NumPy selecting specific column index per row by using a list of indexes

You can do something like this:

In [7]: a = np.array([[1, 2, 3],
   ...: [4, 5, 6],
   ...: [7, 8, 9]])

In [8]: lst = [1, 0, 2]

In [9]: a[np.arange(len(a)), lst]
Out[9]: array([2, 4, 9])

More on indexing multi-dimensional arrays: http://docs.scipy.org/doc/numpy/user/basics.indexing.html#indexing-multi-dimensional-arrays

Recent numpy versions have added a take_along_axis (and put_along_axis) that does this indexing cleanly.

In [101]: a = np.arange(1,10).reshape(3,3)                                                             
In [102]: b = np.array([1,0,2])                                                                        
In [103]: np.take_along_axis(a, b[:,None], axis=1)                                                     
Out[103]: 
array([[2],
       [4],
       [9]])

It operates in the same way as:

In [104]: a[np.arange(3), b]                                                                           
Out[104]: array([2, 4, 9])

but with different axis handling. It's especially aimed at applying the results of argsort and argmax.

If you've got a boolean array you can do direct selection based on that like so:

>>> a = np.array([True, True, True, False, False])
>>> b = np.array([1,2,3,4,5])
>>> b[a]
array([1, 2, 3])

To go along with your initial example you could do the following:

>>> a = np.array([[1,2,3], [4,5,6], [7,8,9]])
>>> b = np.array([[False,True,False],[True,False,False],[False,False,True]])
>>> a[b]
array([2, 4, 9])

You can also add in an arange and do direct selection on that, though depending on how you're generating your boolean array and what your code looks like YMMV.

>>> a = np.array([[1,2,3], [4,5,6], [7,8,9]])
>>> a[np.arange(len(a)), [1,0,2]]
array([2, 4, 9])