The optical path error, the position-independent geometric error, and the form and position tolerance of the substrate will lead to position deviations of the laser focus resulting in the inconsistency of the large area micro-structure and limiting the processing range of the femtosecond laser fabrication platform. To realize continuous defocus compensation along the processing trajectory, an autofocus scheme consisting of an optimized depth from focus (DFF) method based on grid division and the bilinear interpolation algorithm is proposed in this paper. The optimized DFF method includes the Laplace-DWT evaluation function combining the advantages of spatial domain and frequency domain sharpness evaluation function, an adaptive focusing window selection method, and an adaptive step length three-step hill-climbing search method. The optimized DFF method was used to obtain the best focus position of each grid point. Compared with the traditional DFF method, the optimized algorithm has higher focusing precision and avoids the disadvantage of time-consuming focusing. Then, to compensate for interpolating points of the processing trajectory, the bilinear interpolation algorithm was introduced to achieve online focusing during two-photon lithography processing. Finally, the feasibility and effectiveness of the auto-focusing scheme were validated by experiments. Through defocus compensation, the sharpness evaluation value of the focus image on the processing trajectory improved by 90%, which indicated the successful focus of the laser beam on the workpiece surface. Moreover, a high-precision and large-area encoded micro-polarizer array with consistent structure were fabricated successfully. This paper provides a simple way to identify and compensate the defocus errors online with high accuracy and efficiency. The proposed method can improve the machining accuracy and quality of the femtosecond laser direct writing.
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