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The electron density map of a block copolymer thin film having the hexagonally perforated layer (HPL) structure was directly obtained from the measured grazing-incidence small-angle X-ray scattering (GISAXS) pattern, exploiting the multiple-scattering phenomena present in GISAXS. It is shown that GISAXS is in principle equivalent to three-beam diffraction, which has been used to extract phases of diffraction peaks. In addition, X-ray reflectivity analysis has been performed which, when combined with the GISAXS results, provides full details of the HPL structure.