I wrote a blog entry on the Unity site called Automatic Setup of a Humanoid detailing the work I did for the Mecanim animation system in Unity 4 on automatically detecting human bones in arbitrary skeleton rigs.
Names of bones, bone directions, bone length ratios, and bone topology all provide hints to which bones should be mapped to what. While none of those sources are very reliable on their own, they can be combined and used in a search algorithm to get rather reliable results.
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Names of bones, bone directions, bone length ratios, and bone topology all provide hints to which bones should be mapped to what. While none of those sources are very reliable on their own, they can be combined and used in a search algorithm to get rather reliable results.