Merge_Meshes_for_3DP.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "9d2eef78",
   "metadata": {
    "id": "9d2eef78"
   },
   "outputs": [],
   "source": [
    "import os\n",
    "import pymeshlab\n",
    "from vedo import Mesh, Plotter, Volume\n",
    "import numpy as np"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "e124a4d4",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Specify the input folder containing OBJ files\n",
    "input_folder = \"/Users/minoue/Desktop/Raphy_skull\"\n",
    "\n",
    "# Specify the output STL file\n",
    "output_obj_file = \"/Users/minoue/Desktop/Raphy_skull/single_mesh.obj\"\n",
    "\n",
    "# Specigy the isotropic volume voxel size and output image stack \n",
    "voxel = 7 # This is in the same unit as your mesh\n",
    "output_tiff_file = \"/Users/minoue/Desktop/Raphy_skull/voxelized_img.tiff\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "c0f4ce82",
   "metadata": {
    "id": "c0f4ce82"
   },
   "outputs": [],
   "source": [
    "def flatten_meshes(input_folder):\n",
    "    # Initialize a MeshSet object\n",
    "    ms = pymeshlab.MeshSet()\n",
    "\n",
    "    # Iterate through each input OBJ file\n",
    "    for obj_file in os.listdir(input_folder):\n",
    "        if obj_file.endswith(\".obj\"):\n",
    "            # Construct the full path to the input OBJ file\n",
    "            obj_path = os.path.join(input_folder, obj_file)\n",
    "\n",
    "            # Load the OBJ file into the MeshSet\n",
    "            ms.load_new_mesh(obj_path)\n",
    "\n",
    "    # Merge all loaded meshes into one\n",
    "    ms.generate_by_merging_visible_meshes()\n",
    "    return ms"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "370b684d",
   "metadata": {
    "id": "370b684d"
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processed mesh saved as '/Users/minoue/Desktop/Raphy_skull/single_mesh.obj'\n"
     ]
    }
   ],
   "source": [
    "if __name__ == \"__main__\":\n",
    "\n",
    "    # Create the MeshSet by flattening all OBJ files\n",
    "    flattened_mesh = flatten_meshes(input_folder)\n",
    "\n",
    "    # Perform Laplacian smoothing\n",
    "    flattened_mesh.apply_filter('apply_coord_laplacian_smoothing')\n",
    "\n",
    "    # Decimate the mesh to the target face number (e.g., 1,000,000)\n",
    "    flattened_mesh.apply_filter(\"meshing_decimation_quadric_edge_collapse\", targetfacenum=1000000)\n",
    "\n",
    "    # Save the merged and processed mesh as a single STL file\n",
    "    flattened_mesh.save_current_mesh(output_obj_file, save_face_color=False)\n",
    "\n",
    "    print(f\"Processed mesh saved as '{output_obj_file}'\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "d144a171",
   "metadata": {
    "id": "d144a171"
   },
   "outputs": [
    {
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       "</td>\n",
       "<td style='text-align: center; vertical-align: center;'><br/>\n",
       "<b><a href=\"https://vedo.embl.es/docs/vedo/volume.html\" target=\"_blank\">vedo.volume.Volume</a></b>\n",
       "<table>\n",
       "<tr><td><b> bounds </b> <br/> (x/y/z) </td><td>7626 ... 1.146e+4<br/>7998 ... 9055<br/>2150 ... 6056</td></tr>\n",
       "<tr><td><b> dimensions </b></td><td>(548, 152, 559)</td></tr>\n",
       "<tr><td><b> voxel spacing </b></td><td>(7.00, 7.00, 7.00)</td></tr>\n",
       "<tr><td><b> in memory size </b></td><td>44MB</td></tr>\n",
       "<tr><td><b> point data array </b></td><td>ImageScalars</td></tr>\n",
       "\n",
       "<tr><td><b> scalar range </b></td><td>(0, 255.0)</td></tr>\n",
       "</table>\n",
       "</table>"
      ],
      "text/plain": [
       "<Volume(0x7fcdb724c600) at 0x7fcdcb643580>"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Binarize and export as tiff\n",
    "# Set export voxel size\n",
    "surf = Mesh(output_obj_file)\n",
    "vol = surf.binarize(spacing=(voxel,voxel,voxel))\n",
    "vol.write(output_tiff_file)"
   ]
  }
 ],
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