[SciPy-dev] manifold_learning

[Nils Wagner]

On Wed, 21 Jan 2009 20:32:24 +0100
  Matthieu Brucher <matthieu.brucher at gmail.com> wrote:
> 2009/1/21 Nils Wagner <nwagner at iam.uni-stuttgart.de>:
>> On Wed, 21 Jan 2009 20:06:41 +0100
>>  Matthieu Brucher <matthieu.brucher at gmail.com> wrote:
>>>>> Who can shed some light on that problem ?
>>>>
>>>> This is strange. I must have made a mistake when
>>>>changing the
>>>> extension, but even with Windows, it shouldn't have been
>>>>a pyd
>>>> extension.
>>>
>>> No idea. I'm using load_library, it should be correct.
>>> Is there a _cost_function.so in
>>> /home/nwagner/local/lib64/python2.6/site-packages/scikits.learn-0.0.0-py2.6-linux-x86_64.egg/scikits/learn/machine/manifold_learning/compression/cost_function/
>>> ?
>>>
>>>
>>> --
>>> Information System Engineer, Ph.D.
>>> Website: http://matthieu-brucher.developpez.com/
>>> Blogs: http://matt.eifelle.com and
>>>http://blog.developpez.com/?blog=92
>>> LinkedIn: http://www.linkedin.com/in/matthieubrucher
>>> _______________________________________________
>>> Scipy-dev mailing list
>>> Scipy-dev at scipy.org
>>> http://projects.scipy.org/mailman/listinfo/scipy-dev
>>
>> No.
>>
>> /home/nwagner/local/lib64/python2.6/site-packages/scikits.learn-0.0.0-py2.6.egg-info
>>
>> nwagner at linux-mogv:~/local/lib64/python2.6/site-packages/scikits.learn-0.0.0-py2.6.egg-info>
>> ll
>> insgesamt 68
>> -rw-r--r-- 1 nwagner users     1 21. Jan 19:25
>> dependency_links.txt
>> -rw-r--r-- 1 nwagner users     8 21. Jan 19:25
>> namespace_packages.txt
>> -rw-r--r-- 1 nwagner users   686 21. Jan 19:25 PKG-INFO
>> -rw-r--r-- 1 nwagner users     5 21. Jan 19:25
>> requires.txt
>> -rw-r--r-- 1 nwagner users 15201 21. Jan 19:25 
>>SOURCES.txt
>> -rw-r--r-- 1 nwagner users     8 21. Jan 19:25
>> top_level.txt
>> -rw-r--r-- 1 nwagner users     1 21. Jan 18:34 zip-safe
>>
>> Nils
>> _______________________________________________
>> Scipy-dev mailing list
>> Scipy-dev at scipy.org
>> http://projects.scipy.org/mailman/listinfo/scipy-dev
>>
> 
> in the compression/cost_function folder
> 
> -- 
> Information System Engineer, Ph.D.
> Website: http://matthieu-brucher.developpez.com/
> Blogs: http://matt.eifelle.com and 
>http://blog.developpez.com/?blog=92
> LinkedIn: http://www.linkedin.com/in/matthieubrucher
> _______________________________________________
> Scipy-dev mailing list
> Scipy-dev at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-dev


O.k. I have removed everything under site-packages and
reinstalled learn.

Now

python -i regression.py
Importing dataset swissroll.pickled
Importing compressed dataset swissroll.isomap.pickled
Regression using MLPLMR
/home/nwagner/local/lib64/python2.6/site-packages/scipy/stats/stats.py:1471: 
DeprecationWarning: scipy.stats.cov is deprecated; please 
update your code to use numpy.cov.
Please note that:
     - numpy.cov rowvar argument defaults to true, not 
false
     - numpy.cov bias argument defaults to false, not true

   """, DeprecationWarning)
Traceback (most recent call last):
   File "regression.py", line 56, in <module>
     model = regressionalgo(data, coords, neighbors = 9)
   File 
"/home/nwagner/local/lib64/python2.6/site-packages/scikits/learn/machine/manifold_learning/regression/MLPLMR.py", 
line 38, in __init__
     super(MLPLMR, self).__init__(points, coords, 
**kwargs)
   File 
"/home/nwagner/local/lib64/python2.6/site-packages/scikits/learn/machine/manifold_learning/regression/PLMR.py", 
line 36, in __init__
     self.coords_field = RBF_field(coords, weight = 1)
   File 
"/home/nwagner/local/lib64/python2.6/site-packages/scikits/learn/machine/manifold_learning/stats/radial_basis_functions_field.py", 
line 29, in __init__
     gaussian_kde.__init__(self, dataset = samples.T)
   File 
"/home/nwagner/local/lib64/python2.6/site-packages/scipy/stats/kde.py", 
line 81, in __init__
     self._compute_covariance()
   File 
"/home/nwagner/local/lib64/python2.6/site-packages/scipy/stats/kde.py", 
line 333, in _compute_covariance
     self.factor * self.factor)
   File 
"/home/nwagner/local/lib64/python2.6/site-packages/scipy/stats/stats.py", 
line 1483, in cov
     m = m - mean(m,axis=0)
   File 
"/home/nwagner/local/lib64/python2.6/site-packages/scipy/stats/stats.py", 
line 418, in mean
     axis=0, ddof=1).""")
DeprecationWarning: scipy.stats.mean is deprecated; please 
update your code to use numpy.mean.
Please note that:
     - numpy.mean axis argument defaults to None, not 0
     - numpy.mean has a ddof argument to replace bias in a 
more general manner.
       scipy.stats.mean(a, bias=True) can be replaced by 
numpy.mean(x,
axis=0, ddof=1).
  

Nils