model/comp_surface/prepare_target/fixmesh.py

import numpy as np
from numpy.linalg import norm
import pymesh

"""
Modified from: 
fixmesh.py - MaSIF
Pablo Gainza - LPDI STI EPFL 2019
"""

"""
fixmesh.py: Regularize a protein surface mesh. 
- based on code from the PyMESH documentation. 
"""

def fix_mesh(mesh, resolution, detail="normal"):
    bbox_min, bbox_max = mesh.bbox;
    diag_len = norm(bbox_max - bbox_min);
    if detail == "normal":
        target_len = diag_len * 5e-3;
    elif detail == "high":
        target_len = diag_len * 2.5e-3;
    elif detail == "low":
        target_len = diag_len * 1e-2;
    
    target_len = resolution
    #print("Target resolution: {} mm".format(target_len));
    # PGC 2017: Remove duplicated vertices first
    mesh, _ = pymesh.remove_duplicated_vertices(mesh, 0.001)


    count = 0;
    print("Removing degenerated triangles")
    mesh, __ = pymesh.remove_degenerated_triangles(mesh, 100);
    mesh, __ = pymesh.split_long_edges(mesh, target_len);
    num_vertices = mesh.num_vertices;
    while True:
        mesh, __ = pymesh.collapse_short_edges(mesh, 1e-6);
        mesh, __ = pymesh.collapse_short_edges(mesh, target_len,
                preserve_feature=True);
        mesh, __ = pymesh.remove_obtuse_triangles(mesh, 150.0, 100);
        if mesh.num_vertices == num_vertices:
            break;

        num_vertices = mesh.num_vertices;
        #print("#v: {}".format(num_vertices));
        count += 1;
        if count > 10: break;

    mesh = pymesh.resolve_self_intersection(mesh);
    mesh, __ = pymesh.remove_duplicated_faces(mesh);
    #mesh = pymesh.compute_outer_hull(mesh);

    ############ Added by Oscar Mendez Lucio ##############
    mesh = pymesh.compute_outer_hull(mesh, all_layers=True);
    num_nodes = [i.num_nodes for i in mesh]
    mesh = mesh[np.argmax(num_nodes)]
    ############################################################

    mesh, __ = pymesh.remove_duplicated_faces(mesh);
    mesh, __ = pymesh.remove_obtuse_triangles(mesh, 179.0, 5);
    mesh, __ = pymesh.remove_isolated_vertices(mesh);
    mesh, _ = pymesh.remove_duplicated_vertices(mesh, 0.001)

    ############ Added by Oscar Mendez Lucio ##############
    mesh = pymesh.separate_mesh(mesh)
    num_nodes = [i.num_nodes for i in mesh]
    mesh = mesh[np.argmax(num_nodes)]
    ############################################################

    return mesh