The problem was one of numerical stability. Approx 30 hours of work on this over the course of 2 months, only to figure out I was doing it right from the very start. When I ortho-normalized the rotation matrices before plugging them into the retarget code, the simple solution of multiplying source * inverse(target) worked perfectly. Of course, there's a lot more to retargeting than that (in particular, taking into account the different shapes of the skeleton, ie shoulder width, etc). Here's the code I'm using for the simple, naieve approach, if anyone is curious:
public static SkeletalAnimation retarget(SkeletalAnimation animation, Skeleton target, string boneMapFilePath)
{
if(animation == null) throw new ArgumentNullException("animation");
if(target == null) throw new ArgumentNullException("target");
Skeleton source = animation.skeleton;
if(source == target) return animation;
int nSourceBones = source.count;
int nTargetBones = target.count;
int nFrames = animation.nFrames;
AnimationData[] sourceData = animation.data;
Matrix[] sourceTransforms = new Matrix[nSourceBones];
Matrix[] targetTransforms = new Matrix[nTargetBones];
AnimationData[] temp = new AnimationData[nSourceBones];
AnimationData[] targetData = new AnimationData[nTargetBones * nFrames];
// Get a map where map[iTargetBone] = iSourceBone or -1 if no such bone
int[] map = parseBoneMap(source, target, boneMapFilePath);
for(int iFrame = 0; iFrame < nFrames; iFrame++)
{
int sourceBase = iFrame * nSourceBones;
int targetBase = iFrame * nTargetBones;
// Copy the root translation and rotation directly over
AnimationData rootData = targetData[targetBase] = sourceData[sourceBase];
// Get the source pose for this frame
Array.Copy(sourceData, sourceBase, temp, 0, nSourceBones);
source.getAbsoluteTransforms(temp, sourceTransforms);
// Rotate target bones to face that direction
Matrix m;
AnimationData.toMatrix(ref rootData, out m);
Matrix.Multiply(ref m, ref target.relatives[0], out targetTransforms[0]);
for(int iTargetBone = 1; iTargetBone < nTargetBones; iTargetBone++)
{
int targetIndex = targetBase + iTargetBone;
int iTargetParent = target.hierarchy[iTargetBone];
int iSourceBone = map[iTargetBone];
if(iSourceBone <= 0)
{
targetData[targetIndex].rotation = Quaternion.Identity;
Matrix.Multiply(ref target.relatives[iTargetBone], ref targetTransforms[iTargetParent], out targetTransforms[iTargetBone]);
}
else
{
Matrix currentTransform, inverseCurrent, sourceTransform, final, m2;
Quaternion rot;
// Get the "current" transformation (transform that would be applied if rot is Quaternion.Identity)
Matrix.Multiply(ref target.relatives[iTargetBone], ref targetTransforms[iTargetParent], out currentTransform);
Math2.orthoNormalize(ref currentTransform);
Matrix.Invert(ref currentTransform, out inverseCurrent);
Math2.orthoNormalize(ref inverseCurrent);
// Get the final rotation
Math2.orthoNormalize(ref sourceTransforms[iSourceBone], out sourceTransform);
Matrix.Multiply(ref sourceTransform, ref inverseCurrent, out final);
Math2.orthoNormalize(ref final);
Quaternion.RotationMatrix(ref final, out rot);
// Calculate this bone's absolute position to use as next bone's parent
targetData[targetIndex].rotation = rot;
Matrix.RotationQuaternion(ref rot, out m);
Matrix.Multiply(ref m, ref target.relatives[iTargetBone], out m2);
Matrix.Multiply(ref m2, ref targetTransforms[iTargetParent], out targetTransforms[iTargetBone]);
}
}
}
return new SkeletalAnimation(target, targetData, animation.fps, nFrames);
}