  Quantum process tomography is a necessary tool for verifying quantum gates
and diagnosing faults in architectures and gate design. We show that the
standard approach of process tomography is grossly inaccurate in the case where
the states and measurement operators used to interrogate the system are
generated by gates that have some systematic error, a situation all but
unavoidable in any practical setting. These errors in tomography can not be
fully corrected through oversampling or by performing a larger set of
experiments. We present an alternative method for tomography to reconstruct an
entire library of gates in a self-consistent manner. The essential ingredient
is to define a likelihood function that assumes nothing about the gates used
for preparation and measurement. In order to make the resulting optimization
tractable we linearize about the target, a reasonable approximation when
benchmarking a quantum computer as opposed to probing a black-box function.
