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Since np.where turns out to be so slow (#311), it would be good to remove it where it is not needed.
.gaul files are identical, but currently the test will fail due to #314.
The function numpy.where() is also used in several other places, a quick grep reveals. I didn't look if some of these calls can also be removed safely, but it might be worth a check. If so, I have no objection if you extend this MR to cover the removal of all unnecessary calls to numpy.where().
Generally, np.where is redundant for boolean masking, checking element existence, or counting matching elements. Instead, directly use boolean indexing (arr[mask]), np.any(), or np.count_nonzero(). This avoids unnecessary memory overhead and improves speed.
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Since
np.whereturns out to be so slow (#311), it would be good to remove it where it is not needed..gaul files are identical, but currently the test will fail due to #314.