Trimesh STL loading can lead to vertex indices varying from other programs such as blender or meshlab. Use this function instead to preserve the vertex order. Note: This has been integrated into trimesh since https://github.com/mikedh/trimesh/pull/1546

fix_trimesh_stl_vertex_order.py

import trimesh as tm
import numpy as np

def sorted_uniques(arr):
    """
    np.unique mangles the order of the original array, so that the resulting
    unique values are sorted. To keep them in the order of the original data,
    use this function.
    """
    uniques, uidxs, inverse = np.unique(arr, return_index=True, return_inverse=True)
    
    sorted2ordered = np.argsort(uidxs)
    uniques_ordered = uniques[sorted2ordered]
    
    ordered2sorted = np.argsort(sorted2ordered)
    inv_ordered = ordered2sorted[inverse]
    
    return uniques_ordered, uidxs[sorted2ordered], inv_ordered

def load_stl_fixed(path):
    """
    Fast, correct STL preprocessing. Takes care that the vertex order is not mangled.
    """
    
    with open(path, "rb") as fh:
        mesh = tm.exchange.stl.load_stl(fh)
    
    faces_flat = mesh["faces"].reshape(-1)
    tris = mesh["vertices"][faces_flat]
    
    stacked = [tris * (10 ** 8)]
    stacked = np.column_stack(stacked).round().astype(np.int64)
    
    dtype = np.dtype((np.void, stacked.dtype.itemsize * stacked.shape[1]))
    hashable = np.ascontiguousarray(stacked).view(dtype).reshape(-1)
    
    _, unique, inverse = sorted_uniques(hashable)
    
    verts = tris[unique]
    faces = faces_flat[inverse].reshape(-1, 3)
    
    return tm.Trimesh(verts, faces, process=False)