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Re: Hyperfocal Distance
Stacking, as well as HDR merging, is a merging process, and merging does not work well when the subject has changed between the images. It may result in black "holes" or other artifacts, where image elements are in different phases of movement. Also foliage moving in the wind may suffer from such artifacts, although they might not be as visible as "black holes" in the water.
However, for a subject as the rock in the water, one might merge manually, covering the unsharp image of the rock with the sharp image, without affecting other parts of the scene.
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Re: Hyperfocal Distance
If one uses a programme manually it becomes the person's choice rather than the machine's. I have filled 'holes' in panoramas from time to time, a neccessary task when one makes them hand holding, and a choice made at the time of shooting ... but you have to like editing to happilly accept the result of your choice :)
The advantage of working manually when one has generous overlap between frames is that one can then choose which version of reality or time one uses ... the machine seems to fudge the issue and mixes or dissolves to use a motion picture term. so I would expect PS CC to do much the same as any other programme ... I only use a stitch programme for a quick and maybe nasty job, or if there are no alternative choices to be made, static subjects etc ... but freely admit my programmes are early versions. I gather PTgui is very good but yet to meet it :)
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Re: Hyperfocal Distance
To the question of using HD or stacking I was attracted to these vats, I believe being made for a brewery or suchlike, and 'simply' took three frames so transfering the brainwork to the editing stage ... I expect a pixel peeper will find faults but I'm happy enough in the result of my efforts. I remember that I found little difference between two of the frames and could have simply used two shots ... but three tanks, three shots :)
......... http://i62.tinypic.com/532xh.jpg
Using AF with a small spot target area for each frame [ Panasonic FZ50 ]
Edit 2# In going to camera file to work out which camera I used I noticed that in the final I have removed a large sign on the building as one of my 'editing choices' :)