1. An imaging device, comprising: an image sensor that includes a plurality of pixel units disposed in a two-dimensional array, each equipped with a plurality of imaging pixels with varying spectral sensitivity characteristics set regularly, and focus detection pixels with sensitivity over a range encompassing the spectral sensitivity of the pixel units, which are set in the array of the pixel units; and an estimating circuit that determines an image output structure corresponding to the position of each focus detection pixel based upon outputs from the imaging pixels present around the focus detection pixel and estimates an image output at the focus detection pixel based upon the image output structure and an output from the focus detection pixel.