RuntimeWarning: divide by zero encountered in log

numpy.log10(prob) calculates the base 10 logarithm for all elements of prob, even the ones that aren't selected by the where. If you want, you can fill the zeros of prob with 10**-10 or some dummy value before taking the logarithm to get rid of the problem. (Make sure you don't compute prob > 0.0000000001 with dummy values, though.)

You can turn it off with seterr

numpy.seterr(divide = 'ignore') 

and back on with

numpy.seterr(divide = 'warn') 

Just use the where argument in np.log10

import numpy as np
np.random.seed(0)

prob = np.random.randint(5, size=4) /4
print(prob)

result = np.where(prob > 0.0000000001, prob, -10)
# print(result)
np.log10(result, out=result, where=result > 0)
print(result)

Output

[1.   0.   0.75 0.75]
[  0.         -10.          -0.12493874  -0.12493874]

I solved this by finding the lowest non-zero number in the array and replacing all zeroes by a number lower than the lowest :p

Resulting in a code that would look like:

def replaceZeroes(data):
  min_nonzero = np.min(data[np.nonzero(data)])
  data[data == 0] = min_nonzero
  return data

 ...

prob = replaceZeroes(prob)
result = numpy.where(prob > 0.0000000001, numpy.log10(prob), -10)

Note that all numbers get a tiny fraction added to them.