An autofocus system is system based on a feedback loop, where the AF sensor error reading if fed back to the lens focus motor. Being a closed loop, then theoretically there should be no focusing errors (at least when lighting is good enough).
So I was wondering, what is the source for this kind of error that requires MFA different for each lens?
The one reason I could think of is that the AF sensor is not perfectly aligned with the image sensor - a thing that will create a constant misfocus. But then, this probably needs to be constant for all lenses.
Whet exactly is being calibrated with MFA? Is is it the AF sensor position, the image sensor, control loop gain, etc.?
Answer
Your assumption about it being a closed loop may be wrong. I see numerous references to AF systems generally being "open loop". In other words the AF system calculates the amount of movement needed to achieve focus then moves the lens there, but does not recheck. So it may over- or undershoot the target. I could not find an authoritative reference from any manufacturer. For what it's worth, here are some posts regarding this issue:
http://arstechnica.com/civis/viewtopic.php?f=6&t=157055
http://forums.dpreview.com/forums/readflat.asp?forum=1029&message=16985680
Assuming it is "open loop" then the AF system consults some sort of table of adjustments based on the inputs it gets, which could vary lens to lens.
Even in a "closed loop" system, there would have to be tolerances. If you want speed you can't constantly adjust back and forth until "perfect", you want to quickly get within a margin of error, and small adjustments may just not feasible with the build quality and tolerances of many, if not all, lenses and AF motors
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