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The square size is in whatever units you want to use. A good choice might be cm. Measuring accurately will allow you to make use of your calibration data by allowing you to determine the absolute coordinates of points and objects in such methods as Block Matching, Semi-Global Block Matching, and solvePnP. Also, understand that you need not recompute the distortion coefficients at different image sizes, but that you MUST scale your f_x, f_y, c_x, and c_y to the size of the image in question if it is different from the calibration image size. Some contend that it is good practice to obtain your calibration coefficients at various image sizes and appropriately average/combine the results.
