A method and apparatus are provided to generate tomography images that performs the method. The apparatus and method are configured to determine a basis pattern from modulated phases of incident rays from a spatial light modulator according to a pattern of arranged pixels. The apparatus and method are further configured to perform spatial shift modulation shifting an arrangement of the pixels vertically or horizontally with respect to the basis pattern to obtain shift patterns of the basis pattern. The apparatus and method are configured to generate tomography images for the basis pattern and the shift patterns using spectrum signals of rays obtained from the incident rays passing through the spatial light modulator and entering a subject. The apparatus and method are configured to select a pattern that generates a clearest tomography image of the subject based on the generated tomography images.