{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# 3D Models\n",
    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/VirtualBrainLab/urchin-examples/blob/main/basics/3D.ipynb)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Install Urchin\n",
    "\n",
    "Urchin is a Python package stored on PyPI, the following code needs to be run the first time you use Urchin in a Python environment. \n",
    "\n",
    "Urchin's full documentation can be found [on our website](https://virtualbrainlab.org/urchin/installation_and_use.html)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#Installing urchin\n",
    "!pip install oursin -U"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "!pip install PyWavefront numpy-stl"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Setup Urchin and open the renderer webpage \n",
    "\n",
    "By default Urchin opens the 3D renderer in a webpage. Make sure pop-ups are enabled, or the page won't open properly. You can also open the renderer site yourself by replacing [ID here] with the ID that is output by the call to `.setup()` at https://data.virtualbrainlab.org/Urchin/?ID=[ID here]\n",
    "\n",
    "Note that Urchin communicates to the renderer webpage through an internet connection, we don't currently support offline use (we hope to add support in the future)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(URN) connected to server\n",
      "Login sent with ID: 3f54bbeb, copy this ID into the renderer to connect.\n"
     ]
    }
   ],
   "source": [
    "import oursin as urchin\n",
    "urchin.setup()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "import requests\n",
    "import numpy as np"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Load an STL file\n",
    "\n",
    "We'll just load a cube as an example. The cube is the size of the CCF for convenience."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "# obj_url = 'https://drive.google.com/uc?id=11VIfFz7dO9TOPfkL9sPgihapjs1hNANe'\n",
    "stl_url = 'https://drive.google.com/uc?id=1TUsqumhZWZRL_VEjjlxs4gLeEuicDS34'\n",
    "\n",
    "# obj_response = requests.get(obj_url, stream=True)\n",
    "stl_response = requests.get(stl_url, stream=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "## Load STL/OBJ files\n",
    "from stl import mesh\n",
    "import tempfile\n",
    "\n",
    "def loadSTL(stl_bytes):\n",
    "    # Convert bytes to string\n",
    "    with tempfile.NamedTemporaryFile(delete=False) as temp_stl:\n",
    "        temp_stl.write(stl_bytes)\n",
    "    \n",
    "    # Load STL file using numpy-stl\n",
    "    stl_mesh = mesh.Mesh.from_file(temp_stl.name)\n",
    "\n",
    "    #get unique vertices\n",
    "    vertices = np.unique(np.reshape(stl_mesh.points,(-1,3)), axis=0)\n",
    "\n",
    "    #triangles: go through each triangle and figure out which indexes it corresponds to\n",
    "    triangles = []\n",
    "    for vector in stl_mesh.vectors:\n",
    "        for vi in np.arange(0,3):\n",
    "            index = np.where((vertices == vector[vi]).all(axis=1))[0][0]  \n",
    "            triangles.append(index)\n",
    "\n",
    "    return vertices, triangles"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "\n",
    "# Example usage:\n",
    "stl_vertices, stl_triangles = loadSTL(stl_response.content)\n",
    "\n",
    "vertices = urchin.utils.list_of_list2vector3(stl_vertices)\n",
    "triangles = [int(x) for x in stl_triangles]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 40,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(Warning) Atlas was already loaded, the renderer can have issues if you try to load an atlas twice.\n"
     ]
    }
   ],
   "source": [
    "# Note that an atlas must be loaded to create custom meshes, otherwise no reference coordinate information will be available\n",
    "urchin.ccf25.load()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 41,
   "metadata": {},
   "outputs": [],
   "source": [
    "mesh = urchin.custom.CustomMesh(vertices, triangles)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {},
   "outputs": [],
   "source": [
    "mesh.set_position([3,1,-1], True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 46,
   "metadata": {},
   "outputs": [],
   "source": [
    "mesh.set_scale([1, 1, 1])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 47,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "packet queue is empty, aborting\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(URN) disconnected from server\n",
      "(URN) connected to server\n",
      "Login sent with ID: 3f54bbeb, copy this ID into the renderer to connect.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "packet queue is empty, aborting\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(URN) disconnected from server\n",
      "(URN) connected to server\n",
      "Login sent with ID: 3f54bbeb, copy this ID into the renderer to connect.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "packet queue is empty, aborting\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(URN) disconnected from server\n",
      "(URN) connected to server\n",
      "Login sent with ID: 3f54bbeb, copy this ID into the renderer to connect.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "packet queue is empty, aborting\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(URN) disconnected from server\n",
      "(URN) connected to server\n",
      "Login sent with ID: 3f54bbeb, copy this ID into the renderer to connect.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "packet queue is empty, aborting\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(URN) disconnected from server\n",
      "(URN) connected to server\n",
      "Login sent with ID: 3f54bbeb, copy this ID into the renderer to connect.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "packet queue is empty, aborting\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(URN) disconnected from server\n",
      "(URN) connected to server\n",
      "Login sent with ID: 3f54bbeb, copy this ID into the renderer to connect.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "packet queue is empty, aborting\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(URN) disconnected from server\n",
      "(URN) connected to server\n",
      "Login sent with ID: 3f54bbeb, copy this ID into the renderer to connect.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "packet queue is empty, aborting\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(URN) disconnected from server\n",
      "(URN) connected to server\n",
      "Login sent with ID: 3f54bbeb, copy this ID into the renderer to connect.\n",
      "(URN) disconnected from server\n",
      "(URN) connected to server\n",
      "Login sent with ID: 3f54bbeb, copy this ID into the renderer to connect.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "packet queue is empty, aborting\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(URN) disconnected from server\n",
      "(URN) connected to server\n",
      "Login sent with ID: 3f54bbeb, copy this ID into the renderer to connect.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "packet queue is empty, aborting\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(URN) disconnected from server\n",
      "(URN) connected to server\n",
      "Login sent with ID: 3f54bbeb, copy this ID into the renderer to connect.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "packet queue is empty, aborting\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(URN) disconnected from server\n",
      "(URN) connected to server\n",
      "Login sent with ID: 3f54bbeb, copy this ID into the renderer to connect.\n"
     ]
    }
   ],
   "source": [
    "urchin.custom.clear()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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