What about restricting Animations to not apply their "animation" (rotation, translation etc..) if their referencing bone is manually controlled?
This would make dynamic / procedural animation a lot easier as you could switch back to canned animation all the time (I need to destroy alle animation tracks for a bone i wish to control manually).
Another point: What about having a weight factor, just as for the animations, for the manual controlled values, so you can easily mix-in some dynamic movement?
I'm going to implement this for our project as we do need some dynamic motions on top of our motion-captured animations, so i'm happy to provide a patch for the Eihort version if it's requested.
Don't let animation tracks modify manual controlled bones
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oiking
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http://www.ogre3d.org/phpBB2/viewtopic.php?t=39510
Not quite sure what the status is on the patch, but I've used it before to much success
(to take manual control of a character's arm while holding a weapon, and give it back to animation when dropped)
Not quite sure what the status is on the patch, but I've used it before to much success
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