sampling 2-D numpy array using another array

Question

I have a pretty big numpy matrix (2-D array with more than 1000 * 1000 cells), and another 2-D array of indexes in the following form: [[x1,y1],[x2,y2],...,[xn,yn]], which is also quite large (n > 1000). I want to extract all the cells in the matrix that their (x,y) coordinates appear in the array as efficient as possible, i.e. without loops. If the array was an array of tuples I could just to

cells = matrix[array]

and get what I want, but the array is not in that format, and I couldn't find an efficient way to convert it to the desired form...

matrix[xy[:,0],xy[:,1]]?

Divakar
– Divakar

2017-01-06 10:09:12 +00:00
Commented Jan 6, 2017 at 10:09 — Divakar
– Divakar, Commented Jan 6, 2017 at 10:09
or matrix[tuple(xy.T)] Not sure which is more efficient

Daniel F
– Daniel F

2017-01-06 10:47:47 +00:00
Commented Jan 6, 2017 at 10:47 — Daniel F
– Daniel F, Commented Jan 6, 2017 at 10:47

Daniel F · Accepted Answer · 2017-01-06 10:53:56Z

1

You can make your array into a tuple of arrays like this:

tuple(array.T)

This matches the output style of np.where(), which can be indexed.

cells=matrix[tuple(array.T)]

you can also do standard numpy array slicing and get Divakar's answer in the comments:

cells=matrix[array[:,0],array[:,1]]

answered Jan 6, 2017 at 10:53

Daniel F

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