[Numpy-discussion] numpy.mean problems

[ferreirafm]

Aronne Merrelli wrote:
> 
> I can recreate this error if tab is a structured ndarray - what is the
> dtype of tab?
> 
> If that is correct, I think you could fix this by simplifying things.
> Since
> tab is already an ndarray, you should not need to convert it back into a
> python list. By converting the ndarray back to a list you are making an
> extra level of "wrapping" as a python object, which is ultimately why you
> get that error about adding numpy.void.
> 
> Unfortunately you cannot take directly take a mean of a struct dtype;
> structs are generic so they could have fields with strings, or objects,
> etc, that would be invalid for a mean calculation. However the following
> code fragment should work pretty efficiently. It will make a 1-element
> array of the same dtype as tab, and then populate it with the mean value
> of
> all elements where the length is >= 15. Note that dtype.fields.keys()
> gives
> you a nice way to iterate over the fields in the struct dtype:
> 
> length_mask = tab['length'] >= 15
> tab_means = np.zeros(1, dtype=tab.dtype)
> for k in tab.dtype.fields.keys():
>     tab_means[k] = np.mean( tab[k][mask] )
> 
> In general this would not work if tab has a field that is not a simple
> numeric type, such as a str, object, ... But it looks like your arrays are
> all numeric from your example above.
> 
> Hope that helps,
> Aronne
> 
HI Aronne,
Thanks for your replay. Indeed, tab is a mix of different column types:
tab.dtype:
[('sgi', '<i8'), ('length', '<i8'), ('nident', '<i8'), ('pident', '<f8'),
('positive', '<i8'), ('ppos', '<f8'), ('mismatch', '<i8'), ('qstart',
'<i8'), ('qend', '<i8'), ('sstart', '<i8'), ('send', '<i8'), ('gapopen',
'<i8'), ('gaps', '<i8'), ('evalue', '<f8'), ('bitscore', '<f8'), ('score',
'<f8')]
 Interestingly, I couldn't be able to import some columns of digits as
strings like as with R dataframe objects. 
I'll try to adapt your example to my needs and let you know the results.
Regards.
   
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