{
 "cells": [
  {
   "cell_type": "raw",
   "metadata": {
    "raw_mimetype": "text/restructuredtext"
   },
   "source": [
    "Finite element model from surfaces with per tissue mesh size\n",
    "============================================================\n",
    "\n",
    "A last possibility is to specify a value of characteristic length for each tissue. The process is once again the same."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from shamo import FEM\n",
    "\n",
    "model = FEM(\"fem_from_surfaces_lc-tissue\", \"../../derivatives\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from pathlib import Path\n",
    "\n",
    "data_path = Path(\"../../rawdata/surfaces\")\n",
    "tissues = {\n",
    "    f\"tissue_{i}\": data_path / f\"surfaces_tissue{i}.stl\" for i in range(1, 8)\n",
    "}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "structure = [\n",
    "    \"tissue_1\", [\n",
    "        [\"tissue_2\",\n",
    "            [\"tissue_3\"]\n",
    "        ],\n",
    "        [\"tissue_4\", [\n",
    "            [\"tissue_5\"],\n",
    "            [\"tissue_6\",\n",
    "                [\"tissue_7\"]\n",
    "            ]\n",
    "        ]]\n",
    "    ]\n",
    "]"
   ]
  },
  {
   "cell_type": "raw",
   "metadata": {
    "raw_mimetype": "text/restructuredtext"
   },
   "source": [
    "We simply have to define a dictionary containing the values for the characteristic length. If all the tissues do not have a special value, the `defaut` key must be included."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "lc = {\n",
    "    \"default\": 0.5,\n",
    "    \"tissue_2\": 0.01,\n",
    "    \"tissue_4\": 0.01,\n",
    "}"
   ]
  },
  {
   "cell_type": "raw",
   "metadata": {
    "raw_mimetype": "text/restructuredtext"
   },
   "source": [
    "Finally we pass this dictionary to the :py:func:`~shamo.FEM.mesh_from_surfaces` method."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "model.mesh_from_surfaces(tissues, structure, lc)"
   ]
  }
 ],
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  "kernelspec": {
   "display_name": "shamo",
   "language": "python",
   "name": "shamo"
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   "codemirror_mode": {
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