[SciPy-user] [newbie] standardize a matrix

Mauro Cherubini martigan at gmail.com
Tue Oct 11 09:40:55 CDT 2005


On Oct 11, 2005, at 15:10 , Noel O'Boyle wrote:

> On Tue, 2005-10-11 at 15:04 +0200, Mauro Cherubini wrote:
>
>> Hi Noel,
>> thanks for the reply.
>> Follwoing you advices I implemented this method inside one of my
>> classes:
>>
>> #This method should standardize the matrix
>>      def standardize_matrix(self, matrix, method='standard'):
>>          if method == 'max':
>>              max_x = max(matrix[:,1].flat)
>>              divide(matrix[:,1], max_x, stdmatrix[:,1])
>>              max_y = max(matrix[:,2].flat)
>>              divide(matrix[:,2], max_y, stdmatrix[:,2])
>>              return stdmatrix;
>>          if method == 'standard':
>>              mean_x = mean(matrix[:,1].flat)
>>              stddev_x = std(matrix[:,1].flat)
>>              subtract(matrix[:,1], mean_x, stdmatrix[:,1])
>>              divide(matrix[:,1], stddev_x, stdmatrix[:,1])
>>              mean_y = mean(matrix[:,2].flat)
>>              stddev_y = std(matrix[:,2].flat)
>>              subtract(matrix[:,2], mean_y, stdmatrix[:,2])
>>              divide(matrix[:,2], stddev_y, stdmatrix[:,2])
>>              return stdmatrix;
>>
>> When I call it from the main it throws this error:
>>
>>      mean_x = mean(matrix[:,1].flat)
>> NameError: global name 'mean' is not defined
>>
>> I tried to understand which package are you importing as I initially
>> thought that was the common scipy base. Apparently I was able to find
>> a mean() method only inside scipy.stats.stats. However I am not able
>> to import this. Could you please help me to understand how to call
>> this method mean() and std()?
>>
>> I have a bit of confusion in mind between NumPy and SciPy because I
>> could not find information in the documentation for SciPy.
>>
>
> from scipy import *
> mean should then work (it's actually in stats but some of the stats
> stuff is also imported into the scipy namespace)
>

Actually this doesn't help. Trying to catch the problem I realised  
that I only installed the 'scipy_core-0.4.1', which is obviously  
missing some stuff (if I have well understood). So I tried to  
complete my installation with the old NumPy (which installed fine)  
and f2py2e (which returned some conflicts warnings). Then I tried to  
compile and install the last complete scipy: SciPy_complete-0.3.2.

The setup doesn't complete and it exits. I found lots of __init__.py  
files missing:

package init file 'scipy_core/weave/tests/__init__.py' not found (or  
not a regular file)
package init file 'Lib/tests/__init__.py' not found (or not a regular  
file)
package init file '/Users/mauro/Desktop/python/extra modules/ 
SciPy_complete-0.3.2/Lib/cluster/tests/__init__.py' not found (or not  
a regular file)

And lots of these conflicts:

gcc: Lib/special/cephes/powi.c
In file included from Lib/special/cephes/mconf_BE.h:190,
                  from Lib/special/cephes/mconf.h:3,
                  from Lib/special/cephes/powi.c:46:
Lib/special/cephes/protos.h:27: warning: conflicting types for built- 
in function 'cexp'
Lib/special/cephes/protos.h:28: warning: conflicting types for built- 
in function 'csin'
Lib/special/cephes/protos.h:29: warning: conflicting types for built- 
in function 'ccos'
Lib/special/cephes/protos.h:30: warning: conflicting types for built- 
in function 'ctan'

Finally the install exit this way:

ranlib:@ build/temp.darwin-8.2.0-Power_Macintosh-2.3/libcephes.a
building 'dfftpack' library
compiling Fortran sources
f95(f77) options: '-fixed -O4'
f95(f90) options: '-O4'
f95(fix) options: '-fixed -O4'
creating build/temp.darwin-8.2.0-Power_Macintosh-2.3/Lib/fftpack
creating build/temp.darwin-8.2.0-Power_Macintosh-2.3/Lib/fftpack/ 
dfftpack
compile options: '-c'
f95:f77: Lib/fftpack/dfftpack/dcosqb.f
sh: line 1: f95: command not found
sh: line 1: f95: command not found
error: Command "f95 -fixed -O4 -c -c Lib/fftpack/dfftpack/dcosqb.f -o  
build/temp.darwin-8.2.0-Power_Macintosh-2.3/Lib/fftpack/dfftpack/ 
dcosqb.o" failed with exit status 127
craftmac2:/Users/mauro/Desktop/python/extra modules/ 
SciPy_complete-0.3.2 root#

I have to add that I am running this from a Macintosh running OS X  
10.4.2.
Can anybody suggest something else to try?

Thanks


Mauro


--
web: http://craft.epfl.ch -- blog: http://www.i-cherubini.it/mauro/blog/



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