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 ?.

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

Answer 1

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))

• Daniel F: 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: and to set delimiter = ','if you want a proper *.csv
• Daniel F: Fixed a bit of formatting and added delimiter = ',' to your original answer