From the American Cinematographer article on Star Trek:
"Much of the lighting built into the interior was designed to cause lens flares... "The Enterprise has lights set in the frame that basically point down the lens of the camera in every direction," says Mindel. "Whenever you look, you get a flare. It goes against everything one learns as a camera technician, which is to shield the lens from any extraneous light and stop it from flaring. We'll either get slaughtered by our peers or be really admired for it!" ... If the built-in lighting wasn't providing the desired flare, the crew aimed Xenon flashlights at the lenses as the cameras rolled. "Our A and B camera operators... would tell us if we needed to go a little farther in or out of the frame, or up or down, to get the ultimate flare... it was funny to watch, Dan and I were running around, ducking, jumping, and hiding behind things so we wouldn't be seen by the cameras. The flashlights were so bright that there are probably several instances where Dan's actually in the movie, but you can't really tell!"
Doesn't sound like the net result was that a lens flare only occurred in 2% of the footage despite all that effort and they had to add them to 98% of the footage.
I've shot four movies on Panavision anamorphics, it's not that hard to get a lens to flare... here are two frames from "Akeelah and the Bee":
Zombie thread getting new life?
But yeah, as people have mentioned - flares were mostly practical in the first movie. Second movie is being shot on film/anamorphic again - with much of it on IMAX a la Dark Knight Rises and Ghost Protocol. It is slated to be post-converted to 3D, but was a studio decision, and not JJ's idea (hence not being shot digitally in 3D). There's a couple of articles floating around...I'll have to try and find them.
I was really hoping for my two loves (Star Trek and RED) to come together on the big screen - but not this time, I guess.
yet all the effects shots which was most of the movie, they were added in afterwards. Except for possibally the Enterprises bridge set to which the article talks about.
I watched it again on blue ray as little as a week ago. You'll be amazed how many flares there are even without any point source of light.
One of my favorite films by the way.
Shots that are "all CG" have had "distressing" elements added to them for years in order to make them seem a bit more realistic, and have imperfections that are endemic to live production. That's not news. One of the main sets in the Star Trek movie was the bridge set, which had windows that were composited later and screens that were either composited or replaced. All of those shots were likely done with the same flare treatment done for the rest of the bridge material, and although this makes the compositing quite a bit more difficult, it also allows for more naturalistic photography. I haven't talked to anyone directly involved, but my guess is that some of these shots were done twice, once for a flare reference and once clean, but as we both know, shots done for reference often have a way of becoming final plates if the performance works. So my feeling is that while some shots might have been intentionally shot without practical flares, it was hardly all of them and in fact might have been very few of them if they were on practical sets (i.e., not "full greenscreen" shots).
I believe the new picture has already wrapped principle photography (much of it was shot down the street from me, at the Hughes Hangar in Playa Vista, CA.), so if I run into someone who was involved, I'll ask some questions.
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