How to format in numpy savetxt such that zeros are saved only as “0”

Question

I am saving a numpy sparse array (densed) into a csv. The result is I have a 3GB csv. The problem is 95% of the cells are 0.0000. I used fmt=\'%5.4f\'

Answer 1

It would be much better if you saved only the non-zeros entries in your sparse matrix (m in the example below), you could achieve that doing:

fname = 'row_col_data.txt'
m = m.tocoo()
a = np.vstack((m.row, m.col, m.data)).T
header = '{0}, {1}'.format(*m.shape)
np.savetxt(fname, a, header=header, fmt=('%d', '%d', '%5.4f'))

and the sparse matrix can be recomposed doing:

row, col, data = np.loadtxt(fname, skiprows=1, unpack=True)
shape = map(int, open(fname).next()[1:].split(','))
m = coo_matrix((data, (row, col)), shape=shape)