numpy / python - indexing by arrays with duplicates

Question

I'm trying to make a 3D histogram. Initially h = zeros((6,6,8)).
I'll explain my problem with an example. Suppose I have 3 lists of coordinates for h, each list for one dimension:
x = array([2,1,0,1,2,2])
y = array([1,3,0,3,2,1])
z = array([6,2,0,2,5,6]) (the coordinates (x[0],y[0],z[0]) and (x[6],y[6],z[6]) are duplicates, and (x[1],y[1],z[1]) and (x[3],y[3],z[3]) also are)
and also a list of corresponding quantities to accumulate into h:
q = array([1,2,5,9,8,7])

I tried and h[x,y,z] += q does not work because only q[5] = 7 is added to h[2,1,6] and q[0] = 1 is not.

How can I work around this? Thank you.

DSM · Accepted Answer · 2015-05-02 02:34:53Z

1

IIUC, you want np.add.at. To quote the docs: "For addition ufunc, this method is equivalent to a[indices] += b, except that results are accumulated for elements that are indexed more than once."

For example:

>>> np.add.at(h, [x,y,z], q)
>>> for i, val in np.ndenumerate(h):
...     if val: print(i, val)
...     
((0, 0, 0), 5.0)
((1, 3, 2), 11.0)
((2, 1, 6), 8.0)
((2, 2, 5), 8.0)

answered May 2, 2015 at 2:34

DSM

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