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Using a 3D target lets you tune to a precise point in the DOF range. Even if CDAF in LV were perfect it would still drop you at the 70/30 DOF balance or whatever the balance is for that lens and focusing distance, and some people would prefer to tune to 50/50.
I did a little testing using the ML DotTune (faster to run) and saw differences but I didn't spend much time looking into it.
Alright, here is a good riddle and cautionary note for anyone working on tuning their lenses. I have tested all manner of print targets, lighting, and various setups from indoors to outdoors. The photos below are from a simple test I did using my laptop screen as the target. Both are targets I made up in Illustrator really fast, and both, in theory, should work equally as well on dual-cross center point AF sensor in the 5D3.
The problem is that these two targets consistently test at very different tune values (i.e., the AF system reacts very differently in reading them). In the top image (with the cross-hatch grid lines), the calculated tune value works out to be around a -2. In the bottom image (with the checker board), the calculated tune value work out to be around a +8.
I shot manually focused images of both targets (focus is correct in viewing the RAW files) as a control. Then I used the PDAF system to give me focus confirmation while I focused the lens from both sides of center (one shot focusing from near->far, one shot focusing from far->near). Both gave consistent results of the near focus confirmation being slight in front of the target, and the far focus confirmation being slightly behind the target... with the mid-point between the two being perfect focus.
I don't really know what's going on here, or if my camera is "unique," but it seems as though depending on your target choice, how big you print it, and how far away you are... you could get wildly different results. Which could dovetail into the realworld if the AF system does indeed have some sort of front/back bias depending on your subject.
Anyone care to explain?
24mm @ 5': Target 1 (Tests at a -2 tune value)
24mm @ 5': Target 2 (Tests at a +8 tune value)