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Abstract Disorder is an essential parameter in photonic systems and devices, influencing phenomena such as the robustness of topological photonic states and the Anderson localization of modes in waveguides. We develop and demonstrate a method for both analyzing and visualizing positional, size, and shape disorder in periodic structures such as photonic crystals. This analysis method shows selectivity for disorder type and sensitivity to disorder down to less than 1%. We show that the method can be applied to more complex shapes such as those used in topological photonics. The method provides a powerful tool for process development and quality control, including analyzing the precision of E-Beam Lithography before patterns are transferred; quantifying the precision limits of lithography, deposition, or etch processes; and studying the intentional displacement of individual objects within otherwise periodic arrays.