python save numpy array with only non-zero elements

Question

I have an array with most of the elements are zero.

A =  [ 1,0,2
       2,3,0
       0,0,4 ]

I want to save this as

rowid[0] colid[0] 1
rowid[0] colid[2] 2
rowid[1] colid[0] 2
rowid[1] colid[1] 3
rowid[2] colid[2] 4

here rowid and colid are arrays which maps the array indices to the actual entries in an original file.

How can I do this without using a for loop ?.

There is a scipy.sparse package that handles matrices like this. — hpaulj
– hpaulj, Commented Sep 13, 2018 at 6:33
@hpaulj, i am looking for a way to write such an array in a plaintext file in the specified format — Shew
– Shew, Commented Sep 13, 2018 at 6:38
Should be easy iterating through argwhere.with your own line formatting. — hpaulj
– hpaulj, Commented Sep 13, 2018 at 6:53
Do you want your output to literally have the string "rowid[0]" etc. ? — Daniel F
– Daniel F, Commented Sep 13, 2018 at 7:11
Come to think of it, savetxt could be used a fancier format such as fmt='row[%d] col[%d] %d' — hpaulj
– hpaulj, Commented Sep 15, 2018 at 0:06

Daniel F · Accepted Answer · 2018-09-13 07:06:46Z

3

A = np.array(A).reshape(3, 3) # make A a 3x3 numpy array 
i, j = np.where(A != 0) # find indices where it is nonzero 
v = A[i, j] # extract nonzero values of the array 
np.savetxt('file.csv', np.vstack((i, j, v)).T, delimiter = ',') # stack and save 

# @Daniel F suggestion is to make header with array shape and add delimiter kwarg
np.savetxt('file.csv', np.vstack((i, j, v)).T, delimiter = ',', header = str(A.shape))

edited Sep 13, 2018 at 7:06

Daniel F

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answered Sep 13, 2018 at 6:54

kevinkayaks

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3 Comments

Daniel F Over a year ago

Probably want a header value in savetxt to store the original shape of the array, so it can be rebuilt correctly if it is very sparse.

Daniel F Over a year ago

and to set delimiter = ','if you want a proper *.csv

Daniel F Over a year ago

Fixed a bit of formatting and added delimiter = ',' to your original answer

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