Interpolate values at 3D coordinates
Assuming your data is on a regular grid the xs, ys, and zs need to be unique. Try something like -
xs, ind = np.unique(xs, return_index=True)
xs = xs[np.argsort(ind)]
As an alternative, you can use the interpolators on unstructured data - https://docs.scipy.org/doc/scipy/reference/interpolate.html#multivariate-interpolation.