have to enter a float can enter inf under linux but not
under win32.


Any idea to solve this ?

Thanks a lot.

Sam


-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Samuel Garcia
Universite Claude Bernard LYON 1
CNRS - UMR5020, Laboratoire des Neurosciences et Systemes Sensoriels
50, avenue Tony Garnier
69366 LYON Cedex 07
FRANCE
T?l : 04 37 28 74 64
Fax : 04 37 28 76 01
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~



From robert.kern at gmail.com  Wed Feb 14 12:36:01 2007
From: robert.kern at gmail.com (Robert Kern)
Date: Wed, 14 Feb 2007 11:36:01 -0600
Subject: [SciPy-user] str(numpy.inf)
In-Reply-To: <45D3426B.1050600@olfac.univ-lyon1.fr>
References: <45D3426B.1050600@olfac.univ-lyon1.fr>
Message-ID: <45D34881.3070601@gmail.com>

Samuel GARCIA wrote:
> Hi list,
> 
> I have this problem
> str(numpy.inf) under linux give 'inf'
> str(numpy.inf) under win32 give '1.#INF'
> 
> It is a problem for me because with a GUI in LineEdit, for example, the
> end user who have to enter a float can enter inf under linux but not
> under win32.
> 
> Any idea to solve this ?

No. We (and Python) defer to the C library for such things, and they each use
different representations.

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
 that is made terrible by our own mad attempt to interpret it as though it had
 an underlying truth."
  -- Umberto Eco


From sgarcia at olfac.univ-lyon1.fr  Wed Feb 14 12:51:07 2007
From: sgarcia at olfac.univ-lyon1.fr (Samuel GARCIA)
Date: Wed, 14 Feb 2007 18:51:07 +0100
Subject: [SciPy-user] str(numpy.inf)
In-Reply-To: <45D34881.3070601@gmail.com>
References: <45D3426B.1050600@olfac.univ-lyon1.fr> <45D34881.3070601@gmail.com>
Message-ID: <45D34C0B.3010405@olfac.univ-lyon1.fr>

bad luck,
I will write a patch in my GUI to detect the platform and detect inf
-inf and nan in lineditbox.
If any anyone have a suggestion, thank you because dealing with platform
specificities is boring.

thank you

sam


Robert Kern wrote:
> Samuel GARCIA wrote:
>   
>> Hi list,
>>
>> I have this problem
>> str(numpy.inf) under linux give 'inf'
>> str(numpy.inf) under win32 give '1.#INF'
>>
>> It is a problem for me because with a GUI in LineEdit, for example, the
>> end user who have to enter a float can enter inf under linux but not
>> under win32.
>>
>> Any idea to solve this ?
>>     
>
> No. We (and Python) defer to the C library for such things, and they each use
> different representations.
>
>   

-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Samuel Garcia
Universite Claude Bernard LYON 1
CNRS - UMR5020, Laboratoire des Neurosciences et Systemes Sensoriels
50, avenue Tony Garnier
69366 LYON Cedex 07
FRANCE
T?l : 04 37 28 74 64
Fax : 04 37 28 76 01
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20070214/773c00cb/attachment.html>

From ryanlists at gmail.com  Wed Feb 14 15:36:17 2007
From: ryanlists at gmail.com (Ryan Krauss)
Date: Wed, 14 Feb 2007 14:36:17 -0600
Subject: [SciPy-user] problem with signal.residue
In-Reply-To: <20070214010607.GA5728@localhost>
References: <c5b438120702131157h6ddd045et78436b452397095c@mail.gmail.com>
	<20070214010607.GA5728@localhost>
Message-ID: <c5b438120702141236o25a60163x232b679a7a25feaf@mail.gmail.com>

I will add this to my ticket, but there is also a problem with
signal.residue when the first denominator coefficent isn't zero.  I
think I fixed it and I tested my fix against Maxima's partfrac command
and it looks right.  Bascially, I added the line

rscale = a[0]

near the beginning of the function and then change the last line to return

return r/rscale, p, k

This is (nearly) identical to the approach in residuez, so that and
the agreement with Maxima give me a good feeling about it.

The .wxm file I am attaching is a wxMaxima script for the test, but it
requires a fairly recent version of wxMaxima (I am using 0.7.1).

Ryan

On 2/13/07, Kumar Appaiah <akumar at iitm.ac.in> wrote:
> On Tue, Feb 13, 2007 at 01:57:46PM -0600, Ryan Krauss wrote:
> > I think I have found a small bug in signal.residue and may have found
> > a simple solution.  The problem seems to come from polydiv requiring
> > that the numerator polynomial be of degree at most 1 less than the
> > denominator.  If I have a denominator of s^2+3*s+2, the numerator must
> > have an s coefficient (even if that coefficient is 0) for
> > signal.residue to work:
> >
> > In [75]: a
> > Out[75]: array([1, 3, 2])
> >
> > In [76]: signal.residue([1],a)
> > ---------------------------------------------------------------------------
> > exceptions.ValueError                                Traceback (most recent cal
> >  last)
> [snip]
> > In [77]: signal.residue([0,1],a)
> > Out[77]:
> > (array([ 1.+0.j, -1.+0.j]),
> >  array([-1.+0.j, -2.+0.j]),
> >   array([], dtype=float64))
> >
> >
> > I think the simple solution is to replace line 1056 with these four lines:
> >     if len(b)<len(a):
> >         k=[]
> >     else:
> >         k,b = polydiv(b,a)
> >
> > where the last line above is the old line 1056.  Basically, specify
> > that there is no k term if the len of b is less than the len of a.
> >
> > Is this too simple?  What do I do to actually submit this if it is the
> > right solution?
>
> I think you are right. This seems to be a bug.
> Please register and open a ticket at
> http://projects.scipy.org/scipy/scipy and state the problem and the
> specified solution.
>
> Thanks.
>
> Kumar
> --
> Kumar Appaiah,
> 462, Jamuna Hostel,
> Indian Institute of Technology Madras,
> Chennai - 600 036
>
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user
>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: python_residue_test.wxm
Type: application/octet-stream
Size: 999 bytes
Desc: not available
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20070214/d9e9d7c3/attachment.obj>
-------------- next part --------------
from scipy import *
from pylab import figure, cla, clf, plot, subplot, show, ylabel, xlabel, xlim, ylim, semilogx, legend, title, savefig, yticks, grid, rcParams

from  IPython.Debugger import Pdb

import copy, os, sys

#Test 1
k=100.0
b=10.0
signal.residue([1.0],[b,k,0.0])

#Test2
num=array([1.0,3,-1,10,1,7])
den=array([15.0,3115.5,173311.5,1197300.0,2115000.0])
signal.residue(num,den)
-------------- next part --------------
# Author: Travis Oliphant
# signaltools.py -- 2002

import types
import sigtools
from scipy import special, linalg
from scipy.fftpack import fft, ifft, ifftshift, fft2, ifft2
from numpy import polyadd, polymul, polydiv, polysub, \
     roots, poly, polyval, polyder, cast, asarray, isscalar, atleast_1d, \
     ones, sin, linspace, real, extract, real_if_close, zeros, array, arange, \
     where, sqrt, rank, newaxis, argmax, product, cos, pi, exp, \
     ravel, size, less_equal, sum, r_, iscomplexobj, take, \
     argsort, allclose, expand_dims, unique, prod, sort, reshape, c_, \
     transpose, dot, any, minimum, maximum, mean
import numpy
from scipy.fftpack import fftn, ifftn
from scipy.misc import factorial

from  IPython.Debugger import Pdb

_modedict = {'valid':0, 'same':1, 'full':2}
_boundarydict = {'fill':0, 'pad':0, 'wrap':2, 'circular':2, 'symm':1, 'symmetric':1, 'reflect':4}

def _valfrommode(mode):
    try:
        val = _modedict[mode]
    except KeyError:
        if mode not in [0,1,2]:
            raise ValueError, "Acceptable mode flags are 'valid' (0), 'same' (1), or 'full' (2)."
        val = mode
    return val

def _bvalfromboundary(boundary):
    try:
        val = _boundarydict[boundary] << 2
    except KeyError:
        if val not in [0,1,2] :
            raise ValueError, "Acceptable boundary flags are 'fill', 'wrap' (or 'circular'), \n  and 'symm' (or 'symmetric')."
        val = boundary << 2
    return val


def correlate(in1, in2, mode='full'):
    """Cross-correlate two N-dimensional arrays.

  Description:

     Cross-correlate in1 and in2 with the output size determined by mode.

  Inputs:

    in1 -- an N-dimensional array.
    in2 -- an array with the same number of dimensions as in1.
    mode -- a flag indicating the size of the output
            'valid'  (0): The output consists only of those elements that
                            do not rely on the zero-padding.
            'same'   (1): The output is the same size as the largest input
                            centered with respect to the 'full' output.
            'full'   (2): The output is the full discrete linear
                            cross-correlation of the inputs. (Default)

  Outputs:  (out,)

    out -- an N-dimensional array containing a subset of the discrete linear
           cross-correlation of in1 with in2.

    """
    # Code is faster if kernel is smallest array.
    volume = asarray(in1)
    kernel = asarray(in2)
    if rank(volume) == rank(kernel) == 0:
        return volume*kernel
    if (product(kernel.shape,axis=0) > product(volume.shape,axis=0)):
        temp = kernel
        kernel = volume
        volume = temp
        del temp

    val = _valfrommode(mode)

    return sigtools._correlateND(volume, kernel, val)

def _centered(arr, newsize):
    # Return the center newsize portion of the array.
    newsize = asarray(newsize)
    currsize = array(arr.shape)
    startind = (currsize - newsize) / 2
    endind = startind + newsize
    myslice = [slice(startind[k], endind[k]) for k in range(len(endind))]
    return arr[tuple(myslice)]

def fftconvolve(in1, in2, mode="full"):
    """Convolve two N-dimensional arrays using FFT. See convolve.
    
    """
    s1 = array(in1.shape)
    s2 = array(in2.shape)
    if (s1.dtype.char in ['D','F']) or (s2.dtype.char in ['D', 'F']):
        cmplx=1
    else: cmplx=0
    size = s1+s2-1
    IN1 = fftn(in1,size)
    IN1 *= fftn(in2,size)
    ret = ifftn(IN1)
    del IN1
    if not cmplx:
        ret = real(ret)
    if mode == "full":
        return ret
    elif mode == "same":
        if product(s1,axis=0) > product(s2,axis=0):
            osize = s1
        else:
            osize = s2
        return _centered(ret,osize)
    elif mode == "valid":
        return _centered(ret,abs(s2-s1)+1)


def convolve(in1, in2, mode='full'):
    """Convolve two N-dimensional arrays.

  Description:

     Convolve in1 and in2 with output size determined by mode.

  Inputs:

    in1 -- an N-dimensional array.
    in2 -- an array with the same number of dimensions as in1.
    mode -- a flag indicating the size of the output
            'valid'  (0): The output consists only of those elements that
                            are computed by scaling the larger array with all
                            the values of the smaller array.
            'same'   (1): The output is the same size as the largest input
                            centered with respect to the 'full' output.
            'full'   (2): The output is the full discrete linear convolution
                            of the inputs. (Default)

  Outputs:  (out,)

    out -- an N-dimensional array containing a subset of the discrete linear
           convolution of in1 with in2.

    """
    volume = asarray(in1)
    kernel = asarray(in2)
    if rank(volume) == rank(kernel) == 0:
        return volume*kernel
    if (product(kernel.shape,axis=0) > product(volume.shape,axis=0)):
        temp = kernel
        kernel = volume
        volume = temp
        del temp

    slice_obj = [slice(None,None,-1)]*len(kernel.shape)
    val = _valfrommode(mode)

    return sigtools._correlateND(volume,kernel[slice_obj],val)

def order_filter(a, domain, order):
    """Perform an order filter on an N-dimensional array.

  Description:

    Perform an order filter on the array in.  The domain argument acts as a
    mask centered over each pixel.  The non-zero elements of domain are
    used to select elements surrounding each input pixel which are placed
    in a list.   The list is sorted, and the output for that pixel is the
    element corresponding to rank in the sorted list.

  Inputs:

    in -- an N-dimensional input array.
    domain -- a mask array with the same number of dimensions as in.  Each
              dimension should have an odd number of elements.
    rank -- an non-negative integer which selects the element from the
            sorted list (0 corresponds to the largest element, 1 is the
            next largest element, etc.)

  Output: (out,)

    out -- the results of the order filter in an array with the same
           shape as in.

    """
    domain = asarray(domain)
    size = domain.shape
    for k in range(len(size)):
        if (size[k] % 2) != 1:
            raise ValueError, "Each dimension of domain argument should have an odd number of elements."
    return sigtools._orderfilterND(a, domain, rank)


def medfilt(volume,kernel_size=None):
    """Perform a median filter on an N-dimensional array.

  Description:

    Apply a median filter to the input array using a local window-size
    given by kernel_size.

  Inputs:

    in -- An N-dimensional input array.
    kernel_size -- A scalar or an N-length list giving the size of the
                   median filter window in each dimension.  Elements of
                   kernel_size should be odd.  If kernel_size is a scalar,
                   then this scalar is used as the size in each dimension.

  Outputs: (out,)

    out -- An array the same size as input containing the median filtered
           result.

    """
    volume = asarray(volume)
    if kernel_size is None:
        kernel_size = [3] * len(volume.shape)
    kernel_size = asarray(kernel_size)
    if len(kernel_size.shape) == 0:
        kernel_size = [kernel_size.item()] * len(volume.shape)
    kernel_size = asarray(kernel_size)

    for k in range(len(volume.shape)):
        if (kernel_size[k] % 2) != 1:
            raise ValueError, "Each element of kernel_size should be odd."

    domain = ones(kernel_size)

    numels = product(kernel_size,axis=0)
    order = int(numels/2)
    return sigtools._order_filterND(volume,domain,order)


def wiener(im,mysize=None,noise=None):
    """Perform a Wiener filter on an N-dimensional array.

  Description:

    Apply a Wiener filter to the N-dimensional array in.

  Inputs:

    in -- an N-dimensional array.
    kernel_size -- A scalar or an N-length list giving the size of the
                   median filter window in each dimension.  Elements of
                   kernel_size should be odd.  If kernel_size is a scalar,
                   then this scalar is used as the size in each dimension.
    noise -- The noise-power to use.  If None, then noise is estimated as
             the average of the local variance of the input.

  Outputs: (out,)

    out -- Wiener filtered result with the same shape as in.

    """
    im = asarray(im)
    if mysize is None:
        mysize = [3] * len(im.shape)
    mysize = asarray(mysize);

    # Estimate the local mean
    lMean = correlate(im,ones(mysize),1) / product(mysize,axis=0)

    # Estimate the local variance
    lVar = correlate(im**2,ones(mysize),1) / product(mysize,axis=0) - lMean**2

    # Estimate the noise power if needed.
    if noise==None:
        noise = mean(ravel(lVar),axis=0)

    res = (im - lMean)
    res *= (1-noise / lVar)
    res += lMean
    out = where(lVar < noise, lMean, res)

    return out


def convolve2d(in1, in2, mode='full', boundary='fill', fillvalue=0):
    """Convolve two 2-dimensional arrays.

  Description:

     Convolve in1 and in2 with output size determined by mode and boundary
     conditions determined by boundary and fillvalue.

  Inputs:

    in1 -- a 2-dimensional array.
    in2 -- a 2-dimensional array.
    mode -- a flag indicating the size of the output
            'valid'  (0): The output consists only of those elements that
                            do not rely on the zero-padding.
            'same'   (1): The output is the same size as the input centered
                            with respect to the 'full' output.
            'full'   (2): The output is the full discrete linear convolution
                            of the inputs. (*Default*)
    boundary -- a flag indicating how to handle boundaries
                'fill' : pad input arrays with fillvalue. (*Default*)
                'wrap' : circular boundary conditions.
                'symm' : symmetrical boundary conditions.
    fillvalue -- value to fill pad input arrays with (*Default* = 0)

  Outputs:  (out,)

    out -- a 2-dimensional array containing a subset of the discrete linear
           convolution of in1 with in2.

    """
    val = _valfrommode(mode)
    bval = _bvalfromboundary(boundary)

    return sigtools._convolve2d(in1,in2,1,val,bval,fillvalue)

def correlate2d(in1, in2, mode='full', boundary='fill', fillvalue=0):
    """Cross-correlate two 2-dimensional arrays.

  Description:

     Cross correlate in1 and in2 with output size determined by mode
     and boundary conditions determined by boundary and fillvalue.

  Inputs:

    in1 -- a 2-dimensional array.
    in2 -- a 2-dimensional array.
    mode -- a flag indicating the size of the output
            'valid'  (0): The output consists only of those elements that
                            do not rely on the zero-padding.
            'same'   (1): The output is the same size as the input centered
                            with respect to the 'full' output.
            'full'   (2): The output is the full discrete linear convolution
                            of the inputs. (*Default*)
    boundary -- a flag indicating how to handle boundaries
                'fill' : pad input arrays with fillvalue. (*Default*)
                'wrap' : circular boundary conditions.
                'symm' : symmetrical boundary conditions.
    fillvalue -- value to fill pad input arrays with (*Default* = 0)

  Outputs:  (out,)

    out -- a 2-dimensional array containing a subset of the discrete linear
           cross-correlation of in1 with in2.

    """
    val = _valfrommode(mode)
    bval = _bvalfromboundary(boundary)

    return sigtools._convolve2d(in1, in2, 0,val,bval,fillvalue)

def medfilt2d(input, kernel_size=3):
    """Median filter two 2-dimensional arrays.

  Description:

    Apply a median filter to the input array using a local window-size
    given by kernel_size (must be odd).

  Inputs:

    in -- An 2 dimensional input array.
    kernel_size -- A scalar or an length-2 list giving the size of the
                   median filter window in each dimension.  Elements of
                   kernel_size should be odd.  If kernel_size is a scalar,
                   then this scalar is used as the size in each dimension.

  Outputs: (out,)

    out -- An array the same size as input containing the median filtered
           result.
           
    """
    image = asarray(input)
    if kernel_size is None:
        kernel_size = [3] * 2
    kernel_size = asarray(kernel_size)
    if len(kernel_size.shape) == 0:
        kernel_size = [kernel_size.item()] * 2
    kernel_size = asarray(kernel_size)

    for size in kernel_size:
        if (size % 2) != 1:
            raise ValueError, "Each element of kernel_size should be odd."

    return sigtools._medfilt2d(image, kernel_size)

def remez(numtaps, bands, desired, weight=None, Hz=1, type='bandpass',
          maxiter=25, grid_density=16):
    """Calculate the minimax optimal filter using Remez exchange algorithm.

  Description:

    Calculate the filter-coefficients for the finite impulse response
    (FIR) filter whose transfer function minimizes the maximum error
    between the desired gain and the realized gain in the specified bands
    using the remez exchange algorithm.

  Inputs:

    numtaps -- The desired number of taps in the filter.
    bands -- A montonic sequence containing the band edges.  All elements
             must be non-negative and less than 1/2 the sampling frequency
             as given by Hz.
    desired -- A sequency half the size of bands containing the desired gain
               in each of the specified bands
    weight -- A relative weighting to give to each band region.
    type --- The type of filter:
             'bandpass' : flat response in bands.
             'differentiator' : frequency proportional response in bands.

  Outputs: (out,)

    out -- A rank-1 array containing the coefficients of the optimal
           (in a minimax sense) filter.

    """
    # Convert type
    try:
        tnum = {'bandpass':1, 'differentiator':2}[type]
    except KeyError:
        raise ValueError, "Type must be 'bandpass', or 'differentiator'"

    # Convert weight
    if weight is None:
        weight = [1] * len(desired)

    bands = asarray(bands).copy()
    return sigtools._remez(numtaps, bands, desired, weight, tnum, Hz,
                           maxiter, grid_density)

def lfilter(b, a, x, axis=-1, zi=None):
    """Filter data along one-dimension with an IIR or FIR filter.

  Description

    Filter a data sequence, x, using a digital filter.  This works for many
    fundamental data types (including Object type).  The filter is a direct
    form II transposed implementation of the standard difference equation
    (see "Algorithm").

  Inputs:

    b -- The numerator coefficient vector in a 1-D sequence.
    a -- The denominator coefficient vector in a 1-D sequence.  If a[0]
         is not 1, then both a and b are normalized by a[0].
    x -- An N-dimensional input array.
    axis -- The axis of the input data array along which to apply the
            linear filter. The filter is applied to each subarray along
            this axis (*Default* = -1)
    zi -- Initial conditions for the filter delays.  It is a vector
          (or array of vectors for an N-dimensional input) of length
          max(len(a),len(b)).  If zi=None or is not given then initial
          rest is assumed.  SEE signal.lfiltic for more information.

  Outputs: (y, {zf})

    y -- The output of the digital filter.
    zf -- If zi is None, this is not returned, otherwise, zf holds the
          final filter delay values.

  Algorithm:

    The filter function is implemented as a direct II transposed structure.
    This means that the filter implements

    y[n] = b[0]*x[n] + b[1]*x[n-1] + ... + b[nb]*x[n-nb]
                     - a[1]*y[n-1] + ... + a[na]*y[n-na]

    using the following difference equations:

    y[m] = b[0]*x[m] + z[0,m-1]
    z[0,m] = b[1]*x[m] + z[1,m-1] - a[1]*y[m]
    ...
    z[n-3,m] = b[n-2]*x[m] + z[n-2,m-1] - a[n-2]*y[m]
    z[n-2,m] = b[n-1]*x[m] - a[n-1]*y[m]

    where m is the output sample number and n=max(len(a),len(b)) is the
    model order.

    The rational transfer function describing this filter in the
    z-transform domain is
                                -1               -nb
                    b[0] + b[1]z  + ... + b[nb] z
            Y(z) = ---------------------------------- X(z)
                                -1               -na
                    a[0] + a[1]z  + ... + a[na] z

    """
    if isscalar(a):
        a = [a]
    if zi is None:
        return sigtools._linear_filter(b, a, x, axis)
    else:
        return sigtools._linear_filter(b, a, x, axis, zi)

def lfiltic(b,a,y,x=None):
    """Given a linear filter (b,a) and initial conditions on the output y
    and the input x, return the inital conditions on the state vector zi
    which is used by lfilter to generate the output given the input.

    If M=len(b)-1 and N=len(a)-1.  Then, the initial conditions are given
    in the vectors x and y as

    x = {x[-1],x[-2],...,x[-M]}
    y = {y[-1],y[-2],...,y[-N]}

    If x is not given, its inital conditions are assumed zero.
    If either vector is too short, then zeros are added
      to achieve the proper length.

    The output vector zi contains

    zi = {z_0[-1], z_1[-1], ..., z_K-1[-1]}  where K=max(M,N).
    
    """
    N = size(a)-1
    M = size(b)-1
    K = max(M,N)
    y = asarray(y)
    zi = zeros(K,y.dtype.char)
    if x is None:
        x = zeros(M,y.dtype.char)
    else:
        x = asarray(x)
        L = size(x)
        if L < M:
            x = r_[x,zeros(M-L)]
    L = size(y)
    if L < N:
        y = r_[y,zeros(N-L)]

    for m in range(M):
        zi[m] = sum(b[m+1:]*x[:M-m],axis=0)

    for m in range(N):
        zi[m] -= sum(a[m+1:]*y[:N-m],axis=0)

    return zi

def deconvolve(signal, divisor):
    """Deconvolves divisor out of signal.
    
    """
    num = atleast_1d(signal)
    den = atleast_1d(divisor)
    N = len(num)
    D = len(den)
    if D > N:
        quot = [];
        rem = num;
    else:
        input = ones(N-D+1, float)
        input[1:] = 0
        quot = lfilter(num, den, input)
        rem = num - convolve(den, quot, mode='full')
    return quot, rem


def boxcar(M,sym=1):
    """The M-point boxcar window.
    
    """
    return ones(M, float)

def triang(M,sym=1):
    """The M-point triangular window.
    
    """
    if M < 1:
        return array([])
    if M == 1:
        return ones(1,'d')
    odd = M % 2
    if not sym and not odd:
        M = M + 1
    n = arange(1,int((M+1)/2)+1)
    if M % 2 == 0:
        w = (2*n-1.0)/M
        w = r_[w, w[::-1]]
    else:
        w = 2*n/(M+1.0)
        w = r_[w, w[-2::-1]]

    if not sym and not odd:
        w = w[:-1]
    return w

def parzen(M,sym=1):
    """The M-point Parzen window.
    
    """
    if M < 1:
        return array([])
    if M == 1:
        return ones(1,'d')
    odd = M % 2
    if not sym and not odd:
        M = M+1
    n = arange(-(M-1)/2.0,(M-1)/2.0+0.5,1.0)
    na = extract(n < -(M-1)/4.0, n)
    nb = extract(abs(n) <= (M-1)/4.0, n)
    wa = 2*(1-abs(na)/(M/2.0))**3.0
    wb = 1-6*(abs(nb)/(M/2.0))**2.0 + 6*(abs(nb)/(M/2.0))**3.0
    w = r_[wa,wb,wa[::-1]]
    if not sym and not odd:
        w = w[:-1]
    return w

def bohman(M,sym=1):
    """The M-point Bohman window.
    
    """
    if M < 1:
        return array([])
    if M == 1:
        return ones(1,'d')
    odd = M % 2
    if not sym and not odd:
        M = M+1
    fac = abs(linspace(-1,1,M)[1:-1])
    w = (1 - fac)* cos(pi*fac) + 1.0/pi*sin(pi*fac)
    w = r_[0,w,0]
    if not sym and not odd:
        w = w[:-1]
    return w

def blackman(M,sym=1):
    """The M-point Blackman window.
    
    """
    if M < 1:
        return array([])
    if M == 1:
        return ones(1,'d')
    odd = M % 2
    if not sym and not odd:
        M = M+1
    n = arange(0,M)
    w = 0.42-0.5*cos(2.0*pi*n/(M-1)) + 0.08*cos(4.0*pi*n/(M-1))
    if not sym and not odd:
        w = w[:-1]
    return w

def nuttall(M,sym=1):
    """A minimum 4-term Blackman-Harris window according to Nuttall.
    
    """
    if M < 1:
        return array([])
    if M == 1:
        return ones(1,'d')
    odd = M % 2
    if not sym and not odd:
        M = M+1
    a = [0.3635819, 0.4891775, 0.1365995, 0.0106411]
    n = arange(0,M)
    fac = n*2*pi/(M-1.0)
    w = a[0] - a[1]*cos(fac) + a[2]*cos(2*fac) - a[3]*cos(3*fac)
    if not sym and not odd:
        w = w[:-1]
    return w

def blackmanharris(M,sym=1):
    """The M-point minimum 4-term Blackman-Harris window.
    
    """
    if M < 1:
        return array([])
    if M == 1:
        return ones(1,'d')
    odd = M % 2
    if not sym and not odd:
        M = M+1
    a = [0.35875, 0.48829, 0.14128, 0.01168];
    n = arange(0,M)
    fac = n*2*pi/(M-1.0)
    w = a[0] - a[1]*cos(fac) + a[2]*cos(2*fac) - a[3]*cos(3*fac)
    if not sym and not odd:
        w = w[:-1]
    return w

def flattop(M,sym=1):
    """The M-point Flat top window.
    
    """
    if M < 1:
        return array([])
    if M == 1:
        return ones(1,'d')
    odd = M % 2
    if not sym and not odd:
        M = M+1
    a = [0.2156, 0.4160, 0.2781, 0.0836, 0.0069]
    n = arange(0,M)
    fac = n*2*pi/(M-1.0)
    w = a[0] - a[1]*cos(fac) + a[2]*cos(2*fac) - a[3]*cos(3*fac) + a[4]*cos(4*fac)
    if not sym and not odd:
        w = w[:-1]
    return w


def bartlett(M,sym=1):
    """The M-point Bartlett window.
    
    """
    if M < 1:
        return array([])
    if M == 1:
        return ones(1,'d')
    odd = M % 2
    if not sym and not odd:
        M = M+1
    n = arange(0,M)
    w = where(less_equal(n,(M-1)/2.0),2.0*n/(M-1),2.0-2.0*n/(M-1))
    if not sym and not odd:
        w = w[:-1]
    return w

def hanning(M,sym=1):
    """The M-point Hanning window.
    
    """
    if M < 1:
        return array([])
    if M == 1:
        return ones(1,'d')
    odd = M % 2
    if not sym and not odd:
        M = M+1
    n = arange(0,M)
    w = 0.5-0.5*cos(2.0*pi*n/(M-1))
    if not sym and not odd:
        w = w[:-1]
    return w

hann = hanning

def barthann(M,sym=1):
    """Return the M-point modified Bartlett-Hann window.
    
    """
    if M < 1:
        return array([])
    if M == 1:
        return ones(1,'d')
    odd = M % 2
    if not sym and not odd:
        M = M+1
    n = arange(0,M)
    fac = abs(n/(M-1.0)-0.5)
    w = 0.62 - 0.48*fac + 0.38*cos(2*pi*fac)
    if not sym and not odd:
        w = w[:-1]
    return w

def hamming(M,sym=1):
    """The M-point Hamming window.
    
    """
    if M < 1:
        return array([])
    if M == 1:
        return ones(1,'d')
    odd = M % 2
    if not sym and not odd:
        M = M+1
    n = arange(0,M)
    w = 0.54-0.46*cos(2.0*pi*n/(M-1))
    if not sym and not odd:
        w = w[:-1]
    return w

    

def kaiser(M,beta,sym=1):
    """Return a Kaiser window of length M with shape parameter beta.
    
    """
    if M < 1:
        return array([])
    if M == 1:
        return ones(1,'d')
    odd = M % 2
    if not sym and not odd:
        M = M+1
    n = arange(0,M)
    alpha = (M-1)/2.0
    w = special.i0(beta * sqrt(1-((n-alpha)/alpha)**2.0))/special.i0(beta)
    if not sym and not odd:
        w = w[:-1]
    return w

def gaussian(M,std,sym=1):
    """Return a Gaussian window of length M with standard-deviation std.
    
    """
    if M < 1:
        return array([])
    if M == 1:
        return ones(1,'d')
    odd = M % 2
    if not sym and not odd:
        M = M + 1
    n = arange(0,M)-(M-1.0)/2.0
    sig2 = 2*std*std
    w = exp(-n**2 / sig2)
    if not sym and not odd:
        w = w[:-1]
    return w

def general_gaussian(M,p,sig,sym=1):
    """Return a window with a generalized Gaussian shape.

    exp(-0.5*(x/sig)**(2*p))

    half power point is at (2*log(2)))**(1/(2*p))*sig
    
    """
    if M < 1:
        return array([])
    if M == 1:
        return ones(1,'d')
    odd = M % 2
    if not sym and not odd:
        M = M+1
    n = arange(0,M)-(M-1.0)/2.0
    w = exp(-0.5*(n/sig)**(2*p))
    if not sym and not odd:
        w = w[:-1]
    return w


def slepian(M,width,sym=1):
    """Return the M-point slepian window.

    """
    if (M*width > 27.38):
        raise ValueError, "Cannot reliably obtain slepian sequences for"\
              " M*width > 27.38."
    if M < 1:
        return array([])
    if M == 1:
        return ones(1,'d')
    odd = M % 2
    if not sym and not odd:
        M = M+1

    twoF = width/2.0
    alpha = (M-1)/2.0
    m = arange(0,M)-alpha
    n = m[:,newaxis]
    k = m[newaxis,:]
    AF = twoF*special.sinc(twoF*(n-k))
    [lam,vec] = linalg.eig(AF)
    ind = argmax(abs(lam),axis=-1)
    w = abs(vec[:,ind])
    w = w / max(w)

    if not sym and not odd:
        w = w[:-1]
    return w


def hilbert(x, N=None):
    """Return the hilbert transform of x of length N.
    """
    x = asarray(x)
    if N is None:
        N = len(x)
    if N <=0:
        raise ValueError, "N must be positive."
    if iscomplexobj(x):
        print "Warning: imaginary part of x ignored."
        x = real(x)
    Xf = fft(x,N,axis=0)
    h = zeros(N)
    if N % 2 == 0:
        h[0] = h[N/2] = 1
        h[1:N/2] = 2
    else:
        h[0] = 1
        h[1:(N+1)/2] = 2

    if len(x.shape) > 1:
        h = h[:, newaxis]
    x = ifft(Xf*h)
    return x

def hilbert2(x,N=None):
    """Return the '2-D' hilbert transform of x of length N.
    """
    x = asarray(x)
    x = asarray(x)
    if N is None:
        N = x.shape
    if len(N) < 2:
        if N <=0:
            raise ValueError, "N must be positive."
        N = (N,N)
    if iscomplexobj(x):
        print "Warning: imaginary part of x ignored."
        x = real(x)
    print N
    Xf = fft2(x,N,axes=(0,1))
    h1 = zeros(N[0],'d')
    h2 = zeros(N[1],'d')
    for p in range(2):
        h = eval("h%d"%(p+1))
        N1 = N[p]
        if N1 % 2 == 0:
            h[0] = h[N1/2] = 1
            h[1:N1/2] = 2
        else:
            h[0] = 1
            h[1:(N1+1)/2] = 2
        exec("h%d = h" % (p+1), globals(), locals())

    h = h1[:,newaxis] * h2[newaxis,:]
    k = len(x.shape)
    while k > 2:
        h = h[:, newaxis]
        k -= 1
    x = ifft2(Xf*h,axes=(0,1))
    return x


def cmplx_sort(p):
    "sort roots based on magnitude."
    p = asarray(p)
    if iscomplexobj(p):
        indx = argsort(abs(p))
    else:
        indx = argsort(p)
    return take(p,indx,0), indx

def unique_roots(p,tol=1e-3,rtype='min'):
    """Determine the unique roots and their multiplicities in two lists

    Inputs:

      p -- The list of roots
      tol --- The tolerance for two roots to be considered equal.
      rtype --- How to determine the returned root from the close
                  ones:  'max': pick the maximum
                         'min': pick the minimum
                         'avg': average roots
    Outputs: (pout, mult)

      pout -- The list of sorted roots
      mult -- The multiplicity of each root
    """
    if rtype in ['max','maximum']:
        comproot = numpy.maximum
    elif rtype in ['min','minimum']:
        comproot = numpy.minimum
    elif rtype in ['avg','mean']:
        comproot = numpy.mean
    p = asarray(p)*1.0
    tol = abs(tol)
    p, indx = cmplx_sort(p)
    pout = []
    mult = []
    indx = -1
    curp = p[0] + 5*tol
    sameroots = []
    for k in range(len(p)):
        tr = p[k]
        if abs(tr-curp) < tol:
            sameroots.append(tr)
            curp = comproot(sameroots)
            pout[indx] = curp
            mult[indx] += 1
        else:
            pout.append(tr)
            curp = tr
            sameroots = [tr]
            indx += 1
            mult.append(1)
    return array(pout), array(mult)


def invres(r,p,k,tol=1e-3,rtype='avg'):
    """Compute b(s) and a(s) from partial fraction expansion: r,p,k

    If M = len(b) and N = len(a)

            b(s)     b[0] x**(M-1) + b[1] x**(M-2) + ... + b[M-1]
    H(s) = ------ = ----------------------------------------------
            a(s)     a[0] x**(N-1) + a[1] x**(N-2) + ... + a[N-1]

             r[0]       r[1]             r[-1]
         = -------- + -------- + ... + --------- + k(s)
           (s-p[0])   (s-p[1])         (s-p[-1])

    If there are any repeated roots (closer than tol), then the partial
    fraction expansion has terms like

            r[i]      r[i+1]              r[i+n-1]
          -------- + ----------- + ... + -----------
          (s-p[i])  (s-p[i])**2          (s-p[i])**n

    See also:  residue, poly, polyval, unique_roots
    """
    extra = k
    p, indx = cmplx_sort(p)
    r = take(r,indx,0)
    pout, mult = unique_roots(p,tol=tol,rtype=rtype)
    p = []
    for k in range(len(pout)):
        p.extend([pout[k]]*mult[k])
    a = atleast_1d(poly(p))
    if len(extra) > 0:
        b = polymul(extra,a)
    else:
        b = [0]
    indx = 0
    for k in range(len(pout)):
        temp = []
        for l in range(len(pout)):
            if l != k:
                temp.extend([pout[l]]*mult[l])
        for m in range(mult[k]):
            t2 = temp[:]
            t2.extend([pout[k]]*(mult[k]-m-1))
            b = polyadd(b,r[indx]*poly(t2))
            indx += 1
    b = real_if_close(b)
    while allclose(b[0], 0, rtol=1e-14) and (b.shape[-1] > 1):
        b = b[1:]
    return b, a

def residue(b,a,tol=1e-3,rtype='avg'):
    """Compute partial-fraction expansion of b(s) / a(s).

    If M = len(b) and N = len(a)

            b(s)     b[0] s**(M-1) + b[1] s**(M-2) + ... + b[M-1]
    H(s) = ------ = ----------------------------------------------
            a(s)     a[0] s**(N-1) + a[1] s**(N-2) + ... + a[N-1]

             r[0]       r[1]             r[-1]
         = -------- + -------- + ... + --------- + k(s)
           (s-p[0])   (s-p[1])         (s-p[-1])

    If there are any repeated roots (closer than tol), then the partial
    fraction expansion has terms like

            r[i]      r[i+1]              r[i+n-1]
          -------- + ----------- + ... + -----------
          (s-p[i])  (s-p[i])**2          (s-p[i])**n

    See also:  invres, poly, polyval, unique_roots
    """

    b,a = map(asarray,(b,a))
    rscale = a[0]
    if len(b)<len(a):
        k=[]
    else:
        k,b = polydiv(b,a)
#    k,b = polydiv(b,a)
#    Pdb().set_trace()
    p = roots(a)
    r = p*0.0
    pout, mult = unique_roots(p,tol=tol,rtype=rtype)
    p = []
    for n in range(len(pout)):
        p.extend([pout[n]]*mult[n])
    p = asarray(p)
    # Compute the residue from the general formula
    indx = 0
    for n in range(len(pout)):
        bn = b.copy()
        pn = []
        for l in range(len(pout)):
            if l != n:
                pn.extend([pout[l]]*mult[l])
        an = atleast_1d(poly(pn))
        # bn(s) / an(s) is (s-po[n])**Nn * b(s) / a(s) where Nn is
        # multiplicity of pole at po[n]
        sig = mult[n]
        for m in range(sig,0,-1):
            if sig > m:
                # compute next derivative of bn(s) / an(s)
                term1 = polymul(polyder(bn,1),an)
                term2 = polymul(bn,polyder(an,1))
                bn = polysub(term1,term2)
                an = polymul(an,an)
            r[indx+m-1] = polyval(bn,pout[n]) / polyval(an,pout[n]) \
                          / factorial(sig-m)
        indx += sig
    return r/rscale, p, k

def residuez(b,a,tol=1e-3,rtype='avg'):
    """Compute partial-fraction expansion of b(z) / a(z).

    If M = len(b) and N = len(a)

            b(z)     b[0] + b[1] z**(-1) + ... + b[M-1] z**(-M+1)
    H(z) = ------ = ----------------------------------------------
            a(z)     a[0] + a[1] z**(-1) + ... + a[N-1] z**(-N+1)

                 r[0]                   r[-1]
         = --------------- + ... + ---------------- + k[0] + k[1]z**(-1) ...
           (1-p[0]z**(-1))         (1-p[-1]z**(-1))

    If there are any repeated roots (closer than tol), then the partial
    fraction expansion has terms like

               r[i]              r[i+1]                    r[i+n-1]
          -------------- + ------------------ + ... + ------------------
          (1-p[i]z**(-1))  (1-p[i]z**(-1))**2         (1-p[i]z**(-1))**n

    See also:  invresz, poly, polyval, unique_roots
    """
    b,a = map(asarray,(b,a))
    gain = a[0]
    brev, arev = b[::-1],a[::-1]
    krev,brev = polydiv(brev,arev)
    if krev == []:
        k = []
    else:
        k = krev[::-1]
    b = brev[::-1]
    p = roots(a)
    r = p*0.0
    pout, mult = unique_roots(p,tol=tol,rtype=rtype)
    p = []
    for n in range(len(pout)):
        p.extend([pout[n]]*mult[n])
    p = asarray(p)
    # Compute the residue from the general formula (for discrete-time)
    #  the polynomial is in z**(-1) and the multiplication is by terms
    #  like this (1-p[i] z**(-1))**mult[i].  After differentiation,
    #  we must divide by (-p[i])**(m-k) as well as (m-k)!
    indx = 0
    for n in range(len(pout)):
        bn = brev.copy()
        pn = []
        for l in range(len(pout)):
            if l != n:
                pn.extend([pout[l]]*mult[l])
        an = atleast_1d(poly(pn))[::-1]
        # bn(z) / an(z) is (1-po[n] z**(-1))**Nn * b(z) / a(z) where Nn is
        # multiplicity of pole at po[n] and b(z) and a(z) are polynomials.
        sig = mult[n]
        for m in range(sig,0,-1):
            if sig > m:
                # compute next derivative of bn(s) / an(s)
                term1 = polymul(polyder(bn,1),an)
                term2 = polymul(bn,polyder(an,1))
                bn = polysub(term1,term2)
                an = polymul(an,an)
            r[indx+m-1] = polyval(bn,1.0/pout[n]) / polyval(an,1.0/pout[n]) \
                          / factorial(sig-m) / (-pout[n])**(sig-m)
        indx += sig
    return r/gain, p, k

def invresz(r,p,k,tol=1e-3,rtype='avg'):
    """Compute b(z) and a(z) from partial fraction expansion: r,p,k

    If M = len(b) and N = len(a)

            b(z)     b[0] + b[1] z**(-1) + ... + b[M-1] z**(-M+1)
    H(z) = ------ = ----------------------------------------------
            a(z)     a[0] + a[1] z**(-1) + ... + a[N-1] z**(-N+1)

                 r[0]                   r[-1]
         = --------------- + ... + ---------------- + k[0] + k[1]z**(-1) ...
           (1-p[0]z**(-1))         (1-p[-1]z**(-1))

    If there are any repeated roots (closer than tol), then the partial
    fraction expansion has terms like

               r[i]              r[i+1]                    r[i+n-1]
          -------------- + ------------------ + ... + ------------------
          (1-p[i]z**(-1))  (1-p[i]z**(-1))**2         (1-p[i]z**(-1))**n

    See also:  residuez, poly, polyval, unique_roots
    """
    extra = asarray(k)
    p, indx = cmplx_sort(p)
    r = take(r,indx,0)
    pout, mult = unique_roots(p,tol=tol,rtype=rtype)
    p = []
    for k in range(len(pout)):
        p.extend([pout[k]]*mult[k])
    a = atleast_1d(poly(p))
    if len(extra) > 0:
        b = polymul(extra,a)
    else:
        b = [0]
    indx = 0
    brev = asarray(b)[::-1]
    for k in range(len(pout)):
        temp = []
        # Construct polynomial which does not include any of this root
        for l in range(len(pout)):
            if l != k:
                temp.extend([pout[l]]*mult[l])
        for m in range(mult[k]):
            t2 = temp[:]
            t2.extend([pout[k]]*(mult[k]-m-1))
            brev = polyadd(brev,(r[indx]*poly(t2))[::-1])
            indx += 1
    b = real_if_close(brev[::-1])
    return b, a


def get_window(window,Nx,fftbins=1):
    """Return a window of length Nx and type window.

    If fftbins is 1, create a "periodic" window ready to use with ifftshift
    and be multiplied by the result of an fft (SEE ALSO fftfreq).

    Window types:  boxcar, triang, blackman, hamming, hanning, bartlett,
                   parzen, bohman, blackmanharris, nuttall, barthann,
                   kaiser (needs beta), gaussian (needs std),
                   general_gaussian (needs power, width),
                   slepian (needs width)

    If the window requires no parameters, then it can be a string.
    If the window requires parameters, the window argument should be a tuple
        with the first argument the string name of the window, and the next
        arguments the needed parameters.
    If window is a floating point number, it is interpreted as the beta
        parameter of the kaiser window.
    """

    sym = not fftbins
    try:
        beta = float(window)
    except (TypeError, ValueError):
        args = ()
        if isinstance(window, types.TupleType):
            winstr = window[0]
            if len(window) > 1:
                args = window[1:]
        elif isinstance(window, types.StringType):
            if window in ['kaiser', 'ksr', 'gaussian', 'gauss', 'gss',
                        'general gaussian', 'general_gaussian',
                        'general gauss', 'general_gauss', 'ggs']:
                raise ValueError, "That window needs a parameter -- pass a tuple"
            else:
                winstr = window

        if winstr in ['blackman', 'black', 'blk']:
            winfunc = blackman
        elif winstr in ['triangle', 'triang', 'tri']:
            winfunc = triang
        elif winstr in ['hamming', 'hamm', 'ham']:
            winfunc = hamming
        elif winstr in ['bartlett', 'bart', 'brt']:
            winfunc = bartlett
        elif winstr in ['hanning', 'hann', 'han']:
            winfunc = hanning
        elif winstr in ['blackmanharris', 'blackharr','bkh']:
            winfunc = blackmanharris
        elif winstr in ['parzen', 'parz', 'par']:
            winfunc = parzen
        elif winstr in ['bohman', 'bman', 'bmn']:
            winfunc = bohman
        elif winstr in ['nuttall', 'nutl', 'nut']:
            winfunc = nuttall
        elif winstr in ['barthann', 'brthan', 'bth']:
            winfunc = barthann
        elif winstr in ['flattop', 'flat', 'flt']:
            winfunc = flattop
        elif winstr in ['kaiser', 'ksr']:
            winfunc = kaiser
        elif winstr in ['gaussian', 'gauss', 'gss']:
            winfunc = gaussian
        elif winstr in ['general gaussian', 'general_gaussian',
                        'general gauss', 'general_gauss', 'ggs']:
            winfunc = general_gaussian
        elif winstr in ['boxcar', 'box', 'ones']:
            winfunc = boxcar
        elif winstr in ['slepian', 'slep', 'optimal', 'dss']:
            winfunc = slepian
        else:
            raise ValueError, "Unknown window type."

        params = (Nx,)+args + (sym,)
    else:
        winfunc = kaiser
        params = (Nx,beta,sym)

    return winfunc(*params)


def resample(x,num,t=None,axis=0,window=None):
    """Resample to num samples using Fourier method along the given axis.

    The resampled signal starts at the same value of x but is sampled
    with a spacing of len(x) / num * (spacing of x).  Because a Fourier method
    is used, the signal is assumed periodic.

    Window controls a Fourier-domain window that tapers the Fourier spectrum
    before zero-padding to aleviate ringing in the resampled values for
    sampled signals you didn't intend to be interpreted as band-limited.

    If window is a string then use the named window.  If window is a float, then
    it represents a value of beta for a kaiser window.  If window is a tuple,
    then the first component is a string representing the window, and the next
    arguments are parameters for that window.

    Possible windows are:
           'blackman'       ('black',   'blk')
           'hamming'        ('hamm',    'ham')
           'bartlett'       ('bart',    'brt')
           'hanning'        ('hann',    'han')
           'kaiser'         ('ksr')             # requires parameter (beta)
           'gaussian'       ('gauss',   'gss')  # requires parameter (std.)
           'general gauss'  ('general', 'ggs')  # requires two parameters
                                                      (power, width)

    The first sample of the returned vector is the same as the first sample of the
        input vector, the spacing between samples is changed from dx to
        dx * len(x) / num

    If t is not None, then it represents the old sample positions, and the new
       sample positions will be returned as well as the new samples.
    """
    x = asarray(x)
    X = fft(x,axis=axis)
    Nx = x.shape[axis]
    if window is not None:
        W = ifftshift(get_window(window,Nx))
        newshape = ones(len(x.shape))
        newshape[axis] = len(W)
        W=W.reshape(newshape)
        X = X*W
    sl = [slice(None)]*len(x.shape)
    newshape = list(x.shape)
    newshape[axis] = num
    N = int(numpy.minimum(num,Nx))
    Y = zeros(newshape,'D')
    sl[axis] = slice(0,(N+1)/2)
    Y[sl] = X[sl]
    sl[axis] = slice(-(N-1)/2,None)
    Y[sl] = X[sl]
    y = ifft(Y,axis=axis)*(float(num)/float(Nx))

    if x.dtype.char not in ['F','D']:
        y = y.real

    if t is None:
        return y
    else:
        new_t = arange(0,num)*(t[1]-t[0])* Nx / float(num) + t[0]
        return y, new_t

def detrend(data, axis=-1, type='linear', bp=0):
    """Remove linear trend along axis from data.

    If type is 'constant' then remove mean only.

    If bp is given, then it is a sequence of points at which to
       break a piecewise-linear fit to the data.
       
    """
    if type not in ['linear','l','constant','c']:
        raise ValueError, "Trend type must be linear or constant"
    data = asarray(data)
    dtype = data.dtype.char
    if dtype not in 'dfDF':
        dtype = 'd'
    if type in ['constant','c']:
        ret = data - expand_dims(mean(data,axis),axis)
        return ret
    else:
        dshape = data.shape
        N = dshape[axis]
        bp = sort(unique(r_[0,bp,N]))
        if any(bp > N):
            raise ValueError, "Breakpoints must be less than length of data along given axis."
        Nreg = len(bp) - 1
        # Restructure data so that axis is along first dimension and
        #  all other dimensions are collapsed into second dimension
        rnk = len(dshape)
        if axis < 0: axis = axis + rnk
        newdims = r_[axis,0:axis,axis+1:rnk]
        newdata = reshape(transpose(data,tuple(newdims)),(N,prod(dshape,axis=0)/N))
        newdata = newdata.copy()  # make sure we have a copy
        if newdata.dtype.char not in 'dfDF':
            newdata = newdata.astype(dtype)
        # Find leastsq fit and remove it for each piece
        for m in range(Nreg):
            Npts = bp[m+1] - bp[m]
            A = ones((Npts,2),dtype)
            A[:,0] = cast[dtype](arange(1,Npts+1)*1.0/Npts)
            sl = slice(bp[m],bp[m+1])
            coef,resids,rank,s = linalg.lstsq(A,newdata[sl])
            newdata[sl] = newdata[sl] - dot(A,coef)
        # Put data back in original shape.
        tdshape = take(dshape,newdims,0)
        ret = reshape(newdata,tuple(tdshape))
        vals = range(1,rnk)
        olddims = vals[:axis] + [0] + vals[axis:]
        ret = transpose(ret,tuple(olddims))
        return ret

From tgrav at mac.com  Wed Feb 14 21:16:50 2007
From: tgrav at mac.com (Tommy Grav)
Date: Wed, 14 Feb 2007 21:16:50 -0500
Subject: [SciPy-user] lsq problem
Message-ID: <86E3078D-C9B7-4516-B573-9C731D6FC45E@mac.com>

I need to fit a gaussian profile to a set of points and would like to  
use scipy (or numpy) to
do the least square fitting if possible. I am however unsure if the  
proper routines are
available, so I thought I would ask to get some hints to get going in  
the right direction.

The input are two 1-dimensional arrays x and flux, together with a  
function

def Gaussian(a,b,c,x1):
	return a*exp(-(pow(x1,2)/pow(c,2))) - c

I would like to find the values of (a,b,c), such that the difference  
between the gaussian
and fluxes are minimalized. Would scipy.linalg.lstsq be the right  
function to use, or is this
problem not linear? (I know I could find out this particular problem  
with a little research, but
I am under a little time pressure and I can not for the life of me  
remember my old math
classes). If the problem is not linear, is there another function  
that can be used or do I have
to code up my own lstsq function to solve the problem?

Thanks in advance for any hints to the answers.

Cheers
   Tommy


From amcmorl at gmail.com  Wed Feb 14 23:01:08 2007
From: amcmorl at gmail.com (Angus McMorland)
Date: Thu, 15 Feb 2007 17:01:08 +1300
Subject: [SciPy-user] lsq problem
In-Reply-To: <86E3078D-C9B7-4516-B573-9C731D6FC45E@mac.com>
References: <86E3078D-C9B7-4516-B573-9C731D6FC45E@mac.com>
Message-ID: <e85f13c40702142001u614ca7a6yd29cbee913fa0683@mail.gmail.com>

Hi Tommy,

On 15/02/07, Tommy Grav <tgrav at mac.com> wrote:
> I need to fit a gaussian profile to a set of points and would like to
> use scipy (or numpy) to
> do the least square fitting if possible. I am however unsure if the
> proper routines are
> available, so I thought I would ask to get some hints to get going in
> the right direction.
>
> The input are two 1-dimensional arrays x and flux, together with a
> function
>
> def Gaussian(a,b,c,x1):
>         return a*exp(-(pow(x1,2)/pow(c,2))) - c
>
> I would like to find the values of (a,b,c), such that the difference
> between the gaussian
> and fluxes are minimalized. Would scipy.linalg.lstsq be the right
> function to use, or is this
> problem not linear? (I know I could find out this particular problem
> with a little research, but
> I am under a little time pressure and I can not for the life of me
> remember my old math
> classes). If the problem is not linear, is there another function
> that can be used or do I have
> to code up my own lstsq function to solve the problem?
>
> Thanks in advance for any hints to the answers.

Using scipy.optimize.leastsq, this problem is pretty easy to solve.
Check the docstring for that function. Basically, you need to
construct an error function: I use the one below, but hopefully you
can see how to adapt this to your needs:

def erf(p, I, r):
    (A, k, c) = p
    return I - A * exp( -(r - c)**2 / k**2 )

then in your code:

p0 = (1,1,1) # starting guesses (anything vaguely close seems to be okay)
plsq = scipy.optimize.leastsq(erf, p0, args=(flux, x)
A = plsq[0][0]
k = plsq[0][1]
c = plsq[0][2]

I hope that helps,

A.
-- 
AJC McMorland, PhD Student
Physiology, University of Auckland


From gael.varoquaux at normalesup.org  Thu Feb 15 01:54:59 2007
From: gael.varoquaux at normalesup.org (Gael Varoquaux)
Date: Thu, 15 Feb 2007 07:54:59 +0100
Subject: [SciPy-user] lsq problem
In-Reply-To: <86E3078D-C9B7-4516-B573-9C731D6FC45E@mac.com>
References: <86E3078D-C9B7-4516-B573-9C731D6FC45E@mac.com>
Message-ID: <20070215065459.GA17713@clipper.ens.fr>

Hi Tommy,

Maybe the cookook example at http://scipy.org/Cookbook/FittingData can
help you.

Ga?l

On Wed, Feb 14, 2007 at 09:16:50PM -0500, Tommy Grav wrote:
> I need to fit a gaussian profile to a set of points and would like to  
> use scipy (or numpy) to
> do the least square fitting if possible. I am however unsure if the  
> proper routines are
> available, so I thought I would ask to get some hints to get going in  
> the right direction.

> The input are two 1-dimensional arrays x and flux, together with a  
> function

> def Gaussian(a,b,c,x1):
> 	return a*exp(-(pow(x1,2)/pow(c,2))) - c

> I would like to find the values of (a,b,c), such that the difference  
> between the gaussian
> and fluxes are minimalized. Would scipy.linalg.lstsq be the right  
> function to use, or is this
> problem not linear? (I know I could find out this particular problem  
> with a little research, but
> I am under a little time pressure and I can not for the life of me  
> remember my old math
> classes). If the problem is not linear, is there another function  
> that can be used or do I have
> to code up my own lstsq function to solve the problem?

> Thanks in advance for any hints to the answers.

> Cheers
>    Tommy
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user

-- 
  Gael Varoquaux,
  Groupe d'optique atomique,
  Laboratoire Charles Fabry de l'Institut d'Optique
  Campus Polytechnique, RD 128
  91127 Palaiseau cedex FRANCE
  !!!! NEW Phone number !!!!
  Tel : 33 (0) 1 64 53 33 49 - Fax : 33 (0) 1 64 53 31 01
  Labs: 33 (0) 1 64 53 33 63 - 33 (0) 1 64 53 33 62


From niklassaers at gmail.com  Fri Feb 16 05:15:35 2007
From: niklassaers at gmail.com (Niklas Saers)
Date: Fri, 16 Feb 2007 11:15:35 +0100
Subject: [SciPy-user] Scipy on Python 2.5 / OS X 10.4.8
Message-ID: <D96375DC-3140-4B1A-8108-3BD0A52937BD@gmail.com>

Hi guys,
has anyone successfully compiled Scipy for Python 2.5 under Mac OS X  
10.4.8? I notice that the binaries on the webpage only support up to  
Python 2.4 so I would like to build them. However, running "python  
setup.py build" I get:

g95 -L/sw/lib build/temp.macosx-10.3-fat-2.5/build/src.macosx-10.3- 
fat-2.5/Lib/fftpack/_fftpackmodule.o build/temp.macosx-10.3-fat-2.5/ 
Lib/fftpack/src/zfft.o build/temp.macosx-10.3-fat-2.5/Lib/fftpack/src/ 
drfft.o build/temp.macosx-10.3-fat-2.5/Lib/fftpack/src/zrfft.o build/ 
temp.macosx-10.3-fat-2.5/Lib/fftpack/src/zfftnd.o build/ 
temp.macosx-10.3-fat-2.5/build/src.macosx-10.3-fat-2.5/ 
fortranobject.o -Lbuild/temp.macosx-10.3-fat-2.5 -ldfftpack -o build/ 
lib.macosx-10.3-fat-2.5/scipy/fftpack/_fftpack.so
/sw/lib/odcctools590/bin/ld: Undefined symbols:
_PyArg_ParseTupleAndKeywords
_PyCObject_AsVoidPtr
_PyCObject_Type
_PyComplex_Type
_PyDict_SetItemString
_PyErr_Clear
_PyErr_Format
_PyErr_NewException
_PyErr_Occurred
_PyErr_Print
_PyErr_SetString
_PyExc_ImportError
_PyExc_RuntimeError
_PyImport_ImportModule
_PyInt_Type
_PyModule_GetDict
_PyNumber_Int
_PyObject_GetAttrString
_PySequence_Check
_PySequence_GetItem
_PyString_FromString
_PyString_Type
_PyType_IsSubtype
_PyType_Type
_Py_BuildValue
_Py_InitModule4
__Py_NoneStruct
_PyCObject_FromVoidPtr
_PyDict_DelItemString
_PyDict_GetItemString
_PyDict_New
_PyExc_AttributeError
_PyExc_TypeError
_PyExc_ValueError
_PyMem_Free
_PyObject_Str
_PyObject_Type
_PyString_AsString
_PyString_ConcatAndDel
_Py_FindMethod
__PyObject_New
_MAIN_
/sw/lib/odcctools590/bin/ld: Undefined symbols:
_PyArg_ParseTupleAndKeywords
_PyCObject_AsVoidPtr
_PyCObject_Type
_PyComplex_Type
_PyDict_SetItemString
_PyErr_Clear
_PyErr_Format
_PyErr_NewException
_PyErr_Occurred
_PyErr_Print
_PyErr_SetString
_PyExc_ImportError
_PyExc_RuntimeError
_PyImport_ImportModule
_PyInt_Type
_PyModule_GetDict
_PyNumber_Int
_PyObject_GetAttrString
_PySequence_Check
_PySequence_GetItem
_PyString_FromString
_PyString_Type
_PyType_IsSubtype
_PyType_Type
_Py_BuildValue
_Py_InitModule4
__Py_NoneStruct
_PyCObject_FromVoidPtr
_PyDict_DelItemString
_PyDict_GetItemString
_PyDict_New
_PyExc_AttributeError
_PyExc_TypeError
_PyExc_ValueError
_PyMem_Free
_PyObject_Str
_PyObject_Type
_PyString_AsString
_PyString_ConcatAndDel
_Py_FindMethod
__PyObject_New
_MAIN_
error: Command "g95 -L/sw/lib build/temp.macosx-10.3-fat-2.5/build/ 
src.macosx-10.3-fat-2.5/Lib/fftpack/_fftpackmodule.o build/ 
temp.macosx-10.3-fat-2.5/Lib/fftpack/src/zfft.o build/ 
temp.macosx-10.3-fat-2.5/Lib/fftpack/src/drfft.o build/ 
temp.macosx-10.3-fat-2.5/Lib/fftpack/src/zrfft.o build/ 
temp.macosx-10.3-fat-2.5/Lib/fftpack/src/zfftnd.o build/ 
temp.macosx-10.3-fat-2.5/build/src.macosx-10.3-fat-2.5/ 
fortranobject.o -Lbuild/temp.macosx-10.3-fat-2.5 -ldfftpack -o build/ 
lib.macosx-10.3-fat-2.5/scipy/fftpack/_fftpack.so" failed with exit  
status 1

I have no idea of why it sais 10.3 rather than 10.4, but perhaps this  
is not the OS version? I use FFTW 2.1.5 after the website recommended  
the 2.1 branch for performance over 3.0 and I'm going to be using  
FFTs a lot

Could anyone help me out? :-)

Cheers


	Nik


From sgarcia at olfac.univ-lyon1.fr  Fri Feb 16 06:21:42 2007
From: sgarcia at olfac.univ-lyon1.fr (Samuel GARCIA)
Date: Fri, 16 Feb 2007 12:21:42 +0100
Subject: [SciPy-user] str(numpy.inf)
In-Reply-To: <45D34881.3070601@gmail.com>
References: <45D3426B.1050600@olfac.univ-lyon1.fr> <45D34881.3070601@gmail.com>
Message-ID: <45D593C6.3060400@olfac.univ-lyon1.fr>

Because of that I also have problem with pickle when I want to store a
float which is not finite.

Am I the first with this problem under win32 ?

Sam


Robert Kern wrote:
> Samuel GARCIA wrote:
>   
>> Hi list,
>>
>> I have this problem
>> str(numpy.inf) under linux give 'inf'
>> str(numpy.inf) under win32 give '1.#INF'
>>
>> It is a problem for me because with a GUI in LineEdit, for example, the
>> end user who have to enter a float can enter inf under linux but not
>> under win32.
>>
>> Any idea to solve this ?
>>     
>
> No. We (and Python) defer to the C library for such things, and they each use
> different representations.
>
>   

-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Samuel Garcia
Universite Claude Bernard LYON 1
CNRS - UMR5020, Laboratoire des Neurosciences et Systemes Sensoriels
50, avenue Tony Garnier
69366 LYON Cedex 07
FRANCE
T?l : 04 37 28 74 64
Fax : 04 37 28 76 01
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20070216/ba82e13f/attachment.html>

From gary.pajer at gmail.com  Sat Feb 17 09:46:42 2007
From: gary.pajer at gmail.com (Gary Pajer)
Date: Sat, 17 Feb 2007 09:46:42 -0500
Subject: [SciPy-user] bose-einstein distribution ?
Message-ID: <88fe22a0702170646n57ec4e04p57c89fe835b4e4fb@mail.gmail.com>

Does the Bose-Einstein distribution exist in scipy.stats?
(Perhaps as a name I don't recognize, or a special case of another
distribution?)

-gary


From meesters at uni-mainz.de  Sat Feb 17 19:28:26 2007
From: meesters at uni-mainz.de (Meesters, Christian)
Date: Sun, 18 Feb 2007 01:28:26 +0100
Subject: [SciPy-user] savitzky golay filtering
Message-ID: <A8A156D3954D6F459AB085E7828365ED7DE388@EXCHANGE01.zdv.Uni-Mainz.DE>

Hi

I wanted to do a Savitzky Golay filtering on my data and came aross this piece of code:
http://www.dalkescientific.com/writings/NBN/data/savitzky_golay.py
Well, translating the necessary bits into current numpy/scipy code is driving me crazy. Can somebody give me a hint on the "M = ..."-line, please?
(Or is there a better way to do this filtering with scipy?)

TIA
Christian


From ckkart at hoc.net  Sat Feb 17 20:12:59 2007
From: ckkart at hoc.net (Christian Kristukat)
Date: Sun, 18 Feb 2007 10:12:59 +0900
Subject: [SciPy-user] savitzky golay filtering
In-Reply-To: <A8A156D3954D6F459AB085E7828365ED7DE388@EXCHANGE01.zdv.Uni-Mainz.DE>
References: <A8A156D3954D6F459AB085E7828365ED7DE388@EXCHANGE01.zdv.Uni-Mainz.DE>
Message-ID: <45D7A81B.9010006@hoc.net>


Hi,

Meesters, Christian wrote:
> Hi
> 
> I wanted to do a Savitzky Golay filtering on my data and came aross this piece of code:
> http://www.dalkescientific.com/writings/NBN/data/savitzky_golay.py
> Well, translating the necessary bits into current numpy/scipy code is driving me crazy. Can somebody give me a hint on the "M = ..."-line, please?

import numpy as N
..
..
M = N.dot(N.linalg.inv(N.dot(B.transpose(),B)),B.transpose())

> (Or is there a better way to do this filtering with scipy?)

I don't know.

Christian


From oliphant at ee.byu.edu  Sat Feb 17 20:47:38 2007
From: oliphant at ee.byu.edu (Travis Oliphant)
Date: Sat, 17 Feb 2007 18:47:38 -0700
Subject: [SciPy-user] savitzky golay filtering
In-Reply-To: <45D7A81B.9010006@hoc.net>
References: <A8A156D3954D6F459AB085E7828365ED7DE388@EXCHANGE01.zdv.Uni-Mainz.DE>
	<45D7A81B.9010006@hoc.net>
Message-ID: <45D7B03A.5030603@ee.byu.edu>

Christian Kristukat wrote:
> Hi,
>
> Meesters, Christian wrote:
>   
>> Hi
>>
>> I wanted to do a Savitzky Golay filtering on my data and came aross this piece of code:
>> http://www.dalkescientific.com/writings/NBN/data/savitzky_golay.py
>> Well, translating the necessary bits into current numpy/scipy code is driving me crazy. Can somebody give me a hint on the "M = ..."-line, please?
>>     

You can always import from numpy.oldnumeric
and numpy.oldnumeric.linear_algebra

Or,

import numpy as N

B = N.mat(B)
M = (B.T*B).I * B.T
return M.A  # if you want an array returned.


But, probably what you really want is to replace the whole line with

M = N.linalg.pinv(B)



-Travis



From nwagner at iam.uni-stuttgart.de  Sun Feb 18 05:39:45 2007
From: nwagner at iam.uni-stuttgart.de (Nils Wagner)
Date: Sun, 18 Feb 2007 11:39:45 +0100
Subject: [SciPy-user] numpy/scipy on an Intel(R) Core(TM)2 CPU
Message-ID: <web-79149236@uni-stuttgart.de>

Hi all,

I am going to install numpy/scipy (svn version)
on an Intel(R) Core(TM)2 CPU. And I would like to build 
everything from scratch
(including BLAS/LAPACK/ATLAS).

Which compiler options/flags should I use for BLAS/LAPACK 
in that case ?

Which fortran compiler g77/gfortran is
currently recommended to build numpy/scipy ?

BTW, I am using openSUSE 10.2.

Nils



  


From david at ar.media.kyoto-u.ac.jp  Sun Feb 18 05:44:36 2007
From: david at ar.media.kyoto-u.ac.jp (David Cournapeau)
Date: Sun, 18 Feb 2007 19:44:36 +0900
Subject: [SciPy-user] numpy/scipy on an Intel(R) Core(TM)2 CPU
In-Reply-To: <web-79149236@uni-stuttgart.de>
References: <web-79149236@uni-stuttgart.de>
Message-ID: <45D82E14.6050903@ar.media.kyoto-u.ac.jp>

Nils Wagner wrote:
> Hi all,
>
> I am going to install numpy/scipy (svn version)
> on an Intel(R) Core(TM)2 CPU. And I would like to build 
> everything from scratch
> (including BLAS/LAPACK/ATLAS).
>
> Which compiler options/flags should I use for BLAS/LAPACK 
> in that case ?
>
> Which fortran compiler g77/gfortran is
> currently recommended to build numpy/scipy ?
>
> BTW, I am using openSUSE 10.2.
>
> Nils
>   
For Atlas, you should use the flags set by the ATLAS build system. If 
you use recent ATLAS sources (3.7.* serie), there are some arch default 
for your CPU, I think.

cheers,

David


From nwagner at iam.uni-stuttgart.de  Sun Feb 18 09:37:09 2007
From: nwagner at iam.uni-stuttgart.de (Nils Wagner)
Date: Sun, 18 Feb 2007 15:37:09 +0100
Subject: [SciPy-user] numpy/scipy on an Intel(R) Core(TM)2 CPU and CPU
 THROTTLING
In-Reply-To: <45D82E14.6050903@ar.media.kyoto-u.ac.jp>
References: <web-79149236@uni-stuttgart.de>
	<45D82E14.6050903@ar.media.kyoto-u.ac.jp>
Message-ID: <45D86495.2070905@iam.uni-stuttgart.de>

David Cournapeau wrote:
> Nils Wagner wrote:
>   
>> Hi all,
>>
>> I am going to install numpy/scipy (svn version)
>> on an Intel(R) Core(TM)2 CPU. And I would like to build 
>> everything from scratch
>> (including BLAS/LAPACK/ATLAS).
>>
>> Which compiler options/flags should I use for BLAS/LAPACK 
>> in that case ?
>>
>> Which fortran compiler g77/gfortran is
>> currently recommended to build numpy/scipy ?
>>
>> BTW, I am using openSUSE 10.2.
>>
>> Nils
>>   
>>     
> For Atlas, you should use the flags set by the ATLAS build system. If 
> you use recent ATLAS sources (3.7.* serie), there are some arch default 
> for your CPU, I think.
>
> cheers,
>
> David
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user
>   
 Hi again,

I am confused about CPU THROTTLING.

How can I switch off CPU throttling on SuSE Linux 10.2 ?

I found a command "cpufreq-set" but I don't know how to proceed.

ATLAS uses gfortran by default but I have used g77 to build BLAS/LAPACK.

Can I replace gfortran in Make.inc by g77 ?

I have used

/usr/local/src/ATLAS/configure -Fa alg -fPIC -Si cputhrchk 0

to configure ATLAS (3.7.28)

Nils


http://www.kernel.org/pub/linux/utils/kernel/cpufreq/cpufreq-set.html



From nvf at uwm.edu  Sun Feb 18 13:53:12 2007
From: nvf at uwm.edu (Nick Fotopoulos)
Date: Sun, 18 Feb 2007 12:53:12 -0600
Subject: [SciPy-user] Scipy on Python 2.5 / OS X 10.4.8
Message-ID: <f687be130702181053g60d95f08u47697e7a40f20c71@mail.gmail.com>

On 2/16/07, scipy-user-request at scipy.org <scipy-user-request at scipy.org> wrote:

> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 16 Feb 2007 11:15:35 +0100
> From: Niklas Saers <niklassaers at gmail.com>
> Subject: [SciPy-user] Scipy on Python 2.5 / OS X 10.4.8
> To: SciPy Users List <scipy-user at scipy.org>
> Message-ID: <D96375DC-3140-4B1A-8108-3BD0A52937BD at gmail.com>
> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
>
> Hi guys,
> has anyone successfully compiled Scipy for Python 2.5 under Mac OS X
> 10.4.8? I notice that the binaries on the webpage only support up to
> Python 2.4 so I would like to build them. However, running "python
> setup.py build" I get:
>
> g95 -L/sw/lib build/temp.macosx-10.3-fat-2.5/build/src.macosx-10.3-
> fat-2.5/Lib/fftpack/_fftpackmodule.o build/temp.macosx-10.3-fat-2.5/
> Lib/fftpack/src/zfft.o build/temp.macosx-10.3-fat-2.5/Lib/fftpack/src/
> drfft.o build/temp.macosx-10.3-fat-2.5/Lib/fftpack/src/zrfft.o build/
> temp.macosx-10.3-fat-2.5/Lib/fftpack/src/zfftnd.o build/
> temp.macosx-10.3-fat-2.5/build/src.macosx-10.3-fat-2.5/
> fortranobject.o -Lbuild/temp.macosx-10.3-fat-2.5 -ldfftpack -o build/
> lib.macosx-10.3-fat-2.5/scipy/fftpack/_fftpack.so
> /sw/lib/odcctools590/bin/ld: Undefined symbols:
> _PyArg_ParseTupleAndKeywords
> _PyCObject_AsVoidPtr
> _PyCObject_Type
> _PyComplex_Type
> _PyDict_SetItemString
> _PyErr_Clear
> _PyErr_Format
> _PyErr_NewException
> _PyErr_Occurred
> _PyErr_Print
> _PyErr_SetString
> _PyExc_ImportError
> _PyExc_RuntimeError
> _PyImport_ImportModule
> _PyInt_Type
> _PyModule_GetDict
> _PyNumber_Int
> _PyObject_GetAttrString
> _PySequence_Check
> _PySequence_GetItem
> _PyString_FromString
> _PyString_Type
> _PyType_IsSubtype
> _PyType_Type
> _Py_BuildValue
> _Py_InitModule4
> __Py_NoneStruct
> _PyCObject_FromVoidPtr
> _PyDict_DelItemString
> _PyDict_GetItemString
> _PyDict_New
> _PyExc_AttributeError
> _PyExc_TypeError
> _PyExc_ValueError
> _PyMem_Free
> _PyObject_Str
> _PyObject_Type
> _PyString_AsString
> _PyString_ConcatAndDel
> _Py_FindMethod
> __PyObject_New
> _MAIN_
> /sw/lib/odcctools590/bin/ld: Undefined symbols:
> _PyArg_ParseTupleAndKeywords
> _PyCObject_AsVoidPtr
> _PyCObject_Type
> _PyComplex_Type
> _PyDict_SetItemString
> _PyErr_Clear
> _PyErr_Format
> _PyErr_NewException
> _PyErr_Occurred
> _PyErr_Print
> _PyErr_SetString
> _PyExc_ImportError
> _PyExc_RuntimeError
> _PyImport_ImportModule
> _PyInt_Type
> _PyModule_GetDict
> _PyNumber_Int
> _PyObject_GetAttrString
> _PySequence_Check
> _PySequence_GetItem
> _PyString_FromString
> _PyString_Type
> _PyType_IsSubtype
> _PyType_Type
> _Py_BuildValue
> _Py_InitModule4
> __Py_NoneStruct
> _PyCObject_FromVoidPtr
> _PyDict_DelItemString
> _PyDict_GetItemString
> _PyDict_New
> _PyExc_AttributeError
> _PyExc_TypeError
> _PyExc_ValueError
> _PyMem_Free
> _PyObject_Str
> _PyObject_Type
> _PyString_AsString
> _PyString_ConcatAndDel
> _Py_FindMethod
> __PyObject_New
> _MAIN_
> error: Command "g95 -L/sw/lib build/temp.macosx-10.3-fat-2.5/build/
> src.macosx-10.3-fat-2.5/Lib/fftpack/_fftpackmodule.o build/
> temp.macosx-10.3-fat-2.5/Lib/fftpack/src/zfft.o build/
> temp.macosx-10.3-fat-2.5/Lib/fftpack/src/drfft.o build/
> temp.macosx-10.3-fat-2.5/Lib/fftpack/src/zrfft.o build/
> temp.macosx-10.3-fat-2.5/Lib/fftpack/src/zfftnd.o build/
> temp.macosx-10.3-fat-2.5/build/src.macosx-10.3-fat-2.5/
> fortranobject.o -Lbuild/temp.macosx-10.3-fat-2.5 -ldfftpack -o build/
> lib.macosx-10.3-fat-2.5/scipy/fftpack/_fftpack.so" failed with exit
> status 1
>
> I have no idea of why it sais 10.3 rather than 10.4, but perhaps this
> is not the OS version? I use FFTW 2.1.5 after the website recommended
> the 2.1 branch for performance over 3.0 and I'm going to be using
> FFTs a lot
>
> Could anyone help me out? :-)

I just wanted to chime in that I have had the same problem on a PPC
Mac and on an Intel Mac.  My workaround with the iBook (PPC) was to
compile Python 2.5 from source.  I'll probably do the same on my MBP
(Intel), but that's rather inconvenient.  It'd make me quite happy if
someone could help Nik and I.

As an aside, on my MBP, I am testing (for work) the Python 2.3 that
shipped with OSX 10.4.  Despite the numerous warnings I've found
online not to use it, I have found that numpy, scipy, and matplotlib
work just fine with 2.3, but I will have to do The Readline Fix in
order to make interactive sessions at the command-line usable.

Thanks,
Nick


From cygnusx1 at mac.com  Sun Feb 18 17:22:08 2007
From: cygnusx1 at mac.com (Tom Bridgman)
Date: Sun, 18 Feb 2007 17:22:08 -0500
Subject: [SciPy-user] More elegant solution for binning lookup?
Message-ID: <BF8F070E-2B4D-4A6C-98A3-0DE18AD3CFFB@mac.com>

I've browsed the numpy and scipy lists and available docs and haven't  
found an answer to this.

SciPy v0.5.1, numpy v1.0rc3.

I've got an array of samples through a region and a value 'R' where I  
want to find the proper bin in 'radius'.  'R' will generally not  
match any value in 'radius'.

Here's the cleanest solution I found:

 >>> import scipy
 >>> import numpy
 >>> radius = scipy.arange(0.0, 1.5, 1.5/1000)
 >>> r=0.7274
 >>> bin = numpy.nonzero(numpy.where(radius > r, 0, 1))[0][-1]
 >>> bin
484
 >>> radius[484:486]
array([ 0.726 ,  0.7275])

But even this looks rather ugly and not very intuitive as to what I'm  
doing.  Is there a function built-in to scipy or numpy for this?

Thanks,
Tom
--
W.T. Bridgman, Ph.D.
Physics & Astronomy



From robert.kern at gmail.com  Sun Feb 18 18:09:15 2007
From: robert.kern at gmail.com (Robert Kern)
Date: Sun, 18 Feb 2007 17:09:15 -0600
Subject: [SciPy-user] Scipy on Python 2.5 / OS X 10.4.8
In-Reply-To: <D96375DC-3140-4B1A-8108-3BD0A52937BD@gmail.com>
References: <D96375DC-3140-4B1A-8108-3BD0A52937BD@gmail.com>
Message-ID: <45D8DC9B.9070005@gmail.com>

Niklas Saers wrote:
> Hi guys,
> has anyone successfully compiled Scipy for Python 2.5 under Mac OS X  
> 10.4.8? I notice that the binaries on the webpage only support up to  
> Python 2.4 so I would like to build them. However, running "python  
> setup.py build" I get:
> 
> g95 -L/sw/lib build/temp.macosx-10.3-fat-2.5/build/src.macosx-10.3- 
> fat-2.5/Lib/fftpack/_fftpackmodule.o build/temp.macosx-10.3-fat-2.5/ 
> Lib/fftpack/src/zfft.o build/temp.macosx-10.3-fat-2.5/Lib/fftpack/src/ 
> drfft.o build/temp.macosx-10.3-fat-2.5/Lib/fftpack/src/zrfft.o build/ 
> temp.macosx-10.3-fat-2.5/Lib/fftpack/src/zfftnd.o build/ 
> temp.macosx-10.3-fat-2.5/build/src.macosx-10.3-fat-2.5/ 
> fortranobject.o -Lbuild/temp.macosx-10.3-fat-2.5 -ldfftpack -o build/ 
> lib.macosx-10.3-fat-2.5/scipy/fftpack/_fftpack.so
> /sw/lib/odcctools590/bin/ld: Undefined symbols:

It looks like you have the LDFLAGS environment variable defined. That
*overrides* all of the link flags, including the ones that distutils provides to
link against the Python libraries. Don't use LDFLAGS.

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
 that is made terrible by our own mad attempt to interpret it as though it had
 an underlying truth."
  -- Umberto Eco


From stefan at sun.ac.za  Sun Feb 18 18:21:13 2007
From: stefan at sun.ac.za (Stefan van der Walt)
Date: Mon, 19 Feb 2007 01:21:13 +0200
Subject: [SciPy-user] More elegant solution for binning lookup?
In-Reply-To: <BF8F070E-2B4D-4A6C-98A3-0DE18AD3CFFB@mac.com>
References: <BF8F070E-2B4D-4A6C-98A3-0DE18AD3CFFB@mac.com>
Message-ID: <20070218232113.GG8850@mentat.za.net>

Hi Tom

On Sun, Feb 18, 2007 at 05:22:08PM -0500, Tom Bridgman wrote:
> I've got an array of samples through a region and a value 'R' where I  
> want to find the proper bin in 'radius'.  'R' will generally not  
> match any value in 'radius'.

Would digitize do the job?

    digitize(x,bins)
    
    Return the index of the bin to which each value of x belongs.
    
    Each index i returned is such that bins[i-1] <= x < bins[i] if
    bins is monotonically increasing, or bins [i-1] > x >= bins[i] if
    bins is monotonically decreasing.
    
    Beyond the bounds of the bins 0 or len(bins) is returned as appropriate.

Cheers
St?fan


From david at ar.media.kyoto-u.ac.jp  Sun Feb 18 22:35:11 2007
From: david at ar.media.kyoto-u.ac.jp (David Cournapeau)
Date: Mon, 19 Feb 2007 12:35:11 +0900
Subject: [SciPy-user] numpy/scipy on an Intel(R) Core(TM)2 CPU and CPU
 THROTTLING
In-Reply-To: <45D86495.2070905@iam.uni-stuttgart.de>
References: <web-79149236@uni-stuttgart.de>	<45D82E14.6050903@ar.media.kyoto-u.ac.jp>
	<45D86495.2070905@iam.uni-stuttgart.de>
Message-ID: <45D91AEF.8030809@ar.media.kyoto-u.ac.jp>

Nils Wagner wrote:
> David Cournapeau wrote:
>> Nils Wagner wrote:
>>   
>>> Hi all,
>>>
>>> I am going to install numpy/scipy (svn version)
>>> on an Intel(R) Core(TM)2 CPU. And I would like to build 
>>> everything from scratch
>>> (including BLAS/LAPACK/ATLAS).
>>>
>>> Which compiler options/flags should I use for BLAS/LAPACK 
>>> in that case ?
>>>
>>> Which fortran compiler g77/gfortran is
>>> currently recommended to build numpy/scipy ?
>>>
>>> BTW, I am using openSUSE 10.2.
>>>
>>> Nils
>>>   
>>>     
>> For Atlas, you should use the flags set by the ATLAS build system. If 
>> you use recent ATLAS sources (3.7.* serie), there are some arch default 
>> for your CPU, I think.
>>
>> cheers,
>>
>> David
>> _______________________________________________
>> SciPy-user mailing list
>> SciPy-user at scipy.org
>> http://projects.scipy.org/mailman/listinfo/scipy-user
>>   
>  Hi again,
>
> I am confused about CPU THROTTLING.
>
> How can I switch off CPU throttling on SuSE Linux 10.2 ?
I don't know anything about Suse, but if the command line cupfreq-set 
works, you should try (as root generally) as written in the docs:

cpufreq-selector -g performance

cpufreq works by using so called governor (hence the -g), and the 
performance one is more or less equivalent to disabling cpu throttling, 
as I understand it (note that I don't know much about those things; but 
if I do that on my laptop, it is working as expected).
>
> I found a command "cpufreq-set" but I don't know how to proceed.
>
> ATLAS uses gfortran by default but I have used g77 to build BLAS/LAPACK.
ATLAS is written in C, so in my understanding is that the fortran 
compiler is just used to build the Fortran interface to the C 
blas/lapack built by ATLAS. I think the key point is to always keep the 
same compiler (eg if you use gfortran, make sure you always use it for 
all the libraries used by numpy/scipy like umfpack, etc...).

One way to check which one is "better", would be to check other fortran 
libraries you are using, I guess (eg, what is the Suse default: g77 or 
gfortran ?).

cheers

David



From nwagner at iam.uni-stuttgart.de  Mon Feb 19 02:33:43 2007
From: nwagner at iam.uni-stuttgart.de (Nils Wagner)
Date: Mon, 19 Feb 2007 08:33:43 +0100
Subject: [SciPy-user] numpy/scipy on an Intel(R) Core(TM)2 CPU and CPU
 THROTTLING
In-Reply-To: <45D91AEF.8030809@ar.media.kyoto-u.ac.jp>
References: <web-79149236@uni-stuttgart.de>	<45D82E14.6050903@ar.media.kyoto-u.ac.jp>	<45D86495.2070905@iam.uni-stuttgart.de>
	<45D91AEF.8030809@ar.media.kyoto-u.ac.jp>
Message-ID: <45D952D7.8040009@iam.uni-stuttgart.de>

David Cournapeau wrote:
> Nils Wagner wrote:
>   
>> David Cournapeau wrote:
>>     
>>> Nils Wagner wrote:
>>>   
>>>       
>>>> Hi all,
>>>>
>>>> I am going to install numpy/scipy (svn version)
>>>> on an Intel(R) Core(TM)2 CPU. And I would like to build 
>>>> everything from scratch
>>>> (including BLAS/LAPACK/ATLAS).
>>>>
>>>> Which compiler options/flags should I use for BLAS/LAPACK 
>>>> in that case ?
>>>>
>>>> Which fortran compiler g77/gfortran is
>>>> currently recommended to build numpy/scipy ?
>>>>
>>>> BTW, I am using openSUSE 10.2.
>>>>
>>>> Nils
>>>>   
>>>>     
>>>>         
>>> For Atlas, you should use the flags set by the ATLAS build system. If 
>>> you use recent ATLAS sources (3.7.* serie), there are some arch default 
>>> for your CPU, I think.
>>>
>>> cheers,
>>>
>>> David
>>> _______________________________________________
>>> SciPy-user mailing list
>>> SciPy-user at scipy.org
>>> http://projects.scipy.org/mailman/listinfo/scipy-user
>>>   
>>>       
>>  Hi again,
>>
>> I am confused about CPU THROTTLING.
>>
>> How can I switch off CPU throttling on SuSE Linux 10.2 ?
>>     
> I don't know anything about Suse, but if the command line cupfreq-set 
> works, you should try (as root generally) as written in the docs:
>
> cpufreq-selector -g performance
>
>   
On SuSE Linux you have

cpufreq-set -g performance

> cpufreq works by using so called governor (hence the -g), and the 
> performance one is more or less equivalent to disabling cpu throttling, 
> as I understand it (note that I don't know much about those things; but 
> if I do that on my laptop, it is working as expected).
>   
>> I found a command "cpufreq-set" but I don't know how to proceed.
>>
>> ATLAS uses gfortran by default but I have used g77 to build BLAS/LAPACK.
>>     
> ATLAS is written in C, so in my understanding is that the fortran 
> compiler is just used to build the Fortran interface to the C 
> blas/lapack built by ATLAS. I think the key point is to always keep the 
> same compiler (eg if you use gfortran, make sure you always use it for 
> all the libraries used by numpy/scipy like umfpack, etc...).
>
> One way to check which one is "better", would be to check other fortran 
> libraries you are using, I guess (eg, what is the Suse default: g77 or 
> gfortran ?).
>
>   
In the end I have used g77.
How do I build/install numpy/scipy with gfortran ?

If I just use

python setup.py build
python setup.py install

to build numpy/scipy g77 is called.


Cheers,

Nils

> cheers
>
> David
>
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user
>   

 


From nvf at uwm.edu  Mon Feb 19 18:52:43 2007
From: nvf at uwm.edu (Nick Fotopoulos)
Date: Mon, 19 Feb 2007 17:52:43 -0600
Subject: [SciPy-user] Scipy on Python 2.5 / OS X 10.4.8
Message-ID: <f687be130702191552i4fb825a7m520bc407458893d2@mail.gmail.com>

On 2/19/07, scipy-user-request at scipy.org <scipy-user-request at scipy.org> wrote:

> ------------------------------
>
> Message: 3
> Date: Sun, 18 Feb 2007 17:09:15 -0600
> From: Robert Kern <robert.kern at gmail.com>
> Subject: Re: [SciPy-user] Scipy on Python 2.5 / OS X 10.4.8
> To: SciPy Users List <scipy-user at scipy.org>
> Message-ID: <45D8DC9B.9070005 at gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Niklas Saers wrote:
> > Hi guys,
> > has anyone successfully compiled Scipy for Python 2.5 under Mac OS X
> > 10.4.8? I notice that the binaries on the webpage only support up to
> > Python 2.4 so I would like to build them. However, running "python
> > setup.py build" I get:
> >
> > g95 -L/sw/lib build/temp.macosx-10.3-fat-2.5/build/src.macosx-10.3-
> > fat-2.5/Lib/fftpack/_fftpackmodule.o build/temp.macosx-10.3-fat-2.5/
> > Lib/fftpack/src/zfft.o build/temp.macosx-10.3-fat-2.5/Lib/fftpack/src/
> > drfft.o build/temp.macosx-10.3-fat-2.5/Lib/fftpack/src/zrfft.o build/
> > temp.macosx-10.3-fat-2.5/Lib/fftpack/src/zfftnd.o build/
> > temp.macosx-10.3-fat-2.5/build/src.macosx-10.3-fat-2.5/
> > fortranobject.o -Lbuild/temp.macosx-10.3-fat-2.5 -ldfftpack -o build/
> > lib.macosx-10.3-fat-2.5/scipy/fftpack/_fftpack.so
> > /sw/lib/odcctools590/bin/ld: Undefined symbols:
>
> It looks like you have the LDFLAGS environment variable defined. That
> *overrides* all of the link flags, including the ones that distutils provides to
> link against the Python libraries. Don't use LDFLAGS.

Robert,

At least for me, this is not the case.  LDFLAGS is not set, but I get
the same "ld: Undefined symbols" error, with both MacPython 2.4 and
MacPython 2.5.  The failing command is different than Nik's, though.
Here is my failing command with MacPython 2.4:

error: Command "/usr/local/bin/gfortran -Wall -bundle
build/temp.macosx-10.3-fat-2.4/build/src.macosx-10.3-fat-2.4/Lib/fftpack/_fftpackmodule.o
build/temp.macosx-10.3-fat-2.4/Lib/fftpack/src/zfft.o
build/temp.macosx-10.3-fat-2.4/Lib/fftpack/src/drfft.o
build/temp.macosx-10.3-fat-2.4/Lib/fftpack/src/zrfft.o
build/temp.macosx-10.3-fat-2.4/Lib/fftpack/src/zfftnd.o
build/temp.macosx-10.3-fat-2.4/build/src.macosx-10.3-fat-2.4/fortranobject.o
-L/opt/lscsoft/non-lsc/lib
-L/usr/local/lib/gcc/i386-apple-darwin8.8.1/4.3.0
-Lbuild/temp.macosx-10.3-fat-2.4 -ldfftpack -lfftw3 -lgfortran -o
build/lib.macosx-10.3-fat-2.4/scipy/fftpack/_fftpack.so" failed with
exit status 1

Numpy and scipy are fresh from SVN.  gfortran is from
hpc.sourceforge.net, OS is OSX 10.4, and architecture is Intel  Any
other ideas?  Is there other useful information I could provide?  My
site.cfg and highlights of my python setup.py config are below.

Many thanks,
Nick

=====================
[DEFAULT]
search_static_first=true

[fftw3]
library_dirs = /opt/lscsoft/non-lsc/lib
fftw3_libs = fftw3
include_dirs = /opt/lscsoft/non-lsc/include
=====================

fftw3_info:
  FOUND:
    libraries = ['fftw3']
    library_dirs = ['/opt/lscsoft/non-lsc/lib']
    define_macros = [('SCIPY_FFTW3_H', None)]
    include_dirs = ['/opt/lscsoft/non-lsc/include']

blas_opt_info:
  FOUND:
    extra_link_args = ['-Wl,-framework', '-Wl,Accelerate']
    define_macros = [('NO_ATLAS_INFO', 3)]
    extra_compile_args = ['-faltivec',
'-I/System/Library/Frameworks/vecLib.framework/Headers']

lapack_opt_info:
  FOUND:
    extra_link_args = ['-Wl,-framework', '-Wl,Accelerate']
    define_macros = [('NO_ATLAS_INFO', 3)]
    extra_compile_args = ['-faltivec']

mkl_info, djbfft_info, and umfpack_info are all NOT AVAILABLE, which
seems fine by me.


From meesters at uni-mainz.de  Tue Feb 20 04:53:43 2007
From: meesters at uni-mainz.de (Christian Meesters)
Date: Tue, 20 Feb 2007 10:53:43 +0100
Subject: [SciPy-user] savitzky golay filtering
In-Reply-To: <45D7B03A.5030603@ee.byu.edu>
References: <A8A156D3954D6F459AB085E7828365ED7DE388@EXCHANGE01.zdv.Uni-Mainz.DE>
	<45D7A81B.9010006@hoc.net> <45D7B03A.5030603@ee.byu.edu>
Message-ID: <200702201053.43561.meesters@uni-mainz.de>

Thanks Travis & Christian!

The filter not only looks like expected, the filtering also works like a charm 
on my data - without loosing resolution. Looks like taken from a textbook, 
absolutely great! 

Cheers
Christian



From rhc28 at cornell.edu  Tue Feb 20 15:02:37 2007
From: rhc28 at cornell.edu (Rob Clewley)
Date: Tue, 20 Feb 2007 15:02:37 -0500
Subject: [SciPy-user] ANN: PyDSTool now compatible with numpy 1.0.1,
	scipy 0.5.2 and 64-bit CPUs.
Message-ID: <a749952d0702201202pf72ffc8r339f7bfaf9bf4401@mail.gmail.com>

We are pleased to announce version 0.84 of PyDSTool, an open-source
dynamical systems simulation, modeling, and analysis package.

This long-overdue release is primarily intended to bring existing
PyDSTool functionality up to date with the latest numpy and scipy releases
(previous versions required scipy 0.3.2, numarray, numeric, etc).
Also, PyDSTool is now compatible with 64-bit CPUs.

While we have added a few new features and made several fixes, major
improvements to functionality are in the pipeline for version 0.90.

Please see http://pydstool.sourceforge.net for release notes and documentation,
and http://sourceforge.net/projects/pydstool for downloading. As ever, please
send us feedback if you have any problems with this new release or ideas and
code contributions for future releases.

Regards,

          Rob, Erik, and Drew.
          Center for Applied Mathematics,
          Cornell University.

                             ******************

PyDSTool is an integrated simulation, modeling and analysis package
for dynamical systems, written in Python (and partly in C). It is
being developed at Cornell University, and the source code is
available under the terms of the BSD license. PyDSTool runs on Linux,
Windows, and Macs, and aims to have a minimal number of package
dependencies.


From s.mientki at ru.nl  Tue Feb 20 15:42:45 2007
From: s.mientki at ru.nl (Stef Mientki)
Date: Tue, 20 Feb 2007 21:42:45 +0100
Subject: [SciPy-user] ANN: PyDSTool now compatible with numpy 1.0.1,
 scipy 0.5.2 and 64-bit CPUs.
In-Reply-To: <a749952d0702201202pf72ffc8r339f7bfaf9bf4401@mail.gmail.com>
References: <a749952d0702201202pf72ffc8r339f7bfaf9bf4401@mail.gmail.com>
Message-ID: <45DB5D45.9020108@ru.nl>

Sounds GREAT !
thank you !
I just took a quick look,
the comparison to SimuLink looks good,
now if someone could make a comparison with Modelica ;-)

cheers,
Stef Mientki

Rob Clewley wrote:
> We are pleased to announce version 0.84 of PyDSTool, an open-source
> dynamical systems simulation, modeling, and analysis package.
>
> This long-overdue release is primarily intended to bring existing
> PyDSTool functionality up to date with the latest numpy and scipy releases
> (previous versions required scipy 0.3.2, numarray, numeric, etc).
> Also, PyDSTool is now compatible with 64-bit CPUs.
>
> While we have added a few new features and made several fixes, major
> improvements to functionality are in the pipeline for version 0.90.
>
> Please see http://pydstool.sourceforge.net for release notes and documentation,
> and http://sourceforge.net/projects/pydstool for downloading. As ever, please
> send us feedback if you have any problems with this new release or ideas and
> code contributions for future releases.
>
> Regards,
>
>           Rob, Erik, and Drew.
>           Center for Applied Mathematics,
>           Cornell University.
>
>                              ******************
>
> PyDSTool is an integrated simulation, modeling and analysis package
> for dynamical systems, written in Python (and partly in C). It is
> being developed at Cornell University, and the source code is
> available under the terms of the BSD license. PyDSTool runs on Linux,
> Windows, and Macs, and aims to have a minimal number of package
> dependencies.
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user
>
>
>   


From nwagner at iam.uni-stuttgart.de  Tue Feb 20 15:59:53 2007
From: nwagner at iam.uni-stuttgart.de (Nils Wagner)
Date: Tue, 20 Feb 2007 21:59:53 +0100
Subject: [SciPy-user] ANN: PyDSTool now compatible with numpy 1.0.1,
 scipy 0.5.2 and 64-bit CPUs.
In-Reply-To: <45DB5D45.9020108@ru.nl>
References: <a749952d0702201202pf72ffc8r339f7bfaf9bf4401@mail.gmail.com>
	<45DB5D45.9020108@ru.nl>
Message-ID: <web-79299887@uni-stuttgart.de>

On Tue, 20 Feb 2007 21:42:45 +0100
  Stef Mientki <s.mientki at ru.nl> wrote:
> Sounds GREAT !
> thank you !
> I just took a quick look,
> the comparison to SimuLink looks good,
> now if someone could make a comparison with Modelica ;-)
> 
> cheers,
> Stef Mientki
> 
> Rob Clewley wrote:
>> We are pleased to announce version 0.84 of PyDSTool, an 
>>open-source
>> dynamical systems simulation, modeling, and analysis 
>>package.
>>
>> This long-overdue release is primarily intended to bring 
>>existing
>> PyDSTool functionality up to date with the latest numpy 
>>and scipy releases
>> (previous versions required scipy 0.3.2, numarray, 
>>numeric, etc).
>> Also, PyDSTool is now compatible with 64-bit CPUs.
>>
>> While we have added a few new features and made several 
>>fixes, major
>> improvements to functionality are in the pipeline for 
>>version 0.90.
>>
>> Please see http://pydstool.sourceforge.net for release 
>>notes and documentation,
>> and http://sourceforge.net/projects/pydstool for 
>>downloading. As ever, please
>> send us feedback if you have any problems with this new 
>>release or ideas and
>> code contributions for future releases.
>>
>> Regards,
>>
>>           Rob, Erik, and Drew.
>>           Center for Applied Mathematics,
>>           Cornell University.
>>
>>                              ******************
>>
>> PyDSTool is an integrated simulation, modeling and 
>>analysis package
>> for dynamical systems, written in Python (and partly in 
>>C). It is
>> being developed at Cornell University, and the source 
>>code is
>> available under the terms of the BSD license. PyDSTool 
>>runs on Linux,
>> Windows, and Macs, and aims to have a minimal number of 
>>package
>> dependencies.
>> _______________________________________________
>> SciPy-user mailing list
>> SciPy-user at scipy.org
>> http://projects.scipy.org/mailman/listinfo/scipy-user
>>
>>
>>   
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user

  
Is there a way to get PyDSTool via cvs ?
I cannot find any module at 
http://pydstool.cvs.sourceforge.net/pydstool/

Am I missing something ?

Nils


From rhc28 at cornell.edu  Wed Feb 21 11:30:48 2007
From: rhc28 at cornell.edu (Rob Clewley)
Date: Wed, 21 Feb 2007 11:30:48 -0500
Subject: [SciPy-user] ANN: PyDSTool now compatible with numpy 1.0.1,
	scipy 0.5.2 and 64-bit CPUs.
In-Reply-To: <web-79299887@uni-stuttgart.de>
References: <a749952d0702201202pf72ffc8r339f7bfaf9bf4401@mail.gmail.com>
	<45DB5D45.9020108@ru.nl> <web-79299887@uni-stuttgart.de>
Message-ID: <a749952d0702210830y18da4312q723c420a11118cce@mail.gmail.com>

There is no CVS repository at Sourceforge.  We are moving to trac with
our local SVN repository and you can already get the source from
http://jay.cam.cornell.edu/svn.

Rob


From nwagner at iam.uni-stuttgart.de  Wed Feb 21 11:36:17 2007
From: nwagner at iam.uni-stuttgart.de (Nils Wagner)
Date: Wed, 21 Feb 2007 17:36:17 +0100
Subject: [SciPy-user] ANN: PyDSTool now compatible with numpy 1.0.1,
 scipy 0.5.2 and 64-bit CPUs.
In-Reply-To: <a749952d0702210830y18da4312q723c420a11118cce@mail.gmail.com>
References: <a749952d0702201202pf72ffc8r339f7bfaf9bf4401@mail.gmail.com>	<45DB5D45.9020108@ru.nl>
	<web-79299887@uni-stuttgart.de>
	<a749952d0702210830y18da4312q723c420a11118cce@mail.gmail.com>
Message-ID: <45DC7501.5020304@iam.uni-stuttgart.de>

Rob Clewley wrote:
> There is no CVS repository at Sourceforge.  We are moving to trac with
> our local SVN repository and you can already get the source from
> http://jay.cam.cornell.edu/svn.
>
> Rob
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user
>   
Many thanks!
 I assume it is

svn co http://jay.cam.cornell.edu/svn/PyDSTool/trunk/PyDSTool/

Is that correct ?
 
Nils



From cclarke at chrisdev.com  Wed Feb 21 13:51:18 2007
From: cclarke at chrisdev.com (Christopher Clarke)
Date: Wed, 21 Feb 2007 14:51:18 -0400
Subject: [SciPy-user] Sort and N dimensional array by 1d array
Message-ID: <433D0017-04DE-46D2-B665-8304CD9A4742@chrisdev.com>

Hi
I am looking for an efficient way put a two dimensional array in the  
same order as a 1 d array
In the case of arrays  key, b and c
key=array([1,3,6,0 ,4])
b = array([6,7,8,9,11])
c=array([[6,10],[7,11],[8,6],[2,5],[21,55]])
ixs=argsort(key)
sb=take(b,ixs)

however for when i do
sc=take(c,ixs)
sc.shape=(5,) (i've lost the second column)

does this mean i have to go
take(c[:,0],ixs)
take(c[:,1],ixs)
and concatenate the results. I know i am supposed to figure out how  
to specify the 2d sorted indecies  for the 2 d array but???
Regards
Chris






From jks at iki.fi  Wed Feb 21 14:08:10 2007
From: jks at iki.fi (=?iso-8859-1?Q?Jouni_K=2E_Sepp=E4nen?=)
Date: Wed, 21 Feb 2007 21:08:10 +0200
Subject: [SciPy-user] Sort and N dimensional array by 1d array
References: <433D0017-04DE-46D2-B665-8304CD9A4742@chrisdev.com>
Message-ID: <m2tzxfgwh1.fsf@iki.fi>

Christopher Clarke <cclarke at chrisdev.com> writes:

> however for when i do
> sc=take(c,ixs)
> sc.shape=(5,) (i've lost the second column)

Does take(c,ixs,axis=0) do what you want?

-- 
Jouni K. Sepp?nen
http://www.iki.fi/jks



From cclarke at chrisdev.com  Wed Feb 21 14:18:52 2007
From: cclarke at chrisdev.com (Christopher Clarke)
Date: Wed, 21 Feb 2007 15:18:52 -0400
Subject: [SciPy-user] Sort and N dimensional array by 1d array
In-Reply-To: <m2tzxfgwh1.fsf@iki.fi>
References: <433D0017-04DE-46D2-B665-8304CD9A4742@chrisdev.com>
	<m2tzxfgwh1.fsf@iki.fi>
Message-ID: <694BF6C1-2BA2-468C-8800-C5FD83F630FF@chrisdev.com>

Er Yes!!

Embarrassing i just checked the code!!!
For some reason i  used axis=1 and getting crap so
i  kept thinking that there was something more eloborate
Thanks a lot
Regards
Chris

On 21 Feb 2007, at 15:08, Jouni K. Sepp?nen wrote:

> Christopher Clarke <cclarke at chrisdev.com> writes:
>
>> however for when i do
>> sc=take(c,ixs)
>> sc.shape=(5,) (i've lost the second column)
>
> Does take(c,ixs,axis=0) do what you want?
>
> -- 
> Jouni K. Sepp?nen
> http://www.iki.fi/jks
>
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user



From rhc28 at cornell.edu  Wed Feb 21 14:55:11 2007
From: rhc28 at cornell.edu (Rob Clewley)
Date: Wed, 21 Feb 2007 14:55:11 -0500
Subject: [SciPy-user] ANN: PyDSTool now compatible with numpy 1.0.1,
	scipy 0.5.2 and 64-bit CPUs.
In-Reply-To: <45DC7501.5020304@iam.uni-stuttgart.de>
References: <a749952d0702201202pf72ffc8r339f7bfaf9bf4401@mail.gmail.com>
	<45DB5D45.9020108@ru.nl> <web-79299887@uni-stuttgart.de>
	<a749952d0702210830y18da4312q723c420a11118cce@mail.gmail.com>
	<45DC7501.5020304@iam.uni-stuttgart.de>
Message-ID: <a749952d0702211155n12bf1e04se1f3d51ad11ce5a5@mail.gmail.com>

> svn co http://jay.cam.cornell.edu/svn/PyDSTool/trunk/PyDSTool/
>
> Is that correct ?

Yes, indeed it is.


From fonnesbeck.mailing.lists at gmail.com  Thu Feb 22 11:45:37 2007
From: fonnesbeck.mailing.lists at gmail.com (Christopher Fonnesbeck)
Date: Thu, 22 Feb 2007 11:45:37 -0500
Subject: [SciPy-user] nan bug in distributions.norm.cdf
Message-ID: <563dd7570702220845m58ab43adr9ace08b3a5b1097@mail.gmail.com>

For some reason, perfectly valid normal random variates return a nan when
passed to the normal cdf in the stats.distributions package:
In [10]: from scipy.stats import distributions as d
...
In [31]: d.norm.cdf(-0.73646593092)
Out[31]: array(nan)

In [32]: d.norm.cdf(-0.7)
Out[32]: array(0.24196365222307303)

In [33]: d.norm.cdf(-0.8)
Out[33]: array(0.21185539858339669)

Simply rounding this value makes it work. Not sure why this happens. Using a
relatively recent svn build on OSX.

cf
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20070222/dafe94e0/attachment.html>

From robert.kern at gmail.com  Thu Feb 22 12:15:29 2007
From: robert.kern at gmail.com (Robert Kern)
Date: Thu, 22 Feb 2007 11:15:29 -0600
Subject: [SciPy-user] nan bug in distributions.norm.cdf
In-Reply-To: <563dd7570702220845m58ab43adr9ace08b3a5b1097@mail.gmail.com>
References: <563dd7570702220845m58ab43adr9ace08b3a5b1097@mail.gmail.com>
Message-ID: <45DDCFB1.4050103@gmail.com>

Christopher Fonnesbeck wrote:
> For some reason, perfectly valid normal random variates return a nan
> when passed to the normal cdf in the stats.distributions package:
> 
> In [10]: from scipy.stats import distributions as d
> ...
> In [31]: d.norm.cdf(-0.73646593092)
> Out[31]: array(nan)
> 
> In [32]: d.norm.cdf(-0.7)
> Out[32]: array(0.24196365222307303 )
> 
> In [33]: d.norm.cdf(-0.8)
> Out[33]: array(0.21185539858339669)
> 
> Simply rounding this value makes it work. Not sure why this happens.
> Using a relatively recent svn build on OSX.

Current SVN on Intel OS X:

Python 2.5 (r25:51918, Sep 19 2006, 08:49:13)
[GCC 4.0.1 (Apple Computer, Inc. build 5341)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> from scipy import stats
>>> stats.norm.cdf(-0.73646593092)
array(0.23072359685139249)

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
 that is made terrible by our own mad attempt to interpret it as though it had
 an underlying truth."
  -- Umberto Eco


From bryanv at enthought.com  Thu Feb 22 11:56:21 2007
From: bryanv at enthought.com (Bryan Van de Ven)
Date: Thu, 22 Feb 2007 10:56:21 -0600
Subject: [SciPy-user] nan bug in distributions.norm.cdf
In-Reply-To: <563dd7570702220845m58ab43adr9ace08b3a5b1097@mail.gmail.com>
References: <563dd7570702220845m58ab43adr9ace08b3a5b1097@mail.gmail.com>
Message-ID: <45DDCB35.4020502@enthought.com>

I just tried this on OSX (Intel MacBook, Darwin) and I don't see the 
problem:

In [1]: from scipy.stats import distributions as d

In [2]: d.norm.cdf(-0.73646593092)
Out[2]: array(0.23072359685139249)

In [3]: import scipy

In [4]: scipy.__version__
Out[4]: '0.5.3.dev2409'

What platform/version are you using?


Christopher Fonnesbeck wrote:
> For some reason, perfectly valid normal random variates return a nan 
> when passed to the normal cdf in the stats.distributions package:
> 
> In [10]: from scipy.stats import distributions as d
> ...
> In [31]: d.norm.cdf(-0.73646593092)
> Out[31]: array(nan)
> 
> In [32]: d.norm.cdf(-0.7)
> Out[32]: array(0.24196365222307303 )
> 
> In [33]: d.norm.cdf(-0.8)
> Out[33]: array(0.21185539858339669)
> 
> Simply rounding this value makes it work. Not sure why this happens. 
> Using a relatively recent svn build on OSX.
> 
> cf
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user



From rshepard at appl-ecosys.com  Thu Feb 22 13:17:15 2007
From: rshepard at appl-ecosys.com (Rich Shepard)
Date: Thu, 22 Feb 2007 10:17:15 -0800 (PST)
Subject: [SciPy-user] Need Advice With Arrays and Calculating Eigenvectors
Message-ID: <Pine.LNX.4.64.0702220948190.21009@salmo.appl-ecosys.com>

   As a newcomer to python, NumPy, and SciPy I need to learn how to most
efficiently manipulate data. Today's need is reducing a list of tuples to
three smaller lists of tuples, creating a symmetrical matrix from each list,
and calculating the Eigenvector of each of the three symmetrical matrices.

   The starting list contains 9 tuples. Each tuple has 30 items: a category
name, a subcategory name, and 28 floats. These were selected from a
database, and a tuple looks like this one:

(u'soc', u'pro', 1.3196923076923075, 3.8109999999999999, 1.6943846153846154,
2.7393076923076922, 3.825538461538462, 5.0640769230769234,
3.609923076923077, 3.1429999999999998, 1.5936153846153849,
1.4893846153846153, 2.6563076923076929, 2.2156923076923074,
3.7973076923076921, 2.6884615384615387, 2.7008461538461543,
3.4992307692307687, 2.3813846153846154, 3.2199230769230769,
1.7726923076923078, 2.9855384615384613, 2.8829230769230771,
3.7862307692307695, 2.3791538461538462, 4.0949230769230773,
2.8703846153846153, 2.8296923076923073, 3.319230769230769,
1.8083076923076922)

   The three 'soc' subcategories need to have each of the 28 floats averaged
and assigned to another tuple for 'soc'; same with the other two categories.
That produces a list of three tuples, each with 29 items.

   Each of these 28 floats represents the average of a pair-wise comparison
of values (in the non-numeric sense). So the first float above represents
the cell (1,2), the second float represents the value of the cell (1,3) and
so on. The diagonal of the matrix is 1.

   When I have these three symmetrical matrices, I want to call eigen() on
each one to calculate the principal Eignevector.

   I can think of indirect ways of doing all this, but I'm sure that there
are much more efficient approaches known to those who have done this before.
So, I'd like your suggestions and recommendations. Of course, if I've not
clearly explained my needs, please ask.

Rich

-- 
Richard B. Shepard, Ph.D.               |    The Environmental Permitting
Applied Ecosystem Services, Inc.        |          Accelerator(TM)
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863


From car at melix.org  Thu Feb 22 13:51:21 2007
From: car at melix.org (Charles-Antoine Robelin)
Date: Thu, 22 Feb 2007 10:51:21 -0800
Subject: [SciPy-user] io.read_array with strings
Message-ID: <web-7524275@tin.ucsc.edu>

I have been using io.read_array successfully to read ASCII 
files containing integers and floats, and I would like to 
import strings into arrays as well.

I tried with io.read_array, but did not get it to work:
If I create an array manually (i.e., numpy.array([['a1', 
'd3', 'gg'],['wq', 'ty', 'e']])), the type (dtype) of its 
elements is '|S4', so I suspect numpy.arrays can handle 
strings.

However, io.read_array(<filename>, separator=',') on the 
following file:
a1, d3, gg
wq, ty, e
returns an array of floats with the correct shape, 
containing the numbers it could find (a1 -> 1.; d3 -> 3.) 
and 0. where no number could be found.
I could not find how to force the type "strings," such as 
atype='<strings>' in the call of read_array.

Is importing strings possible with io.read_array, or with 
another function, without having to parse manually?

Thanks in advance.


From fonnesbeck.mailing.lists at gmail.com  Thu Feb 22 15:17:57 2007
From: fonnesbeck.mailing.lists at gmail.com (Christopher Fonnesbeck)
Date: Thu, 22 Feb 2007 15:17:57 -0500
Subject: [SciPy-user] nan bug in distributions.norm.cdf
In-Reply-To: <45DDCB35.4020502@enthought.com>
References: <563dd7570702220845m58ab43adr9ace08b3a5b1097@mail.gmail.com>
	<45DDCB35.4020502@enthought.com>
Message-ID: <563dd7570702221217q3de21385v84fdf82904510588@mail.gmail.com>

On 2/22/07, Bryan Van de Ven <bryanv at enthought.com> wrote:
>
> I just tried this on OSX (Intel MacBook, Darwin) and I don't see the
> problem:
>
> In [1]: from scipy.stats import distributions as d
>
> In [2]: d.norm.cdf(-0.73646593092)
> Out[2]: array(0.23072359685139249)
>
> In [3]: import scipy
>
> In [4]: scipy.__version__
> Out[4]: '0.5.3.dev2409'
>
> What platform/version are you using?



In [61]: scipy.__version__
Out[61]: '0.5.3.dev2095'

on PPC. It seems to occur every so often for a variety of inoccuous-looking
values. I will build anew from a more recent svn update and see if the
problem goes away.

cf
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20070222/4de7409a/attachment.html>

From fperez.net at gmail.com  Thu Feb 22 15:28:33 2007
From: fperez.net at gmail.com (Fernando Perez)
Date: Thu, 22 Feb 2007 13:28:33 -0700
Subject: [SciPy-user] Fwd: [sage-devel] Fwd: (Summer Of Code) are you
	interested in numerical optimization (+solving non-smooth
	non-linear systems of equations)?
In-Reply-To: <85e81ba30702221200o6ff005d7n658e70098a1befd8@mail.gmail.com>
References: <45DD68B9.10801@ukr.net>
	<85e81ba30702221200o6ff005d7n658e70098a1befd8@mail.gmail.com>
Message-ID: <db6b5ecc0702221228n3c9eae4fj518fa182f21a220d@mail.gmail.com>

[ Forwarded from the SAGE dev list, since this may well be right up
someone's alley from the scipy crowd]

---------- Forwarded message ----------
From: William Stein <wstein at gmail.com>
Date: Feb 22, 2007 1:00 PM
Subject: [sage-devel] Fwd: (Summer Of Code) are you interested in
numerical optimization (+solving non-smooth non-linear systems of
equations)?
To: sage-devel at googlegroups.com, suvrit at cs.utexas.edu


Does anybody have any thoughts about this potentially excellent idea
of a package that could help SAGE?

---------- Forwarded message ----------
From: dmitrey <openopt at ukr.net>
Date: Feb 22, 2007 1:56 AM
Subject: (Summer Of Code) are you interested in numerical optimization
(+solving non-smooth non-linear systems of equations)?
 To: wstein at gmail.com

Hallo William Stein!
I found your email address in
http://wiki.python.org/moin/SummerOfCode/Mentors

As far as I understood there are very few constrained solvers for
Python. In google I failed to find anything but the CVXOPT, which consists
mostly of wrappers to commercial mosek, and some LP/MIP wrappers to GNU
C- or f-
code (and some optimization routines from scipy, of course).

So I'm last-year post-graduate (institute of cybernetics, Ukraine national
science academy, optimization department). Our department research
methods of optimization for non-smooth (& noisy) funcs since 1964 or so
(under leadership of academician Naum
Z. Shor till 2002 when he gone away), and parallel department under
leadership
of academician I. Sergienko & dr. V.Shilo researches combinatory
optimization
problems (something like matlab bintprog, MAXCUT etc, some weeks ago they
published article of their GRASP-based code that won comparison vs CPLEX
& some
other commercial solvers).

So all our software is opensourse & free, mostly fortran & C written.
3-4 months ago I began to write (in m-files) OpenOpt for MATLAB/Octave
(1st ver
0.15 had been reliesed in November 25, 2006). It's equivalent to commercial
TOMLAB or GAMS (currently puny of course, but free (GNU GPL2)) and
contains 4  global solvers, that I connected to the OpenOpt environment
from
matworks fileexchange, 2 my local nonsmooth solvers - ShorEllipsoid for
nVars =
1...10 & ralg for nVars = 1...1000, and nonSmoothSolve - MATLAB fsolve
equivalent for non-smooth & noisy funcs. There is a good comparison in
Examples/nonSmoothSolveEx.m, which shows, that fsolve fails even on
low-noise or
low-non-smooth funcs, but nonSmoothSolve - not.
ralg & ShorEllipsoid are MATLAB equivalents to fminsearch; however, they
can handle (as long as nonSmoothSolve):

lb<=x<=ub;
Ax<=b;
Aeq*x=beq;
c(x)<=0;
h(x)=0; %as far as I understood from CVXOPT documentation it can't
handle these constraints - see
http://www.ee.ucla.edu/~vandenbe/cvxopt/doc/e-nlcp.html

as long as gradients or subgradients df, dc, dh of f, c, h.

MATLAB fminsearch can't handle anything mentioned above, and in 95% it
fails
comparison to ralg (but I can't say I tried too much examples). Just
try, for
example, f(x)=sum(abs(x).^1.2.^(0:(length(x)-1)));
x0 = cos(1:60).';
or Lemarechal.m from OpenOpt/test (convex, continuous, non-smooth)
These and some more examples are in OpenOpt/Examples, see ooexample5.m,
ooexample2.m and others. This directory also contains some pictures of
convergence, automatically generated by the files.
Also OpenOpt performs auto scaling (but I not tested properly it yet);
providing
patterns of f, c, h (when no (sub)gradient is provided by user) can greatly
speedup calculations; possibility of parallel calculations while
obtaining df/dx
numerically (via MATLAB dfeval, Octave users must provide similar func in
prob.parallel.fun) and some more features.

So are you interested in Python version of the OpenOpt? If yes, I
probably would
be able to contact with other Kiev institute of System Analis, where a
group
 under leadership of academician Pshenichniy (perished some months ago) &
dr.
Nikitin develop smooth algorithms of optimization, and their IP-based
smooth
solvers (constrained, of course; including 2nd-order solvers) are
considered to be one of essential. So I probably
would be able to write for you Pyhton OpenOpt ver (GNU GPL2) with
essential equivalent of MATLAB fmincon, as long as ralg, ShorEllipsoid,
bintprog; drawing pictures of convergence, using patterns of
dependences, parallel obtaining of (sub)gradients to f(), c(), h();
network problems solvers etc.

If you have any questions, or can add any financial support, or want to
look at
my CV (I had about 1-1.5 years of Python experience & 3-4 years of
optimization in
MATLAB), or anything else - you can contact me via email or icq 275 -
976 - 670 (invisible).
The more financial support can be obtained, the more time can I spend
for the OpenOpt Python version, & the more icyb optim department workers
can be involved into the OpenOpt for Python development (any salary
amount are essential to the Ukraine workers).
If I gain enough money, I propose:
creating the same environment for Python as it is done for
MATLAB/Octave; (1-1.5 months)
writing ralg() & ShorEllipsoid() solvers (Unconstrained: ~1 week,
constrained: +2-3 weeks)
writing nonSmoothSolve() : ~ 1-2 weeks
writing MATLAB bintprog (f*x->min, A*x<=b, Aeq*x=beq) equivalent based
on rd. Shilo (& others) version of GRASP (works better than current
CPLEX!): ~2 weeks
writing MATLAB fmincon equivalent (smooth constrained optimization,
c(x)<=0, h(x)=0, linear constraints +1st & 2nd derivatives) based on
works of dr. Nikitin & academician Pshenichniy: (I can't estimate time
for now, I must contact to him before)
--------
+ following implementation of other solvers, their upgrade & maintenance.

I guess in future you could easily connect the py-code to the SAGE
project, for example like you did with MAXIMA package.

some links:
ftp where OpenOpt versions are storing:
 http://www.box.net/public/6bsuq765t4
(you would better to download OpenOpt0.36.tar.bz2 from here)

my page at matlabexchange area
 http://www.mathworks.com/matlabcentral/fileexchange/loadFile.do?objectId=13115&objectType=file


Let me attach a graphic file generated by the OpenOpt ooexample3.m

WBR, Dmitrey


 --
William Stein
Associate Professor of Mathematics
University of Washington
 --~--~---------~--~----~------------~-------~--~----~
 To post to this group, send email to sage-devel at googlegroups.com
 To unsubscribe from this group, send email to
sage-devel-unsubscribe at googlegroups.com
 For more options, visit this group at
http://groups.google.com/group/sage-devel
 URLs: http://sage.scipy.org/sage/ and http://modular.math.washington.edu/sage/
 -~----------~----~----~----~------~----~------~--~---


From v-nijs at kellogg.northwestern.edu  Thu Feb 22 15:45:26 2007
From: v-nijs at kellogg.northwestern.edu (Vincent Nijs)
Date: Thu, 22 Feb 2007 14:45:26 -0600
Subject: [SciPy-user] io.read_array with strings
In-Reply-To: <web-7524275@tin.ucsc.edu>
Message-ID: <C2035D06.655D%v-nijs@kellogg.northwestern.edu>

Charles,

You could read-in the array using python's csv module. This will return an
array of strings. Then loop through each column and convert to an
appropriate type using something like:

def csvconvert(col):
    try: 
        return col.astype('i')
    except ValueError:
        try: 
            return col.astype('f')
        except ValueError:
            return col

The issue is how to store the returned columns. A normal array can, as far
as I know, only hold one data type. You could use a recarray or store the
data in a dictionary.

I have used both approaches in a data base class I posted on the cookbook
page:

http://www.scipy.org/Cookbook/dbase

Vincent



On 2/22/07 12:51 PM, "Charles-Antoine Robelin" <car at melix.org> wrote:

> I have been using io.read_array successfully to read ASCII
> files containing integers and floats, and I would like to
> import strings into arrays as well.
> 
> I tried with io.read_array, but did not get it to work:
> If I create an array manually (i.e., numpy.array([['a1',
> 'd3', 'gg'],['wq', 'ty', 'e']])), the type (dtype) of its
> elements is '|S4', so I suspect numpy.arrays can handle
> strings.
> 
> However, io.read_array(<filename>, separator=',') on the
> following file:
> a1, d3, gg
> wq, ty, e
> returns an array of floats with the correct shape,
> containing the numbers it could find (a1 -> 1.; d3 -> 3.)
> and 0. where no number could be found.
> I could not find how to force the type "strings," such as
> atype='<strings>' in the call of read_array.
> 
> Is importing strings possible with io.read_array, or with
> another function, without having to parse manually?
> 
> Thanks in advance.
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user
> 

-- 





From jraddison at gmail.com  Fri Feb 23 01:22:16 2007
From: jraddison at gmail.com (Jason Addison)
Date: Thu, 22 Feb 2007 20:22:16 -1000
Subject: [SciPy-user] Mac OS X 10.4 can not import from scipy.linalg
Message-ID: <4ae645d30702222222k6bd2c9d6k2309949b3c4e64f9@mail.gmail.com>

I installed the prebuilts:
MacPython
  python-2.4.4-macosx2006-10-18.dmg
    MacPython.mpkg
SciPy
  ScipySuperpack-Intel-10.4-py2.4.dmg
    PyMC-1.1-py2.4-macosx10.4.mpkg
    gfortranCompleteInstaller.mpkg
    matplotlib-0.87.7-py2.4-macosx10.4.mpkg
    numpy-1.0.2.dev3522-py2.4-macosx10.4.mpkg
    scipy-0.5.3.dev2630-py2.4-macosx10.4.mpkg

I'm using a MacBook Pro with Mac OS 10.4.8 with fink and Mac Developer
Tools installed.

After installing, I tried the tutorial:

jra$ 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.
>>> from numpy import matrix
>>> from scipy.linalg import inv, det, eig
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/linalg/__init__.py",
line 8, in ?
    from basic import *
  File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/linalg/basic.py",
line 17, in ?
    from lapack import get_lapack_funcs
  File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/linalg/lapack.py",
line 17, in ?
    from scipy.linalg import flapack
ImportError: Inappropriate file type for dynamic loading
>>>

Searching for possibly relevent conflicting files I find stuff like:
  lapack: clapack.h in vecLib.framework
  blas: blas.hpp in ublas from boost numeric

Does anyone have any idea on how to fix this? Is it supposed to work?
Do I have something else installed that is conflicting?

Thanks for your help ... jra


From giorgio.luciano at chimica.unige.it  Fri Feb 23 03:57:45 2007
From: giorgio.luciano at chimica.unige.it (Giorgio Luciano)
Date: Fri, 23 Feb 2007 09:57:45 +0100
Subject: [SciPy-user] Clipborad more friendly tha IDE
Message-ID: <45DEAC89.9020908@chimica.unige.it>

Sorry for the easy question, I've searched the web but find nothing 
"really" helpful.
Is there some editor more user friendly for Windows to have a workspace 
where to copy and paste from gnumeric/excel like the matlab workspace
I'm using orange, which is wonderful, but if you have a lot of array to 
copy and paste is not so comfortable as a simple command
line x=[(ctrl+v)]
Thanks in advance to all.
I guess that a workspace like matlab for numpy/scipy will make a lot of 
people to switch more easily form matlab :)))
Giorgio



From robert.vergnes at yahoo.fr  Fri Feb 23 09:40:24 2007
From: robert.vergnes at yahoo.fr (Robert VERGNES)
Date: Fri, 23 Feb 2007 15:40:24 +0100 (CET)
Subject: [SciPy-user] RE :  Clipborad more friendly tha IDE
In-Reply-To: <45DEAC89.9020908@chimica.unige.it>
Message-ID: <20070223144024.31833.qmail@web27408.mail.ukl.yahoo.com>

Hello

You can look at: 

http://sourceforge.net/projects/qme-dev/

But it is in development.

Could you give some info about orange ?


Best Regards,
Robert
Giorgio Luciano <giorgio.luciano at chimica.unige.it> a ?crit : Sorry for the easy question, I've searched the web but find nothing 
"really" helpful.
Is there some editor more user friendly for Windows to have a workspace 
where to copy and paste from gnumeric/excel like the matlab workspace
I'm using orange, which is wonderful, but if you have a lot of array to 
copy and paste is not so comfortable as a simple command
line x=[(ctrl+v)]
Thanks in advance to all.
I guess that a workspace like matlab for numpy/scipy will make a lot of 
people to switch more easily form matlab :)))
Giorgio

_______________________________________________
SciPy-user mailing list
SciPy-user at scipy.org
http://projects.scipy.org/mailman/listinfo/scipy-user


 		
---------------------------------
 D?couvrez une nouvelle fa?on d'obtenir des r?ponses ? toutes vos questions ! Profitez des connaissances, des opinions et des exp?riences des internautes sur Yahoo! Questions/R?ponses.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20070223/0e5002be/attachment.html>

From oliver.tomic at matforsk.no  Fri Feb 23 09:50:43 2007
From: oliver.tomic at matforsk.no (oliver.tomic at matforsk.no)
Date: Fri, 23 Feb 2007 15:50:43 +0100
Subject: [SciPy-user] error in std?
Message-ID: <OF94A96E95.844045DF-ONC125728B.004E6628-C125728B.00519DFA@matforsk.no>


Hi list,

we are in the process of switching our application from:

(OLD configuration)
Python 2.4.2
scipy 0.49
numpy 0.98

to:

(NEW configuration)
Python 2.5
scipy 0.52
numpy 1.0.1


When I do the following in the OLD configuration:

data = array([1,2,3,4,5,6])
stand = std(data)

the result for stand is 1.870828693386..... ,which is exactly what should
be.

However, when I do exactly the same under the NEW configuration the result
for stand is 1.70782512766.



I am clueless. Has anyone experienced the same problem? Any help
appreciated.

Oliver



From olivetti at itc.it  Fri Feb 23 10:00:39 2007
From: olivetti at itc.it (Emanuele Olivetti)
Date: Fri, 23 Feb 2007 16:00:39 +0100
Subject: [SciPy-user] error in std?
In-Reply-To: <OF94A96E95.844045DF-ONC125728B.004E6628-C125728B.00519DFA@matforsk.no>
References: <OF94A96E95.844045DF-ONC125728B.004E6628-C125728B.00519DFA@matforsk.no>
Message-ID: <45DF0197.5080107@itc.it>

oliver.tomic at matforsk.no wrote:
> Hi list,
...
> the result for stand is 1.870828693386..... ,which is exactly what should
> be.
> 
> However, when I do exactly the same under the NEW configuration the result
> for stand is 1.70782512766.
> 
> I am clueless. Has anyone experienced the same problem? Any help
> appreciated.

There was a post on Numpy-discussion about why dividing by N instead
of N-1 in std from some recent release on:
http://projects.scipy.org/pipermail/numpy-discussion/2006-November/024821.html
but there was no answer.

Let see what happens this time ;)

Emanuele



From giorgio.luciano at chimica.unige.it  Fri Feb 23 10:05:27 2007
From: giorgio.luciano at chimica.unige.it (Giorgio Luciano)
Date: Fri, 23 Feb 2007 16:05:27 +0100
Subject: [SciPy-user] error in std?
In-Reply-To: <45DF0197.5080107@itc.it>
References: <OF94A96E95.844045DF-ONC125728B.004E6628-C125728B.00519DFA@matforsk.no>
	<45DF0197.5080107@itc.it>
Message-ID: <45DF02B7.5090908@chimica.unige.it>

Yes it seems no reply,
for me is better this way, since for having results consistent with 
Matlab I had always to manually change it ;)


From oliver.tomic at matforsk.no  Fri Feb 23 10:13:50 2007
From: oliver.tomic at matforsk.no (oliver.tomic at matforsk.no)
Date: Fri, 23 Feb 2007 16:13:50 +0100
Subject: [SciPy-user] error in std?
In-Reply-To: <45DF02B7.5090908@chimica.unige.it>
Message-ID: <OF18BD8C11.ED7C5C2B-ONC125728B.0053527B-C125728B.0053BBAD@matforsk.no>

Thank you guys!

I have to admit that I'd like to have it the old way, since it is
consistent with the commercial software Unscrambler. But I guess everybody
has an own opinion on this. :-)

Thanks again!
Oliver

scipy-user-bounces at scipy.org wrote on 23.02.2007 16:05:27:

> Yes it seems no reply,
> for me is better this way, since for having results consistent with
> Matlab I had always to manually change it ;)
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user



From lists at zopyx.com  Fri Feb 23 14:56:38 2007
From: lists at zopyx.com (Andreas Jung)
Date: Fri, 23 Feb 2007 13:56:38 -0600
Subject: [SciPy-user] [CFP] Zope conference on Zope in Science
Message-ID: <4CD1FCE7AA6F2B571A65C013@suxmac2-local.local>


Dear Python & Zope Community,

the eighth Zope conference organized by the German Zope User Group (DZUG) 
will be held this year at the Potsdam Institute for Climate Impace Research
from 4. to 5 June 2007 (near Berlin). The topic of the conference will be

    Zope in sciences.

Proposals for talks and workshops can be submitted until 01.04.2007

 http://www.zope.de/redaktion/dzug/tagung/potsdam-2007/dzug-conference-2007-call-for-papers-zope-in-science

or

 http://www.zope.de/redaktion/dzug/tagung/potsdam-2007/dzug-conference-2007-call-for-papers-zope-in-science

Both German and English proposals are highly welcome.

You can find further information about the Zope conference here:

   http://www.zope.de/8-dzug-tagung


Regards,
Andreas Jung
Assistant Chairman DZUG e.V.

-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: application/pgp-signature
Size: 186 bytes
Desc: not available
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20070223/2fda1c8c/attachment.sig>

From jraddison at gmail.com  Fri Feb 23 17:12:42 2007
From: jraddison at gmail.com (Jason Addison)
Date: Fri, 23 Feb 2007 12:12:42 -1000
Subject: [SciPy-user] how to uninstall Mac OS X ScipySuperpack Intel?
Message-ID: <4ae645d30702231412j7d1a3ce3seaee457e40839109@mail.gmail.com>

I installed ScipySuperpack-Intel and have had some trouble. I thinking
about just giving up on it and compiling my own. Before I do, I'd like
to clean up from the packages that I installed:

    PyMC-1.1-py2.4-macosx10.4.mpkg
    gfortranCompleteInstaller.mpkg
    matplotlib-0.87.7-py2.4-macosx10.4.mpkg
    numpy-1.0.2.dev3522-py2.4-macosx10.4.mpkg
    scipy-0.5.3.dev2630-py2.4-macosx10.4.mpkg

It looks like these install things deep into the filesystem, but I'm
not sure what and where. Is there an easy way to uninstall? Is there a
hard way? I didn't see any READMEs or such.

Thanks ... jra


From robert.kern at gmail.com  Fri Feb 23 17:30:12 2007
From: robert.kern at gmail.com (Robert Kern)
Date: Fri, 23 Feb 2007 16:30:12 -0600
Subject: [SciPy-user] how to uninstall Mac OS X ScipySuperpack Intel?
In-Reply-To: <4ae645d30702231412j7d1a3ce3seaee457e40839109@mail.gmail.com>
References: <4ae645d30702231412j7d1a3ce3seaee457e40839109@mail.gmail.com>
Message-ID: <45DF6AF4.9010404@gmail.com>

Jason Addison wrote:
> I installed ScipySuperpack-Intel and have had some trouble. I thinking
> about just giving up on it and compiling my own. Before I do, I'd like
> to clean up from the packages that I installed:
> 
>     PyMC-1.1-py2.4-macosx10.4.mpkg
>     gfortranCompleteInstaller.mpkg
>     matplotlib-0.87.7-py2.4-macosx10.4.mpkg
>     numpy-1.0.2.dev3522-py2.4-macosx10.4.mpkg
>     scipy-0.5.3.dev2630-py2.4-macosx10.4.mpkg
> 
> It looks like these install things deep into the filesystem, but I'm
> not sure what and where. Is there an easy way to uninstall? Is there a
> hard way? I didn't see any READMEs or such.

There's no easy way. Blame Apple for that. There is a hard way, though. In
/Library/Receipts, there are bundle directories with metadata about the packages
that you have installed. You need to use the lsbom(1) program to extract the
file names:

$ lsbom
/Library/Receipts/py2app-purelib-0.2.5-py2.5-macosx10.4.pkg/Contents/Archive.bom
.       40775   501/80
./Py2App        40775   501/80
./Py2App/altgraph       40775   501/80
./Py2App/altgraph/Dot.py        100664  501/80  8425    1846799381
./Py2App/altgraph/Dot.pyc       100664  501/80  9409    2590730341
./Py2App/altgraph/Dot.pyo       100664  501/80  9409    2590730341
./Py2App/altgraph/Graph.py      100664  501/80  19562   2645573956
./Py2App/altgraph/Graph.pyc     100664  501/80  25554   1326377293
./Py2App/altgraph/Graph.pyo     100664  501/80  25554   1326377293
...


Note that the paths are relative. Look in the Contents/Info.plist file of the
bundle for the IFPkgFlagDefaultLocation value to find the path it is relative
to. The list of "files" also includes directories. Do not remove these until
they are empty and you know that other packages don't have stuff in there.

Also note that those packages you listed are meta-packages. Inside each of these
are individual packages. You will only see receipts for the individual packages.

PITA, frankly. This is one reason why I gave up on these Installer.app packages.
They're just not suited for distributing Python libraries.

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
 that is made terrible by our own mad attempt to interpret it as though it had
 an underlying truth."
  -- Umberto Eco


From lanceboyle at qwest.net  Fri Feb 23 18:42:30 2007
From: lanceboyle at qwest.net (Jerry)
Date: Fri, 23 Feb 2007 16:42:30 -0700
Subject: [SciPy-user] how to uninstall Mac OS X ScipySuperpack Intel?
In-Reply-To: <4ae645d30702231412j7d1a3ce3seaee457e40839109@mail.gmail.com>
References: <4ae645d30702231412j7d1a3ce3seaee457e40839109@mail.gmail.com>
Message-ID: <890D0024-F5FB-413D-B895-53119FD69223@qwest.net>

Use Desinstaller. http://www.versiontracker.com/dyn/moreinfo/macosx/ 
13955. It's not a PITA.
Jerry

On Feb 23, 2007, at 3:12 PM, Jason Addison wrote:

> I installed ScipySuperpack-Intel and have had some trouble. I thinking
> about just giving up on it and compiling my own. Before I do, I'd like
> to clean up from the packages that I installed:
>
>     PyMC-1.1-py2.4-macosx10.4.mpkg
>     gfortranCompleteInstaller.mpkg
>     matplotlib-0.87.7-py2.4-macosx10.4.mpkg
>     numpy-1.0.2.dev3522-py2.4-macosx10.4.mpkg
>     scipy-0.5.3.dev2630-py2.4-macosx10.4.mpkg
>
> It looks like these install things deep into the filesystem, but I'm
> not sure what and where. Is there an easy way to uninstall? Is there a
> hard way? I didn't see any READMEs or such.
>
> Thanks ... jra



From pwang at enthought.com  Sat Feb 24 01:22:11 2007
From: pwang at enthought.com (Peter Wang)
Date: Sat, 24 Feb 2007 00:22:11 -0600
Subject: [SciPy-user] how to uninstall Mac OS X ScipySuperpack Intel?
In-Reply-To: <890D0024-F5FB-413D-B895-53119FD69223@qwest.net>
References: <4ae645d30702231412j7d1a3ce3seaee457e40839109@mail.gmail.com>
	<890D0024-F5FB-413D-B895-53119FD69223@qwest.net>
Message-ID: <010048B3-61AB-48C1-9FD6-2308293DC2EC@enthought.com>

On Feb 23, 2007, at 5:42 PM, Jerry wrote:

> Use Desinstaller. http://www.versiontracker.com/dyn/moreinfo/macosx/
> 13955. It's not a PITA.
> Jerry

It took me a second to realize that the full URL is:
http://www.versiontracker.com/dyn/moreinfo/macosx/13955

I sat here thinking that "13955" was l33t sp34k for "LEGSS", as in,  
"this DesInstaller program has real legss [sic]".


-Peter



From topengineer at gmail.com  Sat Feb 24 02:04:03 2007
From: topengineer at gmail.com (Hui Chang Moon)
Date: Sat, 24 Feb 2007 16:04:03 +0900
Subject: [SciPy-user] Does Scipy have the differenciation function?
Message-ID: <296323b50702232304m102b7558gea03f63016fe1406@mail.gmail.com>

Hello, Scipy-user Group members,

I want to know if the Scipy has the differencitaion function.
I can find the integration fuction (quad), but I can't know where the
differenciation function.

Whoever knows the differenciation function, let me know.

Thank you.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20070224/cac7508d/attachment.html>

From nwagner at iam.uni-stuttgart.de  Sat Feb 24 02:41:15 2007
From: nwagner at iam.uni-stuttgart.de (Nils Wagner)
Date: Sat, 24 Feb 2007 08:41:15 +0100
Subject: [SciPy-user] Does Scipy have the differenciation function?
In-Reply-To: <296323b50702232304m102b7558gea03f63016fe1406@mail.gmail.com>
References: <296323b50702232304m102b7558gea03f63016fe1406@mail.gmail.com>
Message-ID: <web-79523666@uni-stuttgart.de>

On Sat, 24 Feb 2007 16:04:03 +0900
  "Hui Chang Moon" <topengineer at gmail.com> wrote:
> Hello, Scipy-user Group members,
> 
> I want to know if the Scipy has the differencitaion 
>function.
> I can find the integration fuction (quad), but I can't 
>know where the
> differenciation function.
> 
> Whoever knows the differenciation function, let me know.
> 
> Thank you.
  
You might use
from scipy import *
#
# Using Complex Variables to Estimate Derivatives of Real 
Functions
# William Squire, George Trapp
# SIAM Review, Vol. 40, No. 1 (Mar., 1998), pp. 110-112
#
#
def f(x):

     return sin(x)

def fp(x):
     """ First derivative of f """

     return cos(x)

print 'The derivative of f is fp'

eps = 1.e-8
print
print 'Analytical solution',fp(0.1)
print
print 'Numerical solution',f(0.1+1j*eps).imag/eps

Otherwise you can use interpolate

       splrep    -- find smoothing spline given (x,y) 
points on curve.
       splprep   -- find smoothing spline given 
parametrically defined curve.
       splev     -- evaluate the spline or its 
derivatives.
       splint    -- compute definite integral of a spline.
       sproot    -- find the roots of a cubic spline.
       spalde    -- compute all derivatives of a spline at 
given points.



Nils


From gruben at bigpond.net.au  Sat Feb 24 02:53:43 2007
From: gruben at bigpond.net.au (Gary Ruben)
Date: Sat, 24 Feb 2007 18:53:43 +1100
Subject: [SciPy-user] Does Scipy have the differenciation function?
In-Reply-To: <web-79523666@uni-stuttgart.de>
References: <296323b50702232304m102b7558gea03f63016fe1406@mail.gmail.com>
	<web-79523666@uni-stuttgart.de>
Message-ID: <45DFEF07.4000907@bigpond.net.au>

In [1]: from scipy import derivative

In [2]: derivative?
Type:           function
Base Class:     <type 'function'>
String Form:    <function derivative at 0x01EC5A30>
Namespace:      Interactive
File:           c:\python24\lib\site-packages\scipy\misc\common.py
Definition:     derivative(func, x0, dx=1.0, n=1, args=(), order=3)
Docstring:
     Given a function, use a central difference formula with spacing dx to
compute the nth derivative at x0.

order is the number of points to use and must be odd.

Warning: Decreasing the step size too small can result in
round-off error.


Gary R.

>   "Hui Chang Moon" <topengineer at gmail.com> wrote:
>> Hello, Scipy-user Group members,
>>
>> I want to know if the Scipy has the differencitaion 
>> function.
>> I can find the integration fuction (quad), but I can't 
>> know where the
>> differenciation function.
>>
>> Whoever knows the differenciation function, let me know.
>>
>> Thank you.



From lorenzo.isella at gmail.com  Sat Feb 24 12:44:54 2007
From: lorenzo.isella at gmail.com (Lorenzo Isella)
Date: Sat, 24 Feb 2007 18:44:54 +0100
Subject: [SciPy-user] Optimization
Message-ID: <45E07996.3000307@gmail.com>

Dear All,
I am going through the Scipy manual and I am trying to reproduce, as an 
exercise to learn Python and Scipy, some nonlinear least-square 
optimization which I was able to carry out using another language.
I am collecting some questions which hopefully will help me understand 
Python a bit better:
(1) What is the difference between
from pylab import *
and import pylab?
(2)  the 2nd question may be a non-problem: in running some of the 
examples in the tutorial by Olinfant, I could not use the xplt module, 
no matter whether trying import scipy.xplt, from scipy.xplt import * et 
similia.
I bumped into
http://lists.debian.org/debian-science/2007/01/msg00007.html
which may be the answer (I am running Debian on my box as well and I 
installed Scipy from the Debian repository). Can I install xplt by itself?
BTW, I also visited
http://www.scipy.org/Cookbook/xplt
but even  using
from scipy.sandbox import xplt
does not help.
 (3) Is there a way to have arrays starting with index 1 rather than 
zero in Python? As you can guess, I do not have a strong C background.
(4) This is the main question: I am trying to fit some experimental data 
to a log-normal curve. I would like to follow the same steps as in the 
tutorial, but something seems to be going wrong.
I cut and paste the code I am using and attach a .csv file so that one 
can reproduce step by step my work.
(5) Finally, if I load scipy and then write, e.g., z=10.3, how is z 
handled? Is it a floating point number?
What if, for instance, I need to have a very large number of significant 
digits because they do matter for some computation I want to run? Can I 
have the equivalent of format long [Matlab statement], so that every 
non-integer number is by default treated with a certain precision?


Here is the code:

#! /usr/bin/env python
from pylab import plot, show, ylim, yticks
from scipy import *

import pylab 

# now I want to try reading some .csv file
data = pylab.load("120km-TPM.csv",delimiter=',')

vecdim=shape(data) # now I introduce a vector with the dimensions of 
data, the file I read
print "the dimensions of data are"
print vecdim  # now very careful! in Python the arrays start with index 
zero.
diam=data[0:vecdim[0],0] # it means: slice the rows from the 1st one (0) 
to the last one (
# (vecdim[0]) for the first column (0)
print "the dimensions of diam are"
print shape(diam)



#plot(diam,data[:,1])
#show() # uncomment them to plot a distribution

# 1st problem: if uncomment the previous two lines, I get a warning and 
until I close
# the window, the script does not progress.

# now I try performing a least-square fitting
from scipy.optimize import leastsq


x=diam # just a list of diameters


y_meas=data[0:vecdim[0],1]  # measured data, for example the 2nd column 
of the .csv file



def residuals(p, y, x):
    A1,mu1,myvar1 = p
    err = 
y-log(10.0)*A1/sqrt(2.0*pi)/log(myvar1)*exp(-((log(x/mu1))**2.0)/2.0/log(myvar1)/log(myvar1))
    return err

def peval(x, p):
    return  
log(10.0)*p[0]/sqrt(2.0*pi)/log(p[2])*exp(-((log(x/p[1]))**2.0)/2.0/log(p[2])/log(p[2]))


p0 = [50000.0,90.0, 1.59]
print array(p0)

# now I try actually solving the problem
print "ok up to here"
plsq = leastsq(residuals, p0, args=(y_meas, x))

print "ok up to here2"

print plsq[0]

print array([A, k, theta])

print "So far so good"


which produces this output on my box:

$ ./read-and-plot.py
the dimensions of data are
(104, 10)
the dimensions of diam are
(104,)
[  5.00000000e+04   9.00000000e+01   1.59000000e+00]
ok up to here
TypeError: array cannot be safely cast to required type
Traceback (most recent call last):
  File "./read-and-plot.py", line 51, in ?
    plsq = leastsq(residuals, p0, args=(y_meas, x))
  File "/usr/lib/python2.4/site-packages/scipy/optimize/minpack.py", 
line 266, in leastsq
    retval = 
_minpack._lmdif(func,x0,args,full_output,ftol,xtol,gtol,maxfev,epsfcn,factor,diag)
minpack.error: Result from function call is not a proper array of floats.

Many thanks

Lorenzo
-------------- next part --------------
A non-text attachment was scrubbed...
Name: 120km-TPM.csv
Type: text/csv
Size: 9696 bytes
Desc: not available
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20070224/e4ede6c7/attachment.csv>

From gael.varoquaux at normalesup.org  Sat Feb 24 14:42:00 2007
From: gael.varoquaux at normalesup.org (Gael Varoquaux)
Date: Sat, 24 Feb 2007 20:42:00 +0100
Subject: [SciPy-user] Carateristic distance in a cloud of points
In-Reply-To: <45E07996.3000307@gmail.com>
References: <45E07996.3000307@gmail.com>
Message-ID: <20070224194200.GI7867@clipper.ens.fr>

I have a cloud of points (for instance given as a (n,3) shaped array,
with columns formed by the x, y and z column vectors).

I would like to find the mean distance in this cloud of points. I do not
need an exact value, I am just interested in a typical distance.

I could do it in a brute force way:

++++++++++++++++++++++++++++++++++++++++++
from scipy import *
x = arange(1, 5)

points = c_[x, x, x]
diffs = abs(points[newaxis, :] - points[:, newaxis])
dists = sqrt(diffs[..., 0]**2 + diffs[..., 1]**2 + diffs[..., 2]**2).ravel()
dists = dists[dists>0]
mean(dists)
++++++++++++++++++++++++++++++++++++++++++

This is actually not as ugly and slow as I originaly thought.

Are there any better ways of doing this ?

Thanks,

Ga?l


From peridot.faceted at gmail.com  Sat Feb 24 16:13:57 2007
From: peridot.faceted at gmail.com (Anne Archibald)
Date: Sat, 24 Feb 2007 16:13:57 -0500
Subject: [SciPy-user] Carateristic distance in a cloud of points
In-Reply-To: <20070224194200.GI7867@clipper.ens.fr>
References: <45E07996.3000307@gmail.com> <20070224194200.GI7867@clipper.ens.fr>
Message-ID: <ce557a360702241313p2d67003am92ce8ca92ca8ff86@mail.gmail.com>

On 24/02/07, Gael Varoquaux <gael.varoquaux at normalesup.org> wrote:
> I have a cloud of points (for instance given as a (n,3) shaped array,
> with columns formed by the x, y and z column vectors).
>
> I would like to find the mean distance in this cloud of points. I do not
> need an exact value, I am just interested in a typical distance.

This is actually quite tricky, depending on what you mean by a
"typical" distance - distances can have all sorts of distributions.
Imagine for example a cloud that is actually two small clouds a long
way apart, or a cloud with a few very distant outliers or a Julia set
(for which the distance behaves like a power law whose exponent is
related to the fractal dimension)... well, you get the point.

> I could do it in a brute force way:

This can be tidied slightly:
> ++++++++++++++++++++++++++++++++++++++++++
> from scipy import *
> x = arange(1, 5)
>
> points = c_[x, x, x]
> diffs = abs(points[newaxis, :] - points[:, newaxis])
There's no need for an absolute value here.
> dists = sqrt(diffs[..., 0]**2 + diffs[..., 1]**2 + diffs[..., 2]**2).ravel()
sqrt(sum(diffs**2,axis=2)).ravel() will do the same.
> dists = dists[dists>0]
> mean(dists)
> ++++++++++++++++++++++++++++++++++++++++++

> Are there any better ways of doing this ?

Well, depending what you want from "typical distance" the median might
do a better job (or not). Or you might be satisfied with a random
sample of 100 points (say):

p = points[random.randint(shape(points)[0],size=100)]
and then use the above procedure.

Alternatively, if you're willing to be crude:

lwh = ptp(points,axis=0) # size of the bounding box
d = sqrt(sum((lwh/2)**2))

I end up using sqrt(sum(X**2,axis=Y)) rather often, I wonder if
there's a tidy idiom for it? It's the L2 norm, after all...

Anne


From sidgalt at gmail.com  Sat Feb 24 18:01:38 2007
From: sidgalt at gmail.com (Siddhartha Jain)
Date: Sun, 25 Feb 2007 04:31:38 +0530
Subject: [SciPy-user] fmin_cobyla help-passing constraints and bounds
Message-ID: <8a8343a10702241501i7cb29776k3a8303441d352465@mail.gmail.com>

I am trying to solve an optimization problem with more than 500 variables.
Will fmin_cobyla be able to solve such a large problem in a reasonable
amount of time?

If so, then can anyone help me as to how to pass the variable bounds and
constraints to fmin_cobyla?

Thank you
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20070225/c610abc5/attachment.html>

From gael.varoquaux at normalesup.org  Sat Feb 24 19:03:03 2007
From: gael.varoquaux at normalesup.org (Gael Varoquaux)
Date: Sun, 25 Feb 2007 01:03:03 +0100
Subject: [SciPy-user] Carateristic distance in a cloud of points
In-Reply-To: <ce557a360702241313p2d67003am92ce8ca92ca8ff86@mail.gmail.com>
References: <45E07996.3000307@gmail.com> <20070224194200.GI7867@clipper.ens.fr>
	<ce557a360702241313p2d67003am92ce8ca92ca8ff86@mail.gmail.com>
Message-ID: <20070225000303.GJ7867@clipper.ens.fr>

Interesting remarks. You forced me to think a bit more about what I was
trying to achieve.

What I am trying to do is to find out the right size to use for symbols
when used on a 3D cloud of points. I am not sure what the right "typical
distance" should be used. If those symbols are arrows then it seems that
should be smaller than the typical inter-point distance. I have in mind
something like this:

if you have n points, find out the distribution of distances, divide it
by n**3, then take the value at 0.2 from the smallest. 

I am having diffculties expressing my point, but the idea would be to
consider that the typical distribution will increase as n**3 (which is
not obvious, for instance if the points are along a plane) and take the
lower tail of the distribution, as we are interested in having symbols
smaller than the inter-point distance. Taking not the smallest value, but
the value at "20%" from the bottom helps getting rid of singular
situations where a few points are very close but the major part is spread
out.

The problem is that the "good" solution does depend on the problem, and
there will never be a one size fits all solution. I am interested in
other suggestions.

Cheers,

Ga?l


From gael.varoquaux at normalesup.org  Sat Feb 24 19:10:39 2007
From: gael.varoquaux at normalesup.org (Gael Varoquaux)
Date: Sun, 25 Feb 2007 01:10:39 +0100
Subject: [SciPy-user] Carateristic distance in a cloud of points
In-Reply-To: <20070225000303.GJ7867@clipper.ens.fr>
References: <45E07996.3000307@gmail.com> <20070224194200.GI7867@clipper.ens.fr>
	<ce557a360702241313p2d67003am92ce8ca92ca8ff86@mail.gmail.com>
	<20070225000303.GJ7867@clipper.ens.fr>
Message-ID: <20070225001039.GK7867@clipper.ens.fr>

Correcting a stupid mistake. It bothered me to leave it, sorry for the
noise.

Ga?l

On Sun, Feb 25, 2007 at 01:03:03AM +0100, Gael Varoquaux wrote:
> Interesting remarks. You forced me to think a bit more about what I was
> trying to achieve.

> What I am trying to do is to find out the right size to use for symbols
> when used on a 3D cloud of points. I am not sure what the right "typical
> distance" should be used. If those symbols are arrows then it seems that
> should be smaller than the typical inter-point distance. I have in mind
> something like this:

> if you have n points, find out the distribution of distances, divide it
> by n**3, then take the value at 0.2 from the smallest. 

> I am having diffculties expressing my point, but the idea would be to
> consider that the typical distribution will increase as n**3 (which is
							n**(1/3.)
> not obvious, for instance if the points are along a plane) and take the
> lower tail of the distribution, as we are interested in having symbols
> smaller than the inter-point distance. Taking not the smallest value, but
> the value at "20%" from the bottom helps getting rid of singular
> situations where a few points are very close but the major part is spread
> out.




From anand at soe.ucsc.edu  Sun Feb 25 13:32:55 2007
From: anand at soe.ucsc.edu (Anand Patil)
Date: Sun, 25 Feb 2007 10:32:55 -0800
Subject: [SciPy-user] Carateristic distance in a cloud of points
In-Reply-To: <mailman.3.1172426405.18012.scipy-user@scipy.org>
References: <mailman.3.1172426405.18012.scipy-user@scipy.org>
Message-ID: <45E1D657.8070806@cse.ucsc.edu>


>Correcting a stupid mistake. It bothered me to leave it, sorry for the
>noise.
>
>Ga?l
>
>On Sun, Feb 25, 2007 at 01:03:03AM +0100, Gael Varoquaux wrote:
>  
>
>>Interesting remarks. You forced me to think a bit more about what I was
>>trying to achieve.
>>    
>>
>
>  
>
>>What I am trying to do is to find out the right size to use for symbols
>>when used on a 3D cloud of points. I am not sure what the right "typical
>>distance" should be used. If those symbols are arrows then it seems that
>>should be smaller than the typical inter-point distance. I have in mind
>>something like this:
>>    
>>
>
>  
>
>>if you have n points, find out the distribution of distances, divide it
>>by n**3, then take the value at 0.2 from the smallest. 
>>    
>>
>
>  
>
>>I am having diffculties expressing my point, but the idea would be to
>>consider that the typical distribution will increase as n**3 (which is
>>    
>>
>							n**(1/3.)
>  
>
>>not obvious, for instance if the points are along a plane) and take the
>>lower tail of the distribution, as we are interested in having symbols
>>smaller than the inter-point distance. Taking not the smallest value, but
>>the value at "20%" from the bottom helps getting rid of singular
>>situations where a few points are very close but the major part is spread
>>out.
>>    
>>
Hi Gael,

Scaling relative to the cloud of points might be an easier way to go 
than scaling relative to the actual interpoint spacing. It would make 
sure your arrowheads are readable on the plot, even though some may 
appear oversized relative to their shafts. Also, points that are far 
apart in 3d space might appear close when viewed from particular angles, 
like 'optical doubles' in astronomy.

If you want to make your symbols roughly the right size relative to the 
whole cloud, you might like a widely used quick-and-dirty method from 
statistics.:

from scipy import *
from numpy.linalg import eigh

points = 2.*randn(100,3)
C = cov(points.transpose())
D,V=eigh(points)

Then the `error ellipse', the ellipsoid that kind of sort of tries to 
fit the point cloud, has major axes given by the columns of V with 
length equal to the sqrt of the corresponding elements of D. You could 
then calculate approximately how big or small the point cloud looks by 
projecting the major axes into your viewing plane.

Hope that helps... that would be a milestone for me, my first time 
actually helping someone else on a Python mailing list.

Cheers,
Anand


From rshepard at appl-ecosys.com  Sun Feb 25 14:10:34 2007
From: rshepard at appl-ecosys.com (Rich Shepard)
Date: Sun, 25 Feb 2007 11:10:34 -0800 (PST)
Subject: [SciPy-user] Need Advice With Arrays and Calculating
	Eigenvectors
In-Reply-To: <Pine.LNX.4.64.0702220948190.21009@salmo.appl-ecosys.com>
References: <Pine.LNX.4.64.0702220948190.21009@salmo.appl-ecosys.com>
Message-ID: <Pine.LNX.4.64.0702251058460.25666@salmo.appl-ecosys.com>

On Thu, 22 Feb 2007, Rich Shepard wrote:

>   As a newcomer to python, NumPy, and SciPy I need to learn how to most
> efficiently manipulate data. Today's need is reducing a list of tuples to
> three smaller lists of tuples, creating a symmetrical matrix from each list,
> and calculating the Eigenvector of each of the three symmetrical matrices.

   I have a function that does part of the above. I know that it's highly
crude, inefficient, and not taking advantage of python functional coding features
such as introspection. That's because I'm not yet sure how to code it
better.

   First, a python message when I invoke the application. In this module, I
have 'from scipi import *' per Travis' book. What I see as the application
loads is:

Overwriting info=<function info at 0xb60e2614> from scipy.misc (was
<function info at 0xb60b5d84> from numpy.lib.utils)

This doesn't seem to harm anything, but perhaps it needs fixing.

   Second, here's the function (followed by the output of the print
statements):

def weightcalc():

   # First: average for each position by category
   stmt1 = """select cat, pos, avg(pr1), avg(pr2), avg(pr3), avg(pr4), avg(pr5),
              avg(pr6), avg(pr7), avg(pr8), avg(pr9), avg(pr10), avg(pr11),
              avg(pr12), avg(pr13), avg(pr14), avg(pr15), avg(pr16),
              avg(pr17), avg(pr18), avg(pr19), avg(pr20), avg(pr21), avg(pr22),
              avg(pr23), avg(pr24), avg(pr25), avg(pr26), avg(pr27), avg(pr28)
              from voting group by cat, pos"""
   appData.cur.execute(stmt1)
   prefbar = appData.cur.fetchall()

   # Now, average for all positions within each category
   ec = []
   en = []
   ep = []
   nc = []
   nn = []
   np = []
   sc = []
   sn = []
   sp = []
   catEco = []
   catNat = []
   catSoc = []
   diag = identity(8, dtype=float)

   for item in prefbar:
     if item[0] == 'eco' and item[1] == 'con':
       ec.append(item[2:])
     if item[0] == 'eco' and item[1] == 'neu':
       en.append(item[2:])
     if item[0] == 'eco' and item[1] == 'pro':
       ep.append(item[2:])

     if item[0] == 'nat' and item[1] == 'con':
       nc.append(item[2:])
     if item[0] == 'nat' and item[1] == 'neu':
       nn.append(item[2:])
     if item[0] == 'nat' and item[1] == 'pro':
       np.append(item[2:])

     if item[0] == 'soc' and item[1] == 'con':
       sc.append(item[2:])
     if item[0] == 'soc' and item[1] == 'neu':
       sn.append(item[2:])
     if item[0] == 'soc' and item[1] == 'pro':
       sp.append(item[2:])

   # three lists, each of three tuples. Need to be converted to arrays and averaged.
   catEco.append(ec + en + ep)
   print catEco, '\n'
   catNat.append(nc + nn + np)
   print catNat, '\n'
   catSoc.append(sc + sn + sp)
   print catSoc

and here is the output of catEco:

[[(2.4884848484848487, 3.3123939393939401, 3.144090909090909,
2.5676060606060607, 3.2095151515151517, 3.4157878787878788,
2.5132727272727275, 2.7514242424242425, 2.9628787878787879,
2.446939393939394, 2.7069393939393938, 3.1676666666666669,
2.8530303030303035, 2.6058484848484853, 3.0955454545454546,
2.6283939393939395, 2.4350606060606061, 3.2610303030303034,
2.3926969696969698, 2.4951212121212123, 2.5276666666666676,
2.668848484848485, 3.4265757575757578, 2.9714545454545456,
2.8431818181818187, 3.0674545454545461, 2.8712727272727272,
2.1262424242424243), (2.0477142857142856, 1.0064285714285715,
3.1869285714285711, 3.5895000000000001, 3.9467142857142861,
3.2696428571428569, 2.9104285714285716, 2.5850714285714282,
4.8555714285714293, 3.3554999999999997, 2.3430714285714282,
3.5795714285714282, 1.3627857142857143, 0.83778571428571436,
2.4744999999999999, 2.8067142857142855, 3.143642857142857,
2.4637857142857138, 3.7382142857142857, 3.2875000000000001,
2.1167857142857143, 3.5459285714285715, 3.5667142857142857,
3.1280714285714284, 3.580428571428572, 1.0882857142857143,
3.0217142857142858, 3.8292857142857142), (2.3360769230769227,
2.0547692307692311, 2.8591538461538457, 2.4986923076923073,
2.809769230769231, 2.2041538461538464, 3.9557692307692309,
3.1109230769230769, 1.8777692307692309, 1.6783846153846156,
2.4337692307692307, 1.8520769230769232, 4.0975384615384618,
3.3513846153846147, 1.9008461538461536, 2.9993846153846158,
1.8076923076923079, 2.6881538461538463, 2.453615384615385,
3.5579999999999998, 1.2396153846153848, 3.8225384615384614,
2.8304615384615386, 2.6258461538461537, 2.2387692307692308,
3.381615384615384, 2.8569999999999998, 2.9676153846153848)]]

   Where I am stuck is making catEco (and the other two lists) NumPy arrays,
and calculating the average of the three values in the same position within
each tuple. Also, I need no more than 2 decimal places for each value, but
I don't know where to place a format specifier.

   Please suggest how to both improve the function's structure and produce a
ndarray[] that is the average tuple values in each list.

Rich

-- 
Richard B. Shepard, Ph.D.               |    The Environmental Permitting
Applied Ecosystem Services, Inc.        |          Accelerator(TM)
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863


From rshepard at appl-ecosys.com  Sun Feb 25 16:08:52 2007
From: rshepard at appl-ecosys.com (Rich Shepard)
Date: Sun, 25 Feb 2007 13:08:52 -0800 (PST)
Subject: [SciPy-user] Need Advice With Arrays and Calculating
	Eigenvectors
In-Reply-To: <Pine.LNX.4.64.0702251058460.25666@salmo.appl-ecosys.com>
References: <Pine.LNX.4.64.0702220948190.21009@salmo.appl-ecosys.com>
	<Pine.LNX.4.64.0702251058460.25666@salmo.appl-ecosys.com>
Message-ID: <Pine.LNX.4.64.0702251302350.25666@salmo.appl-ecosys.com>

On Sun, 25 Feb 2007, Rich Shepard wrote:

>   I have a function that does part of the above. I know that it's highly
> crude, inefficient, and not taking advantage of python functional coding features
> such as introspection. That's because I'm not yet sure how to code it
> better.

   Would still appreciate suggestions for tightening it up. The latest
version is this:

def weightcalc():
   # First: average for each position by category
   meanvotes = []
   stmt1 = """select cat, pos, avg(pr1), avg(pr2), avg(pr3), avg(pr4), avg(pr5),
              avg(pr6), avg(pr7), avg(pr8), avg(pr9), avg(pr10), avg(pr11),
              avg(pr12), avg(pr13), avg(pr14), avg(pr15), avg(pr16),
              avg(pr17), avg(pr18), avg(pr19), avg(pr20), avg(pr21), avg(pr22),
              avg(pr23), avg(pr24), avg(pr25), avg(pr26), avg(pr27), avg(pr28)
              from voting group by cat, pos"""
   appData.cur.execute(stmt1)
   prefbar = appData.cur.fetchall()
   # print prefbar

   # Now, average for all positions within each category
   ec = []
   en = []
   ep = []
   nc = []
   nn = []
   np = []
   sc = []
   sn = []
   sp = []
   catEco = []
   catNat = []
   catSoc = []
   diag = identity(8, dtype=float)

   for item in prefbar:
     if item[0] == 'eco' and item[1] == 'con':
       ec.append(item[2:])
     if item[0] == 'eco' and item[1] == 'neu':
       en.append(item[2:])
     if item[0] == 'eco' and item[1] == 'pro':
       ep.append(item[2:])

     if item[0] == 'nat' and item[1] == 'con':
       nc.append(item[2:])
     if item[0] == 'nat' and item[1] == 'neu':
       nn.append(item[2:])
     if item[0] == 'nat' and item[1] == 'pro':
       np.append(item[2:])

     if item[0] == 'soc' and item[1] == 'con':
       sc.append(item[2:])
     if item[0] == 'soc' and item[1] == 'neu':
       sn.append(item[2:])
     if item[0] == 'soc' and item[1] == 'pro':
       sp.append(item[2:])

   # three lists, each of three tuples. Need to be converted to arrays and averaged.
   catEco.append(ec + en + ep)
   catNat.append(nc + nn + np)
   catSoc.append(sc + sn + sp)

   # here are the numpy arrays
   aEco = array(catEco, dtype=float)
   aNat = array(catNat, dtype=float)
   aSoc = array(catSoc, dtype=float)

   # here are the numpy arrays of averages
   barEco = average(aEco, axis=1)
   barNat = average(aNat, axis=1)
   barSoc = average(aSoc, axis=1)

   Got all this worked out by reading the book and trial-and-error.

   Next step is to convert each of barEco, barNat, and barSoc into
symmetrical matrices with unit diagonals. Each of these arrays holds the
values to the right of the diagonal in the symmetrical matrices; the
matching cells to the left of the diagonal are (1.0 / right cell value).

Rich

-- 
Richard B. Shepard, Ph.D.               |    The Environmental Permitting
Applied Ecosystem Services, Inc.        |          Accelerator(TM)
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863


From rshepard at appl-ecosys.com  Sun Feb 25 17:16:52 2007
From: rshepard at appl-ecosys.com (Rich Shepard)
Date: Sun, 25 Feb 2007 14:16:52 -0800 (PST)
Subject: [SciPy-user] Transforming 1-d array to 2-d array
Message-ID: <Pine.LNX.4.64.0702251412500.25666@salmo.appl-ecosys.com>

   I have this array (called barEco):

[[ 2.29075869  2.12453058  3.06339111  2.88526612  3.32199956  2.96319486
    3.12649018  2.81580625  3.23207315  2.493608    2.49459335  2.86643834
    2.77111816  2.26500627  2.4902972   2.81149761  2.46213192  2.80432329
    2.86150888  3.1135404   1.96135592  3.34577184  3.27458386  2.90845738
    2.88745987  2.51245188  2.91666234  2.97438117]]

and I want to convert it to:

[[ -- 2.29075869  2.12453058  3.06339111  2.88526612  3.32199956  2.96319486 3.12649018]
  [ --    --       2.81580625  3.23207315  2.493608    2.49459335  2.86643834 2.77111816]
  [ --    --           --      2.26500627  2.4902972   2.81149761  2.46213192 2.80432329]
  [ --    --           --          --      2.86150888  3.1135404   1.96135592 3.34577184]
  [ --    --           --          --           --     3.27458386  2.90845738 2.88745987]
  [ --    --           --          --           --         --      2.51245188 2.91666234]
  [ --    --           --          --           --         --          --     2.97438117]
  [ --    --           --          --           --         --          --          --   ]]

with 1.00 as the diagonal.

   It appears that the eye() function is the tool, but when I try

 	foo = eye(barEco,8,8,1)
 	print foo

python responds

Traceback (most recent call last):
   File "/data1/eikos/scopingPage.py", line 184, in OnCalcWeights
     inpWts = functions.weightcalc()
   File "/data1/eikos/functions.py", line 164, in weightcalc
     foo = eye(barEco,8,8,1)
   File "/usr/lib/python2.4/site-packages/numpy/lib/twodim_base.py", line 48,
in eye
     m = equal(subtract.outer(arange(N), arange(M)),-k)
TypeError: only length-1 arrays can be converted to Python scalars

   So, either I used eye() incorrectly, or that's not how to make the
conversion. What should I be doing?

Rich

-- 
Richard B. Shepard, Ph.D.               |    The Environmental Permitting
Applied Ecosystem Services, Inc.        |          Accelerator(TM)
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863


From rshepard at appl-ecosys.com  Sun Feb 25 17:31:35 2007
From: rshepard at appl-ecosys.com (Rich Shepard)
Date: Sun, 25 Feb 2007 14:31:35 -0800 (PST)
Subject: [SciPy-user] Transforming 1-d array to 2-d array
In-Reply-To: <Pine.LNX.4.64.0702251412500.25666@salmo.appl-ecosys.com>
References: <Pine.LNX.4.64.0702251412500.25666@salmo.appl-ecosys.com>
Message-ID: <Pine.LNX.4.64.0702251430270.25666@salmo.appl-ecosys.com>

On Sun, 25 Feb 2007, Rich Shepard wrote:

>   It appears that the eye() function is the tool, but when I try
>
> 	foo = eye(barEco,8,8,1)
> 	print foo

   I've also tried triu() and mat(), but neither prints the results I need.

Rich

-- 
Richard B. Shepard, Ph.D.               |    The Environmental Permitting
Applied Ecosystem Services, Inc.        |          Accelerator(TM)
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863


From williams at astro.ox.ac.uk  Sun Feb 25 18:57:22 2007
From: williams at astro.ox.ac.uk (Michael Williams)
Date: Sun, 25 Feb 2007 23:57:22 +0000
Subject: [SciPy-user] how to uninstall Mac OS X ScipySuperpack Intel?
In-Reply-To: <45DF6AF4.9010404@gmail.com>
References: <4ae645d30702231412j7d1a3ce3seaee457e40839109@mail.gmail.com>
	<45DF6AF4.9010404@gmail.com>
Message-ID: <20070225235722.GD11570@astro.ox.ac.uk>

On Fri, Feb 23, 2007 at 04:30:12PM -0600, Robert Kern wrote:
> There's no easy way. Blame Apple for that. There is a hard way,
> though. In /Library/Receipts, there are bundle directories with
> metadata about the packages that you have installed. You need to use
> the lsbom(1) program to extract the file names:

You can also extract this list by double-clicking on the .[m]pkg file,
launching Installer, then choosing Show Files from the File menu.

-- Mike


From ronald at ivec.org  Sun Feb 25 20:49:22 2007
From: ronald at ivec.org (Ronald Jones)
Date: Mon, 26 Feb 2007 10:49:22 +0900
Subject: [SciPy-user] Failed scipy 0.5.2 tests on IA64 Intel platform
Message-ID: <1172454562.4656.4.camel@sambucca.ivec.org>

Hello,

I have recently installed numpy1.0.1/scipy0.5.2 on a IA64 machine using
the intel compiler(v9.1.043) with the mkl (v8.1.014) libraries. 

The code compiles and runs. But six of the scipy.test(1) tests fail. Is
this a known problem?

There is also a problem with scipy.linsolve.umfpack. Is this significant?

I tried the 19 Feb svn version of scipy and it failed 10 tests.


The output of the scipy 0.5.2 tests are attached.

regards, 

Ronald


-- 
Ronald Jones
iVEC, 'The hub of advanced computing in Western Australia'
26 Dick Perry Avenue, Technology Park
Kensington WA 6151
Australia

Phone: +61 8 6436 8633
Fax: +61 8 6436 8555
Email: ronald.jones at ivec.org
WWW:  http://www.ivec.org
-------------- next part --------------
scipy.test(1)
  Found 4 tests for scipy.io.array_import
  Found 1 tests for scipy.cluster.vq
  Found 128 tests for scipy.linalg.fblas
  Found 397 tests for scipy.ndimage
  Found 10 tests for scipy.integrate.quadpack
  Found 98 tests for scipy.stats.stats
  Found 53 tests for scipy.linalg.decomp
  Found 3 tests for scipy.integrate.quadrature
  Found 96 tests for scipy.sparse.sparse
  Found 20 tests for scipy.fftpack.pseudo_diffs
  Found 6 tests for scipy.optimize.optimize
  Found 6 tests for scipy.interpolate.fitpack
  Found 6 tests for scipy.interpolate
  Found 12 tests for scipy.io.mmio
  Found 10 tests for scipy.stats.morestats
  Found 4 tests for scipy.linalg.lapack
  Found 18 tests for scipy.fftpack.basic
  Found 4 tests for scipy.io.recaster
Warning: FAILURE importing tests for <module 'scipy.linsolve.umfpack' from '.../linsolve/umfpack/__init__.pyc'>
/opt/scipy/0.5.2-forceIntel/lib/python2.4/site-packages/scipy/linsolve/umfpack/tests/test_umfpack.py:17: AttributeError: 'module' object has no attribute 'umfpack' (in ?)
  Found 4 tests for scipy.optimize.zeros
  Found 28 tests for scipy.io.mio
  Found 41 tests for scipy.linalg.basic
  Found 2 tests for scipy.maxentropy.maxentropy
  Found 358 tests for scipy.special.basic
  Found 128 tests for scipy.lib.blas.fblas
  Found 7 tests for scipy.linalg.matfuncs

****************************************************************
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.
****************************************************************

  Found 42 tests for scipy.lib.lapack
Warning: FAILURE importing tests for <module 'scipy.linsolve.umfpack.umfpack' from '...y/linsolve/umfpack/umfpack.pyc'>
/opt/scipy/0.5.2-forceIntel/lib/python2.4/site-packages/scipy/linsolve/umfpack/tests/test_umfpack.py:17: AttributeError: 'module' object has no attribute 'umfpack' (in ?)
  Found 1 tests for scipy.optimize.cobyla
  Found 16 tests for scipy.lib.blas
  Found 1 tests for scipy.integrate
  Found 14 tests for scipy.linalg.blas
  Found 70 tests for scipy.stats.distributions
  Found 4 tests for scipy.fftpack.helper
  Found 4 tests for scipy.signal.signaltools
  Found 0 tests for __main__
Warning: 1000000 bytes requested, 20 bytes read.
........caxpy:n=4
..caxpy:n=3
....ccopy:n=4
..ccopy:n=3
.............cscal:n=4
....cswap:n=4
..cswap:n=3
.....daxpy:n=4
..daxpy:n=3
....dcopy:n=4
..dcopy:n=3
.............dscal:n=4
....dswap:n=4
..dswap:n=3
.....saxpy:n=4
..saxpy:n=3
....scopy:n=4
..scopy:n=3
.............sscal:n=4
....sswap:n=4
..sswap:n=3
.....zaxpy:n=4
..zaxpy:n=3
....zcopy:n=4
..zcopy:n=3
.............zscal:n=4
....zswap:n=4
..zswap:n=3
..........F......................................................................................................................................................................................................F.........F.......................................................................................................................F........................................................................................................................................................................................................................................................................................................................................................./opt/scipy/0.5.2/lib/python2.4/site-packages/scipy/interpolate/fitpack2.py:457: 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)
.................................................................................................................................................................................................................................................................................................F..............................................................................................................................................................................................................caxpy:n=4
..caxpy:n=3
....ccopy:n=4
..ccopy:n=3
.............cscal:n=4
....cswap:n=4
..cswap:n=3
.....daxpy:n=4
..daxpy:n=3
....dcopy:n=4
..dcopy:n=3
.............dscal:n=4
....dswap:n=4
..dswap:n=3
.....saxpy:n=4
..saxpy:n=3
....scopy:n=4
..scopy:n=3
.............sscal:n=4
....sswap:n=4
..sswap:n=3
.....zaxpy:n=4
..zaxpy:n=3
....zcopy:n=4
..zcopy:n=3
.............zscal:n=4
....zswap:n=4
..zswap:n=3
.................................F...............................................................................................................................
======================================================================
FAIL: affine transform 9
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/scipy/0.5.2-forceIntel/lib/python2.4/site-packages/scipy/ndimage/tests/test_ndimage.py", line 1849, in test_affine_transform09
AssertionError

======================================================================
FAIL: geometric transform 10
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/scipy/0.5.2-forceIntel/lib/python2.4/site-packages/scipy/ndimage/tests/test_ndimage.py", line 1575, in test_geometric_transform10
AssertionError

======================================================================
FAIL: geometric transform 22
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/scipy/0.5.2-forceIntel/lib/python2.4/site-packages/scipy/ndimage/tests/test_ndimage.py", line 1697, in test_geometric_transform22
AssertionError

======================================================================
FAIL: shift 9
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/scipy/0.5.2-forceIntel/lib/python2.4/site-packages/scipy/ndimage/tests/test_ndimage.py", line 2066, in test_shift09
AssertionError

======================================================================
FAIL: check_pbdv (scipy.special.tests.test_basic.test_cephes)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/scipy/0.5.2-forceIntel/lib/python2.4/site-packages/scipy/special/tests/test_basic.py", line 367, in check_pbdv
  File "/opt/numpy/1.0.1//lib/python2.4/site-packages/numpy/testing/utils.py", line 137, in assert_equal
    assert_equal(actual[k], desired[k], 'item=%r\n%s' % (k,err_msg), verbose)
  File "/opt/numpy/1.0.1//lib/python2.4/site-packages/numpy/testing/utils.py", line 143, in assert_equal
    assert desired == actual, msg
AssertionError: 
Items are not equal:
item=1

 ACTUAL: 1.0
 DESIRED: 0.0

======================================================================
FAIL: check_syev (scipy.lib.tests.test_lapack.test_flapack_float)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/scipy/0.5.2-forceIntel/lib/python2.4/site-packages/scipy/lib/lapack/tests/esv_tests.py", line 15, in check_syev
  File "/opt/numpy/1.0.1//lib/python2.4/site-packages/numpy/testing/utils.py", line 230, in assert_array_almost_equal
    header='Arrays are not almost equal')
  File "/opt/numpy/1.0.1//lib/python2.4/site-packages/numpy/testing/utils.py", line 215, in assert_array_compare
    assert cond, msg
AssertionError: 
Arrays are not almost equal

(mismatch 33.3333333333%)
 x: array([ 0.12523627,  0.38202888, -0.27607083])
 y: array([ 0.1252365 ,  0.38202912, -0.27607253], dtype=float32)

----------------------------------------------------------------------
Ran 1596 tests in 3.633s

FAILED (failures=6)

Don't worry about a warning regarding the number of bytes read.
Took 13 points.
Resizing... 16 17 24
Resizing... 20 7 35
Resizing... 23 7 47
Resizing... 24 25 58
Resizing... 28 7 68
Resizing... 28 27 73
Use minimum degree ordering on A'+A.
Use minimum degree ordering on A'+A.
Resizing... 16 17 24
Resizing... 20 7 35
Resizing... 23 7 47
Resizing... 24 25 58
Resizing... 28 7 68
Resizing... 28 27 73
Use minimum degree ordering on A'+A.
Resizing... 16 17 24
Resizing... 20 7 35
Resizing... 23 7 47
Resizing... 24 25 58
Resizing... 28 7 68
Resizing... 28 27 73
Use minimum degree ordering on A'+A.
Ties preclude use of exact statistic.
Ties preclude use of exact statistic.

****************************************************************
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.
****************************************************************

Result may be inaccurate, approximate err = 1.292748962e-08
Result may be inaccurate, approximate err = 7.27595761418e-12
Residual: 1.05006926991e-07

****************************************************************
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.
****************************************************************

<unittest.TextTestRunner object at 0x20000000048dba90>

From a.u.r.e.l.i.a.n at gmx.net  Mon Feb 26 03:17:02 2007
From: a.u.r.e.l.i.a.n at gmx.net (Johannes Loehnert)
Date: Mon, 26 Feb 2007 09:17:02 +0100
Subject: [SciPy-user] Need Advice With Arrays and Calculating
	Eigenvectors
In-Reply-To: <Pine.LNX.4.64.0702251302350.25666@salmo.appl-ecosys.com>
References: <Pine.LNX.4.64.0702220948190.21009@salmo.appl-ecosys.com>
	<Pine.LNX.4.64.0702251058460.25666@salmo.appl-ecosys.com>
	<Pine.LNX.4.64.0702251302350.25666@salmo.appl-ecosys.com>
Message-ID: <200702260917.02628.a.u.r.e.l.i.a.n@gmx.net>

Hi,

here's your code as I would have written it. :-) My comments are those 
starting with four #'s.

As a side remark, usually one uses four spaces for intendation. I hope I did
not mix it up.

An alternative approach to what I did below would be to map the keys ('eco',
    'nat', 'soc') to integers and use lists instead of dicts.

Johannes


def weightcalc():
   # First: average for each position by category
   meanvotes = []     #### Do you use this?
   #### not much can be done about this
   stmt1 = """select cat, pos, avg(pr1), avg(pr2), avg(pr3), avg(pr4),
avg(pr5), avg(pr6), avg(pr7), avg(pr8), avg(pr9), avg(pr10), avg(pr11),
avg(pr12), avg(pr13), avg(pr14), avg(pr15), avg(pr16), avg(pr17),
avg(pr18), avg(pr19), avg(pr20), avg(pr21), avg(pr22), avg(pr23),
avg(pr24), avg(pr25), avg(pr26), avg(pr27), avg(pr28) from voting group by
cat, pos"""
   appData.cur.execute(stmt1)
   prefbar = appData.cur.fetchall()
   # print prefbar

   #### using a dict saves us from creating all the lists
   data = {}

   for item in prefbar:
      #### create dict entries on demand
      if item[0] not in data:
         data[item[0]] = {}
      if item[1] not in data[item[0]]:
         data[item[0]][item[1]] = []

      #### append to list
      data[item[0]][item[1]].append(item[2:])

   catarrays = {}
   averages = {}
   for key in ['eco', 'nat', 'soc']:
      catarrays[key] = []
      for subkey in ['con', 'neu', 'pro']
         #### btw. I don't understand why you throw con, neu, pro in one list
         #### now after sorting them out in advance.
         try:
            catarrays[key].append(data[key][subkey])
         except KeyError:
             #### data[key][subkey] was not set
             print 'No data for %s,%s'%(key, subkey)
      #### convert to array
      catarrays[key] = array(catarrays[key])
      #### average
      averages[key] = average(catarrays(key), axis=1)


From lev at columbia.edu  Mon Feb 26 05:46:56 2007
From: lev at columbia.edu (Lev Givon)
Date: Mon, 26 Feb 2007 05:46:56 -0500
Subject: [SciPy-user] question re odeint
Message-ID: <20070226104656.GA6348@localhost.cc.columbia.edu>

While using scipy.integrate.odeint recently, I noticed that it
modifies the object passed as the system's initial value. Is this
behavior intentional? It seems that it would be preferable for odeint
to use a copy of the initial value rather than manipulating whatever
is passed as the second parameter directly.

							L.G.


From nwagner at iam.uni-stuttgart.de  Mon Feb 26 06:38:20 2007
From: nwagner at iam.uni-stuttgart.de (Nils Wagner)
Date: Mon, 26 Feb 2007 12:38:20 +0100
Subject: [SciPy-user] question re odeint
In-Reply-To: <20070226104656.GA6348@localhost.cc.columbia.edu>
References: <20070226104656.GA6348@localhost.cc.columbia.edu>
Message-ID: <45E2C6AC.6090409@iam.uni-stuttgart.de>

Lev Givon wrote:
> While using scipy.integrate.odeint recently, I noticed that it
> modifies the object passed as the system's initial value. Is this
> behavior intentional? It seems that it would be preferable for odeint
> to use a copy of the initial value rather than manipulating whatever
> is passed as the second parameter directly.
>
> 							L.G.
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user
>   
Fixed in svn

http://projects.scipy.org/scipy/scipy/changeset/2704

Nils



From novin01 at gmail.com  Mon Feb 26 06:15:43 2007
From: novin01 at gmail.com (Dave)
Date: Mon, 26 Feb 2007 11:15:43 +0000 (UTC)
Subject: [SciPy-user] Transforming 1-d array to 2-d array
References: <Pine.LNX.4.64.0702251412500.25666@salmo.appl-ecosys.com>
	<Pine.LNX.4.64.0702251430270.25666@salmo.appl-ecosys.com>
Message-ID: <loom.20070226T120344-182@post.gmane.org>

Rich Shepard <rshepard <at> appl-ecosys.com> writes:

> 
> On Sun, 25 Feb 2007, Rich Shepard wrote:
> 
> >   It appears that the eye() function is the tool, but when I try
> >
> > 	foo = eye(barEco,8,8,1)
> > 	print foo
> 
>    I've also tried triu() and mat(), but neither prints the results I need.
> 
> Rich
> 

eye simply creates an array with ones on the diagonal. To solve this problem I
would create a zero array of the correct size and then index into the array.

#Define array size
N = 8

#Define the data to put in the upper-diagonal part of the array
myData = rand(N*(N-1)/2)

#Create an index to the upper-diagonal part
idx = triu(ones([8,8])-eye(8)).nonzero()

#Instantiate a zero array and populate the upper-triangular part with myData
A = zeros([N,N],dtype=float)
A[idx] = myData

#Place ones on the diagonal
A += eye(N)






From mjakubik at ta3.sk  Mon Feb 26 08:34:57 2007
From: mjakubik at ta3.sk (Marian Jakubik)
Date: Mon, 26 Feb 2007 14:34:57 +0100
Subject: [SciPy-user] Fitting - Gauss-normal distribution
Message-ID: <20070226143457.4a90b2db@jakubik.ta3.sk>

Hi, I am a SciPy newbie solving this problem:

I would like to fit data with gaussian normal distribution.... First, I
generated data:

list=normal(0.00714,0.0005,140)

Then I plot this data:

pylab.hist(list,20)

And at the end, I'd like to plot a gauss fit in the graph, also....

Could anyone help me, please?

Marian

This is my code:

from numpy import *
from RandomArray import *
import pylab as p

list=normal(0.00714,0.0005,140)

p.hist(list,20)
p.show()





From cimrman3 at ntc.zcu.cz  Mon Feb 26 08:48:01 2007
From: cimrman3 at ntc.zcu.cz (Robert Cimrman)
Date: Mon, 26 Feb 2007 14:48:01 +0100
Subject: [SciPy-user] ANN: new version of SFE (00.18.09) is available
Message-ID: <45E2E511.4040405@ntc.zcu.cz>

Hi,

version 00.18.09 brings an improved problem definition syntax (regions
are now per term, e.g. dw_poisson.Omega( ... )) and Navier-Stokes terms,
see examples at http://ui505p06-mbs.ntc.zcu.cz/sfe

cheers,
r.


From meesters at uni-mainz.de  Mon Feb 26 08:54:27 2007
From: meesters at uni-mainz.de (Christian Meesters)
Date: Mon, 26 Feb 2007 14:54:27 +0100
Subject: [SciPy-user] Fitting - Gauss-normal distribution
In-Reply-To: <20070226143457.4a90b2db@jakubik.ta3.sk>
References: <20070226143457.4a90b2db@jakubik.ta3.sk>
Message-ID: <200702261454.28465.meesters@uni-mainz.de>

Hi,

you are welcome to use this code - not tested, since it is only rougly 
translated from a more complex function of mine:

from scipy import std
from scipy.optimize import leastsq

def fit_gaussian(x_data, y_data): # ?_data should be numpy arrays
	# estimate the expectation value
        expect = y_data[argmax(x_data)]
	# find +/- 10 elements around the peak
        subxdata = x_data[expect-10:expect+11]
        subydata = y_data[expect-10:expect+11]
	#estimate the std 
	sigma = std([inpt for inpt subydata  in if inpt > 100.0])/len(subydata)**2 
#really dirty hack!!
	#estimate the maximum
        maximum = max(y_data)
        #define starting paramters (as 'first guess')
        parameters0 = [sigma, expect, maximum]
	
	def __residuals(params, value, inpt):
            """
                calculates the resdiuals
            """
            sigma, expect, maximum = params
            err = value - (maximum * exp((-((inpt-expect)/sigma)**2)/2)) 
            #the equation above allows for adding a constant
            return err

	def __peval(inpt, params):
            """
                evaluates the function
            """
            sigma, expect, maximum = params
            return (maximum * exp((-((inpt-expect)/sigma)**2)/2))

	#calculate fit paramters    
        plsq = leastsq(__residuals,  parameters0, args=(subintensity, 
subchannel))
        #calculate 'full width half maximum' parameter for a gaussian fit
        fwhm = 2*sqrt(2*log(2))*plsq[0][0]
        return plsq[0], fwhm, subxdata , subydata, __peval(subchannel, 
plsq[0])

The code above is not really neat, but allows for a peak shifted along your 
'y-axis'. The return value is a tuple of (simga,mu,max),FWHMsubarray of x 
data, subarray of ydata,
and the fitted function as an array.

 See 
http://www.scipy.org/Wiki/Documentation?action=AttachFile&do=get&target=scipy_tutorial.pdf 
for more information - the description of leastsq is really good!

HTH
Christian






On Monday 26 February 2007 14:34, Marian Jakubik wrote:
> Hi, I am a SciPy newbie solving this problem:
>
> I would like to fit data with gaussian normal distribution.... First, I
> generated data:
>
> list=normal(0.00714,0.0005,140)
>
> Then I plot this data:
>
> pylab.hist(list,20)
>
> And at the end, I'd like to plot a gauss fit in the graph, also....
>
> Could anyone help me, please?
>
> Marian
>
> This is my code:
>
> from numpy import *
> from RandomArray import *
> import pylab as p
>
> list=normal(0.00714,0.0005,140)
>
> p.hist(list,20)
> p.show()
>
>
>
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user


From david.huard at gmail.com  Mon Feb 26 10:04:16 2007
From: david.huard at gmail.com (David Huard)
Date: Mon, 26 Feb 2007 10:04:16 -0500
Subject: [SciPy-user] Fitting - Gauss-normal distribution
In-Reply-To: <200702261454.28465.meesters@uni-mainz.de>
References: <20070226143457.4a90b2db@jakubik.ta3.sk>
	<200702261454.28465.meesters@uni-mainz.de>
Message-ID: <91cf711d0702260704i2e52d4b1j48927d5dee4678dd@mail.gmail.com>

Hi Marian,

You could fit the normal using the method of moments:

mu = list.mean()
sigma = list.std()

x = linspace(list.min(), list.max(), 100)
pdf = scipy.stats.norm.pdf(x, mu, sigma)
s = subplot(111)
s.plot(x,y)
s.hist(list, 20, normed=True)


David

2007/2/26, Christian Meesters <meesters at uni-mainz.de>:
>
> Hi,
>
> you are welcome to use this code - not tested, since it is only rougly
> translated from a more complex function of mine:
>
> from scipy import std
> from scipy.optimize import leastsq
>
> def fit_gaussian(x_data, y_data): # ?_data should be numpy arrays
>         # estimate the expectation value
>         expect = y_data[argmax(x_data)]
>         # find +/- 10 elements around the peak
>         subxdata = x_data[expect-10:expect+11]
>         subydata = y_data[expect-10:expect+11]
>         #estimate the std
>         sigma = std([inpt for inpt subydata  in if inpt > 100.0
> ])/len(subydata)**2
> #really dirty hack!!
>         #estimate the maximum
>         maximum = max(y_data)
>         #define starting paramters (as 'first guess')
>         parameters0 = [sigma, expect, maximum]
>
>         def __residuals(params, value, inpt):
>             """
>                 calculates the resdiuals
>             """
>             sigma, expect, maximum = params
>             err = value - (maximum * exp((-((inpt-expect)/sigma)**2)/2))
>             #the equation above allows for adding a constant
>             return err
>
>         def __peval(inpt, params):
>             """
>                 evaluates the function
>             """
>             sigma, expect, maximum = params
>             return (maximum * exp((-((inpt-expect)/sigma)**2)/2))
>
>         #calculate fit paramters
>         plsq = leastsq(__residuals,  parameters0, args=(subintensity,
> subchannel))
>         #calculate 'full width half maximum' parameter for a gaussian fit
>         fwhm = 2*sqrt(2*log(2))*plsq[0][0]
>         return plsq[0], fwhm, subxdata , subydata, __peval(subchannel,
> plsq[0])
>
> The code above is not really neat, but allows for a peak shifted along
> your
> 'y-axis'. The return value is a tuple of (simga,mu,max),FWHMsubarray of x
> data, subarray of ydata,
> and the fitted function as an array.
>
> See
>
> http://www.scipy.org/Wiki/Documentation?action=AttachFile&do=get&target=scipy_tutorial.pdf
> for more information - the description of leastsq is really good!
>
> HTH
> Christian
>
>
>
>
>
>
> On Monday 26 February 2007 14:34, Marian Jakubik wrote:
> > Hi, I am a SciPy newbie solving this problem:
> >
> > I would like to fit data with gaussian normal distribution.... First, I
> > generated data:
> >
> > list=normal(0.00714,0.0005,140)
> >
> > Then I plot this data:
> >
> > pylab.hist(list,20)
> >
> > And at the end, I'd like to plot a gauss fit in the graph, also....
> >
> > Could anyone help me, please?
> >
> > Marian
> >
> > This is my code:
> >
> > from numpy import *
> > from RandomArray import *
> > import pylab as p
> >
> > list=normal(0.00714,0.0005,140)
> >
> > p.hist(list,20)
> > p.show()
> >
> >
> >
> > _______________________________________________
> > SciPy-user mailing list
> > SciPy-user at scipy.org
> > http://projects.scipy.org/mailman/listinfo/scipy-user
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20070226/32bc8d1e/attachment.html>

From david.warde.farley at utoronto.ca  Mon Feb 26 13:46:22 2007
From: david.warde.farley at utoronto.ca (David Warde-Farley)
Date: Mon, 26 Feb 2007 13:46:22 -0500
Subject: [SciPy-user] Fitting - Gauss-normal distribution
In-Reply-To: <91cf711d0702260704i2e52d4b1j48927d5dee4678dd@mail.gmail.com>
References: <20070226143457.4a90b2db@jakubik.ta3.sk>
	<200702261454.28465.meesters@uni-mainz.de>
	<91cf711d0702260704i2e52d4b1j48927d5dee4678dd@mail.gmail.com>
Message-ID: <1172515582.19486.17.camel@rodimus>

Hi,

So, it should be noted that the method of moments estimators for a
Gaussian distribution are also the maximum likelihood estimators, i.e.
the ones that maximize p(data|parameters), as well as the best least
square estimator (since taking the log of the density function gives you
scaled squared distance from the mean). So optimizing iteratively is
hardly necessary in this case.

i.e. what David Huard wrote is probably what you're looking for, and the
best you're going to be able to do if your goal is just to fit a
Gaussian to the data.

David


On Mon, 2007-02-26 at 10:04 -0500, David Huard wrote:
> Hi Marian,
> 
> You could fit the normal using the method of moments:
> 
> mu = list.mean()
> sigma = list.std()
> 
> x = linspace(list.min(), list.max(), 100)
> pdf = scipy.stats.norm.pdf(x, mu, sigma)
> s = subplot(111) 
> s.plot(x,y)
> s.hist(list, 20, normed=True)
> 
> 
> David
> 
> 2007/2/26, Christian Meesters <meesters at uni-mainz.de>:
>         Hi,
>         
>         you are welcome to use this code - not tested, since it is
>         only rougly
>         translated from a more complex function of mine:
>         
>         from scipy import std
>         from scipy.optimize import leastsq
>         
>         def fit_gaussian(x_data, y_data): # ?_data should be numpy
>         arrays 
>                 # estimate the expectation value
>                 expect = y_data[argmax(x_data)]
>                 # find +/- 10 elements around the peak
>                 subxdata = x_data[expect-10:expect+11]
>                 subydata = y_data[expect-10:expect+11] 
>                 #estimate the std
>                 sigma = std([inpt for inpt subydata  in if inpt >
>         100.0])/len(subydata)**2
>         #really dirty hack!!
>                 #estimate the maximum
>                 maximum = max(y_data)
>                 #define starting paramters (as 'first guess') 
>                 parameters0 = [sigma, expect, maximum]
>         
>                 def __residuals(params, value, inpt):
>                     """
>                         calculates the resdiuals
>                     """
>                     sigma, expect, maximum = params 
>                     err = value - (maximum *
>         exp((-((inpt-expect)/sigma)**2)/2))
>                     #the equation above allows for adding a constant
>                     return err
>         
>                 def __peval(inpt, params):
>                     """ 
>                         evaluates the function
>                     """
>                     sigma, expect, maximum = params
>                     return (maximum *
>         exp((-((inpt-expect)/sigma)**2)/2))
>         
>                 #calculate fit paramters 
>                 plsq = leastsq(__residuals,  parameters0,
>         args=(subintensity,
>         subchannel))
>                 #calculate 'full width half maximum' parameter for a
>         gaussian fit
>                 fwhm = 2*sqrt(2*log(2))*plsq[0][0]
>                 return plsq[0], fwhm, subxdata , subydata,
>         __peval(subchannel,
>         plsq[0])
>         
>         The code above is not really neat, but allows for a peak
>         shifted along your
>         'y-axis'. The return value is a tuple of
>         (simga,mu,max),FWHMsubarray of x 
>         data, subarray of ydata,
>         and the fitted function as an array.
>         
>         See
>         http://www.scipy.org/Wiki/Documentation?action=AttachFile&do=get&target=scipy_tutorial.pdf
>         for more information - the description of leastsq is really
>         good!
>         
>         HTH
>         Christian
>         
>         
>         
>         
>         
>         
>         On Monday 26 February 2007 14:34, Marian Jakubik wrote:
>         > Hi, I am a SciPy newbie solving this problem: 
>         >
>         > I would like to fit data with gaussian normal
>         distribution.... First, I
>         > generated data:
>         >
>         > list=normal(0.00714,0.0005,140)
>         >
>         > Then I plot this data:
>         >
>         > pylab.hist (list,20)
>         >
>         > And at the end, I'd like to plot a gauss fit in the graph,
>         also....
>         >
>         > Could anyone help me, please?
>         >
>         > Marian
>         >
>         > This is my code:
>         >
>         > from numpy import * 
>         > from RandomArray import *
>         > import pylab as p
>         >
>         > list=normal(0.00714,0.0005,140)
>         >
>         > p.hist(list,20)
>         > p.show()
>         >
>         >
>         >
>         > _______________________________________________ 
>         > SciPy-user mailing list
>         > SciPy-user at scipy.org
>         > http://projects.scipy.org/mailman/listinfo/scipy-user
>         _______________________________________________
>         SciPy-user mailing list
>         SciPy-user at scipy.org
>         http://projects.scipy.org/mailman/listinfo/scipy-user
> 
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user



From rshepard at appl-ecosys.com  Mon Feb 26 15:39:06 2007
From: rshepard at appl-ecosys.com (Rich Shepard)
Date: Mon, 26 Feb 2007 12:39:06 -0800 (PST)
Subject: [SciPy-user] Need Advice With Arrays and Calculating
	Eigenvectors
In-Reply-To: <200702260917.02628.a.u.r.e.l.i.a.n@gmx.net>
References: <Pine.LNX.4.64.0702220948190.21009@salmo.appl-ecosys.com>
	<Pine.LNX.4.64.0702251058460.25666@salmo.appl-ecosys.com>
	<Pine.LNX.4.64.0702251302350.25666@salmo.appl-ecosys.com>
	<200702260917.02628.a.u.r.e.l.i.a.n@gmx.net>
Message-ID: <Pine.LNX.4.64.0702261224061.31240@salmo.appl-ecosys.com>

On Mon, 26 Feb 2007, Johannes Loehnert wrote:

> here's your code as I would have written it. :-) My comments are those
> starting with four #'s.

   Thank you, Johannes.

> As a side remark, usually one uses four spaces for intendation. I hope I did
> not mix it up.

   Yes, I know that's the standard for python code contributed to projects.
I've used two space tabs for indenting C code for a couple of decades now,
and I find it easier to read. Since this code is being used by us, we format
for our convenience.

> An alternative approach to what I did below would be to map the keys ('eco',
>    'nat', 'soc') to integers and use lists instead of dicts.

   That can be done for this function. But, if dicts work, that's OK, too.

> def weightcalc():
>   # First: average for each position by category
>   meanvotes = []     #### Do you use this?

   No, I meant to take that out, and have.

>   #### not much can be done about this
>   stmt1 = """select cat, pos, avg(pr1), avg(pr2), avg(pr3), avg(pr4),
> avg(pr5), avg(pr6), avg(pr7), avg(pr8), avg(pr9), avg(pr10), avg(pr11),
> avg(pr12), avg(pr13), avg(pr14), avg(pr15), avg(pr16), avg(pr17),
> avg(pr18), avg(pr19), avg(pr20), avg(pr21), avg(pr22), avg(pr23),
> avg(pr24), avg(pr25), avg(pr26), avg(pr27), avg(pr28) from voting group by
> cat, pos"""
>   appData.cur.execute(stmt1)
>   prefbar = appData.cur.fetchall()
>   # print prefbar

   This is the source of the data: a SQLite3 database table.

>   #### using a dict saves us from creating all the lists
>   data = {}

>   for item in prefbar:
>      #### create dict entries on demand
>      if item[0] not in data:
>         data[item[0]] = {}
>      if item[1] not in data[item[0]]:
>         data[item[0]][item[1]] = []
>
>      #### append to list
>      data[item[0]][item[1]].append(item[2:])

   The above seems to do the opposite of what I need. 'prefbar' is a list of
tuples, and the first two items of each tuple are strings. I want to remove
those strings and have only the reals. Doesn't the above just copy prefbar
to data?

>   catarrays = {}
>   averages = {}
>   for key in ['eco', 'nat', 'soc']:
>      catarrays[key] = []
>      for subkey in ['con', 'neu', 'pro']
>         #### btw. I don't understand why you throw con, neu, pro in one list
>         #### now after sorting them out in advance.

   Let me try to explain. I have 9 sets of data as records in the database.
The sets are eco/con, eco/neu, eco/pro, nat/con, nat/neu, nat/pro, soc/con,
soc/neu, and soc/pro.

   First, I need to average the 28 items in each of those 9 sets.
   Second, I need to average the three average values for each of the 28
items within the main sets of eco, nat, and soc.

   Results can be skewed if only an single, overall average of the 28 items
is calculated in a single step.

>         try:
>            catarrays[key].append(data[key][subkey])
>         except KeyError:
>             #### data[key][subkey] was not set
>             print 'No data for %s,%s'%(key, subkey)
>      #### convert to array
>      catarrays[key] = array(catarrays[key])
>      #### average
>      averages[key] = average(catarrays(key), axis=1)

   This seems to be taking the averages in one step. We need them to be in
two steps. Am I mis-reading this?

Thanks,

Rich

-- 
Richard B. Shepard, Ph.D.               |    The Environmental Permitting
Applied Ecosystem Services, Inc.        |          Accelerator(TM)
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863


From rshepard at appl-ecosys.com  Mon Feb 26 15:43:37 2007
From: rshepard at appl-ecosys.com (Rich Shepard)
Date: Mon, 26 Feb 2007 12:43:37 -0800 (PST)
Subject: [SciPy-user] Transforming 1-d array to 2-d array
In-Reply-To: <loom.20070226T120344-182@post.gmane.org>
References: <Pine.LNX.4.64.0702251412500.25666@salmo.appl-ecosys.com>
	<Pine.LNX.4.64.0702251430270.25666@salmo.appl-ecosys.com>
	<loom.20070226T120344-182@post.gmane.org>
Message-ID: <Pine.LNX.4.64.0702261239180.31240@salmo.appl-ecosys.com>

On Mon, 26 Feb 2007, Dave wrote:

> eye simply creates an array with ones on the diagonal. To solve this
> problem I would create a zero array of the correct size and then index
> into the array.

Hi, Dave,

   What, then, is the difference between eye() and identity()?

> #Define array size
> N = 8
>
> #Define the data to put in the upper-diagonal part of the array
> myData = rand(N*(N-1)/2)

   Well, rather than random, these data are the averages of averages of each
item in the list of tuples retrieved from the database table.

> #Create an index to the upper-diagonal part
> idx = triu(ones([8,8])-eye(8)).nonzero()

> #Instantiate a zero array and populate the upper-triangular part with myData
> A = zeros([N,N],dtype=float)
> A[idx] = myData
>
> #Place ones on the diagonal
> A += eye(N)

   I don't immediately understand what this is doing. I'll have to play with
it in ipython.

   Ultimately, I need the averaged item values in the upper half of an 8x8
matrix, 1s along the diagonal, and 1/values in the lower half of the matrix.

   Probably not the simplest introduction to NymPy and SciPy, but it's what I
need to do.

Many thanks,

Rich

-- 
Richard B. Shepard, Ph.D.               |    The Environmental Permitting
Applied Ecosystem Services, Inc.        |          Accelerator(TM)
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863


From rshepard at appl-ecosys.com  Mon Feb 26 16:21:46 2007
From: rshepard at appl-ecosys.com (Rich Shepard)
Date: Mon, 26 Feb 2007 13:21:46 -0800 (PST)
Subject: [SciPy-user] Transforming 1-d array to 2-d array
In-Reply-To: <loom.20070226T120344-182@post.gmane.org>
References: <Pine.LNX.4.64.0702251412500.25666@salmo.appl-ecosys.com>
	<Pine.LNX.4.64.0702251430270.25666@salmo.appl-ecosys.com>
	<loom.20070226T120344-182@post.gmane.org>
Message-ID: <Pine.LNX.4.64.0702261319580.31240@salmo.appl-ecosys.com>

On Mon, 26 Feb 2007, Dave wrote:

> #Define array size
> N = 8
> #Define the data to put in the upper-diagonal part of the array
> myData = rand(N*(N-1)/2)
> #Create an index to the upper-diagonal part
> idx = triu(ones([8,8])-eye(8)).nonzero()
> #Instantiate a zero array and populate the upper-triangular part with myData
> A = zeros([N,N],dtype=float)
> A[idx] = myData
> #Place ones on the diagonal
> A += eye(N)

   Wow! It certainly does what I need. If only I understood why ... and how
to create these solutions myself.

   I've read the brief descriptions of eye() and triu() in the book; where
can I read how to apply them to solutions like this?

Many thanks, Dave,

Rich

-- 
Richard B. Shepard, Ph.D.               |    The Environmental Permitting
Applied Ecosystem Services, Inc.        |          Accelerator(TM)
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863


From rshepard at appl-ecosys.com  Mon Feb 26 16:44:42 2007
From: rshepard at appl-ecosys.com (Rich Shepard)
Date: Mon, 26 Feb 2007 13:44:42 -0800 (PST)
Subject: [SciPy-user] Transforming 1-d array to 2-d array
In-Reply-To: <loom.20070226T120344-182@post.gmane.org>
References: <Pine.LNX.4.64.0702251412500.25666@salmo.appl-ecosys.com>
	<Pine.LNX.4.64.0702251430270.25666@salmo.appl-ecosys.com>
	<loom.20070226T120344-182@post.gmane.org>
Message-ID: <Pine.LNX.4.64.0702261335340.31240@salmo.appl-ecosys.com>

On Mon, 26 Feb 2007, Dave wrote:

Dave,

   I tried applying this to one of my data arrays, but it fails at the next
to last step. I'll put in my code and the results of print statements and
ask what's different between your working example and my non-working data.

> #Define array size
> N = 8
>
> #Define the data to put in the upper-diagonal part of the array
> myData = rand(N*(N-1)/2)

   I have three arrays; the first one is named barEco and contains:

[[ 2.29075869  2.12453058  3.06339111  2.88526612  3.32199956  2.96319486
    3.12649018  2.81580625  3.23207315  2.493608    2.49459335  2.86643834
    2.77111816  2.26500627  2.4902972   2.81149761  2.46213192  2.80432329
    2.86150888  3.1135404   1.96135592  3.34577184  3.27458386  2.90845738
    2.88745987  2.51245188  2.91666234  2.97438117]]

   I see that your myData array has only single brackets while my data have
two. That seems to have resulted from manipulations where the database
records were separated into individual lists and then averages computed

> #Create an index to the upper-diagonal part
> idx = triu(ones([8,8])-eye(8)).nonzero()

   idx = triu(ones([8,8])-eye(8)).nonzero()
   print idx

(array([0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 4,
        4, 4, 5, 5, 6]), array([1, 2, 3, 4, 5, 6, 7, 2, 3, 4, 5, 6, 7, 3, 4,
5, 6, 7, 4, 5, 6, 7, 5,
        6, 7, 6, 7, 7]))

So this is OK.

> #Instantiate a zero array and populate the upper-triangular part with myData
> A = zeros([N,N],dtype=float)

   symEco = zeros([N,N],dtype=float)
   print symEco

[[ 0.  0.  0.  0.  0.  0.  0.  0.]
  [ 0.  0.  0.  0.  0.  0.  0.  0.]
  [ 0.  0.  0.  0.  0.  0.  0.  0.]
  [ 0.  0.  0.  0.  0.  0.  0.  0.]
  [ 0.  0.  0.  0.  0.  0.  0.  0.]
  [ 0.  0.  0.  0.  0.  0.  0.  0.]
  [ 0.  0.  0.  0.  0.  0.  0.  0.]
  [ 0.  0.  0.  0.  0.  0.  0.  0.]]

> A[idx] = myData

   symEco[idx] = barEco
   print symEco

Traceback (most recent call last):
   File "/data1/eikos/scopingPage.py", line 184, in OnCalcWeights
     inpWts = functions.weightcalc()
   File "/data1/eikos/functions.py", line 177, in weightcalc
     symEco[idx] = barEco
ValueError: array is not broadcastable to correct shape

Rich

-- 
Richard B. Shepard, Ph.D.               |    The Environmental Permitting
Applied Ecosystem Services, Inc.        |          Accelerator(TM)
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863


From peridot.faceted at gmail.com  Mon Feb 26 19:52:30 2007
From: peridot.faceted at gmail.com (Anne Archibald)
Date: Mon, 26 Feb 2007 19:52:30 -0500
Subject: [SciPy-user] Fitting - Gauss-normal distribution
In-Reply-To: <1172515582.19486.17.camel@rodimus>
References: <20070226143457.4a90b2db@jakubik.ta3.sk>
	<200702261454.28465.meesters@uni-mainz.de>
	<91cf711d0702260704i2e52d4b1j48927d5dee4678dd@mail.gmail.com>
	<1172515582.19486.17.camel@rodimus>
Message-ID: <ce557a360702261652x6e55485ep3b865c3ea1c1f9ca@mail.gmail.com>

On 26/02/07, David Warde-Farley <david.warde.farley at utoronto.ca> wrote:

> So, it should be noted that the method of moments estimators for a
> Gaussian distribution are also the maximum likelihood estimators, i.e.
> the ones that maximize p(data|parameters), as well as the best least
> square estimator (since taking the log of the density function gives you
> scaled squared distance from the mean). So optimizing iteratively is
> hardly necessary in this case.

Indeed, fitting a Gaussian is pretty easy. If you want to fit
something more sphisticated (even just two Gaussians, for a bimodal
distribution), the way to go is probably not to constuct a histogram
first. A good approach is to fit for a maximum-likelihood estimate.
That is, if you have a pdf f(p1, p2, ..., pn, x) that has n parameters
and gives the probability (density) for x given all those parameters,
set up a nonlinear optimization for the product f(p1, ..., pn,
x1)*...*f(p1, ..., xm).

You are likely to have better numerical behaviour if you instead
minimize the negative logarithm of this.

Anne M. Archibald


From david at ar.media.kyoto-u.ac.jp  Mon Feb 26 22:53:58 2007
From: david at ar.media.kyoto-u.ac.jp (David Cournapeau)
Date: Tue, 27 Feb 2007 12:53:58 +0900
Subject: [SciPy-user] Fitting - Gauss-normal distribution
In-Reply-To: <ce557a360702261652x6e55485ep3b865c3ea1c1f9ca@mail.gmail.com>
References: <20070226143457.4a90b2db@jakubik.ta3.sk>	<200702261454.28465.meesters@uni-mainz.de>	<91cf711d0702260704i2e52d4b1j48927d5dee4678dd@mail.gmail.com>	<1172515582.19486.17.camel@rodimus>
	<ce557a360702261652x6e55485ep3b865c3ea1c1f9ca@mail.gmail.com>
Message-ID: <45E3AB56.4060606@ar.media.kyoto-u.ac.jp>

Anne Archibald wrote:
> On 26/02/07, David Warde-Farley <david.warde.farley at utoronto.ca> wrote:
>
>   
>> So, it should be noted that the method of moments estimators for a
>> Gaussian distribution are also the maximum likelihood estimators, i.e.
>> the ones that maximize p(data|parameters), as well as the best least
>> square estimator (since taking the log of the density function gives you
>> scaled squared distance from the mean). So optimizing iteratively is
>> hardly necessary in this case.
>>     
>
> Indeed, fitting a Gaussian is pretty easy. If you want to fit
> something more sphisticated (even just two Gaussians, for a bimodal
> distribution), the way to go is probably not to constuct a histogram
> first. A good approach is to fit for a maximum-likelihood estimate.
> That is, if you have a pdf f(p1, p2, ..., pn, x) that has n parameters
> and gives the probability (density) for x given all those parameters,
> set up a nonlinear optimization for the product f(p1, ..., pn,
> x1)*...*f(p1, ..., xm).
>   
Note that one standard iterative algorithm to fit a mixture of Gaussian 
using maximum likelihood method (Expectation Maximization) is 
implemented in the scipy.sandbox.pyem.

David


From rshepard at appl-ecosys.com  Mon Feb 26 22:57:18 2007
From: rshepard at appl-ecosys.com (Rich Shepard)
Date: Mon, 26 Feb 2007 19:57:18 -0800 (PST)
Subject: [SciPy-user] Transforming 1-d array to 2-d array
In-Reply-To: <Pine.LNX.4.64.0702261335340.31240@salmo.appl-ecosys.com>
References: <Pine.LNX.4.64.0702251412500.25666@salmo.appl-ecosys.com>
	<Pine.LNX.4.64.0702251430270.25666@salmo.appl-ecosys.com>
	<loom.20070226T120344-182@post.gmane.org>
	<Pine.LNX.4.64.0702261335340.31240@salmo.appl-ecosys.com>
Message-ID: <Pine.LNX.4.64.0702261953470.25305@salmo.appl-ecosys.com>

On Mon, 26 Feb 2007, Rich Shepard wrote:

>   I have three arrays; the first one is named barEco and contains:
>
> [[ 2.29075869  2.12453058  3.06339111  2.88526612  3.32199956  2.96319486
>    3.12649018  2.81580625  3.23207315  2.493608    2.49459335  2.86643834
>    2.77111816  2.26500627  2.4902972   2.81149761  2.46213192  2.80432329
>    2.86150888  3.1135404   1.96135592  3.34577184  3.27458386  2.90845738
>    2.88745987  2.51245188  2.91666234  2.97438117]]
>
>   I see that your myData array has only single brackets while my data have
> two. That seems to have resulted from manipulations where the database
> records were separated into individual lists and then averages computed

   Well, duh! I used an intermediate array, then extracted [0] from it, and
everything works. I still don't fully understand the 'idx' variable, but I'm
sure that will come with further reading, thinking about it, and playing
with the python shell.

   The final step is to take the inverse of each of the values in the upper
half and put it in the mirror position of the lower half. More reading
required to figure that one out.

Thanks again,

Rich

-- 
Richard B. Shepard, Ph.D.               |    The Environmental Permitting
Applied Ecosystem Services, Inc.        |          Accelerator(TM)
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863


From rshepard at appl-ecosys.com  Mon Feb 26 23:35:14 2007
From: rshepard at appl-ecosys.com (Rich Shepard)
Date: Mon, 26 Feb 2007 20:35:14 -0800 (PST)
Subject: [SciPy-user] Transforming 1-d array to 2-d array
In-Reply-To: <loom.20070226T120344-182@post.gmane.org>
References: <Pine.LNX.4.64.0702251412500.25666@salmo.appl-ecosys.com>
	<Pine.LNX.4.64.0702251430270.25666@salmo.appl-ecosys.com>
	<loom.20070226T120344-182@post.gmane.org>
Message-ID: <Pine.LNX.4.64.0702262024530.25305@salmo.appl-ecosys.com>

On Mon, 26 Feb 2007, Dave wrote:

> #Define the data to put in the upper-diagonal part of the array
> myData = rand(N*(N-1)/2)
>
> #Create an index to the upper-diagonal part
> idx = triu(ones([8,8])-eye(8)).nonzero()
>
> #Instantiate a zero array and populate the upper-triangular part with myData
> A = zeros([N,N],dtype=float)
> A[idx] = myData
>
> #Place ones on the diagonal
> A += eye(N)

Dave,

   Now I need a bit more guidance, to complete the symmetrical matrices.

   Instead of 'myData' above, my starting arrays are barEco, barNat, and
barSoc. They are the upper halves of the matrix 'A' above, with 1s in the
diagonal.

   I created an index to the lower-diagonal part:
   udx = tril(ones([8,8])-eye(8)).nonzero()

   And used them to produce the bottom halves with 1s as the diagonal; for
example:

[[ 1.          0.          0.          0.          0.          0.  	    0. 		0.]
  [ 0.4365366   1.          0.          0.          0.          0.           0.          0.]
  [ 0.47069221  0.32643563  1.          0.          0.          0.  	    0.          0.]
  [ 0.34658848  0.30102352  0.33747359  1.          0.          0.  	    0.          0.]
  [ 0.31984748  0.35513807  0.30939894  0.40102534  1.          0.  	    0.          0.]
  [ 0.40086694  0.348865    0.36086516  0.44149988  0.4015585   1.           0.          0.]
  [ 0.35568232  0.40615208  0.35659227  0.34946598  0.32117778  0.50985137   1.          0.]
  [ 0.2988847   0.30538231  0.34382488  0.34632516  0.39801757  0.34285765   0.33620439  1.]]

   Now, my question is how to combine the upper half ('A', above) with the
lower half leaving only one diagonal with 1s.

   I've tried several ways, but they're all incorrect: they don't work and
python complains.

Rich

-- 
Richard B. Shepard, Ph.D.               |    The Environmental Permitting
Applied Ecosystem Services, Inc.        |          Accelerator(TM)
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863


From matthieu.brucher at gmail.com  Tue Feb 27 02:36:05 2007
From: matthieu.brucher at gmail.com (Matthieu Brucher)
Date: Tue, 27 Feb 2007 08:36:05 +0100
Subject: [SciPy-user] Proposal for more generic optimizers
In-Reply-To: <e76aa17f0702262334l5434c4a7k95ef5c69b622b86f@mail.gmail.com>
References: <e76aa17f0702262334l5434c4a7k95ef5c69b622b86f@mail.gmail.com>
Message-ID: <e76aa17f0702262336t7fc6b203w10362a611de70caf@mail.gmail.com>

Hi,

I'm migratting toward Python for some weeks, but I do not find the tools I
had to develop for my PhD in SciPy at the moment. I can't, for instance,
find an elegant way to save the set of parameters used in an optimization
for the standard algorithms. What is more, I think they can be more generic.

What I did in C++, and I'd like your opinion about porting it in Python, was
to define a standard optimizer with no iteration loop - iterate was a pure
virtual method called by a optimize method -. This iteration loop was then
defined for standard optimizer or damped optimizer. Each time, the
parameters tested could be saved. Then, the step that had to be taken was an
instance of a class that used a gradient step, a Newton step, ... and the
same was used for the stoping criterion. The function was a class that
defined value, gradient, hessian, ... if needed.
For instance, a simplified instruction could have been :
Optimizer* optimizer = StandardOptimizer</*some more parameters not relevant
in Python*/(function, GradientStep(), SimpleCriterion(NbMaxIterations),
step, saveParameters);
optimizer->optimize();
optimizer->getOptimalParameters();

The "step" argument was a constant by which the computed step had to be
multiplied, by default, it was 1.

I know that this kind of writting is not as clear and lightweight as the
current one, which is used by Matlab too. But perhaps giving more latitude
to the user can be proposed with this system. If people want, I can try
making a real Python example...

Matthieu
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20070227/956e9b10/attachment.html>

From a.u.r.e.l.i.a.n at gmx.net  Tue Feb 27 03:23:10 2007
From: a.u.r.e.l.i.a.n at gmx.net (Johannes Loehnert)
Date: Tue, 27 Feb 2007 09:23:10 +0100
Subject: [SciPy-user] Need Advice With Arrays and Calculating
	Eigenvectors
In-Reply-To: <Pine.LNX.4.64.0702261224061.31240@salmo.appl-ecosys.com>
References: <Pine.LNX.4.64.0702220948190.21009@salmo.appl-ecosys.com>
	<200702260917.02628.a.u.r.e.l.i.a.n@gmx.net>
	<Pine.LNX.4.64.0702261224061.31240@salmo.appl-ecosys.com>
Message-ID: <200702270923.10266.a.u.r.e.l.i.a.n@gmx.net>

Hi,

> >   #### using a dict saves us from creating all the lists
> >   data = {}
> >
> >   for item in prefbar:
> >      #### create dict entries on demand
> >      if item[0] not in data:
> >         data[item[0]] = {}
> >      if item[1] not in data[item[0]]:
> >         data[item[0]][item[1]] = []
> >
> >      #### append to list
> >      data[item[0]][item[1]].append(item[2:])
>
>    The above seems to do the opposite of what I need. 'prefbar' is a list
> of tuples, and the first two items of each tuple are strings. I want to
> remove those strings and have only the reals. Doesn't the above just copy
> prefbar to data?

No. data is a dict containing the three main keys (eco, nat, soc). Each maps 
to a dict containing the subkeys (con, neu, pro). Each of those maps to a 
list of data. E.g. for

item = [('eco', 'con', 1, 2, 3), ('eco', 'con', 4,5,6), ('eco', 'neu', 7,8,9), 
            ('nat', 'neu', 10,11,12)]

the result would be

data == {'eco': {'con': [(1,2,3), (4,5,6)],
                         'neu': [(7,8,9)]},
              'nat': {'neu': [(10,11,12)]}}.

So with data['eco']['con'] you get back [(1,2,3), (4,5,6)].

>
> >   catarrays = {}
> >   averages = {}
> >   for key in ['eco', 'nat', 'soc']:
> >      catarrays[key] = []
> >      for subkey in ['con', 'neu', 'pro']
> >         #### btw. I don't understand why you throw con, neu, pro in one
> > list #### now after sorting them out in advance.
>
>    Let me try to explain. I have 9 sets of data as records in the database.
> The sets are eco/con, eco/neu, eco/pro, nat/con, nat/neu, nat/pro, soc/con,
> soc/neu, and soc/pro.

So you get only one data row for each category/subcategory combination? Or can 
there be multiple?

>    First, I need to average the 28 items in each of those 9 sets.
>    Second, I need to average the three average values for each of the 28
> items within the main sets of eco, nat, and soc.

what do you mean by item? A float number?
>
>    Results can be skewed if only an single, overall average of the 28 items
> is calculated in a single step.
>
> >         try:
> >            catarrays[key].append(data[key][subkey])
> >         except KeyError:
> >             #### data[key][subkey] was not set
> >             print 'No data for %s,%s'%(key, subkey)
> >      #### convert to array
> >      catarrays[key] = array(catarrays[key])
> >      #### average
> >      averages[key] = average(catarrays(key), axis=1)
>
>    This seems to be taking the averages in one step. We need them to be in
> two steps. Am I mis-reading this?

Well, it ought to do exactly what your code did. averages['eco'] == barEco 
IIANM.

Johannes


From rshepard at appl-ecosys.com  Tue Feb 27 08:52:48 2007
From: rshepard at appl-ecosys.com (Rich Shepard)
Date: Tue, 27 Feb 2007 05:52:48 -0800 (PST)
Subject: [SciPy-user] Need Advice With Arrays and Calculating
	Eigenvectors
In-Reply-To: <200702270923.10266.a.u.r.e.l.i.a.n@gmx.net>
References: <Pine.LNX.4.64.0702220948190.21009@salmo.appl-ecosys.com>
	<200702260917.02628.a.u.r.e.l.i.a.n@gmx.net>
	<Pine.LNX.4.64.0702261224061.31240@salmo.appl-ecosys.com>
	<200702270923.10266.a.u.r.e.l.i.a.n@gmx.net>
Message-ID: <Pine.LNX.4.64.0702270549330.15248@salmo.appl-ecosys.com>

On Tue, 27 Feb 2007, Johannes Loehnert wrote:

> No. data is a dict containing the three main keys (eco, nat, soc). Each
> maps to a dict containing the subkeys (con, neu, pro). Each of those maps
> to a list of data. E.g. for
>
> item = [('eco', 'con', 1, 2, 3), ('eco', 'con', 4,5,6), ('eco', 'neu', 7,8,9),
>            ('nat', 'neu', 10,11,12)]
>
> the result would be
>
> data == {'eco': {'con': [(1,2,3), (4,5,6)],
>                         'neu': [(7,8,9)]},
>              'nat': {'neu': [(10,11,12)]}}.
>
> So with data['eco']['con'] you get back [(1,2,3), (4,5,6)].

   A-ha! Now I see it. Thanks very much, Johannes.

> So you get only one data row for each category/subcategory combination? Or
> can there be multiple?

   Multiple rows for each category/subcategory.

>>    First, I need to average the 28 items in each of those 9 sets.
>>    Second, I need to average the three average values for each of the 28
>> items within the main sets of eco, nat, and soc.
>
> what do you mean by item? A float number?

   Yes. The floats are avereaged by subcategory, then the subcategories are
averaged by category.

> Well, it ought to do exactly what your code did. averages['eco'] == barEco
> IIANM.

   I see now how to write the code so it works. I mis-understood the first
message. Again, thank you very much.

Rich

-- 
Richard B. Shepard, Ph.D.               |    The Environmental Permitting
Applied Ecosystem Services, Inc.        |          Accelerator(TM)
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863


From rshepard at appl-ecosys.com  Tue Feb 27 09:04:19 2007
From: rshepard at appl-ecosys.com (Rich Shepard)
Date: Tue, 27 Feb 2007 06:04:19 -0800 (PST)
Subject: [SciPy-user] Transforming 1-d array to 2-d array
In-Reply-To: <Pine.LNX.4.64.0702262024530.25305@salmo.appl-ecosys.com>
References: <Pine.LNX.4.64.0702251412500.25666@salmo.appl-ecosys.com>
	<Pine.LNX.4.64.0702251430270.25666@salmo.appl-ecosys.com>
	<loom.20070226T120344-182@post.gmane.org>
	<Pine.LNX.4.64.0702262024530.25305@salmo.appl-ecosys.com>
Message-ID: <Pine.LNX.4.64.0702270601520.15248@salmo.appl-ecosys.com>

On Mon, 26 Feb 2007, Rich Shepard wrote:

>   Now I need a bit more guidance, to complete the symmetrical matrices.

   It occurred to me after I posted this message that I'm going along the
wrong path. I don't need a lower index, just the lower triangular half of
the array with zeros along the principal diagonal and the upper half. Then
I can add them (cell-wise, not matrix addition) and get the filled array I
need.

Rich

-- 
Richard B. Shepard, Ph.D.               |    The Environmental Permitting
Applied Ecosystem Services, Inc.        |          Accelerator(TM)
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863


From aisaac at american.edu  Tue Feb 27 10:06:12 2007
From: aisaac at american.edu (Alan G Isaac)
Date: Tue, 27 Feb 2007 10:06:12 -0500
Subject: [SciPy-user] Proposal for more generic optimizers
In-Reply-To: <e76aa17f0702262336t7fc6b203w10362a611de70caf@mail.gmail.com>
References: <e76aa17f0702262334l5434c4a7k95ef5c69b622b86f@mail.gmail.com><e76aa17f0702262336t7fc6b203w10362a611de70caf@mail.gmail.com>
Message-ID: <Mahogany-0.67.0-1044-20070227-100612.00@american.edu>

On Tue, 27 Feb 2007, Matthieu Brucher apparently wrote:
> Optimizer* optimizer = StandardOptimizer</*some more 
> parameters not relevant
> in Python*/(function, GradientStep(), SimpleCriterion(NbMaxIterations),
> step, saveParameters);
> optimizer->optimize();
> optimizer->getOptimalParameters();

Seems like a good approach.
(Put step and saveParameters in a keyword dict.)

Cheers,
Alan Isaac




From matthieu.brucher at gmail.com  Tue Feb 27 11:13:46 2007
From: matthieu.brucher at gmail.com (Matthieu Brucher)
Date: Tue, 27 Feb 2007 17:13:46 +0100
Subject: [SciPy-user] Proposal for more generic optimizers
In-Reply-To: <Mahogany-0.67.0-1044-20070227-100612.00@american.edu>
References: <e76aa17f0702262334l5434c4a7k95ef5c69b622b86f@mail.gmail.com>
	<e76aa17f0702262336t7fc6b203w10362a611de70caf@mail.gmail.com>
	<Mahogany-0.67.0-1044-20070227-100612.00@american.edu>
Message-ID: <e76aa17f0702270813j699e9df0t45aeec990729ba6e@mail.gmail.com>

Thanks for the tip :)
I wonder the saveParamaters could be avoided by using a default list that
does nothing - append does nothing -, and pepole could add a container
defining a "append" method. That would save a test as well.

Matthieu

2007/2/27, Alan G Isaac <aisaac at american.edu>:
>
> On Tue, 27 Feb 2007, Matthieu Brucher apparently wrote:
> > Optimizer* optimizer = StandardOptimizer</*some more
> > parameters not relevant
> > in Python*/(function, GradientStep(), SimpleCriterion(NbMaxIterations),
> > step, saveParameters);
> > optimizer->optimize();
> > optimizer->getOptimalParameters();
>
> Seems like a good approach.
> (Put step and saveParameters in a keyword dict.)
>
> Cheers,
> Alan Isaac
>
>
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20070227/f3dfbbdf/attachment.html>

From krish.subramaniam at gmail.com  Tue Feb 27 12:23:17 2007
From: krish.subramaniam at gmail.com (Krish Subramaniam)
Date: Tue, 27 Feb 2007 09:23:17 -0800
Subject: [SciPy-user] A NifTI-1 I/O library for Numpy wrapped through ctypes
Message-ID: <dfc38c640702270923l77a4ff3t6b1bc6d9792c210a@mail.gmail.com>

Hello Folks

I am new here.

 Whipped up a quick tutorial "A NifTI-1 I/O library for Numpy wrapped
through ctypes" for beginners since I am not an advanced user myself.
I have to thank the Numpy developers for their wonderful job. This is
a write-up on how to get a library wrapped in ctypes and "translate"
the data to a Numpy N-D object. First ever draft.

Would it find a way into your wiki or something? so that people who
are in the same background as mine ( scientific, wrap an existing C
module, seriously contemplate using Scipy instead of Matlab) would
benefit. You can find it here :

http://krish.caltech.edu/niftiio.pdf

( Should I have mailed the devel list instead ? )

Regards
Krish Subramaniam

P.S ( I think my previous mail didn't get through. If this is the 2nd
mail you are receiving, please pardon )


From peridot.faceted at gmail.com  Tue Feb 27 12:42:13 2007
From: peridot.faceted at gmail.com (Anne Archibald)
Date: Tue, 27 Feb 2007 12:42:13 -0500
Subject: [SciPy-user] A NifTI-1 I/O library for Numpy wrapped through
	ctypes
In-Reply-To: <dfc38c640702270923l77a4ff3t6b1bc6d9792c210a@mail.gmail.com>
References: <dfc38c640702270923l77a4ff3t6b1bc6d9792c210a@mail.gmail.com>
Message-ID: <ce557a360702270942p27caa640s7499294ff5a8803c@mail.gmail.com>

On 27/02/07, Krish Subramaniam <krish.subramaniam at gmail.com> wrote:
> Hello Folks
>
> I am new here.
>
>  Whipped up a quick tutorial "A NifTI-1 I/O library for Numpy wrapped
> through ctypes" for beginners since I am not an advanced user myself.
> I have to thank the Numpy developers for their wonderful job. This is
> a write-up on how to get a library wrapped in ctypes and "translate"
> the data to a Numpy N-D object. First ever draft.
>
> Would it find a way into your wiki or something? so that people who
> are in the same background as mine ( scientific, wrap an existing C
> module, seriously contemplate using Scipy instead of Matlab) would
> benefit. You can find it here :
>
> http://krish.caltech.edu/niftiio.pdf

That's a handy document!

If you want, you can just register for an account on the wiki (the
usual two-minute thing) and attach it to some page (not sure what's
appropriate just now). If you wanted to take a little longer, you
could copy the text into a wiki page on its own, which would make it
more searchable.

Thanks for writing the document,
Anne M. Archibald


From krish.subramaniam at gmail.com  Tue Feb 27 12:52:02 2007
From: krish.subramaniam at gmail.com (Krish Subramaniam)
Date: Tue, 27 Feb 2007 09:52:02 -0800
Subject: [SciPy-user] A NifTI-1 I/O library for Numpy wrapped through
	ctypes
In-Reply-To: <ce557a360702270942p27caa640s7499294ff5a8803c@mail.gmail.com>
References: <dfc38c640702270923l77a4ff3t6b1bc6d9792c210a@mail.gmail.com>
	<ce557a360702270942p27caa640s7499294ff5a8803c@mail.gmail.com>
Message-ID: <dfc38c640702270952u41707f42scf40d2b4694b02cc@mail.gmail.com>

Cool .. I can write it in the wiki markup language so that it's
searchable.. I can include more code / examples and hopefully a few
figures..

Thanks
Krish

On 2/27/07, Anne Archibald <peridot.faceted at gmail.com> wrote:
> On 27/02/07, Krish Subramaniam <krish.subramaniam at gmail.com> wrote:
> > Hello Folks
> >
> > I am new here.
> >
> >  Whipped up a quick tutorial "A NifTI-1 I/O library for Numpy wrapped
> > through ctypes" for beginners since I am not an advanced user myself.
> > I have to thank the Numpy developers for their wonderful job. This is
> > a write-up on how to get a library wrapped in ctypes and "translate"
> > the data to a Numpy N-D object. First ever draft.
> >
> > Would it find a way into your wiki or something? so that people who
> > are in the same background as mine ( scientific, wrap an existing C
> > module, seriously contemplate using Scipy instead of Matlab) would
> > benefit. You can find it here :
> >
> > http://krish.caltech.edu/niftiio.pdf
>
> That's a handy document!
>
> If you want, you can just register for an account on the wiki (the
> usual two-minute thing) and attach it to some page (not sure what's
> appropriate just now). If you wanted to take a little longer, you
> could copy the text into a wiki page on its own, which would make it
> more searchable.
>
> Thanks for writing the document,
> Anne M. Archibald
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user
>


From rshepard at appl-ecosys.com  Tue Feb 27 14:09:37 2007
From: rshepard at appl-ecosys.com (Rich Shepard)
Date: Tue, 27 Feb 2007 11:09:37 -0800 (PST)
Subject: [SciPy-user] Combining Arrays
Message-ID: <Pine.LNX.4.64.0702271100440.15248@salmo.appl-ecosys.com>

   I have two arrays: one is the upper triangular half with 1s in the
diagonal, the other has the values for the lower triangular half. I also
have an array that specifies how the values in the lower half array are to
be assigned to rows and columns of the 2D array. However, as this is my
first use of NumPy, I am stuck at how to put these together to form what I
need.

   Here's the upper array (call it topArr):

[[ 1.          2.29075869  2.12453058  3.06339111  2.88526612  3.32199956
    2.96319486  3.12649018]
  [ 0.          1.          2.81580625  3.23207315  2.493608    2.49459335
    2.86643834  2.77111816]
  [ 0.          0.          1.          2.26500627  2.4902972   2.81149761
    2.46213192  2.80432329]
  [ 0.          0.          0.          1.          2.86150888  3.1135404
    1.96135592  3.34577184]
  [ 0.          0.          0.          0.          1.          3.27458386
    2.90845738  2.88745987]
  [ 0.          0.          0.          0.          0.          1.
    2.51245188  2.91666234]
  [ 0.          0.          0.          0.          0.          0. 
1.
    2.97438117]
  [ 0.          0.          0.          0.          0.          0. 
0.
    1.        ]]

   Here's the lower array (call it botArr):

[ 0.4365366   0.47069221  0.32643563  0.34658848  0.30102352  0.33747359
   0.31984748  0.35513807  0.30939894  0.40102534  0.40086694  0.348865
   0.36086516  0.44149988  0.4015585   0.35568232  0.40615208  0.35659227
   0.34946598  0.32117778  0.50985137  0.2988847   0.30538231  0.34382488
   0.34632516  0.39801757  0.34285765  0.33620439]

   And, using 'udx = tril(ones([8,8])-eye(8)).nonzero()' this is udx:

(array([1, 2, 2, 3, 3, 3, 4, 4, 4, 4, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 7, 7,
        7, 7, 7, 7, 7]), array([0, 0, 1, 0, 1, 2, 0, 1, 2, 3, 0, 1, 2, 3, 4,
0, 1, 2, 3, 4, 5, 0, 1, 2, 3, 4, 5, 6]))

   What I need is the array:

[[ 1.00		2.29	2.12	3.06 	...	]
  [ 0.44		1.00	2.82	3.23	...	]
  [ 0.47		0.22	1.00	2.26	...	]
 		...
 						]]

   How do I do this, please?

Rich

-- 
Richard B. Shepard, Ph.D.               |    The Environmental Permitting
Applied Ecosystem Services, Inc.        |          Accelerator(TM)
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863


From as8ca at virginia.edu  Tue Feb 27 14:21:29 2007
From: as8ca at virginia.edu (Alok Singhal)
Date: Tue, 27 Feb 2007 14:21:29 -0500
Subject: [SciPy-user] Combining Arrays
In-Reply-To: <Pine.LNX.4.64.0702271100440.15248@salmo.appl-ecosys.com>
References: <Pine.LNX.4.64.0702271100440.15248@salmo.appl-ecosys.com>
Message-ID: <20070227192129.GA3612@virginia.edu>

Hi Rich,

On 27/02/07: 11:09, Rich Shepard wrote:
>    I have two arrays: one is the upper triangular half with 1s in the
> diagonal, the other has the values for the lower triangular half. I also
> have an array that specifies how the values in the lower half array are to
> be assigned to rows and columns of the 2D array. However, as this is my
> first use of NumPy, I am stuck at how to put these together to form what I
> need.

[snip]

>    What I need is the array:
> 
> [[ 1.00		2.29	2.12	3.06 	...	]
>   [ 0.44		1.00	2.82	3.23	...	]
>   [ 0.47		0.22	1.00	2.26	...	]
>  		...
>  						]]
> 
>    How do I do this, please?

This works for me:

new = zeros(topArr.shape, dtype=float)
new[udx] = botArr
new = new + topArr

-Alok

-- 
Alok Singhal                               *   *          
Graduate Student, dept. of Astronomy   *           *     *
University of Virginia                                    
http://www.astro.virginia.edu/~as8ca/              *    * 


From rshepard at appl-ecosys.com  Tue Feb 27 14:53:31 2007
From: rshepard at appl-ecosys.com (Rich Shepard)
Date: Tue, 27 Feb 2007 11:53:31 -0800 (PST)
Subject: [SciPy-user] Combining Arrays
In-Reply-To: <20070227192129.GA3612@virginia.edu>
References: <Pine.LNX.4.64.0702271100440.15248@salmo.appl-ecosys.com>
	<20070227192129.GA3612@virginia.edu>
Message-ID: <Pine.LNX.4.64.0702271149280.15248@salmo.appl-ecosys.com>

On Tue, 27 Feb 2007, Alok Singhal wrote:

> This works for me:
>
> new = zeros(topArr.shape, dtype=float)
> new[udx] = botArr
> new = new + topArr

Alok,

   I had the first two steps, but needed the last one. What I kept trying
borked each time.

   Wonder if this is documented somewhere. I did not see it in the beta of
the tutorial, the numpy example lists, or in Travis' book.

   But, it works like a charm. Thank you very much.

   Now to read how to use the eigen() function ....

Rich


-- 
Richard B. Shepard, Ph.D.               |    The Environmental Permitting
Applied Ecosystem Services, Inc.        |          Accelerator(TM)
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863


From bnuttall at uky.edu  Tue Feb 27 15:09:47 2007
From: bnuttall at uky.edu (Brandon Nuttall)
Date: Tue, 27 Feb 2007 15:09:47 -0500
Subject: [SciPy-user] Using SciPy/NumPy optimization
Message-ID: <6.0.1.1.2.20070227131721.0287bfe0@pop.uky.edu>

Folks,

The usual confessions: I am relatively new to Python programming and SciPy. 
I have a problem I'm looking for some help in solving.

I have a list of data pairs [[x1,y1], [x2,y2], ..., [xn,yn]] and am trying 
to find the best fit of that data to an equation:

      y = a*(1+b*c*y)^(-1/b)

The parameters, b and c, are constrained:
      1) 0<b<=5
      2) -1<=c<=1

Parameter a is only weakly constrained in that x is usually >= max(x1, x2, 
... , xn).

My "best fit" goal is either to minimize the root mean square deviation (or 
consequently maximize the r-square value).

Any suggestions?

Thanks.



Brandon C. Nuttall

BNUTTALL at UKY.EDU                         Kentucky Geological Survey
(859) 257-5500                                     University of Kentucky
(859) 257-1147 (fax)                              228 Mining & Mineral 
Resources Bldg
http://www.uky.edu/KGS/home.htm       Lexington, Kentucky 40506-0107  



From rshepard at appl-ecosys.com  Tue Feb 27 15:24:20 2007
From: rshepard at appl-ecosys.com (Rich Shepard)
Date: Tue, 27 Feb 2007 12:24:20 -0800 (PST)
Subject: [SciPy-user] Proper Use of NumPy's eig()
Message-ID: <Pine.LNX.4.64.0702271219530.15248@salmo.appl-ecosys.com>

   I start the module with
 	from numpy import linalg

and I need to find the principal Eigenvector of the matrix E. But, when I
try

 	eigE = eig(E)

python responds "NameError: global name 'eig' is not defined."

   Do I need another module from NumPy, should I explicitly cast E to a
matrix, or am I calling the function incorrectly?

Rich

-- 
Richard B. Shepard, Ph.D.               |    The Environmental Permitting
Applied Ecosystem Services, Inc.        |          Accelerator(TM)
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863


From robert.kern at gmail.com  Tue Feb 27 15:25:59 2007
From: robert.kern at gmail.com (Robert Kern)
Date: Tue, 27 Feb 2007 14:25:59 -0600
Subject: [SciPy-user] Using SciPy/NumPy optimization
In-Reply-To: <6.0.1.1.2.20070227131721.0287bfe0@pop.uky.edu>
References: <6.0.1.1.2.20070227131721.0287bfe0@pop.uky.edu>
Message-ID: <45E493D7.2070703@gmail.com>

Brandon Nuttall wrote:
> Folks,
> 
> The usual confessions: I am relatively new to Python programming and SciPy. 
> I have a problem I'm looking for some help in solving.
> 
> I have a list of data pairs [[x1,y1], [x2,y2], ..., [xn,yn]] and am trying 
> to find the best fit of that data to an equation:
> 
>       y = a*(1+b*c*y)^(-1/b)

Presumably, you mean

  y = a*(1 + b*c*x) ** (-1.0/b)

to correct a typo and use Python notation.

> The parameters, b and c, are constrained:
>       1) 0<b<=5
>       2) -1<=c<=1
> 
> Parameter a is only weakly constrained in that x is usually >= max(x1, x2, 
> ... , xn).
> 
> My "best fit" goal is either to minimize the root mean square deviation (or 
> consequently maximize the r-square value).

There are a number of constrained optimizers in scipy.optimize .
scipy.optimize.fmin_tnc seems most appropriate for simple bounds like you have.
In order to get a function to minimize that depends on data, I usually like to
use a class:

  import numpy as np
  from scipy.optimize import fmin_tnc

  class LossFunction(object):
    def __init__(self, x, y):
      self.x = x
      self.y = y

    def __call__(self, abc):
      """ A function suitable for passing to the fmin() minimizers.
      """
      a, b, c = abc
      y = a*(1.0 + b*c*self.x) ** (-1.0/b)
      dy = self.y - y
      return dy*dy

  x = np.array([...])
  y = np.array([...])
  lf = LossFunction(x, y)
  abc0 = np.array([x.max(), 2.5, 0.0])  # or whatever
  retcode, nfeval, abc_optimal = fmin_tnc(lf, abc0,
    bounds=[(None, None), (0., 5.), (-1., 1.)])

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
 that is made terrible by our own mad attempt to interpret it as though it had
 an underlying truth."
  -- Umberto Eco


From bryanv at enthought.com  Tue Feb 27 15:26:16 2007
From: bryanv at enthought.com (Bryan Van de Ven)
Date: Tue, 27 Feb 2007 14:26:16 -0600
Subject: [SciPy-user] Proper Use of NumPy's eig()
In-Reply-To: <Pine.LNX.4.64.0702271219530.15248@salmo.appl-ecosys.com>
References: <Pine.LNX.4.64.0702271219530.15248@salmo.appl-ecosys.com>
Message-ID: <45E493E8.8090003@enthought.com>

eig in in the linalg module, so you need to use

eigE = linalg.eig(E)


Rich Shepard wrote:
>    I start the module with
>  	from numpy import linalg
> 
> and I need to find the principal Eigenvector of the matrix E. But, when I
> try
> 
>  	eigE = eig(E)
> 
> python responds "NameError: global name 'eig' is not defined."
> 
>    Do I need another module from NumPy, should I explicitly cast E to a
> matrix, or am I calling the function incorrectly?
> 
> Rich
> 



From david.warde.farley at utoronto.ca  Tue Feb 27 15:27:10 2007
From: david.warde.farley at utoronto.ca (David Warde-Farley)
Date: Tue, 27 Feb 2007 15:27:10 -0500
Subject: [SciPy-user] Proper Use of NumPy's eig()
In-Reply-To: <Pine.LNX.4.64.0702271219530.15248@salmo.appl-ecosys.com>
References: <Pine.LNX.4.64.0702271219530.15248@salmo.appl-ecosys.com>
Message-ID: <52878754-DDDD-4AE2-9601-880BA43DD446@utoronto.ca>

If you're going to do it that way you'll have to call linalg.eig()

David

On 27-Feb-07, at 3:24 PM, Rich Shepard wrote:

>    I start the module with
>  	from numpy import linalg
>
> and I need to find the principal Eigenvector of the matrix E. But,  
> when I
> try
>
>  	eigE = eig(E)
>
> python responds "NameError: global name 'eig' is not defined."
>
>    Do I need another module from NumPy, should I explicitly cast E  
> to a
> matrix, or am I calling the function incorrectly?
>
> Rich
>
> -- 
> Richard B. Shepard, Ph.D.               |    The Environmental  
> Permitting
> Applied Ecosystem Services, Inc.        |          Accelerator(TM)
> <http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax:  
> 503-667-8863
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user



From robert.kern at gmail.com  Tue Feb 27 15:27:37 2007
From: robert.kern at gmail.com (Robert Kern)
Date: Tue, 27 Feb 2007 14:27:37 -0600
Subject: [SciPy-user] Proper Use of NumPy's eig()
In-Reply-To: <Pine.LNX.4.64.0702271219530.15248@salmo.appl-ecosys.com>
References: <Pine.LNX.4.64.0702271219530.15248@salmo.appl-ecosys.com>
Message-ID: <45E49439.4090603@gmail.com>

Rich Shepard wrote:
>    I start the module with
>  	from numpy import linalg
> 
> and I need to find the principal Eigenvector of the matrix E. But, when I
> try
> 
>  	eigE = eig(E)
> 
> python responds "NameError: global name 'eig' is not defined."
> 
>    Do I need another module from NumPy, should I explicitly cast E to a
> matrix, or am I calling the function incorrectly?

eigE = linalg.eig(E)

Importing modules like that doesn't put their contents into the current
namespace; rather it puts the module object itself into the namespace.

  http://docs.python.org/tut/node8.html

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
 that is made terrible by our own mad attempt to interpret it as though it had
 an underlying truth."
  -- Umberto Eco


From jeremit0 at gmail.com  Tue Feb 27 15:31:43 2007
From: jeremit0 at gmail.com (Jeremy Conlin)
Date: Tue, 27 Feb 2007 15:31:43 -0500
Subject: [SciPy-user] no linalg module and failed check_integer test
Message-ID: <3db594f70702271231s2b0f3fd3l79f1342b11d408d2@mail.gmail.com>

I just installed scipy from svn and I am having some problems.  The
most vexing is that I can no longer load the linalg package, at least
I can't do anything with it.  For example:

Python 2.5 (r25:51918, Sep 19 2006, 08:49:13)
[GCC 4.0.1 (Apple Computer, Inc. build 5341)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import scipy
>>> scipy.pkgload('linalg')
>>> help(scipy.linalg)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
AttributeError: 'module' object has no attribute 'linalg'
>>> A = scipy.ones((10,10))
>>> scipy.linalg.eig(A)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
AttributeError: 'module' object has no attribute 'linalg'
>>>

I didn't notice any errors during the installation.  I know this isn't
a lot of information to go on, but does anyone know what the problem
is?

Secondly, and this might be related, when I run

scipy.test(1,10)

I get the error shown below.  Could this be the cause of my linalg problem?
Thanks in advance,
Jeremy


test_init (scipy.io.tests.test_npfile.test_npfile) ... ok
test_parse_endian (scipy.io.tests.test_npfile.test_npfile) ... ok
test_read_write_array (scipy.io.tests.test_npfile.test_npfile) ... ok
test_read_write_raw (scipy.io.tests.test_npfile.test_npfile) ... ok
test_remaining_bytes (scipy.io.tests.test_npfile.test_npfile) ... ok

======================================================================
ERROR: check_integer (scipy.io.tests.test_array_import.test_read_array)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/io/tests/test_array_import.py",
line 55, in check_integer
    from scipy import stats
  File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/stats/__init__.py",
line 7, in <module>
    from stats import *
  File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/stats/stats.py",
line 190, in <module>
    import scipy.special as special
  File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/special/__init__.py",
line 8, in <module>
    from basic import *
  File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/special/basic.py",
line 8, in <module>
    from _cephes import *
ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/special/_cephes.so,
2): Symbol not found: ___dso_handle
  Referenced from:
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/special/_cephes.so
  Expected in: dynamic lookup


----------------------------------------------------------------------
Ran 554 tests in 2.424s

FAILED (errors=1)
<unittest.TextTestRunner object at 0x2a49fb0>


From rshepard at appl-ecosys.com  Tue Feb 27 15:32:16 2007
From: rshepard at appl-ecosys.com (Rich Shepard)
Date: Tue, 27 Feb 2007 12:32:16 -0800 (PST)
Subject: [SciPy-user] Proper Use of NumPy's eig()
In-Reply-To: <45E493E8.8090003@enthought.com>
References: <Pine.LNX.4.64.0702271219530.15248@salmo.appl-ecosys.com>
	<45E493E8.8090003@enthought.com>
Message-ID: <Pine.LNX.4.64.0702271231400.15248@salmo.appl-ecosys.com>

On Tue, 27 Feb 2007, Bryan Van de Ven wrote:

> eig in in the linalg module, so you need to use
> eigE = linalg.eig(E)

   Ah, yes. Thank you very much.

Rich

-- 
Richard B. Shepard, Ph.D.               |    The Environmental Permitting
Applied Ecosystem Services, Inc.        |          Accelerator(TM)
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863


From rshepard at appl-ecosys.com  Tue Feb 27 15:33:31 2007
From: rshepard at appl-ecosys.com (Rich Shepard)
Date: Tue, 27 Feb 2007 12:33:31 -0800 (PST)
Subject: [SciPy-user] Proper Use of NumPy's eig()
In-Reply-To: <52878754-DDDD-4AE2-9601-880BA43DD446@utoronto.ca>
References: <Pine.LNX.4.64.0702271219530.15248@salmo.appl-ecosys.com>
	<52878754-DDDD-4AE2-9601-880BA43DD446@utoronto.ca>
Message-ID: <Pine.LNX.4.64.0702271232320.15248@salmo.appl-ecosys.com>

On Tue, 27 Feb 2007, David Warde-Farley wrote:

> If you're going to do it that way you'll have to call linalg.eig()

David,

   Yes, it was an obvious oversight on my part. Do you recommend another way?

Thanks,

Rich

-- 
Richard B. Shepard, Ph.D.               |    The Environmental Permitting
Applied Ecosystem Services, Inc.        |          Accelerator(TM)
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863


From david.warde.farley at utoronto.ca  Tue Feb 27 15:37:31 2007
From: david.warde.farley at utoronto.ca (David Warde-Farley)
Date: Tue, 27 Feb 2007 15:37:31 -0500
Subject: [SciPy-user] Proper Use of NumPy's eig()
In-Reply-To: <Pine.LNX.4.64.0702271232320.15248@salmo.appl-ecosys.com>
References: <Pine.LNX.4.64.0702271219530.15248@salmo.appl-ecosys.com>
	<52878754-DDDD-4AE2-9601-880BA43DD446@utoronto.ca>
	<Pine.LNX.4.64.0702271232320.15248@salmo.appl-ecosys.com>
Message-ID: <03F2185E-C21E-414D-AF24-BEBF1922BE8A@utoronto.ca>

Hah, it looks like 3 of us all jumped on the question at once. Sorry. :)

If you're really keen on having short names for things you could use

	from scipy.linalg import eig

or

	import scipy.linalg as L

in the latter case you'd use L.eig().  I personally don't like  
cluttering up the namespace too much but I think that's my own  
obsessive streak. :)

David

On 27-Feb-07, at 3:33 PM, Rich Shepard wrote:

> On Tue, 27 Feb 2007, David Warde-Farley wrote:
>
>> If you're going to do it that way you'll have to call linalg.eig()
>
> David,
>
>    Yes, it was an obvious oversight on my part. Do you recommend  
> another way?
>
> Thanks,
>
> Rich
>
> -- 
> Richard B. Shepard, Ph.D.               |    The Environmental  
> Permitting
> Applied Ecosystem Services, Inc.        |          Accelerator(TM)
> <http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax:  
> 503-667-8863
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user



From robert.kern at gmail.com  Tue Feb 27 15:47:33 2007
From: robert.kern at gmail.com (Robert Kern)
Date: Tue, 27 Feb 2007 14:47:33 -0600
Subject: [SciPy-user] no linalg module and failed check_integer test
In-Reply-To: <3db594f70702271231s2b0f3fd3l79f1342b11d408d2@mail.gmail.com>
References: <3db594f70702271231s2b0f3fd3l79f1342b11d408d2@mail.gmail.com>
Message-ID: <45E498E5.4040601@gmail.com>

Jeremy Conlin wrote:
> I just installed scipy from svn and I am having some problems.  The
> most vexing is that I can no longer load the linalg package, at least
> I can't do anything with it.  For example:
> 
> Python 2.5 (r25:51918, Sep 19 2006, 08:49:13)
> [GCC 4.0.1 (Apple Computer, Inc. build 5341)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
>>>> import scipy
>>>> scipy.pkgload('linalg')
>>>> help(scipy.linalg)
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
> AttributeError: 'module' object has no attribute 'linalg'
>>>> A = scipy.ones((10,10))
>>>> scipy.linalg.eig(A)
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
> AttributeError: 'module' object has no attribute 'linalg'
> 
> I didn't notice any errors during the installation.  I know this isn't
> a lot of information to go on, but does anyone know what the problem
> is?

Don't bother with pkgload. Just import scipy.linalg.

> Secondly, and this might be related, when I run
> 
> scipy.test(1,10)
> 
> I get the error shown below.  Could this be the cause of my linalg problem?

> ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/special/_cephes.so,
> 2): Symbol not found: ___dso_handle
>   Referenced from:
> /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/special/_cephes.so
>   Expected in: dynamic lookup

No, it's different. Exactly what versions of OS X (version number and Intel or
PPC), gcc, gfortran (also where you got it from), Xcode do you have installed?
You might need to install the latest version of cctools from here (AFAIK, the
best place to get it):

  ftp://gcc.gnu.org/pub/gcc/infrastructure/cctools-590.36.dmg

That said, I've never installed it on my MacBook, and I've never had this problem.

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
 that is made terrible by our own mad attempt to interpret it as though it had
 an underlying truth."
  -- Umberto Eco


From lists.steve at arachnedesign.net  Tue Feb 27 15:48:42 2007
From: lists.steve at arachnedesign.net (Steve Lianoglou)
Date: Tue, 27 Feb 2007 15:48:42 -0500
Subject: [SciPy-user] Proper Use of NumPy's eig()
In-Reply-To: <03F2185E-C21E-414D-AF24-BEBF1922BE8A@utoronto.ca>
References: <Pine.LNX.4.64.0702271219530.15248@salmo.appl-ecosys.com>
	<52878754-DDDD-4AE2-9601-880BA43DD446@utoronto.ca>
	<Pine.LNX.4.64.0702271232320.15248@salmo.appl-ecosys.com>
	<03F2185E-C21E-414D-AF24-BEBF1922BE8A@utoronto.ca>
Message-ID: <5A3FFD61-82F5-4E71-BA7D-087E1D5D7B45@arachnedesign.net>

> If you're really keen on having short names for things you could use
>
> 	from scipy.linalg import eig
>
> or
>
> 	import scipy.linalg as L
>
> in the latter case you'd use L.eig().  I personally don't like
> cluttering up the namespace too much but I think that's my own
> obsessive streak. :)

And if you just want all of the functions in the scipy.linalg module  
to enter the global namespace, you can do:

from scipy.linalg import *
# ...
eigE = eig(E)

Typically, this approach isn't recommended when you're writing code,  
but if you're just exploring data in the shell and feel like the the  
module prefixes are too much of a hassle for you to keep typing, this  
is your other option.

-steve



From jpeacock at mesoscopic.mines.edu  Tue Feb 27 15:54:07 2007
From: jpeacock at mesoscopic.mines.edu (Jared Peacock)
Date: Tue, 27 Feb 2007 13:54:07 -0700
Subject: [SciPy-user] Using mpfit
Message-ID: <17892.39535.850287.24023@hipparchus.mines.edu>

I'm trying to use mpfit but I can't seem to get it to work.  I'm
testing the code using this program, which is similar to the example
from the mpfit text:

import mpfit2
import Numeric

x=Numeric.arange(1.,stop=100.)
p0=[5.7, 2.2, 500., 1.5, 2000.]
y=6.+3.5*x+200.*x**2+2.7*Numeric.sqrt(x)+2700.*Numeric.log(x)
err=.1

def myfunct(p,fjac=None,x=None,y=None,err=None):
    f=p[0]+p[1]*x+p[2]*x**2+p[3]*Numeric.sqrt(x)+p[4]*Numeric.log(x)
    status=0
    return [status,(y-f)/err]

fa = {'x':x, 'y':y, 'err':err}
m = mpfit2.mpfit(myfunct, xall=p0, functkw=fa)
print 'status = ', m.status
#if (m.status <= 0): print 'error message = ', m.errmsg
print 'parameters = ', m.params


But when I run it I get this error: 

    m = mpfit2.mpfit(myfunct, xall=p0, functkw=fa)
  File "mpfit2.py", line 1007, in __init__
    [self.status, fvec] = self.call(fcn, self.params, functkw)
TypeError: unpack non-sequence

I'm not sure what this means or how to fix it.  Does anybody have and
incite to this problem and using mpfit?

J. Peacock


From rshepard at appl-ecosys.com  Tue Feb 27 15:58:35 2007
From: rshepard at appl-ecosys.com (Rich Shepard)
Date: Tue, 27 Feb 2007 12:58:35 -0800 (PST)
Subject: [SciPy-user] Proper Use of NumPy's eig()
In-Reply-To: <03F2185E-C21E-414D-AF24-BEBF1922BE8A@utoronto.ca>
References: <Pine.LNX.4.64.0702271219530.15248@salmo.appl-ecosys.com>
	<52878754-DDDD-4AE2-9601-880BA43DD446@utoronto.ca>
	<Pine.LNX.4.64.0702271232320.15248@salmo.appl-ecosys.com>
	<03F2185E-C21E-414D-AF24-BEBF1922BE8A@utoronto.ca>
Message-ID: <Pine.LNX.4.64.0702271241340.15248@salmo.appl-ecosys.com>

On Tue, 27 Feb 2007, David Warde-Farley wrote:

> If you're really keen on having short names for things you could use
> 	from scipy.linalg import eig
> or
> 	import scipy.linalg as L
> in the latter case you'd use L.eig().  I personally don't like cluttering up 
> the namespace too much but I think that's my own obsessive streak. :)

David,

   I've no preference one way or the other.

   However, I don't see the answer I expected. My expectation is that all
values would be in the range [0.00-1.00], but they're not.

   When I print eigE I see:

(array([  8.88174744e+00+0.j        ,   3.54286503e-01+2.48721395j,
          3.54286503e-01-2.48721395j,  -3.11162331e-01+1.00980412j,
         -3.11162331e-01-1.00980412j,  -2.79755841e-01+0.46954619j,
         -2.79755841e-01-0.46954619j,  -4.08484096e-01+0.j        ]),
array([[  6.24249034e-01 +0.00000000e+00j,
           4.46875199e-01 -2.63555328e-01j,
           4.46875199e-01 +2.63555328e-01j,
          -1.42390973e-01 -5.61667808e-01j,
          -1.42390973e-01 +5.61667808e-01j,
          -6.46262210e-01 +0.00000000e+00j,
          -6.46262210e-01 -0.00000000e+00j,
           3.21082397e-01 +0.00000000e+00j],
        [  5.11335982e-01 +0.00000000e+00j,
           5.74875531e-01 +0.00000000e+00j,
           5.74875531e-01 -0.00000000e+00j,
           6.00826858e-01 +0.00000000e+00j,
           6.00826858e-01 -0.00000000e+00j,
           3.96191087e-01 -2.86601017e-01j,
           3.96191087e-01 +2.86601017e-01j,
          -1.11778945e-01 +0.00000000e+00j],
        [  3.67333773e-01 +0.00000000e+00j,
           2.17622233e-01 +2.64832461e-01j,
           2.17622233e-01 -2.64832461e-01j,
           5.23950814e-02 +3.20941855e-01j,
           5.23950814e-02 -3.20941855e-01j,
           9.79467401e-02 +4.26775994e-01j,
           9.79467401e-02 -4.26775994e-01j,
           3.25049690e-01 +0.00000000e+00j],
        [  3.01189122e-01 +0.00000000e+00j,
          -1.99915129e-03 +3.51819621e-01j,
          -1.99915129e-03 -3.51819621e-01j,
          -3.31543315e-01 +4.14230032e-02j,
          -3.31543315e-01 -4.14230032e-02j,
          -2.40393098e-01 -1.72385172e-01j,
          -2.40393098e-01 +1.72385172e-01j,
          -5.55853156e-01 +0.00000000e+00j],
        [  2.43449050e-01 +0.00000000e+00j,
          -2.39280748e-01 +1.81665666e-01j,
          -2.39280748e-01 -1.81665666e-01j,
           7.36841917e-02 -2.29964404e-01j,
           7.36841917e-02 +2.29964404e-01j,
           1.64067922e-01 -9.40947682e-02j,
           1.64067922e-01 +9.40947682e-02j,
           5.32558922e-01 +0.00000000e+00j],
        [  1.82948476e-01 +0.00000000e+00j,
          -1.73636742e-01 -5.63298529e-02j,
          -1.73636742e-01 +5.63298529e-02j,
           1.02155185e-01 +6.19835455e-02j,
           1.02155185e-01 -6.19835455e-02j,
          -5.20559632e-02 +1.19076414e-01j,
          -5.20559632e-02 -1.19076414e-01j,
          -3.31196888e-01 +0.00000000e+00j],
        [  1.43655139e-01 +0.00000000e+00j,
          -8.17472085e-02 -1.40491017e-01j,
          -8.17472085e-02 +1.40491017e-01j,
          -3.15727963e-03 +7.94710216e-02j,
          -3.15727963e-03 -7.94710216e-02j,
           4.00006513e-03 -8.97730556e-02j,
           4.00006513e-03 +8.97730556e-02j,
           2.50876482e-01 +0.00000000e+00j],
        [  9.91225725e-02 +0.00000000e+00j,
           3.30357162e-02 -8.93890809e-02j,
           3.30357162e-02 +8.93890809e-02j,
          -8.33994799e-02 +1.92423688e-03j,
          -8.33994799e-02 -1.92423688e-03j,
           4.33406761e-02 +3.72302707e-02j,
           4.33406761e-02 -3.72302707e-02j,
          -1.16327714e-01 +0.00000000e+00j]]))

   Since eig(E) "Return[s] all solutions (lamda, x) to the equation Ax =
lamda x. The first element of the return tuple contains all the eigenvalues.
The second element of the return tuple contains the eigenvectors in the
columns (x[:,i] is the ith eigenvector)."

   I can't interpret the above. If the first tuple has all the Eigenvalues,
how do I extract the principal Eigenvector from the rest? When I did this
manually a couple of years ago, I used Octave to calculate the principal
Eigenvector and the answer was easy for me to see.

Rich

-- 
Richard B. Shepard, Ph.D.               |    The Environmental Permitting
Applied Ecosystem Services, Inc.        |          Accelerator(TM)
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863


From jeremit0 at gmail.com  Tue Feb 27 16:02:31 2007
From: jeremit0 at gmail.com (Jeremy Conlin)
Date: Tue, 27 Feb 2007 16:02:31 -0500
Subject: [SciPy-user] no linalg module and failed check_integer test
In-Reply-To: <45E498E5.4040601@gmail.com>
References: <3db594f70702271231s2b0f3fd3l79f1342b11d408d2@mail.gmail.com>
	<45E498E5.4040601@gmail.com>
Message-ID: <3db594f70702271302t3ebc0785maa65a1211c00fd22@mail.gmail.com>

On 2/27/07, Robert Kern <robert.kern at gmail.com> wrote:
> > I didn't notice any errors during the installation.  I know this isn't
> > a lot of information to go on, but does anyone know what the problem
> > is?
>
> Don't bother with pkgload. Just import scipy.linalg.

I tried that:

Python 2.5 (r25:51918, Sep 19 2006, 08:49:13)
[GCC 4.0.1 (Apple Computer, Inc. build 5341)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import scipy
>>> import scipy.linalg
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/linalg/__init__.py",
line 8, in <module>
    from basic import *
  File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/linalg/basic.py",
line 17, in <module>
    from lapack import get_lapack_funcs
  File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/linalg/lapack.py",
line 17, in <module>
    from scipy.linalg import flapack
ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/linalg/flapack.so,
2): Symbol not found: ___dso_handle
  Referenced from:
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/linalg/flapack.so
  Expected in: dynamic lookup

>>>

Sorry.  I don't understand what all of those mean or I would try something.

> > ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/special/_cephes.so,
> > 2): Symbol not found: ___dso_handle
> >   Referenced from:
> > /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/special/_cephes.so
> >   Expected in: dynamic lookup
>
> No, it's different. Exactly what versions of OS X (version number and Intel or
> PPC), gcc, gfortran (also where you got it from), Xcode do you have installed?
> You might need to install the latest version of cctools from here (AFAIK, the
> best place to get it):
>
>   ftp://gcc.gnu.org/pub/gcc/infrastructure/cctools-590.36.dmg
>
> That said, I've never installed it on my MacBook, and I've never had this problem.
>
I have the latest version of Xcode installed.  I am running on a
MacBook Pro with the latest OS X version.  I am running gcc version
4.0.1 and gfortran version 4.3.0.  I got gfortran by following the
instructions on the install scipy page for Mac OS X; it links to this
package:
http://prdownloads.sourceforge.net/hpc/gfortran-intel-bin.tar.gz?download

Thanks,
Jeremy


From bryanv at enthought.com  Tue Feb 27 16:11:13 2007
From: bryanv at enthought.com (Bryan Van de Ven)
Date: Tue, 27 Feb 2007 15:11:13 -0600
Subject: [SciPy-user] Proper Use of NumPy's eig()
In-Reply-To: <Pine.LNX.4.64.0702271241340.15248@salmo.appl-ecosys.com>
References: <Pine.LNX.4.64.0702271219530.15248@salmo.appl-ecosys.com>	<52878754-DDDD-4AE2-9601-880BA43DD446@utoronto.ca>	<Pine.LNX.4.64.0702271232320.15248@salmo.appl-ecosys.com>	<03F2185E-C21E-414D-AF24-BEBF1922BE8A@utoronto.ca>
	<Pine.LNX.4.64.0702271241340.15248@salmo.appl-ecosys.com>
Message-ID: <45E49E71.6040605@enthought.com>


If by principal eigenvector you mean the eigenvector corresponding to the 
largest-magnitude eigenvalue, then you can try something like:

a=array([[1,0],[0,-3]])
evals, evects = eig(a)
peig = evects[where(abs(evals)==max(abs(evals)))]

Rich Shepard wrote:
> On Tue, 27 Feb 2007, David Warde-Farley wrote:
> 
>> If you're really keen on having short names for things you could use
>> 	from scipy.linalg import eig
>> or
>> 	import scipy.linalg as L
>> in the latter case you'd use L.eig().  I personally don't like cluttering up 
>> the namespace too much but I think that's my own obsessive streak. :)
> 
> David,
> 
>    I've no preference one way or the other.
> 
>    However, I don't see the answer I expected. My expectation is that all
> values would be in the range [0.00-1.00], but they're not.
> 
>    When I print eigE I see:
> 
> (array([  8.88174744e+00+0.j        ,   3.54286503e-01+2.48721395j,
>           3.54286503e-01-2.48721395j,  -3.11162331e-01+1.00980412j,
>          -3.11162331e-01-1.00980412j,  -2.79755841e-01+0.46954619j,
>          -2.79755841e-01-0.46954619j,  -4.08484096e-01+0.j        ]),
> array([[  6.24249034e-01 +0.00000000e+00j,
>            4.46875199e-01 -2.63555328e-01j,
>            4.46875199e-01 +2.63555328e-01j,
>           -1.42390973e-01 -5.61667808e-01j,
>           -1.42390973e-01 +5.61667808e-01j,
>           -6.46262210e-01 +0.00000000e+00j,
>           -6.46262210e-01 -0.00000000e+00j,
>            3.21082397e-01 +0.00000000e+00j],
>         [  5.11335982e-01 +0.00000000e+00j,
>            5.74875531e-01 +0.00000000e+00j,
>            5.74875531e-01 -0.00000000e+00j,
>            6.00826858e-01 +0.00000000e+00j,
>            6.00826858e-01 -0.00000000e+00j,
>            3.96191087e-01 -2.86601017e-01j,
>            3.96191087e-01 +2.86601017e-01j,
>           -1.11778945e-01 +0.00000000e+00j],
>         [  3.67333773e-01 +0.00000000e+00j,
>            2.17622233e-01 +2.64832461e-01j,
>            2.17622233e-01 -2.64832461e-01j,
>            5.23950814e-02 +3.20941855e-01j,
>            5.23950814e-02 -3.20941855e-01j,
>            9.79467401e-02 +4.26775994e-01j,
>            9.79467401e-02 -4.26775994e-01j,
>            3.25049690e-01 +0.00000000e+00j],
>         [  3.01189122e-01 +0.00000000e+00j,
>           -1.99915129e-03 +3.51819621e-01j,
>           -1.99915129e-03 -3.51819621e-01j,
>           -3.31543315e-01 +4.14230032e-02j,
>           -3.31543315e-01 -4.14230032e-02j,
>           -2.40393098e-01 -1.72385172e-01j,
>           -2.40393098e-01 +1.72385172e-01j,
>           -5.55853156e-01 +0.00000000e+00j],
>         [  2.43449050e-01 +0.00000000e+00j,
>           -2.39280748e-01 +1.81665666e-01j,
>           -2.39280748e-01 -1.81665666e-01j,
>            7.36841917e-02 -2.29964404e-01j,
>            7.36841917e-02 +2.29964404e-01j,
>            1.64067922e-01 -9.40947682e-02j,
>            1.64067922e-01 +9.40947682e-02j,
>            5.32558922e-01 +0.00000000e+00j],
>         [  1.82948476e-01 +0.00000000e+00j,
>           -1.73636742e-01 -5.63298529e-02j,
>           -1.73636742e-01 +5.63298529e-02j,
>            1.02155185e-01 +6.19835455e-02j,
>            1.02155185e-01 -6.19835455e-02j,
>           -5.20559632e-02 +1.19076414e-01j,
>           -5.20559632e-02 -1.19076414e-01j,
>           -3.31196888e-01 +0.00000000e+00j],
>         [  1.43655139e-01 +0.00000000e+00j,
>           -8.17472085e-02 -1.40491017e-01j,
>           -8.17472085e-02 +1.40491017e-01j,
>           -3.15727963e-03 +7.94710216e-02j,
>           -3.15727963e-03 -7.94710216e-02j,
>            4.00006513e-03 -8.97730556e-02j,
>            4.00006513e-03 +8.97730556e-02j,
>            2.50876482e-01 +0.00000000e+00j],
>         [  9.91225725e-02 +0.00000000e+00j,
>            3.30357162e-02 -8.93890809e-02j,
>            3.30357162e-02 +8.93890809e-02j,
>           -8.33994799e-02 +1.92423688e-03j,
>           -8.33994799e-02 -1.92423688e-03j,
>            4.33406761e-02 +3.72302707e-02j,
>            4.33406761e-02 -3.72302707e-02j,
>           -1.16327714e-01 +0.00000000e+00j]]))
> 
>    Since eig(E) "Return[s] all solutions (lamda, x) to the equation Ax =
> lamda x. The first element of the return tuple contains all the eigenvalues.
> The second element of the return tuple contains the eigenvectors in the
> columns (x[:,i] is the ith eigenvector)."
> 
>    I can't interpret the above. If the first tuple has all the Eigenvalues,
> how do I extract the principal Eigenvector from the rest? When I did this
> manually a couple of years ago, I used Octave to calculate the principal
> Eigenvector and the answer was easy for me to see.
> 
> Rich
> 



From robert.kern at gmail.com  Tue Feb 27 16:11:21 2007
From: robert.kern at gmail.com (Robert Kern)
Date: Tue, 27 Feb 2007 15:11:21 -0600
Subject: [SciPy-user] Proper Use of NumPy's eig()
In-Reply-To: <Pine.LNX.4.64.0702271241340.15248@salmo.appl-ecosys.com>
References: <Pine.LNX.4.64.0702271219530.15248@salmo.appl-ecosys.com>	<52878754-DDDD-4AE2-9601-880BA43DD446@utoronto.ca>	<Pine.LNX.4.64.0702271232320.15248@salmo.appl-ecosys.com>	<03F2185E-C21E-414D-AF24-BEBF1922BE8A@utoronto.ca>
	<Pine.LNX.4.64.0702271241340.15248@salmo.appl-ecosys.com>
Message-ID: <45E49E79.6080905@gmail.com>

Rich Shepard wrote:

>    However, I don't see the answer I expected. My expectation is that all
> values would be in the range [0.00-1.00], but they're not.
> 
>    When I print eigE I see:
> 
> (array([  8.88174744e+00+0.j        ,   3.54286503e-01+2.48721395j,
>           3.54286503e-01-2.48721395j,  -3.11162331e-01+1.00980412j,
>          -3.11162331e-01-1.00980412j,  -2.79755841e-01+0.46954619j,
>          -2.79755841e-01-0.46954619j,  -4.08484096e-01+0.j        ]),
> array([[  6.24249034e-01 +0.00000000e+00j,

...

Without knowing your input, I can't see anything particularly wrong. Unless if E
were real-symmetric (or complex-Hermitian), you are likely to end up with
complex eigenvalues.

>    Since eig(E) "Return[s] all solutions (lamda, x) to the equation Ax =
> lamda x. The first element of the return tuple contains all the eigenvalues.
> The second element of the return tuple contains the eigenvectors in the
> columns (x[:,i] is the ith eigenvector)."
> 
>    I can't interpret the above. If the first tuple has all the Eigenvalues,
> how do I extract the principal Eigenvector from the rest? When I did this
> manually a couple of years ago, I used Octave to calculate the principal
> Eigenvector and the answer was easy for me to see.

I don't think that the notion of a principal eigenvector is well-defined if the
matrix is not symmetric. But if you do have a symmetric matrix:


import numpy as np
from scipy import linalg

eigvals, eigvecs = linalg.eig(E)
i = np.real_if_close(eigvals).argmax()
principal_eigvec = eigvecs[:, i]

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
 that is made terrible by our own mad attempt to interpret it as though it had
 an underlying truth."
  -- Umberto Eco


From robert.kern at gmail.com  Tue Feb 27 16:14:15 2007
From: robert.kern at gmail.com (Robert Kern)
Date: Tue, 27 Feb 2007 15:14:15 -0600
Subject: [SciPy-user] no linalg module and failed check_integer test
In-Reply-To: <3db594f70702271302t3ebc0785maa65a1211c00fd22@mail.gmail.com>
References: <3db594f70702271231s2b0f3fd3l79f1342b11d408d2@mail.gmail.com>	<45E498E5.4040601@gmail.com>
	<3db594f70702271302t3ebc0785maa65a1211c00fd22@mail.gmail.com>
Message-ID: <45E49F27.1090507@gmail.com>

Jeremy Conlin wrote:
> On 2/27/07, Robert Kern <robert.kern at gmail.com> wrote:
>>> I didn't notice any errors during the installation.  I know this isn't
>>> a lot of information to go on, but does anyone know what the problem
>>> is?
>> Don't bother with pkgload. Just import scipy.linalg.
> 
> I tried that:

> ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/linalg/flapack.so,
> 2): Symbol not found: ___dso_handle
>   Referenced from:
> /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/linalg/flapack.so
>   Expected in: dynamic lookup
> 
> Sorry.  I don't understand what all of those mean or I would try something.

Then I was wrong: the next error is related. The fact that pkgload() hid this
message is why I suggest not using it.

>>> ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/special/_cephes.so,
>>> 2): Symbol not found: ___dso_handle
>>>   Referenced from:
>>> /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/special/_cephes.so
>>>   Expected in: dynamic lookup
>> No, it's different. Exactly what versions of OS X (version number and Intel or
>> PPC), gcc, gfortran (also where you got it from), Xcode do you have installed?
>> You might need to install the latest version of cctools from here (AFAIK, the
>> best place to get it):
>>
>>   ftp://gcc.gnu.org/pub/gcc/infrastructure/cctools-590.36.dmg
>>
>> That said, I've never installed it on my MacBook, and I've never had this problem.
>>
> I have the latest version of Xcode installed.  I am running on a
> MacBook Pro with the latest OS X version.  I am running gcc version
> 4.0.1 and gfortran version 4.3.0.  I got gfortran by following the
> instructions on the install scipy page for Mac OS X; it links to this
> package:
> http://prdownloads.sourceforge.net/hpc/gfortran-intel-bin.tar.gz?download

When did you install gfortran? Gaurav Khanna has the unfortunate habit of
uploading new builds without changing the filename.

Try installing the cctools package I gave and rebuilding scipy.

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
 that is made terrible by our own mad attempt to interpret it as though it had
 an underlying truth."
  -- Umberto Eco


From jeremit0 at gmail.com  Tue Feb 27 16:17:49 2007
From: jeremit0 at gmail.com (Jeremy Conlin)
Date: Tue, 27 Feb 2007 16:17:49 -0500
Subject: [SciPy-user] no linalg module and failed check_integer test
In-Reply-To: <45E49F27.1090507@gmail.com>
References: <3db594f70702271231s2b0f3fd3l79f1342b11d408d2@mail.gmail.com>
	<45E498E5.4040601@gmail.com>
	<3db594f70702271302t3ebc0785maa65a1211c00fd22@mail.gmail.com>
	<45E49F27.1090507@gmail.com>
Message-ID: <3db594f70702271317t4b8de4ffvb4b6330410c8bb1c@mail.gmail.com>

On 2/27/07, Robert Kern <robert.kern at gmail.com> wrote:
> Jeremy Conlin wrote:
> > On 2/27/07, Robert Kern <robert.kern at gmail.com> wrote:
> >>> I didn't notice any errors during the installation.  I know this isn't
> >>> a lot of information to go on, but does anyone know what the problem
> >>> is?
> >> Don't bother with pkgload. Just import scipy.linalg.
> >
> > I tried that:
>
> > ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/linalg/flapack.so,
> > 2): Symbol not found: ___dso_handle
> >   Referenced from:
> > /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/linalg/flapack.so
> >   Expected in: dynamic lookup
> >
> > Sorry.  I don't understand what all of those mean or I would try something.
>
> Then I was wrong: the next error is related. The fact that pkgload() hid this
> message is why I suggest not using it.
>
> >>> ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/special/_cephes.so,
> >>> 2): Symbol not found: ___dso_handle
> >>>   Referenced from:
> >>> /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/special/_cephes.so
> >>>   Expected in: dynamic lookup
> >> No, it's different. Exactly what versions of OS X (version number and Intel or
> >> PPC), gcc, gfortran (also where you got it from), Xcode do you have installed?
> >> You might need to install the latest version of cctools from here (AFAIK, the
> >> best place to get it):
> >>
> >>   ftp://gcc.gnu.org/pub/gcc/infrastructure/cctools-590.36.dmg
> >>
> >> That said, I've never installed it on my MacBook, and I've never had this problem.
> >>
> > I have the latest version of Xcode installed.  I am running on a
> > MacBook Pro with the latest OS X version.  I am running gcc version
> > 4.0.1 and gfortran version 4.3.0.  I got gfortran by following the
> > instructions on the install scipy page for Mac OS X; it links to this
> > package:
> > http://prdownloads.sourceforge.net/hpc/gfortran-intel-bin.tar.gz?download
>
> When did you install gfortran? Gaurav Khanna has the unfortunate habit of
> uploading new builds without changing the filename.

I installed gfortran about a week or two ago.

>
> Try installing the cctools package I gave and rebuilding scipy.

I did just that and it fixed my problem with loading linalg!  Thanks.
However, scipy still fails on some tests, but it did get further this
time.  Can I trust the results from scipy if these tests fail?  I have
copied the failed portions below.
Thanks again,
Jeremy

======================================================================
FAIL: check_expon (scipy.stats.tests.test_morestats.test_anderson)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/stats/tests/test_morestats.py",
line 57, in check_expon
    assert_array_less(A, crit[-2:])
  File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/testing/utils.py",
line 235, in assert_array_less
    header='Arrays are not less-ordered')
  File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/testing/utils.py",
line 215, in assert_array_compare
    assert cond, msg
AssertionError:
Arrays are not less-ordered

(mismatch 100.0%)
 x: array(1.9823844122912462)
 y: array([ 1.587,  1.934])

======================================================================
FAIL: check_dot (scipy.lib.tests.test_blas.test_fblas1_simple)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/lib/blas/tests/test_blas.py",
line 76, in check_dot
    assert_almost_equal(f([3j,-4,3-4j],[2,3,1]),-9+2j)
  File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/testing/utils.py",
line 156, in assert_almost_equal
    assert round(abs(desired - actual),decimal) == 0, msg
AssertionError:
Items are not equal:
 ACTUAL: 6.3815410082967491e-37j
 DESIRED: (-9+2j)

======================================================================
FAIL: check_dot (scipy.linalg.tests.test_blas.test_fblas1_simple)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/linalg/tests/test_blas.py",
line 75, in check_dot
    assert_almost_equal(f([3j,-4,3-4j],[2,3,1]),-9+2j)
  File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/testing/utils.py",
line 156, in assert_almost_equal
    assert round(abs(desired - actual),decimal) == 0, msg
AssertionError:
Items are not equal:
 ACTUAL: 6.4704707719591164e-37j
 DESIRED: (-9+2j)

----------------------------------------------------------------------
Ran 1620 tests in 4.936s

FAILED (failures=3)


From rshepard at appl-ecosys.com  Tue Feb 27 16:44:56 2007
From: rshepard at appl-ecosys.com (Rich Shepard)
Date: Tue, 27 Feb 2007 13:44:56 -0800 (PST)
Subject: [SciPy-user] Proper Use of NumPy's eig()
In-Reply-To: <45E49E71.6040605@enthought.com>
References: <Pine.LNX.4.64.0702271219530.15248@salmo.appl-ecosys.com>
	<52878754-DDDD-4AE2-9601-880BA43DD446@utoronto.ca>
	<Pine.LNX.4.64.0702271232320.15248@salmo.appl-ecosys.com>
	<03F2185E-C21E-414D-AF24-BEBF1922BE8A@utoronto.ca>
	<Pine.LNX.4.64.0702271241340.15248@salmo.appl-ecosys.com>
	<45E49E71.6040605@enthought.com>
Message-ID: <Pine.LNX.4.64.0702271340560.15248@salmo.appl-ecosys.com>

On Tue, 27 Feb 2007, Bryan Van de Ven wrote:

> If by principal eigenvector you mean the eigenvector corresponding to the
> largest-magnitude eigenvalue, then you can try something like:
>
> a=array([[1,0],[0,-3]])
> evals, evects = eig(a)
> peig = evects[where(abs(evals)==max(abs(evals)))]

   Thank you, Bryan. That is just what I meant. The numbers are not coming
out in a way that makes sense, so I assume that my input data -- randomly
generated as a test case -- is incorrect. Either that, or my algorithm to
create the symmetrical matrix is flawed.

   Time to take a very close look from the start.

Rich

-- 
Richard B. Shepard, Ph.D.               |    The Environmental Permitting
Applied Ecosystem Services, Inc.        |          Accelerator(TM)
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863


From as8ca at virginia.edu  Tue Feb 27 16:46:29 2007
From: as8ca at virginia.edu (Alok Singhal)
Date: Tue, 27 Feb 2007 16:46:29 -0500
Subject: [SciPy-user] Using SciPy/NumPy optimization
In-Reply-To: <45E493D7.2070703@gmail.com>
References: <6.0.1.1.2.20070227131721.0287bfe0@pop.uky.edu>
	<45E493D7.2070703@gmail.com>
Message-ID: <20070227214629.GA6215@virginia.edu>

Hi,

Sorry about the long post.  I did not ask the original question, but I
tried the solution posted and could not get it to work.

Original question: given a set of data [[x1, y1], ..., [xn, yn]], how
to fit y = a*(1 + b*c*x) ** (-1.0/b) to it, subject to the
constraints:

 0 <  b <= 5
-1 <= c <= 1
a ~ >= max(x1, ... xn)

On 27/02/07: 14:25, Robert Kern wrote:
> There are a number of constrained optimizers in scipy.optimize .
> scipy.optimize.fmin_tnc seems most appropriate for simple bounds like you have.
> In order to get a function to minimize that depends on data, I usually like to
> use a class:
> 
>   import numpy as np
>   from scipy.optimize import fmin_tnc
> 
>   class LossFunction(object):
>     def __init__(self, x, y):
>       self.x = x
>       self.y = y
> 
>     def __call__(self, abc):
>       """ A function suitable for passing to the fmin() minimizers.
>       """
>       a, b, c = abc
>       y = a*(1.0 + b*c*self.x) ** (-1.0/b)
>       dy = self.y - y
>       return dy*dy
> 
>   x = np.array([...])
>   y = np.array([...])
>   lf = LossFunction(x, y)
>   abc0 = np.array([x.max(), 2.5, 0.0])  # or whatever
>   retcode, nfeval, abc_optimal = fmin_tnc(lf, abc0,
>     bounds=[(None, None), (0., 5.), (-1., 1.)])

I used optimize.leastsq to do the fitting, and it worked well me (see
http://www.scipy.org/Cookbook/FittingData).  But I was trying the
above method, and unfortunately it doesn't work as presented.  When I
define the variables x and y by:

from scipy.optimize import fmin_tnc
from scipy import rand
from numpy import mgrid, log

def f(abc, x):
  return abc[0]*(1.0+abc[1]*abc[2]*x)**(-1.0/abc[1])

a = 15.0
b = 2.5
c = 0.3
abc = (a, b, c)
num_points = 151
x = mgrid[1:10:num_points*1j]

y = f(abc, x) + rand(num_points) - 0.5
abc0 = [x.max(), 2.5, 0.0]
lf = LossFunction(x, y)

retcode, nfeval, abc_optimal = fmin_tnc(lf, abc0, bounds=[(None, None), (0., 5.), (-1., 1.)])

The call to fmin_tnc gives me an error:

File "/usr/lib/python2.4/site-packages/scipy/optimize/tnc.py", line 191, in func_and_grad
    f, g = func(x, *args)
ValueError: too many values to unpack

Looking at the documentation and the source file, the first parameter
to fmin_tnc should be a function that returns the function value and
the gradient vector (with respect to the parameters being estimated).
Also, it seems that I can tell fmin_tnc to estimate the gradient
itself, if I specify approx_grad as True:

retcode, nfeval, abc_optimal = fmin_tnc(lf, abc0, bounds=[(None, None), (0., 5.), (-1., 1.)], approx_grad=True)

But this gives me an error saying:

File "/usr/lib/python2.4/site-packages/scipy/optimize/optimize.py", line 576, in approx_fprime
    grad[k] = (apply(f,(xk+ei,)+args) - f0)/epsilon
ValueError: setting an array element with a sequence.

Then I tried redefining the __call__ in LossFunction to return the
gradient as well:

class LossFunction(object):
  def __init__(self, x, y):
    self.x = x
    self.y = y
  def __call__(self, abc):
    a, b, c = abc
    y = a*(1.0 + b*c*self.x) ** (-1.0/b)
    dy = self.y - y
    d = [0, 0, 0]
    d[0] = (1.0 + b*c*self.x) ** (-1.0/b)
    d[1] = y * (log(a*(1.0+b*c*self.x))/b**2 - c*self.x/(b*(1.0+b*c*self.x)))
    d[2] = -a/b*(1.0 + b*c*self.x) ** (-1.0/b) * b*self.x
    return dy*dy, d

When I call this function instead, I get another error:

File "/usr/lib/python2.4/site-packages/scipy/optimize/tnc.py", line 221, in fmin_tnc
    fmin, ftol, rescale)
ValueError: Bad return value from minimized function.

At this point, I gave up, but I would like to understand what I am
doing wrong.  To me, it seems like fmin_tnc will find the values of
parameters (a, b, c in this case) that minimize a given function that
depends *only* on a, b, c.  I don't understand how to make it work so
as to fit existing data.  I am sure I am missing something, but I
don't know what that is.

Thanks for all your help,
Alok

-- 
Alok Singhal                               *   *          
Graduate Student, dept. of Astronomy   *           *     *
University of Virginia                                    
http://www.astro.virginia.edu/~as8ca/              *    * 


From bnuttall at uky.edu  Tue Feb 27 17:16:23 2007
From: bnuttall at uky.edu (Brandon Nuttall)
Date: Tue, 27 Feb 2007 17:16:23 -0500
Subject: [SciPy-user] Using SciPy/NumPy optimization
In-Reply-To: <45E493D7.2070703@gmail.com>
References: <6.0.1.1.2.20070227131721.0287bfe0@pop.uky.edu>
	<45E493D7.2070703@gmail.com>
Message-ID: <6.0.1.1.2.20070227170539.0283f608@pop.uky.edu>

Robert,

Thanks.

At 03:25 PM 2/27/2007, you wrote:
>Presumably, you mean
>
>   y = a*(1 + b*c*x) ** (-1.0/b)
>
>to correct a typo and use Python notation.

Yes, you are correct.

>   import numpy as np
>   from scipy.optimize import fmin_tnc
>
>   class LossFunction(object):
>     def __init__(self, x, y):
>       self.x = x
>       self.y = y
>
>     def __call__(self, abc):
>       """ A function suitable for passing to the fmin() minimizers.
>       """
>       a, b, c = abc
>       y = a*(1.0 + b*c*self.x) ** (-1.0/b)
>       dy = self.y - y
>       return dy*dy
>
>   x = np.array([...])
>   y = np.array([...])
>   lf = LossFunction(x, y)
>   abc0 = np.array([x.max(), 2.5, 0.0])  # or whatever
>   retcode, nfeval, abc_optimal = fmin_tnc(lf, abc0,
>     bounds=[(None, None), (0., 5.), (-1., 1.)])

OK. I'm on my way home to try it out.



Brandon C. Nuttall

BNUTTALL at UKY.EDU                         Kentucky Geological Survey
(859) 257-5500                                     University of Kentucky
(859) 257-1147 (fax)                              228 Mining & Mineral 
Resources Bldg
http://www.uky.edu/KGS/home.htm       Lexington, Kentucky 40506-0107  



From rshepard at appl-ecosys.com  Tue Feb 27 17:21:25 2007
From: rshepard at appl-ecosys.com (Rich Shepard)
Date: Tue, 27 Feb 2007 14:21:25 -0800 (PST)
Subject: [SciPy-user] Proper Use of NumPy's eig()
In-Reply-To: <45E49E79.6080905@gmail.com>
References: <Pine.LNX.4.64.0702271219530.15248@salmo.appl-ecosys.com>
	<52878754-DDDD-4AE2-9601-880BA43DD446@utoronto.ca>
	<Pine.LNX.4.64.0702271232320.15248@salmo.appl-ecosys.com>
	<03F2185E-C21E-414D-AF24-BEBF1922BE8A@utoronto.ca>
	<Pine.LNX.4.64.0702271241340.15248@salmo.appl-ecosys.com>
	<45E49E79.6080905@gmail.com>
Message-ID: <Pine.LNX.4.64.0702271346150.15248@salmo.appl-ecosys.com>

On Tue, 27 Feb 2007, Robert Kern wrote:

> Without knowing your input, I can't see anything particularly wrong.
> Unless if E were real-symmetric (or complex-Hermitian), you are likely to
> end up with complex eigenvalues.

Robert,

   It's been decades since I last worked a lot with linear algebra. I suspect
that I've mis-handled the calculations between raw input and final
symmectric matrix. It is supposed to be symmetrical. And the values of the
principal eigenvector should add to 1.00 because they should be the relative
weights of input factor.

> I don't think that the notion of a principal eigenvector is well-defined if the
> matrix is not symmetric. But if you do have a symmetric matrix:

> import numpy as np
> from scipy import linalg
>
> eigvals, eigvecs = linalg.eig(E)
> i = np.real_if_close(eigvals).argmax()
> principal_eigvec = eigvecs[:, i]

   This produces:

[  6.24249034e-01+0.j   5.11335982e-01+0.j   3.67333773e-01+0.j
    3.01189122e-01+0.j   2.43449050e-01+0.j   1.82948476e-01+0.j
    1.43655139e-01+0.j   9.91225725e-02+0.j]

   ... and these total approximately 2.472.

   So, it's time to look at the input (which is almost certainly OK) and more
closely at how those input values are extracted, averaged, and reduced to a
symmetrical matrix.

Thanks,

Rich

-- 
Richard B. Shepard, Ph.D.               |    The Environmental Permitting
Applied Ecosystem Services, Inc.        |          Accelerator(TM)
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863


From rshepard at appl-ecosys.com  Tue Feb 27 18:41:23 2007
From: rshepard at appl-ecosys.com (Rich Shepard)
Date: Tue, 27 Feb 2007 15:41:23 -0800 (PST)
Subject: [SciPy-user] Proper Use of NumPy's eig()
In-Reply-To: <Pine.LNX.4.64.0702271346150.15248@salmo.appl-ecosys.com>
References: <Pine.LNX.4.64.0702271219530.15248@salmo.appl-ecosys.com>
	<52878754-DDDD-4AE2-9601-880BA43DD446@utoronto.ca>
	<Pine.LNX.4.64.0702271232320.15248@salmo.appl-ecosys.com>
	<03F2185E-C21E-414D-AF24-BEBF1922BE8A@utoronto.ca>
	<Pine.LNX.4.64.0702271241340.15248@salmo.appl-ecosys.com>
	<45E49E79.6080905@gmail.com>
	<Pine.LNX.4.64.0702271346150.15248@salmo.appl-ecosys.com>
Message-ID: <Pine.LNX.4.64.0702271538200.15248@salmo.appl-ecosys.com>

On Tue, 27 Feb 2007, Rich Shepard wrote:

>   This produces:
>
> [  6.24249034e-01+0.j   5.11335982e-01+0.j   3.67333773e-01+0.j
>    3.01189122e-01+0.j   2.43449050e-01+0.j   1.82948476e-01+0.j
>    1.43655139e-01+0.j   9.91225725e-02+0.j]
>
>   ... and these total approximately 2.472.
>
>   So, it's time to look at the input (which is almost certainly OK) and
> more closely at how those input values are extracted, averaged, and
> reduced to a symmetrical matrix.

All:

   Since it's been almost 2 years since my book was published, and even
longer since I worked the example for the book, I forgot the last -- and
most important -- step: to normalize those values returned as the principal
eigenvector.

   Yes, they are correctly computed, I just need to take the process one more
step.

   My sincere thanks to all of you. I now have a much better understanding
how to apply NumPy and SciPy to address this need.

Rich

-- 
Richard B. Shepard, Ph.D.               |    The Environmental Permitting
Applied Ecosystem Services, Inc.        |          Accelerator(TM)
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863


From rblove at airmail.net  Tue Feb 27 22:10:29 2007
From: rblove at airmail.net (Robert Love)
Date: Tue, 27 Feb 2007 21:10:29 -0600
Subject: [SciPy-user] Any Books on SciPy?
Message-ID: <D73DF6B6-D5A3-45E4-B7BA-F514307B3321@airmail.net>

Are there any good, up to date books that people recommend for  
numerical work with Python?

I see the book

    Python Scripting for Computational Science
    Hans Petter Langtangen

Does anyone have opinions on this?  Is it current?  Are there better  
books?

All pointers appreciated.


From david.warde.farley at utoronto.ca  Tue Feb 27 22:54:34 2007
From: david.warde.farley at utoronto.ca (David Warde-Farley)
Date: Tue, 27 Feb 2007 22:54:34 -0500
Subject: [SciPy-user] Any Books on SciPy?
In-Reply-To: <D73DF6B6-D5A3-45E4-B7BA-F514307B3321@airmail.net>
References: <D73DF6B6-D5A3-45E4-B7BA-F514307B3321@airmail.net>
Message-ID: <1172634874.6867.13.camel@rodimus>

On Tue, 2007-02-27 at 21:10 -0600, Robert Love wrote:
> Are there any good, up to date books that people recommend for  
> numerical work with Python?

Travis Oliphant's "Guide to NumPy" (eBook) tells you more than you'll
probably ever need to know about NumPy specifically, but it's less a
recipe book and more a reference manual. I don't know of any, but I'd
sure like to see them, since it's a bit of a barrier to entry for new
users who see similar books for Matlab, etc.

David



From jdh2358 at gmail.com  Tue Feb 27 22:59:28 2007
From: jdh2358 at gmail.com (John Hunter)
Date: Tue, 27 Feb 2007 21:59:28 -0600
Subject: [SciPy-user] Any Books on SciPy?
In-Reply-To: <D73DF6B6-D5A3-45E4-B7BA-F514307B3321@airmail.net>
References: <D73DF6B6-D5A3-45E4-B7BA-F514307B3321@airmail.net>
Message-ID: <88e473830702271959o6a4dcc2dv3dd2d5fb7db0bfa1@mail.gmail.com>

On 2/27/07, Robert Love <rblove at airmail.net> wrote:
> Are there any good, up to date books that people recommend for
> numerical work with Python?
>
> I see the book
>
>     Python Scripting for Computational Science
>     Hans Petter Langtangen
>
> Does anyone have opinions on this?  Is it current?  Are there better
> books?

I specifically do not recommend this book -- I own it but in my
opinion it is outdated and is more a collection of the author's
personal idioms than the current common practice in the scientific
python community.   For numerical work in python most people use

  * numpy - for array math.  The best documentation is Travis' online
book http://www.tramy.us.  For free, the numarray documentation is
excellent and the API is very similar for common use cases -
http://www.stsci.edu/resources/software_hardware/numarray/doc

 * scipy - there is no comprehensive printed documentation that I know
of.  The online help, site docs, and wiki are your best bet. -
http://www.scipy.org/Documentation

 * ipython - the enhanced python shell which is widely used in the
scientific computing community for interactive work.  Has special
modes to support numpy, scipy, matplotlib and distributed computing.
- http://ipython.scipy.org/moin/Documentation

  * matplotlib - 2D graphics, charts and the like.  ipython has a
'ipython -pylab' mode which loads matplotlib and numpy for a matlab
like environment .  http://matplotlib.sourceforge.net/tutorial.html
and http://matplotlib.sourceforge.net/users_guide_0.87.7.pdf

* Enthought Tool Suite - provides a comprehensive package for
scientific computing including the above modules and many others for
application development and more.  Provides 3D graphics through the
Mayavi2/VTK packages and 2D plotting through Chaco, and lots of tools
to facilitate wx based GUI development -  http://code.enthought.com/

There is a lot more, particularly for domain specific stiff, but these
links are good starting points.  Unfortunately, there is no
one-stop-shop for a guide to scientific computing in python - Travis'
documentation is the closest thing we have but it pretty much just
covers numpy which is *the* core package.  Fernando Perez and I have a
very brief and limited started guide covering multiple packages
(ipython, numpy, matplotlib, scipy, VTK) but I don't have the PDF
handy (Fernando, do you have the roadshow doc handy?).  Eric Jones and
Travis (authors of scipy) have some talk notes at
http://www.nanohub.org/resources/?id=99 but these are a bit out of
date.

JDH


From steve at shrogers.com  Tue Feb 27 23:05:58 2007
From: steve at shrogers.com (Steven H. Rogers)
Date: Tue, 27 Feb 2007 21:05:58 -0700
Subject: [SciPy-user] NumPy in Teaching
Message-ID: <45E4FFA6.9010408@shrogers.com>

I'm doing an informal survey on the use of Array Programming Languages 
for teaching.  If you're using NumPy in this manner I'd like to hear 
from you.  What subject was/is taught, academic level, results, lessons 
learned, etc.

Regards,
Steve



From gary.pajer at gmail.com  Tue Feb 27 23:27:02 2007
From: gary.pajer at gmail.com (Gary Pajer)
Date: Tue, 27 Feb 2007 23:27:02 -0500
Subject: [SciPy-user] Do I have LAPACK or not?
Message-ID: <88fe22a0702272027s214476f8r99852705adb1b544@mail.gmail.com>

When I compile I get the output  below.  Has LAPACK been found or not?
 I'm guessing yes, but I have some doubt ...

thanks,
gary

-----------------------------------------------------
atlas_info:
  libraries f77blas,cblas,atlas not found in /usr/lib/atlas
  libraries lapack_atlas not found in /usr/lib/atlas
  libraries lapack not found in /usr/lib/sse2
  libraries f77blas,cblas,atlas not found in /usr/lib
  libraries lapack_atlas not found in /usr/lib
numpy.distutils.system_info.atlas_info
/usr/lib/python2.4/site-packages/numpy/distutils/system_info.py:903:
UserWarning:
*********************************************************************
    Could not find lapack library within the ATLAS installation.
*********************************************************************

  warnings.warn(message)
  FOUND:
    libraries = ['f77blas', 'cblas', 'atlas']
    library_dirs = ['/usr/lib/sse2']
    language = c
    define_macros = [('ATLAS_WITHOUT_LAPACK', None)]

lapack_info:
  FOUND:
    libraries = ['lapack']
    library_dirs = ['/usr/lib']
    language = f77

  FOUND:
    libraries = ['f77blas', 'cblas', 'atlas', 'lapack']
    library_dirs = ['/usr/lib/sse2', '/usr/lib']
    language = f77
    define_macros = [('ATLAS_WITHOUT_LAPACK', None), ('ATLAS_INFO',
'"\\"3.6.0\\""')]

ATLAS version 3.6.0


From rshepard at appl-ecosys.com  Tue Feb 27 23:55:36 2007
From: rshepard at appl-ecosys.com (Rich Shepard)
Date: Tue, 27 Feb 2007 20:55:36 -0800 (PST)
Subject: [SciPy-user] Do I have LAPACK or not?
In-Reply-To: <88fe22a0702272027s214476f8r99852705adb1b544@mail.gmail.com>
References: <88fe22a0702272027s214476f8r99852705adb1b544@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.0702272054160.23399@salmo.appl-ecosys.com>

On Tue, 27 Feb 2007, Gary Pajer wrote:

> When I compile I get the output  below.  Has LAPACK been found or not?
> I'm guessing yes, but I have some doubt ...

Gary,

   What is the result of 'locate LAPACK?' On my system it returns
/usr/local/scipy/LAPACK/ and all the subdirectories and files therein.

Rich

-- 
Richard B. Shepard, Ph.D.               |    The Environmental Permitting
Applied Ecosystem Services, Inc.        |          Accelerator(TM)
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863


From fperez.net at gmail.com  Wed Feb 28 01:19:51 2007
From: fperez.net at gmail.com (Fernando Perez)
Date: Tue, 27 Feb 2007 23:19:51 -0700
Subject: [SciPy-user] Any Books on SciPy?
In-Reply-To: <88e473830702271959o6a4dcc2dv3dd2d5fb7db0bfa1@mail.gmail.com>
References: <D73DF6B6-D5A3-45E4-B7BA-F514307B3321@airmail.net>
	<88e473830702271959o6a4dcc2dv3dd2d5fb7db0bfa1@mail.gmail.com>
Message-ID: <db6b5ecc0702272219k3a5d67dft7d2f1980b86950d1@mail.gmail.com>

On 2/27/07, John Hunter <jdh2358 at gmail.com> wrote:
> On 2/27/07, Robert Love <rblove at airmail.net> wrote:
> > Are there any good, up to date books that people recommend for
> > numerical work with Python?
> >
> > I see the book
> >
> >     Python Scripting for Computational Science
> >     Hans Petter Langtangen
> >
> > Does anyone have opinions on this?  Is it current?  Are there better
> > books?
>
> I specifically do not recommend this book -- I own it but in my
> opinion it is outdated and is more a collection of the author's
> personal idioms than the current common practice in the scientific
> python community.   For numerical work in python most people use

I happen to share John's opinion, and I also have a copy of this book.
 While it's technically correct, well written and fairly comprehensive
(probably /too/ much, since it's a bit all over the map), I strongly
dislike his approach.  Much of the book uses his custom, home-made
collection of scripts and tools, which you can only download if you go
to a site and type a word from a certain page in the book (a simple
'protection' system).

Now you have an unmaintained, unreleased (publicly), set of tools to
learn from that don't have any licensing explicitly specified.

Oh, and a good chunk of the tools in his distribution (since I have
the book, I have the code) use Perl.  Go figure (there's also a tcl
directory thrown in for good measure).

One of Python's main strengths for scientific work is precisely the
openness and interoperability of the various tools, and we all do our
part to help that be the case.  The fact that this book follows an
approach more or less orthogonal to those ideas makes me very much
uninterested in using it.

> There is a lot more, particularly for domain specific stiff, but these
> links are good starting points.  Unfortunately, there is no
> one-stop-shop for a guide to scientific computing in python - Travis'
> documentation is the closest thing we have but it pretty much just
> covers numpy which is *the* core package.  Fernando Perez and I have a
> very brief and limited started guide covering multiple packages
> (ipython, numpy, matplotlib, scipy, VTK) but I don't have the PDF
> handy (Fernando, do you have the roadshow doc handy?).

Well, you asked for it :)

http://amath.colorado.edu/faculty/fperez/tmp/py4science.pdf

It's worth stressing, in the strongest possible terms, that this
should NOT, in any way, shape or form, be considered anything beyond a
pre-pre-alpha, pre-draft of a project for a possible book :)  Besides,
it's already outdated in several important places (numpy, mayavi, no
TVTK,...).

After all I said about the Langtangen book, at least it's a real one.
Our pdf draft is most certainly not.  So if you need a book, with all
of its limitations, Langtangen's is currently the only game in town
that covers the whole spectrum of python for scientific computing.  If
John and I ever end up stranded on a desert island for 3 months with
great internet access and poor diving gear, we might actually finish
ours, but don't hold your breath.

Honestly, I think that today your best bet is:

1. Buy Travis' book.  It's fantastic, has everything you need to know
about numpy, and you'll be supporting numpy itself.

2. Print Perry Greenfield's tutorial
(http://new.scipy.org/wikis/topical_software/Tutorial).  I think he's
updating it for numpy now.

3. Have a look at some of the other info in
http://new.scipy.org/Documentation, in particular D. Kuhlman's course
is very nice.


Regards,

f


From gael.varoquaux at normalesup.org  Wed Feb 28 02:29:32 2007
From: gael.varoquaux at normalesup.org (Gael Varoquaux)
Date: Wed, 28 Feb 2007 08:29:32 +0100
Subject: [SciPy-user] Any Books on SciPy?
In-Reply-To: <db6b5ecc0702272219k3a5d67dft7d2f1980b86950d1@mail.gmail.com>
References: <D73DF6B6-D5A3-45E4-B7BA-F514307B3321@airmail.net>
	<88e473830702271959o6a4dcc2dv3dd2d5fb7db0bfa1@mail.gmail.com>
	<db6b5ecc0702272219k3a5d67dft7d2f1980b86950d1@mail.gmail.com>
Message-ID: <20070228072932.GA3249@clipper.ens.fr>

On Tue, Feb 27, 2007 at 11:19:51PM -0700, Fernando Perez wrote:
> http://amath.colorado.edu/faculty/fperez/tmp/py4science.pdf

Nice ! Really nice ! I am very happy that someone is writing something
about all this in a consistent way.

I have two questions: what will be the distribution mode (printed matter,
internet and free, both) ? This is important because an easily and freely
available book really helps spreading the word. Second question: what
will be the licence ? The reason I ask this is that I could consider
trying to contribute if I can reuse the part I contribute.

As you are probably aware (I think you follow the enthought-dev ML)
Prabhu and I are currently trying to find time to code a nice "mlab"
interface to mayavi2. Once it has made some progress (expect two to three
months) it will be much nicer than the current way of using mayavi from
python. Of course there is the problem that mayavi2 is not properly
distributed currently. That might change as enthought is currently
pushing for a modular eggs-based version of their tool suite.

Anyway if we can get something out of mayavi's mlab, I could write
document how to use it and contribute a modified version of it to your
book.

Similarly you could use a modified version of my traitsUI tutorial
http://www.gael-varoquaux.info/computers/traits_tutorial/index.html if
you think this is not out of scope.

Thumbs up for such work !

Ga?l



From gael.varoquaux at normalesup.org  Wed Feb 28 02:31:56 2007
From: gael.varoquaux at normalesup.org (Gael Varoquaux)
Date: Wed, 28 Feb 2007 08:31:56 +0100
Subject: [SciPy-user] Any Books on SciPy?
In-Reply-To: <20070228072932.GA3249@clipper.ens.fr>
References: <D73DF6B6-D5A3-45E4-B7BA-F514307B3321@airmail.net>
	<88e473830702271959o6a4dcc2dv3dd2d5fb7db0bfa1@mail.gmail.com>
	<db6b5ecc0702272219k3a5d67dft7d2f1980b86950d1@mail.gmail.com>
	<20070228072932.GA3249@clipper.ens.fr>
Message-ID: <20070228073156.GB3249@clipper.ens.fr>

Damn it, I intended to send this e-mail off list !

On Wed, Feb 28, 2007 at 08:29:32AM +0100, Gael Varoquaux wrote:
> On Tue, Feb 27, 2007 at 11:19:51PM -0700, Fernando Perez wrote:
> > http://amath.colorado.edu/faculty/fperez/tmp/py4science.pdf

> Nice ! Really nice ! I am very happy that someone is writing something
> about all this in a consistent way.

> I have two questions: what will be the distribution mode (printed matter,
> internet and free, both) ? This is important because an easily and freely
> available book really helps spreading the word. Second question: what
> will be the licence ? The reason I ask this is that I could consider
> trying to contribute if I can reuse the part I contribute.

> As you are probably aware (I think you follow the enthought-dev ML)
> Prabhu and I are currently trying to find time to code a nice "mlab"
> interface to mayavi2. Once it has made some progress (expect two to three
> months) it will be much nicer than the current way of using mayavi from
> python. Of course there is the problem that mayavi2 is not properly
> distributed currently. That might change as enthought is currently
> pushing for a modular eggs-based version of their tool suite.

> Anyway if we can get something out of mayavi's mlab, I could write
> document how to use it and contribute a modified version of it to your
> book.

> Similarly you could use a modified version of my traitsUI tutorial
> http://www.gael-varoquaux.info/computers/traits_tutorial/index.html if
> you think this is not out of scope.

> Thumbs up for such work !

> Ga?l



From fperez.net at gmail.com  Wed Feb 28 03:22:34 2007
From: fperez.net at gmail.com (Fernando Perez)
Date: Wed, 28 Feb 2007 01:22:34 -0700
Subject: [SciPy-user] Any Books on SciPy?
In-Reply-To: <20070228072932.GA3249@clipper.ens.fr>
References: <D73DF6B6-D5A3-45E4-B7BA-F514307B3321@airmail.net>
	<88e473830702271959o6a4dcc2dv3dd2d5fb7db0bfa1@mail.gmail.com>
	<db6b5ecc0702272219k3a5d67dft7d2f1980b86950d1@mail.gmail.com>
	<20070228072932.GA3249@clipper.ens.fr>
Message-ID: <db6b5ecc0702280022u1205ff89tcd4376ad27e7a0c2@mail.gmail.com>

On 2/28/07, Gael Varoquaux <gael.varoquaux at normalesup.org> wrote:
> On Tue, Feb 27, 2007 at 11:19:51PM -0700, Fernando Perez wrote:
> > http://amath.colorado.edu/faculty/fperez/tmp/py4science.pdf

I'll reply on-list since you sent it on-list :)  But feel free to ask
off-list anything in particular.

> Nice ! Really nice ! I am very happy that someone is writing something
> about all this in a consistent way.

Thanks, but it's unfortunately a bit of a stillborn effort at this point.

> I have two questions: what will be the distribution mode (printed matter,
> internet and free, both) ? This is important because an easily and freely
> available book really helps spreading the word. Second question: what
> will be the licence ? The reason I ask this is that I could consider
> trying to contribute if I can reuse the part I contribute.

Well, nothing had been set in stone yet, but I'd favor a combination
of a printed book by a publisher with some track record in science,
hopefully with an agreement that would allow free online
redistribution.  Such things have been done recently, so perhaps
convincing a publisher of this might not be altogether impossible.

> As you are probably aware (I think you follow the enthought-dev ML)
> Prabhu and I are currently trying to find time to code a nice "mlab"
> interface to mayavi2. Once it has made some progress (expect two to three
> months) it will be much nicer than the current way of using mayavi from
> python. Of course there is the problem that mayavi2 is not properly
> distributed currently. That might change as enthought is currently
> pushing for a modular eggs-based version of their tool suite.

I know, I've been quietly following that discussion with the utmost
interest.  I'm hoping it will be ready by Saturday, b/c I'm having a
mini-sprint at my house with some students to port some old CFD code
to the new mayavi.  So you have 3 days to finish it :)

> Anyway if we can get something out of mayavi's mlab, I could write
> document how to use it and contribute a modified version of it to your
> book.
>
> Similarly you could use a modified version of my traitsUI tutorial
> http://www.gael-varoquaux.info/computers/traits_tutorial/index.html if
> you think this is not out of scope.
>
> Thumbs up for such work !

Thanks!

But as I said, while I'm quite open on the possibilities for licensing
and distribution, the grim reality is that right now, I simply don't
have /any/ time to put into this.  All of my 'free' (funny, I know)
time right now has to go into pushing the new code effort for
distributed and parallel computing in ipython.  We've made good
progress recently on that front and some of the things that were
holding back integration of the trunk into the dev branch, so that we
might finally have a single codebase.

So while it would be very nice for this to be finished, realistically
I don't see that coming from me in the near future.

Regards,

f


From nwagner at iam.uni-stuttgart.de  Wed Feb 28 03:37:24 2007
From: nwagner at iam.uni-stuttgart.de (Nils Wagner)
Date: Wed, 28 Feb 2007 09:37:24 +0100
Subject: [SciPy-user] Proper Use of NumPy's eig()
In-Reply-To: <45E49E79.6080905@gmail.com>
References: <Pine.LNX.4.64.0702271219530.15248@salmo.appl-ecosys.com>	<52878754-DDDD-4AE2-9601-880BA43DD446@utoronto.ca>	<Pine.LNX.4.64.0702271232320.15248@salmo.appl-ecosys.com>	<03F2185E-C21E-414D-AF24-BEBF1922BE8A@utoronto.ca>	<Pine.LNX.4.64.0702271241340.15248@salmo.appl-ecosys.com>
	<45E49E79.6080905@gmail.com>
Message-ID: <45E53F44.6080308@iam.uni-stuttgart.de>

Robert Kern wrote:
> Rich Shepard wrote:
>
>   
>>    However, I don't see the answer I expected. My expectation is that all
>> values would be in the range [0.00-1.00], but they're not.
>>
>>    When I print eigE I see:
>>
>> (array([  8.88174744e+00+0.j        ,   3.54286503e-01+2.48721395j,
>>           3.54286503e-01-2.48721395j,  -3.11162331e-01+1.00980412j,
>>          -3.11162331e-01-1.00980412j,  -2.79755841e-01+0.46954619j,
>>          -2.79755841e-01-0.46954619j,  -4.08484096e-01+0.j        ]),
>> array([[  6.24249034e-01 +0.00000000e+00j,
>>     
>
> ...
>
> Without knowing your input, I can't see anything particularly wrong. Unless if E
> were real-symmetric (or complex-Hermitian), you are likely to end up with
> complex eigenvalues.
>
>   
>>    Since eig(E) "Return[s] all solutions (lamda, x) to the equation Ax =
>> lamda x. The first element of the return tuple contains all the eigenvalues.
>> The second element of the return tuple contains the eigenvectors in the
>> columns (x[:,i] is the ith eigenvector)."
>>
>>    I can't interpret the above. If the first tuple has all the Eigenvalues,
>> how do I extract the principal Eigenvector from the rest? When I did this
>> manually a couple of years ago, I used Octave to calculate the principal
>> Eigenvector and the answer was easy for me to see.
>>     
>
> I don't think that the notion of a principal eigenvector is well-defined if the
> matrix is not symmetric. But if you do have a symmetric matrix:
>
>
> import numpy as np
> from scipy import linalg
>
> eigvals, eigvecs = linalg.eig(E)
> i = np.real_if_close(eigvals).argmax()
> principal_eigvec = eigvecs[:, i]
>
>   
 
Hi Rich,

here is another approach to compute the principal eigenpair (absil.py)

Nils

-------------- next part --------------
A non-text attachment was scrubbed...
Name: absil.py
Type: text/x-python
Size: 1019 bytes
Desc: not available
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20070228/c9a72330/attachment.py>

From steve at shrogers.com  Wed Feb 28 06:29:38 2007
From: steve at shrogers.com (Steven H. Rogers)
Date: Wed, 28 Feb 2007 04:29:38 -0700
Subject: [SciPy-user] Any Books on SciPy?
In-Reply-To: <db6b5ecc0702272219k3a5d67dft7d2f1980b86950d1@mail.gmail.com>
References: <D73DF6B6-D5A3-45E4-B7BA-F514307B3321@airmail.net>	<88e473830702271959o6a4dcc2dv3dd2d5fb7db0bfa1@mail.gmail.com>
	<db6b5ecc0702272219k3a5d67dft7d2f1980b86950d1@mail.gmail.com>
Message-ID: <45E567A2.3050406@shrogers.com>

Fernando Perez wrote:
> On 2/27/07, John Hunter <jdh2358 at gmail.com> wrote:
>> On 2/27/07, Robert Love <rblove at airmail.net> wrote:
>>> Are there any good, up to date books that people recommend for
>>> numerical work with Python?
>>>
>>> I see the book
>>>
>>>     Python Scripting for Computational Science
>>>     Hans Petter Langtangen
>>>
>>> Does anyone have opinions on this?  Is it current?  Are there better
>>> books?
>> I specifically do not recommend this book -- I own it but in my
>> opinion it is outdated and is more a collection of the author's
>> personal idioms than the current common practice in the scientific
>> python community.   For numerical work in python most people use
> 
> I happen to share John's opinion, and I also have a copy of this book.
>  While it's technically correct, well written and fairly comprehensive
> (probably /too/ much, since it's a bit all over the map), I strongly
> dislike his approach.  Much of the book uses his custom, home-made
> collection of scripts and tools, which you can only download if you go
> to a site and type a word from a certain page in the book (a simple
> 'protection' system).
> 

Concur with John and Fernando.  I found a copy in a local bookstore and 
bought it because it _is_ the only book covering the subject and I 
wanted to show that there is demand for such material.

# Steve



From gary.pajer at gmail.com  Wed Feb 28 07:11:36 2007
From: gary.pajer at gmail.com (Gary Pajer)
Date: Wed, 28 Feb 2007 07:11:36 -0500
Subject: [SciPy-user] Do I have LAPACK or not?
In-Reply-To: <Pine.LNX.4.64.0702272054160.23399@salmo.appl-ecosys.com>
References: <88fe22a0702272027s214476f8r99852705adb1b544@mail.gmail.com>
	<Pine.LNX.4.64.0702272054160.23399@salmo.appl-ecosys.com>
Message-ID: <88fe22a0702280411i335688a7ldd0f8c9f35f1642f@mail.gmail.com>

On 2/27/07, Rich Shepard <rshepard at appl-ecosys.com> wrote:
> On Tue, 27 Feb 2007, Gary Pajer wrote:
>
> > When I compile I get the output  below.  Has LAPACK been found or not?
> > I'm guessing yes, but I have some doubt ...
>
> Gary,
>
>    What is the result of 'locate LAPACK?' On my system it returns
> /usr/local/scipy/LAPACK/ and all the subdirectories and files therein.
>
> Rich

I get
/svn/scipy/trunk/Lib/sandbox/arpack/ARPACK/LAPACK

but locate lapack gets

/usr/lib/sse2/liblapack_atlas.so.3.0
/usr/lib/sse2/liblapack_atlas.so.3
/usr/lib/sse2/liblapack_atlas.a
/usr/lib/sse2/liblapack_atlas.so

and

/usr/lib/python2.4/site-packages/scipy/lib/lapack

and

/usr/lib/python2.4/site-packages/scipy/linalg/flapack.so
/usr/lib/python2.4/site-packages/scipy/linalg/clapack.so

and

/usr/lib/atlas/sse2/liblapack.so.3.0
/usr/lib/atlas/sse2/liblapack.so.3
/usr/lib/atlas/sse2/liblapack.a
/usr/lib/atlas/sse2/liblapack.s

and

/usr/lib/liblapack.so.3.0
/usr/lib/liblapack-3.so
/usr/lib/liblapack-3.a
/usr/lib/liblapack.so.3
/usr/lib/liblapack.a
/usr/lib/liblapack.so

similar for atlas and blas

I did not build ATLAS myself, I apt-got it.  (Kubuntu 6.10, Edgy)
(python 2.4.4, both numpy and scipy from recent SVNs)

(I never did understand the difference between ATLAS, LAPACK, and BLAS
and whether or not (and what) I should build, and why the standard
builds of one of the above is said to be incomplete.  I just cross my
fingers and hit return.)


>
> --
> Richard B. Shepard, Ph.D.               |    The Environmental Permitting
> Applied Ecosystem Services, Inc.        |          Accelerator(TM)
> <http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user
>


From dd55 at cornell.edu  Wed Feb 28 08:21:35 2007
From: dd55 at cornell.edu (Darren Dale)
Date: Wed, 28 Feb 2007 08:21:35 -0500
Subject: [SciPy-user] Any Books on SciPy?
In-Reply-To: <45E567A2.3050406@shrogers.com>
References: <D73DF6B6-D5A3-45E4-B7BA-F514307B3321@airmail.net>
	<db6b5ecc0702272219k3a5d67dft7d2f1980b86950d1@mail.gmail.com>
	<45E567A2.3050406@shrogers.com>
Message-ID: <200702280821.35981.dd55@cornell.edu>

On Wednesday 28 February 2007 06:29:38 am Steven H. Rogers wrote:
> Fernando Perez wrote:
> > On 2/27/07, John Hunter <jdh2358 at gmail.com> wrote:
> >> On 2/27/07, Robert Love <rblove at airmail.net> wrote:
> >>> Are there any good, up to date books that people recommend for
> >>> numerical work with Python?
> >>>
> >>> I see the book
> >>>
> >>>     Python Scripting for Computational Science
> >>>     Hans Petter Langtangen
> >>>
> >>> Does anyone have opinions on this?  Is it current?  Are there better
> >>> books?
> >>
> >> I specifically do not recommend this book -- I own it but in my
> >> opinion it is outdated and is more a collection of the author's
> >> personal idioms than the current common practice in the scientific
> >> python community.   For numerical work in python most people use
> >
> > I happen to share John's opinion, and I also have a copy of this book.
> >  While it's technically correct, well written and fairly comprehensive
> > (probably /too/ much, since it's a bit all over the map), I strongly
> > dislike his approach.  Much of the book uses his custom, home-made
> > collection of scripts and tools, which you can only download if you go
> > to a site and type a word from a certain page in the book (a simple
> > 'protection' system).
>
> Concur with John and Fernando.  I found a copy in a local bookstore and
> bought it because it _is_ the only book covering the subject and I
> wanted to show that there is demand for such material.

I did the same thing, and came to the same conclusion about the book.

I haven't seen anyone mention "Numerical Methods in Engineering with Python" 
by Jaan Kiusalaas. It was published in 2005, and uses numarray, so it is 
somewhat dated considering all the impressive developments with NumPy and 
SciPy. I mention it for the sake of completeness.

Darren


From giorgio.luciano at chimica.unige.it  Wed Feb 28 08:29:39 2007
From: giorgio.luciano at chimica.unige.it (Giorgio Luciano)
Date: Wed, 28 Feb 2007 14:29:39 +0100
Subject: [SciPy-user] Any Books on SciPy?
In-Reply-To: <200702280821.35981.dd55@cornell.edu>
References: <D73DF6B6-D5A3-45E4-B7BA-F514307B3321@airmail.net>	<db6b5ecc0702272219k3a5d67dft7d2f1980b86950d1@mail.gmail.com>	<45E567A2.3050406@shrogers.com>
	<200702280821.35981.dd55@cornell.edu>
Message-ID: <45E583C3.9020307@chimica.unige.it>

I'm setting up a new site about chemometrics hopefully (cross fingered), 
it should be online on Thursday.
With other co-author we are also thinking about writing a "chapter of a 
book"/article about how to use python/scipy to perform common 
chemometric tasks.
Why dont' we all merge our knowledge in different field and try to have 
something more "comprehensive" ?
prbably togheter we can succeed in seeing all in completion without all 
rewriting twice same things
We will also be glade to give to scipy the functions to seem them included
if anyone interested just drop me a line
Giorgio

>   



From gael.varoquaux at normalesup.org  Wed Feb 28 09:08:31 2007
From: gael.varoquaux at normalesup.org (Gael Varoquaux)
Date: Wed, 28 Feb 2007 15:08:31 +0100
Subject: [SciPy-user] Any Books on SciPy?
In-Reply-To: <db6b5ecc0702280022u1205ff89tcd4376ad27e7a0c2@mail.gmail.com>
References: <D73DF6B6-D5A3-45E4-B7BA-F514307B3321@airmail.net>
	<88e473830702271959o6a4dcc2dv3dd2d5fb7db0bfa1@mail.gmail.com>
	<db6b5ecc0702272219k3a5d67dft7d2f1980b86950d1@mail.gmail.com>
	<20070228072932.GA3249@clipper.ens.fr>
	<db6b5ecc0702280022u1205ff89tcd4376ad27e7a0c2@mail.gmail.com>
Message-ID: <20070228140828.GE3249@clipper.ens.fr>

On Wed, Feb 28, 2007 at 01:22:34AM -0700, Fernando Perez wrote:
> > As you are probably aware (I think you follow the enthought-dev ML)
> > Prabhu and I are currently trying to find time to code a nice "mlab"
> > interface to mayavi2. Once it has made some progress (expect two to three
> > months) it will be much nicer than the current way of using mayavi from
> > python. Of course there is the problem that mayavi2 is not properly
> > distributed currently. That might change as enthought is currently
> > pushing for a modular eggs-based version of their tool suite.

> I know, I've been quietly following that discussion with the utmost
> interest.  I'm hoping it will be ready by Saturday, b/c I'm having a
> mini-sprint at my house with some students to port some old CFD code
> to the new mayavi.  So you have 3 days to finish it :)

Well well. Currently the API is not stable at all, and I do not want to
freeze it (cf my last about this on the enthougt-dev ML). I can let this
project steel even more sleep from me than my work already does, and move
a bit forward to try and establish something that is closer to the API
that I am aiming to, but even if I a manage to get something out (and when I
am to tired I am not terribly productive), I need Prabhu to review it.

All I can say is that mayavi.tools.mlab is not currently in its final
form and I do not suggest using it, unless you are planning to modify the
code you are writing. From the user point of view following the API
change should not be a huge amount of work.

The changes I would like do to the API are exposed in the mails:
https://mail.enthought.com/pipermail/enthought-dev/2007-February/004425.html
[[Enthought-dev] Mlab API, and usability]
and
https://mail.enthought.com/pipermail/enthought-dev/2007-February/004442.html
[Enthought-dev] Mlab: contour3d and quiver3d.

I am interested on feedback on these propositions, by the way.

Ga?l


From novin01 at gmail.com  Wed Feb 28 09:13:27 2007
From: novin01 at gmail.com (Dave)
Date: Wed, 28 Feb 2007 14:13:27 +0000 (UTC)
Subject: [SciPy-user] Transforming 1-d array to 2-d array
References: <Pine.LNX.4.64.0702251412500.25666@salmo.appl-ecosys.com>
	<Pine.LNX.4.64.0702251430270.25666@salmo.appl-ecosys.com>
	<loom.20070226T120344-182@post.gmane.org>
	<Pine.LNX.4.64.0702262024530.25305@salmo.appl-ecosys.com>
	<Pine.LNX.4.64.0702270601520.15248@salmo.appl-ecosys.com>
Message-ID: <loom.20070228T143840-989@post.gmane.org>

Rich Shepard <rshepard <at> appl-ecosys.com> writes:

> 
> On Mon, 26 Feb 2007, Rich Shepard wrote:
> 
> >   Now I need a bit more guidance, to complete the symmetrical matrices.
> 
>    It occurred to me after I posted this message that I'm going along the
> wrong path. I don't need a lower index, just the lower triangular half of
> the array with zeros along the principal diagonal and the upper half. Then
> I can add them (cell-wise, not matrix addition) and get the filled array I
> need.
> 
> Rich
> 

Sorry, have been quite busy....

The double brackets was the cause of your original error I suspect - hence
taking [0] fixed the problem.

I'm not sure if your data is in an array but if not you can cast it as an
array as follows:

barEco = asarray(barEco).squeeze()

The .squeeze() method will get rid of any extraneous brackets (singleton 
dimensions)

I'm not too sure what you're now trying to achieve, but hopefully the code
below will help you understang array indexing.

-Dave

from numpy import asarray, ones, tril, triu, zeros
from numpy.random import rand

N = 5

upperData = (10.0*rand(N*(N-1)/2)).round() #dummy data
lowerData = (10.0*rand(N*(N-1)/2)).round() #dummy data

# Index into the upper half of an NxN array
upper_idx = triu(ones([N,N])-eye(N)).nonzero()

# Index into the upper half of an NxN array
lower_idx = tril(ones([N,N])-eye(N)).nonzero()

# Index into the diagonal elements of an NxN array
diag_idx = eye(N).nonzero()

C = zeros([N,N],dtype=float)
print C
C[upper_idx] = upperData
print C
C[lower_idx] = lowerData
print C
C += eye(N)
print C

A = 2.0*ones([N,N],dtype=float)
print A
B = 3.0*ones([N,N],dtype=float)
print B

print triu(A,k=1)
print tril(B,k=-1)
print triu(A,k=1) + tril(B,k=-1)
print triu(A,k=1) + tril(B,k=-1) + eye(N)





From ryanlists at gmail.com  Wed Feb 28 09:16:43 2007
From: ryanlists at gmail.com (Ryan Krauss)
Date: Wed, 28 Feb 2007 08:16:43 -0600
Subject: [SciPy-user] NumPy in Teaching
In-Reply-To: <45E4FFA6.9010408@shrogers.com>
References: <45E4FFA6.9010408@shrogers.com>
Message-ID: <c5b438120702280616x4668ac36qdb68207b093d1060@mail.gmail.com>

I am teaching system dynamics, controls, and mechatronics and letting
the students choose between matlab and python.  I don't know if I have
any lessons learned yet.  Not many of the students choose python.  I
think the problem is that getting everything installed seems
overwhelming.  Enthought python is good, but the packages are slightly
old, because everything is in flux.  So, I tell my students to install
it and then update Numpy/Scipy/Matplotlib.  My other problem is that
the other faculty don't know python, so Matlab is taught and expected.

On 2/27/07, Steven H. Rogers <steve at shrogers.com> wrote:
> I'm doing an informal survey on the use of Array Programming Languages
> for teaching.  If you're using NumPy in this manner I'd like to hear
> from you.  What subject was/is taught, academic level, results, lessons
> learned, etc.
>
> Regards,
> Steve
>
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user
>


From rshepard at appl-ecosys.com  Wed Feb 28 09:20:06 2007
From: rshepard at appl-ecosys.com (Rich Shepard)
Date: Wed, 28 Feb 2007 06:20:06 -0800 (PST)
Subject: [SciPy-user] Transforming 1-d array to 2-d array
In-Reply-To: <loom.20070228T143840-989@post.gmane.org>
References: <Pine.LNX.4.64.0702251412500.25666@salmo.appl-ecosys.com>
	<Pine.LNX.4.64.0702251430270.25666@salmo.appl-ecosys.com>
	<loom.20070226T120344-182@post.gmane.org>
	<Pine.LNX.4.64.0702262024530.25305@salmo.appl-ecosys.com>
	<Pine.LNX.4.64.0702270601520.15248@salmo.appl-ecosys.com>
	<loom.20070228T143840-989@post.gmane.org>
Message-ID: <Pine.LNX.4.64.0702280618280.8243@salmo.appl-ecosys.com>

On Wed, 28 Feb 2007, Dave wrote:

> Sorry, have been quite busy....

Dave,

   Apologies not necessary.

> The double brackets was the cause of your original error I suspect - hence
> taking [0] fixed the problem.

   That's true.

> I'm not too sure what you're now trying to achieve, but hopefully the code
> below will help you understand array indexing.

   Thank you. I've read the indexing section of Travis' book several times
and have a general understanding. It will become clearer as I use NumPy
more.

Rich

-- 
Richard B. Shepard, Ph.D.               |    The Environmental Permitting
Applied Ecosystem Services, Inc.        |          Accelerator(TM)
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863


From nwagner at iam.uni-stuttgart.de  Wed Feb 28 09:25:46 2007
From: nwagner at iam.uni-stuttgart.de (Nils Wagner)
Date: Wed, 28 Feb 2007 15:25:46 +0100
Subject: [SciPy-user] Optimizers and the number of iterations
Message-ID: <45E590EA.7010308@iam.uni-stuttgart.de>

Hi all,

AFAIK, only the number of function and gradient evaluations are directly
available via full_output=1.

Is there a better way to get the number of iterations ?

What I have used so far, is

x_opt, allvec=optimize.fmin_cg(func,x_0,retall=1)
print 'The number of iterations is',shape(allvec)[0]-1



Nils
 


From perry at stsci.edu  Wed Feb 28 09:34:04 2007
From: perry at stsci.edu (Perry Greenfield)
Date: Wed, 28 Feb 2007 09:34:04 -0500
Subject: [SciPy-user] Any Books on SciPy?
In-Reply-To: <db6b5ecc0702272219k3a5d67dft7d2f1980b86950d1@mail.gmail.com>
References: <D73DF6B6-D5A3-45E4-B7BA-F514307B3321@airmail.net>
	<88e473830702271959o6a4dcc2dv3dd2d5fb7db0bfa1@mail.gmail.com>
	<db6b5ecc0702272219k3a5d67dft7d2f1980b86950d1@mail.gmail.com>
Message-ID: <E9ADD630-F643-4A23-BA9C-FCBC8EFDA5A1@stsci.edu>


On Feb 28, 2007, at 1:19 AM, Fernando Perez wrote:

>
> 2. Print Perry Greenfield's tutorial
> (http://new.scipy.org/wikis/topical_software/Tutorial).  I think he's
> updating it for numpy now.

Yes, that's right. Hopefully it won't take too long to do (a week or  
two depending on my other work).

Perry



From gonzalezmancera+scipy at gmail.com  Wed Feb 28 09:42:14 2007
From: gonzalezmancera+scipy at gmail.com (Andres Gonzalez-Mancera)
Date: Wed, 28 Feb 2007 09:42:14 -0500
Subject: [SciPy-user] Any Books on SciPy?
Message-ID: <c990a6a50702280642m55924baeme6bf52e8ba9ecf13@mail.gmail.com>

I agree that there is a huge void in proper Scipy documentation which
is essential for broader adoption. I know you can always go to the
source files but this is not something everybody will do. Although the
Documentation has been growing over the past year we're still missing
some central 'official' documentation or at least tutorial.

While I'm on the subject, I bought Travis' book early last year. I
understood that we should have received updates as they became
available. I never heard or received anything. Have there been any
updates in the past year or was I left out of the loop? The reason I
ask this is because I understand there were substantial changes to
numpy in the road to 1.0. Are these changes documented anywhere other
than the developers mailing lists?

Thank you very much,

Andres

On 2/28/07, scipy-user-request at scipy.org <scipy-user-request at scipy.org> wrote:

> Message: 8
> Date: Tue, 27 Feb 2007 23:19:51 -0700
> From: "Fernando Perez" <fperez.net at gmail.com>
> Subject: Re: [SciPy-user] Any Books on SciPy?
> To: "SciPy Users List" <scipy-user at scipy.org>
> Message-ID:
>         <db6b5ecc0702272219k3a5d67dft7d2f1980b86950d1 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> On 2/27/07, John Hunter <jdh2358 at gmail.com> wrote:
> > On 2/27/07, Robert Love <rblove at airmail.net> wrote:
> > > Are there any good, up to date books that people recommend for
> > > numerical work with Python?
> > >
> > > I see the book
> > >
> > >     Python Scripting for Computational Science
> > >     Hans Petter Langtangen
> > >
> > > Does anyone have opinions on this?  Is it current?  Are there better
> > > books?
> >
> > I specifically do not recommend this book -- I own it but in my
> > opinion it is outdated and is more a collection of the author's
> > personal idioms than the current common practice in the scientific
> > python community.   For numerical work in python most people use
>
> I happen to share John's opinion, and I also have a copy of this book.
>  While it's technically correct, well written and fairly comprehensive
> (probably /too/ much, since it's a bit all over the map), I strongly
> dislike his approach.  Much of the book uses his custom, home-made
> collection of scripts and tools, which you can only download if you go
> to a site and type a word from a certain page in the book (a simple
> 'protection' system).
>
> Now you have an unmaintained, unreleased (publicly), set of tools to
> learn from that don't have any licensing explicitly specified.
>
> Oh, and a good chunk of the tools in his distribution (since I have
> the book, I have the code) use Perl.  Go figure (there's also a tcl
> directory thrown in for good measure).
>
> One of Python's main strengths for scientific work is precisely the
> openness and interoperability of the various tools, and we all do our
> part to help that be the case.  The fact that this book follows an
> approach more or less orthogonal to those ideas makes me very much
> uninterested in using it.
>
> > There is a lot more, particularly for domain specific stiff, but these
> > links are good starting points.  Unfortunately, there is no
> > one-stop-shop for a guide to scientific computing in python - Travis'
> > documentation is the closest thing we have but it pretty much just
> > covers numpy which is *the* core package.  Fernando Perez and I have a
> > very brief and limited started guide covering multiple packages
> > (ipython, numpy, matplotlib, scipy, VTK) but I don't have the PDF
> > handy (Fernando, do you have the roadshow doc handy?).
>
> Well, you asked for it :)
>
> http://amath.colorado.edu/faculty/fperez/tmp/py4science.pdf
>
> It's worth stressing, in the strongest possible terms, that this
> should NOT, in any way, shape or form, be considered anything beyond a
> pre-pre-alpha, pre-draft of a project for a possible book :)  Besides,
> it's already outdated in several important places (numpy, mayavi, no
> TVTK,...).
>
> After all I said about the Langtangen book, at least it's a real one.
> Our pdf draft is most certainly not.  So if you need a book, with all
> of its limitations, Langtangen's is currently the only game in town
> that covers the whole spectrum of python for scientific computing.  If
> John and I ever end up stranded on a desert island for 3 months with
> great internet access and poor diving gear, we might actually finish
> ours, but don't hold your breath.
>
> Honestly, I think that today your best bet is:
>
> 1. Buy Travis' book.  It's fantastic, has everything you need to know
> about numpy, and you'll be supporting numpy itself.
>
> 2. Print Perry Greenfield's tutorial
> (http://new.scipy.org/wikis/topical_software/Tutorial).  I think he's
> updating it for numpy now.
>
> 3. Have a look at some of the other info in
> http://new.scipy.org/Documentation, in particular D. Kuhlman's course
> is very nice.
>
>
> Regards,
>
> f
>

-- 
Andres Gonzalez-Mancera
Biofluid Mechanics Lab
Department of Mechanical Engineering
University of Maryland, Baltimore County
andres.gonzalez at umbc.edu
410-455-3347


From lou_boog2000 at yahoo.com  Wed Feb 28 10:26:10 2007
From: lou_boog2000 at yahoo.com (Lou Pecora)
Date: Wed, 28 Feb 2007 07:26:10 -0800 (PST)
Subject: [SciPy-user] Any Books on SciPy?
In-Reply-To: <db6b5ecc0702272219k3a5d67dft7d2f1980b86950d1@mail.gmail.com>
Message-ID: <20070228152610.79882.qmail@web34405.mail.mud.yahoo.com>

While I agree with some of the criticisms of the
Langtangen book I do think it covers some topics that
are really hard to find elsewhere.  He does go into
depth and cover a lot of writing C/C++ extensions. 
Overall the book has a lot of information.  Thumbs
down on parts that rely on his own code, especially
the Perl stuff, but Thumbs Up on parts that show you
details you have a hard time finding elsewhere.

The biggest problem with the book is one that ALL
printed documents face with Python (and probably other
open source projects):  staying current.  Things
change fast and books go out of date fast.  Web
sources and discussion list like this one are
essential.

The way I see it as a user of scientific python
packages the biggest barriers to new users and even
veterans are:

* Getting documention, examples and tutorials for
various package.  Can vary greatly depending on each
package.

* Figuring out how to install packages (an on-going
battle for all)

* Figuring out package dependencies (e.g. do I need
wxPython with matplotlib?)

* Figuring out which versions of each package are
compatible with other packages' versions.

I bet I'm not the only one who gets nervous when
he/she has to update a package.

--- Fernando Perez <fperez.net at gmail.com> wrote:

> On 2/27/07, John Hunter <jdh2358 at gmail.com> wrote:
> > On 2/27/07, Robert Love <rblove at airmail.net>
> wrote:
> > > Are there any good, up to date books that people
> recommend for
> > > numerical work with Python?
> > >
> > > I see the book
> > >
> > >     Python Scripting for Computational Science
> > >     Hans Petter Langtangen
> > >
> > > Does anyone have opinions on this?  Is it
> current?  Are there better



-- Lou Pecora,   my views are my own.
---------------
Three laws of thermodynamics:
  First law: "You can't win."
  Second law: "You can't break even."
  Third law: "You can't quit."
  -- Allen Ginsberg, beat poet


 
____________________________________________________________________________________
Expecting? Get great news right away with email Auto-Check. 
Try the Yahoo! Mail Beta.
http://advision.webevents.yahoo.com/mailbeta/newmail_tools.html 


From bnuttall at uky.edu  Wed Feb 28 10:56:04 2007
From: bnuttall at uky.edu (Brandon Nuttall)
Date: Wed, 28 Feb 2007 10:56:04 -0500
Subject: [SciPy-user] Using SciPy/NumPy optimization
In-Reply-To: <6.0.1.1.2.20070227170539.0283f608@pop.uky.edu>
References: <6.0.1.1.2.20070227131721.0287bfe0@pop.uky.edu>
	<45E493D7.2070703@gmail.com>
	<6.0.1.1.2.20070227170539.0283f608@pop.uky.edu>
Message-ID: <6.0.1.1.2.20070228093647.02798d38@pop.uky.edu>

Folks,

I've gotten further, but still am not there. I have the following code:

import numpy as np
from scipy.optimize import fmin_tnc

class hyp_func:
     def __init__(self,*args):
         self.x, self.y = args
         self.avg = y.mean()
     def rmsd(self,*args):
         """A function suitable for passing to the fmin() minimizers
         """
         a, b, c = args[0]
         sse = 0.0
         sst = 0.0
         # minimize the RMSD
         for i in range(len(x)):
             y = a*(1.0+b*c*x[i])**(-1.0/b)
             sse += (self.y[i]-y)**2
             sst += (self.avg-y)**2
         # this won't work because I don't know what x should be or if it 
is related
         diff = [0.0,0.0] # this is just an initial value and won't get any 
results
         # diff[0] = (-a*c-a*c*c*b*?????)**((-1-b)/b)
         # diff[1] = ((-1-b)/b)*(-a*c*c*b)*(-a*c-a*c*c*b*?????)**(((-1-b)/b)-1)
         return (sse / sst, diff)

# fake data for testing
a, b, c = [1.25,0.75,0.25]
x = []
y = []
for i in range(1,61):
     x.append(float(i))
     y.append(a*(1.0+b*c*float(i))**(-1.0/b))

x = np.array(x)
y = np.array(y)

myfunc=hyp_func(x,y)
params0 = [1.0,0.5,0.5]

retcode, nfeval, optimal = fmin_tnc(myfunc.rmsd,params0,
                                     bounds=[(None,None),(0.001,5.0), 
(-1.0,1.0)])

myfunc.rmsd() now returns the root mean square deviation which is to be 
minimized. However, in looking at the example code in 
scipy/optimize/tnc.py, I find that myfunc.rmsd() needs to return a second 
argument, g, the gradient of the function. It looks like this needs to be 
the first and second derivative of my function which if my [really, really] 
rusty calculus should be:

      y' = (-a*c-a*c*c*b*x)**((-1-b)/b)
      y'' = ((-1-b)/b)*(-a*c*c*b)*(-a*c-a*c*c*b*x)**(((-1-b)/b)-1)

I'm not sure these derivatives are particularly informative about which way 
to go to minimize the RMSD. At the moment, the code fails with a 
SystemError (error return without exception set) in the call to 
moduleTNC.minimize(). So, any suggestions on my next step?

FWIW: In tnc.py, in test(), the call to fmin_tnc() has a typo in the 
keyword arguments. "maxnfeval=" should be "maxfun=". When running tnc.py to 
execute the tests, example() and test1fg() run. The test2fg() detects an 
infeasible condition (apparently, I guess that is what was to be tested); 
Python raises an exception and terminates without running the other tests.


Brandon C. Nuttall

BNUTTALL at UKY.EDU                         Kentucky Geological Survey
(859) 257-5500                                     University of Kentucky
(859) 257-1147 (fax)                              228 Mining & Mineral 
Resources Bldg
http://www.uky.edu/KGS/home.htm       Lexington, Kentucky 40506-0107  



From hetland at tamu.edu  Wed Feb 28 11:49:50 2007
From: hetland at tamu.edu (Rob Hetland)
Date: Wed, 28 Feb 2007 10:49:50 -0600
Subject: [SciPy-user] Any Books on SciPy?
In-Reply-To: <20070228152610.79882.qmail@web34405.mail.mud.yahoo.com>
References: <20070228152610.79882.qmail@web34405.mail.mud.yahoo.com>
Message-ID: <1618CF9B-AD0D-4E1C-A0FF-C39289FDFF63@tamu.edu>


I would help write part of a book.  I'm sure others would, too.  But  
none of us have the time to write a whole book ourselves.

Who could coordinate such an effort?

What format would be used (LaTeX, etc.)?

How would consistency be maintained across sections?

I think these are not insurmountable obstacles, and a free, printable  
PDF howto manual (as opposed to a reference book like the NumPy book)  
in the spirit of the Lerning ... O'Reilly books is very, very  
important.  The tutorials on the wiki are a good place to start, but  
in the end, people want a book.  I know I prefer books to online  
documentation when I am really diving into something.

-Rob


----
Rob Hetland, Associate Professor
Dept. of Oceanography, Texas A&M University
http://pong.tamu.edu/~rob
phone: 979-458-0096, fax: 979-845-6331




From grante at visi.com  Wed Feb 28 11:49:34 2007
From: grante at visi.com (Grant Edwards)
Date: Wed, 28 Feb 2007 16:49:34 +0000 (UTC)
Subject: [SciPy-user] Any Books on SciPy?
References: <D73DF6B6-D5A3-45E4-B7BA-F514307B3321@airmail.net>
	<88e473830702271959o6a4dcc2dv3dd2d5fb7db0bfa1@mail.gmail.com>
	<db6b5ecc0702272219k3a5d67dft7d2f1980b86950d1@mail.gmail.com>
Message-ID: <es4bqu$7la$1@sea.gmane.org>

On 2007-02-28, Fernando Perez <fperez.net at gmail.com> wrote:

> Well, you asked for it :)
>
> http://amath.colorado.edu/faculty/fperez/tmp/py4science.pdf

Cool.

If you're interested in suggestions for additional topics, you
might want to add a chapter on scientific python:
http://sourcesup.cru.fr/projects/scientific-py/

Though it's probably not "cool" these days compared to some of
the other visualization options, I still get a _lot_ of use out
of gnuplot-py: http://gnuplot-py.sourceforge.net/

-- 
Grant Edwards                   grante             Yow!  Civilization is
                                  at               fun! Anyway, it keeps
                               visi.com            me busy!!



From as8ca at virginia.edu  Wed Feb 28 11:50:24 2007
From: as8ca at virginia.edu (Alok Singhal)
Date: Wed, 28 Feb 2007 11:50:24 -0500
Subject: [SciPy-user] Using SciPy/NumPy optimization
In-Reply-To: <6.0.1.1.2.20070228093647.02798d38@pop.uky.edu>
References: <6.0.1.1.2.20070227131721.0287bfe0@pop.uky.edu>
	<45E493D7.2070703@gmail.com>
	<6.0.1.1.2.20070227170539.0283f608@pop.uky.edu>
	<6.0.1.1.2.20070228093647.02798d38@pop.uky.edu>
Message-ID: <20070228165024.GA3521@virginia.edu>

On 28/02/07: 10:56, Brandon Nuttall wrote:
> myfunc.rmsd() now returns the root mean square deviation which is to be 
> minimized. However, in looking at the example code in 
> scipy/optimize/tnc.py, I find that myfunc.rmsd() needs to return a second 
> argument, g, the gradient of the function. It looks like this needs to be 
> the first and second derivative of my function which if my [really, really] 
> rusty calculus should be:
> 
>       y' = (-a*c-a*c*c*b*x)**((-1-b)/b)
>       y'' = ((-1-b)/b)*(-a*c*c*b)*(-a*c-a*c*c*b*x)**(((-1-b)/b)-1)
> 

I think the second return value should be a list of (first, partial)
derivatives with respect to the parameters being estimated, i.e., a,
b, c in your case.  The example in optimize/tnc.py defines the
function as pow(x[0],2.0)+pow(abs(x[1]),3.0), and the derivatives g[0]
and g[1] are defined as 2.0*x[0] and
sign(x[1])*3.0*pow(abs(x[1]),2.0), which are derivatives of f with
respect to x[0] and x[1], the parameters.  I calculated those
derivatives (and I think did it right :-) ), you can see them in an
earlier message by me in this thread.

> I'm not sure these derivatives are particularly informative about which way 
> to go to minimize the RMSD.

Yeah, that is why it makes more sense to calculate the derivatives wrt
the parameters being estimated.

Here is another way to do the fitting (adapted from scipy cookbook):

import numpy as np
from scipy import rand
from scipy.optimize import leastsq
import pylab

n = 151
x = np.mgrid[1:10:n*1j]

def f(p, x):
  return p[0]*(1.0+p[1]*p[2]*x)**(-1.0/p[1])

def errf(p, x, y):
  return f(p, x) - y

abc = [15.0, 2.5, 0.3]
y = f(abc, x) + rand(n) - 0.5

abc_guess = [30.0, 4.0, 1.0]
abc1, success = leastsq(errf, abc_guess[:], args = (x, y))

print success	# should be 1
print abc1	# I get [ 14.71976079   2.4536336    0.27560377]

pylab.plot(x, y, x, f(abc1, x))
pylab.show()

-Alok

-- 
Alok Singhal                               *   *          
Graduate Student, dept. of Astronomy   *           *     *
University of Virginia                                    
http://www.astro.virginia.edu/~as8ca/              *    * 


From jdh2358 at gmail.com  Wed Feb 28 12:10:47 2007
From: jdh2358 at gmail.com (John Hunter)
Date: Wed, 28 Feb 2007 11:10:47 -0600
Subject: [SciPy-user] Any Books on SciPy?
In-Reply-To: <1618CF9B-AD0D-4E1C-A0FF-C39289FDFF63@tamu.edu>
References: <20070228152610.79882.qmail@web34405.mail.mud.yahoo.com>
	<1618CF9B-AD0D-4E1C-A0FF-C39289FDFF63@tamu.edu>
Message-ID: <88e473830702280910x3cf80db7sa9991e00c3b65a74@mail.gmail.com>

On 2/28/07, Rob Hetland <hetland at tamu.edu> wrote:

> I would help write part of a book.  I'm sure others would, too.  But
> none of us have the time to write a whole book ourselves.

> Who could coordinate such an effort?

> What format would be used (LaTeX, etc.)?

> How would consistency be maintained across sections?

> I think these are not insurmountable obstacles, and a free, printable
> PDF howto manual (as opposed to a reference book like the NumPy book)

When Fernando and I first started the project, we wanted to keep this
with as few authors as possible simply because most team written books
aren't that good, and are not well integrated.  Maintenance also
becomes difficult since open source is a rapidly moving target (as
Fernando noted several of our chapters are already out of date) and
the more authors you have the more difficult it becomes to herd the
cats. So we decided to try and tackle it alone.  Unfortunately, both
of us are too involved with our other commitments to put the work in
that is necessary, and speaking for myself, I would be happy to
revisit the idea of a collaborative project.  We would need a couple
of people to step up as editors who commit a fair amount of time to
insuring style, cross referencing, proper topics, etc...  We could
then solicit chapters on all the relevant major packages, either from
the authors of the packages or from heavy users.  We would need a few
introductory chapters which emphasize integrated usage, followed by
package specific chapters emphasizing deeper features.  At this point,
I can probably only commit to an mpl chapter and maybe some work on
some integration.  I would be happy to do this under an open document
license, while still striving for  hardcopy printing.

The src for the document Fernando posted lives in matplotlib svn as a
collection of lyx chapters (egad the last commit was 20 months ago)

http://matplotlib.svn.sourceforge.net/viewvc/matplotlib/trunk/course/

I will defer to Fernando's wishes on this, but I am happy to try and
move the ball forward by bringing in any one offering to do some work.

Perry's tutorial is very nice and covers a lot of ground, often in
more detail than what Fernando and I have done, and might be a better
starting point, depending on his interests.  Or some variant of his
tutorial might serve well for the introductory chapters, followed by
the package specific stuff.

JDH


From paul.ray at nrl.navy.mil  Wed Feb 28 12:15:11 2007
From: paul.ray at nrl.navy.mil (Paul Ray)
Date: Wed, 28 Feb 2007 12:15:11 -0500
Subject: [SciPy-user] Numpy eBook
In-Reply-To: <mailman.24086.1172681410.8339.scipy-user@scipy.org>
References: <mailman.24086.1172681410.8339.scipy-user@scipy.org>
Message-ID: <013D2783-DCB2-448F-B23E-A907FB4E9A64@nrl.navy.mil>


On Feb 28, 2007, at 11:50 AM, scipy-user-request at scipy.org wrote:

> While I'm on the subject, I bought Travis' book early last year. I
> understood that we should have received updates as they became
> available. I never heard or received anything. Have there been any
> updates in the past year or was I left out of the loop? The reason I
> ask this is because I understand there were substantial changes to
> numpy in the road to 1.0. Are these changes documented anywhere other
> than the developers mailing lists?

I got one update in late December 2005, and none since then.  I have  
certainly been hoping for a post-1.0 revision as well.

Cheers,

-- Paul

-------------- next part --------------
A non-text attachment was scrubbed...
Name: smime.p7s
Type: application/pkcs7-signature
Size: 5012 bytes
Desc: not available
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20070228/762180b9/attachment.bin>

From coughlan at ski.org  Wed Feb 28 12:20:23 2007
From: coughlan at ski.org (James Coughlan)
Date: Wed, 28 Feb 2007 09:20:23 -0800
Subject: [SciPy-user] Numpy eBook
In-Reply-To: <013D2783-DCB2-448F-B23E-A907FB4E9A64@nrl.navy.mil>
References: <mailman.24086.1172681410.8339.scipy-user@scipy.org>
	<013D2783-DCB2-448F-B23E-A907FB4E9A64@nrl.navy.mil>
Message-ID: <45E5B9D7.4050107@ski.org>

I bought Travis's book in mid-2006 and received an update in December.

-James

Paul Ray wrote:
>
> On Feb 28, 2007, at 11:50 AM, scipy-user-request at scipy.org wrote:
>
>> While I'm on the subject, I bought Travis' book early last year. I
>> understood that we should have received updates as they became
>> available. I never heard or received anything. Have there been any
>> updates in the past year or was I left out of the loop? The reason I
>> ask this is because I understand there were substantial changes to
>> numpy in the road to 1.0. Are these changes documented anywhere other
>> than the developers mailing lists?
>
> I got one update in late December 2005, and none since then.  I have 
> certainly been hoping for a post-1.0 revision as well.
>
> Cheers,
>
> -- Paul
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user
>   


-- 
-------------------------------------------------------
James Coughlan, Ph.D., Associate Scientist                     

Smith-Kettlewell Eye Research Institute

Email: coughlan at ski.org
URL: http://www.ski.org/Rehab/Coughlan_lab/
Phone: 415-345-2146 
Fax: 415-345-8455
-------------------------------------------------------



From robert.kern at gmail.com  Wed Feb 28 12:43:58 2007
From: robert.kern at gmail.com (Robert Kern)
Date: Wed, 28 Feb 2007 11:43:58 -0600
Subject: [SciPy-user] Using SciPy/NumPy optimization
In-Reply-To: <6.0.1.1.2.20070228093647.02798d38@pop.uky.edu>
References: <6.0.1.1.2.20070227131721.0287bfe0@pop.uky.edu>	<45E493D7.2070703@gmail.com>	<6.0.1.1.2.20070227170539.0283f608@pop.uky.edu>
	<6.0.1.1.2.20070228093647.02798d38@pop.uky.edu>
Message-ID: <45E5BF5E.6020601@gmail.com>

Brandon Nuttall wrote:
> Folks,
> 
> I've gotten further, but still am not there. I have the following code:
> 
> import numpy as np
> from scipy.optimize import fmin_tnc
> 
> class hyp_func:
>      def __init__(self,*args):
>          self.x, self.y = args
>          self.avg = y.mean()
>      def rmsd(self,*args):
>          """A function suitable for passing to the fmin() minimizers
>          """
>          a, b, c = args[0]
>          sse = 0.0
>          sst = 0.0
>          # minimize the RMSD
>          for i in range(len(x)):
>              y = a*(1.0+b*c*x[i])**(-1.0/b)
>              sse += (self.y[i]-y)**2
>              sst += (self.avg-y)**2

Don't do this looping. Instead, just make sure that self.x and self.y are arrays
and use array math.

y = a*(1.0 + b*c*self.x) ** (-1.0/b)
dy = self.y - y
sse = (dy*dy).sum()
sst = ((y - avg)**2).sum()

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
 that is made terrible by our own mad attempt to interpret it as though it had
 an underlying truth."
  -- Umberto Eco


From oliphant at ee.byu.edu  Wed Feb 28 12:45:06 2007
From: oliphant at ee.byu.edu (Travis Oliphant)
Date: Wed, 28 Feb 2007 10:45:06 -0700
Subject: [SciPy-user] Any Books on SciPy?
In-Reply-To: <c990a6a50702280642m55924baeme6bf52e8ba9ecf13@mail.gmail.com>
References: <c990a6a50702280642m55924baeme6bf52e8ba9ecf13@mail.gmail.com>
Message-ID: <45E5BFA2.6090302@ee.byu.edu>

Andres Gonzalez-Mancera wrote:

>I agree that there is a huge void in proper Scipy documentation which
>is essential for broader adoption. I know you can always go to the
>source files but this is not something everybody will do. Although the
>Documentation has been growing over the past year we're still missing
>some central 'official' documentation or at least tutorial.
>
>While I'm on the subject, I bought Travis' book early last year. I
>understood that we should have received updates as they became
>available. I never heard or received anything. Have there been any
>updates in the past year or was I left out of the loop? The reason I
>ask this is because I understand there were substantial changes to
>numpy in the road to 1.0. Are these changes documented anywhere other
>than the developers mailing lists?
>  
>

The current version of "Guide to NumPy" is very complete.  There are a 
few editing and typographical changes needed, but that is it.

I sent updates to everyone who I have an email adress for in December.  
If you did not receive it then I don't have the right email address for 
you.  Please let me know and we will get it fixed (I'll send you an 
update right away and you'll be set to receive the final update in 
April/May).

Thank you so much, everybody, for all of your support.   I have received 
approximately 1000 orders so far over the past 18 months which has 
literally saved my skin and made it possible to continue working on NumPy. 

I'm even more enthused that the number of downloads of NumPy 1.0.1 has 
reached 30000.   We are also making inroads with the Python developers 
and uf all goes well should have a working array interface in Python 3.0 
and Python 2.6

Best regards,

-Travis



From cclarke at chrisdev.com  Wed Feb 28 13:01:27 2007
From: cclarke at chrisdev.com (Christopher Clarke)
Date: Wed, 28 Feb 2007 14:01:27 -0400
Subject: [SciPy-user] Any Books on SciPy?
In-Reply-To: <45E5BFA2.6090302@ee.byu.edu>
References: <c990a6a50702280642m55924baeme6bf52e8ba9ecf13@mail.gmail.com>
	<45E5BFA2.6090302@ee.byu.edu>
Message-ID: <65893979-F4DF-416A-AA8F-AF73FB33DF9D@chrisdev.com>

Hi Travis
I agree the the "Guide to Numpy" book was well worth the price
(I was really happy when PayPal started to work in Trinidad!!!)
I am suggesting that the examples i.e http://www.scipy.org/ 
Numpy_Example_List
should also be included
Regards
Chris



On 28 Feb 2007, at 13:45, Travis Oliphant wrote:

> Andres Gonzalez-Mancera wrote:
>
>> I agree that there is a huge void in proper Scipy documentation which
>> is essential for broader adoption. I know you can always go to the
>> source files but this is not something everybody will do. Although  
>> the
>> Documentation has been growing over the past year we're still missing
>> some central 'official' documentation or at least tutorial.
>>
>> While I'm on the subject, I bought Travis' book early last year. I
>> understood that we should have received updates as they became
>> available. I never heard or received anything. Have there been any
>> updates in the past year or was I left out of the loop? The reason I
>> ask this is because I understand there were substantial changes to
>> numpy in the road to 1.0. Are these changes documented anywhere other
>> than the developers mailing lists?
>>
>>
>
> The current version of "Guide to NumPy" is very complete.  There are a
> few editing and typographical changes needed, but that is it.
>
> I sent updates to everyone who I have an email adress for in December.
> If you did not receive it then I don't have the right email address  
> for
> you.  Please let me know and we will get it fixed (I'll send you an
> update right away and you'll be set to receive the final update in
> April/May).
>
> Thank you so much, everybody, for all of your support.   I have  
> received
> approximately 1000 orders so far over the past 18 months which has
> literally saved my skin and made it possible to continue working on  
> NumPy.
>
> I'm even more enthused that the number of downloads of NumPy 1.0.1 has
> reached 30000.   We are also making inroads with the Python developers
> and uf all goes well should have a working array interface in  
> Python 3.0
> and Python 2.6
>
> Best regards,
>
> -Travis
>
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user



From perry at stsci.edu  Wed Feb 28 13:30:15 2007
From: perry at stsci.edu (Perry Greenfield)
Date: Wed, 28 Feb 2007 13:30:15 -0500
Subject: [SciPy-user] Any Books on SciPy?
In-Reply-To: <88e473830702280910x3cf80db7sa9991e00c3b65a74@mail.gmail.com>
References: <20070228152610.79882.qmail@web34405.mail.mud.yahoo.com>
	<1618CF9B-AD0D-4E1C-A0FF-C39289FDFF63@tamu.edu>
	<88e473830702280910x3cf80db7sa9991e00c3b65a74@mail.gmail.com>
Message-ID: <F8435A1F-7EB7-42C5-9E10-99D3AE616E1E@stsci.edu>


On Feb 28, 2007, at 12:10 PM, John Hunter wrote:


>
>
> Perry's tutorial is very nice and covers a lot of ground, often in
> more detail than what Fernando and I have done, and might be a better
> starting point, depending on his interests.  Or some variant of his
> tutorial might serve well for the introductory chapters, followed by
> the package specific stuff.
>
I see it as suitable for a certain class of new users (i.e, those  
that are more task oriented and looking to see what they can  
accomplish interactively without having to learn a lot of preliminary  
material. But it certainly isn't suitable for all.

I was talking to Travis about the need for some sort of lightweight  
intro to numpy. His book is a great technical reference, and very  
suitable for developers. But I worry that it is a bit intimidating  
for new users. So I raised the possibility of writing some sort of  
introduction that did the basics but pointed to the book for details  
for more advanced topics. Travis was ok with that (I didn't want to  
instigate anything that would cut into book sales). I was thinking of  
perhaps taking the old Numeric/numarray user guides and stripping  
them down and modifying that base document after I finish with the  
interactive tutorial (if I have time of course). With having to  
switch our staff over to numpy (we've pretty much completed  
converting most of our distributed software; our next release in  
early summer will be numpy-based) I think we need something that  
isn't too long to read. If others want to take this on, I welcome it  
(and as I said, I don't think Travis objects based on what he told me).

Perry




From rshepard at appl-ecosys.com  Wed Feb 28 13:44:28 2007
From: rshepard at appl-ecosys.com (Rich Shepard)
Date: Wed, 28 Feb 2007 10:44:28 -0800 (PST)
Subject: [SciPy-user] Library Message On Application Start
Message-ID: <Pine.LNX.4.64.0702281043050.19522@salmo.appl-ecosys.com>

   Each time I start my application I see this:

Overwriting info=<function info at 0xb5fa05dc> from scipy.misc (was
<function info at 0xb610d994> from numpy.lib.utils)

   It does not seem to affect the few functions we use, but I wonder if it's
something that should be fixed somewhere.

Rich

-- 
Richard B. Shepard, Ph.D.               |    The Environmental Permitting
Applied Ecosystem Services, Inc.        |          Accelerator(TM)
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863


From lou_boog2000 at yahoo.com  Wed Feb 28 13:45:14 2007
From: lou_boog2000 at yahoo.com (Lou Pecora)
Date: Wed, 28 Feb 2007 10:45:14 -0800 (PST)
Subject: [SciPy-user] Any Books on SciPy?
In-Reply-To: <F8435A1F-7EB7-42C5-9E10-99D3AE616E1E@stsci.edu>
Message-ID: <666570.29413.qm@web34409.mail.mud.yahoo.com>

What's really is needed are Examples, examples, and
examples.   The book is light on that (no offense). 
Some defintions of functions or methods leaves me
scratching my head asking, "How is that done in the
code, really?"


--- Perry Greenfield <perry at stsci.edu> wrote:

> I see it as suitable for a certain class of new
> users (i.e, those  
> that are more task oriented and looking to see what
> they can  
> accomplish interactively without having to learn a
> lot of preliminary  
> material. But it certainly isn't suitable for all.
> 
> I was talking to Travis about the need for some sort
> of lightweight  
> intro to numpy. His book is a great technical
> reference, and very  
> suitable for developers. But I worry that it is a
> bit intimidating  
> for new users. So I raised the possibility of
> writing some sort of  
> introduction that did the basics but pointed to the
> book for details  
> for more advanced topics. Travis was ok with that (I
> didn't want to  
> instigate anything that would cut into book sales).
> I was thinking of  
> perhaps taking the old Numeric/numarray user guides
> and stripping  
> them down and modifying that base document after I
> finish with the  
> interactive tutorial (if I have time of course).
> With having to  
> switch our staff over to numpy (we've pretty much
> completed  
> converting most of our distributed software; our
> next release in  
> early summer will be numpy-based) I think we need
> something that  
> isn't too long to read. If others want to take this
> on, I welcome it  
> (and as I said, I don't think Travis objects based
> on what he told me).
> 
> Perry



-- Lou Pecora,   my views are my own.
---------------
Three laws of thermodynamics:
  First law: "You can't win."
  Second law: "You can't break even."
  Third law: "You can't quit."
  -- Allen Ginsberg, beat poet


 
____________________________________________________________________________________
Finding fabulous fares is fun.  
Let Yahoo! FareChase search your favorite travel sites to find flight and hotel bargains.
http://farechase.yahoo.com/promo-generic-14795097


From rshepard at appl-ecosys.com  Wed Feb 28 14:02:42 2007
From: rshepard at appl-ecosys.com (Rich Shepard)
Date: Wed, 28 Feb 2007 11:02:42 -0800 (PST)
Subject: [SciPy-user] Any Books on SciPy?
In-Reply-To: <666570.29413.qm@web34409.mail.mud.yahoo.com>
References: <666570.29413.qm@web34409.mail.mud.yahoo.com>
Message-ID: <Pine.LNX.4.64.0702281100050.19522@salmo.appl-ecosys.com>

On Wed, 28 Feb 2007, Lou Pecora wrote:

> What's really is needed are Examples, examples, and examples. The book is
> light on that (no offense). Some defintions of functions or methods leaves
> me scratching my head asking, "How is that done in the code, really?"

   I'll second that suggestion. The mail list is very helpful, but it would
be nice to see the actual use of a function in a small program (or function)
in the book.

Rich

-- 
Richard B. Shepard, Ph.D.               |    The Environmental Permitting
Applied Ecosystem Services, Inc.        |          Accelerator(TM)
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863


From pgmdevlist at gmail.com  Wed Feb 28 14:09:11 2007
From: pgmdevlist at gmail.com (Pierre GM)
Date: Wed, 28 Feb 2007 14:09:11 -0500
Subject: [SciPy-user] Any Books on SciPy?
In-Reply-To: <Pine.LNX.4.64.0702281100050.19522@salmo.appl-ecosys.com>
References: <666570.29413.qm@web34409.mail.mud.yahoo.com>
	<Pine.LNX.4.64.0702281100050.19522@salmo.appl-ecosys.com>
Message-ID: <200702281409.11771.pgmdevlist@gmail.com>


>    I'll second that suggestion. The mail list is very helpful, but it would
> be nice to see the actual use of a function in a small program (or
> function) in the book.

Something like that ?
http://www.scipy.org/Numpy_Example_List_With_Doc
http://www.scipy.org/Cookbook


From krish.subramaniam at gmail.com  Wed Feb 28 14:11:17 2007
From: krish.subramaniam at gmail.com (Krish Subramaniam)
Date: Wed, 28 Feb 2007 11:11:17 -0800
Subject: [SciPy-user] Any Books on SciPy?
In-Reply-To: <Pine.LNX.4.64.0702281100050.19522@salmo.appl-ecosys.com>
References: <666570.29413.qm@web34409.mail.mud.yahoo.com>
	<Pine.LNX.4.64.0702281100050.19522@salmo.appl-ecosys.com>
Message-ID: <dfc38c640702281111g503674a9mcaf41115bfc1f6f@mail.gmail.com>

Personally, I think the approach Cleve Moler ( of Mathworks) takes in
the first chapter of "Numerical Computing in Matlab" is the best I
have seen.

http://www.mathworks.com/moler/chapters.html

What he does is, he takes a central concept ( Fibonacci numbers and
Golden Ratio). Explains everything about them using interactive
examples in Matlab-scripts. This approach helps a reader to learn when
to use a function and how to use it. So if one can explain a
lightweight scientific-computing concept using Scipy / Numpy and
exhausts most of the functions that would be a great tutorial.

Just my 2 cents.

--Krish Subramaniam


On 2/28/07, Rich Shepard <rshepard at appl-ecosys.com> wrote:
> On Wed, 28 Feb 2007, Lou Pecora wrote:
>
> > What's really is needed are Examples, examples, and examples. The book is
> > light on that (no offense). Some defintions of functions or methods leaves
> > me scratching my head asking, "How is that done in the code, really?"
>
>    I'll second that suggestion. The mail list is very helpful, but it would
> be nice to see the actual use of a function in a small program (or function)
> in the book.
>
> Rich
>
> --
> Richard B. Shepard, Ph.D.               |    The Environmental Permitting
> Applied Ecosystem Services, Inc.        |          Accelerator(TM)
> <http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user
>


From rshepard at appl-ecosys.com  Wed Feb 28 14:32:48 2007
From: rshepard at appl-ecosys.com (Rich Shepard)
Date: Wed, 28 Feb 2007 11:32:48 -0800 (PST)
Subject: [SciPy-user] Any Books on SciPy?
In-Reply-To: <200702281409.11771.pgmdevlist@gmail.com>
References: <666570.29413.qm@web34409.mail.mud.yahoo.com>
	<Pine.LNX.4.64.0702281100050.19522@salmo.appl-ecosys.com>
	<200702281409.11771.pgmdevlist@gmail.com>
Message-ID: <Pine.LNX.4.64.0702281132360.19522@salmo.appl-ecosys.com>

On Wed, 28 Feb 2007, Pierre GM wrote:

> Something like that ?
> http://www.scipy.org/Numpy_Example_List_With_Doc
> http://www.scipy.org/Cookbook

   Yes.

-- 
Richard B. Shepard, Ph.D.               |    The Environmental Permitting
Applied Ecosystem Services, Inc.        |          Accelerator(TM)
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863


From lou_boog2000 at yahoo.com  Wed Feb 28 15:03:11 2007
From: lou_boog2000 at yahoo.com (Lou Pecora)
Date: Wed, 28 Feb 2007 12:03:11 -0800 (PST)
Subject: [SciPy-user] Any Books on SciPy?
In-Reply-To: <200702281409.11771.pgmdevlist@gmail.com>
Message-ID: <92333.6801.qm@web34408.mail.mud.yahoo.com>

Well... yes, what took you so long?  :-) 

Thanks.  A very good web site.  And right there hiding
under my nose. 

--- Pierre GM <pgmdevlist at gmail.com> wrote:

> Something like that ?
> http://www.scipy.org/Numpy_Example_List_With_Doc
> http://www.scipy.org/Cookbook



-- Lou Pecora,   my views are my own.
---------------
Three laws of thermodynamics:
  First law: "You can't win."
  Second law: "You can't break even."
  Third law: "You can't quit."
  -- Allen Ginsberg, beat poet



 
____________________________________________________________________________________
Need Mail bonding?
Go to the Yahoo! Mail Q&A for great tips from Yahoo! Answers users.
http://answers.yahoo.com/dir/?link=list&sid=396546091


From pgmdevlist at gmail.com  Wed Feb 28 15:19:54 2007
From: pgmdevlist at gmail.com (Pierre GM)
Date: Wed, 28 Feb 2007 15:19:54 -0500
Subject: [SciPy-user] Any Books on SciPy?
In-Reply-To: <92333.6801.qm@web34408.mail.mud.yahoo.com>
References: <92333.6801.qm@web34408.mail.mud.yahoo.com>
Message-ID: <200702281519.54562.pgmdevlist@gmail.com>

On Wednesday 28 February 2007 15:03:11 Lou Pecora wrote:
> Well... yes, what took you so long?  :-)
>
> Thanks.  A very good web site.  And right there hiding
> under my nose.

If I remember my Poe correctly, that's quite often the case.

But seriously: I find the Numpy examples invaluable. However, nothing prevents 
us to start reorganizing these examples in a fashion closer to Moler's 
approach: short, real-life examples, along with the corresponding Numpy code. 
A kind of Guide to numpy's electronic companion, that shouldn't replace the 
Cookbook but complete it. We should first to agree on a basic template, and 
fill it adequately. The wiki organization is ideal for that.


From lou_boog2000 at yahoo.com  Wed Feb 28 15:53:07 2007
From: lou_boog2000 at yahoo.com (Lou Pecora)
Date: Wed, 28 Feb 2007 12:53:07 -0800 (PST)
Subject: [SciPy-user] Any Books on SciPy?
In-Reply-To: <200702281519.54562.pgmdevlist@gmail.com>
Message-ID: <20070228205307.17517.qmail@web34414.mail.mud.yahoo.com>

--- Pierre GM <pgmdevlist at gmail.com> wrote:

> On Wednesday 28 February 2007 15:03:11 Lou Pecora
> wrote:
> > Well... yes, what took you so long?  :-)
> >
> > Thanks.  A very good web site.  And right there
> hiding
> > under my nose.
> 
> If I remember my Poe correctly, that's quite often
> the case.

You know Edgar Allen well.  I think that was "The
Tell-Tale Heart".  Very good knowledge of literature. 


> But seriously: I find the Numpy examples invaluable.
> However, nothing prevents 
> us to start reorganizing these examples in a fashion
> closer to Moler's 
> approach: short, real-life examples, along with the
> corresponding Numpy code. 
> A kind of Guide to numpy's electronic companion,
> that shouldn't replace the 
> Cookbook but complete it. We should first to agree
> on a basic template, and 
> fill it adequately. The wiki organization is ideal
> for that.

You are right.  I'm not sure what the format should
be.  I'm a little out of it about writing up things
even though I have contributed to the NumPy/SciPy
wiki.



-- Lou Pecora,   my views are my own.
---------------
Three laws of thermodynamics:
  First law: "You can't win."
  Second law: "You can't break even."
  Third law: "You can't quit."
  -- Allen Ginsberg, beat poet


 
____________________________________________________________________________________
No need to miss a message. Get email on-the-go 
with Yahoo! Mail for Mobile. Get started.
http://mobile.yahoo.com/mail 


From bnuttall at uky.edu  Wed Feb 28 15:51:36 2007
From: bnuttall at uky.edu (Brandon Nuttall)
Date: Wed, 28 Feb 2007 15:51:36 -0500
Subject: [SciPy-user] Using SciPy/NumPy optimization THANKS!
In-Reply-To: <45E5BF5E.6020601@gmail.com>
References: <6.0.1.1.2.20070227131721.0287bfe0@pop.uky.edu>
	<45E493D7.2070703@gmail.com>
	<6.0.1.1.2.20070227170539.0283f608@pop.uky.edu>
	<6.0.1.1.2.20070228093647.02798d38@pop.uky.edu>
	<45E5BF5E.6020601@gmail.com>
Message-ID: <6.0.1.1.2.20070228135020.026f3008@pop.uky.edu>

Folks,

Thanks to Alok Singhal and Robert Kern I have not only learned a great deal 
about SciPy and NumPy, but I have code that works. Thanks for the tip on 
not looping; it does make cleaner code. I have two issues: 1) there must be 
a better way to convert a list of data pairs to two arrays, 2) I'm not sure 
of a graceful way to transition from one plot to the next and then close.

It works and I'm going to plug it into other code that grabs data from a 
MySQL database.

import numpy as np
from scipy import rand
from scipy.optimize import leastsq
import pylab

class HypObj:
     """Object for best fit to hyperbolic function"""
     def __init__(self,x,y,guess=None,plot=None):
         self.x = x
         self.y = y
         self.plot=plot
         if guess==None:
             self.guess = [y.max(),1.0,0.5]
         else:
             self.guess = guess
         self.parameters, self.success = leastsq(self._errf,
                                                 self.guess[:],
                                                 args = (self.x, self.y))
         self.r2 = self._r2(self.x,self.y,self.parameters)
         if self.plot<>None:
             pylab.plot(self.x, self.y, 'ro',
                        self.x, self._f(self.parameters, self.x), 'b--')
             pylab.show()
             pylab.clf()
     def _f(self,p, x):
         """Evaluate function with parameters, p, and array of x values"""
         return p[0]*(1.0+p[1]*p[2]*x)**(-1.0/p[1])
     def _errf(self,p, x, y):
         """return the difference between calculated and input y values"""
         return self._f(p, x) - y
     def _r2(self,x,y,abc):
         """calculate the correlation coefficient and rmsd"""
         y_calc = self._f(abc,self.x)
         y_avg = y.mean()
         rmsd = ((y-self._f(abc,x))**2).sum()/((y_calc-y_avg)**2).sum()
         return (1.0-rmsd, rmsd)

def list_toarray(data):
     """Convert input list of data pairs to two arrays"""
     x = []
     y = []
     for i in data:
         x.append(float(i[0]))
         y.append(float(i[1]))
     x = np.array(x)
     y = np.array(y)
     return x,y

def test():

     def f(p, x): # for testing, make the objective function available
         return p[0]*(1.0+p[1]*p[2]*x)**(-1.0/p[1])

     # fake data for testing, should get perfect correlation
     print "\nTest 1: should find an exact solution = [1.25,0.75,0.25]"
     print "(No plot)"
     qi, b, di = [1.25,0.75,0.25]
     sample = []
     for i in range(1,61):
         sample.append([float(i),qi*(1.0+b*di*float(i))**(-1.0/b)])
     x, y = list_toarray(sample)
     ex1 = HypObj(x,y)
     if ex1.success==1:
         print ex1.parameters,ex1.r2
     else:
         print "leastsq() error: ",ex1.success

     # generate data with random deviations
     print "\nTest 2: should find a solution close to [15.0, 2.5, 0.3]"
     print "(No plot)"
     n = 151
     x = np.mgrid[1:10:n*1j]
     abc = [15.0, 2.5, 0.3]
     y = f(abc, x) + rand(n) - 0.5
     ex2 = HypObj(x,y,guess=[30.0, 4.0, 1.0])
     if ex2.success==1:
         print ex2.parameters,ex2.r2
     else:
         print "leastsq() error: ",ex2.success

     # real data
     print "\nTest 3: real world data"
     rn115604=[[1, 3233],[2, 3530],[3, 3152],[4, 2088],[6, 3038],
               [7, 2108],[8, 2132],[9, 1654],[10, 1762],[11, 1967],
               [12, 1760],[13, 1649],[14, 1633],[15, 1680],[16, 1398],
               [17, 1622],[18, 1393],[19, 1436],[20, 1352],[21, 1402],
               [22, 1459],[23, 1373],[24, 1262],[25, 1346],[26, 1325],
               [27, 1319],[28, 1309],[29, 1206],[30, 1249],[31, 1446],
               [32, 1255],[33, 1227],[34, 1268],[35, 1233],[36, 1175],
               [37, 1129],[38, 1242],[39, 1247],[40, 1198],[41, 1058],
               [42, 1172],[43, 1242],[44, 1214],[45, 1148],[46, 1689],
               [47, 971],[48, 1084],[49, 1028],[50, 1164],[51, 1297],
               [52, 1040],[53, 1045],[54, 1196],[55, 991],[56, 1065],
               [57, 898],[58, 1020],[59, 966],[60, 1162],[61, 1069],
               [62, 1055],[63, 1035],[64, 1045],[65, 1076],[66, 1108],
               [67, 918],[68, 1051],[69, 1049],[70, 1039],[71, 1133],
               [72, 887],[73, 924],[74, 983],[75, 1077],[76, 1092],
               [77, 973],[78, 920],[79, 1040]]
     x, y = list_toarray(rn115604)
     ex3 = HypObj(x,y,plot=1)
     if ex3.success==1:
         print ex3.parameters,ex3.r2
     else:
         print "leastsq() error: ",ex3.success

if __name__=="__main__":
     test()


Brandon C. Nuttall

BNUTTALL at UKY.EDU                         Kentucky Geological Survey
(859) 257-5500                                     University of Kentucky
(859) 257-1147 (fax)                              228 Mining & Mineral 
Resources Bldg
http://www.uky.edu/KGS/home.htm       Lexington, Kentucky 40506-0107  



From fperez.net at gmail.com  Wed Feb 28 15:57:36 2007
From: fperez.net at gmail.com (Fernando Perez)
Date: Wed, 28 Feb 2007 13:57:36 -0700
Subject: [SciPy-user] Any Books on SciPy?
In-Reply-To: <20070228205307.17517.qmail@web34414.mail.mud.yahoo.com>
References: <200702281519.54562.pgmdevlist@gmail.com>
	<20070228205307.17517.qmail@web34414.mail.mud.yahoo.com>
Message-ID: <db6b5ecc0702281257w6c2ed7bcye86a259e7d8da80e@mail.gmail.com>

On 2/28/07, Lou Pecora <lou_boog2000 at yahoo.com> wrote:
> --- Pierre GM <pgmdevlist at gmail.com> wrote:
>
> > > Thanks.  A very good web site.  And right there
> > hiding
> > > under my nose.
> >
> > If I remember my Poe correctly, that's quite often
> > the case.
>
> You know Edgar Allen well.  I think that was "The
> Tell-Tale Heart".  Very good knowledge of literature.

I suspect the reference was to "The Purloined Letter" (or "La carta
robada", as I originally read it) instead.

Cheers,

f


From robert.kern at gmail.com  Wed Feb 28 16:07:48 2007
From: robert.kern at gmail.com (Robert Kern)
Date: Wed, 28 Feb 2007 15:07:48 -0600
Subject: [SciPy-user] Using SciPy/NumPy optimization THANKS!
In-Reply-To: <6.0.1.1.2.20070228135020.026f3008@pop.uky.edu>
References: <6.0.1.1.2.20070227131721.0287bfe0@pop.uky.edu>	<45E493D7.2070703@gmail.com>	<6.0.1.1.2.20070227170539.0283f608@pop.uky.edu>	<6.0.1.1.2.20070228093647.02798d38@pop.uky.edu>	<45E5BF5E.6020601@gmail.com>
	<6.0.1.1.2.20070228135020.026f3008@pop.uky.edu>
Message-ID: <45E5EF24.8080703@gmail.com>

Brandon Nuttall wrote:
> Folks,
> 
> Thanks to Alok Singhal and Robert Kern I have not only learned a great deal 
> about SciPy and NumPy, but I have code that works. Thanks for the tip on 
> not looping; it does make cleaner code. I have two issues: 1) there must be 
> a better way to convert a list of data pairs to two arrays,

xy = array([[x0, y0], [x1, y1], ...])
x = xy[:,0]
y = xy[:,1]

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
 that is made terrible by our own mad attempt to interpret it as though it had
 an underlying truth."
  -- Umberto Eco


From lou_boog2000 at yahoo.com  Wed Feb 28 16:08:40 2007
From: lou_boog2000 at yahoo.com (Lou Pecora)
Date: Wed, 28 Feb 2007 13:08:40 -0800 (PST)
Subject: [SciPy-user] Any Books on SciPy?
In-Reply-To: <db6b5ecc0702281257w6c2ed7bcye86a259e7d8da80e@mail.gmail.com>
Message-ID: <20070228210841.22939.qmail@web34414.mail.mud.yahoo.com>


--- Fernando Perez <fperez.net at gmail.com> wrote:

> On 2/28/07, Lou Pecora <lou_boog2000 at yahoo.com>
> wrote:
> > You know Edgar Allen well.  I think that was "The
> > Tell-Tale Heart".  Very good knowledge of
> literature.
> 
> I suspect the reference was to "The Purloined
> Letter" (or "La carta
> robada", as I originally read it) instead.

Sigh.  This is why I went into physics and not
literature.  Thanks.  :-) 



-- Lou Pecora,   my views are my own.
---------------
Three laws of thermodynamics:
  First law: "You can't win."
  Second law: "You can't break even."
  Third law: "You can't quit."
  -- Allen Ginsberg, beat poet


 
____________________________________________________________________________________
Have a burning question?  
Go to www.Answers.yahoo.com and get answers from real people who know.


From as8ca at virginia.edu  Wed Feb 28 16:16:26 2007
From: as8ca at virginia.edu (Alok Singhal)
Date: Wed, 28 Feb 2007 16:16:26 -0500
Subject: [SciPy-user] Using SciPy/NumPy optimization THANKS!
In-Reply-To: <6.0.1.1.2.20070228135020.026f3008@pop.uky.edu>
References: <6.0.1.1.2.20070227131721.0287bfe0@pop.uky.edu>
	<45E493D7.2070703@gmail.com>
	<6.0.1.1.2.20070227170539.0283f608@pop.uky.edu>
	<6.0.1.1.2.20070228093647.02798d38@pop.uky.edu>
	<45E5BF5E.6020601@gmail.com>
	<6.0.1.1.2.20070228135020.026f3008@pop.uky.edu>
Message-ID: <20070228211626.GA6423@virginia.edu>

On 28/02/07: 15:51, Brandon Nuttall wrote:
> import numpy as np
> from scipy import rand
> from scipy.optimize import leastsq
> import pylab
> 
> class HypObj:
>      """Object for best fit to hyperbolic function"""
>      def __init__(self,x,y,guess=None,plot=None):
>          self.x = x
>          self.y = y
>          self.plot=plot
>          if guess==None:
>              self.guess = [y.max(),1.0,0.5]
>          else:
>              self.guess = guess
>          self.parameters, self.success = leastsq(self._errf,
>                                                  self.guess[:],
>                                                  args = (self.x, self.y))
>          self.r2 = self._r2(self.x,self.y,self.parameters)
>          if self.plot<>None:

Maybe 

if self.plot is not None:

is better?  See http://www.python.org/dev/peps/pep-0008/, section
'Programming Recommendations'.

> def list_toarray(data):
>      """Convert input list of data pairs to two arrays"""
>      x = []
>      y = []
>      for i in data:
>          x.append(float(i[0]))
>          y.append(float(i[1]))
>      x = np.array(x)
>      y = np.array(y)
>      return x,y

For your data, you can do:

x = [data[i][0] for i in range(60)]
y = [data[i][1] for i in range(60)]

If you want to use numpy, then you could do:

data = np.asarray(data)
x = data[:, 0]
y = data[:, 1]

> def test():
> 
>      def f(p, x): # for testing, make the objective function available
>          return p[0]*(1.0+p[1]*p[2]*x)**(-1.0/p[1])
> 
>      # fake data for testing, should get perfect correlation
>      print "\nTest 1: should find an exact solution = [1.25,0.75,0.25]"
>      print "(No plot)"
>      qi, b, di = [1.25,0.75,0.25]
>      sample = []
>      for i in range(1,61):
>          sample.append([float(i),qi*(1.0+b*di*float(i))**(-1.0/b)])

You don't need the loop:

sample = np.zeros((60, 2), dtype=float)
sample[:, 0] = np.arange(60) + 1
sample[:, 1] = qi*(1. + b*di*sample[:, 0])**(-1.0/b)

Given that you 'unpack' sample at a later stage anyway, you could as
well use two different variables instead of sample.

Cheers,
Alok

-- 
Alok Singhal                               *   *          
Graduate Student, dept. of Astronomy   *           *     *
University of Virginia                                    
http://www.astro.virginia.edu/~as8ca/              *    * 


From emin.shopper at gmail.com  Wed Feb 28 16:40:32 2007
From: emin.shopper at gmail.com (Emin.shopper Martinian.shopper)
Date: Wed, 28 Feb 2007 16:40:32 -0500
Subject: [SciPy-user] scipy and cvxopt
Message-ID: <32e43bb70702281340r39d69ea5t2e1287ed340eee9b@mail.gmail.com>

Dear Experts,

I need to solve some quadratic programs (and potentially other nonlinear
programs). While scipy.optimize.fmin_cobyla seems like it can do this, it
seems orders of magnitude slower than cvxopt. Are there plans to
merge/include cvxopt in scipy or otherwise improve scipy's
quadratic/nonlinear constrained optimization routines?

I saw an old response to this question but the response pointed to a
non-existent URL.

Thanks,
-Emin
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20070228/d1a51eea/attachment.html>

From oliphant.travis at ieee.org  Wed Feb 28 17:31:39 2007
From: oliphant.travis at ieee.org (Travis Oliphant)
Date: Wed, 28 Feb 2007 15:31:39 -0700
Subject: [SciPy-user] NumPy in Teaching
In-Reply-To: <45E4FFA6.9010408@shrogers.com>
References: <45E4FFA6.9010408@shrogers.com>
Message-ID: <es4vsb$2mt$1@sea.gmane.org>

Steven H. Rogers wrote:
> I'm doing an informal survey on the use of Array Programming Languages 
> for teaching.  If you're using NumPy in this manner I'd like to hear 
> from you.  What subject was/is taught, academic level, results, lessons 
> learned, etc.
> 

I've used NumPy in a Signals and Systems class and in a Probability 
Theory class.  These were both Junior/Senior level undergraduate classes.

Students were given the option to use Python or MATLAB.  Most chose 
MATLAB because it was installed on the computers they had access to.  It 
is also the language used when other teachers teach the course.

NumPy/SciPy was a complete replacement for MATLAB however.  I did all of 
the labs using NumPy/SciPy and they worked fine.

-Travis



From oliphant at ee.byu.edu  Wed Feb 28 17:54:05 2007
From: oliphant at ee.byu.edu (Travis Oliphant)
Date: Wed, 28 Feb 2007 15:54:05 -0700
Subject: [SciPy-user] scipy and cvxopt
In-Reply-To: <32e43bb70702281340r39d69ea5t2e1287ed340eee9b@mail.gmail.com>
References: <32e43bb70702281340r39d69ea5t2e1287ed340eee9b@mail.gmail.com>
Message-ID: <45E6080D.8090103@ee.byu.edu>

Emin.shopper Martinian.shopper wrote:

> Dear Experts,
>
> I need to solve some quadratic programs (and potentially other 
> nonlinear programs). While scipy.optimize.fmin_cobyla seems like it 
> can do this, it seems orders of magnitude slower than cvxopt. Are 
> there plans to merge/include cvxopt in scipy or otherwise improve 
> scipy's quadratic/nonlinear constrained optimization routines?


Yes, eventually.  I have talked to the author of CVXOPT at NIPS 2006.  
The plan is to move NumPy's matrix object into C and move CVXOPTs 
implementation over to use it, possibly integrating the cvxopt 
algorithms into at least a scikits library (of GPL code).

But, I won't have time for that until April or May.

-Travis



From david.warde.farley at utoronto.ca  Wed Feb 28 18:00:58 2007
From: david.warde.farley at utoronto.ca (David Warde-Farley)
Date: Wed, 28 Feb 2007 18:00:58 -0500
Subject: [SciPy-user] NumPy in Teaching
In-Reply-To: <es4vsb$2mt$1@sea.gmane.org>
References: <45E4FFA6.9010408@shrogers.com> <es4vsb$2mt$1@sea.gmane.org>
Message-ID: <119A160D-FBC3-4086-A22F-60658961616F@utoronto.ca>

On 28-Feb-07, at 5:31 PM, Travis Oliphant wrote:

> Students were given the option to use Python or MATLAB.  Most chose
> MATLAB because it was installed on the computers they had access  
> to.  It
> is also the language used when other teachers teach the course.
>
> NumPy/SciPy was a complete replacement for MATLAB however.  I did  
> all of
> the labs using NumPy/SciPy and they worked fine.

Travis,

Can I ask how you (or anyone else) deals with saving a "workspace"  
when doing interactive numerical work in Python? I'd imagine this  
might be important in an educational setting, and I'm remiss to still  
be without an equivalent to Matlab's "save" (I understand the  
difficulty in serializing a Python namespace though).

So what do people do? Aside from being somewhat clumsy, even cPickle  
seems intolerably slow at saving large matrices to disk.

David



P.S. Many thanks for all the work you've done making NumPy and SciPy  
usable. I'm currently working on porting a good bit of numerical code  
to Python and your documentation has been invaluable. By the way, was  
it you who gave the presentation at the NIPS workshops? (My  
supervisor came away quite impressed)



From oliphant at ee.byu.edu  Wed Feb 28 18:15:11 2007
From: oliphant at ee.byu.edu (Travis Oliphant)
Date: Wed, 28 Feb 2007 16:15:11 -0700
Subject: [SciPy-user] NumPy in Teaching
In-Reply-To: <119A160D-FBC3-4086-A22F-60658961616F@utoronto.ca>
References: <45E4FFA6.9010408@shrogers.com> <es4vsb$2mt$1@sea.gmane.org>
	<119A160D-FBC3-4086-A22F-60658961616F@utoronto.ca>
Message-ID: <45E60CFF.3090103@ee.byu.edu>

David Warde-Farley wrote:

>On 28-Feb-07, at 5:31 PM, Travis Oliphant wrote:
>
>  
>
>>Students were given the option to use Python or MATLAB.  Most chose
>>MATLAB because it was installed on the computers they had access  
>>to.  It
>>is also the language used when other teachers teach the course.
>>
>>NumPy/SciPy was a complete replacement for MATLAB however.  I did  
>>all of
>>the labs using NumPy/SciPy and they worked fine.
>>    
>>
>
>Travis,
>
>Can I ask how you (or anyone else) deals with saving a "workspace"  
>when doing interactive numerical work in Python? I'd imagine this  
>might be important in an educational setting, and I'm remiss to still  
>be without an equivalent to Matlab's "save" (I understand the  
>difficulty in serializing a Python namespace though).
>  
>
You can save .mat files (which I've done in the past) by passing in a 
list of the names to save to the file to scipy's  scipy.io.savemat function.

I've also used scipy's scipy.io.save command with success in the past.   
The problem with pickling is the copying that occurs to a string before 
pickling can occur.   I think something a little more specialized to 
NumPy would be possible using the .tofile() method. 

There has been some nice work on SciPy's io functionality lately which 
includes using memory-mapping techniques.  It has not been completely 
documented yet, however.

-Travis



From jh at physics.ucf.edu  Wed Feb 28 19:32:41 2007
From: jh at physics.ucf.edu (Joe Harrington)
Date: Wed, 28 Feb 2007 19:32:41 -0500
Subject: [SciPy-user] NumPy in Teaching
Message-ID: <200703010032.l210WfhI005995@glup.physics.ucf.edu>

Hi Steve,

I have taught Astronomical Data Analysis twice at Cornell using IDL,
and I will be teaching it next Fall at UCF using NumPy.  Though I've
been active here in the recent past, I'm actually not a regular NumPy
user myself yet (I used Numeric experimentally for about 6 months in
1997), so I'm a bit nervous.  There isn't the kind of documentation
and how-to support for Numpy that there is for IDL, though our web
site is a start in that direction.  One thought I've had in making the
transition easier is to put up a syntax and function concordance,
similar to that available for MATLAB.  I thought this existed.  Maybe
Perry can point me to it.  Just adding a column to the MATLAB one
would be fine.

My syllabi (there are undergrad and grad versions) are at:

Cornell courses (undergrad only):
http://physics.ucf.edu/~jh/ast/ast234-2003/
http://physics.ucf.edu/~jh/ast/ast234-2004/

UCF course (4xxx is undergrad, 5xxx is grad, numbers not yet assigned):
http://physics.ucf.edu/~jh/ast/dacourse/

The goal of the course is for students to go out and do research with
faculty as soon as they're done, and be useful enough to be included
on papers.  Rather than the usual (and failing) "just do what I do"
model, in which physics students learn to program badly and in
FORTRAN77 from their professors, I teach programming from a CS point
of view, focusing on good top-down design and bottom-up construction
(indentation, documentation, sensible naming, testing, etc.).  I teach
error analysis by first teaching probability.  Then we go into the
physics of detectors and finally do an end-to-end analysis of some
simple spacecraft data sets (photometry and spectroscopy), the
programming of which make up most of their assignments.  There is a
project at the end, in which many in the class seem to get an epiphany
for how all this stuff fits together.  They write up the result in the
format of an Astrophysical Journal article, and while I don't teach
writing as a topic, I do demand that it is done well (and to my shock
it usually is!).

The first two times I taught it, it was way too much material (good
students spent 15+ hours on the class weekly), so I'm ripping out
about half the programming assignments for the undergrads, and giving
simpler project datasets.

My main lesson learned is that the old adage of "They know less than
you think they know but they can do more than you think they can do"
falls completely on its face here.  Many of them actually do know how
to program, and that ability, rather than their academic level, is
really the best predictor of course success.  A computer-savvy
freshman will just kill a computerphobic grad student, because the
rest of the class just isn't that hard.  What I wasn't prepared for
the first time I taught it is just how hard it is to teach debugging.
These kids will stare a simple twiddle-characters bug in the face for
hours and not see it.  It's been twenty-five years since I was at that
stage and it's hard to remember what it was like.  To teach debugging,
I'm emphasizing "fingers as the creators of error" (since you KNOW
your brain didn't do it!), and that they should test each small bit of
code before incorporating it in their function.  I'm also showing them
how to use a debugger, giving them a list of common bug types and how
to find them, and only having them do every other step in the
photometry pipeline.  I'll give them the other half of the steps and
that will teach them how to design to an API.

The other lesson is that it is a hell of a lot of work to grade
programming assignments from even four students, if you care about
grading for good practice and not just whether it runs.  I probably
spent 20 hours a week on the class the second year I taught it.  Since
I'll have 10 students next semester, I plan on doing something here
with peer evaluation.  Wish me luck...

I'm posting here because I'm interested in your results and any advice
you or your respondents have to share.  I hope other respondents will
post here rather than sending private email.  If we get enough people,
let's start a page on the wiki (a mailing list!  a conference!  a
movement!  ok, well, let's start with a wiki page).

--jh--
Prof. Joseph Harrington
Department of Physics
University of Central Florida


From palazzol at comcast.net  Wed Feb 28 21:00:10 2007
From: palazzol at comcast.net (Frank Palazzolo)
Date: Wed, 28 Feb 2007 21:00:10 -0500
Subject: [SciPy-user] Robert Kern's pyCA
Message-ID: <45E633AA.8070107@comcast.net>

Hello,

Has anyone tried to port Robert Kern's pyCA (Geometric Algebra) code to 
use the new NumPy?  It uses a combination of Numeric and NumPy at 
present - as seen here:

http://mail.python.org/pipermail/python-list/2000-August/050443.html

I might have a go at it myself...just thought I'd find out if someone 
did it already.  And I noticed that Robert posts here :)

I wonder if there is interest in having this as part of SciPy?

Thanks,
Frank





From steve at shrogers.com  Wed Feb 28 23:14:48 2007
From: steve at shrogers.com (Steven H. Rogers)
Date: Wed, 28 Feb 2007 21:14:48 -0700
Subject: [SciPy-user] NumPy in Teaching
In-Reply-To: <20070228124928.8D9D2BA05AD@phaser.physics.ucf.edu>
References: <20070228124928.8D9D2BA05AD@phaser.physics.ucf.edu>
Message-ID: <45E65338.9060806@shrogers.com>

Hi Joe:

Thanks for the comprehensive response.  I'll post the results to the 
lists when I've compiled them. 

# Steve


From robert.kern at gmail.com  Wed Feb 28 23:20:17 2007
From: robert.kern at gmail.com (Robert Kern)
Date: Wed, 28 Feb 2007 22:20:17 -0600
Subject: [SciPy-user] Robert Kern's pyCA
In-Reply-To: <45E633AA.8070107@comcast.net>
References: <45E633AA.8070107@comcast.net>
Message-ID: <45E65481.5050505@gmail.com>

Frank Palazzolo wrote:
> Hello,
> 
> Has anyone tried to port Robert Kern's pyCA (Geometric Algebra) code to 
> use the new NumPy?

I made an initial pass at it:

  http://www.enthought.com/~rkern/cgi-bin/hgwebdir.cgi/clifford/

That's a Mercurial repository[1], so after installing Mercurial, you can make a
local branch like so:

  $ hg clone http://www.enthought.com/~rkern/cgi-bin/hgwebdir.cgi/clifford/


[1] http://www.selenic.com/mercurial/wiki

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
 that is made terrible by our own mad attempt to interpret it as though it had
 an underlying truth."
  -- Umberto Eco


From steve at shrogers.com  Wed Feb 28 23:30:16 2007
From: steve at shrogers.com (Steven H. Rogers)
Date: Wed, 28 Feb 2007 21:30:16 -0700
Subject: [SciPy-user] NumPy in Teaching
In-Reply-To: <c5b438120702280616x4668ac36qdb68207b093d1060@mail.gmail.com>
References: <45E4FFA6.9010408@shrogers.com>
	<c5b438120702280616x4668ac36qdb68207b093d1060@mail.gmail.com>
Message-ID: <45E656D8.6030408@shrogers.com>

Thanks Ryan.  Matlab  _is_ rather pervasive in engineering, but I expect 
NumPy/SciPy to make inroads as the rough edges are smoothed out. 

Regards,
Steve