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@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
Cath, The simple answer to your question is to use MA.set_print_limit(0) to change the behavior of str and repr back to the standard Numeric behavior of always printing the entire array. Then you will get the whole array, with the masked values as '--'. Reggie
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@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
------------------------------------------------------- This sf.net email is sponsored by:ThinkGeek Welcome to geek heaven. http://thinkgeek.com/sf _______________________________________________ Numpy-discussion mailing list Numpy-discussion@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/numpy-discussion
participants (2)
-
Cath Lawrence -
Reggie Dugard