The UA9 Experiment at CERN-SPS investigates channeling processes in bent silicon crystals with the aim to manipulate hadron beams. Monitoring and characterization of channeled beams in the high energy accelerators environment ideally requires in-vacuum and radiation hard detectors. For this purpose the Cherenkov detector for proton Flux Measurement (CpFM) was designed and developed. It is based on thin fused silica bars in the beam pipe vacuum which intercept charged particles and generate Cherenkov light. The first version of the CpFM is installed since 2015 in the crystal-assisted collimation setup of the UA9 experiment. In this paper the procedures to make the detector operational and fully integrated in the UA9 setup are described. The most important standard operations of the detector are presented. They have been used to commission and characterize the detector, providing moreover the measurement of the integrated channeled beam profile and several functionality tests as the determination of the crystal bending angle. The calibration has been performed with Lead (Pb) and Xenon (Xe) beams and the results are applied to the flux measurement discussed here in detail.
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