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pythonnumpysumindices

Cumulative summation of a numpy array by index


Assume you have an array of values that will need to be summed together

d = [1,1,1,1,1]

and a second array specifying which elements need to be summed together

i = [0,0,1,2,2]

The result will be stored in a new array of size max(i)+1. So for example i=[0,0,0,0,0] would be equivalent to summing all the elements of d and storing the result at position 0 of a new array of size 1.

I tried to implement this using

c = zeros(max(i)+1)
c[i] += d

However, the += operation adds each element only once, thus giving the unexpected result of

[1,1,1]

instead of

[2,1,2]

How would one correctly implement this kind of summation?


Solution

  • This solution should be more efficient for large arrays (it iterates over the possible index values instead of the individual entries of i):

    import numpy as np
    
    i = np.array([0,0,1,2,2])
    d = np.array([0,1,2,3,4])
    
    i_max = i.max()
    c = np.empty(i_max+1)
    for j in range(i_max+1):
        c[j] = d[i==j].sum()
    
    print c
    [1. 2. 7.]