{
 "cells": [
  {
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   "source": [
    "# Magnetic Skeleton Finder\n",
    "\n",
    "[Magnetic Skeleton Finder]: ../../api_static/plasmapy.analysis.magnetic_skeleton.rst\n",
    "\n",
    "The [magnetic skeleton finder] is functionality that is designed to find and analyze magnetic skeleton structures using a trilinear method as described in [Haynes et al. (2010)](https://doi.org/10.1063/1.3467499)\n",
    "In this notebook we will briefly cover how the [magnetic skeleton finder] utilizes the method described in the paper in order to describe the structures of magnetic field."
   ]
  },
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   "id": "a4069f6d",
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   "outputs": [
    {
     "ename": "ModuleNotFoundError",
     "evalue": "No module named 'plasmapy'",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mModuleNotFoundError\u001b[0m                       Traceback (most recent call last)",
      "Input \u001b[0;32mIn [6]\u001b[0m, in \u001b[0;36m<cell line: 2>\u001b[0;34m()\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mnumpy\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m \u001b[38;5;21;01mnp\u001b[39;00m\n\u001b[0;32m----> 2\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mplasmapy\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01manalysis\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mmagnetic_skeleton\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m (\n\u001b[1;32m      3\u001b[0m     magnetic_skeleton_find\n\u001b[1;32m      4\u001b[0m )\n",
      "\u001b[0;31mModuleNotFoundError\u001b[0m: No module named 'plasmapy'"
     ]
    }
   ],
   "source": [
    "import numpy as np\n",
    "\n",
    "from plasmapy.analysis.magnetic_skeleton import magnetic_skeleton_find"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "8b324d8f",
   "metadata": {},
   "source": [
    "## Contents:\n",
    "\n",
    "1. [How Magnetic Skeleton Finder works](#How-Magnetic-Skeleton-Finder-works)\n",
    "    1. [Locating the null points](#Locating-the-null-points)\n",
    "    1. [Locating the spines](#Locating-the-spines)\n",
    "    1. [Locating the fan and separators](#Locating-the-fan-and-separators)\n",
    "1. [Running through an example](#Running_through-an-example)\n",
    "    1. [Arbitrary Regular Grid](#Arbitrary-regular-grid)\n",
    "        "
   ]
  },
  {
   "cell_type": "markdown",
   "id": "ff2a3f8c",
   "metadata": {},
   "source": [
    "## Running through an example"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "3344c0ba",
   "metadata": {},
   "outputs": [],
   "source": [
    "def example():\n",
    "    x_arr = np.linspace(-5, 5, 60)\n",
    "    y_arr = np.linspace(-5, 5, 60)\n",
    "    z_arr = np.linspace(-5, 5, 60)\n",
    "    x, y, z = np.meshgrid(\n",
    "        x_arr,\n",
    "        y_arr,\n",
    "        z_arr,\n",
    "        indexing=\"ij\",\n",
    "    )\n",
    "    u, v, w = vspace_func_3(x, y, z)\n",
    "    nullpoints, spines, fan, separators = magnetic_skeleton_find(\n",
    "        x_arr, y_arr, z_arr, u, v, w\n",
    "    )\n",
    "\n",
    "\n",
    "example()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "98f802af",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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