1. A reference image generation apparatus, comprising: a point spread function estimating section for estimating a function expressing a coherent optical effect and an incoherent optical effect from an observation image and design information; a convolution image generating section for generating a convolution image by convoluting the point spread function relative to the design information; and a reference image generating section for generating a reference image from the convolution image obtained by the convolution image generating section, wherein the function comprises a plurality of point spread functions, where each point spread function in the plurality expresses a coherent optical effect and an incoherent optical effect, and the function estimates variables of the plurality of point spread functions as uncorrelated variables.