Ray, just a point on testing technique - I think there are two ways of handling the sharpening issue: (1) don't do any so you see only and exactly what the combination of lens settings and sensor is telling you - i.e. the "intrinsic, raw quality", or (2) sharpen the way you would for a "real world" print and see what that tells you, because in the "real world" this is what you would do to achieve the image you will sell/live with. I think both of them have their place, because they each answer a different question; therefore it is good to do it each way. Needless to say - when you get back to your studio - I'm impressed by how you are managing to do what you've already been doing from a laptop on a mountainside and posting it all here.
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Mark makes a good point, which is amplified on by Norman Koren (author of Imatest). If you are using the same camera to measure lens performance, you should not use any sharpening. However, if you are comparing different cameras you have to use sharpening. Otherwise, the camera with the strongest blur filter will be at a disadvantage.
Here is an Imatest plot I made with the D200 and the 50 mm f/1.8 lens at f/5.6 I used autofocus and there may be some focusing error since the maximal MTF is not quite as good as one would expect. The plot shows MTF with and without sharpening. Without sharpening, the MTF falls rapidly with increasing frequency, but with sharpening, the MTF at lower frequencies is improved. At the highest frequencies, the sharpening makes little difference.
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SQF (subjective quality factor) adds information, since the perceived image quality is affected by relatively low frequencies. For example, [a href=\"http://bobatkins.com/photography/technical/mtf/mtf4.html]Bob Atkins[/url] has calculated that for an 8 by 12 inch print made from a 35mm negative and with normal viewing conditions, the most important MTFs on the film are 4-16 lp/mm. For a 16 by 24 inch print, the corresponding MTFs would be 8-32 lp/mm.
This is an Imatest plot for SQF with the D200 and the same conditions.
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Bill