Numpy savetxt Structured Array ValueError: fmt has wrong number of % formats

Question

import numpy as np

row_a = ['0.01722497', '', '0.09496404', '0.03654174', '0.03624997', '0.01583785', '0.02002064', '0.13934049', '0.0405615', '0.05686177', '', '0.08495372', '0.00619173', '0.00515492', '0.01053369', '0.06576333']
row_b = [0.04871661, 0.1122536, 0.20836956, 0.05473605, 0.02344445, 0.01739371, 0.00524003, 0.0640286, 0.02766152, 0.02442267, 0.04183814, 0.04853815, 0.01682549, 0.00263045, 0.00819199, 0.1631007]
dt = np.dtype([('col_1', 'U32'), ('col_2', float)])
arr = np.empty((2, len(row_a)), dtype=dt)
arr['col_1'] = row_a
arr['col_2'] = row_b
np.savetxt('table.csv', arr, delimiter=',', header='col_1,col_2', fmt='%s %f')

Code above (which is supposed to create a structured array out of an str and int array and output it to a csv) gives me the following error, even though I have 2 arrays of same length, 2 columns and 2 formats:

ValueError: fmt has wrong number of % formats:  %s %f

Read this: https://stackoverflow.com/questions/42938436/how-to-use-numpy-savetxt-with-a-structured-array-that-contains-an-array and this: https://stackoverflow.com/questions/51027447/save-structured-numpy-array-using-np-savetxt-with-header — John Zwinck, Apr 04 '21 at 02:56
Check `arr`. I think its shape should be `len(rowa)`, not 2d — hpaulj, Apr 04 '21 at 03:54
I had read both those questions through before posting mine. I wouldn't have posted it if they had answered it. @hpaulj that works! Many thanks. — gargoylebident, Apr 04 '21 at 04:37

score 1 · Accepted Answer · answered Apr 04 '21 at 04:58

Making a 1d structured array (as per my comment):

In [423]: row_a = ['0.01722497', '', '0.09496404', '0.03654174', '0.03624997', '0.01583785', '0
     ...: .02002064', '0.13934049', '0.0405615', '0.05686177', '', '0.08495372', '0.00619173',
     ...: '0.00515492', '0.01053369', '0.06576333']
     ...: row_b = [0.04871661, 0.1122536, 0.20836956, 0.05473605, 0.02344445, 0.01739371, 0.005
     ...: 24003, 0.0640286, 0.02766152, 0.02442267, 0.04183814, 0.04853815, 0.01682549, 0.00263
     ...: 045, 0.00819199, 0.1631007]
     ...: dt = np.dtype([('col_1', 'U32'), ('col_2', float)])
     ...: arr = np.empty(len(row_a), dtype=dt)
     ...: arr['col_1'] = row_a
     ...: arr['col_2'] = row_b
In [424]: 
In [424]: arr
Out[424]: 
array([('0.01722497', 0.04871661), ('', 0.1122536 ),
       ('0.09496404', 0.20836956), ('0.03654174', 0.05473605),
       ('0.03624997', 0.02344445), ('0.01583785', 0.01739371),
       ('0.02002064', 0.00524003), ('0.13934049', 0.0640286 ),
       ('0.0405615', 0.02766152), ('0.05686177', 0.02442267),
       ('', 0.04183814), ('0.08495372', 0.04853815),
       ('0.00619173', 0.01682549), ('0.00515492', 0.00263045),
       ('0.01053369', 0.00819199), ('0.06576333', 0.1631007 )],
      dtype=[('col_1', '<U32'), ('col_2', '<f8')])
In [425]: arr.shape
Out[425]: (16,)

And the save:

In [426]: np.savetxt('table.csv', arr, delimiter=',', header='col_1,col_2', fmt='%s %f')
In [427]: cat table.csv
# col_1,col_2
0.01722497 0.048717
 0.112254
0.09496404 0.208370
0.03654174 0.054736
...

The linked SO that I answered before had a more complex dtype. This is a simple 2 field case, so doesn't need special handling.

The """ values might give problems when file loading. I'd suggest at least using delimiter like ,, so the loader can treat it as missing value.

In [428]: np.savetxt('table.csv', arr, delimiter=',', header='col_1,col_2', fmt='%s, %f')
In [429]: cat table.csv
# col_1,col_2
0.01722497, 0.048717
, 0.112254
0.09496404, 0.208370
0.03654174, 0.054736
...
In [430]: np.genfromtxt('table.csv', dtype=None, names=True, delimiter=',')
Out[430]: 
array([(0.01722497, 0.048717), (       nan, 0.112254),
       (0.09496404, 0.20837 ), (0.03654174, 0.054736),
       (0.03624997, 0.023444), (0.01583785, 0.017394),

In [431]: np.genfromtxt('table.csv', dtype=arr.dtype, names=True, delimiter=',')
Out[431]: 
array([('0.01722497', 0.048717), ('', 0.112254), ('0.09496404', 0.20837 ),
       ('0.03654174', 0.054736), ('0.03624997', 0.023444),
       ('0.01583785', 0.017394), ('0.02002064', 0.00524 ),

Numpy savetxt Structured Array ValueError: fmt has wrong number of % formats

1 Answers1