a = np.array([[  3,   0,   2,  -1],
              [  1, 255,   1,   2],
              [  0,   3,   2,   2]])

d = {0: 1, 1: 2, 2: 3, 3:4, -1: 0, 255: 0}

>>> a.astype(np.uint8) + 1
array([[4, 1, 3, 0],
       [2, 0, 2, 3],
       [1, 4, 3, 3]], dtype=uint8)