1. An array camera system, comprising: an array camera comprising a plurality of cameras that capture images of a scene from different viewpoints; a separate camera having a fixed geometric relationship with array camera and each of the plurality of cameras in the array camera, where the separate camera captures an image of the scene from a different viewpoint to the viewpoints of the cameras in the array camera; a processor; and memory in communication with the processor storing software; wherein the software directs the processor to: obtain a focus window based upon image data from the separate camera, determine a focus window for the array camera based upon the focus window from the separate camera, obtain image data pertaining to the focus window of the array camera module from at least two cameras in the plurality of cameras, determine depth information for the focus window of the array camera from the image data from the at least two cameras, colocate the depth information from the focus window of the array camera to the focus window of the separate camera to generate depth information for the focus window of the separate camera, and determine a focus depth for the separate camera based upon the depth information for the focus window of the separate camera.