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As you experiment with retargeting, you'll quickly find that there are several common cases that the fake-and-bake technique doesn't cover.
One common problem is that the animator needs to decide which bones need to mimic the position of their opposite numbers in the old file, and which ones only need rotations. Positional matches are only needed by character roots or IK targets. Most other bones can be retargeted using just rotations.
You'll need to hone reliable, automatic ways of knowing when to use positional retargets and when not to. You don't want to doom some poor animator to opening hundreds of animations just to select a particular bone and press the "retarget my positions" button by hand.
Another important issue is pose matching. To get good results, you need to get the new skeleton into the right start pose before constraining it to retargeting dummies. Without matching the pose, you can't leverage the power of the constraint offsets. Again, the key is to find reliable ways to automate that.
Once you're comfortable with the basics, you can start expanding your repertoire to handle more puzzling situations. For example, once you have a basic set of retargeting scripts, you can extend them to handle trickier situations.
You could apply a global scale by grouping all your retargeting dummies together and scaling them up or down. You could reorient animations by grouping and rotating retargeting dummies. One of the nice things about the dummies is that they are not hierarchical, so your adjustments are applied in a comprehensible way.
If this sounds pretty easy, it is -- up to a point. Building your own retargeting system, especially if you have no mocap experts in-house, is an important investment in protecting your data and keeping your animators from endless do-overs.
It's important to be realistic, though. Few studios have the technical art chops (or the unscheduled time) to put together a truly bulletproof retargeting system. A successful retarget can involve a serious amount of trial and error. In most cases, there is no truly right way to move motion between skeletons with more than trivial differences, and so you'll have to rely on the instincts of your retargeting specialist and a lot of very tweaky, case-by-case scripts.
Once animators get over the novelty of your retargeting tools, they'll be less grateful for their saved work than resentful of all those dense mo-cap-like keys (it's not fair, but it is human nature). And soon they'll start demanding the ability to retarget between animation rigs as well as skeletons, a vastly trickier proposition.
If you set out to design the perfect system that will survive all skeletal changes without human intervention, you are going to be very frustrated. If, on the other hand, you can cheerfully stick to a glass-half-full outlook, you can get a lot of value from the simple tricks outlined here.
The key is never to forget the terrible curse that is placed on those who trifle with skeletons! Those undead hordes may never be truly laid to rest, but they can certainly be forced back into the shadows where they belong, as long as you are bold enough to grasp the weapons at your disposal.
[EDITOR'S NOTE: This article was independently published by Gamasutra's editors, since it was deemed of value to the community. Its publishing has been made possible by Intel, as a platform and vendor-agnostic part of Intel's Visual Computing microsite.]