Until SMPTE actually sets the stereo standard, you're going to get answers and recommendations all over the road. For example; I can freeview both parallel and cross-eyed, and I prefer to format side-by-side content (when needed) as L|R for logical reasons. I think the left video should be on the left side of the screen, it's easy to remember when this is the case.
Playback devices, for the most part, have the ability to "swap eyes" so you can actually encode however you wish and if there is a problem swap eyes. This is not ideal of course, we should be able to encode to a standard and it should just work across any type of viewing technology. Until SMPTE actually sets the spec, we're left in this gray area.
Seconding an earlier post, when possible encode the full frames and don't mess with anamorphic squeezing, you're already losing resolution on most displays (checkerboard DLP and Xpol being the most prevalent). Use the WMV video layers capability and free utility from Peter Wimmer at
http://www.3dtv.at/. This should reasonably future proof you and retain the highest quality. The 3D BluRay proposed spec is double frame rate interleaved: L|R|L|R|L|R|L|R|L|R|L|R.
For some reason the YouTube engineer working on the YouTube 3D player chose to have the native layout as R|L and we're stuck with this de-facto standard for the time being. I encode L|R and use the yt3d:swap=true flag for the time being. By the way, how can we post a YouTube link without the embedded player function? The embedded player does now show the YT3D viewing options.
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If anyone from SMPTE is reading these fora, please set the spec sooner rather than later. Thanks!
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Chris Eller
* Advanced Visualization Lab - Indiana University
* Chris Eller Photography, LLC
* Starrynight Productions, Inc.