The calorimeter data as stored by the reconstruction program contain the time reported by the digital cards. A time-of-flight correction has been applied to this time online so that the reported time is zero for a particle coming from a collision at the nominal interaction point. This is ideal for the trigger system because it can simply select good events by requiring the average event time to be close to zero.
A traversing muon however is obviously not coming from the nominal interaction point, so in order to allow a measurement of the velocity of the muon the correction is undone.
Whenever calculations involving the time measured in the calorimeter are performed MUFFIN uses the individual photomultiplier time as well as the energy reported by this photomultiplier to calculate an error on the time. For the error calculation it uses the same formula that is used inside the standard offline reconstruction program (see (3.1)).