Hi Bert,
actually, my "first" thought solves this problem. If you turn all your points into an xray_structure, and get the asu_mappings, this gives you the coordinates of the equivalent site in the asu (returned by the "mapped_site" method). However, it won't make a list of equivalent sites unique, i.e. if you have site1 = ( 0.1, 0.1, 0.1 ) and site2 = ( 1.1, 0.1, 0.1 ) (in fractional coordinates), you get a mapping for the same site twice, so perhaps the most efficient method is just to transform your scalar field into the unit cell, and then discard points that are outside the asu. If the grid is not congruent with the unit cell, you are probably better off using asu_mappings, since you will be able to interpolate on a finer grid.
BW, Gabor