1. An information processing apparatus comprising; an acquisition unit that acquires a plurality of image sets obtained by different acquisition methods; a generation unit that generates partial image sets by extracting corresponding partial images from respective images of the image. sets; a first assignment unit that assigns the partial image sets generated by said generation unit to a root node of a tree structure; a setting unit that sets, at each node of the tree structure, positions of a plurality of pixels for each partial image set assigned to the node; a determination unit that determines whether any one of the plurality of pixels in a partial image obtained by a predetermined one of the different aquisition methods in each partial image set has an invalid value; a selection unit that selects the predetermined one of the different acquisition methods for the partial image set when none of the plurality of pixels in the partial image obtained, by the predetermined one of the different acquisition methods has the invalid value and selects another one of the diff different acquisition methods for the partial image set when at least one of the plurality of pixels in the partial image obtained by the predetermined one of the different acquisition methods has the invalid value; a second assignment unit that assigns each partial image set assigned to each node to one of lower nodes based on the pixel values of the set positions in the partial images acquired by the acquisition method selected by said selection unit; and an output unit that outputs information about the set assigned to an end node of the tree structure.