The role of preparation in quantum process tomography

In a recent letter one of us pointed out how differences in preparation procedures for quantum experiments can lead to non-trivial differences in the results of the experiment. The difference arise from the initial correlations between the system and environment. Therefore, any quantum experiment that is prone to the influences from the environment must be prepared carefully. In this paper, we study quantum process tomography in light of this. We suggest several experimental setups, where preparation of initial state plays a role on the final outcome of the experiment. We show that by studying the linearity and the positivity of the resulting maps the experimenter can determine the nature of the initial correlations between the system and the environment.