On Sun, Feb 2, 2014 at 2:58 PM, Mads Ipsen <mads.ipsen@gmail.com> wrote:

Since atoms [1,2,3,7,8] have been
deleted, the remaining atoms with indices larger than the deleted atoms
must be decremented.

Let

>>> x

array([[ 0, 1, 2, 3],

[ 4, 5, 6, 7],

[ 8, 9, 10, 11]])

and

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

Create a shape of x matrix with 1's at (k, i[k]) and zeros elsewhere

>>> b = zeros_like(x)

>>> b.put(i + arange(3)*4 + 1, 1) # there must be a simpler way

>>> x - b.cumsum(1)

array([[ 0, 1, 1, 2],

[ 4, 4, 5, 6],

[ 8, 9, 10, 10]])

seems to be the result you want.