Hey @DanielAsarnow,
We assume that the focus mask is strictly within the solvent mask, so those regions will be clipped off for the purposes of classification. During the E step of classification, we set each class volume to:
where S is the solvent mask, F is the focus mask, and \bar{V} is the consensus volume. If the focus mask is not provided, we set F = 1, and use S * V_k.
(See: Tutorial: 3D Classification (BETA) - CryoSPARC Guide for more info).
Valentin