Focus calibration for “fast” lenses
I have three fast lenses that are causing me focus calibration issues. A Nikkor 85 f/1.4, Sigma 20mm f/1.8, Sigma 50mm f/1.4. Coming across your Focus Shift article, I think has explained the problem I'm seeing, that a different calibration is required at different apertures. However I need some sort of general use choice for the lens. Can you suggest an appropriate aperture to do my lens calibration at for fast glass.
Focus accuracy in general
Inherent focus accuracy is not high in general for fast f/1.4 lenses because contrast is quite low wide open, and it's contrast which helps the autofocus system achieve accurate focus. Pro cameras generally do a better job here, especially under low light, or "flat" lighting.
In general, autofocus accuracy is better thought of as autofocus consistency. A lens/camera combination will generally not focus exactly the same each time; there is a zone of focus, always with some margin of error. The autofocus adjustment on many current DSLRs shifts the focus forward or back in an effort to keep that zone of consistency centered where it should be; one can't expect exactly the same focus each time even so.
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Lens and camera tolerances
Both the lens and camera have tolerances which can work in harmony or at odds with each other; anything but minor focus problems are best handled by sending both the lens(es) and camera(s) in for service. I had exactly this issue with a Canon EF 16-35/2.8L II; it came back focusing very accurately. It's unreasonable, given tolerances, to expect that every camera would focus exactly the same with every lens— that's nirvana and isn't realistic. You must assess and mitigate the reality of your own equipment.
Focus shift and focus consistency
Complicating the situation is focus shift, which is actually no shift at all, but rather an elimination of what I'll term "smeared focus". Wide open, "fast" lenses exhibit uncorrected spherical aberration, which "spreads out" focus over some depth; outer areas of the lens focus differently than inner ones. This effect also varies with focus distance! Thus there is no perfect focus, only a best compromise, one that is also confusing to an autofocus system, as well as the human eye.
In short, when you add focus consistency to focus shift, you must ask yourself for which aperture and distance are key for your work. Focus adjustments thus are a compromise. I advise adjusting focus for your most common working aperture. For all-around work, aperture f/2.8 is a good choice for f/1.2 or f/1.4 lenses.
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DAP coverage of focus shift
My diglloyd's Advanced Photography service has extensive focus shift analysis for a wide variety of lenses, which can be a good starting point for understanding what your lenses are doing.
Focus shift in infrared
If you're shooting in infrared, there is another type of focus issue: "backfocus" caused by the fact that infrared light rays focus much differently than visible light in all but the most superbly corrected optics. This is not focus shift as discussed here, but definitely something to be dealt with. See the diglloyd Guide to Digital Infrared Photography.