In [19]: a[yy,xx]
Out[19]: array([ 0,  3,  6,  9, 12, 15, 18])

In [20]: a[yy,xx] = 999

In [21]: a
Out[21]:
array([[999,   1,   2, 999,   4],
       [  5, 999,   7,   8, 999],
       [ 10,  11, 999,  13,  14],
       [999,  16,  17, 999,  19]])

In [22]: a[yy,xx] = -a[yy,xx]

In [23]: a
Out[23]:
array([[-999,    1,    2, -999,    4],
       [   5, -999,    7,    8, -999],
       [  10,   11, -999,   13,   14],
       [-999,   16,   17, -999,   19]])

In [34]: a[ np.where((a>2) & (a<12)) ]
Out[34]: array([ 3,  4,  5,  6,  7,  8,  9, 10, 11])