[Numpy-discussion] Newbie MA question

Cath Lawrence Cath.Lawrence at anu.edu.au
Wed Aug 7 20:18:01 CDT 2002


Hi,

I'm not sure this is the right list - looking at the archives you guys 
look more like developers more than users.

Any pointers to the proper place, or TFMs to R, are welcome. (Yes, I 
have & have read the Numerical Python documentation.)

That said, I'm trying to use masked arrays (for a bioinformatics app 
calculating stats on distances between pairs of amino acids, if you want 
to know) and am having a little trouble printing.

One possible bug - "x.__str__()" and "x.__repr__()" show different 
typecodes.
Example:
 >>> import MA
 >>> id = MA.identity(20)
 >>> r  = MA.ones((20,20))*1.0
 >>> rm = MA.MaskedArray(r, mask=id)
 >>> rm		       # ie, call x.__repr__()
array(data =
  array (20,20) , type = d, has 400 elements,
       mask =
  array (20,20) , type = 1, has 400 elements,
       fill_value=[  1.00000002e+20,])

 >>> print rm         # ie, call x.__str__()
array (20,20) , type = O, has 400 elements
 >>>

Secondly, I can't see how to make this print the whole thing if I want 
it. Which I do; all my matrices are 20*20 'cause there are 20 amino 
acids.

The Numeric.array2string method can't be used because the data is always 
masked.
The best I've found so far is to make a Numeric array by filling with an 
impossible number like -1, then use array2string. But visually it would 
be nicer to see the masked values as "--".

Thanks for any help,
regards,
Cath
Cath Lawrence,                       Cath.Lawrence at anu.edu.au
Scientific Programmer,  Centre for Bioinformation Science,
John Curtin School of Medical Research
Australian National University,  Canberra ACT 0200
ph: Maths (02) 6125 2904;  JCSMR (02) 6125 0417;
mobile: 0421-902694   fax: (02) 61254712





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