Fitting skeleton to mesh after using shape keys?

Questions
2

i was able to fix it by using reference points on the mesh.

class SkeletonAlignment {
  constructor(mesh, skeletonDataUrl, vertexDataUrl) {
    this.mesh = mesh;
    this.skeletonDataUrl = skeletonDataUrl; //rig data you generate in blender
    this.vertexDataUrl = vertexDataUrl; //vertex group data found in makehuman directory
    this.skeletonData = null;
    this.vertexData = null;
  }

  async loadJSONFiles() {
    try {
      const [skeletonResponse, vertexResponse] = await Promise.all([
        fetch(this.skeletonDataUrl),
        fetch(this.vertexDataUrl),
      ]);

      this.skeletonData = await skeletonResponse.json();
      this.vertexData = await vertexResponse.json();
    } catch (error) {
      console.error("Error loading JSON files:", error.message);
    }
  }
  // put single values in array, flatten those retrieved from vertex data file
  toArray(value) {
    return Array.isArray(value) ? value : [value];
  }

  flattenArray(value) {
    return Array.isArray(value) && Array.isArray(value[0]) ? value.flat() : this.toArray(value);
  }

  getJointPositions(boneName) {
    const boneData = this.skeletonData.bones[boneName];

    if (!boneData) {
      console.warn(`Bone data not found for: ${boneName}`);
      return null;
    }
    // three strategies for each bone: cube, mean, or vertex.
    const headVertices = boneData.head.cube_name
      ? this.flattenArray(this.vertexData[boneData.head.cube_name])
      : this.toArray(boneData.head.vertex_indices || boneData.head.vertex_index);

    const tailVertices = boneData.tail.cube_name
      ? this.flattenArray(this.vertexData[boneData.tail.cube_name])
      : this.toArray(boneData.tail?.vertex_indices || boneData.tail?.vertex_index);

    return {
      bone: boneName,
      head: boneData.head.cube_name || boneData.head.strategy,
      tail: boneData.tail.cube_name || boneData.tail.strategy,
      headVertices,
      tailVertices,
      headPosition: this.calculateAveragePosition(headVertices),
      tailPosition: this.calculateAveragePosition(tailVertices), 
    };
    
  }

  calculateAveragePosition(vertices) {
    if (!vertices[0]) {
      console.warn("invalid or empty vertices array", vertices);
      return null;
    }

    if (vertices.length === 1) {
      const tempVec = new THREE.Vector3();
      this.mesh.getVertexPosition(vertices[0], tempVec);
      return tempVec;
    }
    const [start, end] = vertices;

    const tempVec = new THREE.Vector3();
    let sum = new THREE.Vector3();
    let count = 0;

    for (let i = start; i <= end; i++) {
      this.mesh.getVertexPosition(i, tempVec);
      sum.add(tempVec);
      count++;
    }

    return sum.divideScalar(count);
    
  }

  updateJointPositions() {
    const skeleton = this.mesh.skeleton;
  
    const jointPos = skeleton.bones.map((bone) => {
      if (bone.userData.name === "neutral_bone") {
        //console.warn(`Skipping neutral bone`);
        return null;
      }

      const position = this.getJointPositions(bone.userData.name);
      if (!position) {
        console.error(`Invalid joint position for bone: ${bone.userData.name}`);
      }
      return position;
    });

    skeleton.bones.forEach((bone, i) => {
      if (bone.userData.name === "neutral_bone" || !jointPos[i].headPosition) {
        return;
      }
      const localVec = new THREE.Vector3();
      const parentBone = bone.parent;
      const parentMatrixWorld = parentBone.matrixWorld.clone().invert();
      if (!jointPos[i].headPosition) return;
      localVec.copy(jointPos[i].headPosition).applyMatrix4(parentMatrixWorld);
      bone.position.copy(localVec);
      bone.updateMatrixWorld();
    });
    skeleton.calculateInverses();
    this.mesh.updateMatrixWorld();
  }
}

when i call the updateJointPositions function with dat gui’s onChange function all bones move to their reference positions on the mesh.