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As quantum systems expand in size and complexity, manual qubit characterization and gate optimization will be a non-scalable and time-consuming venture. Physical qubits have to be carefully calibrated because quantum processors are very sensitive to the external environment, with control hardware parameters slowly drifting during operation, affecting gate fidelity. Currently, existing calibration techniques require complex and lengthy measurements to independently control the different parameters of each gate and are unscalable to large quantum systems. Therefore, fully automated protocols with the desired functionalities are required to speed up the calibration process. This paper aims to propose single-qubit calibration of superconducting qubits under continuous weak measurements from a real physical experimental settings point of view. We propose a real-time optimal estimator of qubit states, which utilizes weak measurements and Bayesian optimization to find the optimal control pulses for gate design. Our numerical results demonstrate a significant reduction in the calibration process, obtaining a high gate fidelity. Using the proposed estimator we estimated the qubit state with and without measurement noise and the estimation error between the qubit state and the estimator state is less than 0.02. With this setup, we drive an approximated pi pulse with final fidelity of 0.9928. This shows that our proposed strategy is robust against the presence of measurement and environmental noise and can also be applicable for the calibration of many other quantum computation technologies.