The manufacture of a photonic crystal always produce deviations from the ideal case. In this paper we present a detailed analysis of the influence of the manufacture errors in the resulting electric field distribution of a photonic crystal microcavity. The electromagnetic field has been obtained from a FDTD algorithm. The results are studied by using the Principal Component Analysis method. This approach quantifies the influence of the error in the preservation of the spatial-temporal structure of electromagnetic modes of the ideal microcavity. The results show that the spatial structure of the excited mode is well preserved within the range of imperfection analyzed in the paper. The deviation from the ideal case has been described and quantitatively estimated.
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