I have an irregular (non-rectangular) lon/lat grid and a bunch of points in lon/lat coordinates, which should correspond to points on the grid (though they might be slightly off for numerical reasons). Now I need the indices of the corresponding lon/lat points.

I have written a function which does this, but it is REALLY slow.

def find_indices(lon,lat,x,y):lonlat = np.dstack([lon,lat])delta = np.abs(lonlat-[x,y])ij_1d = np.linalg.norm(delta,axis=2).argmin()i,j = np.unravel_index(ij_1d,lon.shape)return i,jind = [find_indices(lon,lat,p*) for p in points]

I'm pretty sure there's a better (and faster) solution in numpy/scipy. I've already googled quite a lot, but the answer has so far eluded me.

Any suggestions on how to efficiently find the indices of the corresponding (nearest) points?

PS: This question emerged from another one).

If the points are sufficiently localized, you may try directly scipy.spatial's cKDTree implementation, as discussed by myself in another post. That post was about interpolation but you can ignore that and just use the query part.

tl;dr version:

Read up the documentation of scipy.sptial.cKDTree. Create the tree by passing an (n, m)-shaped numpy ndarray object to the initializer, and the tree will be created from the n m-dimensional coordinates.

tree = scipy.spatial.cKDTree(array_of_coordinates)

After that, use tree.query() to retrieve the k-th nearest neighbor (possibly with approximation and parallelization, see docs), or use tree.query_ball_point() to find all neighbors within given distance tolerance.

If the points are not well localized, and the spherical curvature / non-trivial topology kicks in, you can try breaking the manifold into multiple parts, each small enough to be considered local.