numpy array of objects

You can vectorize the class’s __init__ function:

import numpy as np

class Site:
    def __init__(self, a):
        self.a = a
    def set_a(self, new_a):
        self.a = new_a

vSite = np.vectorize(Site)

init_arry = np.arange(9).reshape((3,3))

lattice = np.empty((3,3), dtype=object)
lattice[:,:] = vSite(init_arry)

This may look cleaner but has no performance advantage over your looping solution. The list comprehension answers create an intermediate python list which would cause a performance hit.