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Integrated quantum photonic circuits are becoming increasingly complex. Accurate calibration of device parameters and detailed characterization of the prepared quantum states are critically important for future progress. Here we report on an effective experimental calibration method based on Bayesian updating and Markov chain Monte Carlo integration. We use this calibration technique to characterize a two qubit chip and extract the reflectivities of its directional couplers. An average quantum state tomography fidelity of 93.79 +/- 1.05% against the four Bell states is achieved. Furthermore, comparing the measured density matrices against a model using the non-ideal device parameters derived from the calibration we achieve an average fidelity of 97.57 +/- 0.96%. This pinpoints non-ideality of chip parameters as a major factor in the decrease of Bell state fidelity. We also perform quantum state tomography for Bell states while continuously varying photon distinguishability and find excellent agreement with theory.