In this work a self-configuration system and the frequency characterization for a fully integrated CMOS photodetector sensor is presented. The sensor is composed of pixels with programmable switches that allow each pixel to connect with its neighbors; in this way, an arbitrary detection pattern can be synthesized on it. The design was aimed to be part of an optical encoder based on a non-diffractive light beam, therefore, the purpose of the self-configuration routine is to find the center of the incident non-diffractive beam and then configure the detection pattern around it. The corresponding algorithm is implemented on a Zynq-7000 SoC allowing to automate the alignment of the beam with the detection pattern, without using micrometric positioning procedures. The frequency response of the analog front-end of the entire chip (the pixels and the amplification system) is addressed via SPICE simulations and experimental data, and is consistent with the classical mathematical models, allowing us to propose future improvements to the design.