{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Import supporting package"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import xarray as xr\n",
    "import numpy as np\n",
    "import copy\n",
    "\n",
    "from uncertainties import ufloat\n",
    "from uncertainties import unumpy as unp\n",
    "from uncertainties import umath\n",
    "import random\n",
    "import matplotlib.pyplot as plt\n",
    "plt.rcParams['font.size'] = 12\n",
    "\n",
    "from DataContainer.ReadData import read_hdf5_file\n",
    "from Analyser.ImagingAnalyser import ImageAnalyser\n",
    "from Analyser.FitAnalyser import FitAnalyser\n",
    "from Analyser.FitAnalyser import NewFitModel, DensityProfileBEC2dModel\n",
    "from ToolFunction.ToolFunction import *\n",
    "\n",
    "from scipy.optimize import curve_fit\n",
    "\n",
    "from ToolFunction.HomeMadeXarrayFunction import errorbar, dataarray_plot_errorbar\n",
    "xr.plot.dataarray_plot.errorbar = errorbar\n",
    "xr.plot.accessor.DataArrayPlotAccessor.errorbar = dataarray_plot_errorbar\n",
    "\n",
    "imageAnalyser = ImageAnalyser()\n",
    "\n",
    "# %matplotlib notebook"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Start a client for parallel computing"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "    <div style=\"width: 24px; height: 24px; background-color: #e1e1e1; border: 3px solid #9D9D9D; border-radius: 5px; position: absolute;\"> </div>\n",
       "    <div style=\"margin-left: 48px;\">\n",
       "        <h3 style=\"margin-bottom: 0px;\">Client</h3>\n",
       "        <p style=\"color: #9D9D9D; margin-bottom: 0px;\">Client-a5e5cea6-2fbd-11ee-8430-80e82ce2fa8e</p>\n",
       "        <table style=\"width: 100%; text-align: left;\">\n",
       "\n",
       "        <tr>\n",
       "        \n",
       "            <td style=\"text-align: left;\"><strong>Connection method:</strong> Cluster object</td>\n",
       "            <td style=\"text-align: left;\"><strong>Cluster type:</strong> distributed.LocalCluster</td>\n",
       "        \n",
       "        </tr>\n",
       "\n",
       "        \n",
       "            <tr>\n",
       "                <td style=\"text-align: left;\">\n",
       "                    <strong>Dashboard: </strong> <a href=\"http://127.0.0.1:8787/status\" target=\"_blank\">http://127.0.0.1:8787/status</a>\n",
       "                </td>\n",
       "                <td style=\"text-align: left;\"></td>\n",
       "            </tr>\n",
       "        \n",
       "\n",
       "        </table>\n",
       "\n",
       "        \n",
       "\n",
       "        \n",
       "            <details>\n",
       "            <summary style=\"margin-bottom: 20px;\"><h3 style=\"display: inline;\">Cluster Info</h3></summary>\n",
       "            <div class=\"jp-RenderedHTMLCommon jp-RenderedHTML jp-mod-trusted jp-OutputArea-output\">\n",
       "    <div style=\"width: 24px; height: 24px; background-color: #e1e1e1; border: 3px solid #9D9D9D; border-radius: 5px; position: absolute;\">\n",
       "    </div>\n",
       "    <div style=\"margin-left: 48px;\">\n",
       "        <h3 style=\"margin-bottom: 0px; margin-top: 0px;\">LocalCluster</h3>\n",
       "        <p style=\"color: #9D9D9D; margin-bottom: 0px;\">49266936</p>\n",
       "        <table style=\"width: 100%; text-align: left;\">\n",
       "            <tr>\n",
       "                <td style=\"text-align: left;\">\n",
       "                    <strong>Dashboard:</strong> <a href=\"http://127.0.0.1:8787/status\" target=\"_blank\">http://127.0.0.1:8787/status</a>\n",
       "                </td>\n",
       "                <td style=\"text-align: left;\">\n",
       "                    <strong>Workers:</strong> 8\n",
       "                </td>\n",
       "            </tr>\n",
       "            <tr>\n",
       "                <td style=\"text-align: left;\">\n",
       "                    <strong>Total threads:</strong> 128\n",
       "                </td>\n",
       "                <td style=\"text-align: left;\">\n",
       "                    <strong>Total memory:</strong> 149.01 GiB\n",
       "                </td>\n",
       "            </tr>\n",
       "            \n",
       "            <tr>\n",
       "    <td style=\"text-align: left;\"><strong>Status:</strong> running</td>\n",
       "    <td style=\"text-align: left;\"><strong>Using processes:</strong> True</td>\n",
       "</tr>\n",
       "\n",
       "            \n",
       "        </table>\n",
       "\n",
       "        <details>\n",
       "            <summary style=\"margin-bottom: 20px;\">\n",
       "                <h3 style=\"display: inline;\">Scheduler Info</h3>\n",
       "            </summary>\n",
       "\n",
       "            <div style=\"\">\n",
       "    <div>\n",
       "        <div style=\"width: 24px; height: 24px; background-color: #FFF7E5; border: 3px solid #FF6132; border-radius: 5px; position: absolute;\"> </div>\n",
       "        <div style=\"margin-left: 48px;\">\n",
       "            <h3 style=\"margin-bottom: 0px;\">Scheduler</h3>\n",
       "            <p style=\"color: #9D9D9D; margin-bottom: 0px;\">Scheduler-6db1fb2d-d8be-4f76-9fcf-6a7cc9ed86ee</p>\n",
       "            <table style=\"width: 100%; text-align: left;\">\n",
       "                <tr>\n",
       "                    <td style=\"text-align: left;\">\n",
       "                        <strong>Comm:</strong> tcp://127.0.0.1:63903\n",
       "                    </td>\n",
       "                    <td style=\"text-align: left;\">\n",
       "                        <strong>Workers:</strong> 8\n",
       "                    </td>\n",
       "                </tr>\n",
       "                <tr>\n",
       "                    <td style=\"text-align: left;\">\n",
       "                        <strong>Dashboard:</strong> <a href=\"http://127.0.0.1:8787/status\" target=\"_blank\">http://127.0.0.1:8787/status</a>\n",
       "                    </td>\n",
       "                    <td style=\"text-align: left;\">\n",
       "                        <strong>Total threads:</strong> 128\n",
       "                    </td>\n",
       "                </tr>\n",
       "                <tr>\n",
       "                    <td style=\"text-align: left;\">\n",
       "                        <strong>Started:</strong> Just now\n",
       "                    </td>\n",
       "                    <td style=\"text-align: left;\">\n",
       "                        <strong>Total memory:</strong> 149.01 GiB\n",
       "                    </td>\n",
       "                </tr>\n",
       "            </table>\n",
       "        </div>\n",
       "    </div>\n",
       "\n",
       "    <details style=\"margin-left: 48px;\">\n",
       "        <summary style=\"margin-bottom: 20px;\">\n",
       "            <h3 style=\"display: inline;\">Workers</h3>\n",
       "        </summary>\n",
       "\n",
       "        \n",
       "        <div style=\"margin-bottom: 20px;\">\n",
       "            <div style=\"width: 24px; height: 24px; background-color: #DBF5FF; border: 3px solid #4CC9FF; border-radius: 5px; position: absolute;\"> </div>\n",
       "            <div style=\"margin-left: 48px;\">\n",
       "            <details>\n",
       "                <summary>\n",
       "                    <h4 style=\"margin-bottom: 0px; display: inline;\">Worker: 0</h4>\n",
       "                </summary>\n",
       "                <table style=\"width: 100%; text-align: left;\">\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Comm: </strong> tcp://127.0.0.1:63943\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Total threads: </strong> 16\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Dashboard: </strong> <a href=\"http://127.0.0.1:63946/status\" target=\"_blank\">http://127.0.0.1:63946/status</a>\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Memory: </strong> 18.63 GiB\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Nanny: </strong> tcp://127.0.0.1:63906\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\"></td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td colspan=\"2\" style=\"text-align: left;\">\n",
       "                            <strong>Local directory: </strong> C:\\Users\\data\\AppData\\Local\\Temp\\dask-worker-space\\worker-sctehcfb\n",
       "                        </td>\n",
       "                    </tr>\n",
       "\n",
       "                    \n",
       "\n",
       "                    \n",
       "\n",
       "                </table>\n",
       "            </details>\n",
       "            </div>\n",
       "        </div>\n",
       "        \n",
       "        <div style=\"margin-bottom: 20px;\">\n",
       "            <div style=\"width: 24px; height: 24px; background-color: #DBF5FF; border: 3px solid #4CC9FF; border-radius: 5px; position: absolute;\"> </div>\n",
       "            <div style=\"margin-left: 48px;\">\n",
       "            <details>\n",
       "                <summary>\n",
       "                    <h4 style=\"margin-bottom: 0px; display: inline;\">Worker: 1</h4>\n",
       "                </summary>\n",
       "                <table style=\"width: 100%; text-align: left;\">\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Comm: </strong> tcp://127.0.0.1:63957\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Total threads: </strong> 16\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Dashboard: </strong> <a href=\"http://127.0.0.1:63959/status\" target=\"_blank\">http://127.0.0.1:63959/status</a>\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Memory: </strong> 18.63 GiB\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Nanny: </strong> tcp://127.0.0.1:63907\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\"></td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td colspan=\"2\" style=\"text-align: left;\">\n",
       "                            <strong>Local directory: </strong> C:\\Users\\data\\AppData\\Local\\Temp\\dask-worker-space\\worker-b1kdawd2\n",
       "                        </td>\n",
       "                    </tr>\n",
       "\n",
       "                    \n",
       "\n",
       "                    \n",
       "\n",
       "                </table>\n",
       "            </details>\n",
       "            </div>\n",
       "        </div>\n",
       "        \n",
       "        <div style=\"margin-bottom: 20px;\">\n",
       "            <div style=\"width: 24px; height: 24px; background-color: #DBF5FF; border: 3px solid #4CC9FF; border-radius: 5px; position: absolute;\"> </div>\n",
       "            <div style=\"margin-left: 48px;\">\n",
       "            <details>\n",
       "                <summary>\n",
       "                    <h4 style=\"margin-bottom: 0px; display: inline;\">Worker: 2</h4>\n",
       "                </summary>\n",
       "                <table style=\"width: 100%; text-align: left;\">\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Comm: </strong> tcp://127.0.0.1:63948\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Total threads: </strong> 16\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Dashboard: </strong> <a href=\"http://127.0.0.1:63951/status\" target=\"_blank\">http://127.0.0.1:63951/status</a>\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Memory: </strong> 18.63 GiB\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Nanny: </strong> tcp://127.0.0.1:63908\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\"></td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td colspan=\"2\" style=\"text-align: left;\">\n",
       "                            <strong>Local directory: </strong> C:\\Users\\data\\AppData\\Local\\Temp\\dask-worker-space\\worker-845evwbp\n",
       "                        </td>\n",
       "                    </tr>\n",
       "\n",
       "                    \n",
       "\n",
       "                    \n",
       "\n",
       "                </table>\n",
       "            </details>\n",
       "            </div>\n",
       "        </div>\n",
       "        \n",
       "        <div style=\"margin-bottom: 20px;\">\n",
       "            <div style=\"width: 24px; height: 24px; background-color: #DBF5FF; border: 3px solid #4CC9FF; border-radius: 5px; position: absolute;\"> </div>\n",
       "            <div style=\"margin-left: 48px;\">\n",
       "            <details>\n",
       "                <summary>\n",
       "                    <h4 style=\"margin-bottom: 0px; display: inline;\">Worker: 3</h4>\n",
       "                </summary>\n",
       "                <table style=\"width: 100%; text-align: left;\">\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Comm: </strong> tcp://127.0.0.1:63942\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Total threads: </strong> 16\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Dashboard: </strong> <a href=\"http://127.0.0.1:63944/status\" target=\"_blank\">http://127.0.0.1:63944/status</a>\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Memory: </strong> 18.63 GiB\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Nanny: </strong> tcp://127.0.0.1:63909\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\"></td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td colspan=\"2\" style=\"text-align: left;\">\n",
       "                            <strong>Local directory: </strong> C:\\Users\\data\\AppData\\Local\\Temp\\dask-worker-space\\worker-xneexydx\n",
       "                        </td>\n",
       "                    </tr>\n",
       "\n",
       "                    \n",
       "\n",
       "                    \n",
       "\n",
       "                </table>\n",
       "            </details>\n",
       "            </div>\n",
       "        </div>\n",
       "        \n",
       "        <div style=\"margin-bottom: 20px;\">\n",
       "            <div style=\"width: 24px; height: 24px; background-color: #DBF5FF; border: 3px solid #4CC9FF; border-radius: 5px; position: absolute;\"> </div>\n",
       "            <div style=\"margin-left: 48px;\">\n",
       "            <details>\n",
       "                <summary>\n",
       "                    <h4 style=\"margin-bottom: 0px; display: inline;\">Worker: 4</h4>\n",
       "                </summary>\n",
       "                <table style=\"width: 100%; text-align: left;\">\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Comm: </strong> tcp://127.0.0.1:63949\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Total threads: </strong> 16\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Dashboard: </strong> <a href=\"http://127.0.0.1:63953/status\" target=\"_blank\">http://127.0.0.1:63953/status</a>\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Memory: </strong> 18.63 GiB\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Nanny: </strong> tcp://127.0.0.1:63910\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\"></td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td colspan=\"2\" style=\"text-align: left;\">\n",
       "                            <strong>Local directory: </strong> C:\\Users\\data\\AppData\\Local\\Temp\\dask-worker-space\\worker-zb64b79v\n",
       "                        </td>\n",
       "                    </tr>\n",
       "\n",
       "                    \n",
       "\n",
       "                    \n",
       "\n",
       "                </table>\n",
       "            </details>\n",
       "            </div>\n",
       "        </div>\n",
       "        \n",
       "        <div style=\"margin-bottom: 20px;\">\n",
       "            <div style=\"width: 24px; height: 24px; background-color: #DBF5FF; border: 3px solid #4CC9FF; border-radius: 5px; position: absolute;\"> </div>\n",
       "            <div style=\"margin-left: 48px;\">\n",
       "            <details>\n",
       "                <summary>\n",
       "                    <h4 style=\"margin-bottom: 0px; display: inline;\">Worker: 5</h4>\n",
       "                </summary>\n",
       "                <table style=\"width: 100%; text-align: left;\">\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Comm: </strong> tcp://127.0.0.1:63950\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Total threads: </strong> 16\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Dashboard: </strong> <a href=\"http://127.0.0.1:63954/status\" target=\"_blank\">http://127.0.0.1:63954/status</a>\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Memory: </strong> 18.63 GiB\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Nanny: </strong> tcp://127.0.0.1:63911\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\"></td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td colspan=\"2\" style=\"text-align: left;\">\n",
       "                            <strong>Local directory: </strong> C:\\Users\\data\\AppData\\Local\\Temp\\dask-worker-space\\worker-q6lyanmx\n",
       "                        </td>\n",
       "                    </tr>\n",
       "\n",
       "                    \n",
       "\n",
       "                    \n",
       "\n",
       "                </table>\n",
       "            </details>\n",
       "            </div>\n",
       "        </div>\n",
       "        \n",
       "        <div style=\"margin-bottom: 20px;\">\n",
       "            <div style=\"width: 24px; height: 24px; background-color: #DBF5FF; border: 3px solid #4CC9FF; border-radius: 5px; position: absolute;\"> </div>\n",
       "            <div style=\"margin-left: 48px;\">\n",
       "            <details>\n",
       "                <summary>\n",
       "                    <h4 style=\"margin-bottom: 0px; display: inline;\">Worker: 6</h4>\n",
       "                </summary>\n",
       "                <table style=\"width: 100%; text-align: left;\">\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Comm: </strong> tcp://127.0.0.1:63925\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Total threads: </strong> 16\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Dashboard: </strong> <a href=\"http://127.0.0.1:63934/status\" target=\"_blank\">http://127.0.0.1:63934/status</a>\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Memory: </strong> 18.63 GiB\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Nanny: </strong> tcp://127.0.0.1:63912\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\"></td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td colspan=\"2\" style=\"text-align: left;\">\n",
       "                            <strong>Local directory: </strong> C:\\Users\\data\\AppData\\Local\\Temp\\dask-worker-space\\worker-1cvfk3q5\n",
       "                        </td>\n",
       "                    </tr>\n",
       "\n",
       "                    \n",
       "\n",
       "                    \n",
       "\n",
       "                </table>\n",
       "            </details>\n",
       "            </div>\n",
       "        </div>\n",
       "        \n",
       "        <div style=\"margin-bottom: 20px;\">\n",
       "            <div style=\"width: 24px; height: 24px; background-color: #DBF5FF; border: 3px solid #4CC9FF; border-radius: 5px; position: absolute;\"> </div>\n",
       "            <div style=\"margin-left: 48px;\">\n",
       "            <details>\n",
       "                <summary>\n",
       "                    <h4 style=\"margin-bottom: 0px; display: inline;\">Worker: 7</h4>\n",
       "                </summary>\n",
       "                <table style=\"width: 100%; text-align: left;\">\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Comm: </strong> tcp://127.0.0.1:63958\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Total threads: </strong> 16\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Dashboard: </strong> <a href=\"http://127.0.0.1:63961/status\" target=\"_blank\">http://127.0.0.1:63961/status</a>\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Memory: </strong> 18.63 GiB\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Nanny: </strong> tcp://127.0.0.1:63913\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\"></td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td colspan=\"2\" style=\"text-align: left;\">\n",
       "                            <strong>Local directory: </strong> C:\\Users\\data\\AppData\\Local\\Temp\\dask-worker-space\\worker-0agsu53e\n",
       "                        </td>\n",
       "                    </tr>\n",
       "\n",
       "                    \n",
       "\n",
       "                    \n",
       "\n",
       "                </table>\n",
       "            </details>\n",
       "            </div>\n",
       "        </div>\n",
       "        \n",
       "\n",
       "    </details>\n",
       "</div>\n",
       "\n",
       "        </details>\n",
       "    </div>\n",
       "</div>\n",
       "            </details>\n",
       "        \n",
       "\n",
       "    </div>\n",
       "</div>"
      ],
      "text/plain": [
       "<Client: 'tcp://127.0.0.1:63903' processes=8 threads=128, memory=149.01 GiB>"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from dask.distributed import Client\n",
    "client = Client(n_workers=8, threads_per_worker=16, processes=True, memory_limit='20GB')\n",
    "client"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Start a client for Mongo DB"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pymongo\n",
    "import xarray_mongodb\n",
    "\n",
    "from DataContainer.MongoDB import MongoDB\n",
    "\n",
    "mongoClient = pymongo.MongoClient('mongodb://control:DyLab2021@127.0.0.1:27017/?authMechanism=DEFAULT')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Set global path for experiment"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "groupList = [\n",
    "    \"images/MOT_3D_Camera/in_situ_absorption\",\n",
    "    \"images/ODT_1_Axis_Camera/in_situ_absorption\",\n",
    "    \"images/ODT_2_Axis_Camera/in_situ_absorption\",\n",
    "]\n",
    "\n",
    "dskey = {\n",
    "    \"images/MOT_3D_Camera/in_situ_absorption\": \"camera_0\",\n",
    "    \"images/ODT_1_Axis_Camera/in_situ_absorption\": \"camera_1\",\n",
    "    \"images/ODT_2_Axis_Camera/in_situ_absorption\": \"camera_2\",\n",
    "}\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "img_dir = 'C:/Users/control/DyLab/Experiments/DyBEC/'\n",
    "SequenceName = \"Repetition_scan\"\n",
    "folderPath = img_dir + SequenceName + \"/\" + get_date()\n",
    "\n",
    "mongoDB = mongoClient[SequenceName]\n",
    "\n",
    "DB = MongoDB(mongoClient, mongoDB, date=get_date())"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Repetition Scans"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## scan MOT freq"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The detected scaning axes and values are: \n",
      "\n",
      "{'initial_horz_freq': array([102.75, 102.8 , 102.85, 102.9 , 102.95, 103.  , 103.05]), 'initial_vert_freq': array([101.8 , 101.85, 101.9 , 101.95, 102.  , 102.05, 102.1 , 102.15,\n",
      "       102.2 , 102.25])}\n"
     ]
    },
    {
     "data": {
      "application/javascript": "/* Put everything inside the global mpl namespace */\n/* global mpl */\nwindow.mpl = {};\n\nmpl.get_websocket_type = function () {\n    if (typeof WebSocket !== 'undefined') {\n        return WebSocket;\n    } else if (typeof MozWebSocket !== 'undefined') {\n        return MozWebSocket;\n    } else {\n        alert(\n            'Your browser does not have WebSocket support. ' +\n                'Please try Chrome, Safari or Firefox ≥ 6. ' +\n                'Firefox 4 and 5 are also supported but you ' +\n                'have to enable WebSockets in about:config.'\n        );\n    }\n};\n\nmpl.figure = function (figure_id, websocket, ondownload, parent_element) {\n    this.id = figure_id;\n\n    this.ws = websocket;\n\n    this.supports_binary = this.ws.binaryType !== undefined;\n\n    if (!this.supports_binary) {\n        var warnings = document.getElementById('mpl-warnings');\n        if (warnings) {\n            warnings.style.display = 'block';\n            warnings.textContent =\n                'This browser does not support binary websocket messages. ' +\n                'Performance may be slow.';\n        }\n    }\n\n    this.imageObj = new Image();\n\n    this.context = undefined;\n    this.message = undefined;\n    this.canvas = undefined;\n    this.rubberband_canvas = undefined;\n    this.rubberband_context = undefined;\n    this.format_dropdown = undefined;\n\n    this.image_mode = 'full';\n\n    this.root = document.createElement('div');\n    this.root.setAttribute('style', 'display: inline-block');\n    this._root_extra_style(this.root);\n\n    parent_element.appendChild(this.root);\n\n    this._init_header(this);\n    this._init_canvas(this);\n    this._init_toolbar(this);\n\n    var fig = this;\n\n    this.waiting = false;\n\n    this.ws.onopen = function () {\n        fig.send_message('supports_binary', { value: fig.supports_binary });\n        fig.send_message('send_image_mode', {});\n        if (fig.ratio !== 1) {\n            fig.send_message('set_device_pixel_ratio', {\n                device_pixel_ratio: fig.ratio,\n            });\n        }\n        fig.send_message('refresh', {});\n    };\n\n    this.imageObj.onload = function () {\n        if (fig.image_mode === 'full') {\n            // Full images could contain transparency (where diff images\n            // almost always do), so we need to clear the canvas so that\n            // there is no ghosting.\n            fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n        }\n        fig.context.drawImage(fig.imageObj, 0, 0);\n    };\n\n    this.imageObj.onunload = function () {\n        fig.ws.close();\n    };\n\n    this.ws.onmessage = this._make_on_message_function(this);\n\n    this.ondownload = ondownload;\n};\n\nmpl.figure.prototype._init_header = function () {\n    var titlebar = document.createElement('div');\n    titlebar.classList =\n        'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n    var titletext = document.createElement('div');\n    titletext.classList = 'ui-dialog-title';\n    titletext.setAttribute(\n        'style',\n        'width: 100%; text-align: center; padding: 3px;'\n    );\n    titlebar.appendChild(titletext);\n    this.root.appendChild(titlebar);\n    this.header = titletext;\n};\n\nmpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._init_canvas = function () {\n    var fig = this;\n\n    var canvas_div = (this.canvas_div = document.createElement('div'));\n    canvas_div.setAttribute(\n        'style',\n        'border: 1px solid #ddd;' +\n            'box-sizing: content-box;' +\n            'clear: both;' +\n            'min-height: 1px;' +\n            'min-width: 1px;' +\n            'outline: 0;' +\n            'overflow: hidden;' +\n            'position: relative;' +\n            'resize: both;'\n    );\n\n    function on_keyboard_event_closure(name) {\n        return function (event) {\n            return fig.key_event(event, name);\n        };\n    }\n\n    canvas_div.addEventListener(\n        'keydown',\n        on_keyboard_event_closure('key_press')\n    );\n    canvas_div.addEventListener(\n        'keyup',\n        on_keyboard_event_closure('key_release')\n    );\n\n    this._canvas_extra_style(canvas_div);\n    this.root.appendChild(canvas_div);\n\n    var canvas = (this.canvas = document.createElement('canvas'));\n    canvas.classList.add('mpl-canvas');\n    canvas.setAttribute('style', 'box-sizing: content-box;');\n\n    this.context = canvas.getContext('2d');\n\n    var backingStore =\n        this.context.backingStorePixelRatio ||\n        this.context.webkitBackingStorePixelRatio ||\n        this.context.mozBackingStorePixelRatio ||\n        this.context.msBackingStorePixelRatio ||\n        this.context.oBackingStorePixelRatio ||\n        this.context.backingStorePixelRatio ||\n        1;\n\n    this.ratio = (window.devicePixelRatio || 1) / backingStore;\n\n    var rubberband_canvas = (this.rubberband_canvas = document.createElement(\n        'canvas'\n    ));\n    rubberband_canvas.setAttribute(\n        'style',\n        'box-sizing: content-box; position: absolute; left: 0; top: 0; z-index: 1;'\n    );\n\n    // Apply a ponyfill if ResizeObserver is not implemented by browser.\n    if (this.ResizeObserver === undefined) {\n        if (window.ResizeObserver !== undefined) {\n            this.ResizeObserver = window.ResizeObserver;\n        } else {\n            var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n            this.ResizeObserver = obs.ResizeObserver;\n        }\n    }\n\n    this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n        var nentries = entries.length;\n        for (var i = 0; i < nentries; i++) {\n            var entry = entries[i];\n            var width, height;\n            if (entry.contentBoxSize) {\n                if (entry.contentBoxSize instanceof Array) {\n                    // Chrome 84 implements new version of spec.\n                    width = entry.contentBoxSize[0].inlineSize;\n                    height = entry.contentBoxSize[0].blockSize;\n                } else {\n                    // Firefox implements old version of spec.\n                    width = entry.contentBoxSize.inlineSize;\n                    height = entry.contentBoxSize.blockSize;\n                }\n            } else {\n                // Chrome <84 implements even older version of spec.\n                width = entry.contentRect.width;\n                height = entry.contentRect.height;\n            }\n\n            // Keep the size of the canvas and rubber band canvas in sync with\n            // the canvas container.\n            if (entry.devicePixelContentBoxSize) {\n                // Chrome 84 implements new version of spec.\n                canvas.setAttribute(\n                    'width',\n                    entry.devicePixelContentBoxSize[0].inlineSize\n                );\n                canvas.setAttribute(\n                    'height',\n                    entry.devicePixelContentBoxSize[0].blockSize\n                );\n            } else {\n                canvas.setAttribute('width', width * fig.ratio);\n                canvas.setAttribute('height', height * fig.ratio);\n            }\n            canvas.setAttribute(\n                'style',\n                'width: ' + width + 'px; height: ' + height + 'px;'\n            );\n\n            rubberband_canvas.setAttribute('width', width);\n            rubberband_canvas.setAttribute('height', height);\n\n            // And update the size in Python. We ignore the initial 0/0 size\n            // that occurs as the element is placed into the DOM, which should\n            // otherwise not happen due to the minimum size styling.\n            if (fig.ws.readyState == 1 && width != 0 && height != 0) {\n                fig.request_resize(width, height);\n            }\n        }\n    });\n    this.resizeObserverInstance.observe(canvas_div);\n\n    function on_mouse_event_closure(name) {\n        return function (event) {\n            return fig.mouse_event(event, name);\n        };\n    }\n\n    rubberband_canvas.addEventListener(\n        'mousedown',\n        on_mouse_event_closure('button_press')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseup',\n        on_mouse_event_closure('button_release')\n    );\n    rubberband_canvas.addEventListener(\n        'dblclick',\n        on_mouse_event_closure('dblclick')\n    );\n    // Throttle sequential mouse events to 1 every 20ms.\n    rubberband_canvas.addEventListener(\n        'mousemove',\n        on_mouse_event_closure('motion_notify')\n    );\n\n    rubberband_canvas.addEventListener(\n        'mouseenter',\n        on_mouse_event_closure('figure_enter')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseleave',\n        on_mouse_event_closure('figure_leave')\n    );\n\n    canvas_div.addEventListener('wheel', function (event) {\n        if (event.deltaY < 0) {\n            event.step = 1;\n        } else {\n            event.step = -1;\n        }\n        on_mouse_event_closure('scroll')(event);\n    });\n\n    canvas_div.appendChild(canvas);\n    canvas_div.appendChild(rubberband_canvas);\n\n    this.rubberband_context = rubberband_canvas.getContext('2d');\n    this.rubberband_context.strokeStyle = '#000000';\n\n    this._resize_canvas = function (width, height, forward) {\n        if (forward) {\n            canvas_div.style.width = width + 'px';\n            canvas_div.style.height = height + 'px';\n        }\n    };\n\n    // Disable right mouse context menu.\n    this.rubberband_canvas.addEventListener('contextmenu', function (_e) {\n        event.preventDefault();\n        return false;\n    });\n\n    function set_focus() {\n        canvas.focus();\n        canvas_div.focus();\n    }\n\n    window.setTimeout(set_focus, 100);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'mpl-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'mpl-button-group';\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'mpl-button-group';\n            continue;\n        }\n\n        var button = (fig.buttons[name] = document.createElement('button'));\n        button.classList = 'mpl-widget';\n        button.setAttribute('role', 'button');\n        button.setAttribute('aria-disabled', 'false');\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n\n        var icon_img = document.createElement('img');\n        icon_img.src = '_images/' + image + '.png';\n        icon_img.srcset = '_images/' + image + '_large.png 2x';\n        icon_img.alt = tooltip;\n        button.appendChild(icon_img);\n\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    var fmt_picker = document.createElement('select');\n    fmt_picker.classList = 'mpl-widget';\n    toolbar.appendChild(fmt_picker);\n    this.format_dropdown = fmt_picker;\n\n    for (var ind in mpl.extensions) {\n        var fmt = mpl.extensions[ind];\n        var option = document.createElement('option');\n        option.selected = fmt === mpl.default_extension;\n        option.innerHTML = fmt;\n        fmt_picker.appendChild(option);\n    }\n\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n};\n\nmpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n    // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n    // which will in turn request a refresh of the image.\n    this.send_message('resize', { width: x_pixels, height: y_pixels });\n};\n\nmpl.figure.prototype.send_message = function (type, properties) {\n    properties['type'] = type;\n    properties['figure_id'] = this.id;\n    this.ws.send(JSON.stringify(properties));\n};\n\nmpl.figure.prototype.send_draw_message = function () {\n    if (!this.waiting) {\n        this.waiting = true;\n        this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    var format_dropdown = fig.format_dropdown;\n    var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n    fig.ondownload(fig, format);\n};\n\nmpl.figure.prototype.handle_resize = function (fig, msg) {\n    var size = msg['size'];\n    if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n        fig._resize_canvas(size[0], size[1], msg['forward']);\n        fig.send_message('refresh', {});\n    }\n};\n\nmpl.figure.prototype.handle_rubberband = function (fig, msg) {\n    var x0 = msg['x0'] / fig.ratio;\n    var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n    var x1 = msg['x1'] / fig.ratio;\n    var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n    x0 = Math.floor(x0) + 0.5;\n    y0 = Math.floor(y0) + 0.5;\n    x1 = Math.floor(x1) + 0.5;\n    y1 = Math.floor(y1) + 0.5;\n    var min_x = Math.min(x0, x1);\n    var min_y = Math.min(y0, y1);\n    var width = Math.abs(x1 - x0);\n    var height = Math.abs(y1 - y0);\n\n    fig.rubberband_context.clearRect(\n        0,\n        0,\n        fig.canvas.width / fig.ratio,\n        fig.canvas.height / fig.ratio\n    );\n\n    fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n};\n\nmpl.figure.prototype.handle_figure_label = function (fig, msg) {\n    // Updates the figure title.\n    fig.header.textContent = msg['label'];\n};\n\nmpl.figure.prototype.handle_cursor = function (fig, msg) {\n    fig.rubberband_canvas.style.cursor = msg['cursor'];\n};\n\nmpl.figure.prototype.handle_message = function (fig, msg) {\n    fig.message.textContent = msg['message'];\n};\n\nmpl.figure.prototype.handle_draw = function (fig, _msg) {\n    // Request the server to send over a new figure.\n    fig.send_draw_message();\n};\n\nmpl.figure.prototype.handle_image_mode = function (fig, msg) {\n    fig.image_mode = msg['mode'];\n};\n\nmpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n    for (var key in msg) {\n        if (!(key in fig.buttons)) {\n            continue;\n        }\n        fig.buttons[key].disabled = !msg[key];\n        fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n    }\n};\n\nmpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n    if (msg['mode'] === 'PAN') {\n        fig.buttons['Pan'].classList.add('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    } else if (msg['mode'] === 'ZOOM') {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.add('active');\n    } else {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    }\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Called whenever the canvas gets updated.\n    this.send_message('ack', {});\n};\n\n// A function to construct a web socket function for onmessage handling.\n// Called in the figure constructor.\nmpl.figure.prototype._make_on_message_function = function (fig) {\n    return function socket_on_message(evt) {\n        if (evt.data instanceof Blob) {\n            var img = evt.data;\n            if (img.type !== 'image/png') {\n                /* FIXME: We get \"Resource interpreted as Image but\n                 * transferred with MIME type text/plain:\" errors on\n                 * Chrome.  But how to set the MIME type?  It doesn't seem\n                 * to be part of the websocket stream */\n                img.type = 'image/png';\n            }\n\n            /* Free the memory for the previous frames */\n            if (fig.imageObj.src) {\n                (window.URL || window.webkitURL).revokeObjectURL(\n                    fig.imageObj.src\n                );\n            }\n\n            fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n                img\n            );\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        } else if (\n            typeof evt.data === 'string' &&\n            evt.data.slice(0, 21) === 'data:image/png;base64'\n        ) {\n            fig.imageObj.src = evt.data;\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        }\n\n        var msg = JSON.parse(evt.data);\n        var msg_type = msg['type'];\n\n        // Call the  \"handle_{type}\" callback, which takes\n        // the figure and JSON message as its only arguments.\n        try {\n            var callback = fig['handle_' + msg_type];\n        } catch (e) {\n            console.log(\n                \"No handler for the '\" + msg_type + \"' message type: \",\n                msg\n            );\n            return;\n        }\n\n        if (callback) {\n            try {\n                // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n                callback(fig, msg);\n            } catch (e) {\n                console.log(\n                    \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n                    e,\n                    e.stack,\n                    msg\n                );\n            }\n        }\n    };\n};\n\n// from https://stackoverflow.com/questions/1114465/getting-mouse-location-in-canvas\nmpl.findpos = function (e) {\n    //this section is from http://www.quirksmode.org/js/events_properties.html\n    var targ;\n    if (!e) {\n        e = window.event;\n    }\n    if (e.target) {\n        targ = e.target;\n    } else if (e.srcElement) {\n        targ = e.srcElement;\n    }\n    if (targ.nodeType === 3) {\n        // defeat Safari bug\n        targ = targ.parentNode;\n    }\n\n    // pageX,Y are the mouse positions relative to the document\n    var boundingRect = targ.getBoundingClientRect();\n    var x = e.pageX - (boundingRect.left + document.body.scrollLeft);\n    var y = e.pageY - (boundingRect.top + document.body.scrollTop);\n\n    return { x: x, y: y };\n};\n\n/*\n * return a copy of an object with only non-object keys\n * we need this to avoid circular references\n * https://stackoverflow.com/a/24161582/3208463\n */\nfunction simpleKeys(original) {\n    return Object.keys(original).reduce(function (obj, key) {\n        if (typeof original[key] !== 'object') {\n            obj[key] = original[key];\n        }\n        return obj;\n    }, {});\n}\n\nmpl.figure.prototype.mouse_event = function (event, name) {\n    var canvas_pos = mpl.findpos(event);\n\n    if (name === 'button_press') {\n        this.canvas.focus();\n        this.canvas_div.focus();\n    }\n\n    var x = canvas_pos.x * this.ratio;\n    var y = canvas_pos.y * this.ratio;\n\n    this.send_message(name, {\n        x: x,\n        y: y,\n        button: event.button,\n        step: event.step,\n        guiEvent: simpleKeys(event),\n    });\n\n    /* This prevents the web browser from automatically changing to\n     * the text insertion cursor when the button is pressed.  We want\n     * to control all of the cursor setting manually through the\n     * 'cursor' event from matplotlib */\n    event.preventDefault();\n    return false;\n};\n\nmpl.figure.prototype._key_event_extra = function (_event, _name) {\n    // Handle any extra behaviour associated with a key event\n};\n\nmpl.figure.prototype.key_event = function (event, name) {\n    // Prevent repeat events\n    if (name === 'key_press') {\n        if (event.key === this._key) {\n            return;\n        } else {\n            this._key = event.key;\n        }\n    }\n    if (name === 'key_release') {\n        this._key = null;\n    }\n\n    var value = '';\n    if (event.ctrlKey && event.key !== 'Control') {\n        value += 'ctrl+';\n    }\n    else if (event.altKey && event.key !== 'Alt') {\n        value += 'alt+';\n    }\n    else if (event.shiftKey && event.key !== 'Shift') {\n        value += 'shift+';\n    }\n\n    value += 'k' + event.key;\n\n    this._key_event_extra(event, name);\n\n    this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n    return false;\n};\n\nmpl.figure.prototype.toolbar_button_onclick = function (name) {\n    if (name === 'download') {\n        this.handle_save(this, null);\n    } else {\n        this.send_message('toolbar_button', { name: name });\n    }\n};\n\nmpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n    this.message.textContent = tooltip;\n};\n\n///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n// prettier-ignore\nvar _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\nmpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home icon-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left icon-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right icon-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows icon-move\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis\", \"fa fa-square-o icon-check-empty\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o icon-save\", \"download\"]];\n\nmpl.extensions = [\"eps\", \"jpeg\", \"pgf\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\"];\n\nmpl.default_extension = \"png\";/* global mpl */\n\nvar comm_websocket_adapter = function (comm) {\n    // Create a \"websocket\"-like object which calls the given IPython comm\n    // object with the appropriate methods. Currently this is a non binary\n    // socket, so there is still some room for performance tuning.\n    var ws = {};\n\n    ws.binaryType = comm.kernel.ws.binaryType;\n    ws.readyState = comm.kernel.ws.readyState;\n    function updateReadyState(_event) {\n        if (comm.kernel.ws) {\n            ws.readyState = comm.kernel.ws.readyState;\n        } else {\n            ws.readyState = 3; // Closed state.\n        }\n    }\n    comm.kernel.ws.addEventListener('open', updateReadyState);\n    comm.kernel.ws.addEventListener('close', updateReadyState);\n    comm.kernel.ws.addEventListener('error', updateReadyState);\n\n    ws.close = function () {\n        comm.close();\n    };\n    ws.send = function (m) {\n        //console.log('sending', m);\n        comm.send(m);\n    };\n    // Register the callback with on_msg.\n    comm.on_msg(function (msg) {\n        //console.log('receiving', msg['content']['data'], msg);\n        var data = msg['content']['data'];\n        if (data['blob'] !== undefined) {\n            data = {\n                data: new Blob(msg['buffers'], { type: data['blob'] }),\n            };\n        }\n        // Pass the mpl event to the overridden (by mpl) onmessage function.\n        ws.onmessage(data);\n    });\n    return ws;\n};\n\nmpl.mpl_figure_comm = function (comm, msg) {\n    // This is the function which gets called when the mpl process\n    // starts-up an IPython Comm through the \"matplotlib\" channel.\n\n    var id = msg.content.data.id;\n    // Get hold of the div created by the display call when the Comm\n    // socket was opened in Python.\n    var element = document.getElementById(id);\n    var ws_proxy = comm_websocket_adapter(comm);\n\n    function ondownload(figure, _format) {\n        window.open(figure.canvas.toDataURL());\n    }\n\n    var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n\n    // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n    // web socket which is closed, not our websocket->open comm proxy.\n    ws_proxy.onopen();\n\n    fig.parent_element = element;\n    fig.cell_info = mpl.find_output_cell(\"<div id='\" + id + \"'></div>\");\n    if (!fig.cell_info) {\n        console.error('Failed to find cell for figure', id, fig);\n        return;\n    }\n    fig.cell_info[0].output_area.element.on(\n        'cleared',\n        { fig: fig },\n        fig._remove_fig_handler\n    );\n};\n\nmpl.figure.prototype.handle_close = function (fig, msg) {\n    var width = fig.canvas.width / fig.ratio;\n    fig.cell_info[0].output_area.element.off(\n        'cleared',\n        fig._remove_fig_handler\n    );\n    fig.resizeObserverInstance.unobserve(fig.canvas_div);\n\n    // Update the output cell to use the data from the current canvas.\n    fig.push_to_output();\n    var dataURL = fig.canvas.toDataURL();\n    // Re-enable the keyboard manager in IPython - without this line, in FF,\n    // the notebook keyboard shortcuts fail.\n    IPython.keyboard_manager.enable();\n    fig.parent_element.innerHTML =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n    fig.close_ws(fig, msg);\n};\n\nmpl.figure.prototype.close_ws = function (fig, msg) {\n    fig.send_message('closing', msg);\n    // fig.ws.close()\n};\n\nmpl.figure.prototype.push_to_output = function (_remove_interactive) {\n    // Turn the data on the canvas into data in the output cell.\n    var width = this.canvas.width / this.ratio;\n    var dataURL = this.canvas.toDataURL();\n    this.cell_info[1]['text/html'] =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Tell IPython that the notebook contents must change.\n    IPython.notebook.set_dirty(true);\n    this.send_message('ack', {});\n    var fig = this;\n    // Wait a second, then push the new image to the DOM so\n    // that it is saved nicely (might be nice to debounce this).\n    setTimeout(function () {\n        fig.push_to_output();\n    }, 1000);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'btn-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'btn-group';\n    var button;\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'btn-group';\n            continue;\n        }\n\n        button = fig.buttons[name] = document.createElement('button');\n        button.classList = 'btn btn-default';\n        button.href = '#';\n        button.title = name;\n        button.innerHTML = '<i class=\"fa ' + image + ' fa-lg\"></i>';\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    // Add the status bar.\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message pull-right';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n\n    // Add the close button to the window.\n    var buttongrp = document.createElement('div');\n    buttongrp.classList = 'btn-group inline pull-right';\n    button = document.createElement('button');\n    button.classList = 'btn btn-mini btn-primary';\n    button.href = '#';\n    button.title = 'Stop Interaction';\n    button.innerHTML = '<i class=\"fa fa-power-off icon-remove icon-large\"></i>';\n    button.addEventListener('click', function (_evt) {\n        fig.handle_close(fig, {});\n    });\n    button.addEventListener(\n        'mouseover',\n        on_mouseover_closure('Stop Interaction')\n    );\n    buttongrp.appendChild(button);\n    var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n    titlebar.insertBefore(buttongrp, titlebar.firstChild);\n};\n\nmpl.figure.prototype._remove_fig_handler = function (event) {\n    var fig = event.data.fig;\n    if (event.target !== this) {\n        // Ignore bubbled events from children.\n        return;\n    }\n    fig.close_ws(fig, {});\n};\n\nmpl.figure.prototype._root_extra_style = function (el) {\n    el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n};\n\nmpl.figure.prototype._canvas_extra_style = function (el) {\n    // this is important to make the div 'focusable\n    el.setAttribute('tabindex', 0);\n    // reach out to IPython and tell the keyboard manager to turn it's self\n    // off when our div gets focus\n\n    // location in version 3\n    if (IPython.notebook.keyboard_manager) {\n        IPython.notebook.keyboard_manager.register_events(el);\n    } else {\n        // location in version 2\n        IPython.keyboard_manager.register_events(el);\n    }\n};\n\nmpl.figure.prototype._key_event_extra = function (event, _name) {\n    // Check for shift+enter\n    if (event.shiftKey && event.which === 13) {\n        this.canvas_div.blur();\n        // select the cell after this one\n        var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n        IPython.notebook.select(index + 1);\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    fig.ondownload(fig, null);\n};\n\nmpl.find_output_cell = function (html_output) {\n    // Return the cell and output element which can be found *uniquely* in the notebook.\n    // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n    // IPython event is triggered only after the cells have been serialised, which for\n    // our purposes (turning an active figure into a static one), is too late.\n    var cells = IPython.notebook.get_cells();\n    var ncells = cells.length;\n    for (var i = 0; i < ncells; i++) {\n        var cell = cells[i];\n        if (cell.cell_type === 'code') {\n            for (var j = 0; j < cell.output_area.outputs.length; j++) {\n                var data = cell.output_area.outputs[j];\n                if (data.data) {\n                    // IPython >= 3 moved mimebundle to data attribute of output\n                    data = data.data;\n                }\n                if (data['text/html'] === html_output) {\n                    return [cell, data, j];\n                }\n            }\n        }\n    }\n};\n\n// Register the function which deals with the matplotlib target/channel.\n// The kernel may be null if the page has been refreshed.\nif (IPython.notebook.kernel !== null) {\n    IPython.notebook.kernel.comm_manager.register_target(\n        'matplotlib',\n        mpl.mpl_figure_comm\n    );\n}\n",
      "text/plain": [
       "<IPython.core.display.Javascript object>"
      ]
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     "output_type": "display_data"
    },
    {
     "data": {
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       "<img src=\"data:image/png;base64,[encoded data, 50208 characters]\" width=\"640\">"
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   ],
   "source": [
    "%matplotlib notebook\n",
    "shotNum = \"0014\"\n",
    "filePath = folderPath + \"/\" + shotNum + \"/*.h5\"\n",
    "\n",
    "dataSetDict = {\n",
    "    dskey[groupList[i]]: read_hdf5_file(filePath, groupList[i])\n",
    "    for i in [0,1]\n",
    "}\n",
    "\n",
    "dataSet = dataSetDict[\"camera_1\"]\n",
    "\n",
    "print_scanAxis(dataSet)\n",
    "\n",
    "scanAxis = get_scanAxis(dataSet)\n",
    "\n",
    "dataSet = auto_rechunk(dataSet)\n",
    "\n",
    "dataSet = imageAnalyser.get_absorption_images(dataSet)\n",
    "\n",
    "imageAnalyser.center = (310, 815)\n",
    "imageAnalyser.span = (550, 1275)\n",
    "imageAnalyser.fraction = (0.1, 0.1)\n",
    "\n",
    "dataSet_cropOD = imageAnalyser.crop_image(dataSet.OD)\n",
    "dataSet_cropOD = imageAnalyser.substract_offset(dataSet_cropOD).load()\n",
    "\n",
    "Ncount = imageAnalyser.get_Ncount(dataSet_cropOD)\n",
    "Ncount_mean = calculate_mean(Ncount)\n",
    "Ncount_std = calculate_std(Ncount)\n",
    "\n",
    "fig = plt.figure()\n",
    "ax = fig.gca()\n",
    "Ncount_mean.plot.pcolormesh(ax=ax, vmin=0, cmap='jet', cbar_kwargs = dict(label='NCount'))\n",
    "plt.xlabel('Vert AOM Frequency')\n",
    "plt.ylabel('Horz AOM Frequency')\n",
    "plt.tight_layout()\n",
    "plt.show()\n",
    "\n",
    "# DB.create_global(shotNum, dataSet)\n",
    "# DB.add_data(shotNum, dataSet_cropOD, engine='xarray')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
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       "}\n",
       "\n",
       ".xr-header > div,\n",
       ".xr-header > ul {\n",
       "  display: inline;\n",
       "  margin-top: 0;\n",
       "  margin-bottom: 0;\n",
       "}\n",
       "\n",
       ".xr-obj-type,\n",
       ".xr-array-name {\n",
       "  margin-left: 2px;\n",
       "  margin-right: 10px;\n",
       "}\n",
       "\n",
       ".xr-obj-type {\n",
       "  color: var(--xr-font-color2);\n",
       "}\n",
       "\n",
       ".xr-sections {\n",
       "  padding-left: 0 !important;\n",
       "  display: grid;\n",
       "  grid-template-columns: 150px auto auto 1fr 20px 20px;\n",
       "}\n",
       "\n",
       ".xr-section-item {\n",
       "  display: contents;\n",
       "}\n",
       "\n",
       ".xr-section-item input {\n",
       "  display: none;\n",
       "}\n",
       "\n",
       ".xr-section-item input + label {\n",
       "  color: var(--xr-disabled-color);\n",
       "}\n",
       "\n",
       ".xr-section-item input:enabled + label {\n",
       "  cursor: pointer;\n",
       "  color: var(--xr-font-color2);\n",
       "}\n",
       "\n",
       ".xr-section-item input:enabled + label:hover {\n",
       "  color: var(--xr-font-color0);\n",
       "}\n",
       "\n",
       ".xr-section-summary {\n",
       "  grid-column: 1;\n",
       "  color: var(--xr-font-color2);\n",
       "  font-weight: 500;\n",
       "}\n",
       "\n",
       ".xr-section-summary > span {\n",
       "  display: inline-block;\n",
       "  padding-left: 0.5em;\n",
       "}\n",
       "\n",
       ".xr-section-summary-in:disabled + label {\n",
       "  color: var(--xr-font-color2);\n",
       "}\n",
       "\n",
       ".xr-section-summary-in + label:before {\n",
       "  display: inline-block;\n",
       "  content: '►';\n",
       "  font-size: 11px;\n",
       "  width: 15px;\n",
       "  text-align: center;\n",
       "}\n",
       "\n",
       ".xr-section-summary-in:disabled + label:before {\n",
       "  color: var(--xr-disabled-color);\n",
       "}\n",
       "\n",
       ".xr-section-summary-in:checked + label:before {\n",
       "  content: '▼';\n",
       "}\n",
       "\n",
       ".xr-section-summary-in:checked + label > span {\n",
       "  display: none;\n",
       "}\n",
       "\n",
       ".xr-section-summary,\n",
       ".xr-section-inline-details {\n",
       "  padding-top: 4px;\n",
       "  padding-bottom: 4px;\n",
       "}\n",
       "\n",
       ".xr-section-inline-details {\n",
       "  grid-column: 2 / -1;\n",
       "}\n",
       "\n",
       ".xr-section-details {\n",
       "  display: none;\n",
       "  grid-column: 1 / -1;\n",
       "  margin-bottom: 5px;\n",
       "}\n",
       "\n",
       ".xr-section-summary-in:checked ~ .xr-section-details {\n",
       "  display: contents;\n",
       "}\n",
       "\n",
       ".xr-array-wrap {\n",
       "  grid-column: 1 / -1;\n",
       "  display: grid;\n",
       "  grid-template-columns: 20px auto;\n",
       "}\n",
       "\n",
       ".xr-array-wrap > label {\n",
       "  grid-column: 1;\n",
       "  vertical-align: top;\n",
       "}\n",
       "\n",
       ".xr-preview {\n",
       "  color: var(--xr-font-color3);\n",
       "}\n",
       "\n",
       ".xr-array-preview,\n",
       ".xr-array-data {\n",
       "  padding: 0 5px !important;\n",
       "  grid-column: 2;\n",
       "}\n",
       "\n",
       ".xr-array-data,\n",
       ".xr-array-in:checked ~ .xr-array-preview {\n",
       "  display: none;\n",
       "}\n",
       "\n",
       ".xr-array-in:checked ~ .xr-array-data,\n",
       ".xr-array-preview {\n",
       "  display: inline-block;\n",
       "}\n",
       "\n",
       ".xr-dim-list {\n",
       "  display: inline-block !important;\n",
       "  list-style: none;\n",
       "  padding: 0 !important;\n",
       "  margin: 0;\n",
       "}\n",
       "\n",
       ".xr-dim-list li {\n",
       "  display: inline-block;\n",
       "  padding: 0;\n",
       "  margin: 0;\n",
       "}\n",
       "\n",
       ".xr-dim-list:before {\n",
       "  content: '(';\n",
       "}\n",
       "\n",
       ".xr-dim-list:after {\n",
       "  content: ')';\n",
       "}\n",
       "\n",
       ".xr-dim-list li:not(:last-child):after {\n",
       "  content: ',';\n",
       "  padding-right: 5px;\n",
       "}\n",
       "\n",
       ".xr-has-index {\n",
       "  font-weight: bold;\n",
       "}\n",
       "\n",
       ".xr-var-list,\n",
       ".xr-var-item {\n",
       "  display: contents;\n",
       "}\n",
       "\n",
       ".xr-var-item > div,\n",
       ".xr-var-item label,\n",
       ".xr-var-item > .xr-var-name span {\n",
       "  background-color: var(--xr-background-color-row-even);\n",
       "  margin-bottom: 0;\n",
       "}\n",
       "\n",
       ".xr-var-item > .xr-var-name:hover span {\n",
       "  padding-right: 5px;\n",
       "}\n",
       "\n",
       ".xr-var-list > li:nth-child(odd) > div,\n",
       ".xr-var-list > li:nth-child(odd) > label,\n",
       ".xr-var-list > li:nth-child(odd) > .xr-var-name span {\n",
       "  background-color: var(--xr-background-color-row-odd);\n",
       "}\n",
       "\n",
       ".xr-var-name {\n",
       "  grid-column: 1;\n",
       "}\n",
       "\n",
       ".xr-var-dims {\n",
       "  grid-column: 2;\n",
       "}\n",
       "\n",
       ".xr-var-dtype {\n",
       "  grid-column: 3;\n",
       "  text-align: right;\n",
       "  color: var(--xr-font-color2);\n",
       "}\n",
       "\n",
       ".xr-var-preview {\n",
       "  grid-column: 4;\n",
       "}\n",
       "\n",
       ".xr-index-preview {\n",
       "  grid-column: 2 / 5;\n",
       "  color: var(--xr-font-color2);\n",
       "}\n",
       "\n",
       ".xr-var-name,\n",
       ".xr-var-dims,\n",
       ".xr-var-dtype,\n",
       ".xr-preview,\n",
       ".xr-attrs dt {\n",
       "  white-space: nowrap;\n",
       "  overflow: hidden;\n",
       "  text-overflow: ellipsis;\n",
       "  padding-right: 10px;\n",
       "}\n",
       "\n",
       ".xr-var-name:hover,\n",
       ".xr-var-dims:hover,\n",
       ".xr-var-dtype:hover,\n",
       ".xr-attrs dt:hover {\n",
       "  overflow: visible;\n",
       "  width: auto;\n",
       "  z-index: 1;\n",
       "}\n",
       "\n",
       ".xr-var-attrs,\n",
       ".xr-var-data,\n",
       ".xr-index-data {\n",
       "  display: none;\n",
       "  background-color: var(--xr-background-color) !important;\n",
       "  padding-bottom: 5px !important;\n",
       "}\n",
       "\n",
       ".xr-var-attrs-in:checked ~ .xr-var-attrs,\n",
       ".xr-var-data-in:checked ~ .xr-var-data,\n",
       ".xr-index-data-in:checked ~ .xr-index-data {\n",
       "  display: block;\n",
       "}\n",
       "\n",
       ".xr-var-data > table {\n",
       "  float: right;\n",
       "}\n",
       "\n",
       ".xr-var-name span,\n",
       ".xr-var-data,\n",
       ".xr-index-name div,\n",
       ".xr-index-data,\n",
       ".xr-attrs {\n",
       "  padding-left: 25px !important;\n",
       "}\n",
       "\n",
       ".xr-attrs,\n",
       ".xr-var-attrs,\n",
       ".xr-var-data,\n",
       ".xr-index-data {\n",
       "  grid-column: 1 / -1;\n",
       "}\n",
       "\n",
       "dl.xr-attrs {\n",
       "  padding: 0;\n",
       "  margin: 0;\n",
       "  display: grid;\n",
       "  grid-template-columns: 125px auto;\n",
       "}\n",
       "\n",
       ".xr-attrs dt,\n",
       ".xr-attrs dd {\n",
       "  padding: 0;\n",
       "  margin: 0;\n",
       "  float: left;\n",
       "  padding-right: 10px;\n",
       "  width: auto;\n",
       "}\n",
       "\n",
       ".xr-attrs dt {\n",
       "  font-weight: normal;\n",
       "  grid-column: 1;\n",
       "}\n",
       "\n",
       ".xr-attrs dt:hover span {\n",
       "  display: inline-block;\n",
       "  background: var(--xr-background-color);\n",
       "  padding-right: 10px;\n",
       "}\n",
       "\n",
       ".xr-attrs dd {\n",
       "  grid-column: 2;\n",
       "  white-space: pre-wrap;\n",
       "  word-break: break-all;\n",
       "}\n",
       "\n",
       ".xr-icon-database,\n",
       ".xr-icon-file-text2,\n",
       ".xr-no-icon {\n",
       "  display: inline-block;\n",
       "  vertical-align: middle;\n",
       "  width: 1em;\n",
       "  height: 1.5em !important;\n",
       "  stroke-width: 0;\n",
       "  stroke: currentColor;\n",
       "  fill: currentColor;\n",
       "}\n",
       "</style><pre class='xr-text-repr-fallback'>&lt;xarray.DataArray &#x27;OD&#x27; (initial_horz_freq: 1, initial_vert_freq: 1)&gt;\n",
       "array([[65351.30239154]])\n",
       "Coordinates:\n",
       "  * initial_horz_freq  (initial_horz_freq) float64 103.0\n",
       "  * initial_vert_freq  (initial_vert_freq) float64 101.8</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.DataArray</div><div class='xr-array-name'>'OD'</div><ul class='xr-dim-list'><li><span class='xr-has-index'>initial_horz_freq</span>: 1</li><li><span class='xr-has-index'>initial_vert_freq</span>: 1</li></ul></div><ul class='xr-sections'><li class='xr-section-item'><div class='xr-array-wrap'><input id='section-1a84307d-0552-4450-aa56-34b422ac9c57' class='xr-array-in' type='checkbox' checked><label for='section-1a84307d-0552-4450-aa56-34b422ac9c57' title='Show/hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-array-preview xr-preview'><span>6.535e+04</span></div><div class='xr-array-data'><pre>array([[65351.30239154]])</pre></div></div></li><li class='xr-section-item'><input id='section-fc5fcc47-c424-4595-8493-b6fb33ab058a' class='xr-section-summary-in' type='checkbox'  checked><label for='section-fc5fcc47-c424-4595-8493-b6fb33ab058a' class='xr-section-summary' >Coordinates: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>initial_horz_freq</span></div><div class='xr-var-dims'>(initial_horz_freq)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>103.0</div><input id='attrs-2cb7430e-3fbe-4518-a5b0-c4ffa0684653' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-2cb7430e-3fbe-4518-a5b0-c4ffa0684653' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-601e3bd6-edb0-4887-b832-a015a068cfbd' class='xr-var-data-in' type='checkbox'><label for='data-601e3bd6-edb0-4887-b832-a015a068cfbd' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([103.05])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>initial_vert_freq</span></div><div class='xr-var-dims'>(initial_vert_freq)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>101.8</div><input id='attrs-ceb926a9-c49d-45f6-b305-c3026f758a01' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ceb926a9-c49d-45f6-b305-c3026f758a01' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-cdbc3fd8-77d8-4bda-8dc6-706f8c67e989' class='xr-var-data-in' type='checkbox'><label for='data-cdbc3fd8-77d8-4bda-8dc6-706f8c67e989' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([101.85])</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-510b5835-0192-48da-a654-eee9ac81726a' class='xr-section-summary-in' type='checkbox'  ><label for='section-510b5835-0192-48da-a654-eee9ac81726a' class='xr-section-summary' >Indexes: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-index-name'><div>initial_horz_freq</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-7f10b146-9ec5-442b-9b19-2080607460c7' class='xr-index-data-in' type='checkbox'/><label for='index-7f10b146-9ec5-442b-9b19-2080607460c7' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Float64Index([103.05], dtype=&#x27;float64&#x27;, name=&#x27;initial_horz_freq&#x27;))</pre></div></li><li class='xr-var-item'><div class='xr-index-name'><div>initial_vert_freq</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-bd796bae-f9a5-43d3-9805-41d56c0daed1' class='xr-index-data-in' type='checkbox'/><label for='index-bd796bae-f9a5-43d3-9805-41d56c0daed1' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Float64Index([101.85], dtype=&#x27;float64&#x27;, name=&#x27;initial_vert_freq&#x27;))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-316a92ba-57fa-476c-8a3d-03a5d5c15ba6' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-316a92ba-57fa-476c-8a3d-03a5d5c15ba6' class='xr-section-summary'  title='Expand/collapse section'>Attributes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'></dl></div></li></ul></div></div>"
      ],
      "text/plain": [
       "<xarray.DataArray 'OD' (initial_horz_freq: 1, initial_vert_freq: 1)>\n",
       "array([[65351.30239154]])\n",
       "Coordinates:\n",
       "  * initial_horz_freq  (initial_horz_freq) float64 103.0\n",
       "  * initial_vert_freq  (initial_vert_freq) float64 101.8"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Ncount_mean.where(Ncount_mean==Ncount_mean.max(), drop=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## scan MOT amp"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The detected scaning axes and values are: \n",
      "\n",
      "{'initial_horz_amp': array([0.45, 0.49, 0.53, 0.57, 0.61, 0.65, 0.69, 0.73, 0.77, 0.81]), 'initial_vert_amp': array([0.35, 0.39, 0.43, 0.47, 0.51, 0.55, 0.59, 0.63, 0.67, 0.71])}\n"
     ]
    },
    {
     "data": {
      "application/javascript": "/* Put everything inside the global mpl namespace */\n/* global mpl */\nwindow.mpl = {};\n\nmpl.get_websocket_type = function () {\n    if (typeof WebSocket !== 'undefined') {\n        return WebSocket;\n    } else if (typeof MozWebSocket !== 'undefined') {\n        return MozWebSocket;\n    } else {\n        alert(\n            'Your browser does not have WebSocket support. ' +\n                'Please try Chrome, Safari or Firefox ≥ 6. ' +\n                'Firefox 4 and 5 are also supported but you ' +\n                'have to enable WebSockets in about:config.'\n        );\n    }\n};\n\nmpl.figure = function (figure_id, websocket, ondownload, parent_element) {\n    this.id = figure_id;\n\n    this.ws = websocket;\n\n    this.supports_binary = this.ws.binaryType !== undefined;\n\n    if (!this.supports_binary) {\n        var warnings = document.getElementById('mpl-warnings');\n        if (warnings) {\n            warnings.style.display = 'block';\n            warnings.textContent =\n                'This browser does not support binary websocket messages. ' +\n                'Performance may be slow.';\n        }\n    }\n\n    this.imageObj = new Image();\n\n    this.context = undefined;\n    this.message = undefined;\n    this.canvas = undefined;\n    this.rubberband_canvas = undefined;\n    this.rubberband_context = undefined;\n    this.format_dropdown = undefined;\n\n    this.image_mode = 'full';\n\n    this.root = document.createElement('div');\n    this.root.setAttribute('style', 'display: inline-block');\n    this._root_extra_style(this.root);\n\n    parent_element.appendChild(this.root);\n\n    this._init_header(this);\n    this._init_canvas(this);\n    this._init_toolbar(this);\n\n    var fig = this;\n\n    this.waiting = false;\n\n    this.ws.onopen = function () {\n        fig.send_message('supports_binary', { value: fig.supports_binary });\n        fig.send_message('send_image_mode', {});\n        if (fig.ratio !== 1) {\n            fig.send_message('set_device_pixel_ratio', {\n                device_pixel_ratio: fig.ratio,\n            });\n        }\n        fig.send_message('refresh', {});\n    };\n\n    this.imageObj.onload = function () {\n        if (fig.image_mode === 'full') {\n            // Full images could contain transparency (where diff images\n            // almost always do), so we need to clear the canvas so that\n            // there is no ghosting.\n            fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n        }\n        fig.context.drawImage(fig.imageObj, 0, 0);\n    };\n\n    this.imageObj.onunload = function () {\n        fig.ws.close();\n    };\n\n    this.ws.onmessage = this._make_on_message_function(this);\n\n    this.ondownload = ondownload;\n};\n\nmpl.figure.prototype._init_header = function () {\n    var titlebar = document.createElement('div');\n    titlebar.classList =\n        'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n    var titletext = document.createElement('div');\n    titletext.classList = 'ui-dialog-title';\n    titletext.setAttribute(\n        'style',\n        'width: 100%; text-align: center; padding: 3px;'\n    );\n    titlebar.appendChild(titletext);\n    this.root.appendChild(titlebar);\n    this.header = titletext;\n};\n\nmpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._init_canvas = function () {\n    var fig = this;\n\n    var canvas_div = (this.canvas_div = document.createElement('div'));\n    canvas_div.setAttribute(\n        'style',\n        'border: 1px solid #ddd;' +\n            'box-sizing: content-box;' +\n            'clear: both;' +\n            'min-height: 1px;' +\n            'min-width: 1px;' +\n            'outline: 0;' +\n            'overflow: hidden;' +\n            'position: relative;' +\n            'resize: both;'\n    );\n\n    function on_keyboard_event_closure(name) {\n        return function (event) {\n            return fig.key_event(event, name);\n        };\n    }\n\n    canvas_div.addEventListener(\n        'keydown',\n        on_keyboard_event_closure('key_press')\n    );\n    canvas_div.addEventListener(\n        'keyup',\n        on_keyboard_event_closure('key_release')\n    );\n\n    this._canvas_extra_style(canvas_div);\n    this.root.appendChild(canvas_div);\n\n    var canvas = (this.canvas = document.createElement('canvas'));\n    canvas.classList.add('mpl-canvas');\n    canvas.setAttribute('style', 'box-sizing: content-box;');\n\n    this.context = canvas.getContext('2d');\n\n    var backingStore =\n        this.context.backingStorePixelRatio ||\n        this.context.webkitBackingStorePixelRatio ||\n        this.context.mozBackingStorePixelRatio ||\n        this.context.msBackingStorePixelRatio ||\n        this.context.oBackingStorePixelRatio ||\n        this.context.backingStorePixelRatio ||\n        1;\n\n    this.ratio = (window.devicePixelRatio || 1) / backingStore;\n\n    var rubberband_canvas = (this.rubberband_canvas = document.createElement(\n        'canvas'\n    ));\n    rubberband_canvas.setAttribute(\n        'style',\n        'box-sizing: content-box; position: absolute; left: 0; top: 0; z-index: 1;'\n    );\n\n    // Apply a ponyfill if ResizeObserver is not implemented by browser.\n    if (this.ResizeObserver === undefined) {\n        if (window.ResizeObserver !== undefined) {\n            this.ResizeObserver = window.ResizeObserver;\n        } else {\n            var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n            this.ResizeObserver = obs.ResizeObserver;\n        }\n    }\n\n    this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n        var nentries = entries.length;\n        for (var i = 0; i < nentries; i++) {\n            var entry = entries[i];\n            var width, height;\n            if (entry.contentBoxSize) {\n                if (entry.contentBoxSize instanceof Array) {\n                    // Chrome 84 implements new version of spec.\n                    width = entry.contentBoxSize[0].inlineSize;\n                    height = entry.contentBoxSize[0].blockSize;\n                } else {\n                    // Firefox implements old version of spec.\n                    width = entry.contentBoxSize.inlineSize;\n                    height = entry.contentBoxSize.blockSize;\n                }\n            } else {\n                // Chrome <84 implements even older version of spec.\n                width = entry.contentRect.width;\n                height = entry.contentRect.height;\n            }\n\n            // Keep the size of the canvas and rubber band canvas in sync with\n            // the canvas container.\n            if (entry.devicePixelContentBoxSize) {\n                // Chrome 84 implements new version of spec.\n                canvas.setAttribute(\n                    'width',\n                    entry.devicePixelContentBoxSize[0].inlineSize\n                );\n                canvas.setAttribute(\n                    'height',\n                    entry.devicePixelContentBoxSize[0].blockSize\n                );\n            } else {\n                canvas.setAttribute('width', width * fig.ratio);\n                canvas.setAttribute('height', height * fig.ratio);\n            }\n            canvas.setAttribute(\n                'style',\n                'width: ' + width + 'px; height: ' + height + 'px;'\n            );\n\n            rubberband_canvas.setAttribute('width', width);\n            rubberband_canvas.setAttribute('height', height);\n\n            // And update the size in Python. We ignore the initial 0/0 size\n            // that occurs as the element is placed into the DOM, which should\n            // otherwise not happen due to the minimum size styling.\n            if (fig.ws.readyState == 1 && width != 0 && height != 0) {\n                fig.request_resize(width, height);\n            }\n        }\n    });\n    this.resizeObserverInstance.observe(canvas_div);\n\n    function on_mouse_event_closure(name) {\n        return function (event) {\n            return fig.mouse_event(event, name);\n        };\n    }\n\n    rubberband_canvas.addEventListener(\n        'mousedown',\n        on_mouse_event_closure('button_press')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseup',\n        on_mouse_event_closure('button_release')\n    );\n    rubberband_canvas.addEventListener(\n        'dblclick',\n        on_mouse_event_closure('dblclick')\n    );\n    // Throttle sequential mouse events to 1 every 20ms.\n    rubberband_canvas.addEventListener(\n        'mousemove',\n        on_mouse_event_closure('motion_notify')\n    );\n\n    rubberband_canvas.addEventListener(\n        'mouseenter',\n        on_mouse_event_closure('figure_enter')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseleave',\n        on_mouse_event_closure('figure_leave')\n    );\n\n    canvas_div.addEventListener('wheel', function (event) {\n        if (event.deltaY < 0) {\n            event.step = 1;\n        } else {\n            event.step = -1;\n        }\n        on_mouse_event_closure('scroll')(event);\n    });\n\n    canvas_div.appendChild(canvas);\n    canvas_div.appendChild(rubberband_canvas);\n\n    this.rubberband_context = rubberband_canvas.getContext('2d');\n    this.rubberband_context.strokeStyle = '#000000';\n\n    this._resize_canvas = function (width, height, forward) {\n        if (forward) {\n            canvas_div.style.width = width + 'px';\n            canvas_div.style.height = height + 'px';\n        }\n    };\n\n    // Disable right mouse context menu.\n    this.rubberband_canvas.addEventListener('contextmenu', function (_e) {\n        event.preventDefault();\n        return false;\n    });\n\n    function set_focus() {\n        canvas.focus();\n        canvas_div.focus();\n    }\n\n    window.setTimeout(set_focus, 100);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'mpl-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'mpl-button-group';\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'mpl-button-group';\n            continue;\n        }\n\n        var button = (fig.buttons[name] = document.createElement('button'));\n        button.classList = 'mpl-widget';\n        button.setAttribute('role', 'button');\n        button.setAttribute('aria-disabled', 'false');\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n\n        var icon_img = document.createElement('img');\n        icon_img.src = '_images/' + image + '.png';\n        icon_img.srcset = '_images/' + image + '_large.png 2x';\n        icon_img.alt = tooltip;\n        button.appendChild(icon_img);\n\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    var fmt_picker = document.createElement('select');\n    fmt_picker.classList = 'mpl-widget';\n    toolbar.appendChild(fmt_picker);\n    this.format_dropdown = fmt_picker;\n\n    for (var ind in mpl.extensions) {\n        var fmt = mpl.extensions[ind];\n        var option = document.createElement('option');\n        option.selected = fmt === mpl.default_extension;\n        option.innerHTML = fmt;\n        fmt_picker.appendChild(option);\n    }\n\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n};\n\nmpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n    // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n    // which will in turn request a refresh of the image.\n    this.send_message('resize', { width: x_pixels, height: y_pixels });\n};\n\nmpl.figure.prototype.send_message = function (type, properties) {\n    properties['type'] = type;\n    properties['figure_id'] = this.id;\n    this.ws.send(JSON.stringify(properties));\n};\n\nmpl.figure.prototype.send_draw_message = function () {\n    if (!this.waiting) {\n        this.waiting = true;\n        this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    var format_dropdown = fig.format_dropdown;\n    var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n    fig.ondownload(fig, format);\n};\n\nmpl.figure.prototype.handle_resize = function (fig, msg) {\n    var size = msg['size'];\n    if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n        fig._resize_canvas(size[0], size[1], msg['forward']);\n        fig.send_message('refresh', {});\n    }\n};\n\nmpl.figure.prototype.handle_rubberband = function (fig, msg) {\n    var x0 = msg['x0'] / fig.ratio;\n    var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n    var x1 = msg['x1'] / fig.ratio;\n    var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n    x0 = Math.floor(x0) + 0.5;\n    y0 = Math.floor(y0) + 0.5;\n    x1 = Math.floor(x1) + 0.5;\n    y1 = Math.floor(y1) + 0.5;\n    var min_x = Math.min(x0, x1);\n    var min_y = Math.min(y0, y1);\n    var width = Math.abs(x1 - x0);\n    var height = Math.abs(y1 - y0);\n\n    fig.rubberband_context.clearRect(\n        0,\n        0,\n        fig.canvas.width / fig.ratio,\n        fig.canvas.height / fig.ratio\n    );\n\n    fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n};\n\nmpl.figure.prototype.handle_figure_label = function (fig, msg) {\n    // Updates the figure title.\n    fig.header.textContent = msg['label'];\n};\n\nmpl.figure.prototype.handle_cursor = function (fig, msg) {\n    fig.rubberband_canvas.style.cursor = msg['cursor'];\n};\n\nmpl.figure.prototype.handle_message = function (fig, msg) {\n    fig.message.textContent = msg['message'];\n};\n\nmpl.figure.prototype.handle_draw = function (fig, _msg) {\n    // Request the server to send over a new figure.\n    fig.send_draw_message();\n};\n\nmpl.figure.prototype.handle_image_mode = function (fig, msg) {\n    fig.image_mode = msg['mode'];\n};\n\nmpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n    for (var key in msg) {\n        if (!(key in fig.buttons)) {\n            continue;\n        }\n        fig.buttons[key].disabled = !msg[key];\n        fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n    }\n};\n\nmpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n    if (msg['mode'] === 'PAN') {\n        fig.buttons['Pan'].classList.add('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    } else if (msg['mode'] === 'ZOOM') {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.add('active');\n    } else {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    }\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Called whenever the canvas gets updated.\n    this.send_message('ack', {});\n};\n\n// A function to construct a web socket function for onmessage handling.\n// Called in the figure constructor.\nmpl.figure.prototype._make_on_message_function = function (fig) {\n    return function socket_on_message(evt) {\n        if (evt.data instanceof Blob) {\n            var img = evt.data;\n            if (img.type !== 'image/png') {\n                /* FIXME: We get \"Resource interpreted as Image but\n                 * transferred with MIME type text/plain:\" errors on\n                 * Chrome.  But how to set the MIME type?  It doesn't seem\n                 * to be part of the websocket stream */\n                img.type = 'image/png';\n            }\n\n            /* Free the memory for the previous frames */\n            if (fig.imageObj.src) {\n                (window.URL || window.webkitURL).revokeObjectURL(\n                    fig.imageObj.src\n                );\n            }\n\n            fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n                img\n            );\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        } else if (\n            typeof evt.data === 'string' &&\n            evt.data.slice(0, 21) === 'data:image/png;base64'\n        ) {\n            fig.imageObj.src = evt.data;\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        }\n\n        var msg = JSON.parse(evt.data);\n        var msg_type = msg['type'];\n\n        // Call the  \"handle_{type}\" callback, which takes\n        // the figure and JSON message as its only arguments.\n        try {\n            var callback = fig['handle_' + msg_type];\n        } catch (e) {\n            console.log(\n                \"No handler for the '\" + msg_type + \"' message type: \",\n                msg\n            );\n            return;\n        }\n\n        if (callback) {\n            try {\n                // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n                callback(fig, msg);\n            } catch (e) {\n                console.log(\n                    \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n                    e,\n                    e.stack,\n                    msg\n                );\n            }\n        }\n    };\n};\n\n// from https://stackoverflow.com/questions/1114465/getting-mouse-location-in-canvas\nmpl.findpos = function (e) {\n    //this section is from http://www.quirksmode.org/js/events_properties.html\n    var targ;\n    if (!e) {\n        e = window.event;\n    }\n    if (e.target) {\n        targ = e.target;\n    } else if (e.srcElement) {\n        targ = e.srcElement;\n    }\n    if (targ.nodeType === 3) {\n        // defeat Safari bug\n        targ = targ.parentNode;\n    }\n\n    // pageX,Y are the mouse positions relative to the document\n    var boundingRect = targ.getBoundingClientRect();\n    var x = e.pageX - (boundingRect.left + document.body.scrollLeft);\n    var y = e.pageY - (boundingRect.top + document.body.scrollTop);\n\n    return { x: x, y: y };\n};\n\n/*\n * return a copy of an object with only non-object keys\n * we need this to avoid circular references\n * https://stackoverflow.com/a/24161582/3208463\n */\nfunction simpleKeys(original) {\n    return Object.keys(original).reduce(function (obj, key) {\n        if (typeof original[key] !== 'object') {\n            obj[key] = original[key];\n        }\n        return obj;\n    }, {});\n}\n\nmpl.figure.prototype.mouse_event = function (event, name) {\n    var canvas_pos = mpl.findpos(event);\n\n    if (name === 'button_press') {\n        this.canvas.focus();\n        this.canvas_div.focus();\n    }\n\n    var x = canvas_pos.x * this.ratio;\n    var y = canvas_pos.y * this.ratio;\n\n    this.send_message(name, {\n        x: x,\n        y: y,\n        button: event.button,\n        step: event.step,\n        guiEvent: simpleKeys(event),\n    });\n\n    /* This prevents the web browser from automatically changing to\n     * the text insertion cursor when the button is pressed.  We want\n     * to control all of the cursor setting manually through the\n     * 'cursor' event from matplotlib */\n    event.preventDefault();\n    return false;\n};\n\nmpl.figure.prototype._key_event_extra = function (_event, _name) {\n    // Handle any extra behaviour associated with a key event\n};\n\nmpl.figure.prototype.key_event = function (event, name) {\n    // Prevent repeat events\n    if (name === 'key_press') {\n        if (event.key === this._key) {\n            return;\n        } else {\n            this._key = event.key;\n        }\n    }\n    if (name === 'key_release') {\n        this._key = null;\n    }\n\n    var value = '';\n    if (event.ctrlKey && event.key !== 'Control') {\n        value += 'ctrl+';\n    }\n    else if (event.altKey && event.key !== 'Alt') {\n        value += 'alt+';\n    }\n    else if (event.shiftKey && event.key !== 'Shift') {\n        value += 'shift+';\n    }\n\n    value += 'k' + event.key;\n\n    this._key_event_extra(event, name);\n\n    this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n    return false;\n};\n\nmpl.figure.prototype.toolbar_button_onclick = function (name) {\n    if (name === 'download') {\n        this.handle_save(this, null);\n    } else {\n        this.send_message('toolbar_button', { name: name });\n    }\n};\n\nmpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n    this.message.textContent = tooltip;\n};\n\n///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n// prettier-ignore\nvar _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\nmpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home icon-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left icon-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right icon-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows icon-move\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis\", \"fa fa-square-o icon-check-empty\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o icon-save\", \"download\"]];\n\nmpl.extensions = [\"eps\", \"jpeg\", \"pgf\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\"];\n\nmpl.default_extension = \"png\";/* global mpl */\n\nvar comm_websocket_adapter = function (comm) {\n    // Create a \"websocket\"-like object which calls the given IPython comm\n    // object with the appropriate methods. Currently this is a non binary\n    // socket, so there is still some room for performance tuning.\n    var ws = {};\n\n    ws.binaryType = comm.kernel.ws.binaryType;\n    ws.readyState = comm.kernel.ws.readyState;\n    function updateReadyState(_event) {\n        if (comm.kernel.ws) {\n            ws.readyState = comm.kernel.ws.readyState;\n        } else {\n            ws.readyState = 3; // Closed state.\n        }\n    }\n    comm.kernel.ws.addEventListener('open', updateReadyState);\n    comm.kernel.ws.addEventListener('close', updateReadyState);\n    comm.kernel.ws.addEventListener('error', updateReadyState);\n\n    ws.close = function () {\n        comm.close();\n    };\n    ws.send = function (m) {\n        //console.log('sending', m);\n        comm.send(m);\n    };\n    // Register the callback with on_msg.\n    comm.on_msg(function (msg) {\n        //console.log('receiving', msg['content']['data'], msg);\n        var data = msg['content']['data'];\n        if (data['blob'] !== undefined) {\n            data = {\n                data: new Blob(msg['buffers'], { type: data['blob'] }),\n            };\n        }\n        // Pass the mpl event to the overridden (by mpl) onmessage function.\n        ws.onmessage(data);\n    });\n    return ws;\n};\n\nmpl.mpl_figure_comm = function (comm, msg) {\n    // This is the function which gets called when the mpl process\n    // starts-up an IPython Comm through the \"matplotlib\" channel.\n\n    var id = msg.content.data.id;\n    // Get hold of the div created by the display call when the Comm\n    // socket was opened in Python.\n    var element = document.getElementById(id);\n    var ws_proxy = comm_websocket_adapter(comm);\n\n    function ondownload(figure, _format) {\n        window.open(figure.canvas.toDataURL());\n    }\n\n    var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n\n    // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n    // web socket which is closed, not our websocket->open comm proxy.\n    ws_proxy.onopen();\n\n    fig.parent_element = element;\n    fig.cell_info = mpl.find_output_cell(\"<div id='\" + id + \"'></div>\");\n    if (!fig.cell_info) {\n        console.error('Failed to find cell for figure', id, fig);\n        return;\n    }\n    fig.cell_info[0].output_area.element.on(\n        'cleared',\n        { fig: fig },\n        fig._remove_fig_handler\n    );\n};\n\nmpl.figure.prototype.handle_close = function (fig, msg) {\n    var width = fig.canvas.width / fig.ratio;\n    fig.cell_info[0].output_area.element.off(\n        'cleared',\n        fig._remove_fig_handler\n    );\n    fig.resizeObserverInstance.unobserve(fig.canvas_div);\n\n    // Update the output cell to use the data from the current canvas.\n    fig.push_to_output();\n    var dataURL = fig.canvas.toDataURL();\n    // Re-enable the keyboard manager in IPython - without this line, in FF,\n    // the notebook keyboard shortcuts fail.\n    IPython.keyboard_manager.enable();\n    fig.parent_element.innerHTML =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n    fig.close_ws(fig, msg);\n};\n\nmpl.figure.prototype.close_ws = function (fig, msg) {\n    fig.send_message('closing', msg);\n    // fig.ws.close()\n};\n\nmpl.figure.prototype.push_to_output = function (_remove_interactive) {\n    // Turn the data on the canvas into data in the output cell.\n    var width = this.canvas.width / this.ratio;\n    var dataURL = this.canvas.toDataURL();\n    this.cell_info[1]['text/html'] =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Tell IPython that the notebook contents must change.\n    IPython.notebook.set_dirty(true);\n    this.send_message('ack', {});\n    var fig = this;\n    // Wait a second, then push the new image to the DOM so\n    // that it is saved nicely (might be nice to debounce this).\n    setTimeout(function () {\n        fig.push_to_output();\n    }, 1000);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'btn-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'btn-group';\n    var button;\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'btn-group';\n            continue;\n        }\n\n        button = fig.buttons[name] = document.createElement('button');\n        button.classList = 'btn btn-default';\n        button.href = '#';\n        button.title = name;\n        button.innerHTML = '<i class=\"fa ' + image + ' fa-lg\"></i>';\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    // Add the status bar.\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message pull-right';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n\n    // Add the close button to the window.\n    var buttongrp = document.createElement('div');\n    buttongrp.classList = 'btn-group inline pull-right';\n    button = document.createElement('button');\n    button.classList = 'btn btn-mini btn-primary';\n    button.href = '#';\n    button.title = 'Stop Interaction';\n    button.innerHTML = '<i class=\"fa fa-power-off icon-remove icon-large\"></i>';\n    button.addEventListener('click', function (_evt) {\n        fig.handle_close(fig, {});\n    });\n    button.addEventListener(\n        'mouseover',\n        on_mouseover_closure('Stop Interaction')\n    );\n    buttongrp.appendChild(button);\n    var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n    titlebar.insertBefore(buttongrp, titlebar.firstChild);\n};\n\nmpl.figure.prototype._remove_fig_handler = function (event) {\n    var fig = event.data.fig;\n    if (event.target !== this) {\n        // Ignore bubbled events from children.\n        return;\n    }\n    fig.close_ws(fig, {});\n};\n\nmpl.figure.prototype._root_extra_style = function (el) {\n    el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n};\n\nmpl.figure.prototype._canvas_extra_style = function (el) {\n    // this is important to make the div 'focusable\n    el.setAttribute('tabindex', 0);\n    // reach out to IPython and tell the keyboard manager to turn it's self\n    // off when our div gets focus\n\n    // location in version 3\n    if (IPython.notebook.keyboard_manager) {\n        IPython.notebook.keyboard_manager.register_events(el);\n    } else {\n        // location in version 2\n        IPython.keyboard_manager.register_events(el);\n    }\n};\n\nmpl.figure.prototype._key_event_extra = function (event, _name) {\n    // Check for shift+enter\n    if (event.shiftKey && event.which === 13) {\n        this.canvas_div.blur();\n        // select the cell after this one\n        var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n        IPython.notebook.select(index + 1);\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    fig.ondownload(fig, null);\n};\n\nmpl.find_output_cell = function (html_output) {\n    // Return the cell and output element which can be found *uniquely* in the notebook.\n    // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n    // IPython event is triggered only after the cells have been serialised, which for\n    // our purposes (turning an active figure into a static one), is too late.\n    var cells = IPython.notebook.get_cells();\n    var ncells = cells.length;\n    for (var i = 0; i < ncells; i++) {\n        var cell = cells[i];\n        if (cell.cell_type === 'code') {\n            for (var j = 0; j < cell.output_area.outputs.length; j++) {\n                var data = cell.output_area.outputs[j];\n                if (data.data) {\n                    // IPython >= 3 moved mimebundle to data attribute of output\n                    data = data.data;\n                }\n                if (data['text/html'] === html_output) {\n                    return [cell, data, j];\n                }\n            }\n        }\n    }\n};\n\n// Register the function which deals with the matplotlib target/channel.\n// The kernel may be null if the page has been refreshed.\nif (IPython.notebook.kernel !== null) {\n    IPython.notebook.kernel.comm_manager.register_target(\n        'matplotlib',\n        mpl.mpl_figure_comm\n    );\n}\n",
      "text/plain": [
       "<IPython.core.display.Javascript object>"
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     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<img src=\"data:image/png;base64,[encoded data, 52768 characters]\" width=\"640\">"
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   "source": [
    "%matplotlib notebook\n",
    "shotNum = \"0015\"\n",
    "filePath = folderPath + \"/\" + shotNum + \"/*.h5\"\n",
    "\n",
    "dataSetDict = {\n",
    "    dskey[groupList[i]]: read_hdf5_file(filePath, groupList[i])\n",
    "    for i in [0,1]\n",
    "}\n",
    "\n",
    "dataSet = dataSetDict[\"camera_1\"]\n",
    "\n",
    "print_scanAxis(dataSet)\n",
    "\n",
    "scanAxis = get_scanAxis(dataSet)\n",
    "\n",
    "dataSet = auto_rechunk(dataSet)\n",
    "\n",
    "dataSet = imageAnalyser.get_absorption_images(dataSet)\n",
    "\n",
    "imageAnalyser.center = (310, 815)\n",
    "imageAnalyser.span = (550, 1275)\n",
    "imageAnalyser.fraction = (0.1, 0.1)\n",
    "\n",
    "dataSet_cropOD = imageAnalyser.crop_image(dataSet.OD)\n",
    "dataSet_cropOD = imageAnalyser.substract_offset(dataSet_cropOD).load()\n",
    "\n",
    "Ncount = imageAnalyser.get_Ncount(dataSet_cropOD)\n",
    "Ncount_mean = calculate_mean(Ncount)\n",
    "Ncount_std = calculate_std(Ncount)\n",
    "\n",
    "fig = plt.figure()\n",
    "ax = fig.gca()\n",
    "Ncount_mean.plot.pcolormesh(ax=ax, vmin=0, cmap='jet', cbar_kwargs = dict(label='NCount'))\n",
    "plt.xlabel('Vert AOM Frequency')\n",
    "plt.ylabel('Horz AOM Frequency')\n",
    "plt.tight_layout()\n",
    "plt.show()\n",
    "\n",
    "# DB.create_global(shotNum, dataSet)\n",
    "# DB.add_data(shotNum, dataSet_cropOD, engine='xarray')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
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       ".xr-index-data {\n",
       "  display: none;\n",
       "  background-color: var(--xr-background-color) !important;\n",
       "  padding-bottom: 5px !important;\n",
       "}\n",
       "\n",
       ".xr-var-attrs-in:checked ~ .xr-var-attrs,\n",
       ".xr-var-data-in:checked ~ .xr-var-data,\n",
       ".xr-index-data-in:checked ~ .xr-index-data {\n",
       "  display: block;\n",
       "}\n",
       "\n",
       ".xr-var-data > table {\n",
       "  float: right;\n",
       "}\n",
       "\n",
       ".xr-var-name span,\n",
       ".xr-var-data,\n",
       ".xr-index-name div,\n",
       ".xr-index-data,\n",
       ".xr-attrs {\n",
       "  padding-left: 25px !important;\n",
       "}\n",
       "\n",
       ".xr-attrs,\n",
       ".xr-var-attrs,\n",
       ".xr-var-data,\n",
       ".xr-index-data {\n",
       "  grid-column: 1 / -1;\n",
       "}\n",
       "\n",
       "dl.xr-attrs {\n",
       "  padding: 0;\n",
       "  margin: 0;\n",
       "  display: grid;\n",
       "  grid-template-columns: 125px auto;\n",
       "}\n",
       "\n",
       ".xr-attrs dt,\n",
       ".xr-attrs dd {\n",
       "  padding: 0;\n",
       "  margin: 0;\n",
       "  float: left;\n",
       "  padding-right: 10px;\n",
       "  width: auto;\n",
       "}\n",
       "\n",
       ".xr-attrs dt {\n",
       "  font-weight: normal;\n",
       "  grid-column: 1;\n",
       "}\n",
       "\n",
       ".xr-attrs dt:hover span {\n",
       "  display: inline-block;\n",
       "  background: var(--xr-background-color);\n",
       "  padding-right: 10px;\n",
       "}\n",
       "\n",
       ".xr-attrs dd {\n",
       "  grid-column: 2;\n",
       "  white-space: pre-wrap;\n",
       "  word-break: break-all;\n",
       "}\n",
       "\n",
       ".xr-icon-database,\n",
       ".xr-icon-file-text2,\n",
       ".xr-no-icon {\n",
       "  display: inline-block;\n",
       "  vertical-align: middle;\n",
       "  width: 1em;\n",
       "  height: 1.5em !important;\n",
       "  stroke-width: 0;\n",
       "  stroke: currentColor;\n",
       "  fill: currentColor;\n",
       "}\n",
       "</style><pre class='xr-text-repr-fallback'>&lt;xarray.DataArray &#x27;OD&#x27; (initial_horz_amp: 1, initial_vert_amp: 1)&gt;\n",
       "array([[70751.40524034]])\n",
       "Coordinates:\n",
       "  * initial_horz_amp  (initial_horz_amp) float64 0.81\n",
       "  * initial_vert_amp  (initial_vert_amp) float64 0.59</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.DataArray</div><div class='xr-array-name'>'OD'</div><ul class='xr-dim-list'><li><span class='xr-has-index'>initial_horz_amp</span>: 1</li><li><span class='xr-has-index'>initial_vert_amp</span>: 1</li></ul></div><ul class='xr-sections'><li class='xr-section-item'><div class='xr-array-wrap'><input id='section-177509d9-805b-470b-a14d-b81705fd4a60' class='xr-array-in' type='checkbox' checked><label for='section-177509d9-805b-470b-a14d-b81705fd4a60' title='Show/hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-array-preview xr-preview'><span>7.075e+04</span></div><div class='xr-array-data'><pre>array([[70751.40524034]])</pre></div></div></li><li class='xr-section-item'><input id='section-76e14a22-fe3b-447b-b2dd-2bb3ba9aabbf' class='xr-section-summary-in' type='checkbox'  checked><label for='section-76e14a22-fe3b-447b-b2dd-2bb3ba9aabbf' class='xr-section-summary' >Coordinates: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>initial_horz_amp</span></div><div class='xr-var-dims'>(initial_horz_amp)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>0.81</div><input id='attrs-94907e0a-18ce-4351-bfaf-d564533bd62f' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-94907e0a-18ce-4351-bfaf-d564533bd62f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e22171f2-c0a0-45f8-84b3-b4e8ef1bb135' class='xr-var-data-in' type='checkbox'><label for='data-e22171f2-c0a0-45f8-84b3-b4e8ef1bb135' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([0.81])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>initial_vert_amp</span></div><div class='xr-var-dims'>(initial_vert_amp)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>0.59</div><input id='attrs-8ec82677-4202-4a42-869f-e24cda492fcb' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-8ec82677-4202-4a42-869f-e24cda492fcb' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d4611850-9260-41d7-b5c7-4bf79a2b8bba' class='xr-var-data-in' type='checkbox'><label for='data-d4611850-9260-41d7-b5c7-4bf79a2b8bba' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([0.59])</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-4f941a64-d6be-490e-8286-4af1fee95797' class='xr-section-summary-in' type='checkbox'  ><label for='section-4f941a64-d6be-490e-8286-4af1fee95797' class='xr-section-summary' >Indexes: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-index-name'><div>initial_horz_amp</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-7335d05f-250d-4928-af8b-4bf9e657a1f1' class='xr-index-data-in' type='checkbox'/><label for='index-7335d05f-250d-4928-af8b-4bf9e657a1f1' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Float64Index([0.81], dtype=&#x27;float64&#x27;, name=&#x27;initial_horz_amp&#x27;))</pre></div></li><li class='xr-var-item'><div class='xr-index-name'><div>initial_vert_amp</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-a2197422-b511-436b-a0cf-e953f218a55d' class='xr-index-data-in' type='checkbox'/><label for='index-a2197422-b511-436b-a0cf-e953f218a55d' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Float64Index([0.59], dtype=&#x27;float64&#x27;, name=&#x27;initial_vert_amp&#x27;))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-57d22b47-c86e-46e6-801b-f9ca3622dd9b' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-57d22b47-c86e-46e6-801b-f9ca3622dd9b' class='xr-section-summary'  title='Expand/collapse section'>Attributes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'></dl></div></li></ul></div></div>"
      ],
      "text/plain": [
       "<xarray.DataArray 'OD' (initial_horz_amp: 1, initial_vert_amp: 1)>\n",
       "array([[70751.40524034]])\n",
       "Coordinates:\n",
       "  * initial_horz_amp  (initial_horz_amp) float64 0.81\n",
       "  * initial_vert_amp  (initial_vert_amp) float64 0.59"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Ncount_mean.where(Ncount_mean==Ncount_mean.max(), drop=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Scan final Z Comp Current"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The detected scaning axes and values are: \n",
      "\n",
      "{'compZ_final_current': array([0.233, 0.234, 0.235, 0.236, 0.237, 0.238, 0.239, 0.24 , 0.241,\n",
      "       0.242]), 'runs': array([0., 1., 2.])}\n"
     ]
    },
    {
     "data": {
      "application/javascript": "/* Put everything inside the global mpl namespace */\n/* global mpl */\nwindow.mpl = {};\n\nmpl.get_websocket_type = function () {\n    if (typeof WebSocket !== 'undefined') {\n        return WebSocket;\n    } else if (typeof MozWebSocket !== 'undefined') {\n        return MozWebSocket;\n    } else {\n        alert(\n            'Your browser does not have WebSocket support. ' +\n                'Please try Chrome, Safari or Firefox ≥ 6. ' +\n                'Firefox 4 and 5 are also supported but you ' +\n                'have to enable WebSockets in about:config.'\n        );\n    }\n};\n\nmpl.figure = function (figure_id, websocket, ondownload, parent_element) {\n    this.id = figure_id;\n\n    this.ws = websocket;\n\n    this.supports_binary = this.ws.binaryType !== undefined;\n\n    if (!this.supports_binary) {\n        var warnings = document.getElementById('mpl-warnings');\n        if (warnings) {\n            warnings.style.display = 'block';\n            warnings.textContent =\n                'This browser does not support binary websocket messages. ' +\n                'Performance may be slow.';\n        }\n    }\n\n    this.imageObj = new Image();\n\n    this.context = undefined;\n    this.message = undefined;\n    this.canvas = undefined;\n    this.rubberband_canvas = undefined;\n    this.rubberband_context = undefined;\n    this.format_dropdown = undefined;\n\n    this.image_mode = 'full';\n\n    this.root = document.createElement('div');\n    this.root.setAttribute('style', 'display: inline-block');\n    this._root_extra_style(this.root);\n\n    parent_element.appendChild(this.root);\n\n    this._init_header(this);\n    this._init_canvas(this);\n    this._init_toolbar(this);\n\n    var fig = this;\n\n    this.waiting = false;\n\n    this.ws.onopen = function () {\n        fig.send_message('supports_binary', { value: fig.supports_binary });\n        fig.send_message('send_image_mode', {});\n        if (fig.ratio !== 1) {\n            fig.send_message('set_device_pixel_ratio', {\n                device_pixel_ratio: fig.ratio,\n            });\n        }\n        fig.send_message('refresh', {});\n    };\n\n    this.imageObj.onload = function () {\n        if (fig.image_mode === 'full') {\n            // Full images could contain transparency (where diff images\n            // almost always do), so we need to clear the canvas so that\n            // there is no ghosting.\n            fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n        }\n        fig.context.drawImage(fig.imageObj, 0, 0);\n    };\n\n    this.imageObj.onunload = function () {\n        fig.ws.close();\n    };\n\n    this.ws.onmessage = this._make_on_message_function(this);\n\n    this.ondownload = ondownload;\n};\n\nmpl.figure.prototype._init_header = function () {\n    var titlebar = document.createElement('div');\n    titlebar.classList =\n        'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n    var titletext = document.createElement('div');\n    titletext.classList = 'ui-dialog-title';\n    titletext.setAttribute(\n        'style',\n        'width: 100%; text-align: center; padding: 3px;'\n    );\n    titlebar.appendChild(titletext);\n    this.root.appendChild(titlebar);\n    this.header = titletext;\n};\n\nmpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._init_canvas = function () {\n    var fig = this;\n\n    var canvas_div = (this.canvas_div = document.createElement('div'));\n    canvas_div.setAttribute(\n        'style',\n        'border: 1px solid #ddd;' +\n            'box-sizing: content-box;' +\n            'clear: both;' +\n            'min-height: 1px;' +\n            'min-width: 1px;' +\n            'outline: 0;' +\n            'overflow: hidden;' +\n            'position: relative;' +\n            'resize: both;'\n    );\n\n    function on_keyboard_event_closure(name) {\n        return function (event) {\n            return fig.key_event(event, name);\n        };\n    }\n\n    canvas_div.addEventListener(\n        'keydown',\n        on_keyboard_event_closure('key_press')\n    );\n    canvas_div.addEventListener(\n        'keyup',\n        on_keyboard_event_closure('key_release')\n    );\n\n    this._canvas_extra_style(canvas_div);\n    this.root.appendChild(canvas_div);\n\n    var canvas = (this.canvas = document.createElement('canvas'));\n    canvas.classList.add('mpl-canvas');\n    canvas.setAttribute('style', 'box-sizing: content-box;');\n\n    this.context = canvas.getContext('2d');\n\n    var backingStore =\n        this.context.backingStorePixelRatio ||\n        this.context.webkitBackingStorePixelRatio ||\n        this.context.mozBackingStorePixelRatio ||\n        this.context.msBackingStorePixelRatio ||\n        this.context.oBackingStorePixelRatio ||\n        this.context.backingStorePixelRatio ||\n        1;\n\n    this.ratio = (window.devicePixelRatio || 1) / backingStore;\n\n    var rubberband_canvas = (this.rubberband_canvas = document.createElement(\n        'canvas'\n    ));\n    rubberband_canvas.setAttribute(\n        'style',\n        'box-sizing: content-box; position: absolute; left: 0; top: 0; z-index: 1;'\n    );\n\n    // Apply a ponyfill if ResizeObserver is not implemented by browser.\n    if (this.ResizeObserver === undefined) {\n        if (window.ResizeObserver !== undefined) {\n            this.ResizeObserver = window.ResizeObserver;\n        } else {\n            var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n            this.ResizeObserver = obs.ResizeObserver;\n        }\n    }\n\n    this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n        var nentries = entries.length;\n        for (var i = 0; i < nentries; i++) {\n            var entry = entries[i];\n            var width, height;\n            if (entry.contentBoxSize) {\n                if (entry.contentBoxSize instanceof Array) {\n                    // Chrome 84 implements new version of spec.\n                    width = entry.contentBoxSize[0].inlineSize;\n                    height = entry.contentBoxSize[0].blockSize;\n                } else {\n                    // Firefox implements old version of spec.\n                    width = entry.contentBoxSize.inlineSize;\n                    height = entry.contentBoxSize.blockSize;\n                }\n            } else {\n                // Chrome <84 implements even older version of spec.\n                width = entry.contentRect.width;\n                height = entry.contentRect.height;\n            }\n\n            // Keep the size of the canvas and rubber band canvas in sync with\n            // the canvas container.\n            if (entry.devicePixelContentBoxSize) {\n                // Chrome 84 implements new version of spec.\n                canvas.setAttribute(\n                    'width',\n                    entry.devicePixelContentBoxSize[0].inlineSize\n                );\n                canvas.setAttribute(\n                    'height',\n                    entry.devicePixelContentBoxSize[0].blockSize\n                );\n            } else {\n                canvas.setAttribute('width', width * fig.ratio);\n                canvas.setAttribute('height', height * fig.ratio);\n            }\n            canvas.setAttribute(\n                'style',\n                'width: ' + width + 'px; height: ' + height + 'px;'\n            );\n\n            rubberband_canvas.setAttribute('width', width);\n            rubberband_canvas.setAttribute('height', height);\n\n            // And update the size in Python. We ignore the initial 0/0 size\n            // that occurs as the element is placed into the DOM, which should\n            // otherwise not happen due to the minimum size styling.\n            if (fig.ws.readyState == 1 && width != 0 && height != 0) {\n                fig.request_resize(width, height);\n            }\n        }\n    });\n    this.resizeObserverInstance.observe(canvas_div);\n\n    function on_mouse_event_closure(name) {\n        return function (event) {\n            return fig.mouse_event(event, name);\n        };\n    }\n\n    rubberband_canvas.addEventListener(\n        'mousedown',\n        on_mouse_event_closure('button_press')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseup',\n        on_mouse_event_closure('button_release')\n    );\n    rubberband_canvas.addEventListener(\n        'dblclick',\n        on_mouse_event_closure('dblclick')\n    );\n    // Throttle sequential mouse events to 1 every 20ms.\n    rubberband_canvas.addEventListener(\n        'mousemove',\n        on_mouse_event_closure('motion_notify')\n    );\n\n    rubberband_canvas.addEventListener(\n        'mouseenter',\n        on_mouse_event_closure('figure_enter')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseleave',\n        on_mouse_event_closure('figure_leave')\n    );\n\n    canvas_div.addEventListener('wheel', function (event) {\n        if (event.deltaY < 0) {\n            event.step = 1;\n        } else {\n            event.step = -1;\n        }\n        on_mouse_event_closure('scroll')(event);\n    });\n\n    canvas_div.appendChild(canvas);\n    canvas_div.appendChild(rubberband_canvas);\n\n    this.rubberband_context = rubberband_canvas.getContext('2d');\n    this.rubberband_context.strokeStyle = '#000000';\n\n    this._resize_canvas = function (width, height, forward) {\n        if (forward) {\n            canvas_div.style.width = width + 'px';\n            canvas_div.style.height = height + 'px';\n        }\n    };\n\n    // Disable right mouse context menu.\n    this.rubberband_canvas.addEventListener('contextmenu', function (_e) {\n        event.preventDefault();\n        return false;\n    });\n\n    function set_focus() {\n        canvas.focus();\n        canvas_div.focus();\n    }\n\n    window.setTimeout(set_focus, 100);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'mpl-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'mpl-button-group';\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'mpl-button-group';\n            continue;\n        }\n\n        var button = (fig.buttons[name] = document.createElement('button'));\n        button.classList = 'mpl-widget';\n        button.setAttribute('role', 'button');\n        button.setAttribute('aria-disabled', 'false');\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n\n        var icon_img = document.createElement('img');\n        icon_img.src = '_images/' + image + '.png';\n        icon_img.srcset = '_images/' + image + '_large.png 2x';\n        icon_img.alt = tooltip;\n        button.appendChild(icon_img);\n\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    var fmt_picker = document.createElement('select');\n    fmt_picker.classList = 'mpl-widget';\n    toolbar.appendChild(fmt_picker);\n    this.format_dropdown = fmt_picker;\n\n    for (var ind in mpl.extensions) {\n        var fmt = mpl.extensions[ind];\n        var option = document.createElement('option');\n        option.selected = fmt === mpl.default_extension;\n        option.innerHTML = fmt;\n        fmt_picker.appendChild(option);\n    }\n\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n};\n\nmpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n    // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n    // which will in turn request a refresh of the image.\n    this.send_message('resize', { width: x_pixels, height: y_pixels });\n};\n\nmpl.figure.prototype.send_message = function (type, properties) {\n    properties['type'] = type;\n    properties['figure_id'] = this.id;\n    this.ws.send(JSON.stringify(properties));\n};\n\nmpl.figure.prototype.send_draw_message = function () {\n    if (!this.waiting) {\n        this.waiting = true;\n        this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    var format_dropdown = fig.format_dropdown;\n    var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n    fig.ondownload(fig, format);\n};\n\nmpl.figure.prototype.handle_resize = function (fig, msg) {\n    var size = msg['size'];\n    if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n        fig._resize_canvas(size[0], size[1], msg['forward']);\n        fig.send_message('refresh', {});\n    }\n};\n\nmpl.figure.prototype.handle_rubberband = function (fig, msg) {\n    var x0 = msg['x0'] / fig.ratio;\n    var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n    var x1 = msg['x1'] / fig.ratio;\n    var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n    x0 = Math.floor(x0) + 0.5;\n    y0 = Math.floor(y0) + 0.5;\n    x1 = Math.floor(x1) + 0.5;\n    y1 = Math.floor(y1) + 0.5;\n    var min_x = Math.min(x0, x1);\n    var min_y = Math.min(y0, y1);\n    var width = Math.abs(x1 - x0);\n    var height = Math.abs(y1 - y0);\n\n    fig.rubberband_context.clearRect(\n        0,\n        0,\n        fig.canvas.width / fig.ratio,\n        fig.canvas.height / fig.ratio\n    );\n\n    fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n};\n\nmpl.figure.prototype.handle_figure_label = function (fig, msg) {\n    // Updates the figure title.\n    fig.header.textContent = msg['label'];\n};\n\nmpl.figure.prototype.handle_cursor = function (fig, msg) {\n    fig.rubberband_canvas.style.cursor = msg['cursor'];\n};\n\nmpl.figure.prototype.handle_message = function (fig, msg) {\n    fig.message.textContent = msg['message'];\n};\n\nmpl.figure.prototype.handle_draw = function (fig, _msg) {\n    // Request the server to send over a new figure.\n    fig.send_draw_message();\n};\n\nmpl.figure.prototype.handle_image_mode = function (fig, msg) {\n    fig.image_mode = msg['mode'];\n};\n\nmpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n    for (var key in msg) {\n        if (!(key in fig.buttons)) {\n            continue;\n        }\n        fig.buttons[key].disabled = !msg[key];\n        fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n    }\n};\n\nmpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n    if (msg['mode'] === 'PAN') {\n        fig.buttons['Pan'].classList.add('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    } else if (msg['mode'] === 'ZOOM') {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.add('active');\n    } else {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    }\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Called whenever the canvas gets updated.\n    this.send_message('ack', {});\n};\n\n// A function to construct a web socket function for onmessage handling.\n// Called in the figure constructor.\nmpl.figure.prototype._make_on_message_function = function (fig) {\n    return function socket_on_message(evt) {\n        if (evt.data instanceof Blob) {\n            var img = evt.data;\n            if (img.type !== 'image/png') {\n                /* FIXME: We get \"Resource interpreted as Image but\n                 * transferred with MIME type text/plain:\" errors on\n                 * Chrome.  But how to set the MIME type?  It doesn't seem\n                 * to be part of the websocket stream */\n                img.type = 'image/png';\n            }\n\n            /* Free the memory for the previous frames */\n            if (fig.imageObj.src) {\n                (window.URL || window.webkitURL).revokeObjectURL(\n                    fig.imageObj.src\n                );\n            }\n\n            fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n                img\n            );\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        } else if (\n            typeof evt.data === 'string' &&\n            evt.data.slice(0, 21) === 'data:image/png;base64'\n        ) {\n            fig.imageObj.src = evt.data;\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        }\n\n        var msg = JSON.parse(evt.data);\n        var msg_type = msg['type'];\n\n        // Call the  \"handle_{type}\" callback, which takes\n        // the figure and JSON message as its only arguments.\n        try {\n            var callback = fig['handle_' + msg_type];\n        } catch (e) {\n            console.log(\n                \"No handler for the '\" + msg_type + \"' message type: \",\n                msg\n            );\n            return;\n        }\n\n        if (callback) {\n            try {\n                // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n                callback(fig, msg);\n            } catch (e) {\n                console.log(\n                    \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n                    e,\n                    e.stack,\n                    msg\n                );\n            }\n        }\n    };\n};\n\n// from https://stackoverflow.com/questions/1114465/getting-mouse-location-in-canvas\nmpl.findpos = function (e) {\n    //this section is from http://www.quirksmode.org/js/events_properties.html\n    var targ;\n    if (!e) {\n        e = window.event;\n    }\n    if (e.target) {\n        targ = e.target;\n    } else if (e.srcElement) {\n        targ = e.srcElement;\n    }\n    if (targ.nodeType === 3) {\n        // defeat Safari bug\n        targ = targ.parentNode;\n    }\n\n    // pageX,Y are the mouse positions relative to the document\n    var boundingRect = targ.getBoundingClientRect();\n    var x = e.pageX - (boundingRect.left + document.body.scrollLeft);\n    var y = e.pageY - (boundingRect.top + document.body.scrollTop);\n\n    return { x: x, y: y };\n};\n\n/*\n * return a copy of an object with only non-object keys\n * we need this to avoid circular references\n * https://stackoverflow.com/a/24161582/3208463\n */\nfunction simpleKeys(original) {\n    return Object.keys(original).reduce(function (obj, key) {\n        if (typeof original[key] !== 'object') {\n            obj[key] = original[key];\n        }\n        return obj;\n    }, {});\n}\n\nmpl.figure.prototype.mouse_event = function (event, name) {\n    var canvas_pos = mpl.findpos(event);\n\n    if (name === 'button_press') {\n        this.canvas.focus();\n        this.canvas_div.focus();\n    }\n\n    var x = canvas_pos.x * this.ratio;\n    var y = canvas_pos.y * this.ratio;\n\n    this.send_message(name, {\n        x: x,\n        y: y,\n        button: event.button,\n        step: event.step,\n        guiEvent: simpleKeys(event),\n    });\n\n    /* This prevents the web browser from automatically changing to\n     * the text insertion cursor when the button is pressed.  We want\n     * to control all of the cursor setting manually through the\n     * 'cursor' event from matplotlib */\n    event.preventDefault();\n    return false;\n};\n\nmpl.figure.prototype._key_event_extra = function (_event, _name) {\n    // Handle any extra behaviour associated with a key event\n};\n\nmpl.figure.prototype.key_event = function (event, name) {\n    // Prevent repeat events\n    if (name === 'key_press') {\n        if (event.key === this._key) {\n            return;\n        } else {\n            this._key = event.key;\n        }\n    }\n    if (name === 'key_release') {\n        this._key = null;\n    }\n\n    var value = '';\n    if (event.ctrlKey && event.key !== 'Control') {\n        value += 'ctrl+';\n    }\n    else if (event.altKey && event.key !== 'Alt') {\n        value += 'alt+';\n    }\n    else if (event.shiftKey && event.key !== 'Shift') {\n        value += 'shift+';\n    }\n\n    value += 'k' + event.key;\n\n    this._key_event_extra(event, name);\n\n    this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n    return false;\n};\n\nmpl.figure.prototype.toolbar_button_onclick = function (name) {\n    if (name === 'download') {\n        this.handle_save(this, null);\n    } else {\n        this.send_message('toolbar_button', { name: name });\n    }\n};\n\nmpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n    this.message.textContent = tooltip;\n};\n\n///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n// prettier-ignore\nvar _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\nmpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home icon-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left icon-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right icon-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows icon-move\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis\", \"fa fa-square-o icon-check-empty\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o icon-save\", \"download\"]];\n\nmpl.extensions = [\"eps\", \"jpeg\", \"pgf\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\"];\n\nmpl.default_extension = \"png\";/* global mpl */\n\nvar comm_websocket_adapter = function (comm) {\n    // Create a \"websocket\"-like object which calls the given IPython comm\n    // object with the appropriate methods. Currently this is a non binary\n    // socket, so there is still some room for performance tuning.\n    var ws = {};\n\n    ws.binaryType = comm.kernel.ws.binaryType;\n    ws.readyState = comm.kernel.ws.readyState;\n    function updateReadyState(_event) {\n        if (comm.kernel.ws) {\n            ws.readyState = comm.kernel.ws.readyState;\n        } else {\n            ws.readyState = 3; // Closed state.\n        }\n    }\n    comm.kernel.ws.addEventListener('open', updateReadyState);\n    comm.kernel.ws.addEventListener('close', updateReadyState);\n    comm.kernel.ws.addEventListener('error', updateReadyState);\n\n    ws.close = function () {\n        comm.close();\n    };\n    ws.send = function (m) {\n        //console.log('sending', m);\n        comm.send(m);\n    };\n    // Register the callback with on_msg.\n    comm.on_msg(function (msg) {\n        //console.log('receiving', msg['content']['data'], msg);\n        var data = msg['content']['data'];\n        if (data['blob'] !== undefined) {\n            data = {\n                data: new Blob(msg['buffers'], { type: data['blob'] }),\n            };\n        }\n        // Pass the mpl event to the overridden (by mpl) onmessage function.\n        ws.onmessage(data);\n    });\n    return ws;\n};\n\nmpl.mpl_figure_comm = function (comm, msg) {\n    // This is the function which gets called when the mpl process\n    // starts-up an IPython Comm through the \"matplotlib\" channel.\n\n    var id = msg.content.data.id;\n    // Get hold of the div created by the display call when the Comm\n    // socket was opened in Python.\n    var element = document.getElementById(id);\n    var ws_proxy = comm_websocket_adapter(comm);\n\n    function ondownload(figure, _format) {\n        window.open(figure.canvas.toDataURL());\n    }\n\n    var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n\n    // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n    // web socket which is closed, not our websocket->open comm proxy.\n    ws_proxy.onopen();\n\n    fig.parent_element = element;\n    fig.cell_info = mpl.find_output_cell(\"<div id='\" + id + \"'></div>\");\n    if (!fig.cell_info) {\n        console.error('Failed to find cell for figure', id, fig);\n        return;\n    }\n    fig.cell_info[0].output_area.element.on(\n        'cleared',\n        { fig: fig },\n        fig._remove_fig_handler\n    );\n};\n\nmpl.figure.prototype.handle_close = function (fig, msg) {\n    var width = fig.canvas.width / fig.ratio;\n    fig.cell_info[0].output_area.element.off(\n        'cleared',\n        fig._remove_fig_handler\n    );\n    fig.resizeObserverInstance.unobserve(fig.canvas_div);\n\n    // Update the output cell to use the data from the current canvas.\n    fig.push_to_output();\n    var dataURL = fig.canvas.toDataURL();\n    // Re-enable the keyboard manager in IPython - without this line, in FF,\n    // the notebook keyboard shortcuts fail.\n    IPython.keyboard_manager.enable();\n    fig.parent_element.innerHTML =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n    fig.close_ws(fig, msg);\n};\n\nmpl.figure.prototype.close_ws = function (fig, msg) {\n    fig.send_message('closing', msg);\n    // fig.ws.close()\n};\n\nmpl.figure.prototype.push_to_output = function (_remove_interactive) {\n    // Turn the data on the canvas into data in the output cell.\n    var width = this.canvas.width / this.ratio;\n    var dataURL = this.canvas.toDataURL();\n    this.cell_info[1]['text/html'] =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Tell IPython that the notebook contents must change.\n    IPython.notebook.set_dirty(true);\n    this.send_message('ack', {});\n    var fig = this;\n    // Wait a second, then push the new image to the DOM so\n    // that it is saved nicely (might be nice to debounce this).\n    setTimeout(function () {\n        fig.push_to_output();\n    }, 1000);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'btn-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'btn-group';\n    var button;\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'btn-group';\n            continue;\n        }\n\n        button = fig.buttons[name] = document.createElement('button');\n        button.classList = 'btn btn-default';\n        button.href = '#';\n        button.title = name;\n        button.innerHTML = '<i class=\"fa ' + image + ' fa-lg\"></i>';\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    // Add the status bar.\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message pull-right';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n\n    // Add the close button to the window.\n    var buttongrp = document.createElement('div');\n    buttongrp.classList = 'btn-group inline pull-right';\n    button = document.createElement('button');\n    button.classList = 'btn btn-mini btn-primary';\n    button.href = '#';\n    button.title = 'Stop Interaction';\n    button.innerHTML = '<i class=\"fa fa-power-off icon-remove icon-large\"></i>';\n    button.addEventListener('click', function (_evt) {\n        fig.handle_close(fig, {});\n    });\n    button.addEventListener(\n        'mouseover',\n        on_mouseover_closure('Stop Interaction')\n    );\n    buttongrp.appendChild(button);\n    var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n    titlebar.insertBefore(buttongrp, titlebar.firstChild);\n};\n\nmpl.figure.prototype._remove_fig_handler = function (event) {\n    var fig = event.data.fig;\n    if (event.target !== this) {\n        // Ignore bubbled events from children.\n        return;\n    }\n    fig.close_ws(fig, {});\n};\n\nmpl.figure.prototype._root_extra_style = function (el) {\n    el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n};\n\nmpl.figure.prototype._canvas_extra_style = function (el) {\n    // this is important to make the div 'focusable\n    el.setAttribute('tabindex', 0);\n    // reach out to IPython and tell the keyboard manager to turn it's self\n    // off when our div gets focus\n\n    // location in version 3\n    if (IPython.notebook.keyboard_manager) {\n        IPython.notebook.keyboard_manager.register_events(el);\n    } else {\n        // location in version 2\n        IPython.keyboard_manager.register_events(el);\n    }\n};\n\nmpl.figure.prototype._key_event_extra = function (event, _name) {\n    // Check for shift+enter\n    if (event.shiftKey && event.which === 13) {\n        this.canvas_div.blur();\n        // select the cell after this one\n        var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n        IPython.notebook.select(index + 1);\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    fig.ondownload(fig, null);\n};\n\nmpl.find_output_cell = function (html_output) {\n    // Return the cell and output element which can be found *uniquely* in the notebook.\n    // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n    // IPython event is triggered only after the cells have been serialised, which for\n    // our purposes (turning an active figure into a static one), is too late.\n    var cells = IPython.notebook.get_cells();\n    var ncells = cells.length;\n    for (var i = 0; i < ncells; i++) {\n        var cell = cells[i];\n        if (cell.cell_type === 'code') {\n            for (var j = 0; j < cell.output_area.outputs.length; j++) {\n                var data = cell.output_area.outputs[j];\n                if (data.data) {\n                    // IPython >= 3 moved mimebundle to data attribute of output\n                    data = data.data;\n                }\n                if (data['text/html'] === html_output) {\n                    return [cell, data, j];\n                }\n            }\n        }\n    }\n};\n\n// Register the function which deals with the matplotlib target/channel.\n// The kernel may be null if the page has been refreshed.\nif (IPython.notebook.kernel !== null) {\n    IPython.notebook.kernel.comm_manager.register_target(\n        'matplotlib',\n        mpl.mpl_figure_comm\n    );\n}\n",
      "text/plain": [
       "<IPython.core.display.Javascript object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<img src=\"data:image/png;base64,[encoded data, 41900 characters]\" width=\"640\">"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "%matplotlib notebook\n",
    "shotNum = \"0018\"\n",
    "filePath = folderPath + \"/\" + shotNum + \"/*.h5\"\n",
    "\n",
    "dataSetDict = {\n",
    "    dskey[groupList[i]]: read_hdf5_file(filePath, groupList[i])\n",
    "    for i in [0, 1]\n",
    "}\n",
    "\n",
    "dataSet = dataSetDict[\"camera_1\"]\n",
    "\n",
    "print_scanAxis(dataSet)\n",
    "\n",
    "scanAxis = get_scanAxis(dataSet)\n",
    "\n",
    "dataSet = auto_rechunk(dataSet)\n",
    "\n",
    "dataSet = imageAnalyser.get_absorption_images(dataSet)\n",
    "\n",
    "imageAnalyser.center = (325, 875)\n",
    "imageAnalyser.span = (500, 500)\n",
    "imageAnalyser.fraction = (0.1, 0.1)\n",
    "\n",
    "dataSet_cropOD = imageAnalyser.crop_image(dataSet.OD)\n",
    "dataSet_cropOD = imageAnalyser.substract_offset(dataSet_cropOD).load()\n",
    "\n",
    "Ncount = imageAnalyser.get_Ncount(dataSet_cropOD)\n",
    "Ncount_mean = calculate_mean(Ncount)\n",
    "Ncount_std = calculate_std(Ncount)\n",
    "\n",
    "fig = plt.figure()\n",
    "ax = fig.gca()\n",
    "Ncount_mean.plot.errorbar(ax=ax, yerr = Ncount_std, fmt='ob')\n",
    "#plt.xlabel('')\n",
    "plt.ylabel('NCount')\n",
    "plt.tight_layout()\n",
    "plt.grid(visible=1)\n",
    "plt.show()\n",
    "\n",
    "# DB.create_global(shotNum, dataSet)\n",
    "# DB.add_data(shotNum, dataSet_cropOD, engine='xarray')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "}\n",
       "\n",
       ".xr-attrs dt,\n",
       ".xr-attrs dd {\n",
       "  padding: 0;\n",
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       "}\n",
       "\n",
       ".xr-attrs dt {\n",
       "  font-weight: normal;\n",
       "  grid-column: 1;\n",
       "}\n",
       "\n",
       ".xr-attrs dt:hover span {\n",
       "  display: inline-block;\n",
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       "  padding-right: 10px;\n",
       "}\n",
       "\n",
       ".xr-attrs dd {\n",
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       ".xr-icon-file-text2,\n",
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       "  display: inline-block;\n",
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       "</style><pre class='xr-text-repr-fallback'>&lt;xarray.DataArray &#x27;OD&#x27; (compZ_final_current: 1)&gt;\n",
       "array([26642.0066982])\n",
       "Coordinates:\n",
       "  * compZ_final_current  (compZ_final_current) float64 0.238</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.DataArray</div><div class='xr-array-name'>'OD'</div><ul class='xr-dim-list'><li><span class='xr-has-index'>compZ_final_current</span>: 1</li></ul></div><ul class='xr-sections'><li class='xr-section-item'><div class='xr-array-wrap'><input id='section-c81e0e81-6867-48a8-817b-0270bf8320f5' class='xr-array-in' type='checkbox' checked><label for='section-c81e0e81-6867-48a8-817b-0270bf8320f5' title='Show/hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-array-preview xr-preview'><span>2.664e+04</span></div><div class='xr-array-data'><pre>array([26642.0066982])</pre></div></div></li><li class='xr-section-item'><input id='section-213a9602-e7c9-4a8d-872a-0a9a224c9c77' class='xr-section-summary-in' type='checkbox'  checked><label for='section-213a9602-e7c9-4a8d-872a-0a9a224c9c77' class='xr-section-summary' >Coordinates: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>compZ_final_current</span></div><div class='xr-var-dims'>(compZ_final_current)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>0.238</div><input id='attrs-97b5d183-12a2-43d2-bc55-2ce7784bfe38' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-97b5d183-12a2-43d2-bc55-2ce7784bfe38' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ac436865-f3d0-4ffc-8f65-960c2f4ccf32' class='xr-var-data-in' type='checkbox'><label for='data-ac436865-f3d0-4ffc-8f65-960c2f4ccf32' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([0.238])</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-084aa2db-fadf-4f9c-9080-822a3683ad63' class='xr-section-summary-in' type='checkbox'  ><label for='section-084aa2db-fadf-4f9c-9080-822a3683ad63' class='xr-section-summary' >Indexes: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-index-name'><div>compZ_final_current</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-8f148761-2dbb-435d-b8e1-c7a944c677c6' class='xr-index-data-in' type='checkbox'/><label for='index-8f148761-2dbb-435d-b8e1-c7a944c677c6' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Float64Index([0.238], dtype=&#x27;float64&#x27;, name=&#x27;compZ_final_current&#x27;))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-e55ccffc-8a2c-4845-bb7e-8ecd0686637c' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-e55ccffc-8a2c-4845-bb7e-8ecd0686637c' class='xr-section-summary'  title='Expand/collapse section'>Attributes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'></dl></div></li></ul></div></div>"
      ],
      "text/plain": [
       "<xarray.DataArray 'OD' (compZ_final_current: 1)>\n",
       "array([26642.0066982])\n",
       "Coordinates:\n",
       "  * compZ_final_current  (compZ_final_current) float64 0.238"
      ]
     },
     "execution_count": 26,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Ncount_mean.where(Ncount_mean==Ncount_mean.max(), drop=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Scan final horz amp"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The detected scaning axes and values are: \n",
      "\n",
      "{'final_horz_amp': array([5.0e-05, 7.0e-05, 9.0e-05, 1.1e-04, 1.3e-04, 1.5e-04, 1.7e-04,\n",
      "       1.9e-04, 2.1e-04, 2.3e-04, 2.5e-04]), 'runs': array([0., 1., 2.])}\n"
     ]
    },
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' +\n                'Firefox 4 and 5 are also supported but you ' +\n                'have to enable WebSockets in about:config.'\n        );\n    }\n};\n\nmpl.figure = function (figure_id, websocket, ondownload, parent_element) {\n    this.id = figure_id;\n\n    this.ws = websocket;\n\n    this.supports_binary = this.ws.binaryType !== undefined;\n\n    if (!this.supports_binary) {\n        var warnings = document.getElementById('mpl-warnings');\n        if (warnings) {\n            warnings.style.display = 'block';\n            warnings.textContent =\n                'This browser does not support binary websocket messages. ' +\n                'Performance may be slow.';\n        }\n    }\n\n    this.imageObj = new Image();\n\n    this.context = undefined;\n    this.message = undefined;\n    this.canvas = undefined;\n    this.rubberband_canvas = undefined;\n    this.rubberband_context = undefined;\n    this.format_dropdown = undefined;\n\n    this.image_mode = 'full';\n\n    this.root = document.createElement('div');\n    this.root.setAttribute('style', 'display: inline-block');\n    this._root_extra_style(this.root);\n\n    parent_element.appendChild(this.root);\n\n    this._init_header(this);\n    this._init_canvas(this);\n    this._init_toolbar(this);\n\n    var fig = this;\n\n    this.waiting = false;\n\n    this.ws.onopen = function () {\n        fig.send_message('supports_binary', { value: fig.supports_binary });\n        fig.send_message('send_image_mode', {});\n        if (fig.ratio !== 1) {\n            fig.send_message('set_device_pixel_ratio', {\n                device_pixel_ratio: fig.ratio,\n            });\n        }\n        fig.send_message('refresh', {});\n    };\n\n    this.imageObj.onload = function () {\n        if (fig.image_mode === 'full') {\n            // Full images could contain transparency (where diff images\n            // almost always do), so we need to clear the canvas so that\n            // there is no ghosting.\n            fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n        }\n        fig.context.drawImage(fig.imageObj, 0, 0);\n    };\n\n    this.imageObj.onunload = function () {\n        fig.ws.close();\n    };\n\n    this.ws.onmessage = this._make_on_message_function(this);\n\n    this.ondownload = ondownload;\n};\n\nmpl.figure.prototype._init_header = function () {\n    var titlebar = document.createElement('div');\n    titlebar.classList =\n        'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n    var titletext = document.createElement('div');\n    titletext.classList = 'ui-dialog-title';\n    titletext.setAttribute(\n        'style',\n        'width: 100%; text-align: center; padding: 3px;'\n    );\n    titlebar.appendChild(titletext);\n    this.root.appendChild(titlebar);\n    this.header = titletext;\n};\n\nmpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._init_canvas = function () {\n    var fig = this;\n\n    var canvas_div = (this.canvas_div = document.createElement('div'));\n    canvas_div.setAttribute(\n        'style',\n        'border: 1px solid #ddd;' +\n            'box-sizing: content-box;' +\n            'clear: both;' +\n            'min-height: 1px;' +\n            'min-width: 1px;' +\n            'outline: 0;' +\n            'overflow: hidden;' +\n            'position: relative;' +\n            'resize: both;'\n    );\n\n    function on_keyboard_event_closure(name) {\n        return function (event) {\n            return fig.key_event(event, name);\n        };\n    }\n\n    canvas_div.addEventListener(\n        'keydown',\n        on_keyboard_event_closure('key_press')\n    );\n    canvas_div.addEventListener(\n        'keyup',\n        on_keyboard_event_closure('key_release')\n    );\n\n    this._canvas_extra_style(canvas_div);\n    this.root.appendChild(canvas_div);\n\n    var canvas = (this.canvas = document.createElement('canvas'));\n    canvas.classList.add('mpl-canvas');\n    canvas.setAttribute('style', 'box-sizing: content-box;');\n\n    this.context = canvas.getContext('2d');\n\n    var backingStore =\n        this.context.backingStorePixelRatio ||\n        this.context.webkitBackingStorePixelRatio ||\n        this.context.mozBackingStorePixelRatio ||\n        this.context.msBackingStorePixelRatio ||\n        this.context.oBackingStorePixelRatio ||\n        this.context.backingStorePixelRatio ||\n        1;\n\n    this.ratio = (window.devicePixelRatio || 1) / backingStore;\n\n    var rubberband_canvas = (this.rubberband_canvas = document.createElement(\n        'canvas'\n    ));\n    rubberband_canvas.setAttribute(\n        'style',\n        'box-sizing: content-box; position: absolute; left: 0; top: 0; z-index: 1;'\n    );\n\n    // Apply a ponyfill if ResizeObserver is not implemented by browser.\n    if (this.ResizeObserver === undefined) {\n        if (window.ResizeObserver !== undefined) {\n            this.ResizeObserver = window.ResizeObserver;\n        } else {\n            var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n            this.ResizeObserver = obs.ResizeObserver;\n        }\n    }\n\n    this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n        var nentries = entries.length;\n        for (var i = 0; i < nentries; i++) {\n            var entry = entries[i];\n            var width, height;\n            if (entry.contentBoxSize) {\n                if (entry.contentBoxSize instanceof Array) {\n                    // Chrome 84 implements new version of spec.\n                    width = entry.contentBoxSize[0].inlineSize;\n                    height = entry.contentBoxSize[0].blockSize;\n                } else {\n                    // Firefox implements old version of spec.\n                    width = entry.contentBoxSize.inlineSize;\n                    height = entry.contentBoxSize.blockSize;\n                }\n            } else {\n                // Chrome <84 implements even older version of spec.\n                width = entry.contentRect.width;\n                height = entry.contentRect.height;\n            }\n\n            // Keep the size of the canvas and rubber band canvas in sync with\n            // the canvas container.\n            if (entry.devicePixelContentBoxSize) {\n                // Chrome 84 implements new version of spec.\n                canvas.setAttribute(\n                    'width',\n                    entry.devicePixelContentBoxSize[0].inlineSize\n                );\n                canvas.setAttribute(\n                    'height',\n                    entry.devicePixelContentBoxSize[0].blockSize\n                );\n            } else {\n                canvas.setAttribute('width', width * fig.ratio);\n                canvas.setAttribute('height', height * fig.ratio);\n            }\n            canvas.setAttribute(\n                'style',\n                'width: ' + width + 'px; height: ' + height + 'px;'\n            );\n\n            rubberband_canvas.setAttribute('width', width);\n            rubberband_canvas.setAttribute('height', height);\n\n            // And update the size in Python. We ignore the initial 0/0 size\n            // that occurs as the element is placed into the DOM, which should\n            // otherwise not happen due to the minimum size styling.\n            if (fig.ws.readyState == 1 && width != 0 && height != 0) {\n                fig.request_resize(width, height);\n            }\n        }\n    });\n    this.resizeObserverInstance.observe(canvas_div);\n\n    function on_mouse_event_closure(name) {\n        return function (event) {\n            return fig.mouse_event(event, name);\n        };\n    }\n\n    rubberband_canvas.addEventListener(\n        'mousedown',\n        on_mouse_event_closure('button_press')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseup',\n        on_mouse_event_closure('button_release')\n    );\n    rubberband_canvas.addEventListener(\n        'dblclick',\n        on_mouse_event_closure('dblclick')\n    );\n    // Throttle sequential mouse events to 1 every 20ms.\n    rubberband_canvas.addEventListener(\n        'mousemove',\n        on_mouse_event_closure('motion_notify')\n    );\n\n    rubberband_canvas.addEventListener(\n        'mouseenter',\n        on_mouse_event_closure('figure_enter')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseleave',\n        on_mouse_event_closure('figure_leave')\n    );\n\n    canvas_div.addEventListener('wheel', function (event) {\n        if (event.deltaY < 0) {\n            event.step = 1;\n        } else {\n            event.step = -1;\n        }\n        on_mouse_event_closure('scroll')(event);\n    });\n\n    canvas_div.appendChild(canvas);\n    canvas_div.appendChild(rubberband_canvas);\n\n    this.rubberband_context = rubberband_canvas.getContext('2d');\n    this.rubberband_context.strokeStyle = '#000000';\n\n    this._resize_canvas = function (width, height, forward) {\n        if (forward) {\n            canvas_div.style.width = width + 'px';\n            canvas_div.style.height = height + 'px';\n        }\n    };\n\n    // Disable right mouse context menu.\n    this.rubberband_canvas.addEventListener('contextmenu', function (_e) {\n        event.preventDefault();\n        return false;\n    });\n\n    function set_focus() {\n        canvas.focus();\n        canvas_div.focus();\n    }\n\n    window.setTimeout(set_focus, 100);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'mpl-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'mpl-button-group';\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'mpl-button-group';\n            continue;\n        }\n\n        var button = (fig.buttons[name] = document.createElement('button'));\n        button.classList = 'mpl-widget';\n        button.setAttribute('role', 'button');\n        button.setAttribute('aria-disabled', 'false');\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n\n        var icon_img = document.createElement('img');\n        icon_img.src = '_images/' + image + '.png';\n        icon_img.srcset = '_images/' + image + '_large.png 2x';\n        icon_img.alt = tooltip;\n        button.appendChild(icon_img);\n\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    var fmt_picker = document.createElement('select');\n    fmt_picker.classList = 'mpl-widget';\n    toolbar.appendChild(fmt_picker);\n    this.format_dropdown = fmt_picker;\n\n    for (var ind in mpl.extensions) {\n        var fmt = mpl.extensions[ind];\n        var option = document.createElement('option');\n        option.selected = fmt === mpl.default_extension;\n        option.innerHTML = fmt;\n        fmt_picker.appendChild(option);\n    }\n\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n};\n\nmpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n    // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n    // which will in turn request a refresh of the image.\n    this.send_message('resize', { width: x_pixels, height: y_pixels });\n};\n\nmpl.figure.prototype.send_message = function (type, properties) {\n    properties['type'] = type;\n    properties['figure_id'] = this.id;\n    this.ws.send(JSON.stringify(properties));\n};\n\nmpl.figure.prototype.send_draw_message = function () {\n    if (!this.waiting) {\n        this.waiting = true;\n        this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    var format_dropdown = fig.format_dropdown;\n    var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n    fig.ondownload(fig, format);\n};\n\nmpl.figure.prototype.handle_resize = function (fig, msg) {\n    var size = msg['size'];\n    if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n        fig._resize_canvas(size[0], size[1], msg['forward']);\n        fig.send_message('refresh', {});\n    }\n};\n\nmpl.figure.prototype.handle_rubberband = function (fig, msg) {\n    var x0 = msg['x0'] / fig.ratio;\n    var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n    var x1 = msg['x1'] / fig.ratio;\n    var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n    x0 = Math.floor(x0) + 0.5;\n    y0 = Math.floor(y0) + 0.5;\n    x1 = Math.floor(x1) + 0.5;\n    y1 = Math.floor(y1) + 0.5;\n    var min_x = Math.min(x0, x1);\n    var min_y = Math.min(y0, y1);\n    var width = Math.abs(x1 - x0);\n    var height = Math.abs(y1 - y0);\n\n    fig.rubberband_context.clearRect(\n        0,\n        0,\n        fig.canvas.width / fig.ratio,\n        fig.canvas.height / fig.ratio\n    );\n\n    fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n};\n\nmpl.figure.prototype.handle_figure_label = function (fig, msg) {\n    // Updates the figure title.\n    fig.header.textContent = msg['label'];\n};\n\nmpl.figure.prototype.handle_cursor = function (fig, msg) {\n    fig.rubberband_canvas.style.cursor = msg['cursor'];\n};\n\nmpl.figure.prototype.handle_message = function (fig, msg) {\n    fig.message.textContent = msg['message'];\n};\n\nmpl.figure.prototype.handle_draw = function (fig, _msg) {\n    // Request the server to send over a new figure.\n    fig.send_draw_message();\n};\n\nmpl.figure.prototype.handle_image_mode = function (fig, msg) {\n    fig.image_mode = msg['mode'];\n};\n\nmpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n    for (var key in msg) {\n        if (!(key in fig.buttons)) {\n            continue;\n        }\n        fig.buttons[key].disabled = !msg[key];\n        fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n    }\n};\n\nmpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n    if (msg['mode'] === 'PAN') {\n        fig.buttons['Pan'].classList.add('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    } else if (msg['mode'] === 'ZOOM') {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.add('active');\n    } else {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    }\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Called whenever the canvas gets updated.\n    this.send_message('ack', {});\n};\n\n// A function to construct a web socket function for onmessage handling.\n// Called in the figure constructor.\nmpl.figure.prototype._make_on_message_function = function (fig) {\n    return function socket_on_message(evt) {\n        if (evt.data instanceof Blob) {\n            var img = evt.data;\n            if (img.type !== 'image/png') {\n                /* FIXME: We get \"Resource interpreted as Image but\n                 * transferred with MIME type text/plain:\" errors on\n                 * Chrome.  But how to set the MIME type?  It doesn't seem\n                 * to be part of the websocket stream */\n                img.type = 'image/png';\n            }\n\n            /* Free the memory for the previous frames */\n            if (fig.imageObj.src) {\n                (window.URL || window.webkitURL).revokeObjectURL(\n                    fig.imageObj.src\n                );\n            }\n\n            fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n                img\n            );\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        } else if (\n            typeof evt.data === 'string' &&\n            evt.data.slice(0, 21) === 'data:image/png;base64'\n        ) {\n            fig.imageObj.src = evt.data;\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        }\n\n        var msg = JSON.parse(evt.data);\n        var msg_type = msg['type'];\n\n        // Call the  \"handle_{type}\" callback, which takes\n        // the figure and JSON message as its only arguments.\n        try {\n            var callback = fig['handle_' + msg_type];\n        } catch (e) {\n            console.log(\n                \"No handler for the '\" + msg_type + \"' message type: \",\n                msg\n            );\n            return;\n        }\n\n        if (callback) {\n            try {\n                // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n                callback(fig, msg);\n            } catch (e) {\n                console.log(\n                    \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n                    e,\n                    e.stack,\n                    msg\n                );\n            }\n        }\n    };\n};\n\n// from https://stackoverflow.com/questions/1114465/getting-mouse-location-in-canvas\nmpl.findpos = function (e) {\n    //this section is from http://www.quirksmode.org/js/events_properties.html\n    var targ;\n    if (!e) {\n        e = window.event;\n    }\n    if (e.target) {\n        targ = e.target;\n    } else if (e.srcElement) {\n        targ = e.srcElement;\n    }\n    if (targ.nodeType === 3) {\n        // defeat Safari bug\n        targ = targ.parentNode;\n    }\n\n    // pageX,Y are the mouse positions relative to the document\n    var boundingRect = targ.getBoundingClientRect();\n    var x = e.pageX - (boundingRect.left + document.body.scrollLeft);\n    var y = e.pageY - (boundingRect.top + document.body.scrollTop);\n\n    return { x: x, y: y };\n};\n\n/*\n * return a copy of an object with only non-object keys\n * we need this to avoid circular references\n * https://stackoverflow.com/a/24161582/3208463\n */\nfunction simpleKeys(original) {\n    return Object.keys(original).reduce(function (obj, key) {\n        if (typeof original[key] !== 'object') {\n            obj[key] = original[key];\n        }\n        return obj;\n    }, {});\n}\n\nmpl.figure.prototype.mouse_event = function (event, name) {\n    var canvas_pos = mpl.findpos(event);\n\n    if (name === 'button_press') {\n        this.canvas.focus();\n        this.canvas_div.focus();\n    }\n\n    var x = canvas_pos.x * this.ratio;\n    var y = canvas_pos.y * this.ratio;\n\n    this.send_message(name, {\n        x: x,\n        y: y,\n        button: event.button,\n        step: event.step,\n        guiEvent: simpleKeys(event),\n    });\n\n    /* This prevents the web browser from automatically changing to\n     * the text insertion cursor when the button is pressed.  We want\n     * to control all of the cursor setting manually through the\n     * 'cursor' event from matplotlib */\n    event.preventDefault();\n    return false;\n};\n\nmpl.figure.prototype._key_event_extra = function (_event, _name) {\n    // Handle any extra behaviour associated with a key event\n};\n\nmpl.figure.prototype.key_event = function (event, name) {\n    // Prevent repeat events\n    if (name === 'key_press') {\n        if (event.key === this._key) {\n            return;\n        } else {\n            this._key = event.key;\n        }\n    }\n    if (name === 'key_release') {\n        this._key = null;\n    }\n\n    var value = '';\n    if (event.ctrlKey && event.key !== 'Control') {\n        value += 'ctrl+';\n    }\n    else if (event.altKey && event.key !== 'Alt') {\n        value += 'alt+';\n    }\n    else if (event.shiftKey && event.key !== 'Shift') {\n        value += 'shift+';\n    }\n\n    value += 'k' + event.key;\n\n    this._key_event_extra(event, name);\n\n    this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n    return false;\n};\n\nmpl.figure.prototype.toolbar_button_onclick = function (name) {\n    if (name === 'download') {\n        this.handle_save(this, null);\n    } else {\n        this.send_message('toolbar_button', { name: name });\n    }\n};\n\nmpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n    this.message.textContent = tooltip;\n};\n\n///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n// prettier-ignore\nvar _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\nmpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home icon-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left icon-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right icon-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows icon-move\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis\", \"fa fa-square-o icon-check-empty\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o icon-save\", \"download\"]];\n\nmpl.extensions = [\"eps\", \"jpeg\", \"pgf\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\"];\n\nmpl.default_extension = \"png\";/* global mpl */\n\nvar comm_websocket_adapter = function (comm) {\n    // Create a \"websocket\"-like object which calls the given IPython comm\n    // object with the appropriate methods. Currently this is a non binary\n    // socket, so there is still some room for performance tuning.\n    var ws = {};\n\n    ws.binaryType = comm.kernel.ws.binaryType;\n    ws.readyState = comm.kernel.ws.readyState;\n    function updateReadyState(_event) {\n        if (comm.kernel.ws) {\n            ws.readyState = comm.kernel.ws.readyState;\n        } else {\n            ws.readyState = 3; // Closed state.\n        }\n    }\n    comm.kernel.ws.addEventListener('open', updateReadyState);\n    comm.kernel.ws.addEventListener('close', updateReadyState);\n    comm.kernel.ws.addEventListener('error', updateReadyState);\n\n    ws.close = function () {\n        comm.close();\n    };\n    ws.send = function (m) {\n        //console.log('sending', m);\n        comm.send(m);\n    };\n    // Register the callback with on_msg.\n    comm.on_msg(function (msg) {\n        //console.log('receiving', msg['content']['data'], msg);\n        var data = msg['content']['data'];\n        if (data['blob'] !== undefined) {\n            data = {\n                data: new Blob(msg['buffers'], { type: data['blob'] }),\n            };\n        }\n        // Pass the mpl event to the overridden (by mpl) onmessage function.\n        ws.onmessage(data);\n    });\n    return ws;\n};\n\nmpl.mpl_figure_comm = function (comm, msg) {\n    // This is the function which gets called when the mpl process\n    // starts-up an IPython Comm through the \"matplotlib\" channel.\n\n    var id = msg.content.data.id;\n    // Get hold of the div created by the display call when the Comm\n    // socket was opened in Python.\n    var element = document.getElementById(id);\n    var ws_proxy = comm_websocket_adapter(comm);\n\n    function ondownload(figure, _format) {\n        window.open(figure.canvas.toDataURL());\n    }\n\n    var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n\n    // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n    // web socket which is closed, not our websocket->open comm proxy.\n    ws_proxy.onopen();\n\n    fig.parent_element = element;\n    fig.cell_info = mpl.find_output_cell(\"<div id='\" + id + \"'></div>\");\n    if (!fig.cell_info) {\n        console.error('Failed to find cell for figure', id, fig);\n        return;\n    }\n    fig.cell_info[0].output_area.element.on(\n        'cleared',\n        { fig: fig },\n        fig._remove_fig_handler\n    );\n};\n\nmpl.figure.prototype.handle_close = function (fig, msg) {\n    var width = fig.canvas.width / fig.ratio;\n    fig.cell_info[0].output_area.element.off(\n        'cleared',\n        fig._remove_fig_handler\n    );\n    fig.resizeObserverInstance.unobserve(fig.canvas_div);\n\n    // Update the output cell to use the data from the current canvas.\n    fig.push_to_output();\n    var dataURL = fig.canvas.toDataURL();\n    // Re-enable the keyboard manager in IPython - without this line, in FF,\n    // the notebook keyboard shortcuts fail.\n    IPython.keyboard_manager.enable();\n    fig.parent_element.innerHTML =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n    fig.close_ws(fig, msg);\n};\n\nmpl.figure.prototype.close_ws = function (fig, msg) {\n    fig.send_message('closing', msg);\n    // fig.ws.close()\n};\n\nmpl.figure.prototype.push_to_output = function (_remove_interactive) {\n    // Turn the data on the canvas into data in the output cell.\n    var width = this.canvas.width / this.ratio;\n    var dataURL = this.canvas.toDataURL();\n    this.cell_info[1]['text/html'] =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Tell IPython that the notebook contents must change.\n    IPython.notebook.set_dirty(true);\n    this.send_message('ack', {});\n    var fig = this;\n    // Wait a second, then push the new image to the DOM so\n    // that it is saved nicely (might be nice to debounce this).\n    setTimeout(function () {\n        fig.push_to_output();\n    }, 1000);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'btn-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'btn-group';\n    var button;\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'btn-group';\n            continue;\n        }\n\n        button = fig.buttons[name] = document.createElement('button');\n        button.classList = 'btn btn-default';\n        button.href = '#';\n        button.title = name;\n        button.innerHTML = '<i class=\"fa ' + image + ' fa-lg\"></i>';\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    // Add the status bar.\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message pull-right';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n\n    // Add the close button to the window.\n    var buttongrp = document.createElement('div');\n    buttongrp.classList = 'btn-group inline pull-right';\n    button = document.createElement('button');\n    button.classList = 'btn btn-mini btn-primary';\n    button.href = '#';\n    button.title = 'Stop Interaction';\n    button.innerHTML = '<i class=\"fa fa-power-off icon-remove icon-large\"></i>';\n    button.addEventListener('click', function (_evt) {\n        fig.handle_close(fig, {});\n    });\n    button.addEventListener(\n        'mouseover',\n        on_mouseover_closure('Stop Interaction')\n    );\n    buttongrp.appendChild(button);\n    var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n    titlebar.insertBefore(buttongrp, titlebar.firstChild);\n};\n\nmpl.figure.prototype._remove_fig_handler = function (event) {\n    var fig = event.data.fig;\n    if (event.target !== this) {\n        // Ignore bubbled events from children.\n        return;\n    }\n    fig.close_ws(fig, {});\n};\n\nmpl.figure.prototype._root_extra_style = function (el) {\n    el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n};\n\nmpl.figure.prototype._canvas_extra_style = function (el) {\n    // this is important to make the div 'focusable\n    el.setAttribute('tabindex', 0);\n    // reach out to IPython and tell the keyboard manager to turn it's self\n    // off when our div gets focus\n\n    // location in version 3\n    if (IPython.notebook.keyboard_manager) {\n        IPython.notebook.keyboard_manager.register_events(el);\n    } else {\n        // location in version 2\n        IPython.keyboard_manager.register_events(el);\n    }\n};\n\nmpl.figure.prototype._key_event_extra = function (event, _name) {\n    // Check for shift+enter\n    if (event.shiftKey && event.which === 13) {\n        this.canvas_div.blur();\n        // select the cell after this one\n        var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n        IPython.notebook.select(index + 1);\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    fig.ondownload(fig, null);\n};\n\nmpl.find_output_cell = function (html_output) {\n    // Return the cell and output element which can be found *uniquely* in the notebook.\n    // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n    // IPython event is triggered only after the cells have been serialised, which for\n    // our purposes (turning an active figure into a static one), is too late.\n    var cells = IPython.notebook.get_cells();\n    var ncells = cells.length;\n    for (var i = 0; i < ncells; i++) {\n        var cell = cells[i];\n        if (cell.cell_type === 'code') {\n            for (var j = 0; j < cell.output_area.outputs.length; j++) {\n                var data = cell.output_area.outputs[j];\n                if (data.data) {\n                    // IPython >= 3 moved mimebundle to data attribute of output\n                    data = data.data;\n                }\n                if (data['text/html'] === html_output) {\n                    return [cell, data, j];\n                }\n            }\n        }\n    }\n};\n\n// Register the function which deals with the matplotlib target/channel.\n// The kernel may be null if the page has been refreshed.\nif (IPython.notebook.kernel !== null) {\n    IPython.notebook.kernel.comm_manager.register_target(\n        'matplotlib',\n        mpl.mpl_figure_comm\n    );\n}\n",
      "text/plain": [
       "<IPython.core.display.Javascript object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<img src=\"data:image/png;base64,[encoded data, 39804 characters]\" width=\"640\">"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "%matplotlib notebook\n",
    "shotNum = \"0019\"\n",
    "filePath = folderPath + \"/\" + shotNum + \"/*.h5\"\n",
    "\n",
    "dataSetDict = {\n",
    "    dskey[groupList[i]]: read_hdf5_file(filePath, groupList[i])\n",
    "    for i in [0, 1]\n",
    "}\n",
    "\n",
    "dataSet = dataSetDict[\"camera_1\"]\n",
    "\n",
    "print_scanAxis(dataSet)\n",
    "\n",
    "scanAxis = get_scanAxis(dataSet)\n",
    "\n",
    "dataSet = auto_rechunk(dataSet)\n",
    "\n",
    "dataSet = imageAnalyser.get_absorption_images(dataSet)\n",
    "\n",
    "imageAnalyser.center = (325, 875)\n",
    "imageAnalyser.span = (500, 500)\n",
    "imageAnalyser.fraction = (0.1, 0.1)\n",
    "\n",
    "dataSet_cropOD = imageAnalyser.crop_image(dataSet.OD)\n",
    "dataSet_cropOD = imageAnalyser.substract_offset(dataSet_cropOD).load()\n",
    "\n",
    "Ncount = imageAnalyser.get_Ncount(dataSet_cropOD)\n",
    "Ncount_mean = calculate_mean(Ncount)\n",
    "Ncount_std = calculate_std(Ncount)\n",
    "\n",
    "fig = plt.figure()\n",
    "ax = fig.gca()\n",
    "Ncount_mean.plot.errorbar(ax=ax, yerr = Ncount_std, fmt='ob')\n",
    "#plt.xlabel('')\n",
    "plt.ylabel('NCount')\n",
    "plt.tight_layout()\n",
    "plt.grid(visible=1)\n",
    "plt.show()\n",
    "\n",
    "# DB.create_global(shotNum, dataSet)\n",
    "# DB.add_data(shotNum, dataSet_cropOD, engine='xarray')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "Ncount_mean.where(Ncount_mean==Ncount_mean.max(), drop=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Scan final horz freq"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The detected scaning axes and values are: \n",
      "\n",
      "{'final_horz_freq': array([104.05 , 104.055, 104.06 , 104.065, 104.07 , 104.075, 104.08 ,\n",
      "       104.085, 104.09 , 104.095, 104.1  ]), 'runs': array([0., 1., 2.])}\n"
     ]
    },
    {
     "data": {
      "application/javascript": "/* Put everything inside the global mpl namespace */\n/* global mpl */\nwindow.mpl = {};\n\nmpl.get_websocket_type = function () {\n    if (typeof WebSocket !== 'undefined') {\n        return WebSocket;\n    } else if (typeof MozWebSocket !== 'undefined') {\n        return MozWebSocket;\n    } else {\n        alert(\n            'Your browser does not have WebSocket support. ' +\n                'Please try Chrome, Safari or Firefox ≥ 6. ' +\n                'Firefox 4 and 5 are also supported but you ' +\n                'have to enable WebSockets in about:config.'\n        );\n    }\n};\n\nmpl.figure = function (figure_id, websocket, ondownload, parent_element) {\n    this.id = figure_id;\n\n    this.ws = websocket;\n\n    this.supports_binary = this.ws.binaryType !== undefined;\n\n    if (!this.supports_binary) {\n        var warnings = document.getElementById('mpl-warnings');\n        if (warnings) {\n            warnings.style.display = 'block';\n            warnings.textContent =\n                'This browser does not support binary websocket messages. ' +\n                'Performance may be slow.';\n        }\n    }\n\n    this.imageObj = new Image();\n\n    this.context = undefined;\n    this.message = undefined;\n    this.canvas = undefined;\n    this.rubberband_canvas = undefined;\n    this.rubberband_context = undefined;\n    this.format_dropdown = undefined;\n\n    this.image_mode = 'full';\n\n    this.root = document.createElement('div');\n    this.root.setAttribute('style', 'display: inline-block');\n    this._root_extra_style(this.root);\n\n    parent_element.appendChild(this.root);\n\n    this._init_header(this);\n    this._init_canvas(this);\n    this._init_toolbar(this);\n\n    var fig = this;\n\n    this.waiting = false;\n\n    this.ws.onopen = function () {\n        fig.send_message('supports_binary', { value: fig.supports_binary });\n        fig.send_message('send_image_mode', {});\n        if (fig.ratio !== 1) {\n            fig.send_message('set_device_pixel_ratio', {\n                device_pixel_ratio: fig.ratio,\n            });\n        }\n        fig.send_message('refresh', {});\n    };\n\n    this.imageObj.onload = function () {\n        if (fig.image_mode === 'full') {\n            // Full images could contain transparency (where diff images\n            // almost always do), so we need to clear the canvas so that\n            // there is no ghosting.\n            fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n        }\n        fig.context.drawImage(fig.imageObj, 0, 0);\n    };\n\n    this.imageObj.onunload = function () {\n        fig.ws.close();\n    };\n\n    this.ws.onmessage = this._make_on_message_function(this);\n\n    this.ondownload = ondownload;\n};\n\nmpl.figure.prototype._init_header = function () {\n    var titlebar = document.createElement('div');\n    titlebar.classList =\n        'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n    var titletext = document.createElement('div');\n    titletext.classList = 'ui-dialog-title';\n    titletext.setAttribute(\n        'style',\n        'width: 100%; text-align: center; padding: 3px;'\n    );\n    titlebar.appendChild(titletext);\n    this.root.appendChild(titlebar);\n    this.header = titletext;\n};\n\nmpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._init_canvas = function () {\n    var fig = this;\n\n    var canvas_div = (this.canvas_div = document.createElement('div'));\n    canvas_div.setAttribute(\n        'style',\n        'border: 1px solid #ddd;' +\n            'box-sizing: content-box;' +\n            'clear: both;' +\n            'min-height: 1px;' +\n            'min-width: 1px;' +\n            'outline: 0;' +\n            'overflow: hidden;' +\n            'position: relative;' +\n            'resize: both;'\n    );\n\n    function on_keyboard_event_closure(name) {\n        return function (event) {\n            return fig.key_event(event, name);\n        };\n    }\n\n    canvas_div.addEventListener(\n        'keydown',\n        on_keyboard_event_closure('key_press')\n    );\n    canvas_div.addEventListener(\n        'keyup',\n        on_keyboard_event_closure('key_release')\n    );\n\n    this._canvas_extra_style(canvas_div);\n    this.root.appendChild(canvas_div);\n\n    var canvas = (this.canvas = document.createElement('canvas'));\n    canvas.classList.add('mpl-canvas');\n    canvas.setAttribute('style', 'box-sizing: content-box;');\n\n    this.context = canvas.getContext('2d');\n\n    var backingStore =\n        this.context.backingStorePixelRatio ||\n        this.context.webkitBackingStorePixelRatio ||\n        this.context.mozBackingStorePixelRatio ||\n        this.context.msBackingStorePixelRatio ||\n        this.context.oBackingStorePixelRatio ||\n        this.context.backingStorePixelRatio ||\n        1;\n\n    this.ratio = (window.devicePixelRatio || 1) / backingStore;\n\n    var rubberband_canvas = (this.rubberband_canvas = document.createElement(\n        'canvas'\n    ));\n    rubberband_canvas.setAttribute(\n        'style',\n        'box-sizing: content-box; position: absolute; left: 0; top: 0; z-index: 1;'\n    );\n\n    // Apply a ponyfill if ResizeObserver is not implemented by browser.\n    if (this.ResizeObserver === undefined) {\n        if (window.ResizeObserver !== undefined) {\n            this.ResizeObserver = window.ResizeObserver;\n        } else {\n            var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n            this.ResizeObserver = obs.ResizeObserver;\n        }\n    }\n\n    this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n        var nentries = entries.length;\n        for (var i = 0; i < nentries; i++) {\n            var entry = entries[i];\n            var width, height;\n            if (entry.contentBoxSize) {\n                if (entry.contentBoxSize instanceof Array) {\n                    // Chrome 84 implements new version of spec.\n                    width = entry.contentBoxSize[0].inlineSize;\n                    height = entry.contentBoxSize[0].blockSize;\n                } else {\n                    // Firefox implements old version of spec.\n                    width = entry.contentBoxSize.inlineSize;\n                    height = entry.contentBoxSize.blockSize;\n                }\n            } else {\n                // Chrome <84 implements even older version of spec.\n                width = entry.contentRect.width;\n                height = entry.contentRect.height;\n            }\n\n            // Keep the size of the canvas and rubber band canvas in sync with\n            // the canvas container.\n            if (entry.devicePixelContentBoxSize) {\n                // Chrome 84 implements new version of spec.\n                canvas.setAttribute(\n                    'width',\n                    entry.devicePixelContentBoxSize[0].inlineSize\n                );\n                canvas.setAttribute(\n                    'height',\n                    entry.devicePixelContentBoxSize[0].blockSize\n                );\n            } else {\n                canvas.setAttribute('width', width * fig.ratio);\n                canvas.setAttribute('height', height * fig.ratio);\n            }\n            canvas.setAttribute(\n                'style',\n                'width: ' + width + 'px; height: ' + height + 'px;'\n            );\n\n            rubberband_canvas.setAttribute('width', width);\n            rubberband_canvas.setAttribute('height', height);\n\n            // And update the size in Python. We ignore the initial 0/0 size\n            // that occurs as the element is placed into the DOM, which should\n            // otherwise not happen due to the minimum size styling.\n            if (fig.ws.readyState == 1 && width != 0 && height != 0) {\n                fig.request_resize(width, height);\n            }\n        }\n    });\n    this.resizeObserverInstance.observe(canvas_div);\n\n    function on_mouse_event_closure(name) {\n        return function (event) {\n            return fig.mouse_event(event, name);\n        };\n    }\n\n    rubberband_canvas.addEventListener(\n        'mousedown',\n        on_mouse_event_closure('button_press')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseup',\n        on_mouse_event_closure('button_release')\n    );\n    rubberband_canvas.addEventListener(\n        'dblclick',\n        on_mouse_event_closure('dblclick')\n    );\n    // Throttle sequential mouse events to 1 every 20ms.\n    rubberband_canvas.addEventListener(\n        'mousemove',\n        on_mouse_event_closure('motion_notify')\n    );\n\n    rubberband_canvas.addEventListener(\n        'mouseenter',\n        on_mouse_event_closure('figure_enter')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseleave',\n        on_mouse_event_closure('figure_leave')\n    );\n\n    canvas_div.addEventListener('wheel', function (event) {\n        if (event.deltaY < 0) {\n            event.step = 1;\n        } else {\n            event.step = -1;\n        }\n        on_mouse_event_closure('scroll')(event);\n    });\n\n    canvas_div.appendChild(canvas);\n    canvas_div.appendChild(rubberband_canvas);\n\n    this.rubberband_context = rubberband_canvas.getContext('2d');\n    this.rubberband_context.strokeStyle = '#000000';\n\n    this._resize_canvas = function (width, height, forward) {\n        if (forward) {\n            canvas_div.style.width = width + 'px';\n            canvas_div.style.height = height + 'px';\n        }\n    };\n\n    // Disable right mouse context menu.\n    this.rubberband_canvas.addEventListener('contextmenu', function (_e) {\n        event.preventDefault();\n        return false;\n    });\n\n    function set_focus() {\n        canvas.focus();\n        canvas_div.focus();\n    }\n\n    window.setTimeout(set_focus, 100);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'mpl-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'mpl-button-group';\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'mpl-button-group';\n            continue;\n        }\n\n        var button = (fig.buttons[name] = document.createElement('button'));\n        button.classList = 'mpl-widget';\n        button.setAttribute('role', 'button');\n        button.setAttribute('aria-disabled', 'false');\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n\n        var icon_img = document.createElement('img');\n        icon_img.src = '_images/' + image + '.png';\n        icon_img.srcset = '_images/' + image + '_large.png 2x';\n        icon_img.alt = tooltip;\n        button.appendChild(icon_img);\n\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    var fmt_picker = document.createElement('select');\n    fmt_picker.classList = 'mpl-widget';\n    toolbar.appendChild(fmt_picker);\n    this.format_dropdown = fmt_picker;\n\n    for (var ind in mpl.extensions) {\n        var fmt = mpl.extensions[ind];\n        var option = document.createElement('option');\n        option.selected = fmt === mpl.default_extension;\n        option.innerHTML = fmt;\n        fmt_picker.appendChild(option);\n    }\n\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n};\n\nmpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n    // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n    // which will in turn request a refresh of the image.\n    this.send_message('resize', { width: x_pixels, height: y_pixels });\n};\n\nmpl.figure.prototype.send_message = function (type, properties) {\n    properties['type'] = type;\n    properties['figure_id'] = this.id;\n    this.ws.send(JSON.stringify(properties));\n};\n\nmpl.figure.prototype.send_draw_message = function () {\n    if (!this.waiting) {\n        this.waiting = true;\n        this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    var format_dropdown = fig.format_dropdown;\n    var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n    fig.ondownload(fig, format);\n};\n\nmpl.figure.prototype.handle_resize = function (fig, msg) {\n    var size = msg['size'];\n    if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n        fig._resize_canvas(size[0], size[1], msg['forward']);\n        fig.send_message('refresh', {});\n    }\n};\n\nmpl.figure.prototype.handle_rubberband = function (fig, msg) {\n    var x0 = msg['x0'] / fig.ratio;\n    var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n    var x1 = msg['x1'] / fig.ratio;\n    var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n    x0 = Math.floor(x0) + 0.5;\n    y0 = Math.floor(y0) + 0.5;\n    x1 = Math.floor(x1) + 0.5;\n    y1 = Math.floor(y1) + 0.5;\n    var min_x = Math.min(x0, x1);\n    var min_y = Math.min(y0, y1);\n    var width = Math.abs(x1 - x0);\n    var height = Math.abs(y1 - y0);\n\n    fig.rubberband_context.clearRect(\n        0,\n        0,\n        fig.canvas.width / fig.ratio,\n        fig.canvas.height / fig.ratio\n    );\n\n    fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n};\n\nmpl.figure.prototype.handle_figure_label = function (fig, msg) {\n    // Updates the figure title.\n    fig.header.textContent = msg['label'];\n};\n\nmpl.figure.prototype.handle_cursor = function (fig, msg) {\n    fig.rubberband_canvas.style.cursor = msg['cursor'];\n};\n\nmpl.figure.prototype.handle_message = function (fig, msg) {\n    fig.message.textContent = msg['message'];\n};\n\nmpl.figure.prototype.handle_draw = function (fig, _msg) {\n    // Request the server to send over a new figure.\n    fig.send_draw_message();\n};\n\nmpl.figure.prototype.handle_image_mode = function (fig, msg) {\n    fig.image_mode = msg['mode'];\n};\n\nmpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n    for (var key in msg) {\n        if (!(key in fig.buttons)) {\n            continue;\n        }\n        fig.buttons[key].disabled = !msg[key];\n        fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n    }\n};\n\nmpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n    if (msg['mode'] === 'PAN') {\n        fig.buttons['Pan'].classList.add('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    } else if (msg['mode'] === 'ZOOM') {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.add('active');\n    } else {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    }\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Called whenever the canvas gets updated.\n    this.send_message('ack', {});\n};\n\n// A function to construct a web socket function for onmessage handling.\n// Called in the figure constructor.\nmpl.figure.prototype._make_on_message_function = function (fig) {\n    return function socket_on_message(evt) {\n        if (evt.data instanceof Blob) {\n            var img = evt.data;\n            if (img.type !== 'image/png') {\n                /* FIXME: We get \"Resource interpreted as Image but\n                 * transferred with MIME type text/plain:\" errors on\n                 * Chrome.  But how to set the MIME type?  It doesn't seem\n                 * to be part of the websocket stream */\n                img.type = 'image/png';\n            }\n\n            /* Free the memory for the previous frames */\n            if (fig.imageObj.src) {\n                (window.URL || window.webkitURL).revokeObjectURL(\n                    fig.imageObj.src\n                );\n            }\n\n            fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n                img\n            );\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        } else if (\n            typeof evt.data === 'string' &&\n            evt.data.slice(0, 21) === 'data:image/png;base64'\n        ) {\n            fig.imageObj.src = evt.data;\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        }\n\n        var msg = JSON.parse(evt.data);\n        var msg_type = msg['type'];\n\n        // Call the  \"handle_{type}\" callback, which takes\n        // the figure and JSON message as its only arguments.\n        try {\n            var callback = fig['handle_' + msg_type];\n        } catch (e) {\n            console.log(\n                \"No handler for the '\" + msg_type + \"' message type: \",\n                msg\n            );\n            return;\n        }\n\n        if (callback) {\n            try {\n                // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n                callback(fig, msg);\n            } catch (e) {\n                console.log(\n                    \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n                    e,\n                    e.stack,\n                    msg\n                );\n            }\n        }\n    };\n};\n\n// from https://stackoverflow.com/questions/1114465/getting-mouse-location-in-canvas\nmpl.findpos = function (e) {\n    //this section is from http://www.quirksmode.org/js/events_properties.html\n    var targ;\n    if (!e) {\n        e = window.event;\n    }\n    if (e.target) {\n        targ = e.target;\n    } else if (e.srcElement) {\n        targ = e.srcElement;\n    }\n    if (targ.nodeType === 3) {\n        // defeat Safari bug\n        targ = targ.parentNode;\n    }\n\n    // pageX,Y are the mouse positions relative to the document\n    var boundingRect = targ.getBoundingClientRect();\n    var x = e.pageX - (boundingRect.left + document.body.scrollLeft);\n    var y = e.pageY - (boundingRect.top + document.body.scrollTop);\n\n    return { x: x, y: y };\n};\n\n/*\n * return a copy of an object with only non-object keys\n * we need this to avoid circular references\n * https://stackoverflow.com/a/24161582/3208463\n */\nfunction simpleKeys(original) {\n    return Object.keys(original).reduce(function (obj, key) {\n        if (typeof original[key] !== 'object') {\n            obj[key] = original[key];\n        }\n        return obj;\n    }, {});\n}\n\nmpl.figure.prototype.mouse_event = function (event, name) {\n    var canvas_pos = mpl.findpos(event);\n\n    if (name === 'button_press') {\n        this.canvas.focus();\n        this.canvas_div.focus();\n    }\n\n    var x = canvas_pos.x * this.ratio;\n    var y = canvas_pos.y * this.ratio;\n\n    this.send_message(name, {\n        x: x,\n        y: y,\n        button: event.button,\n        step: event.step,\n        guiEvent: simpleKeys(event),\n    });\n\n    /* This prevents the web browser from automatically changing to\n     * the text insertion cursor when the button is pressed.  We want\n     * to control all of the cursor setting manually through the\n     * 'cursor' event from matplotlib */\n    event.preventDefault();\n    return false;\n};\n\nmpl.figure.prototype._key_event_extra = function (_event, _name) {\n    // Handle any extra behaviour associated with a key event\n};\n\nmpl.figure.prototype.key_event = function (event, name) {\n    // Prevent repeat events\n    if (name === 'key_press') {\n        if (event.key === this._key) {\n            return;\n        } else {\n            this._key = event.key;\n        }\n    }\n    if (name === 'key_release') {\n        this._key = null;\n    }\n\n    var value = '';\n    if (event.ctrlKey && event.key !== 'Control') {\n        value += 'ctrl+';\n    }\n    else if (event.altKey && event.key !== 'Alt') {\n        value += 'alt+';\n    }\n    else if (event.shiftKey && event.key !== 'Shift') {\n        value += 'shift+';\n    }\n\n    value += 'k' + event.key;\n\n    this._key_event_extra(event, name);\n\n    this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n    return false;\n};\n\nmpl.figure.prototype.toolbar_button_onclick = function (name) {\n    if (name === 'download') {\n        this.handle_save(this, null);\n    } else {\n        this.send_message('toolbar_button', { name: name });\n    }\n};\n\nmpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n    this.message.textContent = tooltip;\n};\n\n///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n// prettier-ignore\nvar _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\nmpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home icon-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left icon-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right icon-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows icon-move\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis\", \"fa fa-square-o icon-check-empty\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o icon-save\", \"download\"]];\n\nmpl.extensions = [\"eps\", \"jpeg\", \"pgf\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\"];\n\nmpl.default_extension = \"png\";/* global mpl */\n\nvar comm_websocket_adapter = function (comm) {\n    // Create a \"websocket\"-like object which calls the given IPython comm\n    // object with the appropriate methods. Currently this is a non binary\n    // socket, so there is still some room for performance tuning.\n    var ws = {};\n\n    ws.binaryType = comm.kernel.ws.binaryType;\n    ws.readyState = comm.kernel.ws.readyState;\n    function updateReadyState(_event) {\n        if (comm.kernel.ws) {\n            ws.readyState = comm.kernel.ws.readyState;\n        } else {\n            ws.readyState = 3; // Closed state.\n        }\n    }\n    comm.kernel.ws.addEventListener('open', updateReadyState);\n    comm.kernel.ws.addEventListener('close', updateReadyState);\n    comm.kernel.ws.addEventListener('error', updateReadyState);\n\n    ws.close = function () {\n        comm.close();\n    };\n    ws.send = function (m) {\n        //console.log('sending', m);\n        comm.send(m);\n    };\n    // Register the callback with on_msg.\n    comm.on_msg(function (msg) {\n        //console.log('receiving', msg['content']['data'], msg);\n        var data = msg['content']['data'];\n        if (data['blob'] !== undefined) {\n            data = {\n                data: new Blob(msg['buffers'], { type: data['blob'] }),\n            };\n        }\n        // Pass the mpl event to the overridden (by mpl) onmessage function.\n        ws.onmessage(data);\n    });\n    return ws;\n};\n\nmpl.mpl_figure_comm = function (comm, msg) {\n    // This is the function which gets called when the mpl process\n    // starts-up an IPython Comm through the \"matplotlib\" channel.\n\n    var id = msg.content.data.id;\n    // Get hold of the div created by the display call when the Comm\n    // socket was opened in Python.\n    var element = document.getElementById(id);\n    var ws_proxy = comm_websocket_adapter(comm);\n\n    function ondownload(figure, _format) {\n        window.open(figure.canvas.toDataURL());\n    }\n\n    var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n\n    // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n    // web socket which is closed, not our websocket->open comm proxy.\n    ws_proxy.onopen();\n\n    fig.parent_element = element;\n    fig.cell_info = mpl.find_output_cell(\"<div id='\" + id + \"'></div>\");\n    if (!fig.cell_info) {\n        console.error('Failed to find cell for figure', id, fig);\n        return;\n    }\n    fig.cell_info[0].output_area.element.on(\n        'cleared',\n        { fig: fig },\n        fig._remove_fig_handler\n    );\n};\n\nmpl.figure.prototype.handle_close = function (fig, msg) {\n    var width = fig.canvas.width / fig.ratio;\n    fig.cell_info[0].output_area.element.off(\n        'cleared',\n        fig._remove_fig_handler\n    );\n    fig.resizeObserverInstance.unobserve(fig.canvas_div);\n\n    // Update the output cell to use the data from the current canvas.\n    fig.push_to_output();\n    var dataURL = fig.canvas.toDataURL();\n    // Re-enable the keyboard manager in IPython - without this line, in FF,\n    // the notebook keyboard shortcuts fail.\n    IPython.keyboard_manager.enable();\n    fig.parent_element.innerHTML =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n    fig.close_ws(fig, msg);\n};\n\nmpl.figure.prototype.close_ws = function (fig, msg) {\n    fig.send_message('closing', msg);\n    // fig.ws.close()\n};\n\nmpl.figure.prototype.push_to_output = function (_remove_interactive) {\n    // Turn the data on the canvas into data in the output cell.\n    var width = this.canvas.width / this.ratio;\n    var dataURL = this.canvas.toDataURL();\n    this.cell_info[1]['text/html'] =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Tell IPython that the notebook contents must change.\n    IPython.notebook.set_dirty(true);\n    this.send_message('ack', {});\n    var fig = this;\n    // Wait a second, then push the new image to the DOM so\n    // that it is saved nicely (might be nice to debounce this).\n    setTimeout(function () {\n        fig.push_to_output();\n    }, 1000);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'btn-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'btn-group';\n    var button;\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'btn-group';\n            continue;\n        }\n\n        button = fig.buttons[name] = document.createElement('button');\n        button.classList = 'btn btn-default';\n        button.href = '#';\n        button.title = name;\n        button.innerHTML = '<i class=\"fa ' + image + ' fa-lg\"></i>';\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    // Add the status bar.\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message pull-right';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n\n    // Add the close button to the window.\n    var buttongrp = document.createElement('div');\n    buttongrp.classList = 'btn-group inline pull-right';\n    button = document.createElement('button');\n    button.classList = 'btn btn-mini btn-primary';\n    button.href = '#';\n    button.title = 'Stop Interaction';\n    button.innerHTML = '<i class=\"fa fa-power-off icon-remove icon-large\"></i>';\n    button.addEventListener('click', function (_evt) {\n        fig.handle_close(fig, {});\n    });\n    button.addEventListener(\n        'mouseover',\n        on_mouseover_closure('Stop Interaction')\n    );\n    buttongrp.appendChild(button);\n    var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n    titlebar.insertBefore(buttongrp, titlebar.firstChild);\n};\n\nmpl.figure.prototype._remove_fig_handler = function (event) {\n    var fig = event.data.fig;\n    if (event.target !== this) {\n        // Ignore bubbled events from children.\n        return;\n    }\n    fig.close_ws(fig, {});\n};\n\nmpl.figure.prototype._root_extra_style = function (el) {\n    el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n};\n\nmpl.figure.prototype._canvas_extra_style = function (el) {\n    // this is important to make the div 'focusable\n    el.setAttribute('tabindex', 0);\n    // reach out to IPython and tell the keyboard manager to turn it's self\n    // off when our div gets focus\n\n    // location in version 3\n    if (IPython.notebook.keyboard_manager) {\n        IPython.notebook.keyboard_manager.register_events(el);\n    } else {\n        // location in version 2\n        IPython.keyboard_manager.register_events(el);\n    }\n};\n\nmpl.figure.prototype._key_event_extra = function (event, _name) {\n    // Check for shift+enter\n    if (event.shiftKey && event.which === 13) {\n        this.canvas_div.blur();\n        // select the cell after this one\n        var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n        IPython.notebook.select(index + 1);\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    fig.ondownload(fig, null);\n};\n\nmpl.find_output_cell = function (html_output) {\n    // Return the cell and output element which can be found *uniquely* in the notebook.\n    // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n    // IPython event is triggered only after the cells have been serialised, which for\n    // our purposes (turning an active figure into a static one), is too late.\n    var cells = IPython.notebook.get_cells();\n    var ncells = cells.length;\n    for (var i = 0; i < ncells; i++) {\n        var cell = cells[i];\n        if (cell.cell_type === 'code') {\n            for (var j = 0; j < cell.output_area.outputs.length; j++) {\n                var data = cell.output_area.outputs[j];\n                if (data.data) {\n                    // IPython >= 3 moved mimebundle to data attribute of output\n                    data = data.data;\n                }\n                if (data['text/html'] === html_output) {\n                    return [cell, data, j];\n                }\n            }\n        }\n    }\n};\n\n// Register the function which deals with the matplotlib target/channel.\n// The kernel may be null if the page has been refreshed.\nif (IPython.notebook.kernel !== null) {\n    IPython.notebook.kernel.comm_manager.register_target(\n        'matplotlib',\n        mpl.mpl_figure_comm\n    );\n}\n",
      "text/plain": [
       "<IPython.core.display.Javascript object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<img src=\"data:image/png;base64,[encoded data, 42008 characters]\" width=\"640\">"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "%matplotlib notebook\n",
    "shotNum = \"0020\"\n",
    "filePath = folderPath + \"/\" + shotNum + \"/*.h5\"\n",
    "\n",
    "dataSetDict = {\n",
    "    dskey[groupList[i]]: read_hdf5_file(filePath, groupList[i])\n",
    "    for i in [0, 1]\n",
    "}\n",
    "\n",
    "dataSet = dataSetDict[\"camera_1\"]\n",
    "\n",
    "print_scanAxis(dataSet)\n",
    "\n",
    "scanAxis = get_scanAxis(dataSet)\n",
    "\n",
    "dataSet = auto_rechunk(dataSet)\n",
    "\n",
    "dataSet = imageAnalyser.get_absorption_images(dataSet)\n",
    "\n",
    "imageAnalyser.center = (325, 875)\n",
    "imageAnalyser.span = (500, 500)\n",
    "imageAnalyser.fraction = (0.1, 0.1)\n",
    "\n",
    "dataSet_cropOD = imageAnalyser.crop_image(dataSet.OD)\n",
    "dataSet_cropOD = imageAnalyser.substract_offset(dataSet_cropOD).load()\n",
    "\n",
    "Ncount = imageAnalyser.get_Ncount(dataSet_cropOD)\n",
    "Ncount_mean = calculate_mean(Ncount)\n",
    "Ncount_std = calculate_std(Ncount)\n",
    "\n",
    "fig = plt.figure()\n",
    "ax = fig.gca()\n",
    "Ncount_mean.plot.errorbar(ax=ax, yerr = Ncount_std, fmt='ob')\n",
    "#plt.xlabel('')\n",
    "plt.ylabel('NCount')\n",
    "plt.tight_layout()\n",
    "plt.grid(visible=1)\n",
    "plt.show()\n",
    "\n",
    "# DB.create_global(shotNum, dataSet)\n",
    "# DB.add_data(shotNum, dataSet_cropOD, engine='xarray')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\n",
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       "\n",
       "dl.xr-attrs {\n",
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       "  grid-template-columns: 125px auto;\n",
       "}\n",
       "\n",
       ".xr-attrs dt,\n",
       ".xr-attrs dd {\n",
       "  padding: 0;\n",
       "  margin: 0;\n",
       "  float: left;\n",
       "  padding-right: 10px;\n",
       "  width: auto;\n",
       "}\n",
       "\n",
       ".xr-attrs dt {\n",
       "  font-weight: normal;\n",
       "  grid-column: 1;\n",
       "}\n",
       "\n",
       ".xr-attrs dt:hover span {\n",
       "  display: inline-block;\n",
       "  background: var(--xr-background-color);\n",
       "  padding-right: 10px;\n",
       "}\n",
       "\n",
       ".xr-attrs dd {\n",
       "  grid-column: 2;\n",
       "  white-space: pre-wrap;\n",
       "  word-break: break-all;\n",
       "}\n",
       "\n",
       ".xr-icon-database,\n",
       ".xr-icon-file-text2,\n",
       ".xr-no-icon {\n",
       "  display: inline-block;\n",
       "  vertical-align: middle;\n",
       "  width: 1em;\n",
       "  height: 1.5em !important;\n",
       "  stroke-width: 0;\n",
       "  stroke: currentColor;\n",
       "  fill: currentColor;\n",
       "}\n",
       "</style><pre class='xr-text-repr-fallback'>&lt;xarray.DataArray &#x27;OD&#x27; (final_horz_freq: 1)&gt;\n",
       "array([28952.76637914])\n",
       "Coordinates:\n",
       "  * final_horz_freq  (final_horz_freq) float64 104.1</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.DataArray</div><div class='xr-array-name'>'OD'</div><ul class='xr-dim-list'><li><span class='xr-has-index'>final_horz_freq</span>: 1</li></ul></div><ul class='xr-sections'><li class='xr-section-item'><div class='xr-array-wrap'><input id='section-ed0434fd-e803-4855-844d-70b0c3e842c8' class='xr-array-in' type='checkbox' checked><label for='section-ed0434fd-e803-4855-844d-70b0c3e842c8' title='Show/hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-array-preview xr-preview'><span>2.895e+04</span></div><div class='xr-array-data'><pre>array([28952.76637914])</pre></div></div></li><li class='xr-section-item'><input id='section-d2a4729c-d36d-44fa-a8c1-4885a8e7593b' class='xr-section-summary-in' type='checkbox'  checked><label for='section-d2a4729c-d36d-44fa-a8c1-4885a8e7593b' class='xr-section-summary' >Coordinates: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>final_horz_freq</span></div><div class='xr-var-dims'>(final_horz_freq)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>104.1</div><input id='attrs-6f10bdef-1163-4796-8266-ab9332d89ea4' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-6f10bdef-1163-4796-8266-ab9332d89ea4' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-343afb05-ab34-4141-92a8-e56c8c309e66' class='xr-var-data-in' type='checkbox'><label for='data-343afb05-ab34-4141-92a8-e56c8c309e66' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([104.06])</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-d4d0971f-b5b7-4977-91e5-3ef6807a4b2f' class='xr-section-summary-in' type='checkbox'  ><label for='section-d4d0971f-b5b7-4977-91e5-3ef6807a4b2f' class='xr-section-summary' >Indexes: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-index-name'><div>final_horz_freq</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-81425834-189f-4154-bdb4-8c5e8e7207d1' class='xr-index-data-in' type='checkbox'/><label for='index-81425834-189f-4154-bdb4-8c5e8e7207d1' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Float64Index([104.06], dtype=&#x27;float64&#x27;, name=&#x27;final_horz_freq&#x27;))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-813756c4-49be-4230-a482-541103019f9c' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-813756c4-49be-4230-a482-541103019f9c' class='xr-section-summary'  title='Expand/collapse section'>Attributes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'></dl></div></li></ul></div></div>"
      ],
      "text/plain": [
       "<xarray.DataArray 'OD' (final_horz_freq: 1)>\n",
       "array([28952.76637914])\n",
       "Coordinates:\n",
       "  * final_horz_freq  (final_horz_freq) float64 104.1"
      ]
     },
     "execution_count": 29,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Ncount_mean.where(Ncount_mean==Ncount_mean.max(), drop=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Scan final vert amp"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The detected scaning axes and values are: \n",
      "\n",
      "{'final_vert_amp': array([0.035, 0.037, 0.039, 0.041, 0.043, 0.045, 0.047, 0.049, 0.051,\n",
      "       0.053, 0.055, 0.057, 0.059, 0.061, 0.063]), 'runs': array([0., 1., 2.])}\n"
     ]
    },
    {
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' +\n                'Firefox 4 and 5 are also supported but you ' +\n                'have to enable WebSockets in about:config.'\n        );\n    }\n};\n\nmpl.figure = function (figure_id, websocket, ondownload, parent_element) {\n    this.id = figure_id;\n\n    this.ws = websocket;\n\n    this.supports_binary = this.ws.binaryType !== undefined;\n\n    if (!this.supports_binary) {\n        var warnings = document.getElementById('mpl-warnings');\n        if (warnings) {\n            warnings.style.display = 'block';\n            warnings.textContent =\n                'This browser does not support binary websocket messages. ' +\n                'Performance may be slow.';\n        }\n    }\n\n    this.imageObj = new Image();\n\n    this.context = undefined;\n    this.message = undefined;\n    this.canvas = undefined;\n    this.rubberband_canvas = undefined;\n    this.rubberband_context = undefined;\n    this.format_dropdown = undefined;\n\n    this.image_mode = 'full';\n\n    this.root = document.createElement('div');\n    this.root.setAttribute('style', 'display: inline-block');\n    this._root_extra_style(this.root);\n\n    parent_element.appendChild(this.root);\n\n    this._init_header(this);\n    this._init_canvas(this);\n    this._init_toolbar(this);\n\n    var fig = this;\n\n    this.waiting = false;\n\n    this.ws.onopen = function () {\n        fig.send_message('supports_binary', { value: fig.supports_binary });\n        fig.send_message('send_image_mode', {});\n        if (fig.ratio !== 1) {\n            fig.send_message('set_device_pixel_ratio', {\n                device_pixel_ratio: fig.ratio,\n            });\n        }\n        fig.send_message('refresh', {});\n    };\n\n    this.imageObj.onload = function () {\n        if (fig.image_mode === 'full') {\n            // Full images could contain transparency (where diff images\n            // almost always do), so we need to clear the canvas so that\n            // there is no ghosting.\n            fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n        }\n        fig.context.drawImage(fig.imageObj, 0, 0);\n    };\n\n    this.imageObj.onunload = function () {\n        fig.ws.close();\n    };\n\n    this.ws.onmessage = this._make_on_message_function(this);\n\n    this.ondownload = ondownload;\n};\n\nmpl.figure.prototype._init_header = function () {\n    var titlebar = document.createElement('div');\n    titlebar.classList =\n        'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n    var titletext = document.createElement('div');\n    titletext.classList = 'ui-dialog-title';\n    titletext.setAttribute(\n        'style',\n        'width: 100%; text-align: center; padding: 3px;'\n    );\n    titlebar.appendChild(titletext);\n    this.root.appendChild(titlebar);\n    this.header = titletext;\n};\n\nmpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._init_canvas = function () {\n    var fig = this;\n\n    var canvas_div = (this.canvas_div = document.createElement('div'));\n    canvas_div.setAttribute(\n        'style',\n        'border: 1px solid #ddd;' +\n            'box-sizing: content-box;' +\n            'clear: both;' +\n            'min-height: 1px;' +\n            'min-width: 1px;' +\n            'outline: 0;' +\n            'overflow: hidden;' +\n            'position: relative;' +\n            'resize: both;'\n    );\n\n    function on_keyboard_event_closure(name) {\n        return function (event) {\n            return fig.key_event(event, name);\n        };\n    }\n\n    canvas_div.addEventListener(\n        'keydown',\n        on_keyboard_event_closure('key_press')\n    );\n    canvas_div.addEventListener(\n        'keyup',\n        on_keyboard_event_closure('key_release')\n    );\n\n    this._canvas_extra_style(canvas_div);\n    this.root.appendChild(canvas_div);\n\n    var canvas = (this.canvas = document.createElement('canvas'));\n    canvas.classList.add('mpl-canvas');\n    canvas.setAttribute('style', 'box-sizing: content-box;');\n\n    this.context = canvas.getContext('2d');\n\n    var backingStore =\n        this.context.backingStorePixelRatio ||\n        this.context.webkitBackingStorePixelRatio ||\n        this.context.mozBackingStorePixelRatio ||\n        this.context.msBackingStorePixelRatio ||\n        this.context.oBackingStorePixelRatio ||\n        this.context.backingStorePixelRatio ||\n        1;\n\n    this.ratio = (window.devicePixelRatio || 1) / backingStore;\n\n    var rubberband_canvas = (this.rubberband_canvas = document.createElement(\n        'canvas'\n    ));\n    rubberband_canvas.setAttribute(\n        'style',\n        'box-sizing: content-box; position: absolute; left: 0; top: 0; z-index: 1;'\n    );\n\n    // Apply a ponyfill if ResizeObserver is not implemented by browser.\n    if (this.ResizeObserver === undefined) {\n        if (window.ResizeObserver !== undefined) {\n            this.ResizeObserver = window.ResizeObserver;\n        } else {\n            var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n            this.ResizeObserver = obs.ResizeObserver;\n        }\n    }\n\n    this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n        var nentries = entries.length;\n        for (var i = 0; i < nentries; i++) {\n            var entry = entries[i];\n            var width, height;\n            if (entry.contentBoxSize) {\n                if (entry.contentBoxSize instanceof Array) {\n                    // Chrome 84 implements new version of spec.\n                    width = entry.contentBoxSize[0].inlineSize;\n                    height = entry.contentBoxSize[0].blockSize;\n                } else {\n                    // Firefox implements old version of spec.\n                    width = entry.contentBoxSize.inlineSize;\n                    height = entry.contentBoxSize.blockSize;\n                }\n            } else {\n                // Chrome <84 implements even older version of spec.\n                width = entry.contentRect.width;\n                height = entry.contentRect.height;\n            }\n\n            // Keep the size of the canvas and rubber band canvas in sync with\n            // the canvas container.\n            if (entry.devicePixelContentBoxSize) {\n                // Chrome 84 implements new version of spec.\n                canvas.setAttribute(\n                    'width',\n                    entry.devicePixelContentBoxSize[0].inlineSize\n                );\n                canvas.setAttribute(\n                    'height',\n                    entry.devicePixelContentBoxSize[0].blockSize\n                );\n            } else {\n                canvas.setAttribute('width', width * fig.ratio);\n                canvas.setAttribute('height', height * fig.ratio);\n            }\n            canvas.setAttribute(\n                'style',\n                'width: ' + width + 'px; height: ' + height + 'px;'\n            );\n\n            rubberband_canvas.setAttribute('width', width);\n            rubberband_canvas.setAttribute('height', height);\n\n            // And update the size in Python. We ignore the initial 0/0 size\n            // that occurs as the element is placed into the DOM, which should\n            // otherwise not happen due to the minimum size styling.\n            if (fig.ws.readyState == 1 && width != 0 && height != 0) {\n                fig.request_resize(width, height);\n            }\n        }\n    });\n    this.resizeObserverInstance.observe(canvas_div);\n\n    function on_mouse_event_closure(name) {\n        return function (event) {\n            return fig.mouse_event(event, name);\n        };\n    }\n\n    rubberband_canvas.addEventListener(\n        'mousedown',\n        on_mouse_event_closure('button_press')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseup',\n        on_mouse_event_closure('button_release')\n    );\n    rubberband_canvas.addEventListener(\n        'dblclick',\n        on_mouse_event_closure('dblclick')\n    );\n    // Throttle sequential mouse events to 1 every 20ms.\n    rubberband_canvas.addEventListener(\n        'mousemove',\n        on_mouse_event_closure('motion_notify')\n    );\n\n    rubberband_canvas.addEventListener(\n        'mouseenter',\n        on_mouse_event_closure('figure_enter')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseleave',\n        on_mouse_event_closure('figure_leave')\n    );\n\n    canvas_div.addEventListener('wheel', function (event) {\n        if (event.deltaY < 0) {\n            event.step = 1;\n        } else {\n            event.step = -1;\n        }\n        on_mouse_event_closure('scroll')(event);\n    });\n\n    canvas_div.appendChild(canvas);\n    canvas_div.appendChild(rubberband_canvas);\n\n    this.rubberband_context = rubberband_canvas.getContext('2d');\n    this.rubberband_context.strokeStyle = '#000000';\n\n    this._resize_canvas = function (width, height, forward) {\n        if (forward) {\n            canvas_div.style.width = width + 'px';\n            canvas_div.style.height = height + 'px';\n        }\n    };\n\n    // Disable right mouse context menu.\n    this.rubberband_canvas.addEventListener('contextmenu', function (_e) {\n        event.preventDefault();\n        return false;\n    });\n\n    function set_focus() {\n        canvas.focus();\n        canvas_div.focus();\n    }\n\n    window.setTimeout(set_focus, 100);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'mpl-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'mpl-button-group';\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'mpl-button-group';\n            continue;\n        }\n\n        var button = (fig.buttons[name] = document.createElement('button'));\n        button.classList = 'mpl-widget';\n        button.setAttribute('role', 'button');\n        button.setAttribute('aria-disabled', 'false');\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n\n        var icon_img = document.createElement('img');\n        icon_img.src = '_images/' + image + '.png';\n        icon_img.srcset = '_images/' + image + '_large.png 2x';\n        icon_img.alt = tooltip;\n        button.appendChild(icon_img);\n\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    var fmt_picker = document.createElement('select');\n    fmt_picker.classList = 'mpl-widget';\n    toolbar.appendChild(fmt_picker);\n    this.format_dropdown = fmt_picker;\n\n    for (var ind in mpl.extensions) {\n        var fmt = mpl.extensions[ind];\n        var option = document.createElement('option');\n        option.selected = fmt === mpl.default_extension;\n        option.innerHTML = fmt;\n        fmt_picker.appendChild(option);\n    }\n\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n};\n\nmpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n    // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n    // which will in turn request a refresh of the image.\n    this.send_message('resize', { width: x_pixels, height: y_pixels });\n};\n\nmpl.figure.prototype.send_message = function (type, properties) {\n    properties['type'] = type;\n    properties['figure_id'] = this.id;\n    this.ws.send(JSON.stringify(properties));\n};\n\nmpl.figure.prototype.send_draw_message = function () {\n    if (!this.waiting) {\n        this.waiting = true;\n        this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    var format_dropdown = fig.format_dropdown;\n    var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n    fig.ondownload(fig, format);\n};\n\nmpl.figure.prototype.handle_resize = function (fig, msg) {\n    var size = msg['size'];\n    if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n        fig._resize_canvas(size[0], size[1], msg['forward']);\n        fig.send_message('refresh', {});\n    }\n};\n\nmpl.figure.prototype.handle_rubberband = function (fig, msg) {\n    var x0 = msg['x0'] / fig.ratio;\n    var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n    var x1 = msg['x1'] / fig.ratio;\n    var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n    x0 = Math.floor(x0) + 0.5;\n    y0 = Math.floor(y0) + 0.5;\n    x1 = Math.floor(x1) + 0.5;\n    y1 = Math.floor(y1) + 0.5;\n    var min_x = Math.min(x0, x1);\n    var min_y = Math.min(y0, y1);\n    var width = Math.abs(x1 - x0);\n    var height = Math.abs(y1 - y0);\n\n    fig.rubberband_context.clearRect(\n        0,\n        0,\n        fig.canvas.width / fig.ratio,\n        fig.canvas.height / fig.ratio\n    );\n\n    fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n};\n\nmpl.figure.prototype.handle_figure_label = function (fig, msg) {\n    // Updates the figure title.\n    fig.header.textContent = msg['label'];\n};\n\nmpl.figure.prototype.handle_cursor = function (fig, msg) {\n    fig.rubberband_canvas.style.cursor = msg['cursor'];\n};\n\nmpl.figure.prototype.handle_message = function (fig, msg) {\n    fig.message.textContent = msg['message'];\n};\n\nmpl.figure.prototype.handle_draw = function (fig, _msg) {\n    // Request the server to send over a new figure.\n    fig.send_draw_message();\n};\n\nmpl.figure.prototype.handle_image_mode = function (fig, msg) {\n    fig.image_mode = msg['mode'];\n};\n\nmpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n    for (var key in msg) {\n        if (!(key in fig.buttons)) {\n            continue;\n        }\n        fig.buttons[key].disabled = !msg[key];\n        fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n    }\n};\n\nmpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n    if (msg['mode'] === 'PAN') {\n        fig.buttons['Pan'].classList.add('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    } else if (msg['mode'] === 'ZOOM') {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.add('active');\n    } else {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    }\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Called whenever the canvas gets updated.\n    this.send_message('ack', {});\n};\n\n// A function to construct a web socket function for onmessage handling.\n// Called in the figure constructor.\nmpl.figure.prototype._make_on_message_function = function (fig) {\n    return function socket_on_message(evt) {\n        if (evt.data instanceof Blob) {\n            var img = evt.data;\n            if (img.type !== 'image/png') {\n                /* FIXME: We get \"Resource interpreted as Image but\n                 * transferred with MIME type text/plain:\" errors on\n                 * Chrome.  But how to set the MIME type?  It doesn't seem\n                 * to be part of the websocket stream */\n                img.type = 'image/png';\n            }\n\n            /* Free the memory for the previous frames */\n            if (fig.imageObj.src) {\n                (window.URL || window.webkitURL).revokeObjectURL(\n                    fig.imageObj.src\n                );\n            }\n\n            fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n                img\n            );\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        } else if (\n            typeof evt.data === 'string' &&\n            evt.data.slice(0, 21) === 'data:image/png;base64'\n        ) {\n            fig.imageObj.src = evt.data;\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        }\n\n        var msg = JSON.parse(evt.data);\n        var msg_type = msg['type'];\n\n        // Call the  \"handle_{type}\" callback, which takes\n        // the figure and JSON message as its only arguments.\n        try {\n            var callback = fig['handle_' + msg_type];\n        } catch (e) {\n            console.log(\n                \"No handler for the '\" + msg_type + \"' message type: \",\n                msg\n            );\n            return;\n        }\n\n        if (callback) {\n            try {\n                // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n                callback(fig, msg);\n            } catch (e) {\n                console.log(\n                    \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n                    e,\n                    e.stack,\n                    msg\n                );\n            }\n        }\n    };\n};\n\n// from https://stackoverflow.com/questions/1114465/getting-mouse-location-in-canvas\nmpl.findpos = function (e) {\n    //this section is from http://www.quirksmode.org/js/events_properties.html\n    var targ;\n    if (!e) {\n        e = window.event;\n    }\n    if (e.target) {\n        targ = e.target;\n    } else if (e.srcElement) {\n        targ = e.srcElement;\n    }\n    if (targ.nodeType === 3) {\n        // defeat Safari bug\n        targ = targ.parentNode;\n    }\n\n    // pageX,Y are the mouse positions relative to the document\n    var boundingRect = targ.getBoundingClientRect();\n    var x = e.pageX - (boundingRect.left + document.body.scrollLeft);\n    var y = e.pageY - (boundingRect.top + document.body.scrollTop);\n\n    return { x: x, y: y };\n};\n\n/*\n * return a copy of an object with only non-object keys\n * we need this to avoid circular references\n * https://stackoverflow.com/a/24161582/3208463\n */\nfunction simpleKeys(original) {\n    return Object.keys(original).reduce(function (obj, key) {\n        if (typeof original[key] !== 'object') {\n            obj[key] = original[key];\n        }\n        return obj;\n    }, {});\n}\n\nmpl.figure.prototype.mouse_event = function (event, name) {\n    var canvas_pos = mpl.findpos(event);\n\n    if (name === 'button_press') {\n        this.canvas.focus();\n        this.canvas_div.focus();\n    }\n\n    var x = canvas_pos.x * this.ratio;\n    var y = canvas_pos.y * this.ratio;\n\n    this.send_message(name, {\n        x: x,\n        y: y,\n        button: event.button,\n        step: event.step,\n        guiEvent: simpleKeys(event),\n    });\n\n    /* This prevents the web browser from automatically changing to\n     * the text insertion cursor when the button is pressed.  We want\n     * to control all of the cursor setting manually through the\n     * 'cursor' event from matplotlib */\n    event.preventDefault();\n    return false;\n};\n\nmpl.figure.prototype._key_event_extra = function (_event, _name) {\n    // Handle any extra behaviour associated with a key event\n};\n\nmpl.figure.prototype.key_event = function (event, name) {\n    // Prevent repeat events\n    if (name === 'key_press') {\n        if (event.key === this._key) {\n            return;\n        } else {\n            this._key = event.key;\n        }\n    }\n    if (name === 'key_release') {\n        this._key = null;\n    }\n\n    var value = '';\n    if (event.ctrlKey && event.key !== 'Control') {\n        value += 'ctrl+';\n    }\n    else if (event.altKey && event.key !== 'Alt') {\n        value += 'alt+';\n    }\n    else if (event.shiftKey && event.key !== 'Shift') {\n        value += 'shift+';\n    }\n\n    value += 'k' + event.key;\n\n    this._key_event_extra(event, name);\n\n    this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n    return false;\n};\n\nmpl.figure.prototype.toolbar_button_onclick = function (name) {\n    if (name === 'download') {\n        this.handle_save(this, null);\n    } else {\n        this.send_message('toolbar_button', { name: name });\n    }\n};\n\nmpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n    this.message.textContent = tooltip;\n};\n\n///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n// prettier-ignore\nvar _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\nmpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home icon-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left icon-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right icon-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows icon-move\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis\", \"fa fa-square-o icon-check-empty\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o icon-save\", \"download\"]];\n\nmpl.extensions = [\"eps\", \"jpeg\", \"pgf\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\"];\n\nmpl.default_extension = \"png\";/* global mpl */\n\nvar comm_websocket_adapter = function (comm) {\n    // Create a \"websocket\"-like object which calls the given IPython comm\n    // object with the appropriate methods. Currently this is a non binary\n    // socket, so there is still some room for performance tuning.\n    var ws = {};\n\n    ws.binaryType = comm.kernel.ws.binaryType;\n    ws.readyState = comm.kernel.ws.readyState;\n    function updateReadyState(_event) {\n        if (comm.kernel.ws) {\n            ws.readyState = comm.kernel.ws.readyState;\n        } else {\n            ws.readyState = 3; // Closed state.\n        }\n    }\n    comm.kernel.ws.addEventListener('open', updateReadyState);\n    comm.kernel.ws.addEventListener('close', updateReadyState);\n    comm.kernel.ws.addEventListener('error', updateReadyState);\n\n    ws.close = function () {\n        comm.close();\n    };\n    ws.send = function (m) {\n        //console.log('sending', m);\n        comm.send(m);\n    };\n    // Register the callback with on_msg.\n    comm.on_msg(function (msg) {\n        //console.log('receiving', msg['content']['data'], msg);\n        var data = msg['content']['data'];\n        if (data['blob'] !== undefined) {\n            data = {\n                data: new Blob(msg['buffers'], { type: data['blob'] }),\n            };\n        }\n        // Pass the mpl event to the overridden (by mpl) onmessage function.\n        ws.onmessage(data);\n    });\n    return ws;\n};\n\nmpl.mpl_figure_comm = function (comm, msg) {\n    // This is the function which gets called when the mpl process\n    // starts-up an IPython Comm through the \"matplotlib\" channel.\n\n    var id = msg.content.data.id;\n    // Get hold of the div created by the display call when the Comm\n    // socket was opened in Python.\n    var element = document.getElementById(id);\n    var ws_proxy = comm_websocket_adapter(comm);\n\n    function ondownload(figure, _format) {\n        window.open(figure.canvas.toDataURL());\n    }\n\n    var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n\n    // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n    // web socket which is closed, not our websocket->open comm proxy.\n    ws_proxy.onopen();\n\n    fig.parent_element = element;\n    fig.cell_info = mpl.find_output_cell(\"<div id='\" + id + \"'></div>\");\n    if (!fig.cell_info) {\n        console.error('Failed to find cell for figure', id, fig);\n        return;\n    }\n    fig.cell_info[0].output_area.element.on(\n        'cleared',\n        { fig: fig },\n        fig._remove_fig_handler\n    );\n};\n\nmpl.figure.prototype.handle_close = function (fig, msg) {\n    var width = fig.canvas.width / fig.ratio;\n    fig.cell_info[0].output_area.element.off(\n        'cleared',\n        fig._remove_fig_handler\n    );\n    fig.resizeObserverInstance.unobserve(fig.canvas_div);\n\n    // Update the output cell to use the data from the current canvas.\n    fig.push_to_output();\n    var dataURL = fig.canvas.toDataURL();\n    // Re-enable the keyboard manager in IPython - without this line, in FF,\n    // the notebook keyboard shortcuts fail.\n    IPython.keyboard_manager.enable();\n    fig.parent_element.innerHTML =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n    fig.close_ws(fig, msg);\n};\n\nmpl.figure.prototype.close_ws = function (fig, msg) {\n    fig.send_message('closing', msg);\n    // fig.ws.close()\n};\n\nmpl.figure.prototype.push_to_output = function (_remove_interactive) {\n    // Turn the data on the canvas into data in the output cell.\n    var width = this.canvas.width / this.ratio;\n    var dataURL = this.canvas.toDataURL();\n    this.cell_info[1]['text/html'] =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Tell IPython that the notebook contents must change.\n    IPython.notebook.set_dirty(true);\n    this.send_message('ack', {});\n    var fig = this;\n    // Wait a second, then push the new image to the DOM so\n    // that it is saved nicely (might be nice to debounce this).\n    setTimeout(function () {\n        fig.push_to_output();\n    }, 1000);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'btn-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'btn-group';\n    var button;\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'btn-group';\n            continue;\n        }\n\n        button = fig.buttons[name] = document.createElement('button');\n        button.classList = 'btn btn-default';\n        button.href = '#';\n        button.title = name;\n        button.innerHTML = '<i class=\"fa ' + image + ' fa-lg\"></i>';\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    // Add the status bar.\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message pull-right';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n\n    // Add the close button to the window.\n    var buttongrp = document.createElement('div');\n    buttongrp.classList = 'btn-group inline pull-right';\n    button = document.createElement('button');\n    button.classList = 'btn btn-mini btn-primary';\n    button.href = '#';\n    button.title = 'Stop Interaction';\n    button.innerHTML = '<i class=\"fa fa-power-off icon-remove icon-large\"></i>';\n    button.addEventListener('click', function (_evt) {\n        fig.handle_close(fig, {});\n    });\n    button.addEventListener(\n        'mouseover',\n        on_mouseover_closure('Stop Interaction')\n    );\n    buttongrp.appendChild(button);\n    var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n    titlebar.insertBefore(buttongrp, titlebar.firstChild);\n};\n\nmpl.figure.prototype._remove_fig_handler = function (event) {\n    var fig = event.data.fig;\n    if (event.target !== this) {\n        // Ignore bubbled events from children.\n        return;\n    }\n    fig.close_ws(fig, {});\n};\n\nmpl.figure.prototype._root_extra_style = function (el) {\n    el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n};\n\nmpl.figure.prototype._canvas_extra_style = function (el) {\n    // this is important to make the div 'focusable\n    el.setAttribute('tabindex', 0);\n    // reach out to IPython and tell the keyboard manager to turn it's self\n    // off when our div gets focus\n\n    // location in version 3\n    if (IPython.notebook.keyboard_manager) {\n        IPython.notebook.keyboard_manager.register_events(el);\n    } else {\n        // location in version 2\n        IPython.keyboard_manager.register_events(el);\n    }\n};\n\nmpl.figure.prototype._key_event_extra = function (event, _name) {\n    // Check for shift+enter\n    if (event.shiftKey && event.which === 13) {\n        this.canvas_div.blur();\n        // select the cell after this one\n        var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n        IPython.notebook.select(index + 1);\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    fig.ondownload(fig, null);\n};\n\nmpl.find_output_cell = function (html_output) {\n    // Return the cell and output element which can be found *uniquely* in the notebook.\n    // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n    // IPython event is triggered only after the cells have been serialised, which for\n    // our purposes (turning an active figure into a static one), is too late.\n    var cells = IPython.notebook.get_cells();\n    var ncells = cells.length;\n    for (var i = 0; i < ncells; i++) {\n        var cell = cells[i];\n        if (cell.cell_type === 'code') {\n            for (var j = 0; j < cell.output_area.outputs.length; j++) {\n                var data = cell.output_area.outputs[j];\n                if (data.data) {\n                    // IPython >= 3 moved mimebundle to data attribute of output\n                    data = data.data;\n                }\n                if (data['text/html'] === html_output) {\n                    return [cell, data, j];\n                }\n            }\n        }\n    }\n};\n\n// Register the function which deals with the matplotlib target/channel.\n// The kernel may be null if the page has been refreshed.\nif (IPython.notebook.kernel !== null) {\n    IPython.notebook.kernel.comm_manager.register_target(\n        'matplotlib',\n        mpl.mpl_figure_comm\n    );\n}\n",
      "text/plain": [
       "<IPython.core.display.Javascript object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<img src=\"data:image/png;base64,[encoded data, 39628 characters]\" width=\"640\">"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
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   ],
   "source": [
    "%matplotlib notebook\n",
    "shotNum = \"0021\"\n",
    "filePath = folderPath + \"/\" + shotNum + \"/*.h5\"\n",
    "\n",
    "dataSetDict = {\n",
    "    dskey[groupList[i]]: read_hdf5_file(filePath, groupList[i])\n",
    "    for i in [0, 1]\n",
    "}\n",
    "\n",
    "dataSet = dataSetDict[\"camera_1\"]\n",
    "\n",
    "print_scanAxis(dataSet)\n",
    "\n",
    "scanAxis = get_scanAxis(dataSet)\n",
    "\n",
    "dataSet = auto_rechunk(dataSet)\n",
    "\n",
    "dataSet = imageAnalyser.get_absorption_images(dataSet)\n",
    "\n",
    "imageAnalyser.center = (325, 875)\n",
    "imageAnalyser.span = (500, 500)\n",
    "imageAnalyser.fraction = (0.1, 0.1)\n",
    "\n",
    "dataSet_cropOD = imageAnalyser.crop_image(dataSet.OD)\n",
    "dataSet_cropOD = imageAnalyser.substract_offset(dataSet_cropOD).load()\n",
    "\n",
    "Ncount = imageAnalyser.get_Ncount(dataSet_cropOD)\n",
    "Ncount_mean = calculate_mean(Ncount)\n",
    "Ncount_std = calculate_std(Ncount)\n",
    "\n",
    "fig = plt.figure()\n",
    "ax = fig.gca()\n",
    "Ncount_mean.plot.errorbar(ax=ax, yerr = Ncount_std, fmt='ob')\n",
    "#plt.xlabel('')\n",
    "plt.ylabel('NCount')\n",
    "plt.tight_layout()\n",
    "plt.grid(visible=1)\n",
    "plt.show()\n",
    "\n",
    "# DB.create_global(shotNum, dataSet)\n",
    "# DB.add_data(shotNum, dataSet_cropOD, engine='xarray')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {},
   "outputs": [
    {
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       ".xr-index-data {\n",
       "  display: none;\n",
       "  background-color: var(--xr-background-color) !important;\n",
       "  padding-bottom: 5px !important;\n",
       "}\n",
       "\n",
       ".xr-var-attrs-in:checked ~ .xr-var-attrs,\n",
       ".xr-var-data-in:checked ~ .xr-var-data,\n",
       ".xr-index-data-in:checked ~ .xr-index-data {\n",
       "  display: block;\n",
       "}\n",
       "\n",
       ".xr-var-data > table {\n",
       "  float: right;\n",
       "}\n",
       "\n",
       ".xr-var-name span,\n",
       ".xr-var-data,\n",
       ".xr-index-name div,\n",
       ".xr-index-data,\n",
       ".xr-attrs {\n",
       "  padding-left: 25px !important;\n",
       "}\n",
       "\n",
       ".xr-attrs,\n",
       ".xr-var-attrs,\n",
       ".xr-var-data,\n",
       ".xr-index-data {\n",
       "  grid-column: 1 / -1;\n",
       "}\n",
       "\n",
       "dl.xr-attrs {\n",
       "  padding: 0;\n",
       "  margin: 0;\n",
       "  display: grid;\n",
       "  grid-template-columns: 125px auto;\n",
       "}\n",
       "\n",
       ".xr-attrs dt,\n",
       ".xr-attrs dd {\n",
       "  padding: 0;\n",
       "  margin: 0;\n",
       "  float: left;\n",
       "  padding-right: 10px;\n",
       "  width: auto;\n",
       "}\n",
       "\n",
       ".xr-attrs dt {\n",
       "  font-weight: normal;\n",
       "  grid-column: 1;\n",
       "}\n",
       "\n",
       ".xr-attrs dt:hover span {\n",
       "  display: inline-block;\n",
       "  background: var(--xr-background-color);\n",
       "  padding-right: 10px;\n",
       "}\n",
       "\n",
       ".xr-attrs dd {\n",
       "  grid-column: 2;\n",
       "  white-space: pre-wrap;\n",
       "  word-break: break-all;\n",
       "}\n",
       "\n",
       ".xr-icon-database,\n",
       ".xr-icon-file-text2,\n",
       ".xr-no-icon {\n",
       "  display: inline-block;\n",
       "  vertical-align: middle;\n",
       "  width: 1em;\n",
       "  height: 1.5em !important;\n",
       "  stroke-width: 0;\n",
       "  stroke: currentColor;\n",
       "  fill: currentColor;\n",
       "}\n",
       "</style><pre class='xr-text-repr-fallback'>&lt;xarray.DataArray &#x27;OD&#x27; (final_vert_amp: 1)&gt;\n",
       "array([29676.45060443])\n",
       "Coordinates:\n",
       "  * final_vert_amp  (final_vert_amp) float64 0.045</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.DataArray</div><div class='xr-array-name'>'OD'</div><ul class='xr-dim-list'><li><span class='xr-has-index'>final_vert_amp</span>: 1</li></ul></div><ul class='xr-sections'><li class='xr-section-item'><div class='xr-array-wrap'><input id='section-afcf31cf-2ab4-4ec0-bbe4-f6342cf64b8b' class='xr-array-in' type='checkbox' checked><label for='section-afcf31cf-2ab4-4ec0-bbe4-f6342cf64b8b' title='Show/hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-array-preview xr-preview'><span>2.968e+04</span></div><div class='xr-array-data'><pre>array([29676.45060443])</pre></div></div></li><li class='xr-section-item'><input id='section-3064ec8b-148e-48c2-a58b-98b70a9fbf8e' class='xr-section-summary-in' type='checkbox'  checked><label for='section-3064ec8b-148e-48c2-a58b-98b70a9fbf8e' class='xr-section-summary' >Coordinates: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>final_vert_amp</span></div><div class='xr-var-dims'>(final_vert_amp)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>0.045</div><input id='attrs-6fa74f1c-255e-4f85-9eda-30c219bff7d4' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-6fa74f1c-255e-4f85-9eda-30c219bff7d4' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a737f7e3-553a-4474-9fc0-5c8fa128a3ec' class='xr-var-data-in' type='checkbox'><label for='data-a737f7e3-553a-4474-9fc0-5c8fa128a3ec' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([0.045])</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-4343ca55-551c-45a4-a744-a92bbc669a71' class='xr-section-summary-in' type='checkbox'  ><label for='section-4343ca55-551c-45a4-a744-a92bbc669a71' class='xr-section-summary' >Indexes: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-index-name'><div>final_vert_amp</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-e63c7b75-53c2-4eec-8e4c-e6725f45889a' class='xr-index-data-in' type='checkbox'/><label for='index-e63c7b75-53c2-4eec-8e4c-e6725f45889a' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Float64Index([0.045], dtype=&#x27;float64&#x27;, name=&#x27;final_vert_amp&#x27;))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-e98f96d0-b3a2-4063-9b37-a341ae427357' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-e98f96d0-b3a2-4063-9b37-a341ae427357' class='xr-section-summary'  title='Expand/collapse section'>Attributes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'></dl></div></li></ul></div></div>"
      ],
      "text/plain": [
       "<xarray.DataArray 'OD' (final_vert_amp: 1)>\n",
       "array([29676.45060443])\n",
       "Coordinates:\n",
       "  * final_vert_amp  (final_vert_amp) float64 0.045"
      ]
     },
     "execution_count": 31,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Ncount_mean.where(Ncount_mean==Ncount_mean.max(), drop=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Evaporative Cooling"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "metadata": {},
   "outputs": [],
   "source": [
    "img_dir = 'C:/Users/control/DyLab/Experiments/DyBEC/'\n",
    "# img_dir = '//DyLabNAS/Data/'\n",
    "SequenceName = \"Evaporative_Cooling\"\n",
    "folderPath = img_dir + SequenceName + \"/\" + get_date()\n",
    "\n",
    "mongoDB = mongoClient[SequenceName]\n",
    "\n",
    "DB = MongoDB(mongoClient, mongoDB, date=get_date())"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Measure trap frequency at various points of evap 2"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Horz TF due to arm 1: blink on modulation = 0, blink_off_modulation = 0.35 in 700 µs, hold of 1 s"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Truncation: 0.5"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 56,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The detected scaning axes and values are: \n",
      "\n",
      "{'mod_blink_on_time': array([0.005, 0.006, 0.007, 0.008, 0.009, 0.01 , 0.011, 0.012, 0.013,\n",
      "       0.014, 0.015, 0.016, 0.017, 0.018, 0.019]), 'runs': array([0., 1., 2., 3.])}\n"
     ]
    },
    {
     "data": {
      "application/javascript": "/* Put everything inside the global mpl namespace */\n/* global mpl */\nwindow.mpl = {};\n\nmpl.get_websocket_type = function () {\n    if (typeof WebSocket !== 'undefined') {\n        return WebSocket;\n    } else if (typeof MozWebSocket !== 'undefined') {\n        return MozWebSocket;\n    } else {\n        alert(\n            'Your browser does not have WebSocket support. ' +\n                'Please try Chrome, Safari or Firefox ≥ 6. ' +\n                'Firefox 4 and 5 are also supported but you ' +\n                'have to enable WebSockets in about:config.'\n        );\n    }\n};\n\nmpl.figure = function (figure_id, websocket, ondownload, parent_element) {\n    this.id = figure_id;\n\n    this.ws = websocket;\n\n    this.supports_binary = this.ws.binaryType !== undefined;\n\n    if (!this.supports_binary) {\n        var warnings = document.getElementById('mpl-warnings');\n        if (warnings) {\n            warnings.style.display = 'block';\n            warnings.textContent =\n                'This browser does not support binary websocket messages. ' +\n                'Performance may be slow.';\n        }\n    }\n\n    this.imageObj = new Image();\n\n    this.context = undefined;\n    this.message = undefined;\n    this.canvas = undefined;\n    this.rubberband_canvas = undefined;\n    this.rubberband_context = undefined;\n    this.format_dropdown = undefined;\n\n    this.image_mode = 'full';\n\n    this.root = document.createElement('div');\n    this.root.setAttribute('style', 'display: inline-block');\n    this._root_extra_style(this.root);\n\n    parent_element.appendChild(this.root);\n\n    this._init_header(this);\n    this._init_canvas(this);\n    this._init_toolbar(this);\n\n    var fig = this;\n\n    this.waiting = false;\n\n    this.ws.onopen = function () {\n        fig.send_message('supports_binary', { value: fig.supports_binary });\n        fig.send_message('send_image_mode', {});\n        if (fig.ratio !== 1) {\n            fig.send_message('set_device_pixel_ratio', {\n                device_pixel_ratio: fig.ratio,\n            });\n        }\n        fig.send_message('refresh', {});\n    };\n\n    this.imageObj.onload = function () {\n        if (fig.image_mode === 'full') {\n            // Full images could contain transparency (where diff images\n            // almost always do), so we need to clear the canvas so that\n            // there is no ghosting.\n            fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n        }\n        fig.context.drawImage(fig.imageObj, 0, 0);\n    };\n\n    this.imageObj.onunload = function () {\n        fig.ws.close();\n    };\n\n    this.ws.onmessage = this._make_on_message_function(this);\n\n    this.ondownload = ondownload;\n};\n\nmpl.figure.prototype._init_header = function () {\n    var titlebar = document.createElement('div');\n    titlebar.classList =\n        'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n    var titletext = document.createElement('div');\n    titletext.classList = 'ui-dialog-title';\n    titletext.setAttribute(\n        'style',\n        'width: 100%; text-align: center; padding: 3px;'\n    );\n    titlebar.appendChild(titletext);\n    this.root.appendChild(titlebar);\n    this.header = titletext;\n};\n\nmpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._init_canvas = function () {\n    var fig = this;\n\n    var canvas_div = (this.canvas_div = document.createElement('div'));\n    canvas_div.setAttribute(\n        'style',\n        'border: 1px solid #ddd;' +\n            'box-sizing: content-box;' +\n            'clear: both;' +\n            'min-height: 1px;' +\n            'min-width: 1px;' +\n            'outline: 0;' +\n            'overflow: hidden;' +\n            'position: relative;' +\n            'resize: both;'\n    );\n\n    function on_keyboard_event_closure(name) {\n        return function (event) {\n            return fig.key_event(event, name);\n        };\n    }\n\n    canvas_div.addEventListener(\n        'keydown',\n        on_keyboard_event_closure('key_press')\n    );\n    canvas_div.addEventListener(\n        'keyup',\n        on_keyboard_event_closure('key_release')\n    );\n\n    this._canvas_extra_style(canvas_div);\n    this.root.appendChild(canvas_div);\n\n    var canvas = (this.canvas = document.createElement('canvas'));\n    canvas.classList.add('mpl-canvas');\n    canvas.setAttribute('style', 'box-sizing: content-box;');\n\n    this.context = canvas.getContext('2d');\n\n    var backingStore =\n        this.context.backingStorePixelRatio ||\n        this.context.webkitBackingStorePixelRatio ||\n        this.context.mozBackingStorePixelRatio ||\n        this.context.msBackingStorePixelRatio ||\n        this.context.oBackingStorePixelRatio ||\n        this.context.backingStorePixelRatio ||\n        1;\n\n    this.ratio = (window.devicePixelRatio || 1) / backingStore;\n\n    var rubberband_canvas = (this.rubberband_canvas = document.createElement(\n        'canvas'\n    ));\n    rubberband_canvas.setAttribute(\n        'style',\n        'box-sizing: content-box; position: absolute; left: 0; top: 0; z-index: 1;'\n    );\n\n    // Apply a ponyfill if ResizeObserver is not implemented by browser.\n    if (this.ResizeObserver === undefined) {\n        if (window.ResizeObserver !== undefined) {\n            this.ResizeObserver = window.ResizeObserver;\n        } else {\n            var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n            this.ResizeObserver = obs.ResizeObserver;\n        }\n    }\n\n    this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n        var nentries = entries.length;\n        for (var i = 0; i < nentries; i++) {\n            var entry = entries[i];\n            var width, height;\n            if (entry.contentBoxSize) {\n                if (entry.contentBoxSize instanceof Array) {\n                    // Chrome 84 implements new version of spec.\n                    width = entry.contentBoxSize[0].inlineSize;\n                    height = entry.contentBoxSize[0].blockSize;\n                } else {\n                    // Firefox implements old version of spec.\n                    width = entry.contentBoxSize.inlineSize;\n                    height = entry.contentBoxSize.blockSize;\n                }\n            } else {\n                // Chrome <84 implements even older version of spec.\n                width = entry.contentRect.width;\n                height = entry.contentRect.height;\n            }\n\n            // Keep the size of the canvas and rubber band canvas in sync with\n            // the canvas container.\n            if (entry.devicePixelContentBoxSize) {\n                // Chrome 84 implements new version of spec.\n                canvas.setAttribute(\n                    'width',\n                    entry.devicePixelContentBoxSize[0].inlineSize\n                );\n                canvas.setAttribute(\n                    'height',\n                    entry.devicePixelContentBoxSize[0].blockSize\n                );\n            } else {\n                canvas.setAttribute('width', width * fig.ratio);\n                canvas.setAttribute('height', height * fig.ratio);\n            }\n            canvas.setAttribute(\n                'style',\n                'width: ' + width + 'px; height: ' + height + 'px;'\n            );\n\n            rubberband_canvas.setAttribute('width', width);\n            rubberband_canvas.setAttribute('height', height);\n\n            // And update the size in Python. We ignore the initial 0/0 size\n            // that occurs as the element is placed into the DOM, which should\n            // otherwise not happen due to the minimum size styling.\n            if (fig.ws.readyState == 1 && width != 0 && height != 0) {\n                fig.request_resize(width, height);\n            }\n        }\n    });\n    this.resizeObserverInstance.observe(canvas_div);\n\n    function on_mouse_event_closure(name) {\n        return function (event) {\n            return fig.mouse_event(event, name);\n        };\n    }\n\n    rubberband_canvas.addEventListener(\n        'mousedown',\n        on_mouse_event_closure('button_press')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseup',\n        on_mouse_event_closure('button_release')\n    );\n    rubberband_canvas.addEventListener(\n        'dblclick',\n        on_mouse_event_closure('dblclick')\n    );\n    // Throttle sequential mouse events to 1 every 20ms.\n    rubberband_canvas.addEventListener(\n        'mousemove',\n        on_mouse_event_closure('motion_notify')\n    );\n\n    rubberband_canvas.addEventListener(\n        'mouseenter',\n        on_mouse_event_closure('figure_enter')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseleave',\n        on_mouse_event_closure('figure_leave')\n    );\n\n    canvas_div.addEventListener('wheel', function (event) {\n        if (event.deltaY < 0) {\n            event.step = 1;\n        } else {\n            event.step = -1;\n        }\n        on_mouse_event_closure('scroll')(event);\n    });\n\n    canvas_div.appendChild(canvas);\n    canvas_div.appendChild(rubberband_canvas);\n\n    this.rubberband_context = rubberband_canvas.getContext('2d');\n    this.rubberband_context.strokeStyle = '#000000';\n\n    this._resize_canvas = function (width, height, forward) {\n        if (forward) {\n            canvas_div.style.width = width + 'px';\n            canvas_div.style.height = height + 'px';\n        }\n    };\n\n    // Disable right mouse context menu.\n    this.rubberband_canvas.addEventListener('contextmenu', function (_e) {\n        event.preventDefault();\n        return false;\n    });\n\n    function set_focus() {\n        canvas.focus();\n        canvas_div.focus();\n    }\n\n    window.setTimeout(set_focus, 100);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'mpl-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'mpl-button-group';\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'mpl-button-group';\n            continue;\n        }\n\n        var button = (fig.buttons[name] = document.createElement('button'));\n        button.classList = 'mpl-widget';\n        button.setAttribute('role', 'button');\n        button.setAttribute('aria-disabled', 'false');\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n\n        var icon_img = document.createElement('img');\n        icon_img.src = '_images/' + image + '.png';\n        icon_img.srcset = '_images/' + image + '_large.png 2x';\n        icon_img.alt = tooltip;\n        button.appendChild(icon_img);\n\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    var fmt_picker = document.createElement('select');\n    fmt_picker.classList = 'mpl-widget';\n    toolbar.appendChild(fmt_picker);\n    this.format_dropdown = fmt_picker;\n\n    for (var ind in mpl.extensions) {\n        var fmt = mpl.extensions[ind];\n        var option = document.createElement('option');\n        option.selected = fmt === mpl.default_extension;\n        option.innerHTML = fmt;\n        fmt_picker.appendChild(option);\n    }\n\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n};\n\nmpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n    // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n    // which will in turn request a refresh of the image.\n    this.send_message('resize', { width: x_pixels, height: y_pixels });\n};\n\nmpl.figure.prototype.send_message = function (type, properties) {\n    properties['type'] = type;\n    properties['figure_id'] = this.id;\n    this.ws.send(JSON.stringify(properties));\n};\n\nmpl.figure.prototype.send_draw_message = function () {\n    if (!this.waiting) {\n        this.waiting = true;\n        this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    var format_dropdown = fig.format_dropdown;\n    var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n    fig.ondownload(fig, format);\n};\n\nmpl.figure.prototype.handle_resize = function (fig, msg) {\n    var size = msg['size'];\n    if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n        fig._resize_canvas(size[0], size[1], msg['forward']);\n        fig.send_message('refresh', {});\n    }\n};\n\nmpl.figure.prototype.handle_rubberband = function (fig, msg) {\n    var x0 = msg['x0'] / fig.ratio;\n    var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n    var x1 = msg['x1'] / fig.ratio;\n    var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n    x0 = Math.floor(x0) + 0.5;\n    y0 = Math.floor(y0) + 0.5;\n    x1 = Math.floor(x1) + 0.5;\n    y1 = Math.floor(y1) + 0.5;\n    var min_x = Math.min(x0, x1);\n    var min_y = Math.min(y0, y1);\n    var width = Math.abs(x1 - x0);\n    var height = Math.abs(y1 - y0);\n\n    fig.rubberband_context.clearRect(\n        0,\n        0,\n        fig.canvas.width / fig.ratio,\n        fig.canvas.height / fig.ratio\n    );\n\n    fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n};\n\nmpl.figure.prototype.handle_figure_label = function (fig, msg) {\n    // Updates the figure title.\n    fig.header.textContent = msg['label'];\n};\n\nmpl.figure.prototype.handle_cursor = function (fig, msg) {\n    fig.rubberband_canvas.style.cursor = msg['cursor'];\n};\n\nmpl.figure.prototype.handle_message = function (fig, msg) {\n    fig.message.textContent = msg['message'];\n};\n\nmpl.figure.prototype.handle_draw = function (fig, _msg) {\n    // Request the server to send over a new figure.\n    fig.send_draw_message();\n};\n\nmpl.figure.prototype.handle_image_mode = function (fig, msg) {\n    fig.image_mode = msg['mode'];\n};\n\nmpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n    for (var key in msg) {\n        if (!(key in fig.buttons)) {\n            continue;\n        }\n        fig.buttons[key].disabled = !msg[key];\n        fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n    }\n};\n\nmpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n    if (msg['mode'] === 'PAN') {\n        fig.buttons['Pan'].classList.add('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    } else if (msg['mode'] === 'ZOOM') {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.add('active');\n    } else {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    }\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Called whenever the canvas gets updated.\n    this.send_message('ack', {});\n};\n\n// A function to construct a web socket function for onmessage handling.\n// Called in the figure constructor.\nmpl.figure.prototype._make_on_message_function = function (fig) {\n    return function socket_on_message(evt) {\n        if (evt.data instanceof Blob) {\n            var img = evt.data;\n            if (img.type !== 'image/png') {\n                /* FIXME: We get \"Resource interpreted as Image but\n                 * transferred with MIME type text/plain:\" errors on\n                 * Chrome.  But how to set the MIME type?  It doesn't seem\n                 * to be part of the websocket stream */\n                img.type = 'image/png';\n            }\n\n            /* Free the memory for the previous frames */\n            if (fig.imageObj.src) {\n                (window.URL || window.webkitURL).revokeObjectURL(\n                    fig.imageObj.src\n                );\n            }\n\n            fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n                img\n            );\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        } else if (\n            typeof evt.data === 'string' &&\n            evt.data.slice(0, 21) === 'data:image/png;base64'\n        ) {\n            fig.imageObj.src = evt.data;\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        }\n\n        var msg = JSON.parse(evt.data);\n        var msg_type = msg['type'];\n\n        // Call the  \"handle_{type}\" callback, which takes\n        // the figure and JSON message as its only arguments.\n        try {\n            var callback = fig['handle_' + msg_type];\n        } catch (e) {\n            console.log(\n                \"No handler for the '\" + msg_type + \"' message type: \",\n                msg\n            );\n            return;\n        }\n\n        if (callback) {\n            try {\n                // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n                callback(fig, msg);\n            } catch (e) {\n                console.log(\n                    \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n                    e,\n                    e.stack,\n                    msg\n                );\n            }\n        }\n    };\n};\n\n// from https://stackoverflow.com/questions/1114465/getting-mouse-location-in-canvas\nmpl.findpos = function (e) {\n    //this section is from http://www.quirksmode.org/js/events_properties.html\n    var targ;\n    if (!e) {\n        e = window.event;\n    }\n    if (e.target) {\n        targ = e.target;\n    } else if (e.srcElement) {\n        targ = e.srcElement;\n    }\n    if (targ.nodeType === 3) {\n        // defeat Safari bug\n        targ = targ.parentNode;\n    }\n\n    // pageX,Y are the mouse positions relative to the document\n    var boundingRect = targ.getBoundingClientRect();\n    var x = e.pageX - (boundingRect.left + document.body.scrollLeft);\n    var y = e.pageY - (boundingRect.top + document.body.scrollTop);\n\n    return { x: x, y: y };\n};\n\n/*\n * return a copy of an object with only non-object keys\n * we need this to avoid circular references\n * https://stackoverflow.com/a/24161582/3208463\n */\nfunction simpleKeys(original) {\n    return Object.keys(original).reduce(function (obj, key) {\n        if (typeof original[key] !== 'object') {\n            obj[key] = original[key];\n        }\n        return obj;\n    }, {});\n}\n\nmpl.figure.prototype.mouse_event = function (event, name) {\n    var canvas_pos = mpl.findpos(event);\n\n    if (name === 'button_press') {\n        this.canvas.focus();\n        this.canvas_div.focus();\n    }\n\n    var x = canvas_pos.x * this.ratio;\n    var y = canvas_pos.y * this.ratio;\n\n    this.send_message(name, {\n        x: x,\n        y: y,\n        button: event.button,\n        step: event.step,\n        guiEvent: simpleKeys(event),\n    });\n\n    /* This prevents the web browser from automatically changing to\n     * the text insertion cursor when the button is pressed.  We want\n     * to control all of the cursor setting manually through the\n     * 'cursor' event from matplotlib */\n    event.preventDefault();\n    return false;\n};\n\nmpl.figure.prototype._key_event_extra = function (_event, _name) {\n    // Handle any extra behaviour associated with a key event\n};\n\nmpl.figure.prototype.key_event = function (event, name) {\n    // Prevent repeat events\n    if (name === 'key_press') {\n        if (event.key === this._key) {\n            return;\n        } else {\n            this._key = event.key;\n        }\n    }\n    if (name === 'key_release') {\n        this._key = null;\n    }\n\n    var value = '';\n    if (event.ctrlKey && event.key !== 'Control') {\n        value += 'ctrl+';\n    }\n    else if (event.altKey && event.key !== 'Alt') {\n        value += 'alt+';\n    }\n    else if (event.shiftKey && event.key !== 'Shift') {\n        value += 'shift+';\n    }\n\n    value += 'k' + event.key;\n\n    this._key_event_extra(event, name);\n\n    this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n    return false;\n};\n\nmpl.figure.prototype.toolbar_button_onclick = function (name) {\n    if (name === 'download') {\n        this.handle_save(this, null);\n    } else {\n        this.send_message('toolbar_button', { name: name });\n    }\n};\n\nmpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n    this.message.textContent = tooltip;\n};\n\n///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n// prettier-ignore\nvar _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\nmpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home icon-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left icon-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right icon-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows icon-move\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis\", \"fa fa-square-o icon-check-empty\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o icon-save\", \"download\"]];\n\nmpl.extensions = [\"eps\", \"jpeg\", \"pgf\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\"];\n\nmpl.default_extension = \"png\";/* global mpl */\n\nvar comm_websocket_adapter = function (comm) {\n    // Create a \"websocket\"-like object which calls the given IPython comm\n    // object with the appropriate methods. Currently this is a non binary\n    // socket, so there is still some room for performance tuning.\n    var ws = {};\n\n    ws.binaryType = comm.kernel.ws.binaryType;\n    ws.readyState = comm.kernel.ws.readyState;\n    function updateReadyState(_event) {\n        if (comm.kernel.ws) {\n            ws.readyState = comm.kernel.ws.readyState;\n        } else {\n            ws.readyState = 3; // Closed state.\n        }\n    }\n    comm.kernel.ws.addEventListener('open', updateReadyState);\n    comm.kernel.ws.addEventListener('close', updateReadyState);\n    comm.kernel.ws.addEventListener('error', updateReadyState);\n\n    ws.close = function () {\n        comm.close();\n    };\n    ws.send = function (m) {\n        //console.log('sending', m);\n        comm.send(m);\n    };\n    // Register the callback with on_msg.\n    comm.on_msg(function (msg) {\n        //console.log('receiving', msg['content']['data'], msg);\n        var data = msg['content']['data'];\n        if (data['blob'] !== undefined) {\n            data = {\n                data: new Blob(msg['buffers'], { type: data['blob'] }),\n            };\n        }\n        // Pass the mpl event to the overridden (by mpl) onmessage function.\n        ws.onmessage(data);\n    });\n    return ws;\n};\n\nmpl.mpl_figure_comm = function (comm, msg) {\n    // This is the function which gets called when the mpl process\n    // starts-up an IPython Comm through the \"matplotlib\" channel.\n\n    var id = msg.content.data.id;\n    // Get hold of the div created by the display call when the Comm\n    // socket was opened in Python.\n    var element = document.getElementById(id);\n    var ws_proxy = comm_websocket_adapter(comm);\n\n    function ondownload(figure, _format) {\n        window.open(figure.canvas.toDataURL());\n    }\n\n    var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n\n    // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n    // web socket which is closed, not our websocket->open comm proxy.\n    ws_proxy.onopen();\n\n    fig.parent_element = element;\n    fig.cell_info = mpl.find_output_cell(\"<div id='\" + id + \"'></div>\");\n    if (!fig.cell_info) {\n        console.error('Failed to find cell for figure', id, fig);\n        return;\n    }\n    fig.cell_info[0].output_area.element.on(\n        'cleared',\n        { fig: fig },\n        fig._remove_fig_handler\n    );\n};\n\nmpl.figure.prototype.handle_close = function (fig, msg) {\n    var width = fig.canvas.width / fig.ratio;\n    fig.cell_info[0].output_area.element.off(\n        'cleared',\n        fig._remove_fig_handler\n    );\n    fig.resizeObserverInstance.unobserve(fig.canvas_div);\n\n    // Update the output cell to use the data from the current canvas.\n    fig.push_to_output();\n    var dataURL = fig.canvas.toDataURL();\n    // Re-enable the keyboard manager in IPython - without this line, in FF,\n    // the notebook keyboard shortcuts fail.\n    IPython.keyboard_manager.enable();\n    fig.parent_element.innerHTML =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n    fig.close_ws(fig, msg);\n};\n\nmpl.figure.prototype.close_ws = function (fig, msg) {\n    fig.send_message('closing', msg);\n    // fig.ws.close()\n};\n\nmpl.figure.prototype.push_to_output = function (_remove_interactive) {\n    // Turn the data on the canvas into data in the output cell.\n    var width = this.canvas.width / this.ratio;\n    var dataURL = this.canvas.toDataURL();\n    this.cell_info[1]['text/html'] =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Tell IPython that the notebook contents must change.\n    IPython.notebook.set_dirty(true);\n    this.send_message('ack', {});\n    var fig = this;\n    // Wait a second, then push the new image to the DOM so\n    // that it is saved nicely (might be nice to debounce this).\n    setTimeout(function () {\n        fig.push_to_output();\n    }, 1000);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'btn-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'btn-group';\n    var button;\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'btn-group';\n            continue;\n        }\n\n        button = fig.buttons[name] = document.createElement('button');\n        button.classList = 'btn btn-default';\n        button.href = '#';\n        button.title = name;\n        button.innerHTML = '<i class=\"fa ' + image + ' fa-lg\"></i>';\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    // Add the status bar.\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message pull-right';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n\n    // Add the close button to the window.\n    var buttongrp = document.createElement('div');\n    buttongrp.classList = 'btn-group inline pull-right';\n    button = document.createElement('button');\n    button.classList = 'btn btn-mini btn-primary';\n    button.href = '#';\n    button.title = 'Stop Interaction';\n    button.innerHTML = '<i class=\"fa fa-power-off icon-remove icon-large\"></i>';\n    button.addEventListener('click', function (_evt) {\n        fig.handle_close(fig, {});\n    });\n    button.addEventListener(\n        'mouseover',\n        on_mouseover_closure('Stop Interaction')\n    );\n    buttongrp.appendChild(button);\n    var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n    titlebar.insertBefore(buttongrp, titlebar.firstChild);\n};\n\nmpl.figure.prototype._remove_fig_handler = function (event) {\n    var fig = event.data.fig;\n    if (event.target !== this) {\n        // Ignore bubbled events from children.\n        return;\n    }\n    fig.close_ws(fig, {});\n};\n\nmpl.figure.prototype._root_extra_style = function (el) {\n    el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n};\n\nmpl.figure.prototype._canvas_extra_style = function (el) {\n    // this is important to make the div 'focusable\n    el.setAttribute('tabindex', 0);\n    // reach out to IPython and tell the keyboard manager to turn it's self\n    // off when our div gets focus\n\n    // location in version 3\n    if (IPython.notebook.keyboard_manager) {\n        IPython.notebook.keyboard_manager.register_events(el);\n    } else {\n        // location in version 2\n        IPython.keyboard_manager.register_events(el);\n    }\n};\n\nmpl.figure.prototype._key_event_extra = function (event, _name) {\n    // Check for shift+enter\n    if (event.shiftKey && event.which === 13) {\n        this.canvas_div.blur();\n        // select the cell after this one\n        var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n        IPython.notebook.select(index + 1);\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    fig.ondownload(fig, null);\n};\n\nmpl.find_output_cell = function (html_output) {\n    // Return the cell and output element which can be found *uniquely* in the notebook.\n    // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n    // IPython event is triggered only after the cells have been serialised, which for\n    // our purposes (turning an active figure into a static one), is too late.\n    var cells = IPython.notebook.get_cells();\n    var ncells = cells.length;\n    for (var i = 0; i < ncells; i++) {\n        var cell = cells[i];\n        if (cell.cell_type === 'code') {\n            for (var j = 0; j < cell.output_area.outputs.length; j++) {\n                var data = cell.output_area.outputs[j];\n                if (data.data) {\n                    // IPython >= 3 moved mimebundle to data attribute of output\n                    data = data.data;\n                }\n                if (data['text/html'] === html_output) {\n                    return [cell, data, j];\n                }\n            }\n        }\n    }\n};\n\n// Register the function which deals with the matplotlib target/channel.\n// The kernel may be null if the page has been refreshed.\nif (IPython.notebook.kernel !== null) {\n    IPython.notebook.kernel.comm_manager.register_target(\n        'matplotlib',\n        mpl.mpl_figure_comm\n    );\n}\n",
      "text/plain": [
       "<IPython.core.display.Javascript object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<img src=\"data:image/png;base64,[encoded data, 37840 characters]\" width=\"640\">"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "%matplotlib notebook\n",
    "shotNum = \"0004\"\n",
    "filePath = folderPath + \"/\" + shotNum + \"/*.h5\"\n",
    "\n",
    "dataSetDict = {\n",
    "    dskey[groupList[i]]: read_hdf5_file(filePath, groupList[i], excludeAxis = ['sweep_start_freq', 'sweep_stop_freq'])\n",
    "    for i in [0]\n",
    "}\n",
    "\n",
    "dataSet = dataSetDict[\"camera_0\"]\n",
    "\n",
    "print_scanAxis(dataSet)\n",
    "\n",
    "scanAxis = get_scanAxis(dataSet)\n",
    "\n",
    "dataSet = auto_rechunk(dataSet)\n",
    "\n",
    "dataSet = imageAnalyser.get_absorption_images(dataSet)\n",
    "\n",
    "imageAnalyser.center = (800, 900)\n",
    "imageAnalyser.span = (300, 300)\n",
    "imageAnalyser.fraction = (0.1, 0.1)\n",
    "\n",
    "dataSet_cropOD = imageAnalyser.crop_image(dataSet.OD)\n",
    "dataSet_cropOD = imageAnalyser.substract_offset(dataSet_cropOD).load()\n",
    "\n",
    "Ncount = imageAnalyser.get_Ncount(dataSet_cropOD)\n",
    "Ncount_mean = calculate_mean(Ncount)\n",
    "Ncount_std = calculate_std(Ncount)\n",
    "\n",
    "fig = plt.figure()\n",
    "ax = fig.gca()\n",
    "Ncount_mean.plot.errorbar(ax=ax, yerr = None, fmt='ob')\n",
    "plt.ylabel('NCount')\n",
    "plt.tight_layout()\n",
    "plt.grid(visible=1)\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 57,
   "metadata": {},
   "outputs": [],
   "source": [
    "dataSet_cropOD_chunk = dataSet_cropOD.chunk((1, 300, 300))\n",
    "fitAnalyser = FitAnalyser(\"Gaussian-2D\", fitDim=2)\n",
    "params = fitAnalyser.guess(dataSet_cropOD_chunk, dask=\"parallelized\")\n",
    "fitResult = fitAnalyser.fit(dataSet_cropOD_chunk, params, dask=\"parallelized\").load()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 58,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/javascript": "/* Put everything inside the global mpl namespace */\n/* global mpl */\nwindow.mpl = {};\n\nmpl.get_websocket_type = function () {\n    if (typeof WebSocket !== 'undefined') {\n        return WebSocket;\n    } else if (typeof MozWebSocket !== 'undefined') {\n        return MozWebSocket;\n    } else {\n        alert(\n            'Your browser does not have WebSocket support. ' +\n                'Please try Chrome, Safari or Firefox ≥ 6. ' +\n                'Firefox 4 and 5 are also supported but you ' +\n                'have to enable WebSockets in about:config.'\n        );\n    }\n};\n\nmpl.figure = function (figure_id, websocket, ondownload, parent_element) {\n    this.id = figure_id;\n\n    this.ws = websocket;\n\n    this.supports_binary = this.ws.binaryType !== undefined;\n\n    if (!this.supports_binary) {\n        var warnings = document.getElementById('mpl-warnings');\n        if (warnings) {\n            warnings.style.display = 'block';\n            warnings.textContent =\n                'This browser does not support binary websocket messages. ' +\n                'Performance may be slow.';\n        }\n    }\n\n    this.imageObj = new Image();\n\n    this.context = undefined;\n    this.message = undefined;\n    this.canvas = undefined;\n    this.rubberband_canvas = undefined;\n    this.rubberband_context = undefined;\n    this.format_dropdown = undefined;\n\n    this.image_mode = 'full';\n\n    this.root = document.createElement('div');\n    this.root.setAttribute('style', 'display: inline-block');\n    this._root_extra_style(this.root);\n\n    parent_element.appendChild(this.root);\n\n    this._init_header(this);\n    this._init_canvas(this);\n    this._init_toolbar(this);\n\n    var fig = this;\n\n    this.waiting = false;\n\n    this.ws.onopen = function () {\n        fig.send_message('supports_binary', { value: fig.supports_binary });\n        fig.send_message('send_image_mode', {});\n        if (fig.ratio !== 1) {\n            fig.send_message('set_device_pixel_ratio', {\n                device_pixel_ratio: fig.ratio,\n            });\n        }\n        fig.send_message('refresh', {});\n    };\n\n    this.imageObj.onload = function () {\n        if (fig.image_mode === 'full') {\n            // Full images could contain transparency (where diff images\n            // almost always do), so we need to clear the canvas so that\n            // there is no ghosting.\n            fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n        }\n        fig.context.drawImage(fig.imageObj, 0, 0);\n    };\n\n    this.imageObj.onunload = function () {\n        fig.ws.close();\n    };\n\n    this.ws.onmessage = this._make_on_message_function(this);\n\n    this.ondownload = ondownload;\n};\n\nmpl.figure.prototype._init_header = function () {\n    var titlebar = document.createElement('div');\n    titlebar.classList =\n        'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n    var titletext = document.createElement('div');\n    titletext.classList = 'ui-dialog-title';\n    titletext.setAttribute(\n        'style',\n        'width: 100%; text-align: center; padding: 3px;'\n    );\n    titlebar.appendChild(titletext);\n    this.root.appendChild(titlebar);\n    this.header = titletext;\n};\n\nmpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._init_canvas = function () {\n    var fig = this;\n\n    var canvas_div = (this.canvas_div = document.createElement('div'));\n    canvas_div.setAttribute(\n        'style',\n        'border: 1px solid #ddd;' +\n            'box-sizing: content-box;' +\n            'clear: both;' +\n            'min-height: 1px;' +\n            'min-width: 1px;' +\n            'outline: 0;' +\n            'overflow: hidden;' +\n            'position: relative;' +\n            'resize: both;'\n    );\n\n    function on_keyboard_event_closure(name) {\n        return function (event) {\n            return fig.key_event(event, name);\n        };\n    }\n\n    canvas_div.addEventListener(\n        'keydown',\n        on_keyboard_event_closure('key_press')\n    );\n    canvas_div.addEventListener(\n        'keyup',\n        on_keyboard_event_closure('key_release')\n    );\n\n    this._canvas_extra_style(canvas_div);\n    this.root.appendChild(canvas_div);\n\n    var canvas = (this.canvas = document.createElement('canvas'));\n    canvas.classList.add('mpl-canvas');\n    canvas.setAttribute('style', 'box-sizing: content-box;');\n\n    this.context = canvas.getContext('2d');\n\n    var backingStore =\n        this.context.backingStorePixelRatio ||\n        this.context.webkitBackingStorePixelRatio ||\n        this.context.mozBackingStorePixelRatio ||\n        this.context.msBackingStorePixelRatio ||\n        this.context.oBackingStorePixelRatio ||\n        this.context.backingStorePixelRatio ||\n        1;\n\n    this.ratio = (window.devicePixelRatio || 1) / backingStore;\n\n    var rubberband_canvas = (this.rubberband_canvas = document.createElement(\n        'canvas'\n    ));\n    rubberband_canvas.setAttribute(\n        'style',\n        'box-sizing: content-box; position: absolute; left: 0; top: 0; z-index: 1;'\n    );\n\n    // Apply a ponyfill if ResizeObserver is not implemented by browser.\n    if (this.ResizeObserver === undefined) {\n        if (window.ResizeObserver !== undefined) {\n            this.ResizeObserver = window.ResizeObserver;\n        } else {\n            var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n            this.ResizeObserver = obs.ResizeObserver;\n        }\n    }\n\n    this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n        var nentries = entries.length;\n        for (var i = 0; i < nentries; i++) {\n            var entry = entries[i];\n            var width, height;\n            if (entry.contentBoxSize) {\n                if (entry.contentBoxSize instanceof Array) {\n                    // Chrome 84 implements new version of spec.\n                    width = entry.contentBoxSize[0].inlineSize;\n                    height = entry.contentBoxSize[0].blockSize;\n                } else {\n                    // Firefox implements old version of spec.\n                    width = entry.contentBoxSize.inlineSize;\n                    height = entry.contentBoxSize.blockSize;\n                }\n            } else {\n                // Chrome <84 implements even older version of spec.\n                width = entry.contentRect.width;\n                height = entry.contentRect.height;\n            }\n\n            // Keep the size of the canvas and rubber band canvas in sync with\n            // the canvas container.\n            if (entry.devicePixelContentBoxSize) {\n                // Chrome 84 implements new version of spec.\n                canvas.setAttribute(\n                    'width',\n                    entry.devicePixelContentBoxSize[0].inlineSize\n                );\n                canvas.setAttribute(\n                    'height',\n                    entry.devicePixelContentBoxSize[0].blockSize\n                );\n            } else {\n                canvas.setAttribute('width', width * fig.ratio);\n                canvas.setAttribute('height', height * fig.ratio);\n            }\n            canvas.setAttribute(\n                'style',\n                'width: ' + width + 'px; height: ' + height + 'px;'\n            );\n\n            rubberband_canvas.setAttribute('width', width);\n            rubberband_canvas.setAttribute('height', height);\n\n            // And update the size in Python. We ignore the initial 0/0 size\n            // that occurs as the element is placed into the DOM, which should\n            // otherwise not happen due to the minimum size styling.\n            if (fig.ws.readyState == 1 && width != 0 && height != 0) {\n                fig.request_resize(width, height);\n            }\n        }\n    });\n    this.resizeObserverInstance.observe(canvas_div);\n\n    function on_mouse_event_closure(name) {\n        return function (event) {\n            return fig.mouse_event(event, name);\n        };\n    }\n\n    rubberband_canvas.addEventListener(\n        'mousedown',\n        on_mouse_event_closure('button_press')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseup',\n        on_mouse_event_closure('button_release')\n    );\n    rubberband_canvas.addEventListener(\n        'dblclick',\n        on_mouse_event_closure('dblclick')\n    );\n    // Throttle sequential mouse events to 1 every 20ms.\n    rubberband_canvas.addEventListener(\n        'mousemove',\n        on_mouse_event_closure('motion_notify')\n    );\n\n    rubberband_canvas.addEventListener(\n        'mouseenter',\n        on_mouse_event_closure('figure_enter')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseleave',\n        on_mouse_event_closure('figure_leave')\n    );\n\n    canvas_div.addEventListener('wheel', function (event) {\n        if (event.deltaY < 0) {\n            event.step = 1;\n        } else {\n            event.step = -1;\n        }\n        on_mouse_event_closure('scroll')(event);\n    });\n\n    canvas_div.appendChild(canvas);\n    canvas_div.appendChild(rubberband_canvas);\n\n    this.rubberband_context = rubberband_canvas.getContext('2d');\n    this.rubberband_context.strokeStyle = '#000000';\n\n    this._resize_canvas = function (width, height, forward) {\n        if (forward) {\n            canvas_div.style.width = width + 'px';\n            canvas_div.style.height = height + 'px';\n        }\n    };\n\n    // Disable right mouse context menu.\n    this.rubberband_canvas.addEventListener('contextmenu', function (_e) {\n        event.preventDefault();\n        return false;\n    });\n\n    function set_focus() {\n        canvas.focus();\n        canvas_div.focus();\n    }\n\n    window.setTimeout(set_focus, 100);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'mpl-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'mpl-button-group';\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'mpl-button-group';\n            continue;\n        }\n\n        var button = (fig.buttons[name] = document.createElement('button'));\n        button.classList = 'mpl-widget';\n        button.setAttribute('role', 'button');\n        button.setAttribute('aria-disabled', 'false');\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n\n        var icon_img = document.createElement('img');\n        icon_img.src = '_images/' + image + '.png';\n        icon_img.srcset = '_images/' + image + '_large.png 2x';\n        icon_img.alt = tooltip;\n        button.appendChild(icon_img);\n\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    var fmt_picker = document.createElement('select');\n    fmt_picker.classList = 'mpl-widget';\n    toolbar.appendChild(fmt_picker);\n    this.format_dropdown = fmt_picker;\n\n    for (var ind in mpl.extensions) {\n        var fmt = mpl.extensions[ind];\n        var option = document.createElement('option');\n        option.selected = fmt === mpl.default_extension;\n        option.innerHTML = fmt;\n        fmt_picker.appendChild(option);\n    }\n\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n};\n\nmpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n    // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n    // which will in turn request a refresh of the image.\n    this.send_message('resize', { width: x_pixels, height: y_pixels });\n};\n\nmpl.figure.prototype.send_message = function (type, properties) {\n    properties['type'] = type;\n    properties['figure_id'] = this.id;\n    this.ws.send(JSON.stringify(properties));\n};\n\nmpl.figure.prototype.send_draw_message = function () {\n    if (!this.waiting) {\n        this.waiting = true;\n        this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    var format_dropdown = fig.format_dropdown;\n    var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n    fig.ondownload(fig, format);\n};\n\nmpl.figure.prototype.handle_resize = function (fig, msg) {\n    var size = msg['size'];\n    if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n        fig._resize_canvas(size[0], size[1], msg['forward']);\n        fig.send_message('refresh', {});\n    }\n};\n\nmpl.figure.prototype.handle_rubberband = function (fig, msg) {\n    var x0 = msg['x0'] / fig.ratio;\n    var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n    var x1 = msg['x1'] / fig.ratio;\n    var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n    x0 = Math.floor(x0) + 0.5;\n    y0 = Math.floor(y0) + 0.5;\n    x1 = Math.floor(x1) + 0.5;\n    y1 = Math.floor(y1) + 0.5;\n    var min_x = Math.min(x0, x1);\n    var min_y = Math.min(y0, y1);\n    var width = Math.abs(x1 - x0);\n    var height = Math.abs(y1 - y0);\n\n    fig.rubberband_context.clearRect(\n        0,\n        0,\n        fig.canvas.width / fig.ratio,\n        fig.canvas.height / fig.ratio\n    );\n\n    fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n};\n\nmpl.figure.prototype.handle_figure_label = function (fig, msg) {\n    // Updates the figure title.\n    fig.header.textContent = msg['label'];\n};\n\nmpl.figure.prototype.handle_cursor = function (fig, msg) {\n    fig.rubberband_canvas.style.cursor = msg['cursor'];\n};\n\nmpl.figure.prototype.handle_message = function (fig, msg) {\n    fig.message.textContent = msg['message'];\n};\n\nmpl.figure.prototype.handle_draw = function (fig, _msg) {\n    // Request the server to send over a new figure.\n    fig.send_draw_message();\n};\n\nmpl.figure.prototype.handle_image_mode = function (fig, msg) {\n    fig.image_mode = msg['mode'];\n};\n\nmpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n    for (var key in msg) {\n        if (!(key in fig.buttons)) {\n            continue;\n        }\n        fig.buttons[key].disabled = !msg[key];\n        fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n    }\n};\n\nmpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n    if (msg['mode'] === 'PAN') {\n        fig.buttons['Pan'].classList.add('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    } else if (msg['mode'] === 'ZOOM') {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.add('active');\n    } else {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    }\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Called whenever the canvas gets updated.\n    this.send_message('ack', {});\n};\n\n// A function to construct a web socket function for onmessage handling.\n// Called in the figure constructor.\nmpl.figure.prototype._make_on_message_function = function (fig) {\n    return function socket_on_message(evt) {\n        if (evt.data instanceof Blob) {\n            var img = evt.data;\n            if (img.type !== 'image/png') {\n                /* FIXME: We get \"Resource interpreted as Image but\n                 * transferred with MIME type text/plain:\" errors on\n                 * Chrome.  But how to set the MIME type?  It doesn't seem\n                 * to be part of the websocket stream */\n                img.type = 'image/png';\n            }\n\n            /* Free the memory for the previous frames */\n            if (fig.imageObj.src) {\n                (window.URL || window.webkitURL).revokeObjectURL(\n                    fig.imageObj.src\n                );\n            }\n\n            fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n                img\n            );\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        } else if (\n            typeof evt.data === 'string' &&\n            evt.data.slice(0, 21) === 'data:image/png;base64'\n        ) {\n            fig.imageObj.src = evt.data;\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        }\n\n        var msg = JSON.parse(evt.data);\n        var msg_type = msg['type'];\n\n        // Call the  \"handle_{type}\" callback, which takes\n        // the figure and JSON message as its only arguments.\n        try {\n            var callback = fig['handle_' + msg_type];\n        } catch (e) {\n            console.log(\n                \"No handler for the '\" + msg_type + \"' message type: \",\n                msg\n            );\n            return;\n        }\n\n        if (callback) {\n            try {\n                // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n                callback(fig, msg);\n            } catch (e) {\n                console.log(\n                    \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n                    e,\n                    e.stack,\n                    msg\n                );\n            }\n        }\n    };\n};\n\n// from https://stackoverflow.com/questions/1114465/getting-mouse-location-in-canvas\nmpl.findpos = function (e) {\n    //this section is from http://www.quirksmode.org/js/events_properties.html\n    var targ;\n    if (!e) {\n        e = window.event;\n    }\n    if (e.target) {\n        targ = e.target;\n    } else if (e.srcElement) {\n        targ = e.srcElement;\n    }\n    if (targ.nodeType === 3) {\n        // defeat Safari bug\n        targ = targ.parentNode;\n    }\n\n    // pageX,Y are the mouse positions relative to the document\n    var boundingRect = targ.getBoundingClientRect();\n    var x = e.pageX - (boundingRect.left + document.body.scrollLeft);\n    var y = e.pageY - (boundingRect.top + document.body.scrollTop);\n\n    return { x: x, y: y };\n};\n\n/*\n * return a copy of an object with only non-object keys\n * we need this to avoid circular references\n * https://stackoverflow.com/a/24161582/3208463\n */\nfunction simpleKeys(original) {\n    return Object.keys(original).reduce(function (obj, key) {\n        if (typeof original[key] !== 'object') {\n            obj[key] = original[key];\n        }\n        return obj;\n    }, {});\n}\n\nmpl.figure.prototype.mouse_event = function (event, name) {\n    var canvas_pos = mpl.findpos(event);\n\n    if (name === 'button_press') {\n        this.canvas.focus();\n        this.canvas_div.focus();\n    }\n\n    var x = canvas_pos.x * this.ratio;\n    var y = canvas_pos.y * this.ratio;\n\n    this.send_message(name, {\n        x: x,\n        y: y,\n        button: event.button,\n        step: event.step,\n        guiEvent: simpleKeys(event),\n    });\n\n    /* This prevents the web browser from automatically changing to\n     * the text insertion cursor when the button is pressed.  We want\n     * to control all of the cursor setting manually through the\n     * 'cursor' event from matplotlib */\n    event.preventDefault();\n    return false;\n};\n\nmpl.figure.prototype._key_event_extra = function (_event, _name) {\n    // Handle any extra behaviour associated with a key event\n};\n\nmpl.figure.prototype.key_event = function (event, name) {\n    // Prevent repeat events\n    if (name === 'key_press') {\n        if (event.key === this._key) {\n            return;\n        } else {\n            this._key = event.key;\n        }\n    }\n    if (name === 'key_release') {\n        this._key = null;\n    }\n\n    var value = '';\n    if (event.ctrlKey && event.key !== 'Control') {\n        value += 'ctrl+';\n    }\n    else if (event.altKey && event.key !== 'Alt') {\n        value += 'alt+';\n    }\n    else if (event.shiftKey && event.key !== 'Shift') {\n        value += 'shift+';\n    }\n\n    value += 'k' + event.key;\n\n    this._key_event_extra(event, name);\n\n    this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n    return false;\n};\n\nmpl.figure.prototype.toolbar_button_onclick = function (name) {\n    if (name === 'download') {\n        this.handle_save(this, null);\n    } else {\n        this.send_message('toolbar_button', { name: name });\n    }\n};\n\nmpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n    this.message.textContent = tooltip;\n};\n\n///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n// prettier-ignore\nvar _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\nmpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home icon-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left icon-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right icon-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows icon-move\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis\", \"fa fa-square-o icon-check-empty\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o icon-save\", \"download\"]];\n\nmpl.extensions = [\"eps\", \"jpeg\", \"pgf\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\"];\n\nmpl.default_extension = \"png\";/* global mpl */\n\nvar comm_websocket_adapter = function (comm) {\n    // Create a \"websocket\"-like object which calls the given IPython comm\n    // object with the appropriate methods. Currently this is a non binary\n    // socket, so there is still some room for performance tuning.\n    var ws = {};\n\n    ws.binaryType = comm.kernel.ws.binaryType;\n    ws.readyState = comm.kernel.ws.readyState;\n    function updateReadyState(_event) {\n        if (comm.kernel.ws) {\n            ws.readyState = comm.kernel.ws.readyState;\n        } else {\n            ws.readyState = 3; // Closed state.\n        }\n    }\n    comm.kernel.ws.addEventListener('open', updateReadyState);\n    comm.kernel.ws.addEventListener('close', updateReadyState);\n    comm.kernel.ws.addEventListener('error', updateReadyState);\n\n    ws.close = function () {\n        comm.close();\n    };\n    ws.send = function (m) {\n        //console.log('sending', m);\n        comm.send(m);\n    };\n    // Register the callback with on_msg.\n    comm.on_msg(function (msg) {\n        //console.log('receiving', msg['content']['data'], msg);\n        var data = msg['content']['data'];\n        if (data['blob'] !== undefined) {\n            data = {\n                data: new Blob(msg['buffers'], { type: data['blob'] }),\n            };\n        }\n        // Pass the mpl event to the overridden (by mpl) onmessage function.\n        ws.onmessage(data);\n    });\n    return ws;\n};\n\nmpl.mpl_figure_comm = function (comm, msg) {\n    // This is the function which gets called when the mpl process\n    // starts-up an IPython Comm through the \"matplotlib\" channel.\n\n    var id = msg.content.data.id;\n    // Get hold of the div created by the display call when the Comm\n    // socket was opened in Python.\n    var element = document.getElementById(id);\n    var ws_proxy = comm_websocket_adapter(comm);\n\n    function ondownload(figure, _format) {\n        window.open(figure.canvas.toDataURL());\n    }\n\n    var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n\n    // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n    // web socket which is closed, not our websocket->open comm proxy.\n    ws_proxy.onopen();\n\n    fig.parent_element = element;\n    fig.cell_info = mpl.find_output_cell(\"<div id='\" + id + \"'></div>\");\n    if (!fig.cell_info) {\n        console.error('Failed to find cell for figure', id, fig);\n        return;\n    }\n    fig.cell_info[0].output_area.element.on(\n        'cleared',\n        { fig: fig },\n        fig._remove_fig_handler\n    );\n};\n\nmpl.figure.prototype.handle_close = function (fig, msg) {\n    var width = fig.canvas.width / fig.ratio;\n    fig.cell_info[0].output_area.element.off(\n        'cleared',\n        fig._remove_fig_handler\n    );\n    fig.resizeObserverInstance.unobserve(fig.canvas_div);\n\n    // Update the output cell to use the data from the current canvas.\n    fig.push_to_output();\n    var dataURL = fig.canvas.toDataURL();\n    // Re-enable the keyboard manager in IPython - without this line, in FF,\n    // the notebook keyboard shortcuts fail.\n    IPython.keyboard_manager.enable();\n    fig.parent_element.innerHTML =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n    fig.close_ws(fig, msg);\n};\n\nmpl.figure.prototype.close_ws = function (fig, msg) {\n    fig.send_message('closing', msg);\n    // fig.ws.close()\n};\n\nmpl.figure.prototype.push_to_output = function (_remove_interactive) {\n    // Turn the data on the canvas into data in the output cell.\n    var width = this.canvas.width / this.ratio;\n    var dataURL = this.canvas.toDataURL();\n    this.cell_info[1]['text/html'] =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Tell IPython that the notebook contents must change.\n    IPython.notebook.set_dirty(true);\n    this.send_message('ack', {});\n    var fig = this;\n    // Wait a second, then push the new image to the DOM so\n    // that it is saved nicely (might be nice to debounce this).\n    setTimeout(function () {\n        fig.push_to_output();\n    }, 1000);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'btn-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'btn-group';\n    var button;\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'btn-group';\n            continue;\n        }\n\n        button = fig.buttons[name] = document.createElement('button');\n        button.classList = 'btn btn-default';\n        button.href = '#';\n        button.title = name;\n        button.innerHTML = '<i class=\"fa ' + image + ' fa-lg\"></i>';\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    // Add the status bar.\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message pull-right';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n\n    // Add the close button to the window.\n    var buttongrp = document.createElement('div');\n    buttongrp.classList = 'btn-group inline pull-right';\n    button = document.createElement('button');\n    button.classList = 'btn btn-mini btn-primary';\n    button.href = '#';\n    button.title = 'Stop Interaction';\n    button.innerHTML = '<i class=\"fa fa-power-off icon-remove icon-large\"></i>';\n    button.addEventListener('click', function (_evt) {\n        fig.handle_close(fig, {});\n    });\n    button.addEventListener(\n        'mouseover',\n        on_mouseover_closure('Stop Interaction')\n    );\n    buttongrp.appendChild(button);\n    var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n    titlebar.insertBefore(buttongrp, titlebar.firstChild);\n};\n\nmpl.figure.prototype._remove_fig_handler = function (event) {\n    var fig = event.data.fig;\n    if (event.target !== this) {\n        // Ignore bubbled events from children.\n        return;\n    }\n    fig.close_ws(fig, {});\n};\n\nmpl.figure.prototype._root_extra_style = function (el) {\n    el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n};\n\nmpl.figure.prototype._canvas_extra_style = function (el) {\n    // this is important to make the div 'focusable\n    el.setAttribute('tabindex', 0);\n    // reach out to IPython and tell the keyboard manager to turn it's self\n    // off when our div gets focus\n\n    // location in version 3\n    if (IPython.notebook.keyboard_manager) {\n        IPython.notebook.keyboard_manager.register_events(el);\n    } else {\n        // location in version 2\n        IPython.keyboard_manager.register_events(el);\n    }\n};\n\nmpl.figure.prototype._key_event_extra = function (event, _name) {\n    // Check for shift+enter\n    if (event.shiftKey && event.which === 13) {\n        this.canvas_div.blur();\n        // select the cell after this one\n        var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n        IPython.notebook.select(index + 1);\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    fig.ondownload(fig, null);\n};\n\nmpl.find_output_cell = function (html_output) {\n    // Return the cell and output element which can be found *uniquely* in the notebook.\n    // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n    // IPython event is triggered only after the cells have been serialised, which for\n    // our purposes (turning an active figure into a static one), is too late.\n    var cells = IPython.notebook.get_cells();\n    var ncells = cells.length;\n    for (var i = 0; i < ncells; i++) {\n        var cell = cells[i];\n        if (cell.cell_type === 'code') {\n            for (var j = 0; j < cell.output_area.outputs.length; j++) {\n                var data = cell.output_area.outputs[j];\n                if (data.data) {\n                    // IPython >= 3 moved mimebundle to data attribute of output\n                    data = data.data;\n                }\n                if (data['text/html'] === html_output) {\n                    return [cell, data, j];\n                }\n            }\n        }\n    }\n};\n\n// Register the function which deals with the matplotlib target/channel.\n// The kernel may be null if the page has been refreshed.\nif (IPython.notebook.kernel !== null) {\n    IPython.notebook.kernel.comm_manager.register_target(\n        'matplotlib',\n        mpl.mpl_figure_comm\n    );\n}\n",
      "text/plain": [
       "<IPython.core.display.Javascript object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<img src=\"data:image/png;base64,[encoded data, 52448 characters]\" width=\"640\">"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "val = fitAnalyser.get_fit_value(fitResult)\n",
    "std = fitAnalyser.get_fit_std(fitResult)\n",
    "\n",
    "fitCurve = fitAnalyser.eval(fitResult, x=np.arange(300), y=np.arange(300), dask=\"parallelized\").load()\n",
    "\n",
    "# dataKey = 'sigmax'\n",
    "# dataKey = 'centerx'\n",
    "# dataKey = 'sigmay'\n",
    "dataKey = 'centery'\n",
    "\n",
    "# val_mean = val[dataKey].mean(dim='runs')\n",
    "# std_mean = val[dataKey].std(dim='runs')\n",
    "\n",
    "val_mean = calculate_mean(val[dataKey])\n",
    "std_mean = calculate_std(val[dataKey])\n",
    "\n",
    "fig = plt.figure()\n",
    "ax = fig.gca()\n",
    "\n",
    "val_mean.plot.errorbar(yerr=std_mean, fmt='--ob')\n",
    "\n",
    "plt.grid()\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 61,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/javascript": "/* Put everything inside the global mpl namespace */\n/* global mpl */\nwindow.mpl = {};\n\nmpl.get_websocket_type = function () {\n    if (typeof WebSocket !== 'undefined') {\n        return WebSocket;\n    } else if (typeof MozWebSocket !== 'undefined') {\n        return MozWebSocket;\n    } else {\n        alert(\n            'Your browser does not have WebSocket support. ' +\n                'Please try Chrome, Safari or Firefox ≥ 6. ' +\n                'Firefox 4 and 5 are also supported but you ' +\n                'have to enable WebSockets in about:config.'\n        );\n    }\n};\n\nmpl.figure = function (figure_id, websocket, ondownload, parent_element) {\n    this.id = figure_id;\n\n    this.ws = websocket;\n\n    this.supports_binary = this.ws.binaryType !== undefined;\n\n    if (!this.supports_binary) {\n        var warnings = document.getElementById('mpl-warnings');\n        if (warnings) {\n            warnings.style.display = 'block';\n            warnings.textContent =\n                'This browser does not support binary websocket messages. ' +\n                'Performance may be slow.';\n        }\n    }\n\n    this.imageObj = new Image();\n\n    this.context = undefined;\n    this.message = undefined;\n    this.canvas = undefined;\n    this.rubberband_canvas = undefined;\n    this.rubberband_context = undefined;\n    this.format_dropdown = undefined;\n\n    this.image_mode = 'full';\n\n    this.root = document.createElement('div');\n    this.root.setAttribute('style', 'display: inline-block');\n    this._root_extra_style(this.root);\n\n    parent_element.appendChild(this.root);\n\n    this._init_header(this);\n    this._init_canvas(this);\n    this._init_toolbar(this);\n\n    var fig = this;\n\n    this.waiting = false;\n\n    this.ws.onopen = function () {\n        fig.send_message('supports_binary', { value: fig.supports_binary });\n        fig.send_message('send_image_mode', {});\n        if (fig.ratio !== 1) {\n            fig.send_message('set_device_pixel_ratio', {\n                device_pixel_ratio: fig.ratio,\n            });\n        }\n        fig.send_message('refresh', {});\n    };\n\n    this.imageObj.onload = function () {\n        if (fig.image_mode === 'full') {\n            // Full images could contain transparency (where diff images\n            // almost always do), so we need to clear the canvas so that\n            // there is no ghosting.\n            fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n        }\n        fig.context.drawImage(fig.imageObj, 0, 0);\n    };\n\n    this.imageObj.onunload = function () {\n        fig.ws.close();\n    };\n\n    this.ws.onmessage = this._make_on_message_function(this);\n\n    this.ondownload = ondownload;\n};\n\nmpl.figure.prototype._init_header = function () {\n    var titlebar = document.createElement('div');\n    titlebar.classList =\n        'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n    var titletext = document.createElement('div');\n    titletext.classList = 'ui-dialog-title';\n    titletext.setAttribute(\n        'style',\n        'width: 100%; text-align: center; padding: 3px;'\n    );\n    titlebar.appendChild(titletext);\n    this.root.appendChild(titlebar);\n    this.header = titletext;\n};\n\nmpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._init_canvas = function () {\n    var fig = this;\n\n    var canvas_div = (this.canvas_div = document.createElement('div'));\n    canvas_div.setAttribute(\n        'style',\n        'border: 1px solid #ddd;' +\n            'box-sizing: content-box;' +\n            'clear: both;' +\n            'min-height: 1px;' +\n            'min-width: 1px;' +\n            'outline: 0;' +\n            'overflow: hidden;' +\n            'position: relative;' +\n            'resize: both;'\n    );\n\n    function on_keyboard_event_closure(name) {\n        return function (event) {\n            return fig.key_event(event, name);\n        };\n    }\n\n    canvas_div.addEventListener(\n        'keydown',\n        on_keyboard_event_closure('key_press')\n    );\n    canvas_div.addEventListener(\n        'keyup',\n        on_keyboard_event_closure('key_release')\n    );\n\n    this._canvas_extra_style(canvas_div);\n    this.root.appendChild(canvas_div);\n\n    var canvas = (this.canvas = document.createElement('canvas'));\n    canvas.classList.add('mpl-canvas');\n    canvas.setAttribute('style', 'box-sizing: content-box;');\n\n    this.context = canvas.getContext('2d');\n\n    var backingStore =\n        this.context.backingStorePixelRatio ||\n        this.context.webkitBackingStorePixelRatio ||\n        this.context.mozBackingStorePixelRatio ||\n        this.context.msBackingStorePixelRatio ||\n        this.context.oBackingStorePixelRatio ||\n        this.context.backingStorePixelRatio ||\n        1;\n\n    this.ratio = (window.devicePixelRatio || 1) / backingStore;\n\n    var rubberband_canvas = (this.rubberband_canvas = document.createElement(\n        'canvas'\n    ));\n    rubberband_canvas.setAttribute(\n        'style',\n        'box-sizing: content-box; position: absolute; left: 0; top: 0; z-index: 1;'\n    );\n\n    // Apply a ponyfill if ResizeObserver is not implemented by browser.\n    if (this.ResizeObserver === undefined) {\n        if (window.ResizeObserver !== undefined) {\n            this.ResizeObserver = window.ResizeObserver;\n        } else {\n            var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n            this.ResizeObserver = obs.ResizeObserver;\n        }\n    }\n\n    this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n        var nentries = entries.length;\n        for (var i = 0; i < nentries; i++) {\n            var entry = entries[i];\n            var width, height;\n            if (entry.contentBoxSize) {\n                if (entry.contentBoxSize instanceof Array) {\n                    // Chrome 84 implements new version of spec.\n                    width = entry.contentBoxSize[0].inlineSize;\n                    height = entry.contentBoxSize[0].blockSize;\n                } else {\n                    // Firefox implements old version of spec.\n                    width = entry.contentBoxSize.inlineSize;\n                    height = entry.contentBoxSize.blockSize;\n                }\n            } else {\n                // Chrome <84 implements even older version of spec.\n                width = entry.contentRect.width;\n                height = entry.contentRect.height;\n            }\n\n            // Keep the size of the canvas and rubber band canvas in sync with\n            // the canvas container.\n            if (entry.devicePixelContentBoxSize) {\n                // Chrome 84 implements new version of spec.\n                canvas.setAttribute(\n                    'width',\n                    entry.devicePixelContentBoxSize[0].inlineSize\n                );\n                canvas.setAttribute(\n                    'height',\n                    entry.devicePixelContentBoxSize[0].blockSize\n                );\n            } else {\n                canvas.setAttribute('width', width * fig.ratio);\n                canvas.setAttribute('height', height * fig.ratio);\n            }\n            canvas.setAttribute(\n                'style',\n                'width: ' + width + 'px; height: ' + height + 'px;'\n            );\n\n            rubberband_canvas.setAttribute('width', width);\n            rubberband_canvas.setAttribute('height', height);\n\n            // And update the size in Python. We ignore the initial 0/0 size\n            // that occurs as the element is placed into the DOM, which should\n            // otherwise not happen due to the minimum size styling.\n            if (fig.ws.readyState == 1 && width != 0 && height != 0) {\n                fig.request_resize(width, height);\n            }\n        }\n    });\n    this.resizeObserverInstance.observe(canvas_div);\n\n    function on_mouse_event_closure(name) {\n        return function (event) {\n            return fig.mouse_event(event, name);\n        };\n    }\n\n    rubberband_canvas.addEventListener(\n        'mousedown',\n        on_mouse_event_closure('button_press')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseup',\n        on_mouse_event_closure('button_release')\n    );\n    rubberband_canvas.addEventListener(\n        'dblclick',\n        on_mouse_event_closure('dblclick')\n    );\n    // Throttle sequential mouse events to 1 every 20ms.\n    rubberband_canvas.addEventListener(\n        'mousemove',\n        on_mouse_event_closure('motion_notify')\n    );\n\n    rubberband_canvas.addEventListener(\n        'mouseenter',\n        on_mouse_event_closure('figure_enter')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseleave',\n        on_mouse_event_closure('figure_leave')\n    );\n\n    canvas_div.addEventListener('wheel', function (event) {\n        if (event.deltaY < 0) {\n            event.step = 1;\n        } else {\n            event.step = -1;\n        }\n        on_mouse_event_closure('scroll')(event);\n    });\n\n    canvas_div.appendChild(canvas);\n    canvas_div.appendChild(rubberband_canvas);\n\n    this.rubberband_context = rubberband_canvas.getContext('2d');\n    this.rubberband_context.strokeStyle = '#000000';\n\n    this._resize_canvas = function (width, height, forward) {\n        if (forward) {\n            canvas_div.style.width = width + 'px';\n            canvas_div.style.height = height + 'px';\n        }\n    };\n\n    // Disable right mouse context menu.\n    this.rubberband_canvas.addEventListener('contextmenu', function (_e) {\n        event.preventDefault();\n        return false;\n    });\n\n    function set_focus() {\n        canvas.focus();\n        canvas_div.focus();\n    }\n\n    window.setTimeout(set_focus, 100);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'mpl-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'mpl-button-group';\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'mpl-button-group';\n            continue;\n        }\n\n        var button = (fig.buttons[name] = document.createElement('button'));\n        button.classList = 'mpl-widget';\n        button.setAttribute('role', 'button');\n        button.setAttribute('aria-disabled', 'false');\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n\n        var icon_img = document.createElement('img');\n        icon_img.src = '_images/' + image + '.png';\n        icon_img.srcset = '_images/' + image + '_large.png 2x';\n        icon_img.alt = tooltip;\n        button.appendChild(icon_img);\n\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    var fmt_picker = document.createElement('select');\n    fmt_picker.classList = 'mpl-widget';\n    toolbar.appendChild(fmt_picker);\n    this.format_dropdown = fmt_picker;\n\n    for (var ind in mpl.extensions) {\n        var fmt = mpl.extensions[ind];\n        var option = document.createElement('option');\n        option.selected = fmt === mpl.default_extension;\n        option.innerHTML = fmt;\n        fmt_picker.appendChild(option);\n    }\n\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n};\n\nmpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n    // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n    // which will in turn request a refresh of the image.\n    this.send_message('resize', { width: x_pixels, height: y_pixels });\n};\n\nmpl.figure.prototype.send_message = function (type, properties) {\n    properties['type'] = type;\n    properties['figure_id'] = this.id;\n    this.ws.send(JSON.stringify(properties));\n};\n\nmpl.figure.prototype.send_draw_message = function () {\n    if (!this.waiting) {\n        this.waiting = true;\n        this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    var format_dropdown = fig.format_dropdown;\n    var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n    fig.ondownload(fig, format);\n};\n\nmpl.figure.prototype.handle_resize = function (fig, msg) {\n    var size = msg['size'];\n    if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n        fig._resize_canvas(size[0], size[1], msg['forward']);\n        fig.send_message('refresh', {});\n    }\n};\n\nmpl.figure.prototype.handle_rubberband = function (fig, msg) {\n    var x0 = msg['x0'] / fig.ratio;\n    var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n    var x1 = msg['x1'] / fig.ratio;\n    var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n    x0 = Math.floor(x0) + 0.5;\n    y0 = Math.floor(y0) + 0.5;\n    x1 = Math.floor(x1) + 0.5;\n    y1 = Math.floor(y1) + 0.5;\n    var min_x = Math.min(x0, x1);\n    var min_y = Math.min(y0, y1);\n    var width = Math.abs(x1 - x0);\n    var height = Math.abs(y1 - y0);\n\n    fig.rubberband_context.clearRect(\n        0,\n        0,\n        fig.canvas.width / fig.ratio,\n        fig.canvas.height / fig.ratio\n    );\n\n    fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n};\n\nmpl.figure.prototype.handle_figure_label = function (fig, msg) {\n    // Updates the figure title.\n    fig.header.textContent = msg['label'];\n};\n\nmpl.figure.prototype.handle_cursor = function (fig, msg) {\n    fig.rubberband_canvas.style.cursor = msg['cursor'];\n};\n\nmpl.figure.prototype.handle_message = function (fig, msg) {\n    fig.message.textContent = msg['message'];\n};\n\nmpl.figure.prototype.handle_draw = function (fig, _msg) {\n    // Request the server to send over a new figure.\n    fig.send_draw_message();\n};\n\nmpl.figure.prototype.handle_image_mode = function (fig, msg) {\n    fig.image_mode = msg['mode'];\n};\n\nmpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n    for (var key in msg) {\n        if (!(key in fig.buttons)) {\n            continue;\n        }\n        fig.buttons[key].disabled = !msg[key];\n        fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n    }\n};\n\nmpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n    if (msg['mode'] === 'PAN') {\n        fig.buttons['Pan'].classList.add('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    } else if (msg['mode'] === 'ZOOM') {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.add('active');\n    } else {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    }\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Called whenever the canvas gets updated.\n    this.send_message('ack', {});\n};\n\n// A function to construct a web socket function for onmessage handling.\n// Called in the figure constructor.\nmpl.figure.prototype._make_on_message_function = function (fig) {\n    return function socket_on_message(evt) {\n        if (evt.data instanceof Blob) {\n            var img = evt.data;\n            if (img.type !== 'image/png') {\n                /* FIXME: We get \"Resource interpreted as Image but\n                 * transferred with MIME type text/plain:\" errors on\n                 * Chrome.  But how to set the MIME type?  It doesn't seem\n                 * to be part of the websocket stream */\n                img.type = 'image/png';\n            }\n\n            /* Free the memory for the previous frames */\n            if (fig.imageObj.src) {\n                (window.URL || window.webkitURL).revokeObjectURL(\n                    fig.imageObj.src\n                );\n            }\n\n            fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n                img\n            );\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        } else if (\n            typeof evt.data === 'string' &&\n            evt.data.slice(0, 21) === 'data:image/png;base64'\n        ) {\n            fig.imageObj.src = evt.data;\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        }\n\n        var msg = JSON.parse(evt.data);\n        var msg_type = msg['type'];\n\n        // Call the  \"handle_{type}\" callback, which takes\n        // the figure and JSON message as its only arguments.\n        try {\n            var callback = fig['handle_' + msg_type];\n        } catch (e) {\n            console.log(\n                \"No handler for the '\" + msg_type + \"' message type: \",\n                msg\n            );\n            return;\n        }\n\n        if (callback) {\n            try {\n                // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n                callback(fig, msg);\n            } catch (e) {\n                console.log(\n                    \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n                    e,\n                    e.stack,\n                    msg\n                );\n            }\n        }\n    };\n};\n\n// from https://stackoverflow.com/questions/1114465/getting-mouse-location-in-canvas\nmpl.findpos = function (e) {\n    //this section is from http://www.quirksmode.org/js/events_properties.html\n    var targ;\n    if (!e) {\n        e = window.event;\n    }\n    if (e.target) {\n        targ = e.target;\n    } else if (e.srcElement) {\n        targ = e.srcElement;\n    }\n    if (targ.nodeType === 3) {\n        // defeat Safari bug\n        targ = targ.parentNode;\n    }\n\n    // pageX,Y are the mouse positions relative to the document\n    var boundingRect = targ.getBoundingClientRect();\n    var x = e.pageX - (boundingRect.left + document.body.scrollLeft);\n    var y = e.pageY - (boundingRect.top + document.body.scrollTop);\n\n    return { x: x, y: y };\n};\n\n/*\n * return a copy of an object with only non-object keys\n * we need this to avoid circular references\n * https://stackoverflow.com/a/24161582/3208463\n */\nfunction simpleKeys(original) {\n    return Object.keys(original).reduce(function (obj, key) {\n        if (typeof original[key] !== 'object') {\n            obj[key] = original[key];\n        }\n        return obj;\n    }, {});\n}\n\nmpl.figure.prototype.mouse_event = function (event, name) {\n    var canvas_pos = mpl.findpos(event);\n\n    if (name === 'button_press') {\n        this.canvas.focus();\n        this.canvas_div.focus();\n    }\n\n    var x = canvas_pos.x * this.ratio;\n    var y = canvas_pos.y * this.ratio;\n\n    this.send_message(name, {\n        x: x,\n        y: y,\n        button: event.button,\n        step: event.step,\n        guiEvent: simpleKeys(event),\n    });\n\n    /* This prevents the web browser from automatically changing to\n     * the text insertion cursor when the button is pressed.  We want\n     * to control all of the cursor setting manually through the\n     * 'cursor' event from matplotlib */\n    event.preventDefault();\n    return false;\n};\n\nmpl.figure.prototype._key_event_extra = function (_event, _name) {\n    // Handle any extra behaviour associated with a key event\n};\n\nmpl.figure.prototype.key_event = function (event, name) {\n    // Prevent repeat events\n    if (name === 'key_press') {\n        if (event.key === this._key) {\n            return;\n        } else {\n            this._key = event.key;\n        }\n    }\n    if (name === 'key_release') {\n        this._key = null;\n    }\n\n    var value = '';\n    if (event.ctrlKey && event.key !== 'Control') {\n        value += 'ctrl+';\n    }\n    else if (event.altKey && event.key !== 'Alt') {\n        value += 'alt+';\n    }\n    else if (event.shiftKey && event.key !== 'Shift') {\n        value += 'shift+';\n    }\n\n    value += 'k' + event.key;\n\n    this._key_event_extra(event, name);\n\n    this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n    return false;\n};\n\nmpl.figure.prototype.toolbar_button_onclick = function (name) {\n    if (name === 'download') {\n        this.handle_save(this, null);\n    } else {\n        this.send_message('toolbar_button', { name: name });\n    }\n};\n\nmpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n    this.message.textContent = tooltip;\n};\n\n///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n// prettier-ignore\nvar _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\nmpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home icon-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left icon-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right icon-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows icon-move\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis\", \"fa fa-square-o icon-check-empty\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o icon-save\", \"download\"]];\n\nmpl.extensions = [\"eps\", \"jpeg\", \"pgf\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\"];\n\nmpl.default_extension = \"png\";/* global mpl */\n\nvar comm_websocket_adapter = function (comm) {\n    // Create a \"websocket\"-like object which calls the given IPython comm\n    // object with the appropriate methods. Currently this is a non binary\n    // socket, so there is still some room for performance tuning.\n    var ws = {};\n\n    ws.binaryType = comm.kernel.ws.binaryType;\n    ws.readyState = comm.kernel.ws.readyState;\n    function updateReadyState(_event) {\n        if (comm.kernel.ws) {\n            ws.readyState = comm.kernel.ws.readyState;\n        } else {\n            ws.readyState = 3; // Closed state.\n        }\n    }\n    comm.kernel.ws.addEventListener('open', updateReadyState);\n    comm.kernel.ws.addEventListener('close', updateReadyState);\n    comm.kernel.ws.addEventListener('error', updateReadyState);\n\n    ws.close = function () {\n        comm.close();\n    };\n    ws.send = function (m) {\n        //console.log('sending', m);\n        comm.send(m);\n    };\n    // Register the callback with on_msg.\n    comm.on_msg(function (msg) {\n        //console.log('receiving', msg['content']['data'], msg);\n        var data = msg['content']['data'];\n        if (data['blob'] !== undefined) {\n            data = {\n                data: new Blob(msg['buffers'], { type: data['blob'] }),\n            };\n        }\n        // Pass the mpl event to the overridden (by mpl) onmessage function.\n        ws.onmessage(data);\n    });\n    return ws;\n};\n\nmpl.mpl_figure_comm = function (comm, msg) {\n    // This is the function which gets called when the mpl process\n    // starts-up an IPython Comm through the \"matplotlib\" channel.\n\n    var id = msg.content.data.id;\n    // Get hold of the div created by the display call when the Comm\n    // socket was opened in Python.\n    var element = document.getElementById(id);\n    var ws_proxy = comm_websocket_adapter(comm);\n\n    function ondownload(figure, _format) {\n        window.open(figure.canvas.toDataURL());\n    }\n\n    var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n\n    // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n    // web socket which is closed, not our websocket->open comm proxy.\n    ws_proxy.onopen();\n\n    fig.parent_element = element;\n    fig.cell_info = mpl.find_output_cell(\"<div id='\" + id + \"'></div>\");\n    if (!fig.cell_info) {\n        console.error('Failed to find cell for figure', id, fig);\n        return;\n    }\n    fig.cell_info[0].output_area.element.on(\n        'cleared',\n        { fig: fig },\n        fig._remove_fig_handler\n    );\n};\n\nmpl.figure.prototype.handle_close = function (fig, msg) {\n    var width = fig.canvas.width / fig.ratio;\n    fig.cell_info[0].output_area.element.off(\n        'cleared',\n        fig._remove_fig_handler\n    );\n    fig.resizeObserverInstance.unobserve(fig.canvas_div);\n\n    // Update the output cell to use the data from the current canvas.\n    fig.push_to_output();\n    var dataURL = fig.canvas.toDataURL();\n    // Re-enable the keyboard manager in IPython - without this line, in FF,\n    // the notebook keyboard shortcuts fail.\n    IPython.keyboard_manager.enable();\n    fig.parent_element.innerHTML =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n    fig.close_ws(fig, msg);\n};\n\nmpl.figure.prototype.close_ws = function (fig, msg) {\n    fig.send_message('closing', msg);\n    // fig.ws.close()\n};\n\nmpl.figure.prototype.push_to_output = function (_remove_interactive) {\n    // Turn the data on the canvas into data in the output cell.\n    var width = this.canvas.width / this.ratio;\n    var dataURL = this.canvas.toDataURL();\n    this.cell_info[1]['text/html'] =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Tell IPython that the notebook contents must change.\n    IPython.notebook.set_dirty(true);\n    this.send_message('ack', {});\n    var fig = this;\n    // Wait a second, then push the new image to the DOM so\n    // that it is saved nicely (might be nice to debounce this).\n    setTimeout(function () {\n        fig.push_to_output();\n    }, 1000);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'btn-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'btn-group';\n    var button;\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'btn-group';\n            continue;\n        }\n\n        button = fig.buttons[name] = document.createElement('button');\n        button.classList = 'btn btn-default';\n        button.href = '#';\n        button.title = name;\n        button.innerHTML = '<i class=\"fa ' + image + ' fa-lg\"></i>';\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    // Add the status bar.\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message pull-right';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n\n    // Add the close button to the window.\n    var buttongrp = document.createElement('div');\n    buttongrp.classList = 'btn-group inline pull-right';\n    button = document.createElement('button');\n    button.classList = 'btn btn-mini btn-primary';\n    button.href = '#';\n    button.title = 'Stop Interaction';\n    button.innerHTML = '<i class=\"fa fa-power-off icon-remove icon-large\"></i>';\n    button.addEventListener('click', function (_evt) {\n        fig.handle_close(fig, {});\n    });\n    button.addEventListener(\n        'mouseover',\n        on_mouseover_closure('Stop Interaction')\n    );\n    buttongrp.appendChild(button);\n    var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n    titlebar.insertBefore(buttongrp, titlebar.firstChild);\n};\n\nmpl.figure.prototype._remove_fig_handler = function (event) {\n    var fig = event.data.fig;\n    if (event.target !== this) {\n        // Ignore bubbled events from children.\n        return;\n    }\n    fig.close_ws(fig, {});\n};\n\nmpl.figure.prototype._root_extra_style = function (el) {\n    el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n};\n\nmpl.figure.prototype._canvas_extra_style = function (el) {\n    // this is important to make the div 'focusable\n    el.setAttribute('tabindex', 0);\n    // reach out to IPython and tell the keyboard manager to turn it's self\n    // off when our div gets focus\n\n    // location in version 3\n    if (IPython.notebook.keyboard_manager) {\n        IPython.notebook.keyboard_manager.register_events(el);\n    } else {\n        // location in version 2\n        IPython.keyboard_manager.register_events(el);\n    }\n};\n\nmpl.figure.prototype._key_event_extra = function (event, _name) {\n    // Check for shift+enter\n    if (event.shiftKey && event.which === 13) {\n        this.canvas_div.blur();\n        // select the cell after this one\n        var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n        IPython.notebook.select(index + 1);\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    fig.ondownload(fig, null);\n};\n\nmpl.find_output_cell = function (html_output) {\n    // Return the cell and output element which can be found *uniquely* in the notebook.\n    // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n    // IPython event is triggered only after the cells have been serialised, which for\n    // our purposes (turning an active figure into a static one), is too late.\n    var cells = IPython.notebook.get_cells();\n    var ncells = cells.length;\n    for (var i = 0; i < ncells; i++) {\n        var cell = cells[i];\n        if (cell.cell_type === 'code') {\n            for (var j = 0; j < cell.output_area.outputs.length; j++) {\n                var data = cell.output_area.outputs[j];\n                if (data.data) {\n                    // IPython >= 3 moved mimebundle to data attribute of output\n                    data = data.data;\n                }\n                if (data['text/html'] === html_output) {\n                    return [cell, data, j];\n                }\n            }\n        }\n    }\n};\n\n// Register the function which deals with the matplotlib target/channel.\n// The kernel may be null if the page has been refreshed.\nif (IPython.notebook.kernel !== null) {\n    IPython.notebook.kernel.comm_manager.register_target(\n        'matplotlib',\n        mpl.mpl_figure_comm\n    );\n}\n",
      "text/plain": [
       "<IPython.core.display.Javascript object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
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    {
     "data": {
      "text/html": [
       "<img src=\"data:image/png;base64,[encoded data, 71568 characters]\" width=\"640\">"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "f = 303.5930 ± 6.9704 Hz\n"
     ]
    }
   ],
   "source": [
    "def damp_osci(t, t0, A, B, nu, gamma):\n",
    "    return A * np.exp(-gamma*t)*np.sin(2*np.pi*nu*(t-t0)) + B\n",
    "\n",
    "#yvals     = val_mean.sel(blink_on_time=slice(0.005, 0.025))\n",
    "#yvals_std = std_mean.sel(blink_on_time=slice(0.005, 0.025))\n",
    "#xvals     = dataSet_cropOD[scanAxis[0]].sel(blink_on_time=slice(0.005, 0.025))\n",
    "\n",
    "fitted_qtys_1 = val_mean.to_numpy()\n",
    "fitted_qtys_err_1 = std_mean.to_numpy()\n",
    "scan_para = dataSet_cropOD[scanAxis[0]].to_numpy()\n",
    "\n",
    "plt.figure()\n",
    "popt_x, pcov_x = curve_fit(damp_osci, scan_para, fitted_qtys_1, np.array([0, 1, 148, 1e2, 0.1]))\n",
    "freqdata = np.linspace(0.005, 20e-3, 500)\n",
    "plt.plot(freqdata, damp_osci(freqdata, *popt_x), 'g--',label='fit: t0=%5.3f, A=%5.3f, B=%5.3f, nu=%5.3f, Gamma=%5.3f' % tuple(popt_x))\n",
    "plt.errorbar(scan_para, fitted_qtys_1, yerr=fitted_qtys_err_1, fmt='or')\n",
    "plt.xlabel('hold time after switch on the trap (s)')\n",
    "plt.ylabel('Center along gravity direction (pixels)')\n",
    "plt.tight_layout()\n",
    "plt.grid(visible=1)\n",
    "#plt.ylim([0,750])\n",
    "#plt.xlim([0.004, 0.025])\n",
    "#plt.legend(prop={'size': 14})\n",
    "plt.show()\n",
    "\n",
    "f_x = popt_x[3]\n",
    "df_x = pcov_x[3][3]**0.5\n",
    "\n",
    "print('f = %.4f \\u00B1 %.4f Hz'% tuple([np.abs(f_x),df_x]))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Truncation: 0.55"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 62,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The detected scaning axes and values are: \n",
      "\n",
      "{'mod_blink_on_time': array([0.005, 0.006, 0.007, 0.008, 0.009, 0.01 , 0.011, 0.012, 0.013,\n",
      "       0.014, 0.015, 0.016, 0.017, 0.018, 0.019]), 'runs': array([0., 1., 2., 3.])}\n"
     ]
    },
    {
     "data": {
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' +\n                'Firefox 4 and 5 are also supported but you ' +\n                'have to enable WebSockets in about:config.'\n        );\n    }\n};\n\nmpl.figure = function (figure_id, websocket, ondownload, parent_element) {\n    this.id = figure_id;\n\n    this.ws = websocket;\n\n    this.supports_binary = this.ws.binaryType !== undefined;\n\n    if (!this.supports_binary) {\n        var warnings = document.getElementById('mpl-warnings');\n        if (warnings) {\n            warnings.style.display = 'block';\n            warnings.textContent =\n                'This browser does not support binary websocket messages. ' +\n                'Performance may be slow.';\n        }\n    }\n\n    this.imageObj = new Image();\n\n    this.context = undefined;\n    this.message = undefined;\n    this.canvas = undefined;\n    this.rubberband_canvas = undefined;\n    this.rubberband_context = undefined;\n    this.format_dropdown = undefined;\n\n    this.image_mode = 'full';\n\n    this.root = document.createElement('div');\n    this.root.setAttribute('style', 'display: inline-block');\n    this._root_extra_style(this.root);\n\n    parent_element.appendChild(this.root);\n\n    this._init_header(this);\n    this._init_canvas(this);\n    this._init_toolbar(this);\n\n    var fig = this;\n\n    this.waiting = false;\n\n    this.ws.onopen = function () {\n        fig.send_message('supports_binary', { value: fig.supports_binary });\n        fig.send_message('send_image_mode', {});\n        if (fig.ratio !== 1) {\n            fig.send_message('set_device_pixel_ratio', {\n                device_pixel_ratio: fig.ratio,\n            });\n        }\n        fig.send_message('refresh', {});\n    };\n\n    this.imageObj.onload = function () {\n        if (fig.image_mode === 'full') {\n            // Full images could contain transparency (where diff images\n            // almost always do), so we need to clear the canvas so that\n            // there is no ghosting.\n            fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n        }\n        fig.context.drawImage(fig.imageObj, 0, 0);\n    };\n\n    this.imageObj.onunload = function () {\n        fig.ws.close();\n    };\n\n    this.ws.onmessage = this._make_on_message_function(this);\n\n    this.ondownload = ondownload;\n};\n\nmpl.figure.prototype._init_header = function () {\n    var titlebar = document.createElement('div');\n    titlebar.classList =\n        'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n    var titletext = document.createElement('div');\n    titletext.classList = 'ui-dialog-title';\n    titletext.setAttribute(\n        'style',\n        'width: 100%; text-align: center; padding: 3px;'\n    );\n    titlebar.appendChild(titletext);\n    this.root.appendChild(titlebar);\n    this.header = titletext;\n};\n\nmpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._init_canvas = function () {\n    var fig = this;\n\n    var canvas_div = (this.canvas_div = document.createElement('div'));\n    canvas_div.setAttribute(\n        'style',\n        'border: 1px solid #ddd;' +\n            'box-sizing: content-box;' +\n            'clear: both;' +\n            'min-height: 1px;' +\n            'min-width: 1px;' +\n            'outline: 0;' +\n            'overflow: hidden;' +\n            'position: relative;' +\n            'resize: both;'\n    );\n\n    function on_keyboard_event_closure(name) {\n        return function (event) {\n            return fig.key_event(event, name);\n        };\n    }\n\n    canvas_div.addEventListener(\n        'keydown',\n        on_keyboard_event_closure('key_press')\n    );\n    canvas_div.addEventListener(\n        'keyup',\n        on_keyboard_event_closure('key_release')\n    );\n\n    this._canvas_extra_style(canvas_div);\n    this.root.appendChild(canvas_div);\n\n    var canvas = (this.canvas = document.createElement('canvas'));\n    canvas.classList.add('mpl-canvas');\n    canvas.setAttribute('style', 'box-sizing: content-box;');\n\n    this.context = canvas.getContext('2d');\n\n    var backingStore =\n        this.context.backingStorePixelRatio ||\n        this.context.webkitBackingStorePixelRatio ||\n        this.context.mozBackingStorePixelRatio ||\n        this.context.msBackingStorePixelRatio ||\n        this.context.oBackingStorePixelRatio ||\n        this.context.backingStorePixelRatio ||\n        1;\n\n    this.ratio = (window.devicePixelRatio || 1) / backingStore;\n\n    var rubberband_canvas = (this.rubberband_canvas = document.createElement(\n        'canvas'\n    ));\n    rubberband_canvas.setAttribute(\n        'style',\n        'box-sizing: content-box; position: absolute; left: 0; top: 0; z-index: 1;'\n    );\n\n    // Apply a ponyfill if ResizeObserver is not implemented by browser.\n    if (this.ResizeObserver === undefined) {\n        if (window.ResizeObserver !== undefined) {\n            this.ResizeObserver = window.ResizeObserver;\n        } else {\n            var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n            this.ResizeObserver = obs.ResizeObserver;\n        }\n    }\n\n    this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n        var nentries = entries.length;\n        for (var i = 0; i < nentries; i++) {\n            var entry = entries[i];\n            var width, height;\n            if (entry.contentBoxSize) {\n                if (entry.contentBoxSize instanceof Array) {\n                    // Chrome 84 implements new version of spec.\n                    width = entry.contentBoxSize[0].inlineSize;\n                    height = entry.contentBoxSize[0].blockSize;\n                } else {\n                    // Firefox implements old version of spec.\n                    width = entry.contentBoxSize.inlineSize;\n                    height = entry.contentBoxSize.blockSize;\n                }\n            } else {\n                // Chrome <84 implements even older version of spec.\n                width = entry.contentRect.width;\n                height = entry.contentRect.height;\n            }\n\n            // Keep the size of the canvas and rubber band canvas in sync with\n            // the canvas container.\n            if (entry.devicePixelContentBoxSize) {\n                // Chrome 84 implements new version of spec.\n                canvas.setAttribute(\n                    'width',\n                    entry.devicePixelContentBoxSize[0].inlineSize\n                );\n                canvas.setAttribute(\n                    'height',\n                    entry.devicePixelContentBoxSize[0].blockSize\n                );\n            } else {\n                canvas.setAttribute('width', width * fig.ratio);\n                canvas.setAttribute('height', height * fig.ratio);\n            }\n            canvas.setAttribute(\n                'style',\n                'width: ' + width + 'px; height: ' + height + 'px;'\n            );\n\n            rubberband_canvas.setAttribute('width', width);\n            rubberband_canvas.setAttribute('height', height);\n\n            // And update the size in Python. We ignore the initial 0/0 size\n            // that occurs as the element is placed into the DOM, which should\n            // otherwise not happen due to the minimum size styling.\n            if (fig.ws.readyState == 1 && width != 0 && height != 0) {\n                fig.request_resize(width, height);\n            }\n        }\n    });\n    this.resizeObserverInstance.observe(canvas_div);\n\n    function on_mouse_event_closure(name) {\n        return function (event) {\n            return fig.mouse_event(event, name);\n        };\n    }\n\n    rubberband_canvas.addEventListener(\n        'mousedown',\n        on_mouse_event_closure('button_press')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseup',\n        on_mouse_event_closure('button_release')\n    );\n    rubberband_canvas.addEventListener(\n        'dblclick',\n        on_mouse_event_closure('dblclick')\n    );\n    // Throttle sequential mouse events to 1 every 20ms.\n    rubberband_canvas.addEventListener(\n        'mousemove',\n        on_mouse_event_closure('motion_notify')\n    );\n\n    rubberband_canvas.addEventListener(\n        'mouseenter',\n        on_mouse_event_closure('figure_enter')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseleave',\n        on_mouse_event_closure('figure_leave')\n    );\n\n    canvas_div.addEventListener('wheel', function (event) {\n        if (event.deltaY < 0) {\n            event.step = 1;\n        } else {\n            event.step = -1;\n        }\n        on_mouse_event_closure('scroll')(event);\n    });\n\n    canvas_div.appendChild(canvas);\n    canvas_div.appendChild(rubberband_canvas);\n\n    this.rubberband_context = rubberband_canvas.getContext('2d');\n    this.rubberband_context.strokeStyle = '#000000';\n\n    this._resize_canvas = function (width, height, forward) {\n        if (forward) {\n            canvas_div.style.width = width + 'px';\n            canvas_div.style.height = height + 'px';\n        }\n    };\n\n    // Disable right mouse context menu.\n    this.rubberband_canvas.addEventListener('contextmenu', function (_e) {\n        event.preventDefault();\n        return false;\n    });\n\n    function set_focus() {\n        canvas.focus();\n        canvas_div.focus();\n    }\n\n    window.setTimeout(set_focus, 100);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'mpl-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'mpl-button-group';\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'mpl-button-group';\n            continue;\n        }\n\n        var button = (fig.buttons[name] = document.createElement('button'));\n        button.classList = 'mpl-widget';\n        button.setAttribute('role', 'button');\n        button.setAttribute('aria-disabled', 'false');\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n\n        var icon_img = document.createElement('img');\n        icon_img.src = '_images/' + image + '.png';\n        icon_img.srcset = '_images/' + image + '_large.png 2x';\n        icon_img.alt = tooltip;\n        button.appendChild(icon_img);\n\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    var fmt_picker = document.createElement('select');\n    fmt_picker.classList = 'mpl-widget';\n    toolbar.appendChild(fmt_picker);\n    this.format_dropdown = fmt_picker;\n\n    for (var ind in mpl.extensions) {\n        var fmt = mpl.extensions[ind];\n        var option = document.createElement('option');\n        option.selected = fmt === mpl.default_extension;\n        option.innerHTML = fmt;\n        fmt_picker.appendChild(option);\n    }\n\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n};\n\nmpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n    // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n    // which will in turn request a refresh of the image.\n    this.send_message('resize', { width: x_pixels, height: y_pixels });\n};\n\nmpl.figure.prototype.send_message = function (type, properties) {\n    properties['type'] = type;\n    properties['figure_id'] = this.id;\n    this.ws.send(JSON.stringify(properties));\n};\n\nmpl.figure.prototype.send_draw_message = function () {\n    if (!this.waiting) {\n        this.waiting = true;\n        this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    var format_dropdown = fig.format_dropdown;\n    var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n    fig.ondownload(fig, format);\n};\n\nmpl.figure.prototype.handle_resize = function (fig, msg) {\n    var size = msg['size'];\n    if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n        fig._resize_canvas(size[0], size[1], msg['forward']);\n        fig.send_message('refresh', {});\n    }\n};\n\nmpl.figure.prototype.handle_rubberband = function (fig, msg) {\n    var x0 = msg['x0'] / fig.ratio;\n    var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n    var x1 = msg['x1'] / fig.ratio;\n    var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n    x0 = Math.floor(x0) + 0.5;\n    y0 = Math.floor(y0) + 0.5;\n    x1 = Math.floor(x1) + 0.5;\n    y1 = Math.floor(y1) + 0.5;\n    var min_x = Math.min(x0, x1);\n    var min_y = Math.min(y0, y1);\n    var width = Math.abs(x1 - x0);\n    var height = Math.abs(y1 - y0);\n\n    fig.rubberband_context.clearRect(\n        0,\n        0,\n        fig.canvas.width / fig.ratio,\n        fig.canvas.height / fig.ratio\n    );\n\n    fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n};\n\nmpl.figure.prototype.handle_figure_label = function (fig, msg) {\n    // Updates the figure title.\n    fig.header.textContent = msg['label'];\n};\n\nmpl.figure.prototype.handle_cursor = function (fig, msg) {\n    fig.rubberband_canvas.style.cursor = msg['cursor'];\n};\n\nmpl.figure.prototype.handle_message = function (fig, msg) {\n    fig.message.textContent = msg['message'];\n};\n\nmpl.figure.prototype.handle_draw = function (fig, _msg) {\n    // Request the server to send over a new figure.\n    fig.send_draw_message();\n};\n\nmpl.figure.prototype.handle_image_mode = function (fig, msg) {\n    fig.image_mode = msg['mode'];\n};\n\nmpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n    for (var key in msg) {\n        if (!(key in fig.buttons)) {\n            continue;\n        }\n        fig.buttons[key].disabled = !msg[key];\n        fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n    }\n};\n\nmpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n    if (msg['mode'] === 'PAN') {\n        fig.buttons['Pan'].classList.add('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    } else if (msg['mode'] === 'ZOOM') {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.add('active');\n    } else {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    }\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Called whenever the canvas gets updated.\n    this.send_message('ack', {});\n};\n\n// A function to construct a web socket function for onmessage handling.\n// Called in the figure constructor.\nmpl.figure.prototype._make_on_message_function = function (fig) {\n    return function socket_on_message(evt) {\n        if (evt.data instanceof Blob) {\n            var img = evt.data;\n            if (img.type !== 'image/png') {\n                /* FIXME: We get \"Resource interpreted as Image but\n                 * transferred with MIME type text/plain:\" errors on\n                 * Chrome.  But how to set the MIME type?  It doesn't seem\n                 * to be part of the websocket stream */\n                img.type = 'image/png';\n            }\n\n            /* Free the memory for the previous frames */\n            if (fig.imageObj.src) {\n                (window.URL || window.webkitURL).revokeObjectURL(\n                    fig.imageObj.src\n                );\n            }\n\n            fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n                img\n            );\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        } else if (\n            typeof evt.data === 'string' &&\n            evt.data.slice(0, 21) === 'data:image/png;base64'\n        ) {\n            fig.imageObj.src = evt.data;\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        }\n\n        var msg = JSON.parse(evt.data);\n        var msg_type = msg['type'];\n\n        // Call the  \"handle_{type}\" callback, which takes\n        // the figure and JSON message as its only arguments.\n        try {\n            var callback = fig['handle_' + msg_type];\n        } catch (e) {\n            console.log(\n                \"No handler for the '\" + msg_type + \"' message type: \",\n                msg\n            );\n            return;\n        }\n\n        if (callback) {\n            try {\n                // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n                callback(fig, msg);\n            } catch (e) {\n                console.log(\n                    \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n                    e,\n                    e.stack,\n                    msg\n                );\n            }\n        }\n    };\n};\n\n// from https://stackoverflow.com/questions/1114465/getting-mouse-location-in-canvas\nmpl.findpos = function (e) {\n    //this section is from http://www.quirksmode.org/js/events_properties.html\n    var targ;\n    if (!e) {\n        e = window.event;\n    }\n    if (e.target) {\n        targ = e.target;\n    } else if (e.srcElement) {\n        targ = e.srcElement;\n    }\n    if (targ.nodeType === 3) {\n        // defeat Safari bug\n        targ = targ.parentNode;\n    }\n\n    // pageX,Y are the mouse positions relative to the document\n    var boundingRect = targ.getBoundingClientRect();\n    var x = e.pageX - (boundingRect.left + document.body.scrollLeft);\n    var y = e.pageY - (boundingRect.top + document.body.scrollTop);\n\n    return { x: x, y: y };\n};\n\n/*\n * return a copy of an object with only non-object keys\n * we need this to avoid circular references\n * https://stackoverflow.com/a/24161582/3208463\n */\nfunction simpleKeys(original) {\n    return Object.keys(original).reduce(function (obj, key) {\n        if (typeof original[key] !== 'object') {\n            obj[key] = original[key];\n        }\n        return obj;\n    }, {});\n}\n\nmpl.figure.prototype.mouse_event = function (event, name) {\n    var canvas_pos = mpl.findpos(event);\n\n    if (name === 'button_press') {\n        this.canvas.focus();\n        this.canvas_div.focus();\n    }\n\n    var x = canvas_pos.x * this.ratio;\n    var y = canvas_pos.y * this.ratio;\n\n    this.send_message(name, {\n        x: x,\n        y: y,\n        button: event.button,\n        step: event.step,\n        guiEvent: simpleKeys(event),\n    });\n\n    /* This prevents the web browser from automatically changing to\n     * the text insertion cursor when the button is pressed.  We want\n     * to control all of the cursor setting manually through the\n     * 'cursor' event from matplotlib */\n    event.preventDefault();\n    return false;\n};\n\nmpl.figure.prototype._key_event_extra = function (_event, _name) {\n    // Handle any extra behaviour associated with a key event\n};\n\nmpl.figure.prototype.key_event = function (event, name) {\n    // Prevent repeat events\n    if (name === 'key_press') {\n        if (event.key === this._key) {\n            return;\n        } else {\n            this._key = event.key;\n        }\n    }\n    if (name === 'key_release') {\n        this._key = null;\n    }\n\n    var value = '';\n    if (event.ctrlKey && event.key !== 'Control') {\n        value += 'ctrl+';\n    }\n    else if (event.altKey && event.key !== 'Alt') {\n        value += 'alt+';\n    }\n    else if (event.shiftKey && event.key !== 'Shift') {\n        value += 'shift+';\n    }\n\n    value += 'k' + event.key;\n\n    this._key_event_extra(event, name);\n\n    this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n    return false;\n};\n\nmpl.figure.prototype.toolbar_button_onclick = function (name) {\n    if (name === 'download') {\n        this.handle_save(this, null);\n    } else {\n        this.send_message('toolbar_button', { name: name });\n    }\n};\n\nmpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n    this.message.textContent = tooltip;\n};\n\n///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n// prettier-ignore\nvar _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\nmpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home icon-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left icon-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right icon-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows icon-move\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis\", \"fa fa-square-o icon-check-empty\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o icon-save\", \"download\"]];\n\nmpl.extensions = [\"eps\", \"jpeg\", \"pgf\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\"];\n\nmpl.default_extension = \"png\";/* global mpl */\n\nvar comm_websocket_adapter = function (comm) {\n    // Create a \"websocket\"-like object which calls the given IPython comm\n    // object with the appropriate methods. Currently this is a non binary\n    // socket, so there is still some room for performance tuning.\n    var ws = {};\n\n    ws.binaryType = comm.kernel.ws.binaryType;\n    ws.readyState = comm.kernel.ws.readyState;\n    function updateReadyState(_event) {\n        if (comm.kernel.ws) {\n            ws.readyState = comm.kernel.ws.readyState;\n        } else {\n            ws.readyState = 3; // Closed state.\n        }\n    }\n    comm.kernel.ws.addEventListener('open', updateReadyState);\n    comm.kernel.ws.addEventListener('close', updateReadyState);\n    comm.kernel.ws.addEventListener('error', updateReadyState);\n\n    ws.close = function () {\n        comm.close();\n    };\n    ws.send = function (m) {\n        //console.log('sending', m);\n        comm.send(m);\n    };\n    // Register the callback with on_msg.\n    comm.on_msg(function (msg) {\n        //console.log('receiving', msg['content']['data'], msg);\n        var data = msg['content']['data'];\n        if (data['blob'] !== undefined) {\n            data = {\n                data: new Blob(msg['buffers'], { type: data['blob'] }),\n            };\n        }\n        // Pass the mpl event to the overridden (by mpl) onmessage function.\n        ws.onmessage(data);\n    });\n    return ws;\n};\n\nmpl.mpl_figure_comm = function (comm, msg) {\n    // This is the function which gets called when the mpl process\n    // starts-up an IPython Comm through the \"matplotlib\" channel.\n\n    var id = msg.content.data.id;\n    // Get hold of the div created by the display call when the Comm\n    // socket was opened in Python.\n    var element = document.getElementById(id);\n    var ws_proxy = comm_websocket_adapter(comm);\n\n    function ondownload(figure, _format) {\n        window.open(figure.canvas.toDataURL());\n    }\n\n    var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n\n    // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n    // web socket which is closed, not our websocket->open comm proxy.\n    ws_proxy.onopen();\n\n    fig.parent_element = element;\n    fig.cell_info = mpl.find_output_cell(\"<div id='\" + id + \"'></div>\");\n    if (!fig.cell_info) {\n        console.error('Failed to find cell for figure', id, fig);\n        return;\n    }\n    fig.cell_info[0].output_area.element.on(\n        'cleared',\n        { fig: fig },\n        fig._remove_fig_handler\n    );\n};\n\nmpl.figure.prototype.handle_close = function (fig, msg) {\n    var width = fig.canvas.width / fig.ratio;\n    fig.cell_info[0].output_area.element.off(\n        'cleared',\n        fig._remove_fig_handler\n    );\n    fig.resizeObserverInstance.unobserve(fig.canvas_div);\n\n    // Update the output cell to use the data from the current canvas.\n    fig.push_to_output();\n    var dataURL = fig.canvas.toDataURL();\n    // Re-enable the keyboard manager in IPython - without this line, in FF,\n    // the notebook keyboard shortcuts fail.\n    IPython.keyboard_manager.enable();\n    fig.parent_element.innerHTML =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n    fig.close_ws(fig, msg);\n};\n\nmpl.figure.prototype.close_ws = function (fig, msg) {\n    fig.send_message('closing', msg);\n    // fig.ws.close()\n};\n\nmpl.figure.prototype.push_to_output = function (_remove_interactive) {\n    // Turn the data on the canvas into data in the output cell.\n    var width = this.canvas.width / this.ratio;\n    var dataURL = this.canvas.toDataURL();\n    this.cell_info[1]['text/html'] =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Tell IPython that the notebook contents must change.\n    IPython.notebook.set_dirty(true);\n    this.send_message('ack', {});\n    var fig = this;\n    // Wait a second, then push the new image to the DOM so\n    // that it is saved nicely (might be nice to debounce this).\n    setTimeout(function () {\n        fig.push_to_output();\n    }, 1000);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'btn-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'btn-group';\n    var button;\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'btn-group';\n            continue;\n        }\n\n        button = fig.buttons[name] = document.createElement('button');\n        button.classList = 'btn btn-default';\n        button.href = '#';\n        button.title = name;\n        button.innerHTML = '<i class=\"fa ' + image + ' fa-lg\"></i>';\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    // Add the status bar.\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message pull-right';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n\n    // Add the close button to the window.\n    var buttongrp = document.createElement('div');\n    buttongrp.classList = 'btn-group inline pull-right';\n    button = document.createElement('button');\n    button.classList = 'btn btn-mini btn-primary';\n    button.href = '#';\n    button.title = 'Stop Interaction';\n    button.innerHTML = '<i class=\"fa fa-power-off icon-remove icon-large\"></i>';\n    button.addEventListener('click', function (_evt) {\n        fig.handle_close(fig, {});\n    });\n    button.addEventListener(\n        'mouseover',\n        on_mouseover_closure('Stop Interaction')\n    );\n    buttongrp.appendChild(button);\n    var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n    titlebar.insertBefore(buttongrp, titlebar.firstChild);\n};\n\nmpl.figure.prototype._remove_fig_handler = function (event) {\n    var fig = event.data.fig;\n    if (event.target !== this) {\n        // Ignore bubbled events from children.\n        return;\n    }\n    fig.close_ws(fig, {});\n};\n\nmpl.figure.prototype._root_extra_style = function (el) {\n    el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n};\n\nmpl.figure.prototype._canvas_extra_style = function (el) {\n    // this is important to make the div 'focusable\n    el.setAttribute('tabindex', 0);\n    // reach out to IPython and tell the keyboard manager to turn it's self\n    // off when our div gets focus\n\n    // location in version 3\n    if (IPython.notebook.keyboard_manager) {\n        IPython.notebook.keyboard_manager.register_events(el);\n    } else {\n        // location in version 2\n        IPython.keyboard_manager.register_events(el);\n    }\n};\n\nmpl.figure.prototype._key_event_extra = function (event, _name) {\n    // Check for shift+enter\n    if (event.shiftKey && event.which === 13) {\n        this.canvas_div.blur();\n        // select the cell after this one\n        var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n        IPython.notebook.select(index + 1);\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    fig.ondownload(fig, null);\n};\n\nmpl.find_output_cell = function (html_output) {\n    // Return the cell and output element which can be found *uniquely* in the notebook.\n    // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n    // IPython event is triggered only after the cells have been serialised, which for\n    // our purposes (turning an active figure into a static one), is too late.\n    var cells = IPython.notebook.get_cells();\n    var ncells = cells.length;\n    for (var i = 0; i < ncells; i++) {\n        var cell = cells[i];\n        if (cell.cell_type === 'code') {\n            for (var j = 0; j < cell.output_area.outputs.length; j++) {\n                var data = cell.output_area.outputs[j];\n                if (data.data) {\n                    // IPython >= 3 moved mimebundle to data attribute of output\n                    data = data.data;\n                }\n                if (data['text/html'] === html_output) {\n                    return [cell, data, j];\n                }\n            }\n        }\n    }\n};\n\n// Register the function which deals with the matplotlib target/channel.\n// The kernel may be null if the page has been refreshed.\nif (IPython.notebook.kernel !== null) {\n    IPython.notebook.kernel.comm_manager.register_target(\n        'matplotlib',\n        mpl.mpl_figure_comm\n    );\n}\n",
      "text/plain": [
       "<IPython.core.display.Javascript object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<img src=\"data:image/png;base64,[encoded data, 42904 characters]\" width=\"640\">"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "%matplotlib notebook\n",
    "shotNum = \"0005\"\n",
    "filePath = folderPath + \"/\" + shotNum + \"/*.h5\"\n",
    "\n",
    "dataSetDict = {\n",
    "    dskey[groupList[i]]: read_hdf5_file(filePath, groupList[i], excludeAxis = ['sweep_start_freq', 'sweep_stop_freq'])\n",
    "    for i in [0]\n",
    "}\n",
    "\n",
    "dataSet = dataSetDict[\"camera_0\"]\n",
    "\n",
    "print_scanAxis(dataSet)\n",
    "\n",
    "scanAxis = get_scanAxis(dataSet)\n",
    "\n",
    "dataSet = auto_rechunk(dataSet)\n",
    "\n",
    "dataSet = imageAnalyser.get_absorption_images(dataSet)\n",
    "\n",
    "imageAnalyser.center = (800, 900)\n",
    "imageAnalyser.span = (300, 300)\n",
    "imageAnalyser.fraction = (0.1, 0.1)\n",
    "\n",
    "dataSet_cropOD = imageAnalyser.crop_image(dataSet.OD)\n",
    "dataSet_cropOD = imageAnalyser.substract_offset(dataSet_cropOD).load()\n",
    "\n",
    "Ncount = imageAnalyser.get_Ncount(dataSet_cropOD)\n",
    "Ncount_mean = calculate_mean(Ncount)\n",
    "Ncount_std = calculate_std(Ncount)\n",
    "\n",
    "fig = plt.figure()\n",
    "ax = fig.gca()\n",
    "Ncount_mean.plot.errorbar(ax=ax, yerr = Ncount_std, fmt='ob')\n",
    "plt.ylabel('NCount')\n",
    "plt.tight_layout()\n",
    "plt.grid(visible=1)\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 63,
   "metadata": {},
   "outputs": [],
   "source": [
    "dataSet_cropOD_chunk = dataSet_cropOD.chunk((1, 1, 300, 300))\n",
    "fitAnalyser = FitAnalyser(\"Gaussian-2D\", fitDim=2)\n",
    "params = fitAnalyser.guess(dataSet_cropOD_chunk, dask=\"parallelized\")\n",
    "fitResult = fitAnalyser.fit(dataSet_cropOD_chunk, params, dask=\"parallelized\").load()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 64,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/javascript": "/* Put everything inside the global mpl namespace */\n/* global mpl */\nwindow.mpl = {};\n\nmpl.get_websocket_type = function () {\n    if (typeof WebSocket !== 'undefined') {\n        return WebSocket;\n    } else if (typeof MozWebSocket !== 'undefined') {\n        return MozWebSocket;\n    } else {\n        alert(\n            'Your browser does not have WebSocket support. ' +\n                'Please try Chrome, Safari or Firefox ≥ 6. ' +\n                'Firefox 4 and 5 are also supported but you ' +\n                'have to enable WebSockets in about:config.'\n        );\n    }\n};\n\nmpl.figure = function (figure_id, websocket, ondownload, parent_element) {\n    this.id = figure_id;\n\n    this.ws = websocket;\n\n    this.supports_binary = this.ws.binaryType !== undefined;\n\n    if (!this.supports_binary) {\n        var warnings = document.getElementById('mpl-warnings');\n        if (warnings) {\n            warnings.style.display = 'block';\n            warnings.textContent =\n                'This browser does not support binary websocket messages. ' +\n                'Performance may be slow.';\n        }\n    }\n\n    this.imageObj = new Image();\n\n    this.context = undefined;\n    this.message = undefined;\n    this.canvas = undefined;\n    this.rubberband_canvas = undefined;\n    this.rubberband_context = undefined;\n    this.format_dropdown = undefined;\n\n    this.image_mode = 'full';\n\n    this.root = document.createElement('div');\n    this.root.setAttribute('style', 'display: inline-block');\n    this._root_extra_style(this.root);\n\n    parent_element.appendChild(this.root);\n\n    this._init_header(this);\n    this._init_canvas(this);\n    this._init_toolbar(this);\n\n    var fig = this;\n\n    this.waiting = false;\n\n    this.ws.onopen = function () {\n        fig.send_message('supports_binary', { value: fig.supports_binary });\n        fig.send_message('send_image_mode', {});\n        if (fig.ratio !== 1) {\n            fig.send_message('set_device_pixel_ratio', {\n                device_pixel_ratio: fig.ratio,\n            });\n        }\n        fig.send_message('refresh', {});\n    };\n\n    this.imageObj.onload = function () {\n        if (fig.image_mode === 'full') {\n            // Full images could contain transparency (where diff images\n            // almost always do), so we need to clear the canvas so that\n            // there is no ghosting.\n            fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n        }\n        fig.context.drawImage(fig.imageObj, 0, 0);\n    };\n\n    this.imageObj.onunload = function () {\n        fig.ws.close();\n    };\n\n    this.ws.onmessage = this._make_on_message_function(this);\n\n    this.ondownload = ondownload;\n};\n\nmpl.figure.prototype._init_header = function () {\n    var titlebar = document.createElement('div');\n    titlebar.classList =\n        'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n    var titletext = document.createElement('div');\n    titletext.classList = 'ui-dialog-title';\n    titletext.setAttribute(\n        'style',\n        'width: 100%; text-align: center; padding: 3px;'\n    );\n    titlebar.appendChild(titletext);\n    this.root.appendChild(titlebar);\n    this.header = titletext;\n};\n\nmpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._init_canvas = function () {\n    var fig = this;\n\n    var canvas_div = (this.canvas_div = document.createElement('div'));\n    canvas_div.setAttribute(\n        'style',\n        'border: 1px solid #ddd;' +\n            'box-sizing: content-box;' +\n            'clear: both;' +\n            'min-height: 1px;' +\n            'min-width: 1px;' +\n            'outline: 0;' +\n            'overflow: hidden;' +\n            'position: relative;' +\n            'resize: both;'\n    );\n\n    function on_keyboard_event_closure(name) {\n        return function (event) {\n            return fig.key_event(event, name);\n        };\n    }\n\n    canvas_div.addEventListener(\n        'keydown',\n        on_keyboard_event_closure('key_press')\n    );\n    canvas_div.addEventListener(\n        'keyup',\n        on_keyboard_event_closure('key_release')\n    );\n\n    this._canvas_extra_style(canvas_div);\n    this.root.appendChild(canvas_div);\n\n    var canvas = (this.canvas = document.createElement('canvas'));\n    canvas.classList.add('mpl-canvas');\n    canvas.setAttribute('style', 'box-sizing: content-box;');\n\n    this.context = canvas.getContext('2d');\n\n    var backingStore =\n        this.context.backingStorePixelRatio ||\n        this.context.webkitBackingStorePixelRatio ||\n        this.context.mozBackingStorePixelRatio ||\n        this.context.msBackingStorePixelRatio ||\n        this.context.oBackingStorePixelRatio ||\n        this.context.backingStorePixelRatio ||\n        1;\n\n    this.ratio = (window.devicePixelRatio || 1) / backingStore;\n\n    var rubberband_canvas = (this.rubberband_canvas = document.createElement(\n        'canvas'\n    ));\n    rubberband_canvas.setAttribute(\n        'style',\n        'box-sizing: content-box; position: absolute; left: 0; top: 0; z-index: 1;'\n    );\n\n    // Apply a ponyfill if ResizeObserver is not implemented by browser.\n    if (this.ResizeObserver === undefined) {\n        if (window.ResizeObserver !== undefined) {\n            this.ResizeObserver = window.ResizeObserver;\n        } else {\n            var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n            this.ResizeObserver = obs.ResizeObserver;\n        }\n    }\n\n    this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n        var nentries = entries.length;\n        for (var i = 0; i < nentries; i++) {\n            var entry = entries[i];\n            var width, height;\n            if (entry.contentBoxSize) {\n                if (entry.contentBoxSize instanceof Array) {\n                    // Chrome 84 implements new version of spec.\n                    width = entry.contentBoxSize[0].inlineSize;\n                    height = entry.contentBoxSize[0].blockSize;\n                } else {\n                    // Firefox implements old version of spec.\n                    width = entry.contentBoxSize.inlineSize;\n                    height = entry.contentBoxSize.blockSize;\n                }\n            } else {\n                // Chrome <84 implements even older version of spec.\n                width = entry.contentRect.width;\n                height = entry.contentRect.height;\n            }\n\n            // Keep the size of the canvas and rubber band canvas in sync with\n            // the canvas container.\n            if (entry.devicePixelContentBoxSize) {\n                // Chrome 84 implements new version of spec.\n                canvas.setAttribute(\n                    'width',\n                    entry.devicePixelContentBoxSize[0].inlineSize\n                );\n                canvas.setAttribute(\n                    'height',\n                    entry.devicePixelContentBoxSize[0].blockSize\n                );\n            } else {\n                canvas.setAttribute('width', width * fig.ratio);\n                canvas.setAttribute('height', height * fig.ratio);\n            }\n            canvas.setAttribute(\n                'style',\n                'width: ' + width + 'px; height: ' + height + 'px;'\n            );\n\n            rubberband_canvas.setAttribute('width', width);\n            rubberband_canvas.setAttribute('height', height);\n\n            // And update the size in Python. We ignore the initial 0/0 size\n            // that occurs as the element is placed into the DOM, which should\n            // otherwise not happen due to the minimum size styling.\n            if (fig.ws.readyState == 1 && width != 0 && height != 0) {\n                fig.request_resize(width, height);\n            }\n        }\n    });\n    this.resizeObserverInstance.observe(canvas_div);\n\n    function on_mouse_event_closure(name) {\n        return function (event) {\n            return fig.mouse_event(event, name);\n        };\n    }\n\n    rubberband_canvas.addEventListener(\n        'mousedown',\n        on_mouse_event_closure('button_press')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseup',\n        on_mouse_event_closure('button_release')\n    );\n    rubberband_canvas.addEventListener(\n        'dblclick',\n        on_mouse_event_closure('dblclick')\n    );\n    // Throttle sequential mouse events to 1 every 20ms.\n    rubberband_canvas.addEventListener(\n        'mousemove',\n        on_mouse_event_closure('motion_notify')\n    );\n\n    rubberband_canvas.addEventListener(\n        'mouseenter',\n        on_mouse_event_closure('figure_enter')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseleave',\n        on_mouse_event_closure('figure_leave')\n    );\n\n    canvas_div.addEventListener('wheel', function (event) {\n        if (event.deltaY < 0) {\n            event.step = 1;\n        } else {\n            event.step = -1;\n        }\n        on_mouse_event_closure('scroll')(event);\n    });\n\n    canvas_div.appendChild(canvas);\n    canvas_div.appendChild(rubberband_canvas);\n\n    this.rubberband_context = rubberband_canvas.getContext('2d');\n    this.rubberband_context.strokeStyle = '#000000';\n\n    this._resize_canvas = function (width, height, forward) {\n        if (forward) {\n            canvas_div.style.width = width + 'px';\n            canvas_div.style.height = height + 'px';\n        }\n    };\n\n    // Disable right mouse context menu.\n    this.rubberband_canvas.addEventListener('contextmenu', function (_e) {\n        event.preventDefault();\n        return false;\n    });\n\n    function set_focus() {\n        canvas.focus();\n        canvas_div.focus();\n    }\n\n    window.setTimeout(set_focus, 100);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'mpl-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'mpl-button-group';\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'mpl-button-group';\n            continue;\n        }\n\n        var button = (fig.buttons[name] = document.createElement('button'));\n        button.classList = 'mpl-widget';\n        button.setAttribute('role', 'button');\n        button.setAttribute('aria-disabled', 'false');\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n\n        var icon_img = document.createElement('img');\n        icon_img.src = '_images/' + image + '.png';\n        icon_img.srcset = '_images/' + image + '_large.png 2x';\n        icon_img.alt = tooltip;\n        button.appendChild(icon_img);\n\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    var fmt_picker = document.createElement('select');\n    fmt_picker.classList = 'mpl-widget';\n    toolbar.appendChild(fmt_picker);\n    this.format_dropdown = fmt_picker;\n\n    for (var ind in mpl.extensions) {\n        var fmt = mpl.extensions[ind];\n        var option = document.createElement('option');\n        option.selected = fmt === mpl.default_extension;\n        option.innerHTML = fmt;\n        fmt_picker.appendChild(option);\n    }\n\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n};\n\nmpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n    // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n    // which will in turn request a refresh of the image.\n    this.send_message('resize', { width: x_pixels, height: y_pixels });\n};\n\nmpl.figure.prototype.send_message = function (type, properties) {\n    properties['type'] = type;\n    properties['figure_id'] = this.id;\n    this.ws.send(JSON.stringify(properties));\n};\n\nmpl.figure.prototype.send_draw_message = function () {\n    if (!this.waiting) {\n        this.waiting = true;\n        this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    var format_dropdown = fig.format_dropdown;\n    var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n    fig.ondownload(fig, format);\n};\n\nmpl.figure.prototype.handle_resize = function (fig, msg) {\n    var size = msg['size'];\n    if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n        fig._resize_canvas(size[0], size[1], msg['forward']);\n        fig.send_message('refresh', {});\n    }\n};\n\nmpl.figure.prototype.handle_rubberband = function (fig, msg) {\n    var x0 = msg['x0'] / fig.ratio;\n    var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n    var x1 = msg['x1'] / fig.ratio;\n    var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n    x0 = Math.floor(x0) + 0.5;\n    y0 = Math.floor(y0) + 0.5;\n    x1 = Math.floor(x1) + 0.5;\n    y1 = Math.floor(y1) + 0.5;\n    var min_x = Math.min(x0, x1);\n    var min_y = Math.min(y0, y1);\n    var width = Math.abs(x1 - x0);\n    var height = Math.abs(y1 - y0);\n\n    fig.rubberband_context.clearRect(\n        0,\n        0,\n        fig.canvas.width / fig.ratio,\n        fig.canvas.height / fig.ratio\n    );\n\n    fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n};\n\nmpl.figure.prototype.handle_figure_label = function (fig, msg) {\n    // Updates the figure title.\n    fig.header.textContent = msg['label'];\n};\n\nmpl.figure.prototype.handle_cursor = function (fig, msg) {\n    fig.rubberband_canvas.style.cursor = msg['cursor'];\n};\n\nmpl.figure.prototype.handle_message = function (fig, msg) {\n    fig.message.textContent = msg['message'];\n};\n\nmpl.figure.prototype.handle_draw = function (fig, _msg) {\n    // Request the server to send over a new figure.\n    fig.send_draw_message();\n};\n\nmpl.figure.prototype.handle_image_mode = function (fig, msg) {\n    fig.image_mode = msg['mode'];\n};\n\nmpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n    for (var key in msg) {\n        if (!(key in fig.buttons)) {\n            continue;\n        }\n        fig.buttons[key].disabled = !msg[key];\n        fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n    }\n};\n\nmpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n    if (msg['mode'] === 'PAN') {\n        fig.buttons['Pan'].classList.add('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    } else if (msg['mode'] === 'ZOOM') {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.add('active');\n    } else {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    }\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Called whenever the canvas gets updated.\n    this.send_message('ack', {});\n};\n\n// A function to construct a web socket function for onmessage handling.\n// Called in the figure constructor.\nmpl.figure.prototype._make_on_message_function = function (fig) {\n    return function socket_on_message(evt) {\n        if (evt.data instanceof Blob) {\n            var img = evt.data;\n            if (img.type !== 'image/png') {\n                /* FIXME: We get \"Resource interpreted as Image but\n                 * transferred with MIME type text/plain:\" errors on\n                 * Chrome.  But how to set the MIME type?  It doesn't seem\n                 * to be part of the websocket stream */\n                img.type = 'image/png';\n            }\n\n            /* Free the memory for the previous frames */\n            if (fig.imageObj.src) {\n                (window.URL || window.webkitURL).revokeObjectURL(\n                    fig.imageObj.src\n                );\n            }\n\n            fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n                img\n            );\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        } else if (\n            typeof evt.data === 'string' &&\n            evt.data.slice(0, 21) === 'data:image/png;base64'\n        ) {\n            fig.imageObj.src = evt.data;\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        }\n\n        var msg = JSON.parse(evt.data);\n        var msg_type = msg['type'];\n\n        // Call the  \"handle_{type}\" callback, which takes\n        // the figure and JSON message as its only arguments.\n        try {\n            var callback = fig['handle_' + msg_type];\n        } catch (e) {\n            console.log(\n                \"No handler for the '\" + msg_type + \"' message type: \",\n                msg\n            );\n            return;\n        }\n\n        if (callback) {\n            try {\n                // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n                callback(fig, msg);\n            } catch (e) {\n                console.log(\n                    \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n                    e,\n                    e.stack,\n                    msg\n                );\n            }\n        }\n    };\n};\n\n// from https://stackoverflow.com/questions/1114465/getting-mouse-location-in-canvas\nmpl.findpos = function (e) {\n    //this section is from http://www.quirksmode.org/js/events_properties.html\n    var targ;\n    if (!e) {\n        e = window.event;\n    }\n    if (e.target) {\n        targ = e.target;\n    } else if (e.srcElement) {\n        targ = e.srcElement;\n    }\n    if (targ.nodeType === 3) {\n        // defeat Safari bug\n        targ = targ.parentNode;\n    }\n\n    // pageX,Y are the mouse positions relative to the document\n    var boundingRect = targ.getBoundingClientRect();\n    var x = e.pageX - (boundingRect.left + document.body.scrollLeft);\n    var y = e.pageY - (boundingRect.top + document.body.scrollTop);\n\n    return { x: x, y: y };\n};\n\n/*\n * return a copy of an object with only non-object keys\n * we need this to avoid circular references\n * https://stackoverflow.com/a/24161582/3208463\n */\nfunction simpleKeys(original) {\n    return Object.keys(original).reduce(function (obj, key) {\n        if (typeof original[key] !== 'object') {\n            obj[key] = original[key];\n        }\n        return obj;\n    }, {});\n}\n\nmpl.figure.prototype.mouse_event = function (event, name) {\n    var canvas_pos = mpl.findpos(event);\n\n    if (name === 'button_press') {\n        this.canvas.focus();\n        this.canvas_div.focus();\n    }\n\n    var x = canvas_pos.x * this.ratio;\n    var y = canvas_pos.y * this.ratio;\n\n    this.send_message(name, {\n        x: x,\n        y: y,\n        button: event.button,\n        step: event.step,\n        guiEvent: simpleKeys(event),\n    });\n\n    /* This prevents the web browser from automatically changing to\n     * the text insertion cursor when the button is pressed.  We want\n     * to control all of the cursor setting manually through the\n     * 'cursor' event from matplotlib */\n    event.preventDefault();\n    return false;\n};\n\nmpl.figure.prototype._key_event_extra = function (_event, _name) {\n    // Handle any extra behaviour associated with a key event\n};\n\nmpl.figure.prototype.key_event = function (event, name) {\n    // Prevent repeat events\n    if (name === 'key_press') {\n        if (event.key === this._key) {\n            return;\n        } else {\n            this._key = event.key;\n        }\n    }\n    if (name === 'key_release') {\n        this._key = null;\n    }\n\n    var value = '';\n    if (event.ctrlKey && event.key !== 'Control') {\n        value += 'ctrl+';\n    }\n    else if (event.altKey && event.key !== 'Alt') {\n        value += 'alt+';\n    }\n    else if (event.shiftKey && event.key !== 'Shift') {\n        value += 'shift+';\n    }\n\n    value += 'k' + event.key;\n\n    this._key_event_extra(event, name);\n\n    this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n    return false;\n};\n\nmpl.figure.prototype.toolbar_button_onclick = function (name) {\n    if (name === 'download') {\n        this.handle_save(this, null);\n    } else {\n        this.send_message('toolbar_button', { name: name });\n    }\n};\n\nmpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n    this.message.textContent = tooltip;\n};\n\n///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n// prettier-ignore\nvar _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\nmpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home icon-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left icon-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right icon-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows icon-move\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis\", \"fa fa-square-o icon-check-empty\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o icon-save\", \"download\"]];\n\nmpl.extensions = [\"eps\", \"jpeg\", \"pgf\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\"];\n\nmpl.default_extension = \"png\";/* global mpl */\n\nvar comm_websocket_adapter = function (comm) {\n    // Create a \"websocket\"-like object which calls the given IPython comm\n    // object with the appropriate methods. Currently this is a non binary\n    // socket, so there is still some room for performance tuning.\n    var ws = {};\n\n    ws.binaryType = comm.kernel.ws.binaryType;\n    ws.readyState = comm.kernel.ws.readyState;\n    function updateReadyState(_event) {\n        if (comm.kernel.ws) {\n            ws.readyState = comm.kernel.ws.readyState;\n        } else {\n            ws.readyState = 3; // Closed state.\n        }\n    }\n    comm.kernel.ws.addEventListener('open', updateReadyState);\n    comm.kernel.ws.addEventListener('close', updateReadyState);\n    comm.kernel.ws.addEventListener('error', updateReadyState);\n\n    ws.close = function () {\n        comm.close();\n    };\n    ws.send = function (m) {\n        //console.log('sending', m);\n        comm.send(m);\n    };\n    // Register the callback with on_msg.\n    comm.on_msg(function (msg) {\n        //console.log('receiving', msg['content']['data'], msg);\n        var data = msg['content']['data'];\n        if (data['blob'] !== undefined) {\n            data = {\n                data: new Blob(msg['buffers'], { type: data['blob'] }),\n            };\n        }\n        // Pass the mpl event to the overridden (by mpl) onmessage function.\n        ws.onmessage(data);\n    });\n    return ws;\n};\n\nmpl.mpl_figure_comm = function (comm, msg) {\n    // This is the function which gets called when the mpl process\n    // starts-up an IPython Comm through the \"matplotlib\" channel.\n\n    var id = msg.content.data.id;\n    // Get hold of the div created by the display call when the Comm\n    // socket was opened in Python.\n    var element = document.getElementById(id);\n    var ws_proxy = comm_websocket_adapter(comm);\n\n    function ondownload(figure, _format) {\n        window.open(figure.canvas.toDataURL());\n    }\n\n    var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n\n    // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n    // web socket which is closed, not our websocket->open comm proxy.\n    ws_proxy.onopen();\n\n    fig.parent_element = element;\n    fig.cell_info = mpl.find_output_cell(\"<div id='\" + id + \"'></div>\");\n    if (!fig.cell_info) {\n        console.error('Failed to find cell for figure', id, fig);\n        return;\n    }\n    fig.cell_info[0].output_area.element.on(\n        'cleared',\n        { fig: fig },\n        fig._remove_fig_handler\n    );\n};\n\nmpl.figure.prototype.handle_close = function (fig, msg) {\n    var width = fig.canvas.width / fig.ratio;\n    fig.cell_info[0].output_area.element.off(\n        'cleared',\n        fig._remove_fig_handler\n    );\n    fig.resizeObserverInstance.unobserve(fig.canvas_div);\n\n    // Update the output cell to use the data from the current canvas.\n    fig.push_to_output();\n    var dataURL = fig.canvas.toDataURL();\n    // Re-enable the keyboard manager in IPython - without this line, in FF,\n    // the notebook keyboard shortcuts fail.\n    IPython.keyboard_manager.enable();\n    fig.parent_element.innerHTML =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n    fig.close_ws(fig, msg);\n};\n\nmpl.figure.prototype.close_ws = function (fig, msg) {\n    fig.send_message('closing', msg);\n    // fig.ws.close()\n};\n\nmpl.figure.prototype.push_to_output = function (_remove_interactive) {\n    // Turn the data on the canvas into data in the output cell.\n    var width = this.canvas.width / this.ratio;\n    var dataURL = this.canvas.toDataURL();\n    this.cell_info[1]['text/html'] =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Tell IPython that the notebook contents must change.\n    IPython.notebook.set_dirty(true);\n    this.send_message('ack', {});\n    var fig = this;\n    // Wait a second, then push the new image to the DOM so\n    // that it is saved nicely (might be nice to debounce this).\n    setTimeout(function () {\n        fig.push_to_output();\n    }, 1000);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'btn-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'btn-group';\n    var button;\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'btn-group';\n            continue;\n        }\n\n        button = fig.buttons[name] = document.createElement('button');\n        button.classList = 'btn btn-default';\n        button.href = '#';\n        button.title = name;\n        button.innerHTML = '<i class=\"fa ' + image + ' fa-lg\"></i>';\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    // Add the status bar.\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message pull-right';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n\n    // Add the close button to the window.\n    var buttongrp = document.createElement('div');\n    buttongrp.classList = 'btn-group inline pull-right';\n    button = document.createElement('button');\n    button.classList = 'btn btn-mini btn-primary';\n    button.href = '#';\n    button.title = 'Stop Interaction';\n    button.innerHTML = '<i class=\"fa fa-power-off icon-remove icon-large\"></i>';\n    button.addEventListener('click', function (_evt) {\n        fig.handle_close(fig, {});\n    });\n    button.addEventListener(\n        'mouseover',\n        on_mouseover_closure('Stop Interaction')\n    );\n    buttongrp.appendChild(button);\n    var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n    titlebar.insertBefore(buttongrp, titlebar.firstChild);\n};\n\nmpl.figure.prototype._remove_fig_handler = function (event) {\n    var fig = event.data.fig;\n    if (event.target !== this) {\n        // Ignore bubbled events from children.\n        return;\n    }\n    fig.close_ws(fig, {});\n};\n\nmpl.figure.prototype._root_extra_style = function (el) {\n    el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n};\n\nmpl.figure.prototype._canvas_extra_style = function (el) {\n    // this is important to make the div 'focusable\n    el.setAttribute('tabindex', 0);\n    // reach out to IPython and tell the keyboard manager to turn it's self\n    // off when our div gets focus\n\n    // location in version 3\n    if (IPython.notebook.keyboard_manager) {\n        IPython.notebook.keyboard_manager.register_events(el);\n    } else {\n        // location in version 2\n        IPython.keyboard_manager.register_events(el);\n    }\n};\n\nmpl.figure.prototype._key_event_extra = function (event, _name) {\n    // Check for shift+enter\n    if (event.shiftKey && event.which === 13) {\n        this.canvas_div.blur();\n        // select the cell after this one\n        var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n        IPython.notebook.select(index + 1);\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    fig.ondownload(fig, null);\n};\n\nmpl.find_output_cell = function (html_output) {\n    // Return the cell and output element which can be found *uniquely* in the notebook.\n    // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n    // IPython event is triggered only after the cells have been serialised, which for\n    // our purposes (turning an active figure into a static one), is too late.\n    var cells = IPython.notebook.get_cells();\n    var ncells = cells.length;\n    for (var i = 0; i < ncells; i++) {\n        var cell = cells[i];\n        if (cell.cell_type === 'code') {\n            for (var j = 0; j < cell.output_area.outputs.length; j++) {\n                var data = cell.output_area.outputs[j];\n                if (data.data) {\n                    // IPython >= 3 moved mimebundle to data attribute of output\n                    data = data.data;\n                }\n                if (data['text/html'] === html_output) {\n                    return [cell, data, j];\n                }\n            }\n        }\n    }\n};\n\n// Register the function which deals with the matplotlib target/channel.\n// The kernel may be null if the page has been refreshed.\nif (IPython.notebook.kernel !== null) {\n    IPython.notebook.kernel.comm_manager.register_target(\n        'matplotlib',\n        mpl.mpl_figure_comm\n    );\n}\n",
      "text/plain": [
       "<IPython.core.display.Javascript object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<img src=\"data:image/png;base64,[encoded data, 54280 characters]\" width=\"640\">"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "val = fitAnalyser.get_fit_value(fitResult)\n",
    "std = fitAnalyser.get_fit_std(fitResult)\n",
    "\n",
    "fitCurve = fitAnalyser.eval(fitResult, x=np.arange(300), y=np.arange(300), dask=\"parallelized\").load()\n",
    "\n",
    "# dataKey = 'sigmax'\n",
    "# dataKey = 'centerx'\n",
    "# dataKey = 'sigmay'\n",
    "dataKey = 'centery'\n",
    "\n",
    "# val_mean = val[dataKey].mean(dim='runs')\n",
    "# std_mean = val[dataKey].std(dim='runs')\n",
    "\n",
    "val_mean = calculate_mean(val[dataKey])\n",
    "std_mean = calculate_std(val[dataKey])\n",
    "\n",
    "fig = plt.figure()\n",
    "ax = fig.gca()\n",
    "\n",
    "val_mean.plot.errorbar(yerr=std_mean, fmt='--ob')\n",
    "\n",
    "plt.grid()\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 67,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/javascript": "/* Put everything inside the global mpl namespace */\n/* global mpl */\nwindow.mpl = {};\n\nmpl.get_websocket_type = function () {\n    if (typeof WebSocket !== 'undefined') {\n        return WebSocket;\n    } else if (typeof MozWebSocket !== 'undefined') {\n        return MozWebSocket;\n    } else {\n        alert(\n            'Your browser does not have WebSocket support. ' +\n                'Please try Chrome, Safari or Firefox ≥ 6. ' +\n                'Firefox 4 and 5 are also supported but you ' +\n                'have to enable WebSockets in about:config.'\n        );\n    }\n};\n\nmpl.figure = function (figure_id, websocket, ondownload, parent_element) {\n    this.id = figure_id;\n\n    this.ws = websocket;\n\n    this.supports_binary = this.ws.binaryType !== undefined;\n\n    if (!this.supports_binary) {\n        var warnings = document.getElementById('mpl-warnings');\n        if (warnings) {\n            warnings.style.display = 'block';\n            warnings.textContent =\n                'This browser does not support binary websocket messages. ' +\n                'Performance may be slow.';\n        }\n    }\n\n    this.imageObj = new Image();\n\n    this.context = undefined;\n    this.message = undefined;\n    this.canvas = undefined;\n    this.rubberband_canvas = undefined;\n    this.rubberband_context = undefined;\n    this.format_dropdown = undefined;\n\n    this.image_mode = 'full';\n\n    this.root = document.createElement('div');\n    this.root.setAttribute('style', 'display: inline-block');\n    this._root_extra_style(this.root);\n\n    parent_element.appendChild(this.root);\n\n    this._init_header(this);\n    this._init_canvas(this);\n    this._init_toolbar(this);\n\n    var fig = this;\n\n    this.waiting = false;\n\n    this.ws.onopen = function () {\n        fig.send_message('supports_binary', { value: fig.supports_binary });\n        fig.send_message('send_image_mode', {});\n        if (fig.ratio !== 1) {\n            fig.send_message('set_device_pixel_ratio', {\n                device_pixel_ratio: fig.ratio,\n            });\n        }\n        fig.send_message('refresh', {});\n    };\n\n    this.imageObj.onload = function () {\n        if (fig.image_mode === 'full') {\n            // Full images could contain transparency (where diff images\n            // almost always do), so we need to clear the canvas so that\n            // there is no ghosting.\n            fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n        }\n        fig.context.drawImage(fig.imageObj, 0, 0);\n    };\n\n    this.imageObj.onunload = function () {\n        fig.ws.close();\n    };\n\n    this.ws.onmessage = this._make_on_message_function(this);\n\n    this.ondownload = ondownload;\n};\n\nmpl.figure.prototype._init_header = function () {\n    var titlebar = document.createElement('div');\n    titlebar.classList =\n        'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n    var titletext = document.createElement('div');\n    titletext.classList = 'ui-dialog-title';\n    titletext.setAttribute(\n        'style',\n        'width: 100%; text-align: center; padding: 3px;'\n    );\n    titlebar.appendChild(titletext);\n    this.root.appendChild(titlebar);\n    this.header = titletext;\n};\n\nmpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._init_canvas = function () {\n    var fig = this;\n\n    var canvas_div = (this.canvas_div = document.createElement('div'));\n    canvas_div.setAttribute(\n        'style',\n        'border: 1px solid #ddd;' +\n            'box-sizing: content-box;' +\n            'clear: both;' +\n            'min-height: 1px;' +\n            'min-width: 1px;' +\n            'outline: 0;' +\n            'overflow: hidden;' +\n            'position: relative;' +\n            'resize: both;'\n    );\n\n    function on_keyboard_event_closure(name) {\n        return function (event) {\n            return fig.key_event(event, name);\n        };\n    }\n\n    canvas_div.addEventListener(\n        'keydown',\n        on_keyboard_event_closure('key_press')\n    );\n    canvas_div.addEventListener(\n        'keyup',\n        on_keyboard_event_closure('key_release')\n    );\n\n    this._canvas_extra_style(canvas_div);\n    this.root.appendChild(canvas_div);\n\n    var canvas = (this.canvas = document.createElement('canvas'));\n    canvas.classList.add('mpl-canvas');\n    canvas.setAttribute('style', 'box-sizing: content-box;');\n\n    this.context = canvas.getContext('2d');\n\n    var backingStore =\n        this.context.backingStorePixelRatio ||\n        this.context.webkitBackingStorePixelRatio ||\n        this.context.mozBackingStorePixelRatio ||\n        this.context.msBackingStorePixelRatio ||\n        this.context.oBackingStorePixelRatio ||\n        this.context.backingStorePixelRatio ||\n        1;\n\n    this.ratio = (window.devicePixelRatio || 1) / backingStore;\n\n    var rubberband_canvas = (this.rubberband_canvas = document.createElement(\n        'canvas'\n    ));\n    rubberband_canvas.setAttribute(\n        'style',\n        'box-sizing: content-box; position: absolute; left: 0; top: 0; z-index: 1;'\n    );\n\n    // Apply a ponyfill if ResizeObserver is not implemented by browser.\n    if (this.ResizeObserver === undefined) {\n        if (window.ResizeObserver !== undefined) {\n            this.ResizeObserver = window.ResizeObserver;\n        } else {\n            var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n            this.ResizeObserver = obs.ResizeObserver;\n        }\n    }\n\n    this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n        var nentries = entries.length;\n        for (var i = 0; i < nentries; i++) {\n            var entry = entries[i];\n            var width, height;\n            if (entry.contentBoxSize) {\n                if (entry.contentBoxSize instanceof Array) {\n                    // Chrome 84 implements new version of spec.\n                    width = entry.contentBoxSize[0].inlineSize;\n                    height = entry.contentBoxSize[0].blockSize;\n                } else {\n                    // Firefox implements old version of spec.\n                    width = entry.contentBoxSize.inlineSize;\n                    height = entry.contentBoxSize.blockSize;\n                }\n            } else {\n                // Chrome <84 implements even older version of spec.\n                width = entry.contentRect.width;\n                height = entry.contentRect.height;\n            }\n\n            // Keep the size of the canvas and rubber band canvas in sync with\n            // the canvas container.\n            if (entry.devicePixelContentBoxSize) {\n                // Chrome 84 implements new version of spec.\n                canvas.setAttribute(\n                    'width',\n                    entry.devicePixelContentBoxSize[0].inlineSize\n                );\n                canvas.setAttribute(\n                    'height',\n                    entry.devicePixelContentBoxSize[0].blockSize\n                );\n            } else {\n                canvas.setAttribute('width', width * fig.ratio);\n                canvas.setAttribute('height', height * fig.ratio);\n            }\n            canvas.setAttribute(\n                'style',\n                'width: ' + width + 'px; height: ' + height + 'px;'\n            );\n\n            rubberband_canvas.setAttribute('width', width);\n            rubberband_canvas.setAttribute('height', height);\n\n            // And update the size in Python. We ignore the initial 0/0 size\n            // that occurs as the element is placed into the DOM, which should\n            // otherwise not happen due to the minimum size styling.\n            if (fig.ws.readyState == 1 && width != 0 && height != 0) {\n                fig.request_resize(width, height);\n            }\n        }\n    });\n    this.resizeObserverInstance.observe(canvas_div);\n\n    function on_mouse_event_closure(name) {\n        return function (event) {\n            return fig.mouse_event(event, name);\n        };\n    }\n\n    rubberband_canvas.addEventListener(\n        'mousedown',\n        on_mouse_event_closure('button_press')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseup',\n        on_mouse_event_closure('button_release')\n    );\n    rubberband_canvas.addEventListener(\n        'dblclick',\n        on_mouse_event_closure('dblclick')\n    );\n    // Throttle sequential mouse events to 1 every 20ms.\n    rubberband_canvas.addEventListener(\n        'mousemove',\n        on_mouse_event_closure('motion_notify')\n    );\n\n    rubberband_canvas.addEventListener(\n        'mouseenter',\n        on_mouse_event_closure('figure_enter')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseleave',\n        on_mouse_event_closure('figure_leave')\n    );\n\n    canvas_div.addEventListener('wheel', function (event) {\n        if (event.deltaY < 0) {\n            event.step = 1;\n        } else {\n            event.step = -1;\n        }\n        on_mouse_event_closure('scroll')(event);\n    });\n\n    canvas_div.appendChild(canvas);\n    canvas_div.appendChild(rubberband_canvas);\n\n    this.rubberband_context = rubberband_canvas.getContext('2d');\n    this.rubberband_context.strokeStyle = '#000000';\n\n    this._resize_canvas = function (width, height, forward) {\n        if (forward) {\n            canvas_div.style.width = width + 'px';\n            canvas_div.style.height = height + 'px';\n        }\n    };\n\n    // Disable right mouse context menu.\n    this.rubberband_canvas.addEventListener('contextmenu', function (_e) {\n        event.preventDefault();\n        return false;\n    });\n\n    function set_focus() {\n        canvas.focus();\n        canvas_div.focus();\n    }\n\n    window.setTimeout(set_focus, 100);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'mpl-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'mpl-button-group';\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'mpl-button-group';\n            continue;\n        }\n\n        var button = (fig.buttons[name] = document.createElement('button'));\n        button.classList = 'mpl-widget';\n        button.setAttribute('role', 'button');\n        button.setAttribute('aria-disabled', 'false');\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n\n        var icon_img = document.createElement('img');\n        icon_img.src = '_images/' + image + '.png';\n        icon_img.srcset = '_images/' + image + '_large.png 2x';\n        icon_img.alt = tooltip;\n        button.appendChild(icon_img);\n\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    var fmt_picker = document.createElement('select');\n    fmt_picker.classList = 'mpl-widget';\n    toolbar.appendChild(fmt_picker);\n    this.format_dropdown = fmt_picker;\n\n    for (var ind in mpl.extensions) {\n        var fmt = mpl.extensions[ind];\n        var option = document.createElement('option');\n        option.selected = fmt === mpl.default_extension;\n        option.innerHTML = fmt;\n        fmt_picker.appendChild(option);\n    }\n\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n};\n\nmpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n    // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n    // which will in turn request a refresh of the image.\n    this.send_message('resize', { width: x_pixels, height: y_pixels });\n};\n\nmpl.figure.prototype.send_message = function (type, properties) {\n    properties['type'] = type;\n    properties['figure_id'] = this.id;\n    this.ws.send(JSON.stringify(properties));\n};\n\nmpl.figure.prototype.send_draw_message = function () {\n    if (!this.waiting) {\n        this.waiting = true;\n        this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    var format_dropdown = fig.format_dropdown;\n    var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n    fig.ondownload(fig, format);\n};\n\nmpl.figure.prototype.handle_resize = function (fig, msg) {\n    var size = msg['size'];\n    if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n        fig._resize_canvas(size[0], size[1], msg['forward']);\n        fig.send_message('refresh', {});\n    }\n};\n\nmpl.figure.prototype.handle_rubberband = function (fig, msg) {\n    var x0 = msg['x0'] / fig.ratio;\n    var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n    var x1 = msg['x1'] / fig.ratio;\n    var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n    x0 = Math.floor(x0) + 0.5;\n    y0 = Math.floor(y0) + 0.5;\n    x1 = Math.floor(x1) + 0.5;\n    y1 = Math.floor(y1) + 0.5;\n    var min_x = Math.min(x0, x1);\n    var min_y = Math.min(y0, y1);\n    var width = Math.abs(x1 - x0);\n    var height = Math.abs(y1 - y0);\n\n    fig.rubberband_context.clearRect(\n        0,\n        0,\n        fig.canvas.width / fig.ratio,\n        fig.canvas.height / fig.ratio\n    );\n\n    fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n};\n\nmpl.figure.prototype.handle_figure_label = function (fig, msg) {\n    // Updates the figure title.\n    fig.header.textContent = msg['label'];\n};\n\nmpl.figure.prototype.handle_cursor = function (fig, msg) {\n    fig.rubberband_canvas.style.cursor = msg['cursor'];\n};\n\nmpl.figure.prototype.handle_message = function (fig, msg) {\n    fig.message.textContent = msg['message'];\n};\n\nmpl.figure.prototype.handle_draw = function (fig, _msg) {\n    // Request the server to send over a new figure.\n    fig.send_draw_message();\n};\n\nmpl.figure.prototype.handle_image_mode = function (fig, msg) {\n    fig.image_mode = msg['mode'];\n};\n\nmpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n    for (var key in msg) {\n        if (!(key in fig.buttons)) {\n            continue;\n        }\n        fig.buttons[key].disabled = !msg[key];\n        fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n    }\n};\n\nmpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n    if (msg['mode'] === 'PAN') {\n        fig.buttons['Pan'].classList.add('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    } else if (msg['mode'] === 'ZOOM') {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.add('active');\n    } else {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    }\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Called whenever the canvas gets updated.\n    this.send_message('ack', {});\n};\n\n// A function to construct a web socket function for onmessage handling.\n// Called in the figure constructor.\nmpl.figure.prototype._make_on_message_function = function (fig) {\n    return function socket_on_message(evt) {\n        if (evt.data instanceof Blob) {\n            var img = evt.data;\n            if (img.type !== 'image/png') {\n                /* FIXME: We get \"Resource interpreted as Image but\n                 * transferred with MIME type text/plain:\" errors on\n                 * Chrome.  But how to set the MIME type?  It doesn't seem\n                 * to be part of the websocket stream */\n                img.type = 'image/png';\n            }\n\n            /* Free the memory for the previous frames */\n            if (fig.imageObj.src) {\n                (window.URL || window.webkitURL).revokeObjectURL(\n                    fig.imageObj.src\n                );\n            }\n\n            fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n                img\n            );\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        } else if (\n            typeof evt.data === 'string' &&\n            evt.data.slice(0, 21) === 'data:image/png;base64'\n        ) {\n            fig.imageObj.src = evt.data;\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        }\n\n        var msg = JSON.parse(evt.data);\n        var msg_type = msg['type'];\n\n        // Call the  \"handle_{type}\" callback, which takes\n        // the figure and JSON message as its only arguments.\n        try {\n            var callback = fig['handle_' + msg_type];\n        } catch (e) {\n            console.log(\n                \"No handler for the '\" + msg_type + \"' message type: \",\n                msg\n            );\n            return;\n        }\n\n        if (callback) {\n            try {\n                // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n                callback(fig, msg);\n            } catch (e) {\n                console.log(\n                    \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n                    e,\n                    e.stack,\n                    msg\n                );\n            }\n        }\n    };\n};\n\n// from https://stackoverflow.com/questions/1114465/getting-mouse-location-in-canvas\nmpl.findpos = function (e) {\n    //this section is from http://www.quirksmode.org/js/events_properties.html\n    var targ;\n    if (!e) {\n        e = window.event;\n    }\n    if (e.target) {\n        targ = e.target;\n    } else if (e.srcElement) {\n        targ = e.srcElement;\n    }\n    if (targ.nodeType === 3) {\n        // defeat Safari bug\n        targ = targ.parentNode;\n    }\n\n    // pageX,Y are the mouse positions relative to the document\n    var boundingRect = targ.getBoundingClientRect();\n    var x = e.pageX - (boundingRect.left + document.body.scrollLeft);\n    var y = e.pageY - (boundingRect.top + document.body.scrollTop);\n\n    return { x: x, y: y };\n};\n\n/*\n * return a copy of an object with only non-object keys\n * we need this to avoid circular references\n * https://stackoverflow.com/a/24161582/3208463\n */\nfunction simpleKeys(original) {\n    return Object.keys(original).reduce(function (obj, key) {\n        if (typeof original[key] !== 'object') {\n            obj[key] = original[key];\n        }\n        return obj;\n    }, {});\n}\n\nmpl.figure.prototype.mouse_event = function (event, name) {\n    var canvas_pos = mpl.findpos(event);\n\n    if (name === 'button_press') {\n        this.canvas.focus();\n        this.canvas_div.focus();\n    }\n\n    var x = canvas_pos.x * this.ratio;\n    var y = canvas_pos.y * this.ratio;\n\n    this.send_message(name, {\n        x: x,\n        y: y,\n        button: event.button,\n        step: event.step,\n        guiEvent: simpleKeys(event),\n    });\n\n    /* This prevents the web browser from automatically changing to\n     * the text insertion cursor when the button is pressed.  We want\n     * to control all of the cursor setting manually through the\n     * 'cursor' event from matplotlib */\n    event.preventDefault();\n    return false;\n};\n\nmpl.figure.prototype._key_event_extra = function (_event, _name) {\n    // Handle any extra behaviour associated with a key event\n};\n\nmpl.figure.prototype.key_event = function (event, name) {\n    // Prevent repeat events\n    if (name === 'key_press') {\n        if (event.key === this._key) {\n            return;\n        } else {\n            this._key = event.key;\n        }\n    }\n    if (name === 'key_release') {\n        this._key = null;\n    }\n\n    var value = '';\n    if (event.ctrlKey && event.key !== 'Control') {\n        value += 'ctrl+';\n    }\n    else if (event.altKey && event.key !== 'Alt') {\n        value += 'alt+';\n    }\n    else if (event.shiftKey && event.key !== 'Shift') {\n        value += 'shift+';\n    }\n\n    value += 'k' + event.key;\n\n    this._key_event_extra(event, name);\n\n    this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n    return false;\n};\n\nmpl.figure.prototype.toolbar_button_onclick = function (name) {\n    if (name === 'download') {\n        this.handle_save(this, null);\n    } else {\n        this.send_message('toolbar_button', { name: name });\n    }\n};\n\nmpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n    this.message.textContent = tooltip;\n};\n\n///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n// prettier-ignore\nvar _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\nmpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home icon-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left icon-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right icon-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows icon-move\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis\", \"fa fa-square-o icon-check-empty\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o icon-save\", \"download\"]];\n\nmpl.extensions = [\"eps\", \"jpeg\", \"pgf\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\"];\n\nmpl.default_extension = \"png\";/* global mpl */\n\nvar comm_websocket_adapter = function (comm) {\n    // Create a \"websocket\"-like object which calls the given IPython comm\n    // object with the appropriate methods. Currently this is a non binary\n    // socket, so there is still some room for performance tuning.\n    var ws = {};\n\n    ws.binaryType = comm.kernel.ws.binaryType;\n    ws.readyState = comm.kernel.ws.readyState;\n    function updateReadyState(_event) {\n        if (comm.kernel.ws) {\n            ws.readyState = comm.kernel.ws.readyState;\n        } else {\n            ws.readyState = 3; // Closed state.\n        }\n    }\n    comm.kernel.ws.addEventListener('open', updateReadyState);\n    comm.kernel.ws.addEventListener('close', updateReadyState);\n    comm.kernel.ws.addEventListener('error', updateReadyState);\n\n    ws.close = function () {\n        comm.close();\n    };\n    ws.send = function (m) {\n        //console.log('sending', m);\n        comm.send(m);\n    };\n    // Register the callback with on_msg.\n    comm.on_msg(function (msg) {\n        //console.log('receiving', msg['content']['data'], msg);\n        var data = msg['content']['data'];\n        if (data['blob'] !== undefined) {\n            data = {\n                data: new Blob(msg['buffers'], { type: data['blob'] }),\n            };\n        }\n        // Pass the mpl event to the overridden (by mpl) onmessage function.\n        ws.onmessage(data);\n    });\n    return ws;\n};\n\nmpl.mpl_figure_comm = function (comm, msg) {\n    // This is the function which gets called when the mpl process\n    // starts-up an IPython Comm through the \"matplotlib\" channel.\n\n    var id = msg.content.data.id;\n    // Get hold of the div created by the display call when the Comm\n    // socket was opened in Python.\n    var element = document.getElementById(id);\n    var ws_proxy = comm_websocket_adapter(comm);\n\n    function ondownload(figure, _format) {\n        window.open(figure.canvas.toDataURL());\n    }\n\n    var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n\n    // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n    // web socket which is closed, not our websocket->open comm proxy.\n    ws_proxy.onopen();\n\n    fig.parent_element = element;\n    fig.cell_info = mpl.find_output_cell(\"<div id='\" + id + \"'></div>\");\n    if (!fig.cell_info) {\n        console.error('Failed to find cell for figure', id, fig);\n        return;\n    }\n    fig.cell_info[0].output_area.element.on(\n        'cleared',\n        { fig: fig },\n        fig._remove_fig_handler\n    );\n};\n\nmpl.figure.prototype.handle_close = function (fig, msg) {\n    var width = fig.canvas.width / fig.ratio;\n    fig.cell_info[0].output_area.element.off(\n        'cleared',\n        fig._remove_fig_handler\n    );\n    fig.resizeObserverInstance.unobserve(fig.canvas_div);\n\n    // Update the output cell to use the data from the current canvas.\n    fig.push_to_output();\n    var dataURL = fig.canvas.toDataURL();\n    // Re-enable the keyboard manager in IPython - without this line, in FF,\n    // the notebook keyboard shortcuts fail.\n    IPython.keyboard_manager.enable();\n    fig.parent_element.innerHTML =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n    fig.close_ws(fig, msg);\n};\n\nmpl.figure.prototype.close_ws = function (fig, msg) {\n    fig.send_message('closing', msg);\n    // fig.ws.close()\n};\n\nmpl.figure.prototype.push_to_output = function (_remove_interactive) {\n    // Turn the data on the canvas into data in the output cell.\n    var width = this.canvas.width / this.ratio;\n    var dataURL = this.canvas.toDataURL();\n    this.cell_info[1]['text/html'] =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Tell IPython that the notebook contents must change.\n    IPython.notebook.set_dirty(true);\n    this.send_message('ack', {});\n    var fig = this;\n    // Wait a second, then push the new image to the DOM so\n    // that it is saved nicely (might be nice to debounce this).\n    setTimeout(function () {\n        fig.push_to_output();\n    }, 1000);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'btn-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'btn-group';\n    var button;\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'btn-group';\n            continue;\n        }\n\n        button = fig.buttons[name] = document.createElement('button');\n        button.classList = 'btn btn-default';\n        button.href = '#';\n        button.title = name;\n        button.innerHTML = '<i class=\"fa ' + image + ' fa-lg\"></i>';\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    // Add the status bar.\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message pull-right';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n\n    // Add the close button to the window.\n    var buttongrp = document.createElement('div');\n    buttongrp.classList = 'btn-group inline pull-right';\n    button = document.createElement('button');\n    button.classList = 'btn btn-mini btn-primary';\n    button.href = '#';\n    button.title = 'Stop Interaction';\n    button.innerHTML = '<i class=\"fa fa-power-off icon-remove icon-large\"></i>';\n    button.addEventListener('click', function (_evt) {\n        fig.handle_close(fig, {});\n    });\n    button.addEventListener(\n        'mouseover',\n        on_mouseover_closure('Stop Interaction')\n    );\n    buttongrp.appendChild(button);\n    var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n    titlebar.insertBefore(buttongrp, titlebar.firstChild);\n};\n\nmpl.figure.prototype._remove_fig_handler = function (event) {\n    var fig = event.data.fig;\n    if (event.target !== this) {\n        // Ignore bubbled events from children.\n        return;\n    }\n    fig.close_ws(fig, {});\n};\n\nmpl.figure.prototype._root_extra_style = function (el) {\n    el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n};\n\nmpl.figure.prototype._canvas_extra_style = function (el) {\n    // this is important to make the div 'focusable\n    el.setAttribute('tabindex', 0);\n    // reach out to IPython and tell the keyboard manager to turn it's self\n    // off when our div gets focus\n\n    // location in version 3\n    if (IPython.notebook.keyboard_manager) {\n        IPython.notebook.keyboard_manager.register_events(el);\n    } else {\n        // location in version 2\n        IPython.keyboard_manager.register_events(el);\n    }\n};\n\nmpl.figure.prototype._key_event_extra = function (event, _name) {\n    // Check for shift+enter\n    if (event.shiftKey && event.which === 13) {\n        this.canvas_div.blur();\n        // select the cell after this one\n        var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n        IPython.notebook.select(index + 1);\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    fig.ondownload(fig, null);\n};\n\nmpl.find_output_cell = function (html_output) {\n    // Return the cell and output element which can be found *uniquely* in the notebook.\n    // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n    // IPython event is triggered only after the cells have been serialised, which for\n    // our purposes (turning an active figure into a static one), is too late.\n    var cells = IPython.notebook.get_cells();\n    var ncells = cells.length;\n    for (var i = 0; i < ncells; i++) {\n        var cell = cells[i];\n        if (cell.cell_type === 'code') {\n            for (var j = 0; j < cell.output_area.outputs.length; j++) {\n                var data = cell.output_area.outputs[j];\n                if (data.data) {\n                    // IPython >= 3 moved mimebundle to data attribute of output\n                    data = data.data;\n                }\n                if (data['text/html'] === html_output) {\n                    return [cell, data, j];\n                }\n            }\n        }\n    }\n};\n\n// Register the function which deals with the matplotlib target/channel.\n// The kernel may be null if the page has been refreshed.\nif (IPython.notebook.kernel !== null) {\n    IPython.notebook.kernel.comm_manager.register_target(\n        'matplotlib',\n        mpl.mpl_figure_comm\n    );\n}\n",
      "text/plain": [
       "<IPython.core.display.Javascript object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<img src=\"data:image/png;base64,[encoded data, 76092 characters]\" width=\"640\">"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "f = 286.0152 ± 2.5433 Hz\n"
     ]
    }
   ],
   "source": [
    "def damp_osci(t, t0, A, B, nu, gamma):\n",
    "    return A * np.exp(-gamma*t)*np.sin(2*np.pi*nu*(t-t0)) + B\n",
    "\n",
    "yvals     = val_mean#.sel(blink_on_time=slice(0.005, 0.025))\n",
    "yvals_std = std_mean#.sel(blink_on_time=slice(0.005, 0.025))\n",
    "xvals     = dataSet_cropOD[scanAxis[0]]#.sel(blink_on_time=slice(0.005, 0.025))\n",
    "\n",
    "fitted_qtys_1 = yvals.to_numpy()\n",
    "fitted_qtys_err_1 = yvals_std.to_numpy()\n",
    "scan_para = xvals.to_numpy()\n",
    "\n",
    "plt.figure()\n",
    "popt_x, pcov_x = curve_fit(damp_osci, scan_para, fitted_qtys_1, np.array([0, 3, 145, 1e2, 0.1]))\n",
    "freqdata = np.linspace(0.005,19e-3, 500)\n",
    "plt.plot(freqdata, damp_osci(freqdata, *popt_x), 'g--',label='fit: t0=%5.3f, A=%5.3f, B=%5.3f, nu=%5.3f, Gamma=%5.3f' % tuple(popt_x))\n",
    "plt.errorbar(scan_para, fitted_qtys_1, yerr=fitted_qtys_err_1, fmt='or')\n",
    "plt.xlabel('hold time after switch on the trap (s)')\n",
    "plt.ylabel('Center along gravity direction (pixels)')\n",
    "plt.tight_layout()\n",
    "plt.grid(visible=1)\n",
    "#plt.ylim([0,750])\n",
    "#plt.xlim([0.004, 0.025])\n",
    "#plt.legend(prop={'size': 14})\n",
    "plt.show()\n",
    "\n",
    "f_x = popt_x[3]\n",
    "df_x = pcov_x[3][3]**0.5\n",
    "\n",
    "print('f = %.4f \\u00B1 %.4f Hz'% tuple([np.abs(f_x),df_x]))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Truncation: 0.6"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 69,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The detected scaning axes and values are: \n",
      "\n",
      "{'mod_blink_on_time': array([0.005 , 0.0057, 0.0064, 0.0071, 0.0078, 0.0085, 0.0092, 0.0099,\n",
      "       0.0106, 0.0113, 0.012 , 0.0127, 0.0134, 0.0141, 0.0148, 0.0155,\n",
      "       0.0162, 0.0169, 0.0176, 0.0183, 0.019 , 0.0197]), 'runs': array([0., 1., 2., 3.])}\n"
     ]
    },
    {
     "data": {
      "application/javascript": "/* Put everything inside the global mpl namespace */\n/* global mpl */\nwindow.mpl = {};\n\nmpl.get_websocket_type = function () {\n    if (typeof WebSocket !== 'undefined') {\n        return WebSocket;\n    } else if (typeof MozWebSocket !== 'undefined') {\n        return MozWebSocket;\n    } else {\n        alert(\n            'Your browser does not have WebSocket support. ' +\n                'Please try Chrome, Safari or Firefox ≥ 6. ' +\n                'Firefox 4 and 5 are also supported but you ' +\n                'have to enable WebSockets in about:config.'\n        );\n    }\n};\n\nmpl.figure = function (figure_id, websocket, ondownload, parent_element) {\n    this.id = figure_id;\n\n    this.ws = websocket;\n\n    this.supports_binary = this.ws.binaryType !== undefined;\n\n    if (!this.supports_binary) {\n        var warnings = document.getElementById('mpl-warnings');\n        if (warnings) {\n            warnings.style.display = 'block';\n            warnings.textContent =\n                'This browser does not support binary websocket messages. ' +\n                'Performance may be slow.';\n        }\n    }\n\n    this.imageObj = new Image();\n\n    this.context = undefined;\n    this.message = undefined;\n    this.canvas = undefined;\n    this.rubberband_canvas = undefined;\n    this.rubberband_context = undefined;\n    this.format_dropdown = undefined;\n\n    this.image_mode = 'full';\n\n    this.root = document.createElement('div');\n    this.root.setAttribute('style', 'display: inline-block');\n    this._root_extra_style(this.root);\n\n    parent_element.appendChild(this.root);\n\n    this._init_header(this);\n    this._init_canvas(this);\n    this._init_toolbar(this);\n\n    var fig = this;\n\n    this.waiting = false;\n\n    this.ws.onopen = function () {\n        fig.send_message('supports_binary', { value: fig.supports_binary });\n        fig.send_message('send_image_mode', {});\n        if (fig.ratio !== 1) {\n            fig.send_message('set_device_pixel_ratio', {\n                device_pixel_ratio: fig.ratio,\n            });\n        }\n        fig.send_message('refresh', {});\n    };\n\n    this.imageObj.onload = function () {\n        if (fig.image_mode === 'full') {\n            // Full images could contain transparency (where diff images\n            // almost always do), so we need to clear the canvas so that\n            // there is no ghosting.\n            fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n        }\n        fig.context.drawImage(fig.imageObj, 0, 0);\n    };\n\n    this.imageObj.onunload = function () {\n        fig.ws.close();\n    };\n\n    this.ws.onmessage = this._make_on_message_function(this);\n\n    this.ondownload = ondownload;\n};\n\nmpl.figure.prototype._init_header = function () {\n    var titlebar = document.createElement('div');\n    titlebar.classList =\n        'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n    var titletext = document.createElement('div');\n    titletext.classList = 'ui-dialog-title';\n    titletext.setAttribute(\n        'style',\n        'width: 100%; text-align: center; padding: 3px;'\n    );\n    titlebar.appendChild(titletext);\n    this.root.appendChild(titlebar);\n    this.header = titletext;\n};\n\nmpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._init_canvas = function () {\n    var fig = this;\n\n    var canvas_div = (this.canvas_div = document.createElement('div'));\n    canvas_div.setAttribute(\n        'style',\n        'border: 1px solid #ddd;' +\n            'box-sizing: content-box;' +\n            'clear: both;' +\n            'min-height: 1px;' +\n            'min-width: 1px;' +\n            'outline: 0;' +\n            'overflow: hidden;' +\n            'position: relative;' +\n            'resize: both;'\n    );\n\n    function on_keyboard_event_closure(name) {\n        return function (event) {\n            return fig.key_event(event, name);\n        };\n    }\n\n    canvas_div.addEventListener(\n        'keydown',\n        on_keyboard_event_closure('key_press')\n    );\n    canvas_div.addEventListener(\n        'keyup',\n        on_keyboard_event_closure('key_release')\n    );\n\n    this._canvas_extra_style(canvas_div);\n    this.root.appendChild(canvas_div);\n\n    var canvas = (this.canvas = document.createElement('canvas'));\n    canvas.classList.add('mpl-canvas');\n    canvas.setAttribute('style', 'box-sizing: content-box;');\n\n    this.context = canvas.getContext('2d');\n\n    var backingStore =\n        this.context.backingStorePixelRatio ||\n        this.context.webkitBackingStorePixelRatio ||\n        this.context.mozBackingStorePixelRatio ||\n        this.context.msBackingStorePixelRatio ||\n        this.context.oBackingStorePixelRatio ||\n        this.context.backingStorePixelRatio ||\n        1;\n\n    this.ratio = (window.devicePixelRatio || 1) / backingStore;\n\n    var rubberband_canvas = (this.rubberband_canvas = document.createElement(\n        'canvas'\n    ));\n    rubberband_canvas.setAttribute(\n        'style',\n        'box-sizing: content-box; position: absolute; left: 0; top: 0; z-index: 1;'\n    );\n\n    // Apply a ponyfill if ResizeObserver is not implemented by browser.\n    if (this.ResizeObserver === undefined) {\n        if (window.ResizeObserver !== undefined) {\n            this.ResizeObserver = window.ResizeObserver;\n        } else {\n            var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n            this.ResizeObserver = obs.ResizeObserver;\n        }\n    }\n\n    this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n        var nentries = entries.length;\n        for (var i = 0; i < nentries; i++) {\n            var entry = entries[i];\n            var width, height;\n            if (entry.contentBoxSize) {\n                if (entry.contentBoxSize instanceof Array) {\n                    // Chrome 84 implements new version of spec.\n                    width = entry.contentBoxSize[0].inlineSize;\n                    height = entry.contentBoxSize[0].blockSize;\n                } else {\n                    // Firefox implements old version of spec.\n                    width = entry.contentBoxSize.inlineSize;\n                    height = entry.contentBoxSize.blockSize;\n                }\n            } else {\n                // Chrome <84 implements even older version of spec.\n                width = entry.contentRect.width;\n                height = entry.contentRect.height;\n            }\n\n            // Keep the size of the canvas and rubber band canvas in sync with\n            // the canvas container.\n            if (entry.devicePixelContentBoxSize) {\n                // Chrome 84 implements new version of spec.\n                canvas.setAttribute(\n                    'width',\n                    entry.devicePixelContentBoxSize[0].inlineSize\n                );\n                canvas.setAttribute(\n                    'height',\n                    entry.devicePixelContentBoxSize[0].blockSize\n                );\n            } else {\n                canvas.setAttribute('width', width * fig.ratio);\n                canvas.setAttribute('height', height * fig.ratio);\n            }\n            canvas.setAttribute(\n                'style',\n                'width: ' + width + 'px; height: ' + height + 'px;'\n            );\n\n            rubberband_canvas.setAttribute('width', width);\n            rubberband_canvas.setAttribute('height', height);\n\n            // And update the size in Python. We ignore the initial 0/0 size\n            // that occurs as the element is placed into the DOM, which should\n            // otherwise not happen due to the minimum size styling.\n            if (fig.ws.readyState == 1 && width != 0 && height != 0) {\n                fig.request_resize(width, height);\n            }\n        }\n    });\n    this.resizeObserverInstance.observe(canvas_div);\n\n    function on_mouse_event_closure(name) {\n        return function (event) {\n            return fig.mouse_event(event, name);\n        };\n    }\n\n    rubberband_canvas.addEventListener(\n        'mousedown',\n        on_mouse_event_closure('button_press')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseup',\n        on_mouse_event_closure('button_release')\n    );\n    rubberband_canvas.addEventListener(\n        'dblclick',\n        on_mouse_event_closure('dblclick')\n    );\n    // Throttle sequential mouse events to 1 every 20ms.\n    rubberband_canvas.addEventListener(\n        'mousemove',\n        on_mouse_event_closure('motion_notify')\n    );\n\n    rubberband_canvas.addEventListener(\n        'mouseenter',\n        on_mouse_event_closure('figure_enter')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseleave',\n        on_mouse_event_closure('figure_leave')\n    );\n\n    canvas_div.addEventListener('wheel', function (event) {\n        if (event.deltaY < 0) {\n            event.step = 1;\n        } else {\n            event.step = -1;\n        }\n        on_mouse_event_closure('scroll')(event);\n    });\n\n    canvas_div.appendChild(canvas);\n    canvas_div.appendChild(rubberband_canvas);\n\n    this.rubberband_context = rubberband_canvas.getContext('2d');\n    this.rubberband_context.strokeStyle = '#000000';\n\n    this._resize_canvas = function (width, height, forward) {\n        if (forward) {\n            canvas_div.style.width = width + 'px';\n            canvas_div.style.height = height + 'px';\n        }\n    };\n\n    // Disable right mouse context menu.\n    this.rubberband_canvas.addEventListener('contextmenu', function (_e) {\n        event.preventDefault();\n        return false;\n    });\n\n    function set_focus() {\n        canvas.focus();\n        canvas_div.focus();\n    }\n\n    window.setTimeout(set_focus, 100);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'mpl-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'mpl-button-group';\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'mpl-button-group';\n            continue;\n        }\n\n        var button = (fig.buttons[name] = document.createElement('button'));\n        button.classList = 'mpl-widget';\n        button.setAttribute('role', 'button');\n        button.setAttribute('aria-disabled', 'false');\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n\n        var icon_img = document.createElement('img');\n        icon_img.src = '_images/' + image + '.png';\n        icon_img.srcset = '_images/' + image + '_large.png 2x';\n        icon_img.alt = tooltip;\n        button.appendChild(icon_img);\n\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    var fmt_picker = document.createElement('select');\n    fmt_picker.classList = 'mpl-widget';\n    toolbar.appendChild(fmt_picker);\n    this.format_dropdown = fmt_picker;\n\n    for (var ind in mpl.extensions) {\n        var fmt = mpl.extensions[ind];\n        var option = document.createElement('option');\n        option.selected = fmt === mpl.default_extension;\n        option.innerHTML = fmt;\n        fmt_picker.appendChild(option);\n    }\n\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n};\n\nmpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n    // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n    // which will in turn request a refresh of the image.\n    this.send_message('resize', { width: x_pixels, height: y_pixels });\n};\n\nmpl.figure.prototype.send_message = function (type, properties) {\n    properties['type'] = type;\n    properties['figure_id'] = this.id;\n    this.ws.send(JSON.stringify(properties));\n};\n\nmpl.figure.prototype.send_draw_message = function () {\n    if (!this.waiting) {\n        this.waiting = true;\n        this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    var format_dropdown = fig.format_dropdown;\n    var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n    fig.ondownload(fig, format);\n};\n\nmpl.figure.prototype.handle_resize = function (fig, msg) {\n    var size = msg['size'];\n    if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n        fig._resize_canvas(size[0], size[1], msg['forward']);\n        fig.send_message('refresh', {});\n    }\n};\n\nmpl.figure.prototype.handle_rubberband = function (fig, msg) {\n    var x0 = msg['x0'] / fig.ratio;\n    var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n    var x1 = msg['x1'] / fig.ratio;\n    var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n    x0 = Math.floor(x0) + 0.5;\n    y0 = Math.floor(y0) + 0.5;\n    x1 = Math.floor(x1) + 0.5;\n    y1 = Math.floor(y1) + 0.5;\n    var min_x = Math.min(x0, x1);\n    var min_y = Math.min(y0, y1);\n    var width = Math.abs(x1 - x0);\n    var height = Math.abs(y1 - y0);\n\n    fig.rubberband_context.clearRect(\n        0,\n        0,\n        fig.canvas.width / fig.ratio,\n        fig.canvas.height / fig.ratio\n    );\n\n    fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n};\n\nmpl.figure.prototype.handle_figure_label = function (fig, msg) {\n    // Updates the figure title.\n    fig.header.textContent = msg['label'];\n};\n\nmpl.figure.prototype.handle_cursor = function (fig, msg) {\n    fig.rubberband_canvas.style.cursor = msg['cursor'];\n};\n\nmpl.figure.prototype.handle_message = function (fig, msg) {\n    fig.message.textContent = msg['message'];\n};\n\nmpl.figure.prototype.handle_draw = function (fig, _msg) {\n    // Request the server to send over a new figure.\n    fig.send_draw_message();\n};\n\nmpl.figure.prototype.handle_image_mode = function (fig, msg) {\n    fig.image_mode = msg['mode'];\n};\n\nmpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n    for (var key in msg) {\n        if (!(key in fig.buttons)) {\n            continue;\n        }\n        fig.buttons[key].disabled = !msg[key];\n        fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n    }\n};\n\nmpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n    if (msg['mode'] === 'PAN') {\n        fig.buttons['Pan'].classList.add('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    } else if (msg['mode'] === 'ZOOM') {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.add('active');\n    } else {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    }\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Called whenever the canvas gets updated.\n    this.send_message('ack', {});\n};\n\n// A function to construct a web socket function for onmessage handling.\n// Called in the figure constructor.\nmpl.figure.prototype._make_on_message_function = function (fig) {\n    return function socket_on_message(evt) {\n        if (evt.data instanceof Blob) {\n            var img = evt.data;\n            if (img.type !== 'image/png') {\n                /* FIXME: We get \"Resource interpreted as Image but\n                 * transferred with MIME type text/plain:\" errors on\n                 * Chrome.  But how to set the MIME type?  It doesn't seem\n                 * to be part of the websocket stream */\n                img.type = 'image/png';\n            }\n\n            /* Free the memory for the previous frames */\n            if (fig.imageObj.src) {\n                (window.URL || window.webkitURL).revokeObjectURL(\n                    fig.imageObj.src\n                );\n            }\n\n            fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n                img\n            );\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        } else if (\n            typeof evt.data === 'string' &&\n            evt.data.slice(0, 21) === 'data:image/png;base64'\n        ) {\n            fig.imageObj.src = evt.data;\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        }\n\n        var msg = JSON.parse(evt.data);\n        var msg_type = msg['type'];\n\n        // Call the  \"handle_{type}\" callback, which takes\n        // the figure and JSON message as its only arguments.\n        try {\n            var callback = fig['handle_' + msg_type];\n        } catch (e) {\n            console.log(\n                \"No handler for the '\" + msg_type + \"' message type: \",\n                msg\n            );\n            return;\n        }\n\n        if (callback) {\n            try {\n                // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n                callback(fig, msg);\n            } catch (e) {\n                console.log(\n                    \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n                    e,\n                    e.stack,\n                    msg\n                );\n            }\n        }\n    };\n};\n\n// from https://stackoverflow.com/questions/1114465/getting-mouse-location-in-canvas\nmpl.findpos = function (e) {\n    //this section is from http://www.quirksmode.org/js/events_properties.html\n    var targ;\n    if (!e) {\n        e = window.event;\n    }\n    if (e.target) {\n        targ = e.target;\n    } else if (e.srcElement) {\n        targ = e.srcElement;\n    }\n    if (targ.nodeType === 3) {\n        // defeat Safari bug\n        targ = targ.parentNode;\n    }\n\n    // pageX,Y are the mouse positions relative to the document\n    var boundingRect = targ.getBoundingClientRect();\n    var x = e.pageX - (boundingRect.left + document.body.scrollLeft);\n    var y = e.pageY - (boundingRect.top + document.body.scrollTop);\n\n    return { x: x, y: y };\n};\n\n/*\n * return a copy of an object with only non-object keys\n * we need this to avoid circular references\n * https://stackoverflow.com/a/24161582/3208463\n */\nfunction simpleKeys(original) {\n    return Object.keys(original).reduce(function (obj, key) {\n        if (typeof original[key] !== 'object') {\n            obj[key] = original[key];\n        }\n        return obj;\n    }, {});\n}\n\nmpl.figure.prototype.mouse_event = function (event, name) {\n    var canvas_pos = mpl.findpos(event);\n\n    if (name === 'button_press') {\n        this.canvas.focus();\n        this.canvas_div.focus();\n    }\n\n    var x = canvas_pos.x * this.ratio;\n    var y = canvas_pos.y * this.ratio;\n\n    this.send_message(name, {\n        x: x,\n        y: y,\n        button: event.button,\n        step: event.step,\n        guiEvent: simpleKeys(event),\n    });\n\n    /* This prevents the web browser from automatically changing to\n     * the text insertion cursor when the button is pressed.  We want\n     * to control all of the cursor setting manually through the\n     * 'cursor' event from matplotlib */\n    event.preventDefault();\n    return false;\n};\n\nmpl.figure.prototype._key_event_extra = function (_event, _name) {\n    // Handle any extra behaviour associated with a key event\n};\n\nmpl.figure.prototype.key_event = function (event, name) {\n    // Prevent repeat events\n    if (name === 'key_press') {\n        if (event.key === this._key) {\n            return;\n        } else {\n            this._key = event.key;\n        }\n    }\n    if (name === 'key_release') {\n        this._key = null;\n    }\n\n    var value = '';\n    if (event.ctrlKey && event.key !== 'Control') {\n        value += 'ctrl+';\n    }\n    else if (event.altKey && event.key !== 'Alt') {\n        value += 'alt+';\n    }\n    else if (event.shiftKey && event.key !== 'Shift') {\n        value += 'shift+';\n    }\n\n    value += 'k' + event.key;\n\n    this._key_event_extra(event, name);\n\n    this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n    return false;\n};\n\nmpl.figure.prototype.toolbar_button_onclick = function (name) {\n    if (name === 'download') {\n        this.handle_save(this, null);\n    } else {\n        this.send_message('toolbar_button', { name: name });\n    }\n};\n\nmpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n    this.message.textContent = tooltip;\n};\n\n///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n// prettier-ignore\nvar _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\nmpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home icon-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left icon-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right icon-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows icon-move\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis\", \"fa fa-square-o icon-check-empty\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o icon-save\", \"download\"]];\n\nmpl.extensions = [\"eps\", \"jpeg\", \"pgf\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\"];\n\nmpl.default_extension = \"png\";/* global mpl */\n\nvar comm_websocket_adapter = function (comm) {\n    // Create a \"websocket\"-like object which calls the given IPython comm\n    // object with the appropriate methods. Currently this is a non binary\n    // socket, so there is still some room for performance tuning.\n    var ws = {};\n\n    ws.binaryType = comm.kernel.ws.binaryType;\n    ws.readyState = comm.kernel.ws.readyState;\n    function updateReadyState(_event) {\n        if (comm.kernel.ws) {\n            ws.readyState = comm.kernel.ws.readyState;\n        } else {\n            ws.readyState = 3; // Closed state.\n        }\n    }\n    comm.kernel.ws.addEventListener('open', updateReadyState);\n    comm.kernel.ws.addEventListener('close', updateReadyState);\n    comm.kernel.ws.addEventListener('error', updateReadyState);\n\n    ws.close = function () {\n        comm.close();\n    };\n    ws.send = function (m) {\n        //console.log('sending', m);\n        comm.send(m);\n    };\n    // Register the callback with on_msg.\n    comm.on_msg(function (msg) {\n        //console.log('receiving', msg['content']['data'], msg);\n        var data = msg['content']['data'];\n        if (data['blob'] !== undefined) {\n            data = {\n                data: new Blob(msg['buffers'], { type: data['blob'] }),\n            };\n        }\n        // Pass the mpl event to the overridden (by mpl) onmessage function.\n        ws.onmessage(data);\n    });\n    return ws;\n};\n\nmpl.mpl_figure_comm = function (comm, msg) {\n    // This is the function which gets called when the mpl process\n    // starts-up an IPython Comm through the \"matplotlib\" channel.\n\n    var id = msg.content.data.id;\n    // Get hold of the div created by the display call when the Comm\n    // socket was opened in Python.\n    var element = document.getElementById(id);\n    var ws_proxy = comm_websocket_adapter(comm);\n\n    function ondownload(figure, _format) {\n        window.open(figure.canvas.toDataURL());\n    }\n\n    var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n\n    // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n    // web socket which is closed, not our websocket->open comm proxy.\n    ws_proxy.onopen();\n\n    fig.parent_element = element;\n    fig.cell_info = mpl.find_output_cell(\"<div id='\" + id + \"'></div>\");\n    if (!fig.cell_info) {\n        console.error('Failed to find cell for figure', id, fig);\n        return;\n    }\n    fig.cell_info[0].output_area.element.on(\n        'cleared',\n        { fig: fig },\n        fig._remove_fig_handler\n    );\n};\n\nmpl.figure.prototype.handle_close = function (fig, msg) {\n    var width = fig.canvas.width / fig.ratio;\n    fig.cell_info[0].output_area.element.off(\n        'cleared',\n        fig._remove_fig_handler\n    );\n    fig.resizeObserverInstance.unobserve(fig.canvas_div);\n\n    // Update the output cell to use the data from the current canvas.\n    fig.push_to_output();\n    var dataURL = fig.canvas.toDataURL();\n    // Re-enable the keyboard manager in IPython - without this line, in FF,\n    // the notebook keyboard shortcuts fail.\n    IPython.keyboard_manager.enable();\n    fig.parent_element.innerHTML =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n    fig.close_ws(fig, msg);\n};\n\nmpl.figure.prototype.close_ws = function (fig, msg) {\n    fig.send_message('closing', msg);\n    // fig.ws.close()\n};\n\nmpl.figure.prototype.push_to_output = function (_remove_interactive) {\n    // Turn the data on the canvas into data in the output cell.\n    var width = this.canvas.width / this.ratio;\n    var dataURL = this.canvas.toDataURL();\n    this.cell_info[1]['text/html'] =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Tell IPython that the notebook contents must change.\n    IPython.notebook.set_dirty(true);\n    this.send_message('ack', {});\n    var fig = this;\n    // Wait a second, then push the new image to the DOM so\n    // that it is saved nicely (might be nice to debounce this).\n    setTimeout(function () {\n        fig.push_to_output();\n    }, 1000);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'btn-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'btn-group';\n    var button;\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'btn-group';\n            continue;\n        }\n\n        button = fig.buttons[name] = document.createElement('button');\n        button.classList = 'btn btn-default';\n        button.href = '#';\n        button.title = name;\n        button.innerHTML = '<i class=\"fa ' + image + ' fa-lg\"></i>';\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    // Add the status bar.\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message pull-right';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n\n    // Add the close button to the window.\n    var buttongrp = document.createElement('div');\n    buttongrp.classList = 'btn-group inline pull-right';\n    button = document.createElement('button');\n    button.classList = 'btn btn-mini btn-primary';\n    button.href = '#';\n    button.title = 'Stop Interaction';\n    button.innerHTML = '<i class=\"fa fa-power-off icon-remove icon-large\"></i>';\n    button.addEventListener('click', function (_evt) {\n        fig.handle_close(fig, {});\n    });\n    button.addEventListener(\n        'mouseover',\n        on_mouseover_closure('Stop Interaction')\n    );\n    buttongrp.appendChild(button);\n    var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n    titlebar.insertBefore(buttongrp, titlebar.firstChild);\n};\n\nmpl.figure.prototype._remove_fig_handler = function (event) {\n    var fig = event.data.fig;\n    if (event.target !== this) {\n        // Ignore bubbled events from children.\n        return;\n    }\n    fig.close_ws(fig, {});\n};\n\nmpl.figure.prototype._root_extra_style = function (el) {\n    el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n};\n\nmpl.figure.prototype._canvas_extra_style = function (el) {\n    // this is important to make the div 'focusable\n    el.setAttribute('tabindex', 0);\n    // reach out to IPython and tell the keyboard manager to turn it's self\n    // off when our div gets focus\n\n    // location in version 3\n    if (IPython.notebook.keyboard_manager) {\n        IPython.notebook.keyboard_manager.register_events(el);\n    } else {\n        // location in version 2\n        IPython.keyboard_manager.register_events(el);\n    }\n};\n\nmpl.figure.prototype._key_event_extra = function (event, _name) {\n    // Check for shift+enter\n    if (event.shiftKey && event.which === 13) {\n        this.canvas_div.blur();\n        // select the cell after this one\n        var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n        IPython.notebook.select(index + 1);\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    fig.ondownload(fig, null);\n};\n\nmpl.find_output_cell = function (html_output) {\n    // Return the cell and output element which can be found *uniquely* in the notebook.\n    // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n    // IPython event is triggered only after the cells have been serialised, which for\n    // our purposes (turning an active figure into a static one), is too late.\n    var cells = IPython.notebook.get_cells();\n    var ncells = cells.length;\n    for (var i = 0; i < ncells; i++) {\n        var cell = cells[i];\n        if (cell.cell_type === 'code') {\n            for (var j = 0; j < cell.output_area.outputs.length; j++) {\n                var data = cell.output_area.outputs[j];\n                if (data.data) {\n                    // IPython >= 3 moved mimebundle to data attribute of output\n                    data = data.data;\n                }\n                if (data['text/html'] === html_output) {\n                    return [cell, data, j];\n                }\n            }\n        }\n    }\n};\n\n// Register the function which deals with the matplotlib target/channel.\n// The kernel may be null if the page has been refreshed.\nif (IPython.notebook.kernel !== null) {\n    IPython.notebook.kernel.comm_manager.register_target(\n        'matplotlib',\n        mpl.mpl_figure_comm\n    );\n}\n",
      "text/plain": [
       "<IPython.core.display.Javascript object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<img src=\"data:image/png;base64,[encoded data, 41516 characters]\" width=\"640\">"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "%matplotlib notebook\n",
    "shotNum = \"0008\"\n",
    "filePath = folderPath + \"/\" + shotNum + \"/*.h5\"\n",
    "\n",
    "dataSetDict = {\n",
    "    dskey[groupList[i]]: read_hdf5_file(filePath, groupList[i], excludeAxis = ['sweep_start_freq', 'sweep_stop_freq'])\n",
    "    for i in [0]\n",
    "}\n",
    "\n",
    "dataSet = dataSetDict[\"camera_0\"]\n",
    "\n",
    "print_scanAxis(dataSet)\n",
    "\n",
    "scanAxis = get_scanAxis(dataSet)\n",
    "\n",
    "dataSet = auto_rechunk(dataSet)\n",
    "\n",
    "dataSet = imageAnalyser.get_absorption_images(dataSet)\n",
    "\n",
    "imageAnalyser.center = (800, 900)\n",
    "imageAnalyser.span = (300, 300)\n",
    "imageAnalyser.fraction = (0.1, 0.1)\n",
    "\n",
    "dataSet_cropOD = imageAnalyser.crop_image(dataSet.OD)\n",
    "dataSet_cropOD = imageAnalyser.substract_offset(dataSet_cropOD).load()\n",
    "\n",
    "Ncount = imageAnalyser.get_Ncount(dataSet_cropOD)\n",
    "Ncount_mean = calculate_mean(Ncount)\n",
    "Ncount_std = calculate_std(Ncount)\n",
    "\n",
    "fig = plt.figure()\n",
    "ax = fig.gca()\n",
    "Ncount_mean.plot.errorbar(ax=ax, yerr = None, fmt='ob')\n",
    "plt.ylabel('NCount')\n",
    "plt.tight_layout()\n",
    "plt.grid(visible=1)\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 70,
   "metadata": {},
   "outputs": [],
   "source": [
    "dataSet_cropOD_chunk = dataSet_cropOD.chunk((1, 1, 300, 300))\n",
    "fitAnalyser = FitAnalyser(\"Gaussian-2D\", fitDim=2)\n",
    "params = fitAnalyser.guess(dataSet_cropOD_chunk, dask=\"parallelized\")\n",
    "fitResult = fitAnalyser.fit(dataSet_cropOD_chunk, params, dask=\"parallelized\").load()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 71,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/javascript": "/* Put everything inside the global mpl namespace */\n/* global mpl */\nwindow.mpl = {};\n\nmpl.get_websocket_type = function () {\n    if (typeof WebSocket !== 'undefined') {\n        return WebSocket;\n    } else if (typeof MozWebSocket !== 'undefined') {\n        return MozWebSocket;\n    } else {\n        alert(\n            'Your browser does not have WebSocket support. ' +\n                'Please try Chrome, Safari or Firefox ≥ 6. ' +\n                'Firefox 4 and 5 are also supported but you ' +\n                'have to enable WebSockets in about:config.'\n        );\n    }\n};\n\nmpl.figure = function (figure_id, websocket, ondownload, parent_element) {\n    this.id = figure_id;\n\n    this.ws = websocket;\n\n    this.supports_binary = this.ws.binaryType !== undefined;\n\n    if (!this.supports_binary) {\n        var warnings = document.getElementById('mpl-warnings');\n        if (warnings) {\n            warnings.style.display = 'block';\n            warnings.textContent =\n                'This browser does not support binary websocket messages. ' +\n                'Performance may be slow.';\n        }\n    }\n\n    this.imageObj = new Image();\n\n    this.context = undefined;\n    this.message = undefined;\n    this.canvas = undefined;\n    this.rubberband_canvas = undefined;\n    this.rubberband_context = undefined;\n    this.format_dropdown = undefined;\n\n    this.image_mode = 'full';\n\n    this.root = document.createElement('div');\n    this.root.setAttribute('style', 'display: inline-block');\n    this._root_extra_style(this.root);\n\n    parent_element.appendChild(this.root);\n\n    this._init_header(this);\n    this._init_canvas(this);\n    this._init_toolbar(this);\n\n    var fig = this;\n\n    this.waiting = false;\n\n    this.ws.onopen = function () {\n        fig.send_message('supports_binary', { value: fig.supports_binary });\n        fig.send_message('send_image_mode', {});\n        if (fig.ratio !== 1) {\n            fig.send_message('set_device_pixel_ratio', {\n                device_pixel_ratio: fig.ratio,\n            });\n        }\n        fig.send_message('refresh', {});\n    };\n\n    this.imageObj.onload = function () {\n        if (fig.image_mode === 'full') {\n            // Full images could contain transparency (where diff images\n            // almost always do), so we need to clear the canvas so that\n            // there is no ghosting.\n            fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n        }\n        fig.context.drawImage(fig.imageObj, 0, 0);\n    };\n\n    this.imageObj.onunload = function () {\n        fig.ws.close();\n    };\n\n    this.ws.onmessage = this._make_on_message_function(this);\n\n    this.ondownload = ondownload;\n};\n\nmpl.figure.prototype._init_header = function () {\n    var titlebar = document.createElement('div');\n    titlebar.classList =\n        'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n    var titletext = document.createElement('div');\n    titletext.classList = 'ui-dialog-title';\n    titletext.setAttribute(\n        'style',\n        'width: 100%; text-align: center; padding: 3px;'\n    );\n    titlebar.appendChild(titletext);\n    this.root.appendChild(titlebar);\n    this.header = titletext;\n};\n\nmpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._init_canvas = function () {\n    var fig = this;\n\n    var canvas_div = (this.canvas_div = document.createElement('div'));\n    canvas_div.setAttribute(\n        'style',\n        'border: 1px solid #ddd;' +\n            'box-sizing: content-box;' +\n            'clear: both;' +\n            'min-height: 1px;' +\n            'min-width: 1px;' +\n            'outline: 0;' +\n            'overflow: hidden;' +\n            'position: relative;' +\n            'resize: both;'\n    );\n\n    function on_keyboard_event_closure(name) {\n        return function (event) {\n            return fig.key_event(event, name);\n        };\n    }\n\n    canvas_div.addEventListener(\n        'keydown',\n        on_keyboard_event_closure('key_press')\n    );\n    canvas_div.addEventListener(\n        'keyup',\n        on_keyboard_event_closure('key_release')\n    );\n\n    this._canvas_extra_style(canvas_div);\n    this.root.appendChild(canvas_div);\n\n    var canvas = (this.canvas = document.createElement('canvas'));\n    canvas.classList.add('mpl-canvas');\n    canvas.setAttribute('style', 'box-sizing: content-box;');\n\n    this.context = canvas.getContext('2d');\n\n    var backingStore =\n        this.context.backingStorePixelRatio ||\n        this.context.webkitBackingStorePixelRatio ||\n        this.context.mozBackingStorePixelRatio ||\n        this.context.msBackingStorePixelRatio ||\n        this.context.oBackingStorePixelRatio ||\n        this.context.backingStorePixelRatio ||\n        1;\n\n    this.ratio = (window.devicePixelRatio || 1) / backingStore;\n\n    var rubberband_canvas = (this.rubberband_canvas = document.createElement(\n        'canvas'\n    ));\n    rubberband_canvas.setAttribute(\n        'style',\n        'box-sizing: content-box; position: absolute; left: 0; top: 0; z-index: 1;'\n    );\n\n    // Apply a ponyfill if ResizeObserver is not implemented by browser.\n    if (this.ResizeObserver === undefined) {\n        if (window.ResizeObserver !== undefined) {\n            this.ResizeObserver = window.ResizeObserver;\n        } else {\n            var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n            this.ResizeObserver = obs.ResizeObserver;\n        }\n    }\n\n    this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n        var nentries = entries.length;\n        for (var i = 0; i < nentries; i++) {\n            var entry = entries[i];\n            var width, height;\n            if (entry.contentBoxSize) {\n                if (entry.contentBoxSize instanceof Array) {\n                    // Chrome 84 implements new version of spec.\n                    width = entry.contentBoxSize[0].inlineSize;\n                    height = entry.contentBoxSize[0].blockSize;\n                } else {\n                    // Firefox implements old version of spec.\n                    width = entry.contentBoxSize.inlineSize;\n                    height = entry.contentBoxSize.blockSize;\n                }\n            } else {\n                // Chrome <84 implements even older version of spec.\n                width = entry.contentRect.width;\n                height = entry.contentRect.height;\n            }\n\n            // Keep the size of the canvas and rubber band canvas in sync with\n            // the canvas container.\n            if (entry.devicePixelContentBoxSize) {\n                // Chrome 84 implements new version of spec.\n                canvas.setAttribute(\n                    'width',\n                    entry.devicePixelContentBoxSize[0].inlineSize\n                );\n                canvas.setAttribute(\n                    'height',\n                    entry.devicePixelContentBoxSize[0].blockSize\n                );\n            } else {\n                canvas.setAttribute('width', width * fig.ratio);\n                canvas.setAttribute('height', height * fig.ratio);\n            }\n            canvas.setAttribute(\n                'style',\n                'width: ' + width + 'px; height: ' + height + 'px;'\n            );\n\n            rubberband_canvas.setAttribute('width', width);\n            rubberband_canvas.setAttribute('height', height);\n\n            // And update the size in Python. We ignore the initial 0/0 size\n            // that occurs as the element is placed into the DOM, which should\n            // otherwise not happen due to the minimum size styling.\n            if (fig.ws.readyState == 1 && width != 0 && height != 0) {\n                fig.request_resize(width, height);\n            }\n        }\n    });\n    this.resizeObserverInstance.observe(canvas_div);\n\n    function on_mouse_event_closure(name) {\n        return function (event) {\n            return fig.mouse_event(event, name);\n        };\n    }\n\n    rubberband_canvas.addEventListener(\n        'mousedown',\n        on_mouse_event_closure('button_press')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseup',\n        on_mouse_event_closure('button_release')\n    );\n    rubberband_canvas.addEventListener(\n        'dblclick',\n        on_mouse_event_closure('dblclick')\n    );\n    // Throttle sequential mouse events to 1 every 20ms.\n    rubberband_canvas.addEventListener(\n        'mousemove',\n        on_mouse_event_closure('motion_notify')\n    );\n\n    rubberband_canvas.addEventListener(\n        'mouseenter',\n        on_mouse_event_closure('figure_enter')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseleave',\n        on_mouse_event_closure('figure_leave')\n    );\n\n    canvas_div.addEventListener('wheel', function (event) {\n        if (event.deltaY < 0) {\n            event.step = 1;\n        } else {\n            event.step = -1;\n        }\n        on_mouse_event_closure('scroll')(event);\n    });\n\n    canvas_div.appendChild(canvas);\n    canvas_div.appendChild(rubberband_canvas);\n\n    this.rubberband_context = rubberband_canvas.getContext('2d');\n    this.rubberband_context.strokeStyle = '#000000';\n\n    this._resize_canvas = function (width, height, forward) {\n        if (forward) {\n            canvas_div.style.width = width + 'px';\n            canvas_div.style.height = height + 'px';\n        }\n    };\n\n    // Disable right mouse context menu.\n    this.rubberband_canvas.addEventListener('contextmenu', function (_e) {\n        event.preventDefault();\n        return false;\n    });\n\n    function set_focus() {\n        canvas.focus();\n        canvas_div.focus();\n    }\n\n    window.setTimeout(set_focus, 100);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'mpl-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'mpl-button-group';\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'mpl-button-group';\n            continue;\n        }\n\n        var button = (fig.buttons[name] = document.createElement('button'));\n        button.classList = 'mpl-widget';\n        button.setAttribute('role', 'button');\n        button.setAttribute('aria-disabled', 'false');\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n\n        var icon_img = document.createElement('img');\n        icon_img.src = '_images/' + image + '.png';\n        icon_img.srcset = '_images/' + image + '_large.png 2x';\n        icon_img.alt = tooltip;\n        button.appendChild(icon_img);\n\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    var fmt_picker = document.createElement('select');\n    fmt_picker.classList = 'mpl-widget';\n    toolbar.appendChild(fmt_picker);\n    this.format_dropdown = fmt_picker;\n\n    for (var ind in mpl.extensions) {\n        var fmt = mpl.extensions[ind];\n        var option = document.createElement('option');\n        option.selected = fmt === mpl.default_extension;\n        option.innerHTML = fmt;\n        fmt_picker.appendChild(option);\n    }\n\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n};\n\nmpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n    // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n    // which will in turn request a refresh of the image.\n    this.send_message('resize', { width: x_pixels, height: y_pixels });\n};\n\nmpl.figure.prototype.send_message = function (type, properties) {\n    properties['type'] = type;\n    properties['figure_id'] = this.id;\n    this.ws.send(JSON.stringify(properties));\n};\n\nmpl.figure.prototype.send_draw_message = function () {\n    if (!this.waiting) {\n        this.waiting = true;\n        this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    var format_dropdown = fig.format_dropdown;\n    var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n    fig.ondownload(fig, format);\n};\n\nmpl.figure.prototype.handle_resize = function (fig, msg) {\n    var size = msg['size'];\n    if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n        fig._resize_canvas(size[0], size[1], msg['forward']);\n        fig.send_message('refresh', {});\n    }\n};\n\nmpl.figure.prototype.handle_rubberband = function (fig, msg) {\n    var x0 = msg['x0'] / fig.ratio;\n    var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n    var x1 = msg['x1'] / fig.ratio;\n    var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n    x0 = Math.floor(x0) + 0.5;\n    y0 = Math.floor(y0) + 0.5;\n    x1 = Math.floor(x1) + 0.5;\n    y1 = Math.floor(y1) + 0.5;\n    var min_x = Math.min(x0, x1);\n    var min_y = Math.min(y0, y1);\n    var width = Math.abs(x1 - x0);\n    var height = Math.abs(y1 - y0);\n\n    fig.rubberband_context.clearRect(\n        0,\n        0,\n        fig.canvas.width / fig.ratio,\n        fig.canvas.height / fig.ratio\n    );\n\n    fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n};\n\nmpl.figure.prototype.handle_figure_label = function (fig, msg) {\n    // Updates the figure title.\n    fig.header.textContent = msg['label'];\n};\n\nmpl.figure.prototype.handle_cursor = function (fig, msg) {\n    fig.rubberband_canvas.style.cursor = msg['cursor'];\n};\n\nmpl.figure.prototype.handle_message = function (fig, msg) {\n    fig.message.textContent = msg['message'];\n};\n\nmpl.figure.prototype.handle_draw = function (fig, _msg) {\n    // Request the server to send over a new figure.\n    fig.send_draw_message();\n};\n\nmpl.figure.prototype.handle_image_mode = function (fig, msg) {\n    fig.image_mode = msg['mode'];\n};\n\nmpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n    for (var key in msg) {\n        if (!(key in fig.buttons)) {\n            continue;\n        }\n        fig.buttons[key].disabled = !msg[key];\n        fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n    }\n};\n\nmpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n    if (msg['mode'] === 'PAN') {\n        fig.buttons['Pan'].classList.add('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    } else if (msg['mode'] === 'ZOOM') {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.add('active');\n    } else {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    }\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Called whenever the canvas gets updated.\n    this.send_message('ack', {});\n};\n\n// A function to construct a web socket function for onmessage handling.\n// Called in the figure constructor.\nmpl.figure.prototype._make_on_message_function = function (fig) {\n    return function socket_on_message(evt) {\n        if (evt.data instanceof Blob) {\n            var img = evt.data;\n            if (img.type !== 'image/png') {\n                /* FIXME: We get \"Resource interpreted as Image but\n                 * transferred with MIME type text/plain:\" errors on\n                 * Chrome.  But how to set the MIME type?  It doesn't seem\n                 * to be part of the websocket stream */\n                img.type = 'image/png';\n            }\n\n            /* Free the memory for the previous frames */\n            if (fig.imageObj.src) {\n                (window.URL || window.webkitURL).revokeObjectURL(\n                    fig.imageObj.src\n                );\n            }\n\n            fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n                img\n            );\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        } else if (\n            typeof evt.data === 'string' &&\n            evt.data.slice(0, 21) === 'data:image/png;base64'\n        ) {\n            fig.imageObj.src = evt.data;\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        }\n\n        var msg = JSON.parse(evt.data);\n        var msg_type = msg['type'];\n\n        // Call the  \"handle_{type}\" callback, which takes\n        // the figure and JSON message as its only arguments.\n        try {\n            var callback = fig['handle_' + msg_type];\n        } catch (e) {\n            console.log(\n                \"No handler for the '\" + msg_type + \"' message type: \",\n                msg\n            );\n            return;\n        }\n\n        if (callback) {\n            try {\n                // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n                callback(fig, msg);\n            } catch (e) {\n                console.log(\n                    \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n                    e,\n                    e.stack,\n                    msg\n                );\n            }\n        }\n    };\n};\n\n// from https://stackoverflow.com/questions/1114465/getting-mouse-location-in-canvas\nmpl.findpos = function (e) {\n    //this section is from http://www.quirksmode.org/js/events_properties.html\n    var targ;\n    if (!e) {\n        e = window.event;\n    }\n    if (e.target) {\n        targ = e.target;\n    } else if (e.srcElement) {\n        targ = e.srcElement;\n    }\n    if (targ.nodeType === 3) {\n        // defeat Safari bug\n        targ = targ.parentNode;\n    }\n\n    // pageX,Y are the mouse positions relative to the document\n    var boundingRect = targ.getBoundingClientRect();\n    var x = e.pageX - (boundingRect.left + document.body.scrollLeft);\n    var y = e.pageY - (boundingRect.top + document.body.scrollTop);\n\n    return { x: x, y: y };\n};\n\n/*\n * return a copy of an object with only non-object keys\n * we need this to avoid circular references\n * https://stackoverflow.com/a/24161582/3208463\n */\nfunction simpleKeys(original) {\n    return Object.keys(original).reduce(function (obj, key) {\n        if (typeof original[key] !== 'object') {\n            obj[key] = original[key];\n        }\n        return obj;\n    }, {});\n}\n\nmpl.figure.prototype.mouse_event = function (event, name) {\n    var canvas_pos = mpl.findpos(event);\n\n    if (name === 'button_press') {\n        this.canvas.focus();\n        this.canvas_div.focus();\n    }\n\n    var x = canvas_pos.x * this.ratio;\n    var y = canvas_pos.y * this.ratio;\n\n    this.send_message(name, {\n        x: x,\n        y: y,\n        button: event.button,\n        step: event.step,\n        guiEvent: simpleKeys(event),\n    });\n\n    /* This prevents the web browser from automatically changing to\n     * the text insertion cursor when the button is pressed.  We want\n     * to control all of the cursor setting manually through the\n     * 'cursor' event from matplotlib */\n    event.preventDefault();\n    return false;\n};\n\nmpl.figure.prototype._key_event_extra = function (_event, _name) {\n    // Handle any extra behaviour associated with a key event\n};\n\nmpl.figure.prototype.key_event = function (event, name) {\n    // Prevent repeat events\n    if (name === 'key_press') {\n        if (event.key === this._key) {\n            return;\n        } else {\n            this._key = event.key;\n        }\n    }\n    if (name === 'key_release') {\n        this._key = null;\n    }\n\n    var value = '';\n    if (event.ctrlKey && event.key !== 'Control') {\n        value += 'ctrl+';\n    }\n    else if (event.altKey && event.key !== 'Alt') {\n        value += 'alt+';\n    }\n    else if (event.shiftKey && event.key !== 'Shift') {\n        value += 'shift+';\n    }\n\n    value += 'k' + event.key;\n\n    this._key_event_extra(event, name);\n\n    this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n    return false;\n};\n\nmpl.figure.prototype.toolbar_button_onclick = function (name) {\n    if (name === 'download') {\n        this.handle_save(this, null);\n    } else {\n        this.send_message('toolbar_button', { name: name });\n    }\n};\n\nmpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n    this.message.textContent = tooltip;\n};\n\n///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n// prettier-ignore\nvar _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\nmpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home icon-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left icon-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right icon-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows icon-move\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis\", \"fa fa-square-o icon-check-empty\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o icon-save\", \"download\"]];\n\nmpl.extensions = [\"eps\", \"jpeg\", \"pgf\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\"];\n\nmpl.default_extension = \"png\";/* global mpl */\n\nvar comm_websocket_adapter = function (comm) {\n    // Create a \"websocket\"-like object which calls the given IPython comm\n    // object with the appropriate methods. Currently this is a non binary\n    // socket, so there is still some room for performance tuning.\n    var ws = {};\n\n    ws.binaryType = comm.kernel.ws.binaryType;\n    ws.readyState = comm.kernel.ws.readyState;\n    function updateReadyState(_event) {\n        if (comm.kernel.ws) {\n            ws.readyState = comm.kernel.ws.readyState;\n        } else {\n            ws.readyState = 3; // Closed state.\n        }\n    }\n    comm.kernel.ws.addEventListener('open', updateReadyState);\n    comm.kernel.ws.addEventListener('close', updateReadyState);\n    comm.kernel.ws.addEventListener('error', updateReadyState);\n\n    ws.close = function () {\n        comm.close();\n    };\n    ws.send = function (m) {\n        //console.log('sending', m);\n        comm.send(m);\n    };\n    // Register the callback with on_msg.\n    comm.on_msg(function (msg) {\n        //console.log('receiving', msg['content']['data'], msg);\n        var data = msg['content']['data'];\n        if (data['blob'] !== undefined) {\n            data = {\n                data: new Blob(msg['buffers'], { type: data['blob'] }),\n            };\n        }\n        // Pass the mpl event to the overridden (by mpl) onmessage function.\n        ws.onmessage(data);\n    });\n    return ws;\n};\n\nmpl.mpl_figure_comm = function (comm, msg) {\n    // This is the function which gets called when the mpl process\n    // starts-up an IPython Comm through the \"matplotlib\" channel.\n\n    var id = msg.content.data.id;\n    // Get hold of the div created by the display call when the Comm\n    // socket was opened in Python.\n    var element = document.getElementById(id);\n    var ws_proxy = comm_websocket_adapter(comm);\n\n    function ondownload(figure, _format) {\n        window.open(figure.canvas.toDataURL());\n    }\n\n    var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n\n    // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n    // web socket which is closed, not our websocket->open comm proxy.\n    ws_proxy.onopen();\n\n    fig.parent_element = element;\n    fig.cell_info = mpl.find_output_cell(\"<div id='\" + id + \"'></div>\");\n    if (!fig.cell_info) {\n        console.error('Failed to find cell for figure', id, fig);\n        return;\n    }\n    fig.cell_info[0].output_area.element.on(\n        'cleared',\n        { fig: fig },\n        fig._remove_fig_handler\n    );\n};\n\nmpl.figure.prototype.handle_close = function (fig, msg) {\n    var width = fig.canvas.width / fig.ratio;\n    fig.cell_info[0].output_area.element.off(\n        'cleared',\n        fig._remove_fig_handler\n    );\n    fig.resizeObserverInstance.unobserve(fig.canvas_div);\n\n    // Update the output cell to use the data from the current canvas.\n    fig.push_to_output();\n    var dataURL = fig.canvas.toDataURL();\n    // Re-enable the keyboard manager in IPython - without this line, in FF,\n    // the notebook keyboard shortcuts fail.\n    IPython.keyboard_manager.enable();\n    fig.parent_element.innerHTML =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n    fig.close_ws(fig, msg);\n};\n\nmpl.figure.prototype.close_ws = function (fig, msg) {\n    fig.send_message('closing', msg);\n    // fig.ws.close()\n};\n\nmpl.figure.prototype.push_to_output = function (_remove_interactive) {\n    // Turn the data on the canvas into data in the output cell.\n    var width = this.canvas.width / this.ratio;\n    var dataURL = this.canvas.toDataURL();\n    this.cell_info[1]['text/html'] =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Tell IPython that the notebook contents must change.\n    IPython.notebook.set_dirty(true);\n    this.send_message('ack', {});\n    var fig = this;\n    // Wait a second, then push the new image to the DOM so\n    // that it is saved nicely (might be nice to debounce this).\n    setTimeout(function () {\n        fig.push_to_output();\n    }, 1000);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'btn-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'btn-group';\n    var button;\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'btn-group';\n            continue;\n        }\n\n        button = fig.buttons[name] = document.createElement('button');\n        button.classList = 'btn btn-default';\n        button.href = '#';\n        button.title = name;\n        button.innerHTML = '<i class=\"fa ' + image + ' fa-lg\"></i>';\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    // Add the status bar.\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message pull-right';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n\n    // Add the close button to the window.\n    var buttongrp = document.createElement('div');\n    buttongrp.classList = 'btn-group inline pull-right';\n    button = document.createElement('button');\n    button.classList = 'btn btn-mini btn-primary';\n    button.href = '#';\n    button.title = 'Stop Interaction';\n    button.innerHTML = '<i class=\"fa fa-power-off icon-remove icon-large\"></i>';\n    button.addEventListener('click', function (_evt) {\n        fig.handle_close(fig, {});\n    });\n    button.addEventListener(\n        'mouseover',\n        on_mouseover_closure('Stop Interaction')\n    );\n    buttongrp.appendChild(button);\n    var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n    titlebar.insertBefore(buttongrp, titlebar.firstChild);\n};\n\nmpl.figure.prototype._remove_fig_handler = function (event) {\n    var fig = event.data.fig;\n    if (event.target !== this) {\n        // Ignore bubbled events from children.\n        return;\n    }\n    fig.close_ws(fig, {});\n};\n\nmpl.figure.prototype._root_extra_style = function (el) {\n    el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n};\n\nmpl.figure.prototype._canvas_extra_style = function (el) {\n    // this is important to make the div 'focusable\n    el.setAttribute('tabindex', 0);\n    // reach out to IPython and tell the keyboard manager to turn it's self\n    // off when our div gets focus\n\n    // location in version 3\n    if (IPython.notebook.keyboard_manager) {\n        IPython.notebook.keyboard_manager.register_events(el);\n    } else {\n        // location in version 2\n        IPython.keyboard_manager.register_events(el);\n    }\n};\n\nmpl.figure.prototype._key_event_extra = function (event, _name) {\n    // Check for shift+enter\n    if (event.shiftKey && event.which === 13) {\n        this.canvas_div.blur();\n        // select the cell after this one\n        var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n        IPython.notebook.select(index + 1);\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    fig.ondownload(fig, null);\n};\n\nmpl.find_output_cell = function (html_output) {\n    // Return the cell and output element which can be found *uniquely* in the notebook.\n    // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n    // IPython event is triggered only after the cells have been serialised, which for\n    // our purposes (turning an active figure into a static one), is too late.\n    var cells = IPython.notebook.get_cells();\n    var ncells = cells.length;\n    for (var i = 0; i < ncells; i++) {\n        var cell = cells[i];\n        if (cell.cell_type === 'code') {\n            for (var j = 0; j < cell.output_area.outputs.length; j++) {\n                var data = cell.output_area.outputs[j];\n                if (data.data) {\n                    // IPython >= 3 moved mimebundle to data attribute of output\n                    data = data.data;\n                }\n                if (data['text/html'] === html_output) {\n                    return [cell, data, j];\n                }\n            }\n        }\n    }\n};\n\n// Register the function which deals with the matplotlib target/channel.\n// The kernel may be null if the page has been refreshed.\nif (IPython.notebook.kernel !== null) {\n    IPython.notebook.kernel.comm_manager.register_target(\n        'matplotlib',\n        mpl.mpl_figure_comm\n    );\n}\n",
      "text/plain": [
       "<IPython.core.display.Javascript object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<img src=\"data:image/png;base64,[encoded data, 64932 characters]\" width=\"640\">"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "val = fitAnalyser.get_fit_value(fitResult)\n",
    "std = fitAnalyser.get_fit_std(fitResult)\n",
    "\n",
    "fitCurve = fitAnalyser.eval(fitResult, x=np.arange(300), y=np.arange(300), dask=\"parallelized\").load()\n",
    "\n",
    "# dataKey = 'sigmax'\n",
    "# dataKey = 'centerx'\n",
    "# dataKey = 'sigmay'\n",
    "dataKey = 'centery'\n",
    "\n",
    "# val_mean = val[dataKey].mean(dim='runs')\n",
    "# std_mean = val[dataKey].std(dim='runs')\n",
    "\n",
    "val_mean = calculate_mean(val[dataKey])\n",
    "std_mean = calculate_std(val[dataKey])\n",
    "\n",
    "fig = plt.figure()\n",
    "ax = fig.gca()\n",
    "\n",
    "val_mean.plot.errorbar(yerr=std_mean, fmt='--ob')\n",
    "\n",
    "plt.grid()\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 73,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/javascript": "/* Put everything inside the global mpl namespace */\n/* global mpl */\nwindow.mpl = {};\n\nmpl.get_websocket_type = function () {\n    if (typeof WebSocket !== 'undefined') {\n        return WebSocket;\n    } else if (typeof MozWebSocket !== 'undefined') {\n        return MozWebSocket;\n    } else {\n        alert(\n            'Your browser does not have WebSocket support. ' +\n                'Please try Chrome, Safari or Firefox ≥ 6. ' +\n                'Firefox 4 and 5 are also supported but you ' +\n                'have to enable WebSockets in about:config.'\n        );\n    }\n};\n\nmpl.figure = function (figure_id, websocket, ondownload, parent_element) {\n    this.id = figure_id;\n\n    this.ws = websocket;\n\n    this.supports_binary = this.ws.binaryType !== undefined;\n\n    if (!this.supports_binary) {\n        var warnings = document.getElementById('mpl-warnings');\n        if (warnings) {\n            warnings.style.display = 'block';\n            warnings.textContent =\n                'This browser does not support binary websocket messages. ' +\n                'Performance may be slow.';\n        }\n    }\n\n    this.imageObj = new Image();\n\n    this.context = undefined;\n    this.message = undefined;\n    this.canvas = undefined;\n    this.rubberband_canvas = undefined;\n    this.rubberband_context = undefined;\n    this.format_dropdown = undefined;\n\n    this.image_mode = 'full';\n\n    this.root = document.createElement('div');\n    this.root.setAttribute('style', 'display: inline-block');\n    this._root_extra_style(this.root);\n\n    parent_element.appendChild(this.root);\n\n    this._init_header(this);\n    this._init_canvas(this);\n    this._init_toolbar(this);\n\n    var fig = this;\n\n    this.waiting = false;\n\n    this.ws.onopen = function () {\n        fig.send_message('supports_binary', { value: fig.supports_binary });\n        fig.send_message('send_image_mode', {});\n        if (fig.ratio !== 1) {\n            fig.send_message('set_device_pixel_ratio', {\n                device_pixel_ratio: fig.ratio,\n            });\n        }\n        fig.send_message('refresh', {});\n    };\n\n    this.imageObj.onload = function () {\n        if (fig.image_mode === 'full') {\n            // Full images could contain transparency (where diff images\n            // almost always do), so we need to clear the canvas so that\n            // there is no ghosting.\n            fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n        }\n        fig.context.drawImage(fig.imageObj, 0, 0);\n    };\n\n    this.imageObj.onunload = function () {\n        fig.ws.close();\n    };\n\n    this.ws.onmessage = this._make_on_message_function(this);\n\n    this.ondownload = ondownload;\n};\n\nmpl.figure.prototype._init_header = function () {\n    var titlebar = document.createElement('div');\n    titlebar.classList =\n        'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n    var titletext = document.createElement('div');\n    titletext.classList = 'ui-dialog-title';\n    titletext.setAttribute(\n        'style',\n        'width: 100%; text-align: center; padding: 3px;'\n    );\n    titlebar.appendChild(titletext);\n    this.root.appendChild(titlebar);\n    this.header = titletext;\n};\n\nmpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._init_canvas = function () {\n    var fig = this;\n\n    var canvas_div = (this.canvas_div = document.createElement('div'));\n    canvas_div.setAttribute(\n        'style',\n        'border: 1px solid #ddd;' +\n            'box-sizing: content-box;' +\n            'clear: both;' +\n            'min-height: 1px;' +\n            'min-width: 1px;' +\n            'outline: 0;' +\n            'overflow: hidden;' +\n            'position: relative;' +\n            'resize: both;'\n    );\n\n    function on_keyboard_event_closure(name) {\n        return function (event) {\n            return fig.key_event(event, name);\n        };\n    }\n\n    canvas_div.addEventListener(\n        'keydown',\n        on_keyboard_event_closure('key_press')\n    );\n    canvas_div.addEventListener(\n        'keyup',\n        on_keyboard_event_closure('key_release')\n    );\n\n    this._canvas_extra_style(canvas_div);\n    this.root.appendChild(canvas_div);\n\n    var canvas = (this.canvas = document.createElement('canvas'));\n    canvas.classList.add('mpl-canvas');\n    canvas.setAttribute('style', 'box-sizing: content-box;');\n\n    this.context = canvas.getContext('2d');\n\n    var backingStore =\n        this.context.backingStorePixelRatio ||\n        this.context.webkitBackingStorePixelRatio ||\n        this.context.mozBackingStorePixelRatio ||\n        this.context.msBackingStorePixelRatio ||\n        this.context.oBackingStorePixelRatio ||\n        this.context.backingStorePixelRatio ||\n        1;\n\n    this.ratio = (window.devicePixelRatio || 1) / backingStore;\n\n    var rubberband_canvas = (this.rubberband_canvas = document.createElement(\n        'canvas'\n    ));\n    rubberband_canvas.setAttribute(\n        'style',\n        'box-sizing: content-box; position: absolute; left: 0; top: 0; z-index: 1;'\n    );\n\n    // Apply a ponyfill if ResizeObserver is not implemented by browser.\n    if (this.ResizeObserver === undefined) {\n        if (window.ResizeObserver !== undefined) {\n            this.ResizeObserver = window.ResizeObserver;\n        } else {\n            var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n            this.ResizeObserver = obs.ResizeObserver;\n        }\n    }\n\n    this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n        var nentries = entries.length;\n        for (var i = 0; i < nentries; i++) {\n            var entry = entries[i];\n            var width, height;\n            if (entry.contentBoxSize) {\n                if (entry.contentBoxSize instanceof Array) {\n                    // Chrome 84 implements new version of spec.\n                    width = entry.contentBoxSize[0].inlineSize;\n                    height = entry.contentBoxSize[0].blockSize;\n                } else {\n                    // Firefox implements old version of spec.\n                    width = entry.contentBoxSize.inlineSize;\n                    height = entry.contentBoxSize.blockSize;\n                }\n            } else {\n                // Chrome <84 implements even older version of spec.\n                width = entry.contentRect.width;\n                height = entry.contentRect.height;\n            }\n\n            // Keep the size of the canvas and rubber band canvas in sync with\n            // the canvas container.\n            if (entry.devicePixelContentBoxSize) {\n                // Chrome 84 implements new version of spec.\n                canvas.setAttribute(\n                    'width',\n                    entry.devicePixelContentBoxSize[0].inlineSize\n                );\n                canvas.setAttribute(\n                    'height',\n                    entry.devicePixelContentBoxSize[0].blockSize\n                );\n            } else {\n                canvas.setAttribute('width', width * fig.ratio);\n                canvas.setAttribute('height', height * fig.ratio);\n            }\n            canvas.setAttribute(\n                'style',\n                'width: ' + width + 'px; height: ' + height + 'px;'\n            );\n\n            rubberband_canvas.setAttribute('width', width);\n            rubberband_canvas.setAttribute('height', height);\n\n            // And update the size in Python. We ignore the initial 0/0 size\n            // that occurs as the element is placed into the DOM, which should\n            // otherwise not happen due to the minimum size styling.\n            if (fig.ws.readyState == 1 && width != 0 && height != 0) {\n                fig.request_resize(width, height);\n            }\n        }\n    });\n    this.resizeObserverInstance.observe(canvas_div);\n\n    function on_mouse_event_closure(name) {\n        return function (event) {\n            return fig.mouse_event(event, name);\n        };\n    }\n\n    rubberband_canvas.addEventListener(\n        'mousedown',\n        on_mouse_event_closure('button_press')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseup',\n        on_mouse_event_closure('button_release')\n    );\n    rubberband_canvas.addEventListener(\n        'dblclick',\n        on_mouse_event_closure('dblclick')\n    );\n    // Throttle sequential mouse events to 1 every 20ms.\n    rubberband_canvas.addEventListener(\n        'mousemove',\n        on_mouse_event_closure('motion_notify')\n    );\n\n    rubberband_canvas.addEventListener(\n        'mouseenter',\n        on_mouse_event_closure('figure_enter')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseleave',\n        on_mouse_event_closure('figure_leave')\n    );\n\n    canvas_div.addEventListener('wheel', function (event) {\n        if (event.deltaY < 0) {\n            event.step = 1;\n        } else {\n            event.step = -1;\n        }\n        on_mouse_event_closure('scroll')(event);\n    });\n\n    canvas_div.appendChild(canvas);\n    canvas_div.appendChild(rubberband_canvas);\n\n    this.rubberband_context = rubberband_canvas.getContext('2d');\n    this.rubberband_context.strokeStyle = '#000000';\n\n    this._resize_canvas = function (width, height, forward) {\n        if (forward) {\n            canvas_div.style.width = width + 'px';\n            canvas_div.style.height = height + 'px';\n        }\n    };\n\n    // Disable right mouse context menu.\n    this.rubberband_canvas.addEventListener('contextmenu', function (_e) {\n        event.preventDefault();\n        return false;\n    });\n\n    function set_focus() {\n        canvas.focus();\n        canvas_div.focus();\n    }\n\n    window.setTimeout(set_focus, 100);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'mpl-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'mpl-button-group';\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'mpl-button-group';\n            continue;\n        }\n\n        var button = (fig.buttons[name] = document.createElement('button'));\n        button.classList = 'mpl-widget';\n        button.setAttribute('role', 'button');\n        button.setAttribute('aria-disabled', 'false');\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n\n        var icon_img = document.createElement('img');\n        icon_img.src = '_images/' + image + '.png';\n        icon_img.srcset = '_images/' + image + '_large.png 2x';\n        icon_img.alt = tooltip;\n        button.appendChild(icon_img);\n\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    var fmt_picker = document.createElement('select');\n    fmt_picker.classList = 'mpl-widget';\n    toolbar.appendChild(fmt_picker);\n    this.format_dropdown = fmt_picker;\n\n    for (var ind in mpl.extensions) {\n        var fmt = mpl.extensions[ind];\n        var option = document.createElement('option');\n        option.selected = fmt === mpl.default_extension;\n        option.innerHTML = fmt;\n        fmt_picker.appendChild(option);\n    }\n\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n};\n\nmpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n    // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n    // which will in turn request a refresh of the image.\n    this.send_message('resize', { width: x_pixels, height: y_pixels });\n};\n\nmpl.figure.prototype.send_message = function (type, properties) {\n    properties['type'] = type;\n    properties['figure_id'] = this.id;\n    this.ws.send(JSON.stringify(properties));\n};\n\nmpl.figure.prototype.send_draw_message = function () {\n    if (!this.waiting) {\n        this.waiting = true;\n        this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    var format_dropdown = fig.format_dropdown;\n    var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n    fig.ondownload(fig, format);\n};\n\nmpl.figure.prototype.handle_resize = function (fig, msg) {\n    var size = msg['size'];\n    if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n        fig._resize_canvas(size[0], size[1], msg['forward']);\n        fig.send_message('refresh', {});\n    }\n};\n\nmpl.figure.prototype.handle_rubberband = function (fig, msg) {\n    var x0 = msg['x0'] / fig.ratio;\n    var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n    var x1 = msg['x1'] / fig.ratio;\n    var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n    x0 = Math.floor(x0) + 0.5;\n    y0 = Math.floor(y0) + 0.5;\n    x1 = Math.floor(x1) + 0.5;\n    y1 = Math.floor(y1) + 0.5;\n    var min_x = Math.min(x0, x1);\n    var min_y = Math.min(y0, y1);\n    var width = Math.abs(x1 - x0);\n    var height = Math.abs(y1 - y0);\n\n    fig.rubberband_context.clearRect(\n        0,\n        0,\n        fig.canvas.width / fig.ratio,\n        fig.canvas.height / fig.ratio\n    );\n\n    fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n};\n\nmpl.figure.prototype.handle_figure_label = function (fig, msg) {\n    // Updates the figure title.\n    fig.header.textContent = msg['label'];\n};\n\nmpl.figure.prototype.handle_cursor = function (fig, msg) {\n    fig.rubberband_canvas.style.cursor = msg['cursor'];\n};\n\nmpl.figure.prototype.handle_message = function (fig, msg) {\n    fig.message.textContent = msg['message'];\n};\n\nmpl.figure.prototype.handle_draw = function (fig, _msg) {\n    // Request the server to send over a new figure.\n    fig.send_draw_message();\n};\n\nmpl.figure.prototype.handle_image_mode = function (fig, msg) {\n    fig.image_mode = msg['mode'];\n};\n\nmpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n    for (var key in msg) {\n        if (!(key in fig.buttons)) {\n            continue;\n        }\n        fig.buttons[key].disabled = !msg[key];\n        fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n    }\n};\n\nmpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n    if (msg['mode'] === 'PAN') {\n        fig.buttons['Pan'].classList.add('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    } else if (msg['mode'] === 'ZOOM') {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.add('active');\n    } else {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    }\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Called whenever the canvas gets updated.\n    this.send_message('ack', {});\n};\n\n// A function to construct a web socket function for onmessage handling.\n// Called in the figure constructor.\nmpl.figure.prototype._make_on_message_function = function (fig) {\n    return function socket_on_message(evt) {\n        if (evt.data instanceof Blob) {\n            var img = evt.data;\n            if (img.type !== 'image/png') {\n                /* FIXME: We get \"Resource interpreted as Image but\n                 * transferred with MIME type text/plain:\" errors on\n                 * Chrome.  But how to set the MIME type?  It doesn't seem\n                 * to be part of the websocket stream */\n                img.type = 'image/png';\n            }\n\n            /* Free the memory for the previous frames */\n            if (fig.imageObj.src) {\n                (window.URL || window.webkitURL).revokeObjectURL(\n                    fig.imageObj.src\n                );\n            }\n\n            fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n                img\n            );\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        } else if (\n            typeof evt.data === 'string' &&\n            evt.data.slice(0, 21) === 'data:image/png;base64'\n        ) {\n            fig.imageObj.src = evt.data;\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        }\n\n        var msg = JSON.parse(evt.data);\n        var msg_type = msg['type'];\n\n        // Call the  \"handle_{type}\" callback, which takes\n        // the figure and JSON message as its only arguments.\n        try {\n            var callback = fig['handle_' + msg_type];\n        } catch (e) {\n            console.log(\n                \"No handler for the '\" + msg_type + \"' message type: \",\n                msg\n            );\n            return;\n        }\n\n        if (callback) {\n            try {\n                // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n                callback(fig, msg);\n            } catch (e) {\n                console.log(\n                    \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n                    e,\n                    e.stack,\n                    msg\n                );\n            }\n        }\n    };\n};\n\n// from https://stackoverflow.com/questions/1114465/getting-mouse-location-in-canvas\nmpl.findpos = function (e) {\n    //this section is from http://www.quirksmode.org/js/events_properties.html\n    var targ;\n    if (!e) {\n        e = window.event;\n    }\n    if (e.target) {\n        targ = e.target;\n    } else if (e.srcElement) {\n        targ = e.srcElement;\n    }\n    if (targ.nodeType === 3) {\n        // defeat Safari bug\n        targ = targ.parentNode;\n    }\n\n    // pageX,Y are the mouse positions relative to the document\n    var boundingRect = targ.getBoundingClientRect();\n    var x = e.pageX - (boundingRect.left + document.body.scrollLeft);\n    var y = e.pageY - (boundingRect.top + document.body.scrollTop);\n\n    return { x: x, y: y };\n};\n\n/*\n * return a copy of an object with only non-object keys\n * we need this to avoid circular references\n * https://stackoverflow.com/a/24161582/3208463\n */\nfunction simpleKeys(original) {\n    return Object.keys(original).reduce(function (obj, key) {\n        if (typeof original[key] !== 'object') {\n            obj[key] = original[key];\n        }\n        return obj;\n    }, {});\n}\n\nmpl.figure.prototype.mouse_event = function (event, name) {\n    var canvas_pos = mpl.findpos(event);\n\n    if (name === 'button_press') {\n        this.canvas.focus();\n        this.canvas_div.focus();\n    }\n\n    var x = canvas_pos.x * this.ratio;\n    var y = canvas_pos.y * this.ratio;\n\n    this.send_message(name, {\n        x: x,\n        y: y,\n        button: event.button,\n        step: event.step,\n        guiEvent: simpleKeys(event),\n    });\n\n    /* This prevents the web browser from automatically changing to\n     * the text insertion cursor when the button is pressed.  We want\n     * to control all of the cursor setting manually through the\n     * 'cursor' event from matplotlib */\n    event.preventDefault();\n    return false;\n};\n\nmpl.figure.prototype._key_event_extra = function (_event, _name) {\n    // Handle any extra behaviour associated with a key event\n};\n\nmpl.figure.prototype.key_event = function (event, name) {\n    // Prevent repeat events\n    if (name === 'key_press') {\n        if (event.key === this._key) {\n            return;\n        } else {\n            this._key = event.key;\n        }\n    }\n    if (name === 'key_release') {\n        this._key = null;\n    }\n\n    var value = '';\n    if (event.ctrlKey && event.key !== 'Control') {\n        value += 'ctrl+';\n    }\n    else if (event.altKey && event.key !== 'Alt') {\n        value += 'alt+';\n    }\n    else if (event.shiftKey && event.key !== 'Shift') {\n        value += 'shift+';\n    }\n\n    value += 'k' + event.key;\n\n    this._key_event_extra(event, name);\n\n    this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n    return false;\n};\n\nmpl.figure.prototype.toolbar_button_onclick = function (name) {\n    if (name === 'download') {\n        this.handle_save(this, null);\n    } else {\n        this.send_message('toolbar_button', { name: name });\n    }\n};\n\nmpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n    this.message.textContent = tooltip;\n};\n\n///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n// prettier-ignore\nvar _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\nmpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home icon-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left icon-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right icon-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows icon-move\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis\", \"fa fa-square-o icon-check-empty\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o icon-save\", \"download\"]];\n\nmpl.extensions = [\"eps\", \"jpeg\", \"pgf\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\"];\n\nmpl.default_extension = \"png\";/* global mpl */\n\nvar comm_websocket_adapter = function (comm) {\n    // Create a \"websocket\"-like object which calls the given IPython comm\n    // object with the appropriate methods. Currently this is a non binary\n    // socket, so there is still some room for performance tuning.\n    var ws = {};\n\n    ws.binaryType = comm.kernel.ws.binaryType;\n    ws.readyState = comm.kernel.ws.readyState;\n    function updateReadyState(_event) {\n        if (comm.kernel.ws) {\n            ws.readyState = comm.kernel.ws.readyState;\n        } else {\n            ws.readyState = 3; // Closed state.\n        }\n    }\n    comm.kernel.ws.addEventListener('open', updateReadyState);\n    comm.kernel.ws.addEventListener('close', updateReadyState);\n    comm.kernel.ws.addEventListener('error', updateReadyState);\n\n    ws.close = function () {\n        comm.close();\n    };\n    ws.send = function (m) {\n        //console.log('sending', m);\n        comm.send(m);\n    };\n    // Register the callback with on_msg.\n    comm.on_msg(function (msg) {\n        //console.log('receiving', msg['content']['data'], msg);\n        var data = msg['content']['data'];\n        if (data['blob'] !== undefined) {\n            data = {\n                data: new Blob(msg['buffers'], { type: data['blob'] }),\n            };\n        }\n        // Pass the mpl event to the overridden (by mpl) onmessage function.\n        ws.onmessage(data);\n    });\n    return ws;\n};\n\nmpl.mpl_figure_comm = function (comm, msg) {\n    // This is the function which gets called when the mpl process\n    // starts-up an IPython Comm through the \"matplotlib\" channel.\n\n    var id = msg.content.data.id;\n    // Get hold of the div created by the display call when the Comm\n    // socket was opened in Python.\n    var element = document.getElementById(id);\n    var ws_proxy = comm_websocket_adapter(comm);\n\n    function ondownload(figure, _format) {\n        window.open(figure.canvas.toDataURL());\n    }\n\n    var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n\n    // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n    // web socket which is closed, not our websocket->open comm proxy.\n    ws_proxy.onopen();\n\n    fig.parent_element = element;\n    fig.cell_info = mpl.find_output_cell(\"<div id='\" + id + \"'></div>\");\n    if (!fig.cell_info) {\n        console.error('Failed to find cell for figure', id, fig);\n        return;\n    }\n    fig.cell_info[0].output_area.element.on(\n        'cleared',\n        { fig: fig },\n        fig._remove_fig_handler\n    );\n};\n\nmpl.figure.prototype.handle_close = function (fig, msg) {\n    var width = fig.canvas.width / fig.ratio;\n    fig.cell_info[0].output_area.element.off(\n        'cleared',\n        fig._remove_fig_handler\n    );\n    fig.resizeObserverInstance.unobserve(fig.canvas_div);\n\n    // Update the output cell to use the data from the current canvas.\n    fig.push_to_output();\n    var dataURL = fig.canvas.toDataURL();\n    // Re-enable the keyboard manager in IPython - without this line, in FF,\n    // the notebook keyboard shortcuts fail.\n    IPython.keyboard_manager.enable();\n    fig.parent_element.innerHTML =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n    fig.close_ws(fig, msg);\n};\n\nmpl.figure.prototype.close_ws = function (fig, msg) {\n    fig.send_message('closing', msg);\n    // fig.ws.close()\n};\n\nmpl.figure.prototype.push_to_output = function (_remove_interactive) {\n    // Turn the data on the canvas into data in the output cell.\n    var width = this.canvas.width / this.ratio;\n    var dataURL = this.canvas.toDataURL();\n    this.cell_info[1]['text/html'] =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Tell IPython that the notebook contents must change.\n    IPython.notebook.set_dirty(true);\n    this.send_message('ack', {});\n    var fig = this;\n    // Wait a second, then push the new image to the DOM so\n    // that it is saved nicely (might be nice to debounce this).\n    setTimeout(function () {\n        fig.push_to_output();\n    }, 1000);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'btn-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'btn-group';\n    var button;\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'btn-group';\n            continue;\n        }\n\n        button = fig.buttons[name] = document.createElement('button');\n        button.classList = 'btn btn-default';\n        button.href = '#';\n        button.title = name;\n        button.innerHTML = '<i class=\"fa ' + image + ' fa-lg\"></i>';\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    // Add the status bar.\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message pull-right';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n\n    // Add the close button to the window.\n    var buttongrp = document.createElement('div');\n    buttongrp.classList = 'btn-group inline pull-right';\n    button = document.createElement('button');\n    button.classList = 'btn btn-mini btn-primary';\n    button.href = '#';\n    button.title = 'Stop Interaction';\n    button.innerHTML = '<i class=\"fa fa-power-off icon-remove icon-large\"></i>';\n    button.addEventListener('click', function (_evt) {\n        fig.handle_close(fig, {});\n    });\n    button.addEventListener(\n        'mouseover',\n        on_mouseover_closure('Stop Interaction')\n    );\n    buttongrp.appendChild(button);\n    var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n    titlebar.insertBefore(buttongrp, titlebar.firstChild);\n};\n\nmpl.figure.prototype._remove_fig_handler = function (event) {\n    var fig = event.data.fig;\n    if (event.target !== this) {\n        // Ignore bubbled events from children.\n        return;\n    }\n    fig.close_ws(fig, {});\n};\n\nmpl.figure.prototype._root_extra_style = function (el) {\n    el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n};\n\nmpl.figure.prototype._canvas_extra_style = function (el) {\n    // this is important to make the div 'focusable\n    el.setAttribute('tabindex', 0);\n    // reach out to IPython and tell the keyboard manager to turn it's self\n    // off when our div gets focus\n\n    // location in version 3\n    if (IPython.notebook.keyboard_manager) {\n        IPython.notebook.keyboard_manager.register_events(el);\n    } else {\n        // location in version 2\n        IPython.keyboard_manager.register_events(el);\n    }\n};\n\nmpl.figure.prototype._key_event_extra = function (event, _name) {\n    // Check for shift+enter\n    if (event.shiftKey && event.which === 13) {\n        this.canvas_div.blur();\n        // select the cell after this one\n        var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n        IPython.notebook.select(index + 1);\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    fig.ondownload(fig, null);\n};\n\nmpl.find_output_cell = function (html_output) {\n    // Return the cell and output element which can be found *uniquely* in the notebook.\n    // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n    // IPython event is triggered only after the cells have been serialised, which for\n    // our purposes (turning an active figure into a static one), is too late.\n    var cells = IPython.notebook.get_cells();\n    var ncells = cells.length;\n    for (var i = 0; i < ncells; i++) {\n        var cell = cells[i];\n        if (cell.cell_type === 'code') {\n            for (var j = 0; j < cell.output_area.outputs.length; j++) {\n                var data = cell.output_area.outputs[j];\n                if (data.data) {\n                    // IPython >= 3 moved mimebundle to data attribute of output\n                    data = data.data;\n                }\n                if (data['text/html'] === html_output) {\n                    return [cell, data, j];\n                }\n            }\n        }\n    }\n};\n\n// Register the function which deals with the matplotlib target/channel.\n// The kernel may be null if the page has been refreshed.\nif (IPython.notebook.kernel !== null) {\n    IPython.notebook.kernel.comm_manager.register_target(\n        'matplotlib',\n        mpl.mpl_figure_comm\n    );\n}\n",
      "text/plain": [
       "<IPython.core.display.Javascript object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<img src=\"data:image/png;base64,[encoded data, 86416 characters]\" width=\"640\">"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "f = 272.6675 ± 0.6739 Hz\n"
     ]
    }
   ],
   "source": [
    "def damp_osci(t, t0, A, B, nu, gamma):\n",
    "    return A * np.exp(-gamma*t)*np.sin(2*np.pi*nu*(t-t0)) + B\n",
    "\n",
    "yvals     = val_mean#.sel(blink_on_time=slice(0.005, 0.025))\n",
    "yvals_std = std_mean#.sel(blink_on_time=slice(0.005, 0.025))\n",
    "xvals     = dataSet_cropOD[scanAxis[0]]#.sel(blink_on_time=slice(0.005, 0.025))\n",
    "\n",
    "fitted_qtys_1 = yvals.to_numpy()\n",
    "fitted_qtys_err_1 = yvals_std.to_numpy()\n",
    "scan_para = xvals.to_numpy()\n",
    "\n",
    "plt.figure()\n",
    "popt_x, pcov_x = curve_fit(damp_osci, scan_para, fitted_qtys_1, np.array([0, 3, 145, 1e2, 0.1]))\n",
    "freqdata = np.linspace(0.005, 20e-3, 500)\n",
    "plt.plot(freqdata, damp_osci(freqdata, *popt_x), 'g--',label='fit: t0=%5.3f, A=%5.3f, B=%5.3f, nu=%5.3f, Gamma=%5.3f' % tuple(popt_x))\n",
    "plt.errorbar(scan_para, fitted_qtys_1, yerr=fitted_qtys_err_1, fmt='or')\n",
    "plt.xlabel('hold time after switch on the trap (s)')\n",
    "plt.ylabel('Center along gravity direction (pixels)')\n",
    "plt.tight_layout()\n",
    "plt.grid(visible=1)\n",
    "#plt.ylim([0,750])\n",
    "#plt.xlim([0.004, 0.025])\n",
    "#plt.legend(prop={'size': 14})\n",
    "plt.show()\n",
    "\n",
    "f_x = popt_x[3]\n",
    "df_x = pcov_x[3][3]**0.5\n",
    "\n",
    "print('f = %.4f \\u00B1 %.4f Hz'% tuple([np.abs(f_x),df_x]))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Truncation: 0.65"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 74,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The detected scaning axes and values are: \n",
      "\n",
      "{'mod_blink_on_time': array([0.005 , 0.0057, 0.0064, 0.0071, 0.0078, 0.0085, 0.0092, 0.0099,\n",
      "       0.0106, 0.0113, 0.012 , 0.0127, 0.0134, 0.0141, 0.0148, 0.0155,\n",
      "       0.0162, 0.0169, 0.0176, 0.0183, 0.019 , 0.0197]), 'runs': array([0., 1., 2., 3.])}\n"
     ]
    },
    {
     "data": {
      "application/javascript": "/* Put everything inside the global mpl namespace */\n/* global mpl */\nwindow.mpl = {};\n\nmpl.get_websocket_type = function () {\n    if (typeof WebSocket !== 'undefined') {\n        return WebSocket;\n    } else if (typeof MozWebSocket !== 'undefined') {\n        return MozWebSocket;\n    } else {\n        alert(\n            'Your browser does not have WebSocket support. ' +\n                'Please try Chrome, Safari or Firefox ≥ 6. ' +\n                'Firefox 4 and 5 are also supported but you ' +\n                'have to enable WebSockets in about:config.'\n        );\n    }\n};\n\nmpl.figure = function (figure_id, websocket, ondownload, parent_element) {\n    this.id = figure_id;\n\n    this.ws = websocket;\n\n    this.supports_binary = this.ws.binaryType !== undefined;\n\n    if (!this.supports_binary) {\n        var warnings = document.getElementById('mpl-warnings');\n        if (warnings) {\n            warnings.style.display = 'block';\n            warnings.textContent =\n                'This browser does not support binary websocket messages. ' +\n                'Performance may be slow.';\n        }\n    }\n\n    this.imageObj = new Image();\n\n    this.context = undefined;\n    this.message = undefined;\n    this.canvas = undefined;\n    this.rubberband_canvas = undefined;\n    this.rubberband_context = undefined;\n    this.format_dropdown = undefined;\n\n    this.image_mode = 'full';\n\n    this.root = document.createElement('div');\n    this.root.setAttribute('style', 'display: inline-block');\n    this._root_extra_style(this.root);\n\n    parent_element.appendChild(this.root);\n\n    this._init_header(this);\n    this._init_canvas(this);\n    this._init_toolbar(this);\n\n    var fig = this;\n\n    this.waiting = false;\n\n    this.ws.onopen = function () {\n        fig.send_message('supports_binary', { value: fig.supports_binary });\n        fig.send_message('send_image_mode', {});\n        if (fig.ratio !== 1) {\n            fig.send_message('set_device_pixel_ratio', {\n                device_pixel_ratio: fig.ratio,\n            });\n        }\n        fig.send_message('refresh', {});\n    };\n\n    this.imageObj.onload = function () {\n        if (fig.image_mode === 'full') {\n            // Full images could contain transparency (where diff images\n            // almost always do), so we need to clear the canvas so that\n            // there is no ghosting.\n            fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n        }\n        fig.context.drawImage(fig.imageObj, 0, 0);\n    };\n\n    this.imageObj.onunload = function () {\n        fig.ws.close();\n    };\n\n    this.ws.onmessage = this._make_on_message_function(this);\n\n    this.ondownload = ondownload;\n};\n\nmpl.figure.prototype._init_header = function () {\n    var titlebar = document.createElement('div');\n    titlebar.classList =\n        'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n    var titletext = document.createElement('div');\n    titletext.classList = 'ui-dialog-title';\n    titletext.setAttribute(\n        'style',\n        'width: 100%; text-align: center; padding: 3px;'\n    );\n    titlebar.appendChild(titletext);\n    this.root.appendChild(titlebar);\n    this.header = titletext;\n};\n\nmpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._init_canvas = function () {\n    var fig = this;\n\n    var canvas_div = (this.canvas_div = document.createElement('div'));\n    canvas_div.setAttribute(\n        'style',\n        'border: 1px solid #ddd;' +\n            'box-sizing: content-box;' +\n            'clear: both;' +\n            'min-height: 1px;' +\n            'min-width: 1px;' +\n            'outline: 0;' +\n            'overflow: hidden;' +\n            'position: relative;' +\n            'resize: both;'\n    );\n\n    function on_keyboard_event_closure(name) {\n        return function (event) {\n            return fig.key_event(event, name);\n        };\n    }\n\n    canvas_div.addEventListener(\n        'keydown',\n        on_keyboard_event_closure('key_press')\n    );\n    canvas_div.addEventListener(\n        'keyup',\n        on_keyboard_event_closure('key_release')\n    );\n\n    this._canvas_extra_style(canvas_div);\n    this.root.appendChild(canvas_div);\n\n    var canvas = (this.canvas = document.createElement('canvas'));\n    canvas.classList.add('mpl-canvas');\n    canvas.setAttribute('style', 'box-sizing: content-box;');\n\n    this.context = canvas.getContext('2d');\n\n    var backingStore =\n        this.context.backingStorePixelRatio ||\n        this.context.webkitBackingStorePixelRatio ||\n        this.context.mozBackingStorePixelRatio ||\n        this.context.msBackingStorePixelRatio ||\n        this.context.oBackingStorePixelRatio ||\n        this.context.backingStorePixelRatio ||\n        1;\n\n    this.ratio = (window.devicePixelRatio || 1) / backingStore;\n\n    var rubberband_canvas = (this.rubberband_canvas = document.createElement(\n        'canvas'\n    ));\n    rubberband_canvas.setAttribute(\n        'style',\n        'box-sizing: content-box; position: absolute; left: 0; top: 0; z-index: 1;'\n    );\n\n    // Apply a ponyfill if ResizeObserver is not implemented by browser.\n    if (this.ResizeObserver === undefined) {\n        if (window.ResizeObserver !== undefined) {\n            this.ResizeObserver = window.ResizeObserver;\n        } else {\n            var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n            this.ResizeObserver = obs.ResizeObserver;\n        }\n    }\n\n    this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n        var nentries = entries.length;\n        for (var i = 0; i < nentries; i++) {\n            var entry = entries[i];\n            var width, height;\n            if (entry.contentBoxSize) {\n                if (entry.contentBoxSize instanceof Array) {\n                    // Chrome 84 implements new version of spec.\n                    width = entry.contentBoxSize[0].inlineSize;\n                    height = entry.contentBoxSize[0].blockSize;\n                } else {\n                    // Firefox implements old version of spec.\n                    width = entry.contentBoxSize.inlineSize;\n                    height = entry.contentBoxSize.blockSize;\n                }\n            } else {\n                // Chrome <84 implements even older version of spec.\n                width = entry.contentRect.width;\n                height = entry.contentRect.height;\n            }\n\n            // Keep the size of the canvas and rubber band canvas in sync with\n            // the canvas container.\n            if (entry.devicePixelContentBoxSize) {\n                // Chrome 84 implements new version of spec.\n                canvas.setAttribute(\n                    'width',\n                    entry.devicePixelContentBoxSize[0].inlineSize\n                );\n                canvas.setAttribute(\n                    'height',\n                    entry.devicePixelContentBoxSize[0].blockSize\n                );\n            } else {\n                canvas.setAttribute('width', width * fig.ratio);\n                canvas.setAttribute('height', height * fig.ratio);\n            }\n            canvas.setAttribute(\n                'style',\n                'width: ' + width + 'px; height: ' + height + 'px;'\n            );\n\n            rubberband_canvas.setAttribute('width', width);\n            rubberband_canvas.setAttribute('height', height);\n\n            // And update the size in Python. We ignore the initial 0/0 size\n            // that occurs as the element is placed into the DOM, which should\n            // otherwise not happen due to the minimum size styling.\n            if (fig.ws.readyState == 1 && width != 0 && height != 0) {\n                fig.request_resize(width, height);\n            }\n        }\n    });\n    this.resizeObserverInstance.observe(canvas_div);\n\n    function on_mouse_event_closure(name) {\n        return function (event) {\n            return fig.mouse_event(event, name);\n        };\n    }\n\n    rubberband_canvas.addEventListener(\n        'mousedown',\n        on_mouse_event_closure('button_press')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseup',\n        on_mouse_event_closure('button_release')\n    );\n    rubberband_canvas.addEventListener(\n        'dblclick',\n        on_mouse_event_closure('dblclick')\n    );\n    // Throttle sequential mouse events to 1 every 20ms.\n    rubberband_canvas.addEventListener(\n        'mousemove',\n        on_mouse_event_closure('motion_notify')\n    );\n\n    rubberband_canvas.addEventListener(\n        'mouseenter',\n        on_mouse_event_closure('figure_enter')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseleave',\n        on_mouse_event_closure('figure_leave')\n    );\n\n    canvas_div.addEventListener('wheel', function (event) {\n        if (event.deltaY < 0) {\n            event.step = 1;\n        } else {\n            event.step = -1;\n        }\n        on_mouse_event_closure('scroll')(event);\n    });\n\n    canvas_div.appendChild(canvas);\n    canvas_div.appendChild(rubberband_canvas);\n\n    this.rubberband_context = rubberband_canvas.getContext('2d');\n    this.rubberband_context.strokeStyle = '#000000';\n\n    this._resize_canvas = function (width, height, forward) {\n        if (forward) {\n            canvas_div.style.width = width + 'px';\n            canvas_div.style.height = height + 'px';\n        }\n    };\n\n    // Disable right mouse context menu.\n    this.rubberband_canvas.addEventListener('contextmenu', function (_e) {\n        event.preventDefault();\n        return false;\n    });\n\n    function set_focus() {\n        canvas.focus();\n        canvas_div.focus();\n    }\n\n    window.setTimeout(set_focus, 100);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'mpl-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'mpl-button-group';\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'mpl-button-group';\n            continue;\n        }\n\n        var button = (fig.buttons[name] = document.createElement('button'));\n        button.classList = 'mpl-widget';\n        button.setAttribute('role', 'button');\n        button.setAttribute('aria-disabled', 'false');\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n\n        var icon_img = document.createElement('img');\n        icon_img.src = '_images/' + image + '.png';\n        icon_img.srcset = '_images/' + image + '_large.png 2x';\n        icon_img.alt = tooltip;\n        button.appendChild(icon_img);\n\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    var fmt_picker = document.createElement('select');\n    fmt_picker.classList = 'mpl-widget';\n    toolbar.appendChild(fmt_picker);\n    this.format_dropdown = fmt_picker;\n\n    for (var ind in mpl.extensions) {\n        var fmt = mpl.extensions[ind];\n        var option = document.createElement('option');\n        option.selected = fmt === mpl.default_extension;\n        option.innerHTML = fmt;\n        fmt_picker.appendChild(option);\n    }\n\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n};\n\nmpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n    // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n    // which will in turn request a refresh of the image.\n    this.send_message('resize', { width: x_pixels, height: y_pixels });\n};\n\nmpl.figure.prototype.send_message = function (type, properties) {\n    properties['type'] = type;\n    properties['figure_id'] = this.id;\n    this.ws.send(JSON.stringify(properties));\n};\n\nmpl.figure.prototype.send_draw_message = function () {\n    if (!this.waiting) {\n        this.waiting = true;\n        this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    var format_dropdown = fig.format_dropdown;\n    var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n    fig.ondownload(fig, format);\n};\n\nmpl.figure.prototype.handle_resize = function (fig, msg) {\n    var size = msg['size'];\n    if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n        fig._resize_canvas(size[0], size[1], msg['forward']);\n        fig.send_message('refresh', {});\n    }\n};\n\nmpl.figure.prototype.handle_rubberband = function (fig, msg) {\n    var x0 = msg['x0'] / fig.ratio;\n    var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n    var x1 = msg['x1'] / fig.ratio;\n    var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n    x0 = Math.floor(x0) + 0.5;\n    y0 = Math.floor(y0) + 0.5;\n    x1 = Math.floor(x1) + 0.5;\n    y1 = Math.floor(y1) + 0.5;\n    var min_x = Math.min(x0, x1);\n    var min_y = Math.min(y0, y1);\n    var width = Math.abs(x1 - x0);\n    var height = Math.abs(y1 - y0);\n\n    fig.rubberband_context.clearRect(\n        0,\n        0,\n        fig.canvas.width / fig.ratio,\n        fig.canvas.height / fig.ratio\n    );\n\n    fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n};\n\nmpl.figure.prototype.handle_figure_label = function (fig, msg) {\n    // Updates the figure title.\n    fig.header.textContent = msg['label'];\n};\n\nmpl.figure.prototype.handle_cursor = function (fig, msg) {\n    fig.rubberband_canvas.style.cursor = msg['cursor'];\n};\n\nmpl.figure.prototype.handle_message = function (fig, msg) {\n    fig.message.textContent = msg['message'];\n};\n\nmpl.figure.prototype.handle_draw = function (fig, _msg) {\n    // Request the server to send over a new figure.\n    fig.send_draw_message();\n};\n\nmpl.figure.prototype.handle_image_mode = function (fig, msg) {\n    fig.image_mode = msg['mode'];\n};\n\nmpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n    for (var key in msg) {\n        if (!(key in fig.buttons)) {\n            continue;\n        }\n        fig.buttons[key].disabled = !msg[key];\n        fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n    }\n};\n\nmpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n    if (msg['mode'] === 'PAN') {\n        fig.buttons['Pan'].classList.add('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    } else if (msg['mode'] === 'ZOOM') {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.add('active');\n    } else {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    }\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Called whenever the canvas gets updated.\n    this.send_message('ack', {});\n};\n\n// A function to construct a web socket function for onmessage handling.\n// Called in the figure constructor.\nmpl.figure.prototype._make_on_message_function = function (fig) {\n    return function socket_on_message(evt) {\n        if (evt.data instanceof Blob) {\n            var img = evt.data;\n            if (img.type !== 'image/png') {\n                /* FIXME: We get \"Resource interpreted as Image but\n                 * transferred with MIME type text/plain:\" errors on\n                 * Chrome.  But how to set the MIME type?  It doesn't seem\n                 * to be part of the websocket stream */\n                img.type = 'image/png';\n            }\n\n            /* Free the memory for the previous frames */\n            if (fig.imageObj.src) {\n                (window.URL || window.webkitURL).revokeObjectURL(\n                    fig.imageObj.src\n                );\n            }\n\n            fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n                img\n            );\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        } else if (\n            typeof evt.data === 'string' &&\n            evt.data.slice(0, 21) === 'data:image/png;base64'\n        ) {\n            fig.imageObj.src = evt.data;\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        }\n\n        var msg = JSON.parse(evt.data);\n        var msg_type = msg['type'];\n\n        // Call the  \"handle_{type}\" callback, which takes\n        // the figure and JSON message as its only arguments.\n        try {\n            var callback = fig['handle_' + msg_type];\n        } catch (e) {\n            console.log(\n                \"No handler for the '\" + msg_type + \"' message type: \",\n                msg\n            );\n            return;\n        }\n\n        if (callback) {\n            try {\n                // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n                callback(fig, msg);\n            } catch (e) {\n                console.log(\n                    \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n                    e,\n                    e.stack,\n                    msg\n                );\n            }\n        }\n    };\n};\n\n// from https://stackoverflow.com/questions/1114465/getting-mouse-location-in-canvas\nmpl.findpos = function (e) {\n    //this section is from http://www.quirksmode.org/js/events_properties.html\n    var targ;\n    if (!e) {\n        e = window.event;\n    }\n    if (e.target) {\n        targ = e.target;\n    } else if (e.srcElement) {\n        targ = e.srcElement;\n    }\n    if (targ.nodeType === 3) {\n        // defeat Safari bug\n        targ = targ.parentNode;\n    }\n\n    // pageX,Y are the mouse positions relative to the document\n    var boundingRect = targ.getBoundingClientRect();\n    var x = e.pageX - (boundingRect.left + document.body.scrollLeft);\n    var y = e.pageY - (boundingRect.top + document.body.scrollTop);\n\n    return { x: x, y: y };\n};\n\n/*\n * return a copy of an object with only non-object keys\n * we need this to avoid circular references\n * https://stackoverflow.com/a/24161582/3208463\n */\nfunction simpleKeys(original) {\n    return Object.keys(original).reduce(function (obj, key) {\n        if (typeof original[key] !== 'object') {\n            obj[key] = original[key];\n        }\n        return obj;\n    }, {});\n}\n\nmpl.figure.prototype.mouse_event = function (event, name) {\n    var canvas_pos = mpl.findpos(event);\n\n    if (name === 'button_press') {\n        this.canvas.focus();\n        this.canvas_div.focus();\n    }\n\n    var x = canvas_pos.x * this.ratio;\n    var y = canvas_pos.y * this.ratio;\n\n    this.send_message(name, {\n        x: x,\n        y: y,\n        button: event.button,\n        step: event.step,\n        guiEvent: simpleKeys(event),\n    });\n\n    /* This prevents the web browser from automatically changing to\n     * the text insertion cursor when the button is pressed.  We want\n     * to control all of the cursor setting manually through the\n     * 'cursor' event from matplotlib */\n    event.preventDefault();\n    return false;\n};\n\nmpl.figure.prototype._key_event_extra = function (_event, _name) {\n    // Handle any extra behaviour associated with a key event\n};\n\nmpl.figure.prototype.key_event = function (event, name) {\n    // Prevent repeat events\n    if (name === 'key_press') {\n        if (event.key === this._key) {\n            return;\n        } else {\n            this._key = event.key;\n        }\n    }\n    if (name === 'key_release') {\n        this._key = null;\n    }\n\n    var value = '';\n    if (event.ctrlKey && event.key !== 'Control') {\n        value += 'ctrl+';\n    }\n    else if (event.altKey && event.key !== 'Alt') {\n        value += 'alt+';\n    }\n    else if (event.shiftKey && event.key !== 'Shift') {\n        value += 'shift+';\n    }\n\n    value += 'k' + event.key;\n\n    this._key_event_extra(event, name);\n\n    this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n    return false;\n};\n\nmpl.figure.prototype.toolbar_button_onclick = function (name) {\n    if (name === 'download') {\n        this.handle_save(this, null);\n    } else {\n        this.send_message('toolbar_button', { name: name });\n    }\n};\n\nmpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n    this.message.textContent = tooltip;\n};\n\n///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n// prettier-ignore\nvar _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\nmpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home icon-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left icon-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right icon-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows icon-move\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis\", \"fa fa-square-o icon-check-empty\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o icon-save\", \"download\"]];\n\nmpl.extensions = [\"eps\", \"jpeg\", \"pgf\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\"];\n\nmpl.default_extension = \"png\";/* global mpl */\n\nvar comm_websocket_adapter = function (comm) {\n    // Create a \"websocket\"-like object which calls the given IPython comm\n    // object with the appropriate methods. Currently this is a non binary\n    // socket, so there is still some room for performance tuning.\n    var ws = {};\n\n    ws.binaryType = comm.kernel.ws.binaryType;\n    ws.readyState = comm.kernel.ws.readyState;\n    function updateReadyState(_event) {\n        if (comm.kernel.ws) {\n            ws.readyState = comm.kernel.ws.readyState;\n        } else {\n            ws.readyState = 3; // Closed state.\n        }\n    }\n    comm.kernel.ws.addEventListener('open', updateReadyState);\n    comm.kernel.ws.addEventListener('close', updateReadyState);\n    comm.kernel.ws.addEventListener('error', updateReadyState);\n\n    ws.close = function () {\n        comm.close();\n    };\n    ws.send = function (m) {\n        //console.log('sending', m);\n        comm.send(m);\n    };\n    // Register the callback with on_msg.\n    comm.on_msg(function (msg) {\n        //console.log('receiving', msg['content']['data'], msg);\n        var data = msg['content']['data'];\n        if (data['blob'] !== undefined) {\n            data = {\n                data: new Blob(msg['buffers'], { type: data['blob'] }),\n            };\n        }\n        // Pass the mpl event to the overridden (by mpl) onmessage function.\n        ws.onmessage(data);\n    });\n    return ws;\n};\n\nmpl.mpl_figure_comm = function (comm, msg) {\n    // This is the function which gets called when the mpl process\n    // starts-up an IPython Comm through the \"matplotlib\" channel.\n\n    var id = msg.content.data.id;\n    // Get hold of the div created by the display call when the Comm\n    // socket was opened in Python.\n    var element = document.getElementById(id);\n    var ws_proxy = comm_websocket_adapter(comm);\n\n    function ondownload(figure, _format) {\n        window.open(figure.canvas.toDataURL());\n    }\n\n    var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n\n    // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n    // web socket which is closed, not our websocket->open comm proxy.\n    ws_proxy.onopen();\n\n    fig.parent_element = element;\n    fig.cell_info = mpl.find_output_cell(\"<div id='\" + id + \"'></div>\");\n    if (!fig.cell_info) {\n        console.error('Failed to find cell for figure', id, fig);\n        return;\n    }\n    fig.cell_info[0].output_area.element.on(\n        'cleared',\n        { fig: fig },\n        fig._remove_fig_handler\n    );\n};\n\nmpl.figure.prototype.handle_close = function (fig, msg) {\n    var width = fig.canvas.width / fig.ratio;\n    fig.cell_info[0].output_area.element.off(\n        'cleared',\n        fig._remove_fig_handler\n    );\n    fig.resizeObserverInstance.unobserve(fig.canvas_div);\n\n    // Update the output cell to use the data from the current canvas.\n    fig.push_to_output();\n    var dataURL = fig.canvas.toDataURL();\n    // Re-enable the keyboard manager in IPython - without this line, in FF,\n    // the notebook keyboard shortcuts fail.\n    IPython.keyboard_manager.enable();\n    fig.parent_element.innerHTML =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n    fig.close_ws(fig, msg);\n};\n\nmpl.figure.prototype.close_ws = function (fig, msg) {\n    fig.send_message('closing', msg);\n    // fig.ws.close()\n};\n\nmpl.figure.prototype.push_to_output = function (_remove_interactive) {\n    // Turn the data on the canvas into data in the output cell.\n    var width = this.canvas.width / this.ratio;\n    var dataURL = this.canvas.toDataURL();\n    this.cell_info[1]['text/html'] =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Tell IPython that the notebook contents must change.\n    IPython.notebook.set_dirty(true);\n    this.send_message('ack', {});\n    var fig = this;\n    // Wait a second, then push the new image to the DOM so\n    // that it is saved nicely (might be nice to debounce this).\n    setTimeout(function () {\n        fig.push_to_output();\n    }, 1000);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'btn-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'btn-group';\n    var button;\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'btn-group';\n            continue;\n        }\n\n        button = fig.buttons[name] = document.createElement('button');\n        button.classList = 'btn btn-default';\n        button.href = '#';\n        button.title = name;\n        button.innerHTML = '<i class=\"fa ' + image + ' fa-lg\"></i>';\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    // Add the status bar.\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message pull-right';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n\n    // Add the close button to the window.\n    var buttongrp = document.createElement('div');\n    buttongrp.classList = 'btn-group inline pull-right';\n    button = document.createElement('button');\n    button.classList = 'btn btn-mini btn-primary';\n    button.href = '#';\n    button.title = 'Stop Interaction';\n    button.innerHTML = '<i class=\"fa fa-power-off icon-remove icon-large\"></i>';\n    button.addEventListener('click', function (_evt) {\n        fig.handle_close(fig, {});\n    });\n    button.addEventListener(\n        'mouseover',\n        on_mouseover_closure('Stop Interaction')\n    );\n    buttongrp.appendChild(button);\n    var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n    titlebar.insertBefore(buttongrp, titlebar.firstChild);\n};\n\nmpl.figure.prototype._remove_fig_handler = function (event) {\n    var fig = event.data.fig;\n    if (event.target !== this) {\n        // Ignore bubbled events from children.\n        return;\n    }\n    fig.close_ws(fig, {});\n};\n\nmpl.figure.prototype._root_extra_style = function (el) {\n    el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n};\n\nmpl.figure.prototype._canvas_extra_style = function (el) {\n    // this is important to make the div 'focusable\n    el.setAttribute('tabindex', 0);\n    // reach out to IPython and tell the keyboard manager to turn it's self\n    // off when our div gets focus\n\n    // location in version 3\n    if (IPython.notebook.keyboard_manager) {\n        IPython.notebook.keyboard_manager.register_events(el);\n    } else {\n        // location in version 2\n        IPython.keyboard_manager.register_events(el);\n    }\n};\n\nmpl.figure.prototype._key_event_extra = function (event, _name) {\n    // Check for shift+enter\n    if (event.shiftKey && event.which === 13) {\n        this.canvas_div.blur();\n        // select the cell after this one\n        var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n        IPython.notebook.select(index + 1);\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    fig.ondownload(fig, null);\n};\n\nmpl.find_output_cell = function (html_output) {\n    // Return the cell and output element which can be found *uniquely* in the notebook.\n    // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n    // IPython event is triggered only after the cells have been serialised, which for\n    // our purposes (turning an active figure into a static one), is too late.\n    var cells = IPython.notebook.get_cells();\n    var ncells = cells.length;\n    for (var i = 0; i < ncells; i++) {\n        var cell = cells[i];\n        if (cell.cell_type === 'code') {\n            for (var j = 0; j < cell.output_area.outputs.length; j++) {\n                var data = cell.output_area.outputs[j];\n                if (data.data) {\n                    // IPython >= 3 moved mimebundle to data attribute of output\n                    data = data.data;\n                }\n                if (data['text/html'] === html_output) {\n                    return [cell, data, j];\n                }\n            }\n        }\n    }\n};\n\n// Register the function which deals with the matplotlib target/channel.\n// The kernel may be null if the page has been refreshed.\nif (IPython.notebook.kernel !== null) {\n    IPython.notebook.kernel.comm_manager.register_target(\n        'matplotlib',\n        mpl.mpl_figure_comm\n    );\n}\n",
      "text/plain": [
       "<IPython.core.display.Javascript object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<img src=\"data:image/png;base64,[encoded data, 42224 characters]\" width=\"640\">"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "%matplotlib notebook\n",
    "shotNum = \"0009\"\n",
    "filePath = folderPath + \"/\" + shotNum + \"/*.h5\"\n",
    "\n",
    "dataSetDict = {\n",
    "    dskey[groupList[i]]: read_hdf5_file(filePath, groupList[i], excludeAxis = ['sweep_start_freq', 'sweep_stop_freq'])\n",
    "    for i in [0]\n",
    "}\n",
    "\n",
    "dataSet = dataSetDict[\"camera_0\"]\n",
    "\n",
    "print_scanAxis(dataSet)\n",
    "\n",
    "scanAxis = get_scanAxis(dataSet)\n",
    "\n",
    "dataSet = auto_rechunk(dataSet)\n",
    "\n",
    "dataSet = imageAnalyser.get_absorption_images(dataSet)\n",
    "\n",
    "imageAnalyser.center = (800, 900)\n",
    "imageAnalyser.span = (300, 300)\n",
    "imageAnalyser.fraction = (0.1, 0.1)\n",
    "\n",
    "dataSet_cropOD = imageAnalyser.crop_image(dataSet.OD)\n",
    "dataSet_cropOD = imageAnalyser.substract_offset(dataSet_cropOD).load()\n",
    "\n",
    "Ncount = imageAnalyser.get_Ncount(dataSet_cropOD)\n",
    "Ncount_mean = calculate_mean(Ncount)\n",
    "Ncount_std = calculate_std(Ncount)\n",
    "\n",
    "fig = plt.figure()\n",
    "ax = fig.gca()\n",
    "Ncount_mean.plot.errorbar(ax=ax, yerr = None, fmt='ob')\n",
    "plt.ylabel('NCount')\n",
    "plt.tight_layout()\n",
    "plt.grid(visible=1)\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 75,
   "metadata": {},
   "outputs": [],
   "source": [
    "dataSet_cropOD_chunk = dataSet_cropOD.chunk((1, 1, 300, 300))\n",
    "fitAnalyser = FitAnalyser(\"Gaussian-2D\", fitDim=2)\n",
    "params = fitAnalyser.guess(dataSet_cropOD_chunk, dask=\"parallelized\")\n",
    "fitResult = fitAnalyser.fit(dataSet_cropOD_chunk, params, dask=\"parallelized\").load()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 76,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/javascript": "/* Put everything inside the global mpl namespace */\n/* global mpl */\nwindow.mpl = {};\n\nmpl.get_websocket_type = function () {\n    if (typeof WebSocket !== 'undefined') {\n        return WebSocket;\n    } else if (typeof MozWebSocket !== 'undefined') {\n        return MozWebSocket;\n    } else {\n        alert(\n            'Your browser does not have WebSocket support. ' +\n                'Please try Chrome, Safari or Firefox ≥ 6. ' +\n                'Firefox 4 and 5 are also supported but you ' +\n                'have to enable WebSockets in about:config.'\n        );\n    }\n};\n\nmpl.figure = function (figure_id, websocket, ondownload, parent_element) {\n    this.id = figure_id;\n\n    this.ws = websocket;\n\n    this.supports_binary = this.ws.binaryType !== undefined;\n\n    if (!this.supports_binary) {\n        var warnings = document.getElementById('mpl-warnings');\n        if (warnings) {\n            warnings.style.display = 'block';\n            warnings.textContent =\n                'This browser does not support binary websocket messages. ' +\n                'Performance may be slow.';\n        }\n    }\n\n    this.imageObj = new Image();\n\n    this.context = undefined;\n    this.message = undefined;\n    this.canvas = undefined;\n    this.rubberband_canvas = undefined;\n    this.rubberband_context = undefined;\n    this.format_dropdown = undefined;\n\n    this.image_mode = 'full';\n\n    this.root = document.createElement('div');\n    this.root.setAttribute('style', 'display: inline-block');\n    this._root_extra_style(this.root);\n\n    parent_element.appendChild(this.root);\n\n    this._init_header(this);\n    this._init_canvas(this);\n    this._init_toolbar(this);\n\n    var fig = this;\n\n    this.waiting = false;\n\n    this.ws.onopen = function () {\n        fig.send_message('supports_binary', { value: fig.supports_binary });\n        fig.send_message('send_image_mode', {});\n        if (fig.ratio !== 1) {\n            fig.send_message('set_device_pixel_ratio', {\n                device_pixel_ratio: fig.ratio,\n            });\n        }\n        fig.send_message('refresh', {});\n    };\n\n    this.imageObj.onload = function () {\n        if (fig.image_mode === 'full') {\n            // Full images could contain transparency (where diff images\n            // almost always do), so we need to clear the canvas so that\n            // there is no ghosting.\n            fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n        }\n        fig.context.drawImage(fig.imageObj, 0, 0);\n    };\n\n    this.imageObj.onunload = function () {\n        fig.ws.close();\n    };\n\n    this.ws.onmessage = this._make_on_message_function(this);\n\n    this.ondownload = ondownload;\n};\n\nmpl.figure.prototype._init_header = function () {\n    var titlebar = document.createElement('div');\n    titlebar.classList =\n        'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n    var titletext = document.createElement('div');\n    titletext.classList = 'ui-dialog-title';\n    titletext.setAttribute(\n        'style',\n        'width: 100%; text-align: center; padding: 3px;'\n    );\n    titlebar.appendChild(titletext);\n    this.root.appendChild(titlebar);\n    this.header = titletext;\n};\n\nmpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._init_canvas = function () {\n    var fig = this;\n\n    var canvas_div = (this.canvas_div = document.createElement('div'));\n    canvas_div.setAttribute(\n        'style',\n        'border: 1px solid #ddd;' +\n            'box-sizing: content-box;' +\n            'clear: both;' +\n            'min-height: 1px;' +\n            'min-width: 1px;' +\n            'outline: 0;' +\n            'overflow: hidden;' +\n            'position: relative;' +\n            'resize: both;'\n    );\n\n    function on_keyboard_event_closure(name) {\n        return function (event) {\n            return fig.key_event(event, name);\n        };\n    }\n\n    canvas_div.addEventListener(\n        'keydown',\n        on_keyboard_event_closure('key_press')\n    );\n    canvas_div.addEventListener(\n        'keyup',\n        on_keyboard_event_closure('key_release')\n    );\n\n    this._canvas_extra_style(canvas_div);\n    this.root.appendChild(canvas_div);\n\n    var canvas = (this.canvas = document.createElement('canvas'));\n    canvas.classList.add('mpl-canvas');\n    canvas.setAttribute('style', 'box-sizing: content-box;');\n\n    this.context = canvas.getContext('2d');\n\n    var backingStore =\n        this.context.backingStorePixelRatio ||\n        this.context.webkitBackingStorePixelRatio ||\n        this.context.mozBackingStorePixelRatio ||\n        this.context.msBackingStorePixelRatio ||\n        this.context.oBackingStorePixelRatio ||\n        this.context.backingStorePixelRatio ||\n        1;\n\n    this.ratio = (window.devicePixelRatio || 1) / backingStore;\n\n    var rubberband_canvas = (this.rubberband_canvas = document.createElement(\n        'canvas'\n    ));\n    rubberband_canvas.setAttribute(\n        'style',\n        'box-sizing: content-box; position: absolute; left: 0; top: 0; z-index: 1;'\n    );\n\n    // Apply a ponyfill if ResizeObserver is not implemented by browser.\n    if (this.ResizeObserver === undefined) {\n        if (window.ResizeObserver !== undefined) {\n            this.ResizeObserver = window.ResizeObserver;\n        } else {\n            var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n            this.ResizeObserver = obs.ResizeObserver;\n        }\n    }\n\n    this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n        var nentries = entries.length;\n        for (var i = 0; i < nentries; i++) {\n            var entry = entries[i];\n            var width, height;\n            if (entry.contentBoxSize) {\n                if (entry.contentBoxSize instanceof Array) {\n                    // Chrome 84 implements new version of spec.\n                    width = entry.contentBoxSize[0].inlineSize;\n                    height = entry.contentBoxSize[0].blockSize;\n                } else {\n                    // Firefox implements old version of spec.\n                    width = entry.contentBoxSize.inlineSize;\n                    height = entry.contentBoxSize.blockSize;\n                }\n            } else {\n                // Chrome <84 implements even older version of spec.\n                width = entry.contentRect.width;\n                height = entry.contentRect.height;\n            }\n\n            // Keep the size of the canvas and rubber band canvas in sync with\n            // the canvas container.\n            if (entry.devicePixelContentBoxSize) {\n                // Chrome 84 implements new version of spec.\n                canvas.setAttribute(\n                    'width',\n                    entry.devicePixelContentBoxSize[0].inlineSize\n                );\n                canvas.setAttribute(\n                    'height',\n                    entry.devicePixelContentBoxSize[0].blockSize\n                );\n            } else {\n                canvas.setAttribute('width', width * fig.ratio);\n                canvas.setAttribute('height', height * fig.ratio);\n            }\n            canvas.setAttribute(\n                'style',\n                'width: ' + width + 'px; height: ' + height + 'px;'\n            );\n\n            rubberband_canvas.setAttribute('width', width);\n            rubberband_canvas.setAttribute('height', height);\n\n            // And update the size in Python. We ignore the initial 0/0 size\n            // that occurs as the element is placed into the DOM, which should\n            // otherwise not happen due to the minimum size styling.\n            if (fig.ws.readyState == 1 && width != 0 && height != 0) {\n                fig.request_resize(width, height);\n            }\n        }\n    });\n    this.resizeObserverInstance.observe(canvas_div);\n\n    function on_mouse_event_closure(name) {\n        return function (event) {\n            return fig.mouse_event(event, name);\n        };\n    }\n\n    rubberband_canvas.addEventListener(\n        'mousedown',\n        on_mouse_event_closure('button_press')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseup',\n        on_mouse_event_closure('button_release')\n    );\n    rubberband_canvas.addEventListener(\n        'dblclick',\n        on_mouse_event_closure('dblclick')\n    );\n    // Throttle sequential mouse events to 1 every 20ms.\n    rubberband_canvas.addEventListener(\n        'mousemove',\n        on_mouse_event_closure('motion_notify')\n    );\n\n    rubberband_canvas.addEventListener(\n        'mouseenter',\n        on_mouse_event_closure('figure_enter')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseleave',\n        on_mouse_event_closure('figure_leave')\n    );\n\n    canvas_div.addEventListener('wheel', function (event) {\n        if (event.deltaY < 0) {\n            event.step = 1;\n        } else {\n            event.step = -1;\n        }\n        on_mouse_event_closure('scroll')(event);\n    });\n\n    canvas_div.appendChild(canvas);\n    canvas_div.appendChild(rubberband_canvas);\n\n    this.rubberband_context = rubberband_canvas.getContext('2d');\n    this.rubberband_context.strokeStyle = '#000000';\n\n    this._resize_canvas = function (width, height, forward) {\n        if (forward) {\n            canvas_div.style.width = width + 'px';\n            canvas_div.style.height = height + 'px';\n        }\n    };\n\n    // Disable right mouse context menu.\n    this.rubberband_canvas.addEventListener('contextmenu', function (_e) {\n        event.preventDefault();\n        return false;\n    });\n\n    function set_focus() {\n        canvas.focus();\n        canvas_div.focus();\n    }\n\n    window.setTimeout(set_focus, 100);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'mpl-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'mpl-button-group';\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'mpl-button-group';\n            continue;\n        }\n\n        var button = (fig.buttons[name] = document.createElement('button'));\n        button.classList = 'mpl-widget';\n        button.setAttribute('role', 'button');\n        button.setAttribute('aria-disabled', 'false');\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n\n        var icon_img = document.createElement('img');\n        icon_img.src = '_images/' + image + '.png';\n        icon_img.srcset = '_images/' + image + '_large.png 2x';\n        icon_img.alt = tooltip;\n        button.appendChild(icon_img);\n\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    var fmt_picker = document.createElement('select');\n    fmt_picker.classList = 'mpl-widget';\n    toolbar.appendChild(fmt_picker);\n    this.format_dropdown = fmt_picker;\n\n    for (var ind in mpl.extensions) {\n        var fmt = mpl.extensions[ind];\n        var option = document.createElement('option');\n        option.selected = fmt === mpl.default_extension;\n        option.innerHTML = fmt;\n        fmt_picker.appendChild(option);\n    }\n\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n};\n\nmpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n    // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n    // which will in turn request a refresh of the image.\n    this.send_message('resize', { width: x_pixels, height: y_pixels });\n};\n\nmpl.figure.prototype.send_message = function (type, properties) {\n    properties['type'] = type;\n    properties['figure_id'] = this.id;\n    this.ws.send(JSON.stringify(properties));\n};\n\nmpl.figure.prototype.send_draw_message = function () {\n    if (!this.waiting) {\n        this.waiting = true;\n        this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    var format_dropdown = fig.format_dropdown;\n    var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n    fig.ondownload(fig, format);\n};\n\nmpl.figure.prototype.handle_resize = function (fig, msg) {\n    var size = msg['size'];\n    if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n        fig._resize_canvas(size[0], size[1], msg['forward']);\n        fig.send_message('refresh', {});\n    }\n};\n\nmpl.figure.prototype.handle_rubberband = function (fig, msg) {\n    var x0 = msg['x0'] / fig.ratio;\n    var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n    var x1 = msg['x1'] / fig.ratio;\n    var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n    x0 = Math.floor(x0) + 0.5;\n    y0 = Math.floor(y0) + 0.5;\n    x1 = Math.floor(x1) + 0.5;\n    y1 = Math.floor(y1) + 0.5;\n    var min_x = Math.min(x0, x1);\n    var min_y = Math.min(y0, y1);\n    var width = Math.abs(x1 - x0);\n    var height = Math.abs(y1 - y0);\n\n    fig.rubberband_context.clearRect(\n        0,\n        0,\n        fig.canvas.width / fig.ratio,\n        fig.canvas.height / fig.ratio\n    );\n\n    fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n};\n\nmpl.figure.prototype.handle_figure_label = function (fig, msg) {\n    // Updates the figure title.\n    fig.header.textContent = msg['label'];\n};\n\nmpl.figure.prototype.handle_cursor = function (fig, msg) {\n    fig.rubberband_canvas.style.cursor = msg['cursor'];\n};\n\nmpl.figure.prototype.handle_message = function (fig, msg) {\n    fig.message.textContent = msg['message'];\n};\n\nmpl.figure.prototype.handle_draw = function (fig, _msg) {\n    // Request the server to send over a new figure.\n    fig.send_draw_message();\n};\n\nmpl.figure.prototype.handle_image_mode = function (fig, msg) {\n    fig.image_mode = msg['mode'];\n};\n\nmpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n    for (var key in msg) {\n        if (!(key in fig.buttons)) {\n            continue;\n        }\n        fig.buttons[key].disabled = !msg[key];\n        fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n    }\n};\n\nmpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n    if (msg['mode'] === 'PAN') {\n        fig.buttons['Pan'].classList.add('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    } else if (msg['mode'] === 'ZOOM') {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.add('active');\n    } else {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    }\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Called whenever the canvas gets updated.\n    this.send_message('ack', {});\n};\n\n// A function to construct a web socket function for onmessage handling.\n// Called in the figure constructor.\nmpl.figure.prototype._make_on_message_function = function (fig) {\n    return function socket_on_message(evt) {\n        if (evt.data instanceof Blob) {\n            var img = evt.data;\n            if (img.type !== 'image/png') {\n                /* FIXME: We get \"Resource interpreted as Image but\n                 * transferred with MIME type text/plain:\" errors on\n                 * Chrome.  But how to set the MIME type?  It doesn't seem\n                 * to be part of the websocket stream */\n                img.type = 'image/png';\n            }\n\n            /* Free the memory for the previous frames */\n            if (fig.imageObj.src) {\n                (window.URL || window.webkitURL).revokeObjectURL(\n                    fig.imageObj.src\n                );\n            }\n\n            fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n                img\n            );\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        } else if (\n            typeof evt.data === 'string' &&\n            evt.data.slice(0, 21) === 'data:image/png;base64'\n        ) {\n            fig.imageObj.src = evt.data;\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        }\n\n        var msg = JSON.parse(evt.data);\n        var msg_type = msg['type'];\n\n        // Call the  \"handle_{type}\" callback, which takes\n        // the figure and JSON message as its only arguments.\n        try {\n            var callback = fig['handle_' + msg_type];\n        } catch (e) {\n            console.log(\n                \"No handler for the '\" + msg_type + \"' message type: \",\n                msg\n            );\n            return;\n        }\n\n        if (callback) {\n            try {\n                // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n                callback(fig, msg);\n            } catch (e) {\n                console.log(\n                    \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n                    e,\n                    e.stack,\n                    msg\n                );\n            }\n        }\n    };\n};\n\n// from https://stackoverflow.com/questions/1114465/getting-mouse-location-in-canvas\nmpl.findpos = function (e) {\n    //this section is from http://www.quirksmode.org/js/events_properties.html\n    var targ;\n    if (!e) {\n        e = window.event;\n    }\n    if (e.target) {\n        targ = e.target;\n    } else if (e.srcElement) {\n        targ = e.srcElement;\n    }\n    if (targ.nodeType === 3) {\n        // defeat Safari bug\n        targ = targ.parentNode;\n    }\n\n    // pageX,Y are the mouse positions relative to the document\n    var boundingRect = targ.getBoundingClientRect();\n    var x = e.pageX - (boundingRect.left + document.body.scrollLeft);\n    var y = e.pageY - (boundingRect.top + document.body.scrollTop);\n\n    return { x: x, y: y };\n};\n\n/*\n * return a copy of an object with only non-object keys\n * we need this to avoid circular references\n * https://stackoverflow.com/a/24161582/3208463\n */\nfunction simpleKeys(original) {\n    return Object.keys(original).reduce(function (obj, key) {\n        if (typeof original[key] !== 'object') {\n            obj[key] = original[key];\n        }\n        return obj;\n    }, {});\n}\n\nmpl.figure.prototype.mouse_event = function (event, name) {\n    var canvas_pos = mpl.findpos(event);\n\n    if (name === 'button_press') {\n        this.canvas.focus();\n        this.canvas_div.focus();\n    }\n\n    var x = canvas_pos.x * this.ratio;\n    var y = canvas_pos.y * this.ratio;\n\n    this.send_message(name, {\n        x: x,\n        y: y,\n        button: event.button,\n        step: event.step,\n        guiEvent: simpleKeys(event),\n    });\n\n    /* This prevents the web browser from automatically changing to\n     * the text insertion cursor when the button is pressed.  We want\n     * to control all of the cursor setting manually through the\n     * 'cursor' event from matplotlib */\n    event.preventDefault();\n    return false;\n};\n\nmpl.figure.prototype._key_event_extra = function (_event, _name) {\n    // Handle any extra behaviour associated with a key event\n};\n\nmpl.figure.prototype.key_event = function (event, name) {\n    // Prevent repeat events\n    if (name === 'key_press') {\n        if (event.key === this._key) {\n            return;\n        } else {\n            this._key = event.key;\n        }\n    }\n    if (name === 'key_release') {\n        this._key = null;\n    }\n\n    var value = '';\n    if (event.ctrlKey && event.key !== 'Control') {\n        value += 'ctrl+';\n    }\n    else if (event.altKey && event.key !== 'Alt') {\n        value += 'alt+';\n    }\n    else if (event.shiftKey && event.key !== 'Shift') {\n        value += 'shift+';\n    }\n\n    value += 'k' + event.key;\n\n    this._key_event_extra(event, name);\n\n    this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n    return false;\n};\n\nmpl.figure.prototype.toolbar_button_onclick = function (name) {\n    if (name === 'download') {\n        this.handle_save(this, null);\n    } else {\n        this.send_message('toolbar_button', { name: name });\n    }\n};\n\nmpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n    this.message.textContent = tooltip;\n};\n\n///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n// prettier-ignore\nvar _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\nmpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home icon-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left icon-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right icon-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows icon-move\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis\", \"fa fa-square-o icon-check-empty\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o icon-save\", \"download\"]];\n\nmpl.extensions = [\"eps\", \"jpeg\", \"pgf\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\"];\n\nmpl.default_extension = \"png\";/* global mpl */\n\nvar comm_websocket_adapter = function (comm) {\n    // Create a \"websocket\"-like object which calls the given IPython comm\n    // object with the appropriate methods. Currently this is a non binary\n    // socket, so there is still some room for performance tuning.\n    var ws = {};\n\n    ws.binaryType = comm.kernel.ws.binaryType;\n    ws.readyState = comm.kernel.ws.readyState;\n    function updateReadyState(_event) {\n        if (comm.kernel.ws) {\n            ws.readyState = comm.kernel.ws.readyState;\n        } else {\n            ws.readyState = 3; // Closed state.\n        }\n    }\n    comm.kernel.ws.addEventListener('open', updateReadyState);\n    comm.kernel.ws.addEventListener('close', updateReadyState);\n    comm.kernel.ws.addEventListener('error', updateReadyState);\n\n    ws.close = function () {\n        comm.close();\n    };\n    ws.send = function (m) {\n        //console.log('sending', m);\n        comm.send(m);\n    };\n    // Register the callback with on_msg.\n    comm.on_msg(function (msg) {\n        //console.log('receiving', msg['content']['data'], msg);\n        var data = msg['content']['data'];\n        if (data['blob'] !== undefined) {\n            data = {\n                data: new Blob(msg['buffers'], { type: data['blob'] }),\n            };\n        }\n        // Pass the mpl event to the overridden (by mpl) onmessage function.\n        ws.onmessage(data);\n    });\n    return ws;\n};\n\nmpl.mpl_figure_comm = function (comm, msg) {\n    // This is the function which gets called when the mpl process\n    // starts-up an IPython Comm through the \"matplotlib\" channel.\n\n    var id = msg.content.data.id;\n    // Get hold of the div created by the display call when the Comm\n    // socket was opened in Python.\n    var element = document.getElementById(id);\n    var ws_proxy = comm_websocket_adapter(comm);\n\n    function ondownload(figure, _format) {\n        window.open(figure.canvas.toDataURL());\n    }\n\n    var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n\n    // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n    // web socket which is closed, not our websocket->open comm proxy.\n    ws_proxy.onopen();\n\n    fig.parent_element = element;\n    fig.cell_info = mpl.find_output_cell(\"<div id='\" + id + \"'></div>\");\n    if (!fig.cell_info) {\n        console.error('Failed to find cell for figure', id, fig);\n        return;\n    }\n    fig.cell_info[0].output_area.element.on(\n        'cleared',\n        { fig: fig },\n        fig._remove_fig_handler\n    );\n};\n\nmpl.figure.prototype.handle_close = function (fig, msg) {\n    var width = fig.canvas.width / fig.ratio;\n    fig.cell_info[0].output_area.element.off(\n        'cleared',\n        fig._remove_fig_handler\n    );\n    fig.resizeObserverInstance.unobserve(fig.canvas_div);\n\n    // Update the output cell to use the data from the current canvas.\n    fig.push_to_output();\n    var dataURL = fig.canvas.toDataURL();\n    // Re-enable the keyboard manager in IPython - without this line, in FF,\n    // the notebook keyboard shortcuts fail.\n    IPython.keyboard_manager.enable();\n    fig.parent_element.innerHTML =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n    fig.close_ws(fig, msg);\n};\n\nmpl.figure.prototype.close_ws = function (fig, msg) {\n    fig.send_message('closing', msg);\n    // fig.ws.close()\n};\n\nmpl.figure.prototype.push_to_output = function (_remove_interactive) {\n    // Turn the data on the canvas into data in the output cell.\n    var width = this.canvas.width / this.ratio;\n    var dataURL = this.canvas.toDataURL();\n    this.cell_info[1]['text/html'] =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Tell IPython that the notebook contents must change.\n    IPython.notebook.set_dirty(true);\n    this.send_message('ack', {});\n    var fig = this;\n    // Wait a second, then push the new image to the DOM so\n    // that it is saved nicely (might be nice to debounce this).\n    setTimeout(function () {\n        fig.push_to_output();\n    }, 1000);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'btn-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'btn-group';\n    var button;\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'btn-group';\n            continue;\n        }\n\n        button = fig.buttons[name] = document.createElement('button');\n        button.classList = 'btn btn-default';\n        button.href = '#';\n        button.title = name;\n        button.innerHTML = '<i class=\"fa ' + image + ' fa-lg\"></i>';\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    // Add the status bar.\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message pull-right';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n\n    // Add the close button to the window.\n    var buttongrp = document.createElement('div');\n    buttongrp.classList = 'btn-group inline pull-right';\n    button = document.createElement('button');\n    button.classList = 'btn btn-mini btn-primary';\n    button.href = '#';\n    button.title = 'Stop Interaction';\n    button.innerHTML = '<i class=\"fa fa-power-off icon-remove icon-large\"></i>';\n    button.addEventListener('click', function (_evt) {\n        fig.handle_close(fig, {});\n    });\n    button.addEventListener(\n        'mouseover',\n        on_mouseover_closure('Stop Interaction')\n    );\n    buttongrp.appendChild(button);\n    var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n    titlebar.insertBefore(buttongrp, titlebar.firstChild);\n};\n\nmpl.figure.prototype._remove_fig_handler = function (event) {\n    var fig = event.data.fig;\n    if (event.target !== this) {\n        // Ignore bubbled events from children.\n        return;\n    }\n    fig.close_ws(fig, {});\n};\n\nmpl.figure.prototype._root_extra_style = function (el) {\n    el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n};\n\nmpl.figure.prototype._canvas_extra_style = function (el) {\n    // this is important to make the div 'focusable\n    el.setAttribute('tabindex', 0);\n    // reach out to IPython and tell the keyboard manager to turn it's self\n    // off when our div gets focus\n\n    // location in version 3\n    if (IPython.notebook.keyboard_manager) {\n        IPython.notebook.keyboard_manager.register_events(el);\n    } else {\n        // location in version 2\n        IPython.keyboard_manager.register_events(el);\n    }\n};\n\nmpl.figure.prototype._key_event_extra = function (event, _name) {\n    // Check for shift+enter\n    if (event.shiftKey && event.which === 13) {\n        this.canvas_div.blur();\n        // select the cell after this one\n        var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n        IPython.notebook.select(index + 1);\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    fig.ondownload(fig, null);\n};\n\nmpl.find_output_cell = function (html_output) {\n    // Return the cell and output element which can be found *uniquely* in the notebook.\n    // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n    // IPython event is triggered only after the cells have been serialised, which for\n    // our purposes (turning an active figure into a static one), is too late.\n    var cells = IPython.notebook.get_cells();\n    var ncells = cells.length;\n    for (var i = 0; i < ncells; i++) {\n        var cell = cells[i];\n        if (cell.cell_type === 'code') {\n            for (var j = 0; j < cell.output_area.outputs.length; j++) {\n                var data = cell.output_area.outputs[j];\n                if (data.data) {\n                    // IPython >= 3 moved mimebundle to data attribute of output\n                    data = data.data;\n                }\n                if (data['text/html'] === html_output) {\n                    return [cell, data, j];\n                }\n            }\n        }\n    }\n};\n\n// Register the function which deals with the matplotlib target/channel.\n// The kernel may be null if the page has been refreshed.\nif (IPython.notebook.kernel !== null) {\n    IPython.notebook.kernel.comm_manager.register_target(\n        'matplotlib',\n        mpl.mpl_figure_comm\n    );\n}\n",
      "text/plain": [
       "<IPython.core.display.Javascript object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<img src=\"data:image/png;base64,[encoded data, 61276 characters]\" width=\"640\">"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "val = fitAnalyser.get_fit_value(fitResult)\n",
    "std = fitAnalyser.get_fit_std(fitResult)\n",
    "\n",
    "fitCurve = fitAnalyser.eval(fitResult, x=np.arange(300), y=np.arange(300), dask=\"parallelized\").load()\n",
    "\n",
    "# dataKey = 'sigmax'\n",
    "# dataKey = 'centerx'\n",
    "# dataKey = 'sigmay'\n",
    "dataKey = 'centery'\n",
    "\n",
    "# val_mean = val[dataKey].mean(dim='runs')\n",
    "# std_mean = val[dataKey].std(dim='runs')\n",
    "\n",
    "val_mean = calculate_mean(val[dataKey])\n",
    "std_mean = calculate_std(val[dataKey])\n",
    "\n",
    "fig = plt.figure()\n",
    "ax = fig.gca()\n",
    "\n",
    "val_mean.plot.errorbar(yerr=std_mean, fmt='--ob')\n",
    "\n",
    "plt.grid()\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 79,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/javascript": "/* Put everything inside the global mpl namespace */\n/* global mpl */\nwindow.mpl = {};\n\nmpl.get_websocket_type = function () {\n    if (typeof WebSocket !== 'undefined') {\n        return WebSocket;\n    } else if (typeof MozWebSocket !== 'undefined') {\n        return MozWebSocket;\n    } else {\n        alert(\n            'Your browser does not have WebSocket support. ' +\n                'Please try Chrome, Safari or Firefox ≥ 6. ' +\n                'Firefox 4 and 5 are also supported but you ' +\n                'have to enable WebSockets in about:config.'\n        );\n    }\n};\n\nmpl.figure = function (figure_id, websocket, ondownload, parent_element) {\n    this.id = figure_id;\n\n    this.ws = websocket;\n\n    this.supports_binary = this.ws.binaryType !== undefined;\n\n    if (!this.supports_binary) {\n        var warnings = document.getElementById('mpl-warnings');\n        if (warnings) {\n            warnings.style.display = 'block';\n            warnings.textContent =\n                'This browser does not support binary websocket messages. ' +\n                'Performance may be slow.';\n        }\n    }\n\n    this.imageObj = new Image();\n\n    this.context = undefined;\n    this.message = undefined;\n    this.canvas = undefined;\n    this.rubberband_canvas = undefined;\n    this.rubberband_context = undefined;\n    this.format_dropdown = undefined;\n\n    this.image_mode = 'full';\n\n    this.root = document.createElement('div');\n    this.root.setAttribute('style', 'display: inline-block');\n    this._root_extra_style(this.root);\n\n    parent_element.appendChild(this.root);\n\n    this._init_header(this);\n    this._init_canvas(this);\n    this._init_toolbar(this);\n\n    var fig = this;\n\n    this.waiting = false;\n\n    this.ws.onopen = function () {\n        fig.send_message('supports_binary', { value: fig.supports_binary });\n        fig.send_message('send_image_mode', {});\n        if (fig.ratio !== 1) {\n            fig.send_message('set_device_pixel_ratio', {\n                device_pixel_ratio: fig.ratio,\n            });\n        }\n        fig.send_message('refresh', {});\n    };\n\n    this.imageObj.onload = function () {\n        if (fig.image_mode === 'full') {\n            // Full images could contain transparency (where diff images\n            // almost always do), so we need to clear the canvas so that\n            // there is no ghosting.\n            fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n        }\n        fig.context.drawImage(fig.imageObj, 0, 0);\n    };\n\n    this.imageObj.onunload = function () {\n        fig.ws.close();\n    };\n\n    this.ws.onmessage = this._make_on_message_function(this);\n\n    this.ondownload = ondownload;\n};\n\nmpl.figure.prototype._init_header = function () {\n    var titlebar = document.createElement('div');\n    titlebar.classList =\n        'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n    var titletext = document.createElement('div');\n    titletext.classList = 'ui-dialog-title';\n    titletext.setAttribute(\n        'style',\n        'width: 100%; text-align: center; padding: 3px;'\n    );\n    titlebar.appendChild(titletext);\n    this.root.appendChild(titlebar);\n    this.header = titletext;\n};\n\nmpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._init_canvas = function () {\n    var fig = this;\n\n    var canvas_div = (this.canvas_div = document.createElement('div'));\n    canvas_div.setAttribute(\n        'style',\n        'border: 1px solid #ddd;' +\n            'box-sizing: content-box;' +\n            'clear: both;' +\n            'min-height: 1px;' +\n            'min-width: 1px;' +\n            'outline: 0;' +\n            'overflow: hidden;' +\n            'position: relative;' +\n            'resize: both;'\n    );\n\n    function on_keyboard_event_closure(name) {\n        return function (event) {\n            return fig.key_event(event, name);\n        };\n    }\n\n    canvas_div.addEventListener(\n        'keydown',\n        on_keyboard_event_closure('key_press')\n    );\n    canvas_div.addEventListener(\n        'keyup',\n        on_keyboard_event_closure('key_release')\n    );\n\n    this._canvas_extra_style(canvas_div);\n    this.root.appendChild(canvas_div);\n\n    var canvas = (this.canvas = document.createElement('canvas'));\n    canvas.classList.add('mpl-canvas');\n    canvas.setAttribute('style', 'box-sizing: content-box;');\n\n    this.context = canvas.getContext('2d');\n\n    var backingStore =\n        this.context.backingStorePixelRatio ||\n        this.context.webkitBackingStorePixelRatio ||\n        this.context.mozBackingStorePixelRatio ||\n        this.context.msBackingStorePixelRatio ||\n        this.context.oBackingStorePixelRatio ||\n        this.context.backingStorePixelRatio ||\n        1;\n\n    this.ratio = (window.devicePixelRatio || 1) / backingStore;\n\n    var rubberband_canvas = (this.rubberband_canvas = document.createElement(\n        'canvas'\n    ));\n    rubberband_canvas.setAttribute(\n        'style',\n        'box-sizing: content-box; position: absolute; left: 0; top: 0; z-index: 1;'\n    );\n\n    // Apply a ponyfill if ResizeObserver is not implemented by browser.\n    if (this.ResizeObserver === undefined) {\n        if (window.ResizeObserver !== undefined) {\n            this.ResizeObserver = window.ResizeObserver;\n        } else {\n            var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n            this.ResizeObserver = obs.ResizeObserver;\n        }\n    }\n\n    this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n        var nentries = entries.length;\n        for (var i = 0; i < nentries; i++) {\n            var entry = entries[i];\n            var width, height;\n            if (entry.contentBoxSize) {\n                if (entry.contentBoxSize instanceof Array) {\n                    // Chrome 84 implements new version of spec.\n                    width = entry.contentBoxSize[0].inlineSize;\n                    height = entry.contentBoxSize[0].blockSize;\n                } else {\n                    // Firefox implements old version of spec.\n                    width = entry.contentBoxSize.inlineSize;\n                    height = entry.contentBoxSize.blockSize;\n                }\n            } else {\n                // Chrome <84 implements even older version of spec.\n                width = entry.contentRect.width;\n                height = entry.contentRect.height;\n            }\n\n            // Keep the size of the canvas and rubber band canvas in sync with\n            // the canvas container.\n            if (entry.devicePixelContentBoxSize) {\n                // Chrome 84 implements new version of spec.\n                canvas.setAttribute(\n                    'width',\n                    entry.devicePixelContentBoxSize[0].inlineSize\n                );\n                canvas.setAttribute(\n                    'height',\n                    entry.devicePixelContentBoxSize[0].blockSize\n                );\n            } else {\n                canvas.setAttribute('width', width * fig.ratio);\n                canvas.setAttribute('height', height * fig.ratio);\n            }\n            canvas.setAttribute(\n                'style',\n                'width: ' + width + 'px; height: ' + height + 'px;'\n            );\n\n            rubberband_canvas.setAttribute('width', width);\n            rubberband_canvas.setAttribute('height', height);\n\n            // And update the size in Python. We ignore the initial 0/0 size\n            // that occurs as the element is placed into the DOM, which should\n            // otherwise not happen due to the minimum size styling.\n            if (fig.ws.readyState == 1 && width != 0 && height != 0) {\n                fig.request_resize(width, height);\n            }\n        }\n    });\n    this.resizeObserverInstance.observe(canvas_div);\n\n    function on_mouse_event_closure(name) {\n        return function (event) {\n            return fig.mouse_event(event, name);\n        };\n    }\n\n    rubberband_canvas.addEventListener(\n        'mousedown',\n        on_mouse_event_closure('button_press')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseup',\n        on_mouse_event_closure('button_release')\n    );\n    rubberband_canvas.addEventListener(\n        'dblclick',\n        on_mouse_event_closure('dblclick')\n    );\n    // Throttle sequential mouse events to 1 every 20ms.\n    rubberband_canvas.addEventListener(\n        'mousemove',\n        on_mouse_event_closure('motion_notify')\n    );\n\n    rubberband_canvas.addEventListener(\n        'mouseenter',\n        on_mouse_event_closure('figure_enter')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseleave',\n        on_mouse_event_closure('figure_leave')\n    );\n\n    canvas_div.addEventListener('wheel', function (event) {\n        if (event.deltaY < 0) {\n            event.step = 1;\n        } else {\n            event.step = -1;\n        }\n        on_mouse_event_closure('scroll')(event);\n    });\n\n    canvas_div.appendChild(canvas);\n    canvas_div.appendChild(rubberband_canvas);\n\n    this.rubberband_context = rubberband_canvas.getContext('2d');\n    this.rubberband_context.strokeStyle = '#000000';\n\n    this._resize_canvas = function (width, height, forward) {\n        if (forward) {\n            canvas_div.style.width = width + 'px';\n            canvas_div.style.height = height + 'px';\n        }\n    };\n\n    // Disable right mouse context menu.\n    this.rubberband_canvas.addEventListener('contextmenu', function (_e) {\n        event.preventDefault();\n        return false;\n    });\n\n    function set_focus() {\n        canvas.focus();\n        canvas_div.focus();\n    }\n\n    window.setTimeout(set_focus, 100);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'mpl-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'mpl-button-group';\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'mpl-button-group';\n            continue;\n        }\n\n        var button = (fig.buttons[name] = document.createElement('button'));\n        button.classList = 'mpl-widget';\n        button.setAttribute('role', 'button');\n        button.setAttribute('aria-disabled', 'false');\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n\n        var icon_img = document.createElement('img');\n        icon_img.src = '_images/' + image + '.png';\n        icon_img.srcset = '_images/' + image + '_large.png 2x';\n        icon_img.alt = tooltip;\n        button.appendChild(icon_img);\n\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    var fmt_picker = document.createElement('select');\n    fmt_picker.classList = 'mpl-widget';\n    toolbar.appendChild(fmt_picker);\n    this.format_dropdown = fmt_picker;\n\n    for (var ind in mpl.extensions) {\n        var fmt = mpl.extensions[ind];\n        var option = document.createElement('option');\n        option.selected = fmt === mpl.default_extension;\n        option.innerHTML = fmt;\n        fmt_picker.appendChild(option);\n    }\n\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n};\n\nmpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n    // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n    // which will in turn request a refresh of the image.\n    this.send_message('resize', { width: x_pixels, height: y_pixels });\n};\n\nmpl.figure.prototype.send_message = function (type, properties) {\n    properties['type'] = type;\n    properties['figure_id'] = this.id;\n    this.ws.send(JSON.stringify(properties));\n};\n\nmpl.figure.prototype.send_draw_message = function () {\n    if (!this.waiting) {\n        this.waiting = true;\n        this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    var format_dropdown = fig.format_dropdown;\n    var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n    fig.ondownload(fig, format);\n};\n\nmpl.figure.prototype.handle_resize = function (fig, msg) {\n    var size = msg['size'];\n    if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n        fig._resize_canvas(size[0], size[1], msg['forward']);\n        fig.send_message('refresh', {});\n    }\n};\n\nmpl.figure.prototype.handle_rubberband = function (fig, msg) {\n    var x0 = msg['x0'] / fig.ratio;\n    var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n    var x1 = msg['x1'] / fig.ratio;\n    var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n    x0 = Math.floor(x0) + 0.5;\n    y0 = Math.floor(y0) + 0.5;\n    x1 = Math.floor(x1) + 0.5;\n    y1 = Math.floor(y1) + 0.5;\n    var min_x = Math.min(x0, x1);\n    var min_y = Math.min(y0, y1);\n    var width = Math.abs(x1 - x0);\n    var height = Math.abs(y1 - y0);\n\n    fig.rubberband_context.clearRect(\n        0,\n        0,\n        fig.canvas.width / fig.ratio,\n        fig.canvas.height / fig.ratio\n    );\n\n    fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n};\n\nmpl.figure.prototype.handle_figure_label = function (fig, msg) {\n    // Updates the figure title.\n    fig.header.textContent = msg['label'];\n};\n\nmpl.figure.prototype.handle_cursor = function (fig, msg) {\n    fig.rubberband_canvas.style.cursor = msg['cursor'];\n};\n\nmpl.figure.prototype.handle_message = function (fig, msg) {\n    fig.message.textContent = msg['message'];\n};\n\nmpl.figure.prototype.handle_draw = function (fig, _msg) {\n    // Request the server to send over a new figure.\n    fig.send_draw_message();\n};\n\nmpl.figure.prototype.handle_image_mode = function (fig, msg) {\n    fig.image_mode = msg['mode'];\n};\n\nmpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n    for (var key in msg) {\n        if (!(key in fig.buttons)) {\n            continue;\n        }\n        fig.buttons[key].disabled = !msg[key];\n        fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n    }\n};\n\nmpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n    if (msg['mode'] === 'PAN') {\n        fig.buttons['Pan'].classList.add('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    } else if (msg['mode'] === 'ZOOM') {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.add('active');\n    } else {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    }\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Called whenever the canvas gets updated.\n    this.send_message('ack', {});\n};\n\n// A function to construct a web socket function for onmessage handling.\n// Called in the figure constructor.\nmpl.figure.prototype._make_on_message_function = function (fig) {\n    return function socket_on_message(evt) {\n        if (evt.data instanceof Blob) {\n            var img = evt.data;\n            if (img.type !== 'image/png') {\n                /* FIXME: We get \"Resource interpreted as Image but\n                 * transferred with MIME type text/plain:\" errors on\n                 * Chrome.  But how to set the MIME type?  It doesn't seem\n                 * to be part of the websocket stream */\n                img.type = 'image/png';\n            }\n\n            /* Free the memory for the previous frames */\n            if (fig.imageObj.src) {\n                (window.URL || window.webkitURL).revokeObjectURL(\n                    fig.imageObj.src\n                );\n            }\n\n            fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n                img\n            );\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        } else if (\n            typeof evt.data === 'string' &&\n            evt.data.slice(0, 21) === 'data:image/png;base64'\n        ) {\n            fig.imageObj.src = evt.data;\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        }\n\n        var msg = JSON.parse(evt.data);\n        var msg_type = msg['type'];\n\n        // Call the  \"handle_{type}\" callback, which takes\n        // the figure and JSON message as its only arguments.\n        try {\n            var callback = fig['handle_' + msg_type];\n        } catch (e) {\n            console.log(\n                \"No handler for the '\" + msg_type + \"' message type: \",\n                msg\n            );\n            return;\n        }\n\n        if (callback) {\n            try {\n                // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n                callback(fig, msg);\n            } catch (e) {\n                console.log(\n                    \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n                    e,\n                    e.stack,\n                    msg\n                );\n            }\n        }\n    };\n};\n\n// from https://stackoverflow.com/questions/1114465/getting-mouse-location-in-canvas\nmpl.findpos = function (e) {\n    //this section is from http://www.quirksmode.org/js/events_properties.html\n    var targ;\n    if (!e) {\n        e = window.event;\n    }\n    if (e.target) {\n        targ = e.target;\n    } else if (e.srcElement) {\n        targ = e.srcElement;\n    }\n    if (targ.nodeType === 3) {\n        // defeat Safari bug\n        targ = targ.parentNode;\n    }\n\n    // pageX,Y are the mouse positions relative to the document\n    var boundingRect = targ.getBoundingClientRect();\n    var x = e.pageX - (boundingRect.left + document.body.scrollLeft);\n    var y = e.pageY - (boundingRect.top + document.body.scrollTop);\n\n    return { x: x, y: y };\n};\n\n/*\n * return a copy of an object with only non-object keys\n * we need this to avoid circular references\n * https://stackoverflow.com/a/24161582/3208463\n */\nfunction simpleKeys(original) {\n    return Object.keys(original).reduce(function (obj, key) {\n        if (typeof original[key] !== 'object') {\n            obj[key] = original[key];\n        }\n        return obj;\n    }, {});\n}\n\nmpl.figure.prototype.mouse_event = function (event, name) {\n    var canvas_pos = mpl.findpos(event);\n\n    if (name === 'button_press') {\n        this.canvas.focus();\n        this.canvas_div.focus();\n    }\n\n    var x = canvas_pos.x * this.ratio;\n    var y = canvas_pos.y * this.ratio;\n\n    this.send_message(name, {\n        x: x,\n        y: y,\n        button: event.button,\n        step: event.step,\n        guiEvent: simpleKeys(event),\n    });\n\n    /* This prevents the web browser from automatically changing to\n     * the text insertion cursor when the button is pressed.  We want\n     * to control all of the cursor setting manually through the\n     * 'cursor' event from matplotlib */\n    event.preventDefault();\n    return false;\n};\n\nmpl.figure.prototype._key_event_extra = function (_event, _name) {\n    // Handle any extra behaviour associated with a key event\n};\n\nmpl.figure.prototype.key_event = function (event, name) {\n    // Prevent repeat events\n    if (name === 'key_press') {\n        if (event.key === this._key) {\n            return;\n        } else {\n            this._key = event.key;\n        }\n    }\n    if (name === 'key_release') {\n        this._key = null;\n    }\n\n    var value = '';\n    if (event.ctrlKey && event.key !== 'Control') {\n        value += 'ctrl+';\n    }\n    else if (event.altKey && event.key !== 'Alt') {\n        value += 'alt+';\n    }\n    else if (event.shiftKey && event.key !== 'Shift') {\n        value += 'shift+';\n    }\n\n    value += 'k' + event.key;\n\n    this._key_event_extra(event, name);\n\n    this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n    return false;\n};\n\nmpl.figure.prototype.toolbar_button_onclick = function (name) {\n    if (name === 'download') {\n        this.handle_save(this, null);\n    } else {\n        this.send_message('toolbar_button', { name: name });\n    }\n};\n\nmpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n    this.message.textContent = tooltip;\n};\n\n///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n// prettier-ignore\nvar _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\nmpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home icon-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left icon-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right icon-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows icon-move\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis\", \"fa fa-square-o icon-check-empty\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o icon-save\", \"download\"]];\n\nmpl.extensions = [\"eps\", \"jpeg\", \"pgf\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\"];\n\nmpl.default_extension = \"png\";/* global mpl */\n\nvar comm_websocket_adapter = function (comm) {\n    // Create a \"websocket\"-like object which calls the given IPython comm\n    // object with the appropriate methods. Currently this is a non binary\n    // socket, so there is still some room for performance tuning.\n    var ws = {};\n\n    ws.binaryType = comm.kernel.ws.binaryType;\n    ws.readyState = comm.kernel.ws.readyState;\n    function updateReadyState(_event) {\n        if (comm.kernel.ws) {\n            ws.readyState = comm.kernel.ws.readyState;\n        } else {\n            ws.readyState = 3; // Closed state.\n        }\n    }\n    comm.kernel.ws.addEventListener('open', updateReadyState);\n    comm.kernel.ws.addEventListener('close', updateReadyState);\n    comm.kernel.ws.addEventListener('error', updateReadyState);\n\n    ws.close = function () {\n        comm.close();\n    };\n    ws.send = function (m) {\n        //console.log('sending', m);\n        comm.send(m);\n    };\n    // Register the callback with on_msg.\n    comm.on_msg(function (msg) {\n        //console.log('receiving', msg['content']['data'], msg);\n        var data = msg['content']['data'];\n        if (data['blob'] !== undefined) {\n            data = {\n                data: new Blob(msg['buffers'], { type: data['blob'] }),\n            };\n        }\n        // Pass the mpl event to the overridden (by mpl) onmessage function.\n        ws.onmessage(data);\n    });\n    return ws;\n};\n\nmpl.mpl_figure_comm = function (comm, msg) {\n    // This is the function which gets called when the mpl process\n    // starts-up an IPython Comm through the \"matplotlib\" channel.\n\n    var id = msg.content.data.id;\n    // Get hold of the div created by the display call when the Comm\n    // socket was opened in Python.\n    var element = document.getElementById(id);\n    var ws_proxy = comm_websocket_adapter(comm);\n\n    function ondownload(figure, _format) {\n        window.open(figure.canvas.toDataURL());\n    }\n\n    var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n\n    // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n    // web socket which is closed, not our websocket->open comm proxy.\n    ws_proxy.onopen();\n\n    fig.parent_element = element;\n    fig.cell_info = mpl.find_output_cell(\"<div id='\" + id + \"'></div>\");\n    if (!fig.cell_info) {\n        console.error('Failed to find cell for figure', id, fig);\n        return;\n    }\n    fig.cell_info[0].output_area.element.on(\n        'cleared',\n        { fig: fig },\n        fig._remove_fig_handler\n    );\n};\n\nmpl.figure.prototype.handle_close = function (fig, msg) {\n    var width = fig.canvas.width / fig.ratio;\n    fig.cell_info[0].output_area.element.off(\n        'cleared',\n        fig._remove_fig_handler\n    );\n    fig.resizeObserverInstance.unobserve(fig.canvas_div);\n\n    // Update the output cell to use the data from the current canvas.\n    fig.push_to_output();\n    var dataURL = fig.canvas.toDataURL();\n    // Re-enable the keyboard manager in IPython - without this line, in FF,\n    // the notebook keyboard shortcuts fail.\n    IPython.keyboard_manager.enable();\n    fig.parent_element.innerHTML =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n    fig.close_ws(fig, msg);\n};\n\nmpl.figure.prototype.close_ws = function (fig, msg) {\n    fig.send_message('closing', msg);\n    // fig.ws.close()\n};\n\nmpl.figure.prototype.push_to_output = function (_remove_interactive) {\n    // Turn the data on the canvas into data in the output cell.\n    var width = this.canvas.width / this.ratio;\n    var dataURL = this.canvas.toDataURL();\n    this.cell_info[1]['text/html'] =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Tell IPython that the notebook contents must change.\n    IPython.notebook.set_dirty(true);\n    this.send_message('ack', {});\n    var fig = this;\n    // Wait a second, then push the new image to the DOM so\n    // that it is saved nicely (might be nice to debounce this).\n    setTimeout(function () {\n        fig.push_to_output();\n    }, 1000);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'btn-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'btn-group';\n    var button;\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'btn-group';\n            continue;\n        }\n\n        button = fig.buttons[name] = document.createElement('button');\n        button.classList = 'btn btn-default';\n        button.href = '#';\n        button.title = name;\n        button.innerHTML = '<i class=\"fa ' + image + ' fa-lg\"></i>';\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    // Add the status bar.\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message pull-right';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n\n    // Add the close button to the window.\n    var buttongrp = document.createElement('div');\n    buttongrp.classList = 'btn-group inline pull-right';\n    button = document.createElement('button');\n    button.classList = 'btn btn-mini btn-primary';\n    button.href = '#';\n    button.title = 'Stop Interaction';\n    button.innerHTML = '<i class=\"fa fa-power-off icon-remove icon-large\"></i>';\n    button.addEventListener('click', function (_evt) {\n        fig.handle_close(fig, {});\n    });\n    button.addEventListener(\n        'mouseover',\n        on_mouseover_closure('Stop Interaction')\n    );\n    buttongrp.appendChild(button);\n    var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n    titlebar.insertBefore(buttongrp, titlebar.firstChild);\n};\n\nmpl.figure.prototype._remove_fig_handler = function (event) {\n    var fig = event.data.fig;\n    if (event.target !== this) {\n        // Ignore bubbled events from children.\n        return;\n    }\n    fig.close_ws(fig, {});\n};\n\nmpl.figure.prototype._root_extra_style = function (el) {\n    el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n};\n\nmpl.figure.prototype._canvas_extra_style = function (el) {\n    // this is important to make the div 'focusable\n    el.setAttribute('tabindex', 0);\n    // reach out to IPython and tell the keyboard manager to turn it's self\n    // off when our div gets focus\n\n    // location in version 3\n    if (IPython.notebook.keyboard_manager) {\n        IPython.notebook.keyboard_manager.register_events(el);\n    } else {\n        // location in version 2\n        IPython.keyboard_manager.register_events(el);\n    }\n};\n\nmpl.figure.prototype._key_event_extra = function (event, _name) {\n    // Check for shift+enter\n    if (event.shiftKey && event.which === 13) {\n        this.canvas_div.blur();\n        // select the cell after this one\n        var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n        IPython.notebook.select(index + 1);\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    fig.ondownload(fig, null);\n};\n\nmpl.find_output_cell = function (html_output) {\n    // Return the cell and output element which can be found *uniquely* in the notebook.\n    // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n    // IPython event is triggered only after the cells have been serialised, which for\n    // our purposes (turning an active figure into a static one), is too late.\n    var cells = IPython.notebook.get_cells();\n    var ncells = cells.length;\n    for (var i = 0; i < ncells; i++) {\n        var cell = cells[i];\n        if (cell.cell_type === 'code') {\n            for (var j = 0; j < cell.output_area.outputs.length; j++) {\n                var data = cell.output_area.outputs[j];\n                if (data.data) {\n                    // IPython >= 3 moved mimebundle to data attribute of output\n                    data = data.data;\n                }\n                if (data['text/html'] === html_output) {\n                    return [cell, data, j];\n                }\n            }\n        }\n    }\n};\n\n// Register the function which deals with the matplotlib target/channel.\n// The kernel may be null if the page has been refreshed.\nif (IPython.notebook.kernel !== null) {\n    IPython.notebook.kernel.comm_manager.register_target(\n        'matplotlib',\n        mpl.mpl_figure_comm\n    );\n}\n",
      "text/plain": [
       "<IPython.core.display.Javascript object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<img src=\"data:image/png;base64,[encoded data, 81796 characters]\" width=\"640\">"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "f = 253.6669 ± 0.5183 Hz\n"
     ]
    }
   ],
   "source": [
    "def damp_osci(t, t0, A, B, nu, gamma):\n",
    "    return A * np.exp(-gamma*t)*np.sin(2*np.pi*nu*(t-t0)) + B\n",
    "\n",
    "yvals     = val_mean#.sel(blink_on_time=slice(0.005, 0.025))\n",
    "yvals_std = std_mean#.sel(blink_on_time=slice(0.005, 0.025))\n",
    "xvals     = dataSet_cropOD[scanAxis[0]]#.sel(blink_on_time=slice(0.005, 0.025))\n",
    "\n",
    "fitted_qtys_1 = yvals.to_numpy()\n",
    "fitted_qtys_err_1 = yvals_std.to_numpy()\n",
    "scan_para = xvals.to_numpy()\n",
    "\n",
    "plt.figure()\n",
    "popt_x, pcov_x = curve_fit(damp_osci, scan_para, fitted_qtys_1, np.array([0, 3, 145, 1e2, 0.1]))\n",
    "freqdata = np.linspace(0.005, 20e-3, 500)\n",
    "plt.plot(freqdata, damp_osci(freqdata, *popt_x), 'g--',label='fit: t0=%5.3f, A=%5.3f, B=%5.3f, nu=%5.3f, Gamma=%5.3f' % tuple(popt_x))\n",
    "plt.errorbar(scan_para, fitted_qtys_1, yerr=fitted_qtys_err_1, fmt='or')\n",
    "plt.xlabel('hold time after switch on the trap (s)')\n",
    "plt.ylabel('Center along gravity direction (pixels)')\n",
    "plt.tight_layout()\n",
    "plt.grid(visible=1)\n",
    "#plt.ylim([0,750])\n",
    "#plt.xlim([0.004, 0.025])\n",
    "#plt.legend(prop={'size': 14})\n",
    "plt.show()\n",
    "\n",
    "f_x = popt_x[3]\n",
    "df_x = pcov_x[3][3]**0.5\n",
    "\n",
    "print('f = %.4f \\u00B1 %.4f Hz'% tuple([np.abs(f_x),df_x]))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Truncation: 0.7"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 83,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The detected scaning axes and values are: \n",
      "\n",
      "{'mod_blink_on_time': array([0.005 , 0.0057, 0.0064, 0.0071, 0.0078, 0.0085, 0.0092, 0.0099,\n",
      "       0.0106, 0.0113, 0.012 , 0.0127, 0.0134, 0.0141, 0.0148, 0.0155,\n",
      "       0.0162, 0.0169, 0.0176, 0.0183, 0.019 , 0.0197]), 'runs': array([0., 1., 2., 3.])}\n"
     ]
    },
    {
     "data": {
      "application/javascript": "/* Put everything inside the global mpl namespace */\n/* global mpl */\nwindow.mpl = {};\n\nmpl.get_websocket_type = function () {\n    if (typeof WebSocket !== 'undefined') {\n        return WebSocket;\n    } else if (typeof MozWebSocket !== 'undefined') {\n        return MozWebSocket;\n    } else {\n        alert(\n            'Your browser does not have WebSocket support. ' +\n                'Please try Chrome, Safari or Firefox ≥ 6. ' +\n                'Firefox 4 and 5 are also supported but you ' +\n                'have to enable WebSockets in about:config.'\n        );\n    }\n};\n\nmpl.figure = function (figure_id, websocket, ondownload, parent_element) {\n    this.id = figure_id;\n\n    this.ws = websocket;\n\n    this.supports_binary = this.ws.binaryType !== undefined;\n\n    if (!this.supports_binary) {\n        var warnings = document.getElementById('mpl-warnings');\n        if (warnings) {\n            warnings.style.display = 'block';\n            warnings.textContent =\n                'This browser does not support binary websocket messages. ' +\n                'Performance may be slow.';\n        }\n    }\n\n    this.imageObj = new Image();\n\n    this.context = undefined;\n    this.message = undefined;\n    this.canvas = undefined;\n    this.rubberband_canvas = undefined;\n    this.rubberband_context = undefined;\n    this.format_dropdown = undefined;\n\n    this.image_mode = 'full';\n\n    this.root = document.createElement('div');\n    this.root.setAttribute('style', 'display: inline-block');\n    this._root_extra_style(this.root);\n\n    parent_element.appendChild(this.root);\n\n    this._init_header(this);\n    this._init_canvas(this);\n    this._init_toolbar(this);\n\n    var fig = this;\n\n    this.waiting = false;\n\n    this.ws.onopen = function () {\n        fig.send_message('supports_binary', { value: fig.supports_binary });\n        fig.send_message('send_image_mode', {});\n        if (fig.ratio !== 1) {\n            fig.send_message('set_device_pixel_ratio', {\n                device_pixel_ratio: fig.ratio,\n            });\n        }\n        fig.send_message('refresh', {});\n    };\n\n    this.imageObj.onload = function () {\n        if (fig.image_mode === 'full') {\n            // Full images could contain transparency (where diff images\n            // almost always do), so we need to clear the canvas so that\n            // there is no ghosting.\n            fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n        }\n        fig.context.drawImage(fig.imageObj, 0, 0);\n    };\n\n    this.imageObj.onunload = function () {\n        fig.ws.close();\n    };\n\n    this.ws.onmessage = this._make_on_message_function(this);\n\n    this.ondownload = ondownload;\n};\n\nmpl.figure.prototype._init_header = function () {\n    var titlebar = document.createElement('div');\n    titlebar.classList =\n        'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n    var titletext = document.createElement('div');\n    titletext.classList = 'ui-dialog-title';\n    titletext.setAttribute(\n        'style',\n        'width: 100%; text-align: center; padding: 3px;'\n    );\n    titlebar.appendChild(titletext);\n    this.root.appendChild(titlebar);\n    this.header = titletext;\n};\n\nmpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._init_canvas = function () {\n    var fig = this;\n\n    var canvas_div = (this.canvas_div = document.createElement('div'));\n    canvas_div.setAttribute(\n        'style',\n        'border: 1px solid #ddd;' +\n            'box-sizing: content-box;' +\n            'clear: both;' +\n            'min-height: 1px;' +\n            'min-width: 1px;' +\n            'outline: 0;' +\n            'overflow: hidden;' +\n            'position: relative;' +\n            'resize: both;'\n    );\n\n    function on_keyboard_event_closure(name) {\n        return function (event) {\n            return fig.key_event(event, name);\n        };\n    }\n\n    canvas_div.addEventListener(\n        'keydown',\n        on_keyboard_event_closure('key_press')\n    );\n    canvas_div.addEventListener(\n        'keyup',\n        on_keyboard_event_closure('key_release')\n    );\n\n    this._canvas_extra_style(canvas_div);\n    this.root.appendChild(canvas_div);\n\n    var canvas = (this.canvas = document.createElement('canvas'));\n    canvas.classList.add('mpl-canvas');\n    canvas.setAttribute('style', 'box-sizing: content-box;');\n\n    this.context = canvas.getContext('2d');\n\n    var backingStore =\n        this.context.backingStorePixelRatio ||\n        this.context.webkitBackingStorePixelRatio ||\n        this.context.mozBackingStorePixelRatio ||\n        this.context.msBackingStorePixelRatio ||\n        this.context.oBackingStorePixelRatio ||\n        this.context.backingStorePixelRatio ||\n        1;\n\n    this.ratio = (window.devicePixelRatio || 1) / backingStore;\n\n    var rubberband_canvas = (this.rubberband_canvas = document.createElement(\n        'canvas'\n    ));\n    rubberband_canvas.setAttribute(\n        'style',\n        'box-sizing: content-box; position: absolute; left: 0; top: 0; z-index: 1;'\n    );\n\n    // Apply a ponyfill if ResizeObserver is not implemented by browser.\n    if (this.ResizeObserver === undefined) {\n        if (window.ResizeObserver !== undefined) {\n            this.ResizeObserver = window.ResizeObserver;\n        } else {\n            var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n            this.ResizeObserver = obs.ResizeObserver;\n        }\n    }\n\n    this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n        var nentries = entries.length;\n        for (var i = 0; i < nentries; i++) {\n            var entry = entries[i];\n            var width, height;\n            if (entry.contentBoxSize) {\n                if (entry.contentBoxSize instanceof Array) {\n                    // Chrome 84 implements new version of spec.\n                    width = entry.contentBoxSize[0].inlineSize;\n                    height = entry.contentBoxSize[0].blockSize;\n                } else {\n                    // Firefox implements old version of spec.\n                    width = entry.contentBoxSize.inlineSize;\n                    height = entry.contentBoxSize.blockSize;\n                }\n            } else {\n                // Chrome <84 implements even older version of spec.\n                width = entry.contentRect.width;\n                height = entry.contentRect.height;\n            }\n\n            // Keep the size of the canvas and rubber band canvas in sync with\n            // the canvas container.\n            if (entry.devicePixelContentBoxSize) {\n                // Chrome 84 implements new version of spec.\n                canvas.setAttribute(\n                    'width',\n                    entry.devicePixelContentBoxSize[0].inlineSize\n                );\n                canvas.setAttribute(\n                    'height',\n                    entry.devicePixelContentBoxSize[0].blockSize\n                );\n            } else {\n                canvas.setAttribute('width', width * fig.ratio);\n                canvas.setAttribute('height', height * fig.ratio);\n            }\n            canvas.setAttribute(\n                'style',\n                'width: ' + width + 'px; height: ' + height + 'px;'\n            );\n\n            rubberband_canvas.setAttribute('width', width);\n            rubberband_canvas.setAttribute('height', height);\n\n            // And update the size in Python. We ignore the initial 0/0 size\n            // that occurs as the element is placed into the DOM, which should\n            // otherwise not happen due to the minimum size styling.\n            if (fig.ws.readyState == 1 && width != 0 && height != 0) {\n                fig.request_resize(width, height);\n            }\n        }\n    });\n    this.resizeObserverInstance.observe(canvas_div);\n\n    function on_mouse_event_closure(name) {\n        return function (event) {\n            return fig.mouse_event(event, name);\n        };\n    }\n\n    rubberband_canvas.addEventListener(\n        'mousedown',\n        on_mouse_event_closure('button_press')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseup',\n        on_mouse_event_closure('button_release')\n    );\n    rubberband_canvas.addEventListener(\n        'dblclick',\n        on_mouse_event_closure('dblclick')\n    );\n    // Throttle sequential mouse events to 1 every 20ms.\n    rubberband_canvas.addEventListener(\n        'mousemove',\n        on_mouse_event_closure('motion_notify')\n    );\n\n    rubberband_canvas.addEventListener(\n        'mouseenter',\n        on_mouse_event_closure('figure_enter')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseleave',\n        on_mouse_event_closure('figure_leave')\n    );\n\n    canvas_div.addEventListener('wheel', function (event) {\n        if (event.deltaY < 0) {\n            event.step = 1;\n        } else {\n            event.step = -1;\n        }\n        on_mouse_event_closure('scroll')(event);\n    });\n\n    canvas_div.appendChild(canvas);\n    canvas_div.appendChild(rubberband_canvas);\n\n    this.rubberband_context = rubberband_canvas.getContext('2d');\n    this.rubberband_context.strokeStyle = '#000000';\n\n    this._resize_canvas = function (width, height, forward) {\n        if (forward) {\n            canvas_div.style.width = width + 'px';\n            canvas_div.style.height = height + 'px';\n        }\n    };\n\n    // Disable right mouse context menu.\n    this.rubberband_canvas.addEventListener('contextmenu', function (_e) {\n        event.preventDefault();\n        return false;\n    });\n\n    function set_focus() {\n        canvas.focus();\n        canvas_div.focus();\n    }\n\n    window.setTimeout(set_focus, 100);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'mpl-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'mpl-button-group';\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'mpl-button-group';\n            continue;\n        }\n\n        var button = (fig.buttons[name] = document.createElement('button'));\n        button.classList = 'mpl-widget';\n        button.setAttribute('role', 'button');\n        button.setAttribute('aria-disabled', 'false');\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n\n        var icon_img = document.createElement('img');\n        icon_img.src = '_images/' + image + '.png';\n        icon_img.srcset = '_images/' + image + '_large.png 2x';\n        icon_img.alt = tooltip;\n        button.appendChild(icon_img);\n\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    var fmt_picker = document.createElement('select');\n    fmt_picker.classList = 'mpl-widget';\n    toolbar.appendChild(fmt_picker);\n    this.format_dropdown = fmt_picker;\n\n    for (var ind in mpl.extensions) {\n        var fmt = mpl.extensions[ind];\n        var option = document.createElement('option');\n        option.selected = fmt === mpl.default_extension;\n        option.innerHTML = fmt;\n        fmt_picker.appendChild(option);\n    }\n\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n};\n\nmpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n    // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n    // which will in turn request a refresh of the image.\n    this.send_message('resize', { width: x_pixels, height: y_pixels });\n};\n\nmpl.figure.prototype.send_message = function (type, properties) {\n    properties['type'] = type;\n    properties['figure_id'] = this.id;\n    this.ws.send(JSON.stringify(properties));\n};\n\nmpl.figure.prototype.send_draw_message = function () {\n    if (!this.waiting) {\n        this.waiting = true;\n        this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    var format_dropdown = fig.format_dropdown;\n    var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n    fig.ondownload(fig, format);\n};\n\nmpl.figure.prototype.handle_resize = function (fig, msg) {\n    var size = msg['size'];\n    if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n        fig._resize_canvas(size[0], size[1], msg['forward']);\n        fig.send_message('refresh', {});\n    }\n};\n\nmpl.figure.prototype.handle_rubberband = function (fig, msg) {\n    var x0 = msg['x0'] / fig.ratio;\n    var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n    var x1 = msg['x1'] / fig.ratio;\n    var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n    x0 = Math.floor(x0) + 0.5;\n    y0 = Math.floor(y0) + 0.5;\n    x1 = Math.floor(x1) + 0.5;\n    y1 = Math.floor(y1) + 0.5;\n    var min_x = Math.min(x0, x1);\n    var min_y = Math.min(y0, y1);\n    var width = Math.abs(x1 - x0);\n    var height = Math.abs(y1 - y0);\n\n    fig.rubberband_context.clearRect(\n        0,\n        0,\n        fig.canvas.width / fig.ratio,\n        fig.canvas.height / fig.ratio\n    );\n\n    fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n};\n\nmpl.figure.prototype.handle_figure_label = function (fig, msg) {\n    // Updates the figure title.\n    fig.header.textContent = msg['label'];\n};\n\nmpl.figure.prototype.handle_cursor = function (fig, msg) {\n    fig.rubberband_canvas.style.cursor = msg['cursor'];\n};\n\nmpl.figure.prototype.handle_message = function (fig, msg) {\n    fig.message.textContent = msg['message'];\n};\n\nmpl.figure.prototype.handle_draw = function (fig, _msg) {\n    // Request the server to send over a new figure.\n    fig.send_draw_message();\n};\n\nmpl.figure.prototype.handle_image_mode = function (fig, msg) {\n    fig.image_mode = msg['mode'];\n};\n\nmpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n    for (var key in msg) {\n        if (!(key in fig.buttons)) {\n            continue;\n        }\n        fig.buttons[key].disabled = !msg[key];\n        fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n    }\n};\n\nmpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n    if (msg['mode'] === 'PAN') {\n        fig.buttons['Pan'].classList.add('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    } else if (msg['mode'] === 'ZOOM') {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.add('active');\n    } else {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    }\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Called whenever the canvas gets updated.\n    this.send_message('ack', {});\n};\n\n// A function to construct a web socket function for onmessage handling.\n// Called in the figure constructor.\nmpl.figure.prototype._make_on_message_function = function (fig) {\n    return function socket_on_message(evt) {\n        if (evt.data instanceof Blob) {\n            var img = evt.data;\n            if (img.type !== 'image/png') {\n                /* FIXME: We get \"Resource interpreted as Image but\n                 * transferred with MIME type text/plain:\" errors on\n                 * Chrome.  But how to set the MIME type?  It doesn't seem\n                 * to be part of the websocket stream */\n                img.type = 'image/png';\n            }\n\n            /* Free the memory for the previous frames */\n            if (fig.imageObj.src) {\n                (window.URL || window.webkitURL).revokeObjectURL(\n                    fig.imageObj.src\n                );\n            }\n\n            fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n                img\n            );\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        } else if (\n            typeof evt.data === 'string' &&\n            evt.data.slice(0, 21) === 'data:image/png;base64'\n        ) {\n            fig.imageObj.src = evt.data;\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        }\n\n        var msg = JSON.parse(evt.data);\n        var msg_type = msg['type'];\n\n        // Call the  \"handle_{type}\" callback, which takes\n        // the figure and JSON message as its only arguments.\n        try {\n            var callback = fig['handle_' + msg_type];\n        } catch (e) {\n            console.log(\n                \"No handler for the '\" + msg_type + \"' message type: \",\n                msg\n            );\n            return;\n        }\n\n        if (callback) {\n            try {\n                // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n                callback(fig, msg);\n            } catch (e) {\n                console.log(\n                    \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n                    e,\n                    e.stack,\n                    msg\n                );\n            }\n        }\n    };\n};\n\n// from https://stackoverflow.com/questions/1114465/getting-mouse-location-in-canvas\nmpl.findpos = function (e) {\n    //this section is from http://www.quirksmode.org/js/events_properties.html\n    var targ;\n    if (!e) {\n        e = window.event;\n    }\n    if (e.target) {\n        targ = e.target;\n    } else if (e.srcElement) {\n        targ = e.srcElement;\n    }\n    if (targ.nodeType === 3) {\n        // defeat Safari bug\n        targ = targ.parentNode;\n    }\n\n    // pageX,Y are the mouse positions relative to the document\n    var boundingRect = targ.getBoundingClientRect();\n    var x = e.pageX - (boundingRect.left + document.body.scrollLeft);\n    var y = e.pageY - (boundingRect.top + document.body.scrollTop);\n\n    return { x: x, y: y };\n};\n\n/*\n * return a copy of an object with only non-object keys\n * we need this to avoid circular references\n * https://stackoverflow.com/a/24161582/3208463\n */\nfunction simpleKeys(original) {\n    return Object.keys(original).reduce(function (obj, key) {\n        if (typeof original[key] !== 'object') {\n            obj[key] = original[key];\n        }\n        return obj;\n    }, {});\n}\n\nmpl.figure.prototype.mouse_event = function (event, name) {\n    var canvas_pos = mpl.findpos(event);\n\n    if (name === 'button_press') {\n        this.canvas.focus();\n        this.canvas_div.focus();\n    }\n\n    var x = canvas_pos.x * this.ratio;\n    var y = canvas_pos.y * this.ratio;\n\n    this.send_message(name, {\n        x: x,\n        y: y,\n        button: event.button,\n        step: event.step,\n        guiEvent: simpleKeys(event),\n    });\n\n    /* This prevents the web browser from automatically changing to\n     * the text insertion cursor when the button is pressed.  We want\n     * to control all of the cursor setting manually through the\n     * 'cursor' event from matplotlib */\n    event.preventDefault();\n    return false;\n};\n\nmpl.figure.prototype._key_event_extra = function (_event, _name) {\n    // Handle any extra behaviour associated with a key event\n};\n\nmpl.figure.prototype.key_event = function (event, name) {\n    // Prevent repeat events\n    if (name === 'key_press') {\n        if (event.key === this._key) {\n            return;\n        } else {\n            this._key = event.key;\n        }\n    }\n    if (name === 'key_release') {\n        this._key = null;\n    }\n\n    var value = '';\n    if (event.ctrlKey && event.key !== 'Control') {\n        value += 'ctrl+';\n    }\n    else if (event.altKey && event.key !== 'Alt') {\n        value += 'alt+';\n    }\n    else if (event.shiftKey && event.key !== 'Shift') {\n        value += 'shift+';\n    }\n\n    value += 'k' + event.key;\n\n    this._key_event_extra(event, name);\n\n    this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n    return false;\n};\n\nmpl.figure.prototype.toolbar_button_onclick = function (name) {\n    if (name === 'download') {\n        this.handle_save(this, null);\n    } else {\n        this.send_message('toolbar_button', { name: name });\n    }\n};\n\nmpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n    this.message.textContent = tooltip;\n};\n\n///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n// prettier-ignore\nvar _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\nmpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home icon-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left icon-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right icon-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows icon-move\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis\", \"fa fa-square-o icon-check-empty\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o icon-save\", \"download\"]];\n\nmpl.extensions = [\"eps\", \"jpeg\", \"pgf\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\"];\n\nmpl.default_extension = \"png\";/* global mpl */\n\nvar comm_websocket_adapter = function (comm) {\n    // Create a \"websocket\"-like object which calls the given IPython comm\n    // object with the appropriate methods. Currently this is a non binary\n    // socket, so there is still some room for performance tuning.\n    var ws = {};\n\n    ws.binaryType = comm.kernel.ws.binaryType;\n    ws.readyState = comm.kernel.ws.readyState;\n    function updateReadyState(_event) {\n        if (comm.kernel.ws) {\n            ws.readyState = comm.kernel.ws.readyState;\n        } else {\n            ws.readyState = 3; // Closed state.\n        }\n    }\n    comm.kernel.ws.addEventListener('open', updateReadyState);\n    comm.kernel.ws.addEventListener('close', updateReadyState);\n    comm.kernel.ws.addEventListener('error', updateReadyState);\n\n    ws.close = function () {\n        comm.close();\n    };\n    ws.send = function (m) {\n        //console.log('sending', m);\n        comm.send(m);\n    };\n    // Register the callback with on_msg.\n    comm.on_msg(function (msg) {\n        //console.log('receiving', msg['content']['data'], msg);\n        var data = msg['content']['data'];\n        if (data['blob'] !== undefined) {\n            data = {\n                data: new Blob(msg['buffers'], { type: data['blob'] }),\n            };\n        }\n        // Pass the mpl event to the overridden (by mpl) onmessage function.\n        ws.onmessage(data);\n    });\n    return ws;\n};\n\nmpl.mpl_figure_comm = function (comm, msg) {\n    // This is the function which gets called when the mpl process\n    // starts-up an IPython Comm through the \"matplotlib\" channel.\n\n    var id = msg.content.data.id;\n    // Get hold of the div created by the display call when the Comm\n    // socket was opened in Python.\n    var element = document.getElementById(id);\n    var ws_proxy = comm_websocket_adapter(comm);\n\n    function ondownload(figure, _format) {\n        window.open(figure.canvas.toDataURL());\n    }\n\n    var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n\n    // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n    // web socket which is closed, not our websocket->open comm proxy.\n    ws_proxy.onopen();\n\n    fig.parent_element = element;\n    fig.cell_info = mpl.find_output_cell(\"<div id='\" + id + \"'></div>\");\n    if (!fig.cell_info) {\n        console.error('Failed to find cell for figure', id, fig);\n        return;\n    }\n    fig.cell_info[0].output_area.element.on(\n        'cleared',\n        { fig: fig },\n        fig._remove_fig_handler\n    );\n};\n\nmpl.figure.prototype.handle_close = function (fig, msg) {\n    var width = fig.canvas.width / fig.ratio;\n    fig.cell_info[0].output_area.element.off(\n        'cleared',\n        fig._remove_fig_handler\n    );\n    fig.resizeObserverInstance.unobserve(fig.canvas_div);\n\n    // Update the output cell to use the data from the current canvas.\n    fig.push_to_output();\n    var dataURL = fig.canvas.toDataURL();\n    // Re-enable the keyboard manager in IPython - without this line, in FF,\n    // the notebook keyboard shortcuts fail.\n    IPython.keyboard_manager.enable();\n    fig.parent_element.innerHTML =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n    fig.close_ws(fig, msg);\n};\n\nmpl.figure.prototype.close_ws = function (fig, msg) {\n    fig.send_message('closing', msg);\n    // fig.ws.close()\n};\n\nmpl.figure.prototype.push_to_output = function (_remove_interactive) {\n    // Turn the data on the canvas into data in the output cell.\n    var width = this.canvas.width / this.ratio;\n    var dataURL = this.canvas.toDataURL();\n    this.cell_info[1]['text/html'] =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Tell IPython that the notebook contents must change.\n    IPython.notebook.set_dirty(true);\n    this.send_message('ack', {});\n    var fig = this;\n    // Wait a second, then push the new image to the DOM so\n    // that it is saved nicely (might be nice to debounce this).\n    setTimeout(function () {\n        fig.push_to_output();\n    }, 1000);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'btn-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'btn-group';\n    var button;\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'btn-group';\n            continue;\n        }\n\n        button = fig.buttons[name] = document.createElement('button');\n        button.classList = 'btn btn-default';\n        button.href = '#';\n        button.title = name;\n        button.innerHTML = '<i class=\"fa ' + image + ' fa-lg\"></i>';\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    // Add the status bar.\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message pull-right';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n\n    // Add the close button to the window.\n    var buttongrp = document.createElement('div');\n    buttongrp.classList = 'btn-group inline pull-right';\n    button = document.createElement('button');\n    button.classList = 'btn btn-mini btn-primary';\n    button.href = '#';\n    button.title = 'Stop Interaction';\n    button.innerHTML = '<i class=\"fa fa-power-off icon-remove icon-large\"></i>';\n    button.addEventListener('click', function (_evt) {\n        fig.handle_close(fig, {});\n    });\n    button.addEventListener(\n        'mouseover',\n        on_mouseover_closure('Stop Interaction')\n    );\n    buttongrp.appendChild(button);\n    var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n    titlebar.insertBefore(buttongrp, titlebar.firstChild);\n};\n\nmpl.figure.prototype._remove_fig_handler = function (event) {\n    var fig = event.data.fig;\n    if (event.target !== this) {\n        // Ignore bubbled events from children.\n        return;\n    }\n    fig.close_ws(fig, {});\n};\n\nmpl.figure.prototype._root_extra_style = function (el) {\n    el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n};\n\nmpl.figure.prototype._canvas_extra_style = function (el) {\n    // this is important to make the div 'focusable\n    el.setAttribute('tabindex', 0);\n    // reach out to IPython and tell the keyboard manager to turn it's self\n    // off when our div gets focus\n\n    // location in version 3\n    if (IPython.notebook.keyboard_manager) {\n        IPython.notebook.keyboard_manager.register_events(el);\n    } else {\n        // location in version 2\n        IPython.keyboard_manager.register_events(el);\n    }\n};\n\nmpl.figure.prototype._key_event_extra = function (event, _name) {\n    // Check for shift+enter\n    if (event.shiftKey && event.which === 13) {\n        this.canvas_div.blur();\n        // select the cell after this one\n        var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n        IPython.notebook.select(index + 1);\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    fig.ondownload(fig, null);\n};\n\nmpl.find_output_cell = function (html_output) {\n    // Return the cell and output element which can be found *uniquely* in the notebook.\n    // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n    // IPython event is triggered only after the cells have been serialised, which for\n    // our purposes (turning an active figure into a static one), is too late.\n    var cells = IPython.notebook.get_cells();\n    var ncells = cells.length;\n    for (var i = 0; i < ncells; i++) {\n        var cell = cells[i];\n        if (cell.cell_type === 'code') {\n            for (var j = 0; j < cell.output_area.outputs.length; j++) {\n                var data = cell.output_area.outputs[j];\n                if (data.data) {\n                    // IPython >= 3 moved mimebundle to data attribute of output\n                    data = data.data;\n                }\n                if (data['text/html'] === html_output) {\n                    return [cell, data, j];\n                }\n            }\n        }\n    }\n};\n\n// Register the function which deals with the matplotlib target/channel.\n// The kernel may be null if the page has been refreshed.\nif (IPython.notebook.kernel !== null) {\n    IPython.notebook.kernel.comm_manager.register_target(\n        'matplotlib',\n        mpl.mpl_figure_comm\n    );\n}\n",
      "text/plain": [
       "<IPython.core.display.Javascript object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<img src=\"data:image/png;base64,[encoded data, 37684 characters]\" width=\"640\">"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "%matplotlib notebook\n",
    "shotNum = \"0010\"\n",
    "filePath = folderPath + \"/\" + shotNum + \"/*.h5\"\n",
    "\n",
    "dataSetDict = {\n",
    "    dskey[groupList[i]]: read_hdf5_file(filePath, groupList[i], excludeAxis = ['sweep_start_freq', 'sweep_stop_freq'])\n",
    "    for i in [0]\n",
    "}\n",
    "\n",
    "dataSet = dataSetDict[\"camera_0\"]\n",
    "\n",
    "print_scanAxis(dataSet)\n",
    "\n",
    "scanAxis = get_scanAxis(dataSet)\n",
    "\n",
    "dataSet = auto_rechunk(dataSet)\n",
    "\n",
    "dataSet = imageAnalyser.get_absorption_images(dataSet)\n",
    "\n",
    "imageAnalyser.center = (800, 900)\n",
    "imageAnalyser.span = (300, 300)\n",
    "imageAnalyser.fraction = (0.1, 0.1)\n",
    "\n",
    "dataSet_cropOD = imageAnalyser.crop_image(dataSet.OD)\n",
    "dataSet_cropOD = imageAnalyser.substract_offset(dataSet_cropOD).load()\n",
    "\n",
    "Ncount = imageAnalyser.get_Ncount(dataSet_cropOD)\n",
    "Ncount_mean = calculate_mean(Ncount)\n",
    "Ncount_std = calculate_std(Ncount)\n",
    "\n",
    "fig = plt.figure()\n",
    "ax = fig.gca()\n",
    "Ncount_mean.plot.errorbar(ax=ax, yerr = None, fmt='ob')\n",
    "plt.ylabel('NCount')\n",
    "plt.tight_layout()\n",
    "plt.grid(visible=1)\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 84,
   "metadata": {},
   "outputs": [],
   "source": [
    "dataSet_cropOD_chunk = dataSet_cropOD.chunk((1, 1, 300, 300))\n",
    "fitAnalyser = FitAnalyser(\"Gaussian-2D\", fitDim=2)\n",
    "params = fitAnalyser.guess(dataSet_cropOD_chunk, dask=\"parallelized\")\n",
    "fitResult = fitAnalyser.fit(dataSet_cropOD_chunk, params, dask=\"parallelized\").load()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 85,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/javascript": "/* Put everything inside the global mpl namespace */\n/* global mpl */\nwindow.mpl = {};\n\nmpl.get_websocket_type = function () {\n    if (typeof WebSocket !== 'undefined') {\n        return WebSocket;\n    } else if (typeof MozWebSocket !== 'undefined') {\n        return MozWebSocket;\n    } else {\n        alert(\n            'Your browser does not have WebSocket support. ' +\n                'Please try Chrome, Safari or Firefox ≥ 6. ' +\n                'Firefox 4 and 5 are also supported but you ' +\n                'have to enable WebSockets in about:config.'\n        );\n    }\n};\n\nmpl.figure = function (figure_id, websocket, ondownload, parent_element) {\n    this.id = figure_id;\n\n    this.ws = websocket;\n\n    this.supports_binary = this.ws.binaryType !== undefined;\n\n    if (!this.supports_binary) {\n        var warnings = document.getElementById('mpl-warnings');\n        if (warnings) {\n            warnings.style.display = 'block';\n            warnings.textContent =\n                'This browser does not support binary websocket messages. ' +\n                'Performance may be slow.';\n        }\n    }\n\n    this.imageObj = new Image();\n\n    this.context = undefined;\n    this.message = undefined;\n    this.canvas = undefined;\n    this.rubberband_canvas = undefined;\n    this.rubberband_context = undefined;\n    this.format_dropdown = undefined;\n\n    this.image_mode = 'full';\n\n    this.root = document.createElement('div');\n    this.root.setAttribute('style', 'display: inline-block');\n    this._root_extra_style(this.root);\n\n    parent_element.appendChild(this.root);\n\n    this._init_header(this);\n    this._init_canvas(this);\n    this._init_toolbar(this);\n\n    var fig = this;\n\n    this.waiting = false;\n\n    this.ws.onopen = function () {\n        fig.send_message('supports_binary', { value: fig.supports_binary });\n        fig.send_message('send_image_mode', {});\n        if (fig.ratio !== 1) {\n            fig.send_message('set_device_pixel_ratio', {\n                device_pixel_ratio: fig.ratio,\n            });\n        }\n        fig.send_message('refresh', {});\n    };\n\n    this.imageObj.onload = function () {\n        if (fig.image_mode === 'full') {\n            // Full images could contain transparency (where diff images\n            // almost always do), so we need to clear the canvas so that\n            // there is no ghosting.\n            fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n        }\n        fig.context.drawImage(fig.imageObj, 0, 0);\n    };\n\n    this.imageObj.onunload = function () {\n        fig.ws.close();\n    };\n\n    this.ws.onmessage = this._make_on_message_function(this);\n\n    this.ondownload = ondownload;\n};\n\nmpl.figure.prototype._init_header = function () {\n    var titlebar = document.createElement('div');\n    titlebar.classList =\n        'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n    var titletext = document.createElement('div');\n    titletext.classList = 'ui-dialog-title';\n    titletext.setAttribute(\n        'style',\n        'width: 100%; text-align: center; padding: 3px;'\n    );\n    titlebar.appendChild(titletext);\n    this.root.appendChild(titlebar);\n    this.header = titletext;\n};\n\nmpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._init_canvas = function () {\n    var fig = this;\n\n    var canvas_div = (this.canvas_div = document.createElement('div'));\n    canvas_div.setAttribute(\n        'style',\n        'border: 1px solid #ddd;' +\n            'box-sizing: content-box;' +\n            'clear: both;' +\n            'min-height: 1px;' +\n            'min-width: 1px;' +\n            'outline: 0;' +\n            'overflow: hidden;' +\n            'position: relative;' +\n            'resize: both;'\n    );\n\n    function on_keyboard_event_closure(name) {\n        return function (event) {\n            return fig.key_event(event, name);\n        };\n    }\n\n    canvas_div.addEventListener(\n        'keydown',\n        on_keyboard_event_closure('key_press')\n    );\n    canvas_div.addEventListener(\n        'keyup',\n        on_keyboard_event_closure('key_release')\n    );\n\n    this._canvas_extra_style(canvas_div);\n    this.root.appendChild(canvas_div);\n\n    var canvas = (this.canvas = document.createElement('canvas'));\n    canvas.classList.add('mpl-canvas');\n    canvas.setAttribute('style', 'box-sizing: content-box;');\n\n    this.context = canvas.getContext('2d');\n\n    var backingStore =\n        this.context.backingStorePixelRatio ||\n        this.context.webkitBackingStorePixelRatio ||\n        this.context.mozBackingStorePixelRatio ||\n        this.context.msBackingStorePixelRatio ||\n        this.context.oBackingStorePixelRatio ||\n        this.context.backingStorePixelRatio ||\n        1;\n\n    this.ratio = (window.devicePixelRatio || 1) / backingStore;\n\n    var rubberband_canvas = (this.rubberband_canvas = document.createElement(\n        'canvas'\n    ));\n    rubberband_canvas.setAttribute(\n        'style',\n        'box-sizing: content-box; position: absolute; left: 0; top: 0; z-index: 1;'\n    );\n\n    // Apply a ponyfill if ResizeObserver is not implemented by browser.\n    if (this.ResizeObserver === undefined) {\n        if (window.ResizeObserver !== undefined) {\n            this.ResizeObserver = window.ResizeObserver;\n        } else {\n            var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n            this.ResizeObserver = obs.ResizeObserver;\n        }\n    }\n\n    this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n        var nentries = entries.length;\n        for (var i = 0; i < nentries; i++) {\n            var entry = entries[i];\n            var width, height;\n            if (entry.contentBoxSize) {\n                if (entry.contentBoxSize instanceof Array) {\n                    // Chrome 84 implements new version of spec.\n                    width = entry.contentBoxSize[0].inlineSize;\n                    height = entry.contentBoxSize[0].blockSize;\n                } else {\n                    // Firefox implements old version of spec.\n                    width = entry.contentBoxSize.inlineSize;\n                    height = entry.contentBoxSize.blockSize;\n                }\n            } else {\n                // Chrome <84 implements even older version of spec.\n                width = entry.contentRect.width;\n                height = entry.contentRect.height;\n            }\n\n            // Keep the size of the canvas and rubber band canvas in sync with\n            // the canvas container.\n            if (entry.devicePixelContentBoxSize) {\n                // Chrome 84 implements new version of spec.\n                canvas.setAttribute(\n                    'width',\n                    entry.devicePixelContentBoxSize[0].inlineSize\n                );\n                canvas.setAttribute(\n                    'height',\n                    entry.devicePixelContentBoxSize[0].blockSize\n                );\n            } else {\n                canvas.setAttribute('width', width * fig.ratio);\n                canvas.setAttribute('height', height * fig.ratio);\n            }\n            canvas.setAttribute(\n                'style',\n                'width: ' + width + 'px; height: ' + height + 'px;'\n            );\n\n            rubberband_canvas.setAttribute('width', width);\n            rubberband_canvas.setAttribute('height', height);\n\n            // And update the size in Python. We ignore the initial 0/0 size\n            // that occurs as the element is placed into the DOM, which should\n            // otherwise not happen due to the minimum size styling.\n            if (fig.ws.readyState == 1 && width != 0 && height != 0) {\n                fig.request_resize(width, height);\n            }\n        }\n    });\n    this.resizeObserverInstance.observe(canvas_div);\n\n    function on_mouse_event_closure(name) {\n        return function (event) {\n            return fig.mouse_event(event, name);\n        };\n    }\n\n    rubberband_canvas.addEventListener(\n        'mousedown',\n        on_mouse_event_closure('button_press')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseup',\n        on_mouse_event_closure('button_release')\n    );\n    rubberband_canvas.addEventListener(\n        'dblclick',\n        on_mouse_event_closure('dblclick')\n    );\n    // Throttle sequential mouse events to 1 every 20ms.\n    rubberband_canvas.addEventListener(\n        'mousemove',\n        on_mouse_event_closure('motion_notify')\n    );\n\n    rubberband_canvas.addEventListener(\n        'mouseenter',\n        on_mouse_event_closure('figure_enter')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseleave',\n        on_mouse_event_closure('figure_leave')\n    );\n\n    canvas_div.addEventListener('wheel', function (event) {\n        if (event.deltaY < 0) {\n            event.step = 1;\n        } else {\n            event.step = -1;\n        }\n        on_mouse_event_closure('scroll')(event);\n    });\n\n    canvas_div.appendChild(canvas);\n    canvas_div.appendChild(rubberband_canvas);\n\n    this.rubberband_context = rubberband_canvas.getContext('2d');\n    this.rubberband_context.strokeStyle = '#000000';\n\n    this._resize_canvas = function (width, height, forward) {\n        if (forward) {\n            canvas_div.style.width = width + 'px';\n            canvas_div.style.height = height + 'px';\n        }\n    };\n\n    // Disable right mouse context menu.\n    this.rubberband_canvas.addEventListener('contextmenu', function (_e) {\n        event.preventDefault();\n        return false;\n    });\n\n    function set_focus() {\n        canvas.focus();\n        canvas_div.focus();\n    }\n\n    window.setTimeout(set_focus, 100);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'mpl-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'mpl-button-group';\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'mpl-button-group';\n            continue;\n        }\n\n        var button = (fig.buttons[name] = document.createElement('button'));\n        button.classList = 'mpl-widget';\n        button.setAttribute('role', 'button');\n        button.setAttribute('aria-disabled', 'false');\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n\n        var icon_img = document.createElement('img');\n        icon_img.src = '_images/' + image + '.png';\n        icon_img.srcset = '_images/' + image + '_large.png 2x';\n        icon_img.alt = tooltip;\n        button.appendChild(icon_img);\n\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    var fmt_picker = document.createElement('select');\n    fmt_picker.classList = 'mpl-widget';\n    toolbar.appendChild(fmt_picker);\n    this.format_dropdown = fmt_picker;\n\n    for (var ind in mpl.extensions) {\n        var fmt = mpl.extensions[ind];\n        var option = document.createElement('option');\n        option.selected = fmt === mpl.default_extension;\n        option.innerHTML = fmt;\n        fmt_picker.appendChild(option);\n    }\n\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n};\n\nmpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n    // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n    // which will in turn request a refresh of the image.\n    this.send_message('resize', { width: x_pixels, height: y_pixels });\n};\n\nmpl.figure.prototype.send_message = function (type, properties) {\n    properties['type'] = type;\n    properties['figure_id'] = this.id;\n    this.ws.send(JSON.stringify(properties));\n};\n\nmpl.figure.prototype.send_draw_message = function () {\n    if (!this.waiting) {\n        this.waiting = true;\n        this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    var format_dropdown = fig.format_dropdown;\n    var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n    fig.ondownload(fig, format);\n};\n\nmpl.figure.prototype.handle_resize = function (fig, msg) {\n    var size = msg['size'];\n    if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n        fig._resize_canvas(size[0], size[1], msg['forward']);\n        fig.send_message('refresh', {});\n    }\n};\n\nmpl.figure.prototype.handle_rubberband = function (fig, msg) {\n    var x0 = msg['x0'] / fig.ratio;\n    var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n    var x1 = msg['x1'] / fig.ratio;\n    var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n    x0 = Math.floor(x0) + 0.5;\n    y0 = Math.floor(y0) + 0.5;\n    x1 = Math.floor(x1) + 0.5;\n    y1 = Math.floor(y1) + 0.5;\n    var min_x = Math.min(x0, x1);\n    var min_y = Math.min(y0, y1);\n    var width = Math.abs(x1 - x0);\n    var height = Math.abs(y1 - y0);\n\n    fig.rubberband_context.clearRect(\n        0,\n        0,\n        fig.canvas.width / fig.ratio,\n        fig.canvas.height / fig.ratio\n    );\n\n    fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n};\n\nmpl.figure.prototype.handle_figure_label = function (fig, msg) {\n    // Updates the figure title.\n    fig.header.textContent = msg['label'];\n};\n\nmpl.figure.prototype.handle_cursor = function (fig, msg) {\n    fig.rubberband_canvas.style.cursor = msg['cursor'];\n};\n\nmpl.figure.prototype.handle_message = function (fig, msg) {\n    fig.message.textContent = msg['message'];\n};\n\nmpl.figure.prototype.handle_draw = function (fig, _msg) {\n    // Request the server to send over a new figure.\n    fig.send_draw_message();\n};\n\nmpl.figure.prototype.handle_image_mode = function (fig, msg) {\n    fig.image_mode = msg['mode'];\n};\n\nmpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n    for (var key in msg) {\n        if (!(key in fig.buttons)) {\n            continue;\n        }\n        fig.buttons[key].disabled = !msg[key];\n        fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n    }\n};\n\nmpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n    if (msg['mode'] === 'PAN') {\n        fig.buttons['Pan'].classList.add('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    } else if (msg['mode'] === 'ZOOM') {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.add('active');\n    } else {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    }\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Called whenever the canvas gets updated.\n    this.send_message('ack', {});\n};\n\n// A function to construct a web socket function for onmessage handling.\n// Called in the figure constructor.\nmpl.figure.prototype._make_on_message_function = function (fig) {\n    return function socket_on_message(evt) {\n        if (evt.data instanceof Blob) {\n            var img = evt.data;\n            if (img.type !== 'image/png') {\n                /* FIXME: We get \"Resource interpreted as Image but\n                 * transferred with MIME type text/plain:\" errors on\n                 * Chrome.  But how to set the MIME type?  It doesn't seem\n                 * to be part of the websocket stream */\n                img.type = 'image/png';\n            }\n\n            /* Free the memory for the previous frames */\n            if (fig.imageObj.src) {\n                (window.URL || window.webkitURL).revokeObjectURL(\n                    fig.imageObj.src\n                );\n            }\n\n            fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n                img\n            );\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        } else if (\n            typeof evt.data === 'string' &&\n            evt.data.slice(0, 21) === 'data:image/png;base64'\n        ) {\n            fig.imageObj.src = evt.data;\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        }\n\n        var msg = JSON.parse(evt.data);\n        var msg_type = msg['type'];\n\n        // Call the  \"handle_{type}\" callback, which takes\n        // the figure and JSON message as its only arguments.\n        try {\n            var callback = fig['handle_' + msg_type];\n        } catch (e) {\n            console.log(\n                \"No handler for the '\" + msg_type + \"' message type: \",\n                msg\n            );\n            return;\n        }\n\n        if (callback) {\n            try {\n                // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n                callback(fig, msg);\n            } catch (e) {\n                console.log(\n                    \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n                    e,\n                    e.stack,\n                    msg\n                );\n            }\n        }\n    };\n};\n\n// from https://stackoverflow.com/questions/1114465/getting-mouse-location-in-canvas\nmpl.findpos = function (e) {\n    //this section is from http://www.quirksmode.org/js/events_properties.html\n    var targ;\n    if (!e) {\n        e = window.event;\n    }\n    if (e.target) {\n        targ = e.target;\n    } else if (e.srcElement) {\n        targ = e.srcElement;\n    }\n    if (targ.nodeType === 3) {\n        // defeat Safari bug\n        targ = targ.parentNode;\n    }\n\n    // pageX,Y are the mouse positions relative to the document\n    var boundingRect = targ.getBoundingClientRect();\n    var x = e.pageX - (boundingRect.left + document.body.scrollLeft);\n    var y = e.pageY - (boundingRect.top + document.body.scrollTop);\n\n    return { x: x, y: y };\n};\n\n/*\n * return a copy of an object with only non-object keys\n * we need this to avoid circular references\n * https://stackoverflow.com/a/24161582/3208463\n */\nfunction simpleKeys(original) {\n    return Object.keys(original).reduce(function (obj, key) {\n        if (typeof original[key] !== 'object') {\n            obj[key] = original[key];\n        }\n        return obj;\n    }, {});\n}\n\nmpl.figure.prototype.mouse_event = function (event, name) {\n    var canvas_pos = mpl.findpos(event);\n\n    if (name === 'button_press') {\n        this.canvas.focus();\n        this.canvas_div.focus();\n    }\n\n    var x = canvas_pos.x * this.ratio;\n    var y = canvas_pos.y * this.ratio;\n\n    this.send_message(name, {\n        x: x,\n        y: y,\n        button: event.button,\n        step: event.step,\n        guiEvent: simpleKeys(event),\n    });\n\n    /* This prevents the web browser from automatically changing to\n     * the text insertion cursor when the button is pressed.  We want\n     * to control all of the cursor setting manually through the\n     * 'cursor' event from matplotlib */\n    event.preventDefault();\n    return false;\n};\n\nmpl.figure.prototype._key_event_extra = function (_event, _name) {\n    // Handle any extra behaviour associated with a key event\n};\n\nmpl.figure.prototype.key_event = function (event, name) {\n    // Prevent repeat events\n    if (name === 'key_press') {\n        if (event.key === this._key) {\n            return;\n        } else {\n            this._key = event.key;\n        }\n    }\n    if (name === 'key_release') {\n        this._key = null;\n    }\n\n    var value = '';\n    if (event.ctrlKey && event.key !== 'Control') {\n        value += 'ctrl+';\n    }\n    else if (event.altKey && event.key !== 'Alt') {\n        value += 'alt+';\n    }\n    else if (event.shiftKey && event.key !== 'Shift') {\n        value += 'shift+';\n    }\n\n    value += 'k' + event.key;\n\n    this._key_event_extra(event, name);\n\n    this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n    return false;\n};\n\nmpl.figure.prototype.toolbar_button_onclick = function (name) {\n    if (name === 'download') {\n        this.handle_save(this, null);\n    } else {\n        this.send_message('toolbar_button', { name: name });\n    }\n};\n\nmpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n    this.message.textContent = tooltip;\n};\n\n///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n// prettier-ignore\nvar _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\nmpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home icon-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left icon-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right icon-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows icon-move\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis\", \"fa fa-square-o icon-check-empty\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o icon-save\", \"download\"]];\n\nmpl.extensions = [\"eps\", \"jpeg\", \"pgf\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\"];\n\nmpl.default_extension = \"png\";/* global mpl */\n\nvar comm_websocket_adapter = function (comm) {\n    // Create a \"websocket\"-like object which calls the given IPython comm\n    // object with the appropriate methods. Currently this is a non binary\n    // socket, so there is still some room for performance tuning.\n    var ws = {};\n\n    ws.binaryType = comm.kernel.ws.binaryType;\n    ws.readyState = comm.kernel.ws.readyState;\n    function updateReadyState(_event) {\n        if (comm.kernel.ws) {\n            ws.readyState = comm.kernel.ws.readyState;\n        } else {\n            ws.readyState = 3; // Closed state.\n        }\n    }\n    comm.kernel.ws.addEventListener('open', updateReadyState);\n    comm.kernel.ws.addEventListener('close', updateReadyState);\n    comm.kernel.ws.addEventListener('error', updateReadyState);\n\n    ws.close = function () {\n        comm.close();\n    };\n    ws.send = function (m) {\n        //console.log('sending', m);\n        comm.send(m);\n    };\n    // Register the callback with on_msg.\n    comm.on_msg(function (msg) {\n        //console.log('receiving', msg['content']['data'], msg);\n        var data = msg['content']['data'];\n        if (data['blob'] !== undefined) {\n            data = {\n                data: new Blob(msg['buffers'], { type: data['blob'] }),\n            };\n        }\n        // Pass the mpl event to the overridden (by mpl) onmessage function.\n        ws.onmessage(data);\n    });\n    return ws;\n};\n\nmpl.mpl_figure_comm = function (comm, msg) {\n    // This is the function which gets called when the mpl process\n    // starts-up an IPython Comm through the \"matplotlib\" channel.\n\n    var id = msg.content.data.id;\n    // Get hold of the div created by the display call when the Comm\n    // socket was opened in Python.\n    var element = document.getElementById(id);\n    var ws_proxy = comm_websocket_adapter(comm);\n\n    function ondownload(figure, _format) {\n        window.open(figure.canvas.toDataURL());\n    }\n\n    var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n\n    // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n    // web socket which is closed, not our websocket->open comm proxy.\n    ws_proxy.onopen();\n\n    fig.parent_element = element;\n    fig.cell_info = mpl.find_output_cell(\"<div id='\" + id + \"'></div>\");\n    if (!fig.cell_info) {\n        console.error('Failed to find cell for figure', id, fig);\n        return;\n    }\n    fig.cell_info[0].output_area.element.on(\n        'cleared',\n        { fig: fig },\n        fig._remove_fig_handler\n    );\n};\n\nmpl.figure.prototype.handle_close = function (fig, msg) {\n    var width = fig.canvas.width / fig.ratio;\n    fig.cell_info[0].output_area.element.off(\n        'cleared',\n        fig._remove_fig_handler\n    );\n    fig.resizeObserverInstance.unobserve(fig.canvas_div);\n\n    // Update the output cell to use the data from the current canvas.\n    fig.push_to_output();\n    var dataURL = fig.canvas.toDataURL();\n    // Re-enable the keyboard manager in IPython - without this line, in FF,\n    // the notebook keyboard shortcuts fail.\n    IPython.keyboard_manager.enable();\n    fig.parent_element.innerHTML =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n    fig.close_ws(fig, msg);\n};\n\nmpl.figure.prototype.close_ws = function (fig, msg) {\n    fig.send_message('closing', msg);\n    // fig.ws.close()\n};\n\nmpl.figure.prototype.push_to_output = function (_remove_interactive) {\n    // Turn the data on the canvas into data in the output cell.\n    var width = this.canvas.width / this.ratio;\n    var dataURL = this.canvas.toDataURL();\n    this.cell_info[1]['text/html'] =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Tell IPython that the notebook contents must change.\n    IPython.notebook.set_dirty(true);\n    this.send_message('ack', {});\n    var fig = this;\n    // Wait a second, then push the new image to the DOM so\n    // that it is saved nicely (might be nice to debounce this).\n    setTimeout(function () {\n        fig.push_to_output();\n    }, 1000);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'btn-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'btn-group';\n    var button;\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'btn-group';\n            continue;\n        }\n\n        button = fig.buttons[name] = document.createElement('button');\n        button.classList = 'btn btn-default';\n        button.href = '#';\n        button.title = name;\n        button.innerHTML = '<i class=\"fa ' + image + ' fa-lg\"></i>';\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    // Add the status bar.\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message pull-right';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n\n    // Add the close button to the window.\n    var buttongrp = document.createElement('div');\n    buttongrp.classList = 'btn-group inline pull-right';\n    button = document.createElement('button');\n    button.classList = 'btn btn-mini btn-primary';\n    button.href = '#';\n    button.title = 'Stop Interaction';\n    button.innerHTML = '<i class=\"fa fa-power-off icon-remove icon-large\"></i>';\n    button.addEventListener('click', function (_evt) {\n        fig.handle_close(fig, {});\n    });\n    button.addEventListener(\n        'mouseover',\n        on_mouseover_closure('Stop Interaction')\n    );\n    buttongrp.appendChild(button);\n    var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n    titlebar.insertBefore(buttongrp, titlebar.firstChild);\n};\n\nmpl.figure.prototype._remove_fig_handler = function (event) {\n    var fig = event.data.fig;\n    if (event.target !== this) {\n        // Ignore bubbled events from children.\n        return;\n    }\n    fig.close_ws(fig, {});\n};\n\nmpl.figure.prototype._root_extra_style = function (el) {\n    el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n};\n\nmpl.figure.prototype._canvas_extra_style = function (el) {\n    // this is important to make the div 'focusable\n    el.setAttribute('tabindex', 0);\n    // reach out to IPython and tell the keyboard manager to turn it's self\n    // off when our div gets focus\n\n    // location in version 3\n    if (IPython.notebook.keyboard_manager) {\n        IPython.notebook.keyboard_manager.register_events(el);\n    } else {\n        // location in version 2\n        IPython.keyboard_manager.register_events(el);\n    }\n};\n\nmpl.figure.prototype._key_event_extra = function (event, _name) {\n    // Check for shift+enter\n    if (event.shiftKey && event.which === 13) {\n        this.canvas_div.blur();\n        // select the cell after this one\n        var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n        IPython.notebook.select(index + 1);\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    fig.ondownload(fig, null);\n};\n\nmpl.find_output_cell = function (html_output) {\n    // Return the cell and output element which can be found *uniquely* in the notebook.\n    // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n    // IPython event is triggered only after the cells have been serialised, which for\n    // our purposes (turning an active figure into a static one), is too late.\n    var cells = IPython.notebook.get_cells();\n    var ncells = cells.length;\n    for (var i = 0; i < ncells; i++) {\n        var cell = cells[i];\n        if (cell.cell_type === 'code') {\n            for (var j = 0; j < cell.output_area.outputs.length; j++) {\n                var data = cell.output_area.outputs[j];\n                if (data.data) {\n                    // IPython >= 3 moved mimebundle to data attribute of output\n                    data = data.data;\n                }\n                if (data['text/html'] === html_output) {\n                    return [cell, data, j];\n                }\n            }\n        }\n    }\n};\n\n// Register the function which deals with the matplotlib target/channel.\n// The kernel may be null if the page has been refreshed.\nif (IPython.notebook.kernel !== null) {\n    IPython.notebook.kernel.comm_manager.register_target(\n        'matplotlib',\n        mpl.mpl_figure_comm\n    );\n}\n",
      "text/plain": [
       "<IPython.core.display.Javascript object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<img src=\"data:image/png;base64,[encoded data, 61840 characters]\" width=\"640\">"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "val = fitAnalyser.get_fit_value(fitResult)\n",
    "std = fitAnalyser.get_fit_std(fitResult)\n",
    "\n",
    "fitCurve = fitAnalyser.eval(fitResult, x=np.arange(300), y=np.arange(300), dask=\"parallelized\").load()\n",
    "\n",
    "# dataKey = 'sigmax'\n",
    "# dataKey = 'centerx'\n",
    "# dataKey = 'sigmay'\n",
    "dataKey = 'centery'\n",
    "\n",
    "# val_mean = val[dataKey].mean(dim='runs')\n",
    "# std_mean = val[dataKey].std(dim='runs')\n",
    "\n",
    "val_mean = calculate_mean(val[dataKey])\n",
    "std_mean = calculate_std(val[dataKey])\n",
    "\n",
    "fig = plt.figure()\n",
    "ax = fig.gca()\n",
    "\n",
    "val_mean.plot.errorbar(yerr=std_mean, fmt='--ob')\n",
    "\n",
    "plt.grid()\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 87,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/javascript": "/* Put everything inside the global mpl namespace */\n/* global mpl */\nwindow.mpl = {};\n\nmpl.get_websocket_type = function () {\n    if (typeof WebSocket !== 'undefined') {\n        return WebSocket;\n    } else if (typeof MozWebSocket !== 'undefined') {\n        return MozWebSocket;\n    } else {\n        alert(\n            'Your browser does not have WebSocket support. ' +\n                'Please try Chrome, Safari or Firefox ≥ 6. ' +\n                'Firefox 4 and 5 are also supported but you ' +\n                'have to enable WebSockets in about:config.'\n        );\n    }\n};\n\nmpl.figure = function (figure_id, websocket, ondownload, parent_element) {\n    this.id = figure_id;\n\n    this.ws = websocket;\n\n    this.supports_binary = this.ws.binaryType !== undefined;\n\n    if (!this.supports_binary) {\n        var warnings = document.getElementById('mpl-warnings');\n        if (warnings) {\n            warnings.style.display = 'block';\n            warnings.textContent =\n                'This browser does not support binary websocket messages. ' +\n                'Performance may be slow.';\n        }\n    }\n\n    this.imageObj = new Image();\n\n    this.context = undefined;\n    this.message = undefined;\n    this.canvas = undefined;\n    this.rubberband_canvas = undefined;\n    this.rubberband_context = undefined;\n    this.format_dropdown = undefined;\n\n    this.image_mode = 'full';\n\n    this.root = document.createElement('div');\n    this.root.setAttribute('style', 'display: inline-block');\n    this._root_extra_style(this.root);\n\n    parent_element.appendChild(this.root);\n\n    this._init_header(this);\n    this._init_canvas(this);\n    this._init_toolbar(this);\n\n    var fig = this;\n\n    this.waiting = false;\n\n    this.ws.onopen = function () {\n        fig.send_message('supports_binary', { value: fig.supports_binary });\n        fig.send_message('send_image_mode', {});\n        if (fig.ratio !== 1) {\n            fig.send_message('set_device_pixel_ratio', {\n                device_pixel_ratio: fig.ratio,\n            });\n        }\n        fig.send_message('refresh', {});\n    };\n\n    this.imageObj.onload = function () {\n        if (fig.image_mode === 'full') {\n            // Full images could contain transparency (where diff images\n            // almost always do), so we need to clear the canvas so that\n            // there is no ghosting.\n            fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n        }\n        fig.context.drawImage(fig.imageObj, 0, 0);\n    };\n\n    this.imageObj.onunload = function () {\n        fig.ws.close();\n    };\n\n    this.ws.onmessage = this._make_on_message_function(this);\n\n    this.ondownload = ondownload;\n};\n\nmpl.figure.prototype._init_header = function () {\n    var titlebar = document.createElement('div');\n    titlebar.classList =\n        'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n    var titletext = document.createElement('div');\n    titletext.classList = 'ui-dialog-title';\n    titletext.setAttribute(\n        'style',\n        'width: 100%; text-align: center; padding: 3px;'\n    );\n    titlebar.appendChild(titletext);\n    this.root.appendChild(titlebar);\n    this.header = titletext;\n};\n\nmpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._init_canvas = function () {\n    var fig = this;\n\n    var canvas_div = (this.canvas_div = document.createElement('div'));\n    canvas_div.setAttribute(\n        'style',\n        'border: 1px solid #ddd;' +\n            'box-sizing: content-box;' +\n            'clear: both;' +\n            'min-height: 1px;' +\n            'min-width: 1px;' +\n            'outline: 0;' +\n            'overflow: hidden;' +\n            'position: relative;' +\n            'resize: both;'\n    );\n\n    function on_keyboard_event_closure(name) {\n        return function (event) {\n            return fig.key_event(event, name);\n        };\n    }\n\n    canvas_div.addEventListener(\n        'keydown',\n        on_keyboard_event_closure('key_press')\n    );\n    canvas_div.addEventListener(\n        'keyup',\n        on_keyboard_event_closure('key_release')\n    );\n\n    this._canvas_extra_style(canvas_div);\n    this.root.appendChild(canvas_div);\n\n    var canvas = (this.canvas = document.createElement('canvas'));\n    canvas.classList.add('mpl-canvas');\n    canvas.setAttribute('style', 'box-sizing: content-box;');\n\n    this.context = canvas.getContext('2d');\n\n    var backingStore =\n        this.context.backingStorePixelRatio ||\n        this.context.webkitBackingStorePixelRatio ||\n        this.context.mozBackingStorePixelRatio ||\n        this.context.msBackingStorePixelRatio ||\n        this.context.oBackingStorePixelRatio ||\n        this.context.backingStorePixelRatio ||\n        1;\n\n    this.ratio = (window.devicePixelRatio || 1) / backingStore;\n\n    var rubberband_canvas = (this.rubberband_canvas = document.createElement(\n        'canvas'\n    ));\n    rubberband_canvas.setAttribute(\n        'style',\n        'box-sizing: content-box; position: absolute; left: 0; top: 0; z-index: 1;'\n    );\n\n    // Apply a ponyfill if ResizeObserver is not implemented by browser.\n    if (this.ResizeObserver === undefined) {\n        if (window.ResizeObserver !== undefined) {\n            this.ResizeObserver = window.ResizeObserver;\n        } else {\n            var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n            this.ResizeObserver = obs.ResizeObserver;\n        }\n    }\n\n    this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n        var nentries = entries.length;\n        for (var i = 0; i < nentries; i++) {\n            var entry = entries[i];\n            var width, height;\n            if (entry.contentBoxSize) {\n                if (entry.contentBoxSize instanceof Array) {\n                    // Chrome 84 implements new version of spec.\n                    width = entry.contentBoxSize[0].inlineSize;\n                    height = entry.contentBoxSize[0].blockSize;\n                } else {\n                    // Firefox implements old version of spec.\n                    width = entry.contentBoxSize.inlineSize;\n                    height = entry.contentBoxSize.blockSize;\n                }\n            } else {\n                // Chrome <84 implements even older version of spec.\n                width = entry.contentRect.width;\n                height = entry.contentRect.height;\n            }\n\n            // Keep the size of the canvas and rubber band canvas in sync with\n            // the canvas container.\n            if (entry.devicePixelContentBoxSize) {\n                // Chrome 84 implements new version of spec.\n                canvas.setAttribute(\n                    'width',\n                    entry.devicePixelContentBoxSize[0].inlineSize\n                );\n                canvas.setAttribute(\n                    'height',\n                    entry.devicePixelContentBoxSize[0].blockSize\n                );\n            } else {\n                canvas.setAttribute('width', width * fig.ratio);\n                canvas.setAttribute('height', height * fig.ratio);\n            }\n            canvas.setAttribute(\n                'style',\n                'width: ' + width + 'px; height: ' + height + 'px;'\n            );\n\n            rubberband_canvas.setAttribute('width', width);\n            rubberband_canvas.setAttribute('height', height);\n\n            // And update the size in Python. We ignore the initial 0/0 size\n            // that occurs as the element is placed into the DOM, which should\n            // otherwise not happen due to the minimum size styling.\n            if (fig.ws.readyState == 1 && width != 0 && height != 0) {\n                fig.request_resize(width, height);\n            }\n        }\n    });\n    this.resizeObserverInstance.observe(canvas_div);\n\n    function on_mouse_event_closure(name) {\n        return function (event) {\n            return fig.mouse_event(event, name);\n        };\n    }\n\n    rubberband_canvas.addEventListener(\n        'mousedown',\n        on_mouse_event_closure('button_press')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseup',\n        on_mouse_event_closure('button_release')\n    );\n    rubberband_canvas.addEventListener(\n        'dblclick',\n        on_mouse_event_closure('dblclick')\n    );\n    // Throttle sequential mouse events to 1 every 20ms.\n    rubberband_canvas.addEventListener(\n        'mousemove',\n        on_mouse_event_closure('motion_notify')\n    );\n\n    rubberband_canvas.addEventListener(\n        'mouseenter',\n        on_mouse_event_closure('figure_enter')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseleave',\n        on_mouse_event_closure('figure_leave')\n    );\n\n    canvas_div.addEventListener('wheel', function (event) {\n        if (event.deltaY < 0) {\n            event.step = 1;\n        } else {\n            event.step = -1;\n        }\n        on_mouse_event_closure('scroll')(event);\n    });\n\n    canvas_div.appendChild(canvas);\n    canvas_div.appendChild(rubberband_canvas);\n\n    this.rubberband_context = rubberband_canvas.getContext('2d');\n    this.rubberband_context.strokeStyle = '#000000';\n\n    this._resize_canvas = function (width, height, forward) {\n        if (forward) {\n            canvas_div.style.width = width + 'px';\n            canvas_div.style.height = height + 'px';\n        }\n    };\n\n    // Disable right mouse context menu.\n    this.rubberband_canvas.addEventListener('contextmenu', function (_e) {\n        event.preventDefault();\n        return false;\n    });\n\n    function set_focus() {\n        canvas.focus();\n        canvas_div.focus();\n    }\n\n    window.setTimeout(set_focus, 100);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'mpl-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'mpl-button-group';\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'mpl-button-group';\n            continue;\n        }\n\n        var button = (fig.buttons[name] = document.createElement('button'));\n        button.classList = 'mpl-widget';\n        button.setAttribute('role', 'button');\n        button.setAttribute('aria-disabled', 'false');\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n\n        var icon_img = document.createElement('img');\n        icon_img.src = '_images/' + image + '.png';\n        icon_img.srcset = '_images/' + image + '_large.png 2x';\n        icon_img.alt = tooltip;\n        button.appendChild(icon_img);\n\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    var fmt_picker = document.createElement('select');\n    fmt_picker.classList = 'mpl-widget';\n    toolbar.appendChild(fmt_picker);\n    this.format_dropdown = fmt_picker;\n\n    for (var ind in mpl.extensions) {\n        var fmt = mpl.extensions[ind];\n        var option = document.createElement('option');\n        option.selected = fmt === mpl.default_extension;\n        option.innerHTML = fmt;\n        fmt_picker.appendChild(option);\n    }\n\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n};\n\nmpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n    // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n    // which will in turn request a refresh of the image.\n    this.send_message('resize', { width: x_pixels, height: y_pixels });\n};\n\nmpl.figure.prototype.send_message = function (type, properties) {\n    properties['type'] = type;\n    properties['figure_id'] = this.id;\n    this.ws.send(JSON.stringify(properties));\n};\n\nmpl.figure.prototype.send_draw_message = function () {\n    if (!this.waiting) {\n        this.waiting = true;\n        this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    var format_dropdown = fig.format_dropdown;\n    var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n    fig.ondownload(fig, format);\n};\n\nmpl.figure.prototype.handle_resize = function (fig, msg) {\n    var size = msg['size'];\n    if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n        fig._resize_canvas(size[0], size[1], msg['forward']);\n        fig.send_message('refresh', {});\n    }\n};\n\nmpl.figure.prototype.handle_rubberband = function (fig, msg) {\n    var x0 = msg['x0'] / fig.ratio;\n    var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n    var x1 = msg['x1'] / fig.ratio;\n    var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n    x0 = Math.floor(x0) + 0.5;\n    y0 = Math.floor(y0) + 0.5;\n    x1 = Math.floor(x1) + 0.5;\n    y1 = Math.floor(y1) + 0.5;\n    var min_x = Math.min(x0, x1);\n    var min_y = Math.min(y0, y1);\n    var width = Math.abs(x1 - x0);\n    var height = Math.abs(y1 - y0);\n\n    fig.rubberband_context.clearRect(\n        0,\n        0,\n        fig.canvas.width / fig.ratio,\n        fig.canvas.height / fig.ratio\n    );\n\n    fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n};\n\nmpl.figure.prototype.handle_figure_label = function (fig, msg) {\n    // Updates the figure title.\n    fig.header.textContent = msg['label'];\n};\n\nmpl.figure.prototype.handle_cursor = function (fig, msg) {\n    fig.rubberband_canvas.style.cursor = msg['cursor'];\n};\n\nmpl.figure.prototype.handle_message = function (fig, msg) {\n    fig.message.textContent = msg['message'];\n};\n\nmpl.figure.prototype.handle_draw = function (fig, _msg) {\n    // Request the server to send over a new figure.\n    fig.send_draw_message();\n};\n\nmpl.figure.prototype.handle_image_mode = function (fig, msg) {\n    fig.image_mode = msg['mode'];\n};\n\nmpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n    for (var key in msg) {\n        if (!(key in fig.buttons)) {\n            continue;\n        }\n        fig.buttons[key].disabled = !msg[key];\n        fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n    }\n};\n\nmpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n    if (msg['mode'] === 'PAN') {\n        fig.buttons['Pan'].classList.add('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    } else if (msg['mode'] === 'ZOOM') {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.add('active');\n    } else {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    }\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Called whenever the canvas gets updated.\n    this.send_message('ack', {});\n};\n\n// A function to construct a web socket function for onmessage handling.\n// Called in the figure constructor.\nmpl.figure.prototype._make_on_message_function = function (fig) {\n    return function socket_on_message(evt) {\n        if (evt.data instanceof Blob) {\n            var img = evt.data;\n            if (img.type !== 'image/png') {\n                /* FIXME: We get \"Resource interpreted as Image but\n                 * transferred with MIME type text/plain:\" errors on\n                 * Chrome.  But how to set the MIME type?  It doesn't seem\n                 * to be part of the websocket stream */\n                img.type = 'image/png';\n            }\n\n            /* Free the memory for the previous frames */\n            if (fig.imageObj.src) {\n                (window.URL || window.webkitURL).revokeObjectURL(\n                    fig.imageObj.src\n                );\n            }\n\n            fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n                img\n            );\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        } else if (\n            typeof evt.data === 'string' &&\n            evt.data.slice(0, 21) === 'data:image/png;base64'\n        ) {\n            fig.imageObj.src = evt.data;\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        }\n\n        var msg = JSON.parse(evt.data);\n        var msg_type = msg['type'];\n\n        // Call the  \"handle_{type}\" callback, which takes\n        // the figure and JSON message as its only arguments.\n        try {\n            var callback = fig['handle_' + msg_type];\n        } catch (e) {\n            console.log(\n                \"No handler for the '\" + msg_type + \"' message type: \",\n                msg\n            );\n            return;\n        }\n\n        if (callback) {\n            try {\n                // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n                callback(fig, msg);\n            } catch (e) {\n                console.log(\n                    \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n                    e,\n                    e.stack,\n                    msg\n                );\n            }\n        }\n    };\n};\n\n// from https://stackoverflow.com/questions/1114465/getting-mouse-location-in-canvas\nmpl.findpos = function (e) {\n    //this section is from http://www.quirksmode.org/js/events_properties.html\n    var targ;\n    if (!e) {\n        e = window.event;\n    }\n    if (e.target) {\n        targ = e.target;\n    } else if (e.srcElement) {\n        targ = e.srcElement;\n    }\n    if (targ.nodeType === 3) {\n        // defeat Safari bug\n        targ = targ.parentNode;\n    }\n\n    // pageX,Y are the mouse positions relative to the document\n    var boundingRect = targ.getBoundingClientRect();\n    var x = e.pageX - (boundingRect.left + document.body.scrollLeft);\n    var y = e.pageY - (boundingRect.top + document.body.scrollTop);\n\n    return { x: x, y: y };\n};\n\n/*\n * return a copy of an object with only non-object keys\n * we need this to avoid circular references\n * https://stackoverflow.com/a/24161582/3208463\n */\nfunction simpleKeys(original) {\n    return Object.keys(original).reduce(function (obj, key) {\n        if (typeof original[key] !== 'object') {\n            obj[key] = original[key];\n        }\n        return obj;\n    }, {});\n}\n\nmpl.figure.prototype.mouse_event = function (event, name) {\n    var canvas_pos = mpl.findpos(event);\n\n    if (name === 'button_press') {\n        this.canvas.focus();\n        this.canvas_div.focus();\n    }\n\n    var x = canvas_pos.x * this.ratio;\n    var y = canvas_pos.y * this.ratio;\n\n    this.send_message(name, {\n        x: x,\n        y: y,\n        button: event.button,\n        step: event.step,\n        guiEvent: simpleKeys(event),\n    });\n\n    /* This prevents the web browser from automatically changing to\n     * the text insertion cursor when the button is pressed.  We want\n     * to control all of the cursor setting manually through the\n     * 'cursor' event from matplotlib */\n    event.preventDefault();\n    return false;\n};\n\nmpl.figure.prototype._key_event_extra = function (_event, _name) {\n    // Handle any extra behaviour associated with a key event\n};\n\nmpl.figure.prototype.key_event = function (event, name) {\n    // Prevent repeat events\n    if (name === 'key_press') {\n        if (event.key === this._key) {\n            return;\n        } else {\n            this._key = event.key;\n        }\n    }\n    if (name === 'key_release') {\n        this._key = null;\n    }\n\n    var value = '';\n    if (event.ctrlKey && event.key !== 'Control') {\n        value += 'ctrl+';\n    }\n    else if (event.altKey && event.key !== 'Alt') {\n        value += 'alt+';\n    }\n    else if (event.shiftKey && event.key !== 'Shift') {\n        value += 'shift+';\n    }\n\n    value += 'k' + event.key;\n\n    this._key_event_extra(event, name);\n\n    this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n    return false;\n};\n\nmpl.figure.prototype.toolbar_button_onclick = function (name) {\n    if (name === 'download') {\n        this.handle_save(this, null);\n    } else {\n        this.send_message('toolbar_button', { name: name });\n    }\n};\n\nmpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n    this.message.textContent = tooltip;\n};\n\n///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n// prettier-ignore\nvar _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\nmpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home icon-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left icon-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right icon-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows icon-move\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis\", \"fa fa-square-o icon-check-empty\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o icon-save\", \"download\"]];\n\nmpl.extensions = [\"eps\", \"jpeg\", \"pgf\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\"];\n\nmpl.default_extension = \"png\";/* global mpl */\n\nvar comm_websocket_adapter = function (comm) {\n    // Create a \"websocket\"-like object which calls the given IPython comm\n    // object with the appropriate methods. Currently this is a non binary\n    // socket, so there is still some room for performance tuning.\n    var ws = {};\n\n    ws.binaryType = comm.kernel.ws.binaryType;\n    ws.readyState = comm.kernel.ws.readyState;\n    function updateReadyState(_event) {\n        if (comm.kernel.ws) {\n            ws.readyState = comm.kernel.ws.readyState;\n        } else {\n            ws.readyState = 3; // Closed state.\n        }\n    }\n    comm.kernel.ws.addEventListener('open', updateReadyState);\n    comm.kernel.ws.addEventListener('close', updateReadyState);\n    comm.kernel.ws.addEventListener('error', updateReadyState);\n\n    ws.close = function () {\n        comm.close();\n    };\n    ws.send = function (m) {\n        //console.log('sending', m);\n        comm.send(m);\n    };\n    // Register the callback with on_msg.\n    comm.on_msg(function (msg) {\n        //console.log('receiving', msg['content']['data'], msg);\n        var data = msg['content']['data'];\n        if (data['blob'] !== undefined) {\n            data = {\n                data: new Blob(msg['buffers'], { type: data['blob'] }),\n            };\n        }\n        // Pass the mpl event to the overridden (by mpl) onmessage function.\n        ws.onmessage(data);\n    });\n    return ws;\n};\n\nmpl.mpl_figure_comm = function (comm, msg) {\n    // This is the function which gets called when the mpl process\n    // starts-up an IPython Comm through the \"matplotlib\" channel.\n\n    var id = msg.content.data.id;\n    // Get hold of the div created by the display call when the Comm\n    // socket was opened in Python.\n    var element = document.getElementById(id);\n    var ws_proxy = comm_websocket_adapter(comm);\n\n    function ondownload(figure, _format) {\n        window.open(figure.canvas.toDataURL());\n    }\n\n    var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n\n    // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n    // web socket which is closed, not our websocket->open comm proxy.\n    ws_proxy.onopen();\n\n    fig.parent_element = element;\n    fig.cell_info = mpl.find_output_cell(\"<div id='\" + id + \"'></div>\");\n    if (!fig.cell_info) {\n        console.error('Failed to find cell for figure', id, fig);\n        return;\n    }\n    fig.cell_info[0].output_area.element.on(\n        'cleared',\n        { fig: fig },\n        fig._remove_fig_handler\n    );\n};\n\nmpl.figure.prototype.handle_close = function (fig, msg) {\n    var width = fig.canvas.width / fig.ratio;\n    fig.cell_info[0].output_area.element.off(\n        'cleared',\n        fig._remove_fig_handler\n    );\n    fig.resizeObserverInstance.unobserve(fig.canvas_div);\n\n    // Update the output cell to use the data from the current canvas.\n    fig.push_to_output();\n    var dataURL = fig.canvas.toDataURL();\n    // Re-enable the keyboard manager in IPython - without this line, in FF,\n    // the notebook keyboard shortcuts fail.\n    IPython.keyboard_manager.enable();\n    fig.parent_element.innerHTML =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n    fig.close_ws(fig, msg);\n};\n\nmpl.figure.prototype.close_ws = function (fig, msg) {\n    fig.send_message('closing', msg);\n    // fig.ws.close()\n};\n\nmpl.figure.prototype.push_to_output = function (_remove_interactive) {\n    // Turn the data on the canvas into data in the output cell.\n    var width = this.canvas.width / this.ratio;\n    var dataURL = this.canvas.toDataURL();\n    this.cell_info[1]['text/html'] =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Tell IPython that the notebook contents must change.\n    IPython.notebook.set_dirty(true);\n    this.send_message('ack', {});\n    var fig = this;\n    // Wait a second, then push the new image to the DOM so\n    // that it is saved nicely (might be nice to debounce this).\n    setTimeout(function () {\n        fig.push_to_output();\n    }, 1000);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'btn-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'btn-group';\n    var button;\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'btn-group';\n            continue;\n        }\n\n        button = fig.buttons[name] = document.createElement('button');\n        button.classList = 'btn btn-default';\n        button.href = '#';\n        button.title = name;\n        button.innerHTML = '<i class=\"fa ' + image + ' fa-lg\"></i>';\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    // Add the status bar.\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message pull-right';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n\n    // Add the close button to the window.\n    var buttongrp = document.createElement('div');\n    buttongrp.classList = 'btn-group inline pull-right';\n    button = document.createElement('button');\n    button.classList = 'btn btn-mini btn-primary';\n    button.href = '#';\n    button.title = 'Stop Interaction';\n    button.innerHTML = '<i class=\"fa fa-power-off icon-remove icon-large\"></i>';\n    button.addEventListener('click', function (_evt) {\n        fig.handle_close(fig, {});\n    });\n    button.addEventListener(\n        'mouseover',\n        on_mouseover_closure('Stop Interaction')\n    );\n    buttongrp.appendChild(button);\n    var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n    titlebar.insertBefore(buttongrp, titlebar.firstChild);\n};\n\nmpl.figure.prototype._remove_fig_handler = function (event) {\n    var fig = event.data.fig;\n    if (event.target !== this) {\n        // Ignore bubbled events from children.\n        return;\n    }\n    fig.close_ws(fig, {});\n};\n\nmpl.figure.prototype._root_extra_style = function (el) {\n    el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n};\n\nmpl.figure.prototype._canvas_extra_style = function (el) {\n    // this is important to make the div 'focusable\n    el.setAttribute('tabindex', 0);\n    // reach out to IPython and tell the keyboard manager to turn it's self\n    // off when our div gets focus\n\n    // location in version 3\n    if (IPython.notebook.keyboard_manager) {\n        IPython.notebook.keyboard_manager.register_events(el);\n    } else {\n        // location in version 2\n        IPython.keyboard_manager.register_events(el);\n    }\n};\n\nmpl.figure.prototype._key_event_extra = function (event, _name) {\n    // Check for shift+enter\n    if (event.shiftKey && event.which === 13) {\n        this.canvas_div.blur();\n        // select the cell after this one\n        var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n        IPython.notebook.select(index + 1);\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    fig.ondownload(fig, null);\n};\n\nmpl.find_output_cell = function (html_output) {\n    // Return the cell and output element which can be found *uniquely* in the notebook.\n    // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n    // IPython event is triggered only after the cells have been serialised, which for\n    // our purposes (turning an active figure into a static one), is too late.\n    var cells = IPython.notebook.get_cells();\n    var ncells = cells.length;\n    for (var i = 0; i < ncells; i++) {\n        var cell = cells[i];\n        if (cell.cell_type === 'code') {\n            for (var j = 0; j < cell.output_area.outputs.length; j++) {\n                var data = cell.output_area.outputs[j];\n                if (data.data) {\n                    // IPython >= 3 moved mimebundle to data attribute of output\n                    data = data.data;\n                }\n                if (data['text/html'] === html_output) {\n                    return [cell, data, j];\n                }\n            }\n        }\n    }\n};\n\n// Register the function which deals with the matplotlib target/channel.\n// The kernel may be null if the page has been refreshed.\nif (IPython.notebook.kernel !== null) {\n    IPython.notebook.kernel.comm_manager.register_target(\n        'matplotlib',\n        mpl.mpl_figure_comm\n    );\n}\n",
      "text/plain": [
       "<IPython.core.display.Javascript object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<img src=\"data:image/png;base64,[encoded data, 81984 characters]\" width=\"640\">"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "f = 238.8665 ± 0.3901 Hz\n"
     ]
    }
   ],
   "source": [
    "def damp_osci(t, t0, A, B, nu, gamma):\n",
    "    return A * np.exp(-gamma*t)*np.sin(2*np.pi*nu*(t-t0)) + B\n",
    "\n",
    "yvals     = val_mean#.sel(blink_on_time=slice(0.005, 0.025))\n",
    "yvals_std = std_mean#.sel(blink_on_time=slice(0.005, 0.025))\n",
    "xvals     = dataSet_cropOD[scanAxis[0]]#.sel(blink_on_time=slice(0.005, 0.025))\n",
    "\n",
    "fitted_qtys_1 = yvals.to_numpy()\n",
    "scan_para = xvals.to_numpy()\n",
    "fitted_qtys_err_1 = yvals_std.to_numpy()\n",
    "\n",
    "\n",
    "plt.figure()\n",
    "popt_x, pcov_x = curve_fit(damp_osci, scan_para, fitted_qtys_1, np.array([0, 3, 147, 3e2, 0.1]))\n",
    "freqdata = np.linspace(0.005, 20e-3, 500)\n",
    "plt.plot(freqdata, damp_osci(freqdata, *popt_x), 'g--',label='fit: t0=%5.3f, A=%5.3f, B=%5.3f, nu=%5.3f, Gamma=%5.3f' % tuple(popt_x))\n",
    "plt.errorbar(scan_para, fitted_qtys_1, yerr=fitted_qtys_err_1, fmt='or')\n",
    "plt.xlabel('hold time after switch on the trap (s)')\n",
    "plt.ylabel('Center along gravity direction (pixels)')\n",
    "plt.tight_layout()\n",
    "plt.grid(visible=1)\n",
    "#plt.ylim([0,750])\n",
    "#plt.xlim([0.004, 0.025])\n",
    "#plt.legend(prop={'size': 14})\n",
    "plt.show()\n",
    "\n",
    "f_x = popt_x[3]\n",
    "df_x = pcov_x[3][3]**0.5\n",
    "\n",
    "print('f = %.4f \\u00B1 %.4f Hz'% tuple([np.abs(f_x),df_x]))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Truncation: 0.725"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 93,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The detected scaning axes and values are: \n",
      "\n",
      "{'mod_blink_on_time': array([0.005 , 0.0057, 0.0064, 0.0071, 0.0078, 0.0085, 0.0092, 0.0099,\n",
      "       0.0106, 0.0113, 0.012 , 0.0127, 0.0134, 0.0141, 0.0148, 0.0155,\n",
      "       0.0162, 0.0169, 0.0176, 0.0183, 0.019 , 0.0197]), 'runs': array([0., 1., 2., 3.])}\n"
     ]
    },
    {
     "data": {
      "application/javascript": "/* Put everything inside the global mpl namespace */\n/* global mpl */\nwindow.mpl = {};\n\nmpl.get_websocket_type = function () {\n    if (typeof WebSocket !== 'undefined') {\n        return WebSocket;\n    } else if (typeof MozWebSocket !== 'undefined') {\n        return MozWebSocket;\n    } else {\n        alert(\n            'Your browser does not have WebSocket support. ' +\n                'Please try Chrome, Safari or Firefox ≥ 6. ' +\n                'Firefox 4 and 5 are also supported but you ' +\n                'have to enable WebSockets in about:config.'\n        );\n    }\n};\n\nmpl.figure = function (figure_id, websocket, ondownload, parent_element) {\n    this.id = figure_id;\n\n    this.ws = websocket;\n\n    this.supports_binary = this.ws.binaryType !== undefined;\n\n    if (!this.supports_binary) {\n        var warnings = document.getElementById('mpl-warnings');\n        if (warnings) {\n            warnings.style.display = 'block';\n            warnings.textContent =\n                'This browser does not support binary websocket messages. ' +\n                'Performance may be slow.';\n        }\n    }\n\n    this.imageObj = new Image();\n\n    this.context = undefined;\n    this.message = undefined;\n    this.canvas = undefined;\n    this.rubberband_canvas = undefined;\n    this.rubberband_context = undefined;\n    this.format_dropdown = undefined;\n\n    this.image_mode = 'full';\n\n    this.root = document.createElement('div');\n    this.root.setAttribute('style', 'display: inline-block');\n    this._root_extra_style(this.root);\n\n    parent_element.appendChild(this.root);\n\n    this._init_header(this);\n    this._init_canvas(this);\n    this._init_toolbar(this);\n\n    var fig = this;\n\n    this.waiting = false;\n\n    this.ws.onopen = function () {\n        fig.send_message('supports_binary', { value: fig.supports_binary });\n        fig.send_message('send_image_mode', {});\n        if (fig.ratio !== 1) {\n            fig.send_message('set_device_pixel_ratio', {\n                device_pixel_ratio: fig.ratio,\n            });\n        }\n        fig.send_message('refresh', {});\n    };\n\n    this.imageObj.onload = function () {\n        if (fig.image_mode === 'full') {\n            // Full images could contain transparency (where diff images\n            // almost always do), so we need to clear the canvas so that\n            // there is no ghosting.\n            fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n        }\n        fig.context.drawImage(fig.imageObj, 0, 0);\n    };\n\n    this.imageObj.onunload = function () {\n        fig.ws.close();\n    };\n\n    this.ws.onmessage = this._make_on_message_function(this);\n\n    this.ondownload = ondownload;\n};\n\nmpl.figure.prototype._init_header = function () {\n    var titlebar = document.createElement('div');\n    titlebar.classList =\n        'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n    var titletext = document.createElement('div');\n    titletext.classList = 'ui-dialog-title';\n    titletext.setAttribute(\n        'style',\n        'width: 100%; text-align: center; padding: 3px;'\n    );\n    titlebar.appendChild(titletext);\n    this.root.appendChild(titlebar);\n    this.header = titletext;\n};\n\nmpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._init_canvas = function () {\n    var fig = this;\n\n    var canvas_div = (this.canvas_div = document.createElement('div'));\n    canvas_div.setAttribute(\n        'style',\n        'border: 1px solid #ddd;' +\n            'box-sizing: content-box;' +\n            'clear: both;' +\n            'min-height: 1px;' +\n            'min-width: 1px;' +\n            'outline: 0;' +\n            'overflow: hidden;' +\n            'position: relative;' +\n            'resize: both;'\n    );\n\n    function on_keyboard_event_closure(name) {\n        return function (event) {\n            return fig.key_event(event, name);\n        };\n    }\n\n    canvas_div.addEventListener(\n        'keydown',\n        on_keyboard_event_closure('key_press')\n    );\n    canvas_div.addEventListener(\n        'keyup',\n        on_keyboard_event_closure('key_release')\n    );\n\n    this._canvas_extra_style(canvas_div);\n    this.root.appendChild(canvas_div);\n\n    var canvas = (this.canvas = document.createElement('canvas'));\n    canvas.classList.add('mpl-canvas');\n    canvas.setAttribute('style', 'box-sizing: content-box;');\n\n    this.context = canvas.getContext('2d');\n\n    var backingStore =\n        this.context.backingStorePixelRatio ||\n        this.context.webkitBackingStorePixelRatio ||\n        this.context.mozBackingStorePixelRatio ||\n        this.context.msBackingStorePixelRatio ||\n        this.context.oBackingStorePixelRatio ||\n        this.context.backingStorePixelRatio ||\n        1;\n\n    this.ratio = (window.devicePixelRatio || 1) / backingStore;\n\n    var rubberband_canvas = (this.rubberband_canvas = document.createElement(\n        'canvas'\n    ));\n    rubberband_canvas.setAttribute(\n        'style',\n        'box-sizing: content-box; position: absolute; left: 0; top: 0; z-index: 1;'\n    );\n\n    // Apply a ponyfill if ResizeObserver is not implemented by browser.\n    if (this.ResizeObserver === undefined) {\n        if (window.ResizeObserver !== undefined) {\n            this.ResizeObserver = window.ResizeObserver;\n        } else {\n            var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n            this.ResizeObserver = obs.ResizeObserver;\n        }\n    }\n\n    this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n        var nentries = entries.length;\n        for (var i = 0; i < nentries; i++) {\n            var entry = entries[i];\n            var width, height;\n            if (entry.contentBoxSize) {\n                if (entry.contentBoxSize instanceof Array) {\n                    // Chrome 84 implements new version of spec.\n                    width = entry.contentBoxSize[0].inlineSize;\n                    height = entry.contentBoxSize[0].blockSize;\n                } else {\n                    // Firefox implements old version of spec.\n                    width = entry.contentBoxSize.inlineSize;\n                    height = entry.contentBoxSize.blockSize;\n                }\n            } else {\n                // Chrome <84 implements even older version of spec.\n                width = entry.contentRect.width;\n                height = entry.contentRect.height;\n            }\n\n            // Keep the size of the canvas and rubber band canvas in sync with\n            // the canvas container.\n            if (entry.devicePixelContentBoxSize) {\n                // Chrome 84 implements new version of spec.\n                canvas.setAttribute(\n                    'width',\n                    entry.devicePixelContentBoxSize[0].inlineSize\n                );\n                canvas.setAttribute(\n                    'height',\n                    entry.devicePixelContentBoxSize[0].blockSize\n                );\n            } else {\n                canvas.setAttribute('width', width * fig.ratio);\n                canvas.setAttribute('height', height * fig.ratio);\n            }\n            canvas.setAttribute(\n                'style',\n                'width: ' + width + 'px; height: ' + height + 'px;'\n            );\n\n            rubberband_canvas.setAttribute('width', width);\n            rubberband_canvas.setAttribute('height', height);\n\n            // And update the size in Python. We ignore the initial 0/0 size\n            // that occurs as the element is placed into the DOM, which should\n            // otherwise not happen due to the minimum size styling.\n            if (fig.ws.readyState == 1 && width != 0 && height != 0) {\n                fig.request_resize(width, height);\n            }\n        }\n    });\n    this.resizeObserverInstance.observe(canvas_div);\n\n    function on_mouse_event_closure(name) {\n        return function (event) {\n            return fig.mouse_event(event, name);\n        };\n    }\n\n    rubberband_canvas.addEventListener(\n        'mousedown',\n        on_mouse_event_closure('button_press')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseup',\n        on_mouse_event_closure('button_release')\n    );\n    rubberband_canvas.addEventListener(\n        'dblclick',\n        on_mouse_event_closure('dblclick')\n    );\n    // Throttle sequential mouse events to 1 every 20ms.\n    rubberband_canvas.addEventListener(\n        'mousemove',\n        on_mouse_event_closure('motion_notify')\n    );\n\n    rubberband_canvas.addEventListener(\n        'mouseenter',\n        on_mouse_event_closure('figure_enter')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseleave',\n        on_mouse_event_closure('figure_leave')\n    );\n\n    canvas_div.addEventListener('wheel', function (event) {\n        if (event.deltaY < 0) {\n            event.step = 1;\n        } else {\n            event.step = -1;\n        }\n        on_mouse_event_closure('scroll')(event);\n    });\n\n    canvas_div.appendChild(canvas);\n    canvas_div.appendChild(rubberband_canvas);\n\n    this.rubberband_context = rubberband_canvas.getContext('2d');\n    this.rubberband_context.strokeStyle = '#000000';\n\n    this._resize_canvas = function (width, height, forward) {\n        if (forward) {\n            canvas_div.style.width = width + 'px';\n            canvas_div.style.height = height + 'px';\n        }\n    };\n\n    // Disable right mouse context menu.\n    this.rubberband_canvas.addEventListener('contextmenu', function (_e) {\n        event.preventDefault();\n        return false;\n    });\n\n    function set_focus() {\n        canvas.focus();\n        canvas_div.focus();\n    }\n\n    window.setTimeout(set_focus, 100);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'mpl-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'mpl-button-group';\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'mpl-button-group';\n            continue;\n        }\n\n        var button = (fig.buttons[name] = document.createElement('button'));\n        button.classList = 'mpl-widget';\n        button.setAttribute('role', 'button');\n        button.setAttribute('aria-disabled', 'false');\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n\n        var icon_img = document.createElement('img');\n        icon_img.src = '_images/' + image + '.png';\n        icon_img.srcset = '_images/' + image + '_large.png 2x';\n        icon_img.alt = tooltip;\n        button.appendChild(icon_img);\n\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    var fmt_picker = document.createElement('select');\n    fmt_picker.classList = 'mpl-widget';\n    toolbar.appendChild(fmt_picker);\n    this.format_dropdown = fmt_picker;\n\n    for (var ind in mpl.extensions) {\n        var fmt = mpl.extensions[ind];\n        var option = document.createElement('option');\n        option.selected = fmt === mpl.default_extension;\n        option.innerHTML = fmt;\n        fmt_picker.appendChild(option);\n    }\n\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n};\n\nmpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n    // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n    // which will in turn request a refresh of the image.\n    this.send_message('resize', { width: x_pixels, height: y_pixels });\n};\n\nmpl.figure.prototype.send_message = function (type, properties) {\n    properties['type'] = type;\n    properties['figure_id'] = this.id;\n    this.ws.send(JSON.stringify(properties));\n};\n\nmpl.figure.prototype.send_draw_message = function () {\n    if (!this.waiting) {\n        this.waiting = true;\n        this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    var format_dropdown = fig.format_dropdown;\n    var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n    fig.ondownload(fig, format);\n};\n\nmpl.figure.prototype.handle_resize = function (fig, msg) {\n    var size = msg['size'];\n    if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n        fig._resize_canvas(size[0], size[1], msg['forward']);\n        fig.send_message('refresh', {});\n    }\n};\n\nmpl.figure.prototype.handle_rubberband = function (fig, msg) {\n    var x0 = msg['x0'] / fig.ratio;\n    var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n    var x1 = msg['x1'] / fig.ratio;\n    var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n    x0 = Math.floor(x0) + 0.5;\n    y0 = Math.floor(y0) + 0.5;\n    x1 = Math.floor(x1) + 0.5;\n    y1 = Math.floor(y1) + 0.5;\n    var min_x = Math.min(x0, x1);\n    var min_y = Math.min(y0, y1);\n    var width = Math.abs(x1 - x0);\n    var height = Math.abs(y1 - y0);\n\n    fig.rubberband_context.clearRect(\n        0,\n        0,\n        fig.canvas.width / fig.ratio,\n        fig.canvas.height / fig.ratio\n    );\n\n    fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n};\n\nmpl.figure.prototype.handle_figure_label = function (fig, msg) {\n    // Updates the figure title.\n    fig.header.textContent = msg['label'];\n};\n\nmpl.figure.prototype.handle_cursor = function (fig, msg) {\n    fig.rubberband_canvas.style.cursor = msg['cursor'];\n};\n\nmpl.figure.prototype.handle_message = function (fig, msg) {\n    fig.message.textContent = msg['message'];\n};\n\nmpl.figure.prototype.handle_draw = function (fig, _msg) {\n    // Request the server to send over a new figure.\n    fig.send_draw_message();\n};\n\nmpl.figure.prototype.handle_image_mode = function (fig, msg) {\n    fig.image_mode = msg['mode'];\n};\n\nmpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n    for (var key in msg) {\n        if (!(key in fig.buttons)) {\n            continue;\n        }\n        fig.buttons[key].disabled = !msg[key];\n        fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n    }\n};\n\nmpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n    if (msg['mode'] === 'PAN') {\n        fig.buttons['Pan'].classList.add('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    } else if (msg['mode'] === 'ZOOM') {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.add('active');\n    } else {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    }\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Called whenever the canvas gets updated.\n    this.send_message('ack', {});\n};\n\n// A function to construct a web socket function for onmessage handling.\n// Called in the figure constructor.\nmpl.figure.prototype._make_on_message_function = function (fig) {\n    return function socket_on_message(evt) {\n        if (evt.data instanceof Blob) {\n            var img = evt.data;\n            if (img.type !== 'image/png') {\n                /* FIXME: We get \"Resource interpreted as Image but\n                 * transferred with MIME type text/plain:\" errors on\n                 * Chrome.  But how to set the MIME type?  It doesn't seem\n                 * to be part of the websocket stream */\n                img.type = 'image/png';\n            }\n\n            /* Free the memory for the previous frames */\n            if (fig.imageObj.src) {\n                (window.URL || window.webkitURL).revokeObjectURL(\n                    fig.imageObj.src\n                );\n            }\n\n            fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n                img\n            );\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        } else if (\n            typeof evt.data === 'string' &&\n            evt.data.slice(0, 21) === 'data:image/png;base64'\n        ) {\n            fig.imageObj.src = evt.data;\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        }\n\n        var msg = JSON.parse(evt.data);\n        var msg_type = msg['type'];\n\n        // Call the  \"handle_{type}\" callback, which takes\n        // the figure and JSON message as its only arguments.\n        try {\n            var callback = fig['handle_' + msg_type];\n        } catch (e) {\n            console.log(\n                \"No handler for the '\" + msg_type + \"' message type: \",\n                msg\n            );\n            return;\n        }\n\n        if (callback) {\n            try {\n                // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n                callback(fig, msg);\n            } catch (e) {\n                console.log(\n                    \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n                    e,\n                    e.stack,\n                    msg\n                );\n            }\n        }\n    };\n};\n\n// from https://stackoverflow.com/questions/1114465/getting-mouse-location-in-canvas\nmpl.findpos = function (e) {\n    //this section is from http://www.quirksmode.org/js/events_properties.html\n    var targ;\n    if (!e) {\n        e = window.event;\n    }\n    if (e.target) {\n        targ = e.target;\n    } else if (e.srcElement) {\n        targ = e.srcElement;\n    }\n    if (targ.nodeType === 3) {\n        // defeat Safari bug\n        targ = targ.parentNode;\n    }\n\n    // pageX,Y are the mouse positions relative to the document\n    var boundingRect = targ.getBoundingClientRect();\n    var x = e.pageX - (boundingRect.left + document.body.scrollLeft);\n    var y = e.pageY - (boundingRect.top + document.body.scrollTop);\n\n    return { x: x, y: y };\n};\n\n/*\n * return a copy of an object with only non-object keys\n * we need this to avoid circular references\n * https://stackoverflow.com/a/24161582/3208463\n */\nfunction simpleKeys(original) {\n    return Object.keys(original).reduce(function (obj, key) {\n        if (typeof original[key] !== 'object') {\n            obj[key] = original[key];\n        }\n        return obj;\n    }, {});\n}\n\nmpl.figure.prototype.mouse_event = function (event, name) {\n    var canvas_pos = mpl.findpos(event);\n\n    if (name === 'button_press') {\n        this.canvas.focus();\n        this.canvas_div.focus();\n    }\n\n    var x = canvas_pos.x * this.ratio;\n    var y = canvas_pos.y * this.ratio;\n\n    this.send_message(name, {\n        x: x,\n        y: y,\n        button: event.button,\n        step: event.step,\n        guiEvent: simpleKeys(event),\n    });\n\n    /* This prevents the web browser from automatically changing to\n     * the text insertion cursor when the button is pressed.  We want\n     * to control all of the cursor setting manually through the\n     * 'cursor' event from matplotlib */\n    event.preventDefault();\n    return false;\n};\n\nmpl.figure.prototype._key_event_extra = function (_event, _name) {\n    // Handle any extra behaviour associated with a key event\n};\n\nmpl.figure.prototype.key_event = function (event, name) {\n    // Prevent repeat events\n    if (name === 'key_press') {\n        if (event.key === this._key) {\n            return;\n        } else {\n            this._key = event.key;\n        }\n    }\n    if (name === 'key_release') {\n        this._key = null;\n    }\n\n    var value = '';\n    if (event.ctrlKey && event.key !== 'Control') {\n        value += 'ctrl+';\n    }\n    else if (event.altKey && event.key !== 'Alt') {\n        value += 'alt+';\n    }\n    else if (event.shiftKey && event.key !== 'Shift') {\n        value += 'shift+';\n    }\n\n    value += 'k' + event.key;\n\n    this._key_event_extra(event, name);\n\n    this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n    return false;\n};\n\nmpl.figure.prototype.toolbar_button_onclick = function (name) {\n    if (name === 'download') {\n        this.handle_save(this, null);\n    } else {\n        this.send_message('toolbar_button', { name: name });\n    }\n};\n\nmpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n    this.message.textContent = tooltip;\n};\n\n///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n// prettier-ignore\nvar _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\nmpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home icon-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left icon-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right icon-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows icon-move\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis\", \"fa fa-square-o icon-check-empty\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o icon-save\", \"download\"]];\n\nmpl.extensions = [\"eps\", \"jpeg\", \"pgf\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\"];\n\nmpl.default_extension = \"png\";/* global mpl */\n\nvar comm_websocket_adapter = function (comm) {\n    // Create a \"websocket\"-like object which calls the given IPython comm\n    // object with the appropriate methods. Currently this is a non binary\n    // socket, so there is still some room for performance tuning.\n    var ws = {};\n\n    ws.binaryType = comm.kernel.ws.binaryType;\n    ws.readyState = comm.kernel.ws.readyState;\n    function updateReadyState(_event) {\n        if (comm.kernel.ws) {\n            ws.readyState = comm.kernel.ws.readyState;\n        } else {\n            ws.readyState = 3; // Closed state.\n        }\n    }\n    comm.kernel.ws.addEventListener('open', updateReadyState);\n    comm.kernel.ws.addEventListener('close', updateReadyState);\n    comm.kernel.ws.addEventListener('error', updateReadyState);\n\n    ws.close = function () {\n        comm.close();\n    };\n    ws.send = function (m) {\n        //console.log('sending', m);\n        comm.send(m);\n    };\n    // Register the callback with on_msg.\n    comm.on_msg(function (msg) {\n        //console.log('receiving', msg['content']['data'], msg);\n        var data = msg['content']['data'];\n        if (data['blob'] !== undefined) {\n            data = {\n                data: new Blob(msg['buffers'], { type: data['blob'] }),\n            };\n        }\n        // Pass the mpl event to the overridden (by mpl) onmessage function.\n        ws.onmessage(data);\n    });\n    return ws;\n};\n\nmpl.mpl_figure_comm = function (comm, msg) {\n    // This is the function which gets called when the mpl process\n    // starts-up an IPython Comm through the \"matplotlib\" channel.\n\n    var id = msg.content.data.id;\n    // Get hold of the div created by the display call when the Comm\n    // socket was opened in Python.\n    var element = document.getElementById(id);\n    var ws_proxy = comm_websocket_adapter(comm);\n\n    function ondownload(figure, _format) {\n        window.open(figure.canvas.toDataURL());\n    }\n\n    var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n\n    // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n    // web socket which is closed, not our websocket->open comm proxy.\n    ws_proxy.onopen();\n\n    fig.parent_element = element;\n    fig.cell_info = mpl.find_output_cell(\"<div id='\" + id + \"'></div>\");\n    if (!fig.cell_info) {\n        console.error('Failed to find cell for figure', id, fig);\n        return;\n    }\n    fig.cell_info[0].output_area.element.on(\n        'cleared',\n        { fig: fig },\n        fig._remove_fig_handler\n    );\n};\n\nmpl.figure.prototype.handle_close = function (fig, msg) {\n    var width = fig.canvas.width / fig.ratio;\n    fig.cell_info[0].output_area.element.off(\n        'cleared',\n        fig._remove_fig_handler\n    );\n    fig.resizeObserverInstance.unobserve(fig.canvas_div);\n\n    // Update the output cell to use the data from the current canvas.\n    fig.push_to_output();\n    var dataURL = fig.canvas.toDataURL();\n    // Re-enable the keyboard manager in IPython - without this line, in FF,\n    // the notebook keyboard shortcuts fail.\n    IPython.keyboard_manager.enable();\n    fig.parent_element.innerHTML =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n    fig.close_ws(fig, msg);\n};\n\nmpl.figure.prototype.close_ws = function (fig, msg) {\n    fig.send_message('closing', msg);\n    // fig.ws.close()\n};\n\nmpl.figure.prototype.push_to_output = function (_remove_interactive) {\n    // Turn the data on the canvas into data in the output cell.\n    var width = this.canvas.width / this.ratio;\n    var dataURL = this.canvas.toDataURL();\n    this.cell_info[1]['text/html'] =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Tell IPython that the notebook contents must change.\n    IPython.notebook.set_dirty(true);\n    this.send_message('ack', {});\n    var fig = this;\n    // Wait a second, then push the new image to the DOM so\n    // that it is saved nicely (might be nice to debounce this).\n    setTimeout(function () {\n        fig.push_to_output();\n    }, 1000);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'btn-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'btn-group';\n    var button;\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'btn-group';\n            continue;\n        }\n\n        button = fig.buttons[name] = document.createElement('button');\n        button.classList = 'btn btn-default';\n        button.href = '#';\n        button.title = name;\n        button.innerHTML = '<i class=\"fa ' + image + ' fa-lg\"></i>';\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    // Add the status bar.\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message pull-right';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n\n    // Add the close button to the window.\n    var buttongrp = document.createElement('div');\n    buttongrp.classList = 'btn-group inline pull-right';\n    button = document.createElement('button');\n    button.classList = 'btn btn-mini btn-primary';\n    button.href = '#';\n    button.title = 'Stop Interaction';\n    button.innerHTML = '<i class=\"fa fa-power-off icon-remove icon-large\"></i>';\n    button.addEventListener('click', function (_evt) {\n        fig.handle_close(fig, {});\n    });\n    button.addEventListener(\n        'mouseover',\n        on_mouseover_closure('Stop Interaction')\n    );\n    buttongrp.appendChild(button);\n    var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n    titlebar.insertBefore(buttongrp, titlebar.firstChild);\n};\n\nmpl.figure.prototype._remove_fig_handler = function (event) {\n    var fig = event.data.fig;\n    if (event.target !== this) {\n        // Ignore bubbled events from children.\n        return;\n    }\n    fig.close_ws(fig, {});\n};\n\nmpl.figure.prototype._root_extra_style = function (el) {\n    el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n};\n\nmpl.figure.prototype._canvas_extra_style = function (el) {\n    // this is important to make the div 'focusable\n    el.setAttribute('tabindex', 0);\n    // reach out to IPython and tell the keyboard manager to turn it's self\n    // off when our div gets focus\n\n    // location in version 3\n    if (IPython.notebook.keyboard_manager) {\n        IPython.notebook.keyboard_manager.register_events(el);\n    } else {\n        // location in version 2\n        IPython.keyboard_manager.register_events(el);\n    }\n};\n\nmpl.figure.prototype._key_event_extra = function (event, _name) {\n    // Check for shift+enter\n    if (event.shiftKey && event.which === 13) {\n        this.canvas_div.blur();\n        // select the cell after this one\n        var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n        IPython.notebook.select(index + 1);\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    fig.ondownload(fig, null);\n};\n\nmpl.find_output_cell = function (html_output) {\n    // Return the cell and output element which can be found *uniquely* in the notebook.\n    // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n    // IPython event is triggered only after the cells have been serialised, which for\n    // our purposes (turning an active figure into a static one), is too late.\n    var cells = IPython.notebook.get_cells();\n    var ncells = cells.length;\n    for (var i = 0; i < ncells; i++) {\n        var cell = cells[i];\n        if (cell.cell_type === 'code') {\n            for (var j = 0; j < cell.output_area.outputs.length; j++) {\n                var data = cell.output_area.outputs[j];\n                if (data.data) {\n                    // IPython >= 3 moved mimebundle to data attribute of output\n                    data = data.data;\n                }\n                if (data['text/html'] === html_output) {\n                    return [cell, data, j];\n                }\n            }\n        }\n    }\n};\n\n// Register the function which deals with the matplotlib target/channel.\n// The kernel may be null if the page has been refreshed.\nif (IPython.notebook.kernel !== null) {\n    IPython.notebook.kernel.comm_manager.register_target(\n        'matplotlib',\n        mpl.mpl_figure_comm\n    );\n}\n",
      "text/plain": [
       "<IPython.core.display.Javascript object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<img src=\"data:image/png;base64,[encoded data, 38788 characters]\" width=\"640\">"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "%matplotlib notebook\n",
    "shotNum = \"0011\"\n",
    "filePath = folderPath + \"/\" + shotNum + \"/*.h5\"\n",
    "\n",
    "dataSetDict = {\n",
    "    dskey[groupList[i]]: read_hdf5_file(filePath, groupList[i], excludeAxis = ['sweep_start_freq', 'sweep_stop_freq'])\n",
    "    for i in [0]\n",
    "}\n",
    "\n",
    "dataSet = dataSetDict[\"camera_0\"]\n",
    "\n",
    "print_scanAxis(dataSet)\n",
    "\n",
    "scanAxis = get_scanAxis(dataSet)\n",
    "\n",
    "dataSet = auto_rechunk(dataSet)\n",
    "\n",
    "dataSet = imageAnalyser.get_absorption_images(dataSet)\n",
    "\n",
    "imageAnalyser.center = (800, 900)\n",
    "imageAnalyser.span = (300, 300)\n",
    "imageAnalyser.fraction = (0.1, 0.1)\n",
    "\n",
    "dataSet_cropOD = imageAnalyser.crop_image(dataSet.OD)\n",
    "dataSet_cropOD = imageAnalyser.substract_offset(dataSet_cropOD).load()\n",
    "\n",
    "Ncount = imageAnalyser.get_Ncount(dataSet_cropOD)\n",
    "Ncount_mean = calculate_mean(Ncount)\n",
    "Ncount_std = calculate_std(Ncount)\n",
    "\n",
    "fig = plt.figure()\n",
    "ax = fig.gca()\n",
    "Ncount_mean.plot.errorbar(ax=ax, yerr = None, fmt='ob')\n",
    "plt.ylabel('NCount')\n",
    "plt.tight_layout()\n",
    "plt.grid(visible=1)\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 94,
   "metadata": {},
   "outputs": [],
   "source": [
    "dataSet_cropOD_chunk = dataSet_cropOD.chunk((1, 1, 300, 300))\n",
    "fitAnalyser = FitAnalyser(\"Gaussian-2D\", fitDim=2)\n",
    "params = fitAnalyser.guess(dataSet_cropOD_chunk, dask=\"parallelized\")\n",
    "fitResult = fitAnalyser.fit(dataSet_cropOD_chunk, params, dask=\"parallelized\").load()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 95,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/javascript": "/* Put everything inside the global mpl namespace */\n/* global mpl */\nwindow.mpl = {};\n\nmpl.get_websocket_type = function () {\n    if (typeof WebSocket !== 'undefined') {\n        return WebSocket;\n    } else if (typeof MozWebSocket !== 'undefined') {\n        return MozWebSocket;\n    } else {\n        alert(\n            'Your browser does not have WebSocket support. ' +\n                'Please try Chrome, Safari or Firefox ≥ 6. ' +\n                'Firefox 4 and 5 are also supported but you ' +\n                'have to enable WebSockets in about:config.'\n        );\n    }\n};\n\nmpl.figure = function (figure_id, websocket, ondownload, parent_element) {\n    this.id = figure_id;\n\n    this.ws = websocket;\n\n    this.supports_binary = this.ws.binaryType !== undefined;\n\n    if (!this.supports_binary) {\n        var warnings = document.getElementById('mpl-warnings');\n        if (warnings) {\n            warnings.style.display = 'block';\n            warnings.textContent =\n                'This browser does not support binary websocket messages. ' +\n                'Performance may be slow.';\n        }\n    }\n\n    this.imageObj = new Image();\n\n    this.context = undefined;\n    this.message = undefined;\n    this.canvas = undefined;\n    this.rubberband_canvas = undefined;\n    this.rubberband_context = undefined;\n    this.format_dropdown = undefined;\n\n    this.image_mode = 'full';\n\n    this.root = document.createElement('div');\n    this.root.setAttribute('style', 'display: inline-block');\n    this._root_extra_style(this.root);\n\n    parent_element.appendChild(this.root);\n\n    this._init_header(this);\n    this._init_canvas(this);\n    this._init_toolbar(this);\n\n    var fig = this;\n\n    this.waiting = false;\n\n    this.ws.onopen = function () {\n        fig.send_message('supports_binary', { value: fig.supports_binary });\n        fig.send_message('send_image_mode', {});\n        if (fig.ratio !== 1) {\n            fig.send_message('set_device_pixel_ratio', {\n                device_pixel_ratio: fig.ratio,\n            });\n        }\n        fig.send_message('refresh', {});\n    };\n\n    this.imageObj.onload = function () {\n        if (fig.image_mode === 'full') {\n            // Full images could contain transparency (where diff images\n            // almost always do), so we need to clear the canvas so that\n            // there is no ghosting.\n            fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n        }\n        fig.context.drawImage(fig.imageObj, 0, 0);\n    };\n\n    this.imageObj.onunload = function () {\n        fig.ws.close();\n    };\n\n    this.ws.onmessage = this._make_on_message_function(this);\n\n    this.ondownload = ondownload;\n};\n\nmpl.figure.prototype._init_header = function () {\n    var titlebar = document.createElement('div');\n    titlebar.classList =\n        'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n    var titletext = document.createElement('div');\n    titletext.classList = 'ui-dialog-title';\n    titletext.setAttribute(\n        'style',\n        'width: 100%; text-align: center; padding: 3px;'\n    );\n    titlebar.appendChild(titletext);\n    this.root.appendChild(titlebar);\n    this.header = titletext;\n};\n\nmpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._init_canvas = function () {\n    var fig = this;\n\n    var canvas_div = (this.canvas_div = document.createElement('div'));\n    canvas_div.setAttribute(\n        'style',\n        'border: 1px solid #ddd;' +\n            'box-sizing: content-box;' +\n            'clear: both;' +\n            'min-height: 1px;' +\n            'min-width: 1px;' +\n            'outline: 0;' +\n            'overflow: hidden;' +\n            'position: relative;' +\n            'resize: both;'\n    );\n\n    function on_keyboard_event_closure(name) {\n        return function (event) {\n            return fig.key_event(event, name);\n        };\n    }\n\n    canvas_div.addEventListener(\n        'keydown',\n        on_keyboard_event_closure('key_press')\n    );\n    canvas_div.addEventListener(\n        'keyup',\n        on_keyboard_event_closure('key_release')\n    );\n\n    this._canvas_extra_style(canvas_div);\n    this.root.appendChild(canvas_div);\n\n    var canvas = (this.canvas = document.createElement('canvas'));\n    canvas.classList.add('mpl-canvas');\n    canvas.setAttribute('style', 'box-sizing: content-box;');\n\n    this.context = canvas.getContext('2d');\n\n    var backingStore =\n        this.context.backingStorePixelRatio ||\n        this.context.webkitBackingStorePixelRatio ||\n        this.context.mozBackingStorePixelRatio ||\n        this.context.msBackingStorePixelRatio ||\n        this.context.oBackingStorePixelRatio ||\n        this.context.backingStorePixelRatio ||\n        1;\n\n    this.ratio = (window.devicePixelRatio || 1) / backingStore;\n\n    var rubberband_canvas = (this.rubberband_canvas = document.createElement(\n        'canvas'\n    ));\n    rubberband_canvas.setAttribute(\n        'style',\n        'box-sizing: content-box; position: absolute; left: 0; top: 0; z-index: 1;'\n    );\n\n    // Apply a ponyfill if ResizeObserver is not implemented by browser.\n    if (this.ResizeObserver === undefined) {\n        if (window.ResizeObserver !== undefined) {\n            this.ResizeObserver = window.ResizeObserver;\n        } else {\n            var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n            this.ResizeObserver = obs.ResizeObserver;\n        }\n    }\n\n    this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n        var nentries = entries.length;\n        for (var i = 0; i < nentries; i++) {\n            var entry = entries[i];\n            var width, height;\n            if (entry.contentBoxSize) {\n                if (entry.contentBoxSize instanceof Array) {\n                    // Chrome 84 implements new version of spec.\n                    width = entry.contentBoxSize[0].inlineSize;\n                    height = entry.contentBoxSize[0].blockSize;\n                } else {\n                    // Firefox implements old version of spec.\n                    width = entry.contentBoxSize.inlineSize;\n                    height = entry.contentBoxSize.blockSize;\n                }\n            } else {\n                // Chrome <84 implements even older version of spec.\n                width = entry.contentRect.width;\n                height = entry.contentRect.height;\n            }\n\n            // Keep the size of the canvas and rubber band canvas in sync with\n            // the canvas container.\n            if (entry.devicePixelContentBoxSize) {\n                // Chrome 84 implements new version of spec.\n                canvas.setAttribute(\n                    'width',\n                    entry.devicePixelContentBoxSize[0].inlineSize\n                );\n                canvas.setAttribute(\n                    'height',\n                    entry.devicePixelContentBoxSize[0].blockSize\n                );\n            } else {\n                canvas.setAttribute('width', width * fig.ratio);\n                canvas.setAttribute('height', height * fig.ratio);\n            }\n            canvas.setAttribute(\n                'style',\n                'width: ' + width + 'px; height: ' + height + 'px;'\n            );\n\n            rubberband_canvas.setAttribute('width', width);\n            rubberband_canvas.setAttribute('height', height);\n\n            // And update the size in Python. We ignore the initial 0/0 size\n            // that occurs as the element is placed into the DOM, which should\n            // otherwise not happen due to the minimum size styling.\n            if (fig.ws.readyState == 1 && width != 0 && height != 0) {\n                fig.request_resize(width, height);\n            }\n        }\n    });\n    this.resizeObserverInstance.observe(canvas_div);\n\n    function on_mouse_event_closure(name) {\n        return function (event) {\n            return fig.mouse_event(event, name);\n        };\n    }\n\n    rubberband_canvas.addEventListener(\n        'mousedown',\n        on_mouse_event_closure('button_press')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseup',\n        on_mouse_event_closure('button_release')\n    );\n    rubberband_canvas.addEventListener(\n        'dblclick',\n        on_mouse_event_closure('dblclick')\n    );\n    // Throttle sequential mouse events to 1 every 20ms.\n    rubberband_canvas.addEventListener(\n        'mousemove',\n        on_mouse_event_closure('motion_notify')\n    );\n\n    rubberband_canvas.addEventListener(\n        'mouseenter',\n        on_mouse_event_closure('figure_enter')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseleave',\n        on_mouse_event_closure('figure_leave')\n    );\n\n    canvas_div.addEventListener('wheel', function (event) {\n        if (event.deltaY < 0) {\n            event.step = 1;\n        } else {\n            event.step = -1;\n        }\n        on_mouse_event_closure('scroll')(event);\n    });\n\n    canvas_div.appendChild(canvas);\n    canvas_div.appendChild(rubberband_canvas);\n\n    this.rubberband_context = rubberband_canvas.getContext('2d');\n    this.rubberband_context.strokeStyle = '#000000';\n\n    this._resize_canvas = function (width, height, forward) {\n        if (forward) {\n            canvas_div.style.width = width + 'px';\n            canvas_div.style.height = height + 'px';\n        }\n    };\n\n    // Disable right mouse context menu.\n    this.rubberband_canvas.addEventListener('contextmenu', function (_e) {\n        event.preventDefault();\n        return false;\n    });\n\n    function set_focus() {\n        canvas.focus();\n        canvas_div.focus();\n    }\n\n    window.setTimeout(set_focus, 100);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'mpl-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'mpl-button-group';\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'mpl-button-group';\n            continue;\n        }\n\n        var button = (fig.buttons[name] = document.createElement('button'));\n        button.classList = 'mpl-widget';\n        button.setAttribute('role', 'button');\n        button.setAttribute('aria-disabled', 'false');\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n\n        var icon_img = document.createElement('img');\n        icon_img.src = '_images/' + image + '.png';\n        icon_img.srcset = '_images/' + image + '_large.png 2x';\n        icon_img.alt = tooltip;\n        button.appendChild(icon_img);\n\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    var fmt_picker = document.createElement('select');\n    fmt_picker.classList = 'mpl-widget';\n    toolbar.appendChild(fmt_picker);\n    this.format_dropdown = fmt_picker;\n\n    for (var ind in mpl.extensions) {\n        var fmt = mpl.extensions[ind];\n        var option = document.createElement('option');\n        option.selected = fmt === mpl.default_extension;\n        option.innerHTML = fmt;\n        fmt_picker.appendChild(option);\n    }\n\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n};\n\nmpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n    // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n    // which will in turn request a refresh of the image.\n    this.send_message('resize', { width: x_pixels, height: y_pixels });\n};\n\nmpl.figure.prototype.send_message = function (type, properties) {\n    properties['type'] = type;\n    properties['figure_id'] = this.id;\n    this.ws.send(JSON.stringify(properties));\n};\n\nmpl.figure.prototype.send_draw_message = function () {\n    if (!this.waiting) {\n        this.waiting = true;\n        this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    var format_dropdown = fig.format_dropdown;\n    var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n    fig.ondownload(fig, format);\n};\n\nmpl.figure.prototype.handle_resize = function (fig, msg) {\n    var size = msg['size'];\n    if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n        fig._resize_canvas(size[0], size[1], msg['forward']);\n        fig.send_message('refresh', {});\n    }\n};\n\nmpl.figure.prototype.handle_rubberband = function (fig, msg) {\n    var x0 = msg['x0'] / fig.ratio;\n    var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n    var x1 = msg['x1'] / fig.ratio;\n    var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n    x0 = Math.floor(x0) + 0.5;\n    y0 = Math.floor(y0) + 0.5;\n    x1 = Math.floor(x1) + 0.5;\n    y1 = Math.floor(y1) + 0.5;\n    var min_x = Math.min(x0, x1);\n    var min_y = Math.min(y0, y1);\n    var width = Math.abs(x1 - x0);\n    var height = Math.abs(y1 - y0);\n\n    fig.rubberband_context.clearRect(\n        0,\n        0,\n        fig.canvas.width / fig.ratio,\n        fig.canvas.height / fig.ratio\n    );\n\n    fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n};\n\nmpl.figure.prototype.handle_figure_label = function (fig, msg) {\n    // Updates the figure title.\n    fig.header.textContent = msg['label'];\n};\n\nmpl.figure.prototype.handle_cursor = function (fig, msg) {\n    fig.rubberband_canvas.style.cursor = msg['cursor'];\n};\n\nmpl.figure.prototype.handle_message = function (fig, msg) {\n    fig.message.textContent = msg['message'];\n};\n\nmpl.figure.prototype.handle_draw = function (fig, _msg) {\n    // Request the server to send over a new figure.\n    fig.send_draw_message();\n};\n\nmpl.figure.prototype.handle_image_mode = function (fig, msg) {\n    fig.image_mode = msg['mode'];\n};\n\nmpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n    for (var key in msg) {\n        if (!(key in fig.buttons)) {\n            continue;\n        }\n        fig.buttons[key].disabled = !msg[key];\n        fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n    }\n};\n\nmpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n    if (msg['mode'] === 'PAN') {\n        fig.buttons['Pan'].classList.add('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    } else if (msg['mode'] === 'ZOOM') {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.add('active');\n    } else {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    }\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Called whenever the canvas gets updated.\n    this.send_message('ack', {});\n};\n\n// A function to construct a web socket function for onmessage handling.\n// Called in the figure constructor.\nmpl.figure.prototype._make_on_message_function = function (fig) {\n    return function socket_on_message(evt) {\n        if (evt.data instanceof Blob) {\n            var img = evt.data;\n            if (img.type !== 'image/png') {\n                /* FIXME: We get \"Resource interpreted as Image but\n                 * transferred with MIME type text/plain:\" errors on\n                 * Chrome.  But how to set the MIME type?  It doesn't seem\n                 * to be part of the websocket stream */\n                img.type = 'image/png';\n            }\n\n            /* Free the memory for the previous frames */\n            if (fig.imageObj.src) {\n                (window.URL || window.webkitURL).revokeObjectURL(\n                    fig.imageObj.src\n                );\n            }\n\n            fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n                img\n            );\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        } else if (\n            typeof evt.data === 'string' &&\n            evt.data.slice(0, 21) === 'data:image/png;base64'\n        ) {\n            fig.imageObj.src = evt.data;\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        }\n\n        var msg = JSON.parse(evt.data);\n        var msg_type = msg['type'];\n\n        // Call the  \"handle_{type}\" callback, which takes\n        // the figure and JSON message as its only arguments.\n        try {\n            var callback = fig['handle_' + msg_type];\n        } catch (e) {\n            console.log(\n                \"No handler for the '\" + msg_type + \"' message type: \",\n                msg\n            );\n            return;\n        }\n\n        if (callback) {\n            try {\n                // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n                callback(fig, msg);\n            } catch (e) {\n                console.log(\n                    \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n                    e,\n                    e.stack,\n                    msg\n                );\n            }\n        }\n    };\n};\n\n// from https://stackoverflow.com/questions/1114465/getting-mouse-location-in-canvas\nmpl.findpos = function (e) {\n    //this section is from http://www.quirksmode.org/js/events_properties.html\n    var targ;\n    if (!e) {\n        e = window.event;\n    }\n    if (e.target) {\n        targ = e.target;\n    } else if (e.srcElement) {\n        targ = e.srcElement;\n    }\n    if (targ.nodeType === 3) {\n        // defeat Safari bug\n        targ = targ.parentNode;\n    }\n\n    // pageX,Y are the mouse positions relative to the document\n    var boundingRect = targ.getBoundingClientRect();\n    var x = e.pageX - (boundingRect.left + document.body.scrollLeft);\n    var y = e.pageY - (boundingRect.top + document.body.scrollTop);\n\n    return { x: x, y: y };\n};\n\n/*\n * return a copy of an object with only non-object keys\n * we need this to avoid circular references\n * https://stackoverflow.com/a/24161582/3208463\n */\nfunction simpleKeys(original) {\n    return Object.keys(original).reduce(function (obj, key) {\n        if (typeof original[key] !== 'object') {\n            obj[key] = original[key];\n        }\n        return obj;\n    }, {});\n}\n\nmpl.figure.prototype.mouse_event = function (event, name) {\n    var canvas_pos = mpl.findpos(event);\n\n    if (name === 'button_press') {\n        this.canvas.focus();\n        this.canvas_div.focus();\n    }\n\n    var x = canvas_pos.x * this.ratio;\n    var y = canvas_pos.y * this.ratio;\n\n    this.send_message(name, {\n        x: x,\n        y: y,\n        button: event.button,\n        step: event.step,\n        guiEvent: simpleKeys(event),\n    });\n\n    /* This prevents the web browser from automatically changing to\n     * the text insertion cursor when the button is pressed.  We want\n     * to control all of the cursor setting manually through the\n     * 'cursor' event from matplotlib */\n    event.preventDefault();\n    return false;\n};\n\nmpl.figure.prototype._key_event_extra = function (_event, _name) {\n    // Handle any extra behaviour associated with a key event\n};\n\nmpl.figure.prototype.key_event = function (event, name) {\n    // Prevent repeat events\n    if (name === 'key_press') {\n        if (event.key === this._key) {\n            return;\n        } else {\n            this._key = event.key;\n        }\n    }\n    if (name === 'key_release') {\n        this._key = null;\n    }\n\n    var value = '';\n    if (event.ctrlKey && event.key !== 'Control') {\n        value += 'ctrl+';\n    }\n    else if (event.altKey && event.key !== 'Alt') {\n        value += 'alt+';\n    }\n    else if (event.shiftKey && event.key !== 'Shift') {\n        value += 'shift+';\n    }\n\n    value += 'k' + event.key;\n\n    this._key_event_extra(event, name);\n\n    this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n    return false;\n};\n\nmpl.figure.prototype.toolbar_button_onclick = function (name) {\n    if (name === 'download') {\n        this.handle_save(this, null);\n    } else {\n        this.send_message('toolbar_button', { name: name });\n    }\n};\n\nmpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n    this.message.textContent = tooltip;\n};\n\n///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n// prettier-ignore\nvar _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\nmpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home icon-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left icon-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right icon-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows icon-move\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis\", \"fa fa-square-o icon-check-empty\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o icon-save\", \"download\"]];\n\nmpl.extensions = [\"eps\", \"jpeg\", \"pgf\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\"];\n\nmpl.default_extension = \"png\";/* global mpl */\n\nvar comm_websocket_adapter = function (comm) {\n    // Create a \"websocket\"-like object which calls the given IPython comm\n    // object with the appropriate methods. Currently this is a non binary\n    // socket, so there is still some room for performance tuning.\n    var ws = {};\n\n    ws.binaryType = comm.kernel.ws.binaryType;\n    ws.readyState = comm.kernel.ws.readyState;\n    function updateReadyState(_event) {\n        if (comm.kernel.ws) {\n            ws.readyState = comm.kernel.ws.readyState;\n        } else {\n            ws.readyState = 3; // Closed state.\n        }\n    }\n    comm.kernel.ws.addEventListener('open', updateReadyState);\n    comm.kernel.ws.addEventListener('close', updateReadyState);\n    comm.kernel.ws.addEventListener('error', updateReadyState);\n\n    ws.close = function () {\n        comm.close();\n    };\n    ws.send = function (m) {\n        //console.log('sending', m);\n        comm.send(m);\n    };\n    // Register the callback with on_msg.\n    comm.on_msg(function (msg) {\n        //console.log('receiving', msg['content']['data'], msg);\n        var data = msg['content']['data'];\n        if (data['blob'] !== undefined) {\n            data = {\n                data: new Blob(msg['buffers'], { type: data['blob'] }),\n            };\n        }\n        // Pass the mpl event to the overridden (by mpl) onmessage function.\n        ws.onmessage(data);\n    });\n    return ws;\n};\n\nmpl.mpl_figure_comm = function (comm, msg) {\n    // This is the function which gets called when the mpl process\n    // starts-up an IPython Comm through the \"matplotlib\" channel.\n\n    var id = msg.content.data.id;\n    // Get hold of the div created by the display call when the Comm\n    // socket was opened in Python.\n    var element = document.getElementById(id);\n    var ws_proxy = comm_websocket_adapter(comm);\n\n    function ondownload(figure, _format) {\n        window.open(figure.canvas.toDataURL());\n    }\n\n    var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n\n    // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n    // web socket which is closed, not our websocket->open comm proxy.\n    ws_proxy.onopen();\n\n    fig.parent_element = element;\n    fig.cell_info = mpl.find_output_cell(\"<div id='\" + id + \"'></div>\");\n    if (!fig.cell_info) {\n        console.error('Failed to find cell for figure', id, fig);\n        return;\n    }\n    fig.cell_info[0].output_area.element.on(\n        'cleared',\n        { fig: fig },\n        fig._remove_fig_handler\n    );\n};\n\nmpl.figure.prototype.handle_close = function (fig, msg) {\n    var width = fig.canvas.width / fig.ratio;\n    fig.cell_info[0].output_area.element.off(\n        'cleared',\n        fig._remove_fig_handler\n    );\n    fig.resizeObserverInstance.unobserve(fig.canvas_div);\n\n    // Update the output cell to use the data from the current canvas.\n    fig.push_to_output();\n    var dataURL = fig.canvas.toDataURL();\n    // Re-enable the keyboard manager in IPython - without this line, in FF,\n    // the notebook keyboard shortcuts fail.\n    IPython.keyboard_manager.enable();\n    fig.parent_element.innerHTML =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n    fig.close_ws(fig, msg);\n};\n\nmpl.figure.prototype.close_ws = function (fig, msg) {\n    fig.send_message('closing', msg);\n    // fig.ws.close()\n};\n\nmpl.figure.prototype.push_to_output = function (_remove_interactive) {\n    // Turn the data on the canvas into data in the output cell.\n    var width = this.canvas.width / this.ratio;\n    var dataURL = this.canvas.toDataURL();\n    this.cell_info[1]['text/html'] =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Tell IPython that the notebook contents must change.\n    IPython.notebook.set_dirty(true);\n    this.send_message('ack', {});\n    var fig = this;\n    // Wait a second, then push the new image to the DOM so\n    // that it is saved nicely (might be nice to debounce this).\n    setTimeout(function () {\n        fig.push_to_output();\n    }, 1000);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'btn-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'btn-group';\n    var button;\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'btn-group';\n            continue;\n        }\n\n        button = fig.buttons[name] = document.createElement('button');\n        button.classList = 'btn btn-default';\n        button.href = '#';\n        button.title = name;\n        button.innerHTML = '<i class=\"fa ' + image + ' fa-lg\"></i>';\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    // Add the status bar.\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message pull-right';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n\n    // Add the close button to the window.\n    var buttongrp = document.createElement('div');\n    buttongrp.classList = 'btn-group inline pull-right';\n    button = document.createElement('button');\n    button.classList = 'btn btn-mini btn-primary';\n    button.href = '#';\n    button.title = 'Stop Interaction';\n    button.innerHTML = '<i class=\"fa fa-power-off icon-remove icon-large\"></i>';\n    button.addEventListener('click', function (_evt) {\n        fig.handle_close(fig, {});\n    });\n    button.addEventListener(\n        'mouseover',\n        on_mouseover_closure('Stop Interaction')\n    );\n    buttongrp.appendChild(button);\n    var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n    titlebar.insertBefore(buttongrp, titlebar.firstChild);\n};\n\nmpl.figure.prototype._remove_fig_handler = function (event) {\n    var fig = event.data.fig;\n    if (event.target !== this) {\n        // Ignore bubbled events from children.\n        return;\n    }\n    fig.close_ws(fig, {});\n};\n\nmpl.figure.prototype._root_extra_style = function (el) {\n    el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n};\n\nmpl.figure.prototype._canvas_extra_style = function (el) {\n    // this is important to make the div 'focusable\n    el.setAttribute('tabindex', 0);\n    // reach out to IPython and tell the keyboard manager to turn it's self\n    // off when our div gets focus\n\n    // location in version 3\n    if (IPython.notebook.keyboard_manager) {\n        IPython.notebook.keyboard_manager.register_events(el);\n    } else {\n        // location in version 2\n        IPython.keyboard_manager.register_events(el);\n    }\n};\n\nmpl.figure.prototype._key_event_extra = function (event, _name) {\n    // Check for shift+enter\n    if (event.shiftKey && event.which === 13) {\n        this.canvas_div.blur();\n        // select the cell after this one\n        var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n        IPython.notebook.select(index + 1);\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    fig.ondownload(fig, null);\n};\n\nmpl.find_output_cell = function (html_output) {\n    // Return the cell and output element which can be found *uniquely* in the notebook.\n    // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n    // IPython event is triggered only after the cells have been serialised, which for\n    // our purposes (turning an active figure into a static one), is too late.\n    var cells = IPython.notebook.get_cells();\n    var ncells = cells.length;\n    for (var i = 0; i < ncells; i++) {\n        var cell = cells[i];\n        if (cell.cell_type === 'code') {\n            for (var j = 0; j < cell.output_area.outputs.length; j++) {\n                var data = cell.output_area.outputs[j];\n                if (data.data) {\n                    // IPython >= 3 moved mimebundle to data attribute of output\n                    data = data.data;\n                }\n                if (data['text/html'] === html_output) {\n                    return [cell, data, j];\n                }\n            }\n        }\n    }\n};\n\n// Register the function which deals with the matplotlib target/channel.\n// The kernel may be null if the page has been refreshed.\nif (IPython.notebook.kernel !== null) {\n    IPython.notebook.kernel.comm_manager.register_target(\n        'matplotlib',\n        mpl.mpl_figure_comm\n    );\n}\n",
      "text/plain": [
       "<IPython.core.display.Javascript object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<img src=\"data:image/png;base64,[encoded data, 61572 characters]\" width=\"640\">"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "val = fitAnalyser.get_fit_value(fitResult)\n",
    "std = fitAnalyser.get_fit_std(fitResult)\n",
    "\n",
    "fitCurve = fitAnalyser.eval(fitResult, x=np.arange(300), y=np.arange(300), dask=\"parallelized\").load()\n",
    "\n",
    "# dataKey = 'sigmax'\n",
    "# dataKey = 'centerx'\n",
    "# dataKey = 'sigmay'\n",
    "dataKey = 'centery'\n",
    "\n",
    "# val_mean = val[dataKey].mean(dim='runs')\n",
    "# std_mean = val[dataKey].std(dim='runs')\n",
    "\n",
    "val_mean = calculate_mean(val[dataKey])\n",
    "std_mean = calculate_std(val[dataKey])\n",
    "\n",
    "fig = plt.figure()\n",
    "ax = fig.gca()\n",
    "\n",
    "val_mean.plot.errorbar(yerr=std_mean, fmt='--ob')\n",
    "\n",
    "plt.grid()\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 98,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/javascript": "/* Put everything inside the global mpl namespace */\n/* global mpl */\nwindow.mpl = {};\n\nmpl.get_websocket_type = function () {\n    if (typeof WebSocket !== 'undefined') {\n        return WebSocket;\n    } else if (typeof MozWebSocket !== 'undefined') {\n        return MozWebSocket;\n    } else {\n        alert(\n            'Your browser does not have WebSocket support. ' +\n                'Please try Chrome, Safari or Firefox ≥ 6. ' +\n                'Firefox 4 and 5 are also supported but you ' +\n                'have to enable WebSockets in about:config.'\n        );\n    }\n};\n\nmpl.figure = function (figure_id, websocket, ondownload, parent_element) {\n    this.id = figure_id;\n\n    this.ws = websocket;\n\n    this.supports_binary = this.ws.binaryType !== undefined;\n\n    if (!this.supports_binary) {\n        var warnings = document.getElementById('mpl-warnings');\n        if (warnings) {\n            warnings.style.display = 'block';\n            warnings.textContent =\n                'This browser does not support binary websocket messages. ' +\n                'Performance may be slow.';\n        }\n    }\n\n    this.imageObj = new Image();\n\n    this.context = undefined;\n    this.message = undefined;\n    this.canvas = undefined;\n    this.rubberband_canvas = undefined;\n    this.rubberband_context = undefined;\n    this.format_dropdown = undefined;\n\n    this.image_mode = 'full';\n\n    this.root = document.createElement('div');\n    this.root.setAttribute('style', 'display: inline-block');\n    this._root_extra_style(this.root);\n\n    parent_element.appendChild(this.root);\n\n    this._init_header(this);\n    this._init_canvas(this);\n    this._init_toolbar(this);\n\n    var fig = this;\n\n    this.waiting = false;\n\n    this.ws.onopen = function () {\n        fig.send_message('supports_binary', { value: fig.supports_binary });\n        fig.send_message('send_image_mode', {});\n        if (fig.ratio !== 1) {\n            fig.send_message('set_device_pixel_ratio', {\n                device_pixel_ratio: fig.ratio,\n            });\n        }\n        fig.send_message('refresh', {});\n    };\n\n    this.imageObj.onload = function () {\n        if (fig.image_mode === 'full') {\n            // Full images could contain transparency (where diff images\n            // almost always do), so we need to clear the canvas so that\n            // there is no ghosting.\n            fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n        }\n        fig.context.drawImage(fig.imageObj, 0, 0);\n    };\n\n    this.imageObj.onunload = function () {\n        fig.ws.close();\n    };\n\n    this.ws.onmessage = this._make_on_message_function(this);\n\n    this.ondownload = ondownload;\n};\n\nmpl.figure.prototype._init_header = function () {\n    var titlebar = document.createElement('div');\n    titlebar.classList =\n        'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n    var titletext = document.createElement('div');\n    titletext.classList = 'ui-dialog-title';\n    titletext.setAttribute(\n        'style',\n        'width: 100%; text-align: center; padding: 3px;'\n    );\n    titlebar.appendChild(titletext);\n    this.root.appendChild(titlebar);\n    this.header = titletext;\n};\n\nmpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._init_canvas = function () {\n    var fig = this;\n\n    var canvas_div = (this.canvas_div = document.createElement('div'));\n    canvas_div.setAttribute(\n        'style',\n        'border: 1px solid #ddd;' +\n            'box-sizing: content-box;' +\n            'clear: both;' +\n            'min-height: 1px;' +\n            'min-width: 1px;' +\n            'outline: 0;' +\n            'overflow: hidden;' +\n            'position: relative;' +\n            'resize: both;'\n    );\n\n    function on_keyboard_event_closure(name) {\n        return function (event) {\n            return fig.key_event(event, name);\n        };\n    }\n\n    canvas_div.addEventListener(\n        'keydown',\n        on_keyboard_event_closure('key_press')\n    );\n    canvas_div.addEventListener(\n        'keyup',\n        on_keyboard_event_closure('key_release')\n    );\n\n    this._canvas_extra_style(canvas_div);\n    this.root.appendChild(canvas_div);\n\n    var canvas = (this.canvas = document.createElement('canvas'));\n    canvas.classList.add('mpl-canvas');\n    canvas.setAttribute('style', 'box-sizing: content-box;');\n\n    this.context = canvas.getContext('2d');\n\n    var backingStore =\n        this.context.backingStorePixelRatio ||\n        this.context.webkitBackingStorePixelRatio ||\n        this.context.mozBackingStorePixelRatio ||\n        this.context.msBackingStorePixelRatio ||\n        this.context.oBackingStorePixelRatio ||\n        this.context.backingStorePixelRatio ||\n        1;\n\n    this.ratio = (window.devicePixelRatio || 1) / backingStore;\n\n    var rubberband_canvas = (this.rubberband_canvas = document.createElement(\n        'canvas'\n    ));\n    rubberband_canvas.setAttribute(\n        'style',\n        'box-sizing: content-box; position: absolute; left: 0; top: 0; z-index: 1;'\n    );\n\n    // Apply a ponyfill if ResizeObserver is not implemented by browser.\n    if (this.ResizeObserver === undefined) {\n        if (window.ResizeObserver !== undefined) {\n            this.ResizeObserver = window.ResizeObserver;\n        } else {\n            var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n            this.ResizeObserver = obs.ResizeObserver;\n        }\n    }\n\n    this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n        var nentries = entries.length;\n        for (var i = 0; i < nentries; i++) {\n            var entry = entries[i];\n            var width, height;\n            if (entry.contentBoxSize) {\n                if (entry.contentBoxSize instanceof Array) {\n                    // Chrome 84 implements new version of spec.\n                    width = entry.contentBoxSize[0].inlineSize;\n                    height = entry.contentBoxSize[0].blockSize;\n                } else {\n                    // Firefox implements old version of spec.\n                    width = entry.contentBoxSize.inlineSize;\n                    height = entry.contentBoxSize.blockSize;\n                }\n            } else {\n                // Chrome <84 implements even older version of spec.\n                width = entry.contentRect.width;\n                height = entry.contentRect.height;\n            }\n\n            // Keep the size of the canvas and rubber band canvas in sync with\n            // the canvas container.\n            if (entry.devicePixelContentBoxSize) {\n                // Chrome 84 implements new version of spec.\n                canvas.setAttribute(\n                    'width',\n                    entry.devicePixelContentBoxSize[0].inlineSize\n                );\n                canvas.setAttribute(\n                    'height',\n                    entry.devicePixelContentBoxSize[0].blockSize\n                );\n            } else {\n                canvas.setAttribute('width', width * fig.ratio);\n                canvas.setAttribute('height', height * fig.ratio);\n            }\n            canvas.setAttribute(\n                'style',\n                'width: ' + width + 'px; height: ' + height + 'px;'\n            );\n\n            rubberband_canvas.setAttribute('width', width);\n            rubberband_canvas.setAttribute('height', height);\n\n            // And update the size in Python. We ignore the initial 0/0 size\n            // that occurs as the element is placed into the DOM, which should\n            // otherwise not happen due to the minimum size styling.\n            if (fig.ws.readyState == 1 && width != 0 && height != 0) {\n                fig.request_resize(width, height);\n            }\n        }\n    });\n    this.resizeObserverInstance.observe(canvas_div);\n\n    function on_mouse_event_closure(name) {\n        return function (event) {\n            return fig.mouse_event(event, name);\n        };\n    }\n\n    rubberband_canvas.addEventListener(\n        'mousedown',\n        on_mouse_event_closure('button_press')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseup',\n        on_mouse_event_closure('button_release')\n    );\n    rubberband_canvas.addEventListener(\n        'dblclick',\n        on_mouse_event_closure('dblclick')\n    );\n    // Throttle sequential mouse events to 1 every 20ms.\n    rubberband_canvas.addEventListener(\n        'mousemove',\n        on_mouse_event_closure('motion_notify')\n    );\n\n    rubberband_canvas.addEventListener(\n        'mouseenter',\n        on_mouse_event_closure('figure_enter')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseleave',\n        on_mouse_event_closure('figure_leave')\n    );\n\n    canvas_div.addEventListener('wheel', function (event) {\n        if (event.deltaY < 0) {\n            event.step = 1;\n        } else {\n            event.step = -1;\n        }\n        on_mouse_event_closure('scroll')(event);\n    });\n\n    canvas_div.appendChild(canvas);\n    canvas_div.appendChild(rubberband_canvas);\n\n    this.rubberband_context = rubberband_canvas.getContext('2d');\n    this.rubberband_context.strokeStyle = '#000000';\n\n    this._resize_canvas = function (width, height, forward) {\n        if (forward) {\n            canvas_div.style.width = width + 'px';\n            canvas_div.style.height = height + 'px';\n        }\n    };\n\n    // Disable right mouse context menu.\n    this.rubberband_canvas.addEventListener('contextmenu', function (_e) {\n        event.preventDefault();\n        return false;\n    });\n\n    function set_focus() {\n        canvas.focus();\n        canvas_div.focus();\n    }\n\n    window.setTimeout(set_focus, 100);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'mpl-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'mpl-button-group';\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'mpl-button-group';\n            continue;\n        }\n\n        var button = (fig.buttons[name] = document.createElement('button'));\n        button.classList = 'mpl-widget';\n        button.setAttribute('role', 'button');\n        button.setAttribute('aria-disabled', 'false');\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n\n        var icon_img = document.createElement('img');\n        icon_img.src = '_images/' + image + '.png';\n        icon_img.srcset = '_images/' + image + '_large.png 2x';\n        icon_img.alt = tooltip;\n        button.appendChild(icon_img);\n\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    var fmt_picker = document.createElement('select');\n    fmt_picker.classList = 'mpl-widget';\n    toolbar.appendChild(fmt_picker);\n    this.format_dropdown = fmt_picker;\n\n    for (var ind in mpl.extensions) {\n        var fmt = mpl.extensions[ind];\n        var option = document.createElement('option');\n        option.selected = fmt === mpl.default_extension;\n        option.innerHTML = fmt;\n        fmt_picker.appendChild(option);\n    }\n\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n};\n\nmpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n    // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n    // which will in turn request a refresh of the image.\n    this.send_message('resize', { width: x_pixels, height: y_pixels });\n};\n\nmpl.figure.prototype.send_message = function (type, properties) {\n    properties['type'] = type;\n    properties['figure_id'] = this.id;\n    this.ws.send(JSON.stringify(properties));\n};\n\nmpl.figure.prototype.send_draw_message = function () {\n    if (!this.waiting) {\n        this.waiting = true;\n        this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    var format_dropdown = fig.format_dropdown;\n    var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n    fig.ondownload(fig, format);\n};\n\nmpl.figure.prototype.handle_resize = function (fig, msg) {\n    var size = msg['size'];\n    if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n        fig._resize_canvas(size[0], size[1], msg['forward']);\n        fig.send_message('refresh', {});\n    }\n};\n\nmpl.figure.prototype.handle_rubberband = function (fig, msg) {\n    var x0 = msg['x0'] / fig.ratio;\n    var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n    var x1 = msg['x1'] / fig.ratio;\n    var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n    x0 = Math.floor(x0) + 0.5;\n    y0 = Math.floor(y0) + 0.5;\n    x1 = Math.floor(x1) + 0.5;\n    y1 = Math.floor(y1) + 0.5;\n    var min_x = Math.min(x0, x1);\n    var min_y = Math.min(y0, y1);\n    var width = Math.abs(x1 - x0);\n    var height = Math.abs(y1 - y0);\n\n    fig.rubberband_context.clearRect(\n        0,\n        0,\n        fig.canvas.width / fig.ratio,\n        fig.canvas.height / fig.ratio\n    );\n\n    fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n};\n\nmpl.figure.prototype.handle_figure_label = function (fig, msg) {\n    // Updates the figure title.\n    fig.header.textContent = msg['label'];\n};\n\nmpl.figure.prototype.handle_cursor = function (fig, msg) {\n    fig.rubberband_canvas.style.cursor = msg['cursor'];\n};\n\nmpl.figure.prototype.handle_message = function (fig, msg) {\n    fig.message.textContent = msg['message'];\n};\n\nmpl.figure.prototype.handle_draw = function (fig, _msg) {\n    // Request the server to send over a new figure.\n    fig.send_draw_message();\n};\n\nmpl.figure.prototype.handle_image_mode = function (fig, msg) {\n    fig.image_mode = msg['mode'];\n};\n\nmpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n    for (var key in msg) {\n        if (!(key in fig.buttons)) {\n            continue;\n        }\n        fig.buttons[key].disabled = !msg[key];\n        fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n    }\n};\n\nmpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n    if (msg['mode'] === 'PAN') {\n        fig.buttons['Pan'].classList.add('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    } else if (msg['mode'] === 'ZOOM') {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.add('active');\n    } else {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    }\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Called whenever the canvas gets updated.\n    this.send_message('ack', {});\n};\n\n// A function to construct a web socket function for onmessage handling.\n// Called in the figure constructor.\nmpl.figure.prototype._make_on_message_function = function (fig) {\n    return function socket_on_message(evt) {\n        if (evt.data instanceof Blob) {\n            var img = evt.data;\n            if (img.type !== 'image/png') {\n                /* FIXME: We get \"Resource interpreted as Image but\n                 * transferred with MIME type text/plain:\" errors on\n                 * Chrome.  But how to set the MIME type?  It doesn't seem\n                 * to be part of the websocket stream */\n                img.type = 'image/png';\n            }\n\n            /* Free the memory for the previous frames */\n            if (fig.imageObj.src) {\n                (window.URL || window.webkitURL).revokeObjectURL(\n                    fig.imageObj.src\n                );\n            }\n\n            fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n                img\n            );\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        } else if (\n            typeof evt.data === 'string' &&\n            evt.data.slice(0, 21) === 'data:image/png;base64'\n        ) {\n            fig.imageObj.src = evt.data;\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        }\n\n        var msg = JSON.parse(evt.data);\n        var msg_type = msg['type'];\n\n        // Call the  \"handle_{type}\" callback, which takes\n        // the figure and JSON message as its only arguments.\n        try {\n            var callback = fig['handle_' + msg_type];\n        } catch (e) {\n            console.log(\n                \"No handler for the '\" + msg_type + \"' message type: \",\n                msg\n            );\n            return;\n        }\n\n        if (callback) {\n            try {\n                // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n                callback(fig, msg);\n            } catch (e) {\n                console.log(\n                    \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n                    e,\n                    e.stack,\n                    msg\n                );\n            }\n        }\n    };\n};\n\n// from https://stackoverflow.com/questions/1114465/getting-mouse-location-in-canvas\nmpl.findpos = function (e) {\n    //this section is from http://www.quirksmode.org/js/events_properties.html\n    var targ;\n    if (!e) {\n        e = window.event;\n    }\n    if (e.target) {\n        targ = e.target;\n    } else if (e.srcElement) {\n        targ = e.srcElement;\n    }\n    if (targ.nodeType === 3) {\n        // defeat Safari bug\n        targ = targ.parentNode;\n    }\n\n    // pageX,Y are the mouse positions relative to the document\n    var boundingRect = targ.getBoundingClientRect();\n    var x = e.pageX - (boundingRect.left + document.body.scrollLeft);\n    var y = e.pageY - (boundingRect.top + document.body.scrollTop);\n\n    return { x: x, y: y };\n};\n\n/*\n * return a copy of an object with only non-object keys\n * we need this to avoid circular references\n * https://stackoverflow.com/a/24161582/3208463\n */\nfunction simpleKeys(original) {\n    return Object.keys(original).reduce(function (obj, key) {\n        if (typeof original[key] !== 'object') {\n            obj[key] = original[key];\n        }\n        return obj;\n    }, {});\n}\n\nmpl.figure.prototype.mouse_event = function (event, name) {\n    var canvas_pos = mpl.findpos(event);\n\n    if (name === 'button_press') {\n        this.canvas.focus();\n        this.canvas_div.focus();\n    }\n\n    var x = canvas_pos.x * this.ratio;\n    var y = canvas_pos.y * this.ratio;\n\n    this.send_message(name, {\n        x: x,\n        y: y,\n        button: event.button,\n        step: event.step,\n        guiEvent: simpleKeys(event),\n    });\n\n    /* This prevents the web browser from automatically changing to\n     * the text insertion cursor when the button is pressed.  We want\n     * to control all of the cursor setting manually through the\n     * 'cursor' event from matplotlib */\n    event.preventDefault();\n    return false;\n};\n\nmpl.figure.prototype._key_event_extra = function (_event, _name) {\n    // Handle any extra behaviour associated with a key event\n};\n\nmpl.figure.prototype.key_event = function (event, name) {\n    // Prevent repeat events\n    if (name === 'key_press') {\n        if (event.key === this._key) {\n            return;\n        } else {\n            this._key = event.key;\n        }\n    }\n    if (name === 'key_release') {\n        this._key = null;\n    }\n\n    var value = '';\n    if (event.ctrlKey && event.key !== 'Control') {\n        value += 'ctrl+';\n    }\n    else if (event.altKey && event.key !== 'Alt') {\n        value += 'alt+';\n    }\n    else if (event.shiftKey && event.key !== 'Shift') {\n        value += 'shift+';\n    }\n\n    value += 'k' + event.key;\n\n    this._key_event_extra(event, name);\n\n    this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n    return false;\n};\n\nmpl.figure.prototype.toolbar_button_onclick = function (name) {\n    if (name === 'download') {\n        this.handle_save(this, null);\n    } else {\n        this.send_message('toolbar_button', { name: name });\n    }\n};\n\nmpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n    this.message.textContent = tooltip;\n};\n\n///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n// prettier-ignore\nvar _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\nmpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home icon-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left icon-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right icon-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows icon-move\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis\", \"fa fa-square-o icon-check-empty\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o icon-save\", \"download\"]];\n\nmpl.extensions = [\"eps\", \"jpeg\", \"pgf\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\"];\n\nmpl.default_extension = \"png\";/* global mpl */\n\nvar comm_websocket_adapter = function (comm) {\n    // Create a \"websocket\"-like object which calls the given IPython comm\n    // object with the appropriate methods. Currently this is a non binary\n    // socket, so there is still some room for performance tuning.\n    var ws = {};\n\n    ws.binaryType = comm.kernel.ws.binaryType;\n    ws.readyState = comm.kernel.ws.readyState;\n    function updateReadyState(_event) {\n        if (comm.kernel.ws) {\n            ws.readyState = comm.kernel.ws.readyState;\n        } else {\n            ws.readyState = 3; // Closed state.\n        }\n    }\n    comm.kernel.ws.addEventListener('open', updateReadyState);\n    comm.kernel.ws.addEventListener('close', updateReadyState);\n    comm.kernel.ws.addEventListener('error', updateReadyState);\n\n    ws.close = function () {\n        comm.close();\n    };\n    ws.send = function (m) {\n        //console.log('sending', m);\n        comm.send(m);\n    };\n    // Register the callback with on_msg.\n    comm.on_msg(function (msg) {\n        //console.log('receiving', msg['content']['data'], msg);\n        var data = msg['content']['data'];\n        if (data['blob'] !== undefined) {\n            data = {\n                data: new Blob(msg['buffers'], { type: data['blob'] }),\n            };\n        }\n        // Pass the mpl event to the overridden (by mpl) onmessage function.\n        ws.onmessage(data);\n    });\n    return ws;\n};\n\nmpl.mpl_figure_comm = function (comm, msg) {\n    // This is the function which gets called when the mpl process\n    // starts-up an IPython Comm through the \"matplotlib\" channel.\n\n    var id = msg.content.data.id;\n    // Get hold of the div created by the display call when the Comm\n    // socket was opened in Python.\n    var element = document.getElementById(id);\n    var ws_proxy = comm_websocket_adapter(comm);\n\n    function ondownload(figure, _format) {\n        window.open(figure.canvas.toDataURL());\n    }\n\n    var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n\n    // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n    // web socket which is closed, not our websocket->open comm proxy.\n    ws_proxy.onopen();\n\n    fig.parent_element = element;\n    fig.cell_info = mpl.find_output_cell(\"<div id='\" + id + \"'></div>\");\n    if (!fig.cell_info) {\n        console.error('Failed to find cell for figure', id, fig);\n        return;\n    }\n    fig.cell_info[0].output_area.element.on(\n        'cleared',\n        { fig: fig },\n        fig._remove_fig_handler\n    );\n};\n\nmpl.figure.prototype.handle_close = function (fig, msg) {\n    var width = fig.canvas.width / fig.ratio;\n    fig.cell_info[0].output_area.element.off(\n        'cleared',\n        fig._remove_fig_handler\n    );\n    fig.resizeObserverInstance.unobserve(fig.canvas_div);\n\n    // Update the output cell to use the data from the current canvas.\n    fig.push_to_output();\n    var dataURL = fig.canvas.toDataURL();\n    // Re-enable the keyboard manager in IPython - without this line, in FF,\n    // the notebook keyboard shortcuts fail.\n    IPython.keyboard_manager.enable();\n    fig.parent_element.innerHTML =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n    fig.close_ws(fig, msg);\n};\n\nmpl.figure.prototype.close_ws = function (fig, msg) {\n    fig.send_message('closing', msg);\n    // fig.ws.close()\n};\n\nmpl.figure.prototype.push_to_output = function (_remove_interactive) {\n    // Turn the data on the canvas into data in the output cell.\n    var width = this.canvas.width / this.ratio;\n    var dataURL = this.canvas.toDataURL();\n    this.cell_info[1]['text/html'] =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Tell IPython that the notebook contents must change.\n    IPython.notebook.set_dirty(true);\n    this.send_message('ack', {});\n    var fig = this;\n    // Wait a second, then push the new image to the DOM so\n    // that it is saved nicely (might be nice to debounce this).\n    setTimeout(function () {\n        fig.push_to_output();\n    }, 1000);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'btn-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'btn-group';\n    var button;\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'btn-group';\n            continue;\n        }\n\n        button = fig.buttons[name] = document.createElement('button');\n        button.classList = 'btn btn-default';\n        button.href = '#';\n        button.title = name;\n        button.innerHTML = '<i class=\"fa ' + image + ' fa-lg\"></i>';\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    // Add the status bar.\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message pull-right';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n\n    // Add the close button to the window.\n    var buttongrp = document.createElement('div');\n    buttongrp.classList = 'btn-group inline pull-right';\n    button = document.createElement('button');\n    button.classList = 'btn btn-mini btn-primary';\n    button.href = '#';\n    button.title = 'Stop Interaction';\n    button.innerHTML = '<i class=\"fa fa-power-off icon-remove icon-large\"></i>';\n    button.addEventListener('click', function (_evt) {\n        fig.handle_close(fig, {});\n    });\n    button.addEventListener(\n        'mouseover',\n        on_mouseover_closure('Stop Interaction')\n    );\n    buttongrp.appendChild(button);\n    var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n    titlebar.insertBefore(buttongrp, titlebar.firstChild);\n};\n\nmpl.figure.prototype._remove_fig_handler = function (event) {\n    var fig = event.data.fig;\n    if (event.target !== this) {\n        // Ignore bubbled events from children.\n        return;\n    }\n    fig.close_ws(fig, {});\n};\n\nmpl.figure.prototype._root_extra_style = function (el) {\n    el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n};\n\nmpl.figure.prototype._canvas_extra_style = function (el) {\n    // this is important to make the div 'focusable\n    el.setAttribute('tabindex', 0);\n    // reach out to IPython and tell the keyboard manager to turn it's self\n    // off when our div gets focus\n\n    // location in version 3\n    if (IPython.notebook.keyboard_manager) {\n        IPython.notebook.keyboard_manager.register_events(el);\n    } else {\n        // location in version 2\n        IPython.keyboard_manager.register_events(el);\n    }\n};\n\nmpl.figure.prototype._key_event_extra = function (event, _name) {\n    // Check for shift+enter\n    if (event.shiftKey && event.which === 13) {\n        this.canvas_div.blur();\n        // select the cell after this one\n        var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n        IPython.notebook.select(index + 1);\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    fig.ondownload(fig, null);\n};\n\nmpl.find_output_cell = function (html_output) {\n    // Return the cell and output element which can be found *uniquely* in the notebook.\n    // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n    // IPython event is triggered only after the cells have been serialised, which for\n    // our purposes (turning an active figure into a static one), is too late.\n    var cells = IPython.notebook.get_cells();\n    var ncells = cells.length;\n    for (var i = 0; i < ncells; i++) {\n        var cell = cells[i];\n        if (cell.cell_type === 'code') {\n            for (var j = 0; j < cell.output_area.outputs.length; j++) {\n                var data = cell.output_area.outputs[j];\n                if (data.data) {\n                    // IPython >= 3 moved mimebundle to data attribute of output\n                    data = data.data;\n                }\n                if (data['text/html'] === html_output) {\n                    return [cell, data, j];\n                }\n            }\n        }\n    }\n};\n\n// Register the function which deals with the matplotlib target/channel.\n// The kernel may be null if the page has been refreshed.\nif (IPython.notebook.kernel !== null) {\n    IPython.notebook.kernel.comm_manager.register_target(\n        'matplotlib',\n        mpl.mpl_figure_comm\n    );\n}\n",
      "text/plain": [
       "<IPython.core.display.Javascript object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<img src=\"data:image/png;base64,[encoded data, 80960 characters]\" width=\"640\">"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "f = 232.4375 ± 0.3994 Hz\n"
     ]
    }
   ],
   "source": [
    "def damp_osci(t, t0, A, B, nu, gamma):\n",
    "    return A * np.exp(-gamma*t)*np.sin(2*np.pi*nu*(t-t0)) + B\n",
    "\n",
    "yvals     = val_mean#.sel(blink_on_time=slice(0.005, 0.025))\n",
    "yvals_std = std_mean#.sel(blink_on_time=slice(0.005, 0.025))\n",
    "xvals     = dataSet_cropOD[scanAxis[0]]#.sel(blink_on_time=slice(0.005, 0.025))\n",
    "\n",
    "fitted_qtys_1 = yvals.to_numpy()\n",
    "scan_para = xvals.to_numpy()\n",
    "fitted_qtys_err_1 = yvals_std.to_numpy()\n",
    "\n",
    "\n",
    "plt.figure()\n",
    "popt_x, pcov_x = curve_fit(damp_osci, scan_para, fitted_qtys_1, np.array([0, 3, 147, 3e2, 0.1]))\n",
    "freqdata = np.linspace(0.005, 20e-3, 500)\n",
    "plt.plot(freqdata, damp_osci(freqdata, *popt_x), 'g--',label='fit: t0=%5.3f, A=%5.3f, B=%5.3f, nu=%5.3f, Gamma=%5.3f' % tuple(popt_x))\n",
    "plt.errorbar(scan_para, fitted_qtys_1, yerr=fitted_qtys_err_1, fmt='or')\n",
    "plt.xlabel('hold time after switch on the trap (s)')\n",
    "plt.ylabel('Center along gravity direction (pixels)')\n",
    "plt.tight_layout()\n",
    "plt.grid(visible=1)\n",
    "#plt.ylim([0,750])\n",
    "#plt.xlim([0.004, 0.025])\n",
    "#plt.legend(prop={'size': 14})\n",
    "plt.show()\n",
    "\n",
    "f_x = popt_x[3]\n",
    "df_x = pcov_x[3][3]**0.5\n",
    "\n",
    "print('f = %.4f \\u00B1 %.4f Hz'% tuple([np.abs(f_x),df_x]))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Truncation: 0.75"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 99,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The detected scaning axes and values are: \n",
      "\n",
      "{'mod_blink_on_time': array([0.005 , 0.0057, 0.0064, 0.0071, 0.0078, 0.0085, 0.0092, 0.0099,\n",
      "       0.0106, 0.0113, 0.012 , 0.0127, 0.0134, 0.0141, 0.0148, 0.0155,\n",
      "       0.0162, 0.0169, 0.0176, 0.0183, 0.019 , 0.0197]), 'runs': array([0., 1., 2., 3.])}\n"
     ]
    },
    {
     "data": {
      "application/javascript": "/* Put everything inside the global mpl namespace */\n/* global mpl */\nwindow.mpl = {};\n\nmpl.get_websocket_type = function () {\n    if (typeof WebSocket !== 'undefined') {\n        return WebSocket;\n    } else if (typeof MozWebSocket !== 'undefined') {\n        return MozWebSocket;\n    } else {\n        alert(\n            'Your browser does not have WebSocket support. ' +\n                'Please try Chrome, Safari or Firefox ≥ 6. ' +\n                'Firefox 4 and 5 are also supported but you ' +\n                'have to enable WebSockets in about:config.'\n        );\n    }\n};\n\nmpl.figure = function (figure_id, websocket, ondownload, parent_element) {\n    this.id = figure_id;\n\n    this.ws = websocket;\n\n    this.supports_binary = this.ws.binaryType !== undefined;\n\n    if (!this.supports_binary) {\n        var warnings = document.getElementById('mpl-warnings');\n        if (warnings) {\n            warnings.style.display = 'block';\n            warnings.textContent =\n                'This browser does not support binary websocket messages. ' +\n                'Performance may be slow.';\n        }\n    }\n\n    this.imageObj = new Image();\n\n    this.context = undefined;\n    this.message = undefined;\n    this.canvas = undefined;\n    this.rubberband_canvas = undefined;\n    this.rubberband_context = undefined;\n    this.format_dropdown = undefined;\n\n    this.image_mode = 'full';\n\n    this.root = document.createElement('div');\n    this.root.setAttribute('style', 'display: inline-block');\n    this._root_extra_style(this.root);\n\n    parent_element.appendChild(this.root);\n\n    this._init_header(this);\n    this._init_canvas(this);\n    this._init_toolbar(this);\n\n    var fig = this;\n\n    this.waiting = false;\n\n    this.ws.onopen = function () {\n        fig.send_message('supports_binary', { value: fig.supports_binary });\n        fig.send_message('send_image_mode', {});\n        if (fig.ratio !== 1) {\n            fig.send_message('set_device_pixel_ratio', {\n                device_pixel_ratio: fig.ratio,\n            });\n        }\n        fig.send_message('refresh', {});\n    };\n\n    this.imageObj.onload = function () {\n        if (fig.image_mode === 'full') {\n            // Full images could contain transparency (where diff images\n            // almost always do), so we need to clear the canvas so that\n            // there is no ghosting.\n            fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n        }\n        fig.context.drawImage(fig.imageObj, 0, 0);\n    };\n\n    this.imageObj.onunload = function () {\n        fig.ws.close();\n    };\n\n    this.ws.onmessage = this._make_on_message_function(this);\n\n    this.ondownload = ondownload;\n};\n\nmpl.figure.prototype._init_header = function () {\n    var titlebar = document.createElement('div');\n    titlebar.classList =\n        'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n    var titletext = document.createElement('div');\n    titletext.classList = 'ui-dialog-title';\n    titletext.setAttribute(\n        'style',\n        'width: 100%; text-align: center; padding: 3px;'\n    );\n    titlebar.appendChild(titletext);\n    this.root.appendChild(titlebar);\n    this.header = titletext;\n};\n\nmpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._init_canvas = function () {\n    var fig = this;\n\n    var canvas_div = (this.canvas_div = document.createElement('div'));\n    canvas_div.setAttribute(\n        'style',\n        'border: 1px solid #ddd;' +\n            'box-sizing: content-box;' +\n            'clear: both;' +\n            'min-height: 1px;' +\n            'min-width: 1px;' +\n            'outline: 0;' +\n            'overflow: hidden;' +\n            'position: relative;' +\n            'resize: both;'\n    );\n\n    function on_keyboard_event_closure(name) {\n        return function (event) {\n            return fig.key_event(event, name);\n        };\n    }\n\n    canvas_div.addEventListener(\n        'keydown',\n        on_keyboard_event_closure('key_press')\n    );\n    canvas_div.addEventListener(\n        'keyup',\n        on_keyboard_event_closure('key_release')\n    );\n\n    this._canvas_extra_style(canvas_div);\n    this.root.appendChild(canvas_div);\n\n    var canvas = (this.canvas = document.createElement('canvas'));\n    canvas.classList.add('mpl-canvas');\n    canvas.setAttribute('style', 'box-sizing: content-box;');\n\n    this.context = canvas.getContext('2d');\n\n    var backingStore =\n        this.context.backingStorePixelRatio ||\n        this.context.webkitBackingStorePixelRatio ||\n        this.context.mozBackingStorePixelRatio ||\n        this.context.msBackingStorePixelRatio ||\n        this.context.oBackingStorePixelRatio ||\n        this.context.backingStorePixelRatio ||\n        1;\n\n    this.ratio = (window.devicePixelRatio || 1) / backingStore;\n\n    var rubberband_canvas = (this.rubberband_canvas = document.createElement(\n        'canvas'\n    ));\n    rubberband_canvas.setAttribute(\n        'style',\n        'box-sizing: content-box; position: absolute; left: 0; top: 0; z-index: 1;'\n    );\n\n    // Apply a ponyfill if ResizeObserver is not implemented by browser.\n    if (this.ResizeObserver === undefined) {\n        if (window.ResizeObserver !== undefined) {\n            this.ResizeObserver = window.ResizeObserver;\n        } else {\n            var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n            this.ResizeObserver = obs.ResizeObserver;\n        }\n    }\n\n    this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n        var nentries = entries.length;\n        for (var i = 0; i < nentries; i++) {\n            var entry = entries[i];\n            var width, height;\n            if (entry.contentBoxSize) {\n                if (entry.contentBoxSize instanceof Array) {\n                    // Chrome 84 implements new version of spec.\n                    width = entry.contentBoxSize[0].inlineSize;\n                    height = entry.contentBoxSize[0].blockSize;\n                } else {\n                    // Firefox implements old version of spec.\n                    width = entry.contentBoxSize.inlineSize;\n                    height = entry.contentBoxSize.blockSize;\n                }\n            } else {\n                // Chrome <84 implements even older version of spec.\n                width = entry.contentRect.width;\n                height = entry.contentRect.height;\n            }\n\n            // Keep the size of the canvas and rubber band canvas in sync with\n            // the canvas container.\n            if (entry.devicePixelContentBoxSize) {\n                // Chrome 84 implements new version of spec.\n                canvas.setAttribute(\n                    'width',\n                    entry.devicePixelContentBoxSize[0].inlineSize\n                );\n                canvas.setAttribute(\n                    'height',\n                    entry.devicePixelContentBoxSize[0].blockSize\n                );\n            } else {\n                canvas.setAttribute('width', width * fig.ratio);\n                canvas.setAttribute('height', height * fig.ratio);\n            }\n            canvas.setAttribute(\n                'style',\n                'width: ' + width + 'px; height: ' + height + 'px;'\n            );\n\n            rubberband_canvas.setAttribute('width', width);\n            rubberband_canvas.setAttribute('height', height);\n\n            // And update the size in Python. We ignore the initial 0/0 size\n            // that occurs as the element is placed into the DOM, which should\n            // otherwise not happen due to the minimum size styling.\n            if (fig.ws.readyState == 1 && width != 0 && height != 0) {\n                fig.request_resize(width, height);\n            }\n        }\n    });\n    this.resizeObserverInstance.observe(canvas_div);\n\n    function on_mouse_event_closure(name) {\n        return function (event) {\n            return fig.mouse_event(event, name);\n        };\n    }\n\n    rubberband_canvas.addEventListener(\n        'mousedown',\n        on_mouse_event_closure('button_press')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseup',\n        on_mouse_event_closure('button_release')\n    );\n    rubberband_canvas.addEventListener(\n        'dblclick',\n        on_mouse_event_closure('dblclick')\n    );\n    // Throttle sequential mouse events to 1 every 20ms.\n    rubberband_canvas.addEventListener(\n        'mousemove',\n        on_mouse_event_closure('motion_notify')\n    );\n\n    rubberband_canvas.addEventListener(\n        'mouseenter',\n        on_mouse_event_closure('figure_enter')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseleave',\n        on_mouse_event_closure('figure_leave')\n    );\n\n    canvas_div.addEventListener('wheel', function (event) {\n        if (event.deltaY < 0) {\n            event.step = 1;\n        } else {\n            event.step = -1;\n        }\n        on_mouse_event_closure('scroll')(event);\n    });\n\n    canvas_div.appendChild(canvas);\n    canvas_div.appendChild(rubberband_canvas);\n\n    this.rubberband_context = rubberband_canvas.getContext('2d');\n    this.rubberband_context.strokeStyle = '#000000';\n\n    this._resize_canvas = function (width, height, forward) {\n        if (forward) {\n            canvas_div.style.width = width + 'px';\n            canvas_div.style.height = height + 'px';\n        }\n    };\n\n    // Disable right mouse context menu.\n    this.rubberband_canvas.addEventListener('contextmenu', function (_e) {\n        event.preventDefault();\n        return false;\n    });\n\n    function set_focus() {\n        canvas.focus();\n        canvas_div.focus();\n    }\n\n    window.setTimeout(set_focus, 100);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'mpl-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'mpl-button-group';\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'mpl-button-group';\n            continue;\n        }\n\n        var button = (fig.buttons[name] = document.createElement('button'));\n        button.classList = 'mpl-widget';\n        button.setAttribute('role', 'button');\n        button.setAttribute('aria-disabled', 'false');\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n\n        var icon_img = document.createElement('img');\n        icon_img.src = '_images/' + image + '.png';\n        icon_img.srcset = '_images/' + image + '_large.png 2x';\n        icon_img.alt = tooltip;\n        button.appendChild(icon_img);\n\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    var fmt_picker = document.createElement('select');\n    fmt_picker.classList = 'mpl-widget';\n    toolbar.appendChild(fmt_picker);\n    this.format_dropdown = fmt_picker;\n\n    for (var ind in mpl.extensions) {\n        var fmt = mpl.extensions[ind];\n        var option = document.createElement('option');\n        option.selected = fmt === mpl.default_extension;\n        option.innerHTML = fmt;\n        fmt_picker.appendChild(option);\n    }\n\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n};\n\nmpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n    // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n    // which will in turn request a refresh of the image.\n    this.send_message('resize', { width: x_pixels, height: y_pixels });\n};\n\nmpl.figure.prototype.send_message = function (type, properties) {\n    properties['type'] = type;\n    properties['figure_id'] = this.id;\n    this.ws.send(JSON.stringify(properties));\n};\n\nmpl.figure.prototype.send_draw_message = function () {\n    if (!this.waiting) {\n        this.waiting = true;\n        this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    var format_dropdown = fig.format_dropdown;\n    var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n    fig.ondownload(fig, format);\n};\n\nmpl.figure.prototype.handle_resize = function (fig, msg) {\n    var size = msg['size'];\n    if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n        fig._resize_canvas(size[0], size[1], msg['forward']);\n        fig.send_message('refresh', {});\n    }\n};\n\nmpl.figure.prototype.handle_rubberband = function (fig, msg) {\n    var x0 = msg['x0'] / fig.ratio;\n    var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n    var x1 = msg['x1'] / fig.ratio;\n    var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n    x0 = Math.floor(x0) + 0.5;\n    y0 = Math.floor(y0) + 0.5;\n    x1 = Math.floor(x1) + 0.5;\n    y1 = Math.floor(y1) + 0.5;\n    var min_x = Math.min(x0, x1);\n    var min_y = Math.min(y0, y1);\n    var width = Math.abs(x1 - x0);\n    var height = Math.abs(y1 - y0);\n\n    fig.rubberband_context.clearRect(\n        0,\n        0,\n        fig.canvas.width / fig.ratio,\n        fig.canvas.height / fig.ratio\n    );\n\n    fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n};\n\nmpl.figure.prototype.handle_figure_label = function (fig, msg) {\n    // Updates the figure title.\n    fig.header.textContent = msg['label'];\n};\n\nmpl.figure.prototype.handle_cursor = function (fig, msg) {\n    fig.rubberband_canvas.style.cursor = msg['cursor'];\n};\n\nmpl.figure.prototype.handle_message = function (fig, msg) {\n    fig.message.textContent = msg['message'];\n};\n\nmpl.figure.prototype.handle_draw = function (fig, _msg) {\n    // Request the server to send over a new figure.\n    fig.send_draw_message();\n};\n\nmpl.figure.prototype.handle_image_mode = function (fig, msg) {\n    fig.image_mode = msg['mode'];\n};\n\nmpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n    for (var key in msg) {\n        if (!(key in fig.buttons)) {\n            continue;\n        }\n        fig.buttons[key].disabled = !msg[key];\n        fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n    }\n};\n\nmpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n    if (msg['mode'] === 'PAN') {\n        fig.buttons['Pan'].classList.add('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    } else if (msg['mode'] === 'ZOOM') {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.add('active');\n    } else {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    }\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Called whenever the canvas gets updated.\n    this.send_message('ack', {});\n};\n\n// A function to construct a web socket function for onmessage handling.\n// Called in the figure constructor.\nmpl.figure.prototype._make_on_message_function = function (fig) {\n    return function socket_on_message(evt) {\n        if (evt.data instanceof Blob) {\n            var img = evt.data;\n            if (img.type !== 'image/png') {\n                /* FIXME: We get \"Resource interpreted as Image but\n                 * transferred with MIME type text/plain:\" errors on\n                 * Chrome.  But how to set the MIME type?  It doesn't seem\n                 * to be part of the websocket stream */\n                img.type = 'image/png';\n            }\n\n            /* Free the memory for the previous frames */\n            if (fig.imageObj.src) {\n                (window.URL || window.webkitURL).revokeObjectURL(\n                    fig.imageObj.src\n                );\n            }\n\n            fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n                img\n            );\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        } else if (\n            typeof evt.data === 'string' &&\n            evt.data.slice(0, 21) === 'data:image/png;base64'\n        ) {\n            fig.imageObj.src = evt.data;\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        }\n\n        var msg = JSON.parse(evt.data);\n        var msg_type = msg['type'];\n\n        // Call the  \"handle_{type}\" callback, which takes\n        // the figure and JSON message as its only arguments.\n        try {\n            var callback = fig['handle_' + msg_type];\n        } catch (e) {\n            console.log(\n                \"No handler for the '\" + msg_type + \"' message type: \",\n                msg\n            );\n            return;\n        }\n\n        if (callback) {\n            try {\n                // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n                callback(fig, msg);\n            } catch (e) {\n                console.log(\n                    \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n                    e,\n                    e.stack,\n                    msg\n                );\n            }\n        }\n    };\n};\n\n// from https://stackoverflow.com/questions/1114465/getting-mouse-location-in-canvas\nmpl.findpos = function (e) {\n    //this section is from http://www.quirksmode.org/js/events_properties.html\n    var targ;\n    if (!e) {\n        e = window.event;\n    }\n    if (e.target) {\n        targ = e.target;\n    } else if (e.srcElement) {\n        targ = e.srcElement;\n    }\n    if (targ.nodeType === 3) {\n        // defeat Safari bug\n        targ = targ.parentNode;\n    }\n\n    // pageX,Y are the mouse positions relative to the document\n    var boundingRect = targ.getBoundingClientRect();\n    var x = e.pageX - (boundingRect.left + document.body.scrollLeft);\n    var y = e.pageY - (boundingRect.top + document.body.scrollTop);\n\n    return { x: x, y: y };\n};\n\n/*\n * return a copy of an object with only non-object keys\n * we need this to avoid circular references\n * https://stackoverflow.com/a/24161582/3208463\n */\nfunction simpleKeys(original) {\n    return Object.keys(original).reduce(function (obj, key) {\n        if (typeof original[key] !== 'object') {\n            obj[key] = original[key];\n        }\n        return obj;\n    }, {});\n}\n\nmpl.figure.prototype.mouse_event = function (event, name) {\n    var canvas_pos = mpl.findpos(event);\n\n    if (name === 'button_press') {\n        this.canvas.focus();\n        this.canvas_div.focus();\n    }\n\n    var x = canvas_pos.x * this.ratio;\n    var y = canvas_pos.y * this.ratio;\n\n    this.send_message(name, {\n        x: x,\n        y: y,\n        button: event.button,\n        step: event.step,\n        guiEvent: simpleKeys(event),\n    });\n\n    /* This prevents the web browser from automatically changing to\n     * the text insertion cursor when the button is pressed.  We want\n     * to control all of the cursor setting manually through the\n     * 'cursor' event from matplotlib */\n    event.preventDefault();\n    return false;\n};\n\nmpl.figure.prototype._key_event_extra = function (_event, _name) {\n    // Handle any extra behaviour associated with a key event\n};\n\nmpl.figure.prototype.key_event = function (event, name) {\n    // Prevent repeat events\n    if (name === 'key_press') {\n        if (event.key === this._key) {\n            return;\n        } else {\n            this._key = event.key;\n        }\n    }\n    if (name === 'key_release') {\n        this._key = null;\n    }\n\n    var value = '';\n    if (event.ctrlKey && event.key !== 'Control') {\n        value += 'ctrl+';\n    }\n    else if (event.altKey && event.key !== 'Alt') {\n        value += 'alt+';\n    }\n    else if (event.shiftKey && event.key !== 'Shift') {\n        value += 'shift+';\n    }\n\n    value += 'k' + event.key;\n\n    this._key_event_extra(event, name);\n\n    this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n    return false;\n};\n\nmpl.figure.prototype.toolbar_button_onclick = function (name) {\n    if (name === 'download') {\n        this.handle_save(this, null);\n    } else {\n        this.send_message('toolbar_button', { name: name });\n    }\n};\n\nmpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n    this.message.textContent = tooltip;\n};\n\n///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n// prettier-ignore\nvar _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\nmpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home icon-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left icon-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right icon-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows icon-move\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis\", \"fa fa-square-o icon-check-empty\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o icon-save\", \"download\"]];\n\nmpl.extensions = [\"eps\", \"jpeg\", \"pgf\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\"];\n\nmpl.default_extension = \"png\";/* global mpl */\n\nvar comm_websocket_adapter = function (comm) {\n    // Create a \"websocket\"-like object which calls the given IPython comm\n    // object with the appropriate methods. Currently this is a non binary\n    // socket, so there is still some room for performance tuning.\n    var ws = {};\n\n    ws.binaryType = comm.kernel.ws.binaryType;\n    ws.readyState = comm.kernel.ws.readyState;\n    function updateReadyState(_event) {\n        if (comm.kernel.ws) {\n            ws.readyState = comm.kernel.ws.readyState;\n        } else {\n            ws.readyState = 3; // Closed state.\n        }\n    }\n    comm.kernel.ws.addEventListener('open', updateReadyState);\n    comm.kernel.ws.addEventListener('close', updateReadyState);\n    comm.kernel.ws.addEventListener('error', updateReadyState);\n\n    ws.close = function () {\n        comm.close();\n    };\n    ws.send = function (m) {\n        //console.log('sending', m);\n        comm.send(m);\n    };\n    // Register the callback with on_msg.\n    comm.on_msg(function (msg) {\n        //console.log('receiving', msg['content']['data'], msg);\n        var data = msg['content']['data'];\n        if (data['blob'] !== undefined) {\n            data = {\n                data: new Blob(msg['buffers'], { type: data['blob'] }),\n            };\n        }\n        // Pass the mpl event to the overridden (by mpl) onmessage function.\n        ws.onmessage(data);\n    });\n    return ws;\n};\n\nmpl.mpl_figure_comm = function (comm, msg) {\n    // This is the function which gets called when the mpl process\n    // starts-up an IPython Comm through the \"matplotlib\" channel.\n\n    var id = msg.content.data.id;\n    // Get hold of the div created by the display call when the Comm\n    // socket was opened in Python.\n    var element = document.getElementById(id);\n    var ws_proxy = comm_websocket_adapter(comm);\n\n    function ondownload(figure, _format) {\n        window.open(figure.canvas.toDataURL());\n    }\n\n    var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n\n    // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n    // web socket which is closed, not our websocket->open comm proxy.\n    ws_proxy.onopen();\n\n    fig.parent_element = element;\n    fig.cell_info = mpl.find_output_cell(\"<div id='\" + id + \"'></div>\");\n    if (!fig.cell_info) {\n        console.error('Failed to find cell for figure', id, fig);\n        return;\n    }\n    fig.cell_info[0].output_area.element.on(\n        'cleared',\n        { fig: fig },\n        fig._remove_fig_handler\n    );\n};\n\nmpl.figure.prototype.handle_close = function (fig, msg) {\n    var width = fig.canvas.width / fig.ratio;\n    fig.cell_info[0].output_area.element.off(\n        'cleared',\n        fig._remove_fig_handler\n    );\n    fig.resizeObserverInstance.unobserve(fig.canvas_div);\n\n    // Update the output cell to use the data from the current canvas.\n    fig.push_to_output();\n    var dataURL = fig.canvas.toDataURL();\n    // Re-enable the keyboard manager in IPython - without this line, in FF,\n    // the notebook keyboard shortcuts fail.\n    IPython.keyboard_manager.enable();\n    fig.parent_element.innerHTML =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n    fig.close_ws(fig, msg);\n};\n\nmpl.figure.prototype.close_ws = function (fig, msg) {\n    fig.send_message('closing', msg);\n    // fig.ws.close()\n};\n\nmpl.figure.prototype.push_to_output = function (_remove_interactive) {\n    // Turn the data on the canvas into data in the output cell.\n    var width = this.canvas.width / this.ratio;\n    var dataURL = this.canvas.toDataURL();\n    this.cell_info[1]['text/html'] =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Tell IPython that the notebook contents must change.\n    IPython.notebook.set_dirty(true);\n    this.send_message('ack', {});\n    var fig = this;\n    // Wait a second, then push the new image to the DOM so\n    // that it is saved nicely (might be nice to debounce this).\n    setTimeout(function () {\n        fig.push_to_output();\n    }, 1000);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'btn-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'btn-group';\n    var button;\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'btn-group';\n            continue;\n        }\n\n        button = fig.buttons[name] = document.createElement('button');\n        button.classList = 'btn btn-default';\n        button.href = '#';\n        button.title = name;\n        button.innerHTML = '<i class=\"fa ' + image + ' fa-lg\"></i>';\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    // Add the status bar.\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message pull-right';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n\n    // Add the close button to the window.\n    var buttongrp = document.createElement('div');\n    buttongrp.classList = 'btn-group inline pull-right';\n    button = document.createElement('button');\n    button.classList = 'btn btn-mini btn-primary';\n    button.href = '#';\n    button.title = 'Stop Interaction';\n    button.innerHTML = '<i class=\"fa fa-power-off icon-remove icon-large\"></i>';\n    button.addEventListener('click', function (_evt) {\n        fig.handle_close(fig, {});\n    });\n    button.addEventListener(\n        'mouseover',\n        on_mouseover_closure('Stop Interaction')\n    );\n    buttongrp.appendChild(button);\n    var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n    titlebar.insertBefore(buttongrp, titlebar.firstChild);\n};\n\nmpl.figure.prototype._remove_fig_handler = function (event) {\n    var fig = event.data.fig;\n    if (event.target !== this) {\n        // Ignore bubbled events from children.\n        return;\n    }\n    fig.close_ws(fig, {});\n};\n\nmpl.figure.prototype._root_extra_style = function (el) {\n    el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n};\n\nmpl.figure.prototype._canvas_extra_style = function (el) {\n    // this is important to make the div 'focusable\n    el.setAttribute('tabindex', 0);\n    // reach out to IPython and tell the keyboard manager to turn it's self\n    // off when our div gets focus\n\n    // location in version 3\n    if (IPython.notebook.keyboard_manager) {\n        IPython.notebook.keyboard_manager.register_events(el);\n    } else {\n        // location in version 2\n        IPython.keyboard_manager.register_events(el);\n    }\n};\n\nmpl.figure.prototype._key_event_extra = function (event, _name) {\n    // Check for shift+enter\n    if (event.shiftKey && event.which === 13) {\n        this.canvas_div.blur();\n        // select the cell after this one\n        var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n        IPython.notebook.select(index + 1);\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    fig.ondownload(fig, null);\n};\n\nmpl.find_output_cell = function (html_output) {\n    // Return the cell and output element which can be found *uniquely* in the notebook.\n    // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n    // IPython event is triggered only after the cells have been serialised, which for\n    // our purposes (turning an active figure into a static one), is too late.\n    var cells = IPython.notebook.get_cells();\n    var ncells = cells.length;\n    for (var i = 0; i < ncells; i++) {\n        var cell = cells[i];\n        if (cell.cell_type === 'code') {\n            for (var j = 0; j < cell.output_area.outputs.length; j++) {\n                var data = cell.output_area.outputs[j];\n                if (data.data) {\n                    // IPython >= 3 moved mimebundle to data attribute of output\n                    data = data.data;\n                }\n                if (data['text/html'] === html_output) {\n                    return [cell, data, j];\n                }\n            }\n        }\n    }\n};\n\n// Register the function which deals with the matplotlib target/channel.\n// The kernel may be null if the page has been refreshed.\nif (IPython.notebook.kernel !== null) {\n    IPython.notebook.kernel.comm_manager.register_target(\n        'matplotlib',\n        mpl.mpl_figure_comm\n    );\n}\n",
      "text/plain": [
       "<IPython.core.display.Javascript object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<img src=\"data:image/png;base64,[encoded data, 40844 characters]\" width=\"640\">"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "%matplotlib notebook\n",
    "shotNum = \"0012\"\n",
    "filePath = folderPath + \"/\" + shotNum + \"/*.h5\"\n",
    "\n",
    "dataSetDict = {\n",
    "    dskey[groupList[i]]: read_hdf5_file(filePath, groupList[i], excludeAxis = ['sweep_start_freq', 'sweep_stop_freq'])\n",
    "    for i in [0]\n",
    "}\n",
    "\n",
    "dataSet = dataSetDict[\"camera_0\"]\n",
    "\n",
    "print_scanAxis(dataSet)\n",
    "\n",
    "scanAxis = get_scanAxis(dataSet)\n",
    "\n",
    "dataSet = auto_rechunk(dataSet)\n",
    "\n",
    "dataSet = imageAnalyser.get_absorption_images(dataSet)\n",
    "\n",
    "imageAnalyser.center = (800, 900)\n",
    "imageAnalyser.span = (300, 300)\n",
    "imageAnalyser.fraction = (0.1, 0.1)\n",
    "\n",
    "dataSet_cropOD = imageAnalyser.crop_image(dataSet.OD)\n",
    "dataSet_cropOD = imageAnalyser.substract_offset(dataSet_cropOD).load()\n",
    "\n",
    "Ncount = imageAnalyser.get_Ncount(dataSet_cropOD)\n",
    "Ncount_mean = calculate_mean(Ncount)\n",
    "Ncount_std = calculate_std(Ncount)\n",
    "\n",
    "fig = plt.figure()\n",
    "ax = fig.gca()\n",
    "Ncount_mean.plot.errorbar(ax=ax, yerr = None, fmt='ob')\n",
    "plt.ylabel('NCount')\n",
    "plt.tight_layout()\n",
    "plt.grid(visible=1)\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 100,
   "metadata": {},
   "outputs": [],
   "source": [
    "dataSet_cropOD_chunk = dataSet_cropOD.chunk((1, 1, 300, 300))\n",
    "fitAnalyser = FitAnalyser(\"Gaussian-2D\", fitDim=2)\n",
    "params = fitAnalyser.guess(dataSet_cropOD_chunk, dask=\"parallelized\")\n",
    "fitResult = fitAnalyser.fit(dataSet_cropOD_chunk, params, dask=\"parallelized\").load()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 101,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/javascript": "/* Put everything inside the global mpl namespace */\n/* global mpl */\nwindow.mpl = {};\n\nmpl.get_websocket_type = function () {\n    if (typeof WebSocket !== 'undefined') {\n        return WebSocket;\n    } else if (typeof MozWebSocket !== 'undefined') {\n        return MozWebSocket;\n    } else {\n        alert(\n            'Your browser does not have WebSocket support. ' +\n                'Please try Chrome, Safari or Firefox ≥ 6. ' +\n                'Firefox 4 and 5 are also supported but you ' +\n                'have to enable WebSockets in about:config.'\n        );\n    }\n};\n\nmpl.figure = function (figure_id, websocket, ondownload, parent_element) {\n    this.id = figure_id;\n\n    this.ws = websocket;\n\n    this.supports_binary = this.ws.binaryType !== undefined;\n\n    if (!this.supports_binary) {\n        var warnings = document.getElementById('mpl-warnings');\n        if (warnings) {\n            warnings.style.display = 'block';\n            warnings.textContent =\n                'This browser does not support binary websocket messages. ' +\n                'Performance may be slow.';\n        }\n    }\n\n    this.imageObj = new Image();\n\n    this.context = undefined;\n    this.message = undefined;\n    this.canvas = undefined;\n    this.rubberband_canvas = undefined;\n    this.rubberband_context = undefined;\n    this.format_dropdown = undefined;\n\n    this.image_mode = 'full';\n\n    this.root = document.createElement('div');\n    this.root.setAttribute('style', 'display: inline-block');\n    this._root_extra_style(this.root);\n\n    parent_element.appendChild(this.root);\n\n    this._init_header(this);\n    this._init_canvas(this);\n    this._init_toolbar(this);\n\n    var fig = this;\n\n    this.waiting = false;\n\n    this.ws.onopen = function () {\n        fig.send_message('supports_binary', { value: fig.supports_binary });\n        fig.send_message('send_image_mode', {});\n        if (fig.ratio !== 1) {\n            fig.send_message('set_device_pixel_ratio', {\n                device_pixel_ratio: fig.ratio,\n            });\n        }\n        fig.send_message('refresh', {});\n    };\n\n    this.imageObj.onload = function () {\n        if (fig.image_mode === 'full') {\n            // Full images could contain transparency (where diff images\n            // almost always do), so we need to clear the canvas so that\n            // there is no ghosting.\n            fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n        }\n        fig.context.drawImage(fig.imageObj, 0, 0);\n    };\n\n    this.imageObj.onunload = function () {\n        fig.ws.close();\n    };\n\n    this.ws.onmessage = this._make_on_message_function(this);\n\n    this.ondownload = ondownload;\n};\n\nmpl.figure.prototype._init_header = function () {\n    var titlebar = document.createElement('div');\n    titlebar.classList =\n        'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n    var titletext = document.createElement('div');\n    titletext.classList = 'ui-dialog-title';\n    titletext.setAttribute(\n        'style',\n        'width: 100%; text-align: center; padding: 3px;'\n    );\n    titlebar.appendChild(titletext);\n    this.root.appendChild(titlebar);\n    this.header = titletext;\n};\n\nmpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._init_canvas = function () {\n    var fig = this;\n\n    var canvas_div = (this.canvas_div = document.createElement('div'));\n    canvas_div.setAttribute(\n        'style',\n        'border: 1px solid #ddd;' +\n            'box-sizing: content-box;' +\n            'clear: both;' +\n            'min-height: 1px;' +\n            'min-width: 1px;' +\n            'outline: 0;' +\n            'overflow: hidden;' +\n            'position: relative;' +\n            'resize: both;'\n    );\n\n    function on_keyboard_event_closure(name) {\n        return function (event) {\n            return fig.key_event(event, name);\n        };\n    }\n\n    canvas_div.addEventListener(\n        'keydown',\n        on_keyboard_event_closure('key_press')\n    );\n    canvas_div.addEventListener(\n        'keyup',\n        on_keyboard_event_closure('key_release')\n    );\n\n    this._canvas_extra_style(canvas_div);\n    this.root.appendChild(canvas_div);\n\n    var canvas = (this.canvas = document.createElement('canvas'));\n    canvas.classList.add('mpl-canvas');\n    canvas.setAttribute('style', 'box-sizing: content-box;');\n\n    this.context = canvas.getContext('2d');\n\n    var backingStore =\n        this.context.backingStorePixelRatio ||\n        this.context.webkitBackingStorePixelRatio ||\n        this.context.mozBackingStorePixelRatio ||\n        this.context.msBackingStorePixelRatio ||\n        this.context.oBackingStorePixelRatio ||\n        this.context.backingStorePixelRatio ||\n        1;\n\n    this.ratio = (window.devicePixelRatio || 1) / backingStore;\n\n    var rubberband_canvas = (this.rubberband_canvas = document.createElement(\n        'canvas'\n    ));\n    rubberband_canvas.setAttribute(\n        'style',\n        'box-sizing: content-box; position: absolute; left: 0; top: 0; z-index: 1;'\n    );\n\n    // Apply a ponyfill if ResizeObserver is not implemented by browser.\n    if (this.ResizeObserver === undefined) {\n        if (window.ResizeObserver !== undefined) {\n            this.ResizeObserver = window.ResizeObserver;\n        } else {\n            var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n            this.ResizeObserver = obs.ResizeObserver;\n        }\n    }\n\n    this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n        var nentries = entries.length;\n        for (var i = 0; i < nentries; i++) {\n            var entry = entries[i];\n            var width, height;\n            if (entry.contentBoxSize) {\n                if (entry.contentBoxSize instanceof Array) {\n                    // Chrome 84 implements new version of spec.\n                    width = entry.contentBoxSize[0].inlineSize;\n                    height = entry.contentBoxSize[0].blockSize;\n                } else {\n                    // Firefox implements old version of spec.\n                    width = entry.contentBoxSize.inlineSize;\n                    height = entry.contentBoxSize.blockSize;\n                }\n            } else {\n                // Chrome <84 implements even older version of spec.\n                width = entry.contentRect.width;\n                height = entry.contentRect.height;\n            }\n\n            // Keep the size of the canvas and rubber band canvas in sync with\n            // the canvas container.\n            if (entry.devicePixelContentBoxSize) {\n                // Chrome 84 implements new version of spec.\n                canvas.setAttribute(\n                    'width',\n                    entry.devicePixelContentBoxSize[0].inlineSize\n                );\n                canvas.setAttribute(\n                    'height',\n                    entry.devicePixelContentBoxSize[0].blockSize\n                );\n            } else {\n                canvas.setAttribute('width', width * fig.ratio);\n                canvas.setAttribute('height', height * fig.ratio);\n            }\n            canvas.setAttribute(\n                'style',\n                'width: ' + width + 'px; height: ' + height + 'px;'\n            );\n\n            rubberband_canvas.setAttribute('width', width);\n            rubberband_canvas.setAttribute('height', height);\n\n            // And update the size in Python. We ignore the initial 0/0 size\n            // that occurs as the element is placed into the DOM, which should\n            // otherwise not happen due to the minimum size styling.\n            if (fig.ws.readyState == 1 && width != 0 && height != 0) {\n                fig.request_resize(width, height);\n            }\n        }\n    });\n    this.resizeObserverInstance.observe(canvas_div);\n\n    function on_mouse_event_closure(name) {\n        return function (event) {\n            return fig.mouse_event(event, name);\n        };\n    }\n\n    rubberband_canvas.addEventListener(\n        'mousedown',\n        on_mouse_event_closure('button_press')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseup',\n        on_mouse_event_closure('button_release')\n    );\n    rubberband_canvas.addEventListener(\n        'dblclick',\n        on_mouse_event_closure('dblclick')\n    );\n    // Throttle sequential mouse events to 1 every 20ms.\n    rubberband_canvas.addEventListener(\n        'mousemove',\n        on_mouse_event_closure('motion_notify')\n    );\n\n    rubberband_canvas.addEventListener(\n        'mouseenter',\n        on_mouse_event_closure('figure_enter')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseleave',\n        on_mouse_event_closure('figure_leave')\n    );\n\n    canvas_div.addEventListener('wheel', function (event) {\n        if (event.deltaY < 0) {\n            event.step = 1;\n        } else {\n            event.step = -1;\n        }\n        on_mouse_event_closure('scroll')(event);\n    });\n\n    canvas_div.appendChild(canvas);\n    canvas_div.appendChild(rubberband_canvas);\n\n    this.rubberband_context = rubberband_canvas.getContext('2d');\n    this.rubberband_context.strokeStyle = '#000000';\n\n    this._resize_canvas = function (width, height, forward) {\n        if (forward) {\n            canvas_div.style.width = width + 'px';\n            canvas_div.style.height = height + 'px';\n        }\n    };\n\n    // Disable right mouse context menu.\n    this.rubberband_canvas.addEventListener('contextmenu', function (_e) {\n        event.preventDefault();\n        return false;\n    });\n\n    function set_focus() {\n        canvas.focus();\n        canvas_div.focus();\n    }\n\n    window.setTimeout(set_focus, 100);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'mpl-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'mpl-button-group';\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'mpl-button-group';\n            continue;\n        }\n\n        var button = (fig.buttons[name] = document.createElement('button'));\n        button.classList = 'mpl-widget';\n        button.setAttribute('role', 'button');\n        button.setAttribute('aria-disabled', 'false');\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n\n        var icon_img = document.createElement('img');\n        icon_img.src = '_images/' + image + '.png';\n        icon_img.srcset = '_images/' + image + '_large.png 2x';\n        icon_img.alt = tooltip;\n        button.appendChild(icon_img);\n\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    var fmt_picker = document.createElement('select');\n    fmt_picker.classList = 'mpl-widget';\n    toolbar.appendChild(fmt_picker);\n    this.format_dropdown = fmt_picker;\n\n    for (var ind in mpl.extensions) {\n        var fmt = mpl.extensions[ind];\n        var option = document.createElement('option');\n        option.selected = fmt === mpl.default_extension;\n        option.innerHTML = fmt;\n        fmt_picker.appendChild(option);\n    }\n\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n};\n\nmpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n    // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n    // which will in turn request a refresh of the image.\n    this.send_message('resize', { width: x_pixels, height: y_pixels });\n};\n\nmpl.figure.prototype.send_message = function (type, properties) {\n    properties['type'] = type;\n    properties['figure_id'] = this.id;\n    this.ws.send(JSON.stringify(properties));\n};\n\nmpl.figure.prototype.send_draw_message = function () {\n    if (!this.waiting) {\n        this.waiting = true;\n        this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    var format_dropdown = fig.format_dropdown;\n    var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n    fig.ondownload(fig, format);\n};\n\nmpl.figure.prototype.handle_resize = function (fig, msg) {\n    var size = msg['size'];\n    if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n        fig._resize_canvas(size[0], size[1], msg['forward']);\n        fig.send_message('refresh', {});\n    }\n};\n\nmpl.figure.prototype.handle_rubberband = function (fig, msg) {\n    var x0 = msg['x0'] / fig.ratio;\n    var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n    var x1 = msg['x1'] / fig.ratio;\n    var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n    x0 = Math.floor(x0) + 0.5;\n    y0 = Math.floor(y0) + 0.5;\n    x1 = Math.floor(x1) + 0.5;\n    y1 = Math.floor(y1) + 0.5;\n    var min_x = Math.min(x0, x1);\n    var min_y = Math.min(y0, y1);\n    var width = Math.abs(x1 - x0);\n    var height = Math.abs(y1 - y0);\n\n    fig.rubberband_context.clearRect(\n        0,\n        0,\n        fig.canvas.width / fig.ratio,\n        fig.canvas.height / fig.ratio\n    );\n\n    fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n};\n\nmpl.figure.prototype.handle_figure_label = function (fig, msg) {\n    // Updates the figure title.\n    fig.header.textContent = msg['label'];\n};\n\nmpl.figure.prototype.handle_cursor = function (fig, msg) {\n    fig.rubberband_canvas.style.cursor = msg['cursor'];\n};\n\nmpl.figure.prototype.handle_message = function (fig, msg) {\n    fig.message.textContent = msg['message'];\n};\n\nmpl.figure.prototype.handle_draw = function (fig, _msg) {\n    // Request the server to send over a new figure.\n    fig.send_draw_message();\n};\n\nmpl.figure.prototype.handle_image_mode = function (fig, msg) {\n    fig.image_mode = msg['mode'];\n};\n\nmpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n    for (var key in msg) {\n        if (!(key in fig.buttons)) {\n            continue;\n        }\n        fig.buttons[key].disabled = !msg[key];\n        fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n    }\n};\n\nmpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n    if (msg['mode'] === 'PAN') {\n        fig.buttons['Pan'].classList.add('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    } else if (msg['mode'] === 'ZOOM') {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.add('active');\n    } else {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    }\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Called whenever the canvas gets updated.\n    this.send_message('ack', {});\n};\n\n// A function to construct a web socket function for onmessage handling.\n// Called in the figure constructor.\nmpl.figure.prototype._make_on_message_function = function (fig) {\n    return function socket_on_message(evt) {\n        if (evt.data instanceof Blob) {\n            var img = evt.data;\n            if (img.type !== 'image/png') {\n                /* FIXME: We get \"Resource interpreted as Image but\n                 * transferred with MIME type text/plain:\" errors on\n                 * Chrome.  But how to set the MIME type?  It doesn't seem\n                 * to be part of the websocket stream */\n                img.type = 'image/png';\n            }\n\n            /* Free the memory for the previous frames */\n            if (fig.imageObj.src) {\n                (window.URL || window.webkitURL).revokeObjectURL(\n                    fig.imageObj.src\n                );\n            }\n\n            fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n                img\n            );\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        } else if (\n            typeof evt.data === 'string' &&\n            evt.data.slice(0, 21) === 'data:image/png;base64'\n        ) {\n            fig.imageObj.src = evt.data;\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        }\n\n        var msg = JSON.parse(evt.data);\n        var msg_type = msg['type'];\n\n        // Call the  \"handle_{type}\" callback, which takes\n        // the figure and JSON message as its only arguments.\n        try {\n            var callback = fig['handle_' + msg_type];\n        } catch (e) {\n            console.log(\n                \"No handler for the '\" + msg_type + \"' message type: \",\n                msg\n            );\n            return;\n        }\n\n        if (callback) {\n            try {\n                // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n                callback(fig, msg);\n            } catch (e) {\n                console.log(\n                    \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n                    e,\n                    e.stack,\n                    msg\n                );\n            }\n        }\n    };\n};\n\n// from https://stackoverflow.com/questions/1114465/getting-mouse-location-in-canvas\nmpl.findpos = function (e) {\n    //this section is from http://www.quirksmode.org/js/events_properties.html\n    var targ;\n    if (!e) {\n        e = window.event;\n    }\n    if (e.target) {\n        targ = e.target;\n    } else if (e.srcElement) {\n        targ = e.srcElement;\n    }\n    if (targ.nodeType === 3) {\n        // defeat Safari bug\n        targ = targ.parentNode;\n    }\n\n    // pageX,Y are the mouse positions relative to the document\n    var boundingRect = targ.getBoundingClientRect();\n    var x = e.pageX - (boundingRect.left + document.body.scrollLeft);\n    var y = e.pageY - (boundingRect.top + document.body.scrollTop);\n\n    return { x: x, y: y };\n};\n\n/*\n * return a copy of an object with only non-object keys\n * we need this to avoid circular references\n * https://stackoverflow.com/a/24161582/3208463\n */\nfunction simpleKeys(original) {\n    return Object.keys(original).reduce(function (obj, key) {\n        if (typeof original[key] !== 'object') {\n            obj[key] = original[key];\n        }\n        return obj;\n    }, {});\n}\n\nmpl.figure.prototype.mouse_event = function (event, name) {\n    var canvas_pos = mpl.findpos(event);\n\n    if (name === 'button_press') {\n        this.canvas.focus();\n        this.canvas_div.focus();\n    }\n\n    var x = canvas_pos.x * this.ratio;\n    var y = canvas_pos.y * this.ratio;\n\n    this.send_message(name, {\n        x: x,\n        y: y,\n        button: event.button,\n        step: event.step,\n        guiEvent: simpleKeys(event),\n    });\n\n    /* This prevents the web browser from automatically changing to\n     * the text insertion cursor when the button is pressed.  We want\n     * to control all of the cursor setting manually through the\n     * 'cursor' event from matplotlib */\n    event.preventDefault();\n    return false;\n};\n\nmpl.figure.prototype._key_event_extra = function (_event, _name) {\n    // Handle any extra behaviour associated with a key event\n};\n\nmpl.figure.prototype.key_event = function (event, name) {\n    // Prevent repeat events\n    if (name === 'key_press') {\n        if (event.key === this._key) {\n            return;\n        } else {\n            this._key = event.key;\n        }\n    }\n    if (name === 'key_release') {\n        this._key = null;\n    }\n\n    var value = '';\n    if (event.ctrlKey && event.key !== 'Control') {\n        value += 'ctrl+';\n    }\n    else if (event.altKey && event.key !== 'Alt') {\n        value += 'alt+';\n    }\n    else if (event.shiftKey && event.key !== 'Shift') {\n        value += 'shift+';\n    }\n\n    value += 'k' + event.key;\n\n    this._key_event_extra(event, name);\n\n    this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n    return false;\n};\n\nmpl.figure.prototype.toolbar_button_onclick = function (name) {\n    if (name === 'download') {\n        this.handle_save(this, null);\n    } else {\n        this.send_message('toolbar_button', { name: name });\n    }\n};\n\nmpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n    this.message.textContent = tooltip;\n};\n\n///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n// prettier-ignore\nvar _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\nmpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home icon-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left icon-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right icon-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows icon-move\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis\", \"fa fa-square-o icon-check-empty\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o icon-save\", \"download\"]];\n\nmpl.extensions = [\"eps\", \"jpeg\", \"pgf\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\"];\n\nmpl.default_extension = \"png\";/* global mpl */\n\nvar comm_websocket_adapter = function (comm) {\n    // Create a \"websocket\"-like object which calls the given IPython comm\n    // object with the appropriate methods. Currently this is a non binary\n    // socket, so there is still some room for performance tuning.\n    var ws = {};\n\n    ws.binaryType = comm.kernel.ws.binaryType;\n    ws.readyState = comm.kernel.ws.readyState;\n    function updateReadyState(_event) {\n        if (comm.kernel.ws) {\n            ws.readyState = comm.kernel.ws.readyState;\n        } else {\n            ws.readyState = 3; // Closed state.\n        }\n    }\n    comm.kernel.ws.addEventListener('open', updateReadyState);\n    comm.kernel.ws.addEventListener('close', updateReadyState);\n    comm.kernel.ws.addEventListener('error', updateReadyState);\n\n    ws.close = function () {\n        comm.close();\n    };\n    ws.send = function (m) {\n        //console.log('sending', m);\n        comm.send(m);\n    };\n    // Register the callback with on_msg.\n    comm.on_msg(function (msg) {\n        //console.log('receiving', msg['content']['data'], msg);\n        var data = msg['content']['data'];\n        if (data['blob'] !== undefined) {\n            data = {\n                data: new Blob(msg['buffers'], { type: data['blob'] }),\n            };\n        }\n        // Pass the mpl event to the overridden (by mpl) onmessage function.\n        ws.onmessage(data);\n    });\n    return ws;\n};\n\nmpl.mpl_figure_comm = function (comm, msg) {\n    // This is the function which gets called when the mpl process\n    // starts-up an IPython Comm through the \"matplotlib\" channel.\n\n    var id = msg.content.data.id;\n    // Get hold of the div created by the display call when the Comm\n    // socket was opened in Python.\n    var element = document.getElementById(id);\n    var ws_proxy = comm_websocket_adapter(comm);\n\n    function ondownload(figure, _format) {\n        window.open(figure.canvas.toDataURL());\n    }\n\n    var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n\n    // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n    // web socket which is closed, not our websocket->open comm proxy.\n    ws_proxy.onopen();\n\n    fig.parent_element = element;\n    fig.cell_info = mpl.find_output_cell(\"<div id='\" + id + \"'></div>\");\n    if (!fig.cell_info) {\n        console.error('Failed to find cell for figure', id, fig);\n        return;\n    }\n    fig.cell_info[0].output_area.element.on(\n        'cleared',\n        { fig: fig },\n        fig._remove_fig_handler\n    );\n};\n\nmpl.figure.prototype.handle_close = function (fig, msg) {\n    var width = fig.canvas.width / fig.ratio;\n    fig.cell_info[0].output_area.element.off(\n        'cleared',\n        fig._remove_fig_handler\n    );\n    fig.resizeObserverInstance.unobserve(fig.canvas_div);\n\n    // Update the output cell to use the data from the current canvas.\n    fig.push_to_output();\n    var dataURL = fig.canvas.toDataURL();\n    // Re-enable the keyboard manager in IPython - without this line, in FF,\n    // the notebook keyboard shortcuts fail.\n    IPython.keyboard_manager.enable();\n    fig.parent_element.innerHTML =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n    fig.close_ws(fig, msg);\n};\n\nmpl.figure.prototype.close_ws = function (fig, msg) {\n    fig.send_message('closing', msg);\n    // fig.ws.close()\n};\n\nmpl.figure.prototype.push_to_output = function (_remove_interactive) {\n    // Turn the data on the canvas into data in the output cell.\n    var width = this.canvas.width / this.ratio;\n    var dataURL = this.canvas.toDataURL();\n    this.cell_info[1]['text/html'] =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Tell IPython that the notebook contents must change.\n    IPython.notebook.set_dirty(true);\n    this.send_message('ack', {});\n    var fig = this;\n    // Wait a second, then push the new image to the DOM so\n    // that it is saved nicely (might be nice to debounce this).\n    setTimeout(function () {\n        fig.push_to_output();\n    }, 1000);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'btn-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'btn-group';\n    var button;\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'btn-group';\n            continue;\n        }\n\n        button = fig.buttons[name] = document.createElement('button');\n        button.classList = 'btn btn-default';\n        button.href = '#';\n        button.title = name;\n        button.innerHTML = '<i class=\"fa ' + image + ' fa-lg\"></i>';\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    // Add the status bar.\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message pull-right';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n\n    // Add the close button to the window.\n    var buttongrp = document.createElement('div');\n    buttongrp.classList = 'btn-group inline pull-right';\n    button = document.createElement('button');\n    button.classList = 'btn btn-mini btn-primary';\n    button.href = '#';\n    button.title = 'Stop Interaction';\n    button.innerHTML = '<i class=\"fa fa-power-off icon-remove icon-large\"></i>';\n    button.addEventListener('click', function (_evt) {\n        fig.handle_close(fig, {});\n    });\n    button.addEventListener(\n        'mouseover',\n        on_mouseover_closure('Stop Interaction')\n    );\n    buttongrp.appendChild(button);\n    var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n    titlebar.insertBefore(buttongrp, titlebar.firstChild);\n};\n\nmpl.figure.prototype._remove_fig_handler = function (event) {\n    var fig = event.data.fig;\n    if (event.target !== this) {\n        // Ignore bubbled events from children.\n        return;\n    }\n    fig.close_ws(fig, {});\n};\n\nmpl.figure.prototype._root_extra_style = function (el) {\n    el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n};\n\nmpl.figure.prototype._canvas_extra_style = function (el) {\n    // this is important to make the div 'focusable\n    el.setAttribute('tabindex', 0);\n    // reach out to IPython and tell the keyboard manager to turn it's self\n    // off when our div gets focus\n\n    // location in version 3\n    if (IPython.notebook.keyboard_manager) {\n        IPython.notebook.keyboard_manager.register_events(el);\n    } else {\n        // location in version 2\n        IPython.keyboard_manager.register_events(el);\n    }\n};\n\nmpl.figure.prototype._key_event_extra = function (event, _name) {\n    // Check for shift+enter\n    if (event.shiftKey && event.which === 13) {\n        this.canvas_div.blur();\n        // select the cell after this one\n        var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n        IPython.notebook.select(index + 1);\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    fig.ondownload(fig, null);\n};\n\nmpl.find_output_cell = function (html_output) {\n    // Return the cell and output element which can be found *uniquely* in the notebook.\n    // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n    // IPython event is triggered only after the cells have been serialised, which for\n    // our purposes (turning an active figure into a static one), is too late.\n    var cells = IPython.notebook.get_cells();\n    var ncells = cells.length;\n    for (var i = 0; i < ncells; i++) {\n        var cell = cells[i];\n        if (cell.cell_type === 'code') {\n            for (var j = 0; j < cell.output_area.outputs.length; j++) {\n                var data = cell.output_area.outputs[j];\n                if (data.data) {\n                    // IPython >= 3 moved mimebundle to data attribute of output\n                    data = data.data;\n                }\n                if (data['text/html'] === html_output) {\n                    return [cell, data, j];\n                }\n            }\n        }\n    }\n};\n\n// Register the function which deals with the matplotlib target/channel.\n// The kernel may be null if the page has been refreshed.\nif (IPython.notebook.kernel !== null) {\n    IPython.notebook.kernel.comm_manager.register_target(\n        'matplotlib',\n        mpl.mpl_figure_comm\n    );\n}\n",
      "text/plain": [
       "<IPython.core.display.Javascript object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<img src=\"data:image/png;base64,[encoded data, 62452 characters]\" width=\"640\">"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "val = fitAnalyser.get_fit_value(fitResult)\n",
    "std = fitAnalyser.get_fit_std(fitResult)\n",
    "\n",
    "fitCurve = fitAnalyser.eval(fitResult, x=np.arange(300), y=np.arange(300), dask=\"parallelized\").load()\n",
    "\n",
    "# dataKey = 'sigmax'\n",
    "# dataKey = 'centerx'\n",
    "# dataKey = 'sigmay'\n",
    "dataKey = 'centery'\n",
    "\n",
    "# val_mean = val[dataKey].mean(dim='runs')\n",
    "# std_mean = val[dataKey].std(dim='runs')\n",
    "\n",
    "val_mean = calculate_mean(val[dataKey])\n",
    "std_mean = calculate_std(val[dataKey])\n",
    "\n",
    "fig = plt.figure()\n",
    "ax = fig.gca()\n",
    "\n",
    "val_mean.plot.errorbar(yerr=std_mean, fmt='--ob')\n",
    "\n",
    "plt.grid()\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 103,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/javascript": "/* Put everything inside the global mpl namespace */\n/* global mpl */\nwindow.mpl = {};\n\nmpl.get_websocket_type = function () {\n    if (typeof WebSocket !== 'undefined') {\n        return WebSocket;\n    } else if (typeof MozWebSocket !== 'undefined') {\n        return MozWebSocket;\n    } else {\n        alert(\n            'Your browser does not have WebSocket support. ' +\n                'Please try Chrome, Safari or Firefox ≥ 6. ' +\n                'Firefox 4 and 5 are also supported but you ' +\n                'have to enable WebSockets in about:config.'\n        );\n    }\n};\n\nmpl.figure = function (figure_id, websocket, ondownload, parent_element) {\n    this.id = figure_id;\n\n    this.ws = websocket;\n\n    this.supports_binary = this.ws.binaryType !== undefined;\n\n    if (!this.supports_binary) {\n        var warnings = document.getElementById('mpl-warnings');\n        if (warnings) {\n            warnings.style.display = 'block';\n            warnings.textContent =\n                'This browser does not support binary websocket messages. ' +\n                'Performance may be slow.';\n        }\n    }\n\n    this.imageObj = new Image();\n\n    this.context = undefined;\n    this.message = undefined;\n    this.canvas = undefined;\n    this.rubberband_canvas = undefined;\n    this.rubberband_context = undefined;\n    this.format_dropdown = undefined;\n\n    this.image_mode = 'full';\n\n    this.root = document.createElement('div');\n    this.root.setAttribute('style', 'display: inline-block');\n    this._root_extra_style(this.root);\n\n    parent_element.appendChild(this.root);\n\n    this._init_header(this);\n    this._init_canvas(this);\n    this._init_toolbar(this);\n\n    var fig = this;\n\n    this.waiting = false;\n\n    this.ws.onopen = function () {\n        fig.send_message('supports_binary', { value: fig.supports_binary });\n        fig.send_message('send_image_mode', {});\n        if (fig.ratio !== 1) {\n            fig.send_message('set_device_pixel_ratio', {\n                device_pixel_ratio: fig.ratio,\n            });\n        }\n        fig.send_message('refresh', {});\n    };\n\n    this.imageObj.onload = function () {\n        if (fig.image_mode === 'full') {\n            // Full images could contain transparency (where diff images\n            // almost always do), so we need to clear the canvas so that\n            // there is no ghosting.\n            fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n        }\n        fig.context.drawImage(fig.imageObj, 0, 0);\n    };\n\n    this.imageObj.onunload = function () {\n        fig.ws.close();\n    };\n\n    this.ws.onmessage = this._make_on_message_function(this);\n\n    this.ondownload = ondownload;\n};\n\nmpl.figure.prototype._init_header = function () {\n    var titlebar = document.createElement('div');\n    titlebar.classList =\n        'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n    var titletext = document.createElement('div');\n    titletext.classList = 'ui-dialog-title';\n    titletext.setAttribute(\n        'style',\n        'width: 100%; text-align: center; padding: 3px;'\n    );\n    titlebar.appendChild(titletext);\n    this.root.appendChild(titlebar);\n    this.header = titletext;\n};\n\nmpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._init_canvas = function () {\n    var fig = this;\n\n    var canvas_div = (this.canvas_div = document.createElement('div'));\n    canvas_div.setAttribute(\n        'style',\n        'border: 1px solid #ddd;' +\n            'box-sizing: content-box;' +\n            'clear: both;' +\n            'min-height: 1px;' +\n            'min-width: 1px;' +\n            'outline: 0;' +\n            'overflow: hidden;' +\n            'position: relative;' +\n            'resize: both;'\n    );\n\n    function on_keyboard_event_closure(name) {\n        return function (event) {\n            return fig.key_event(event, name);\n        };\n    }\n\n    canvas_div.addEventListener(\n        'keydown',\n        on_keyboard_event_closure('key_press')\n    );\n    canvas_div.addEventListener(\n        'keyup',\n        on_keyboard_event_closure('key_release')\n    );\n\n    this._canvas_extra_style(canvas_div);\n    this.root.appendChild(canvas_div);\n\n    var canvas = (this.canvas = document.createElement('canvas'));\n    canvas.classList.add('mpl-canvas');\n    canvas.setAttribute('style', 'box-sizing: content-box;');\n\n    this.context = canvas.getContext('2d');\n\n    var backingStore =\n        this.context.backingStorePixelRatio ||\n        this.context.webkitBackingStorePixelRatio ||\n        this.context.mozBackingStorePixelRatio ||\n        this.context.msBackingStorePixelRatio ||\n        this.context.oBackingStorePixelRatio ||\n        this.context.backingStorePixelRatio ||\n        1;\n\n    this.ratio = (window.devicePixelRatio || 1) / backingStore;\n\n    var rubberband_canvas = (this.rubberband_canvas = document.createElement(\n        'canvas'\n    ));\n    rubberband_canvas.setAttribute(\n        'style',\n        'box-sizing: content-box; position: absolute; left: 0; top: 0; z-index: 1;'\n    );\n\n    // Apply a ponyfill if ResizeObserver is not implemented by browser.\n    if (this.ResizeObserver === undefined) {\n        if (window.ResizeObserver !== undefined) {\n            this.ResizeObserver = window.ResizeObserver;\n        } else {\n            var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n            this.ResizeObserver = obs.ResizeObserver;\n        }\n    }\n\n    this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n        var nentries = entries.length;\n        for (var i = 0; i < nentries; i++) {\n            var entry = entries[i];\n            var width, height;\n            if (entry.contentBoxSize) {\n                if (entry.contentBoxSize instanceof Array) {\n                    // Chrome 84 implements new version of spec.\n                    width = entry.contentBoxSize[0].inlineSize;\n                    height = entry.contentBoxSize[0].blockSize;\n                } else {\n                    // Firefox implements old version of spec.\n                    width = entry.contentBoxSize.inlineSize;\n                    height = entry.contentBoxSize.blockSize;\n                }\n            } else {\n                // Chrome <84 implements even older version of spec.\n                width = entry.contentRect.width;\n                height = entry.contentRect.height;\n            }\n\n            // Keep the size of the canvas and rubber band canvas in sync with\n            // the canvas container.\n            if (entry.devicePixelContentBoxSize) {\n                // Chrome 84 implements new version of spec.\n                canvas.setAttribute(\n                    'width',\n                    entry.devicePixelContentBoxSize[0].inlineSize\n                );\n                canvas.setAttribute(\n                    'height',\n                    entry.devicePixelContentBoxSize[0].blockSize\n                );\n            } else {\n                canvas.setAttribute('width', width * fig.ratio);\n                canvas.setAttribute('height', height * fig.ratio);\n            }\n            canvas.setAttribute(\n                'style',\n                'width: ' + width + 'px; height: ' + height + 'px;'\n            );\n\n            rubberband_canvas.setAttribute('width', width);\n            rubberband_canvas.setAttribute('height', height);\n\n            // And update the size in Python. We ignore the initial 0/0 size\n            // that occurs as the element is placed into the DOM, which should\n            // otherwise not happen due to the minimum size styling.\n            if (fig.ws.readyState == 1 && width != 0 && height != 0) {\n                fig.request_resize(width, height);\n            }\n        }\n    });\n    this.resizeObserverInstance.observe(canvas_div);\n\n    function on_mouse_event_closure(name) {\n        return function (event) {\n            return fig.mouse_event(event, name);\n        };\n    }\n\n    rubberband_canvas.addEventListener(\n        'mousedown',\n        on_mouse_event_closure('button_press')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseup',\n        on_mouse_event_closure('button_release')\n    );\n    rubberband_canvas.addEventListener(\n        'dblclick',\n        on_mouse_event_closure('dblclick')\n    );\n    // Throttle sequential mouse events to 1 every 20ms.\n    rubberband_canvas.addEventListener(\n        'mousemove',\n        on_mouse_event_closure('motion_notify')\n    );\n\n    rubberband_canvas.addEventListener(\n        'mouseenter',\n        on_mouse_event_closure('figure_enter')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseleave',\n        on_mouse_event_closure('figure_leave')\n    );\n\n    canvas_div.addEventListener('wheel', function (event) {\n        if (event.deltaY < 0) {\n            event.step = 1;\n        } else {\n            event.step = -1;\n        }\n        on_mouse_event_closure('scroll')(event);\n    });\n\n    canvas_div.appendChild(canvas);\n    canvas_div.appendChild(rubberband_canvas);\n\n    this.rubberband_context = rubberband_canvas.getContext('2d');\n    this.rubberband_context.strokeStyle = '#000000';\n\n    this._resize_canvas = function (width, height, forward) {\n        if (forward) {\n            canvas_div.style.width = width + 'px';\n            canvas_div.style.height = height + 'px';\n        }\n    };\n\n    // Disable right mouse context menu.\n    this.rubberband_canvas.addEventListener('contextmenu', function (_e) {\n        event.preventDefault();\n        return false;\n    });\n\n    function set_focus() {\n        canvas.focus();\n        canvas_div.focus();\n    }\n\n    window.setTimeout(set_focus, 100);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'mpl-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'mpl-button-group';\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'mpl-button-group';\n            continue;\n        }\n\n        var button = (fig.buttons[name] = document.createElement('button'));\n        button.classList = 'mpl-widget';\n        button.setAttribute('role', 'button');\n        button.setAttribute('aria-disabled', 'false');\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n\n        var icon_img = document.createElement('img');\n        icon_img.src = '_images/' + image + '.png';\n        icon_img.srcset = '_images/' + image + '_large.png 2x';\n        icon_img.alt = tooltip;\n        button.appendChild(icon_img);\n\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    var fmt_picker = document.createElement('select');\n    fmt_picker.classList = 'mpl-widget';\n    toolbar.appendChild(fmt_picker);\n    this.format_dropdown = fmt_picker;\n\n    for (var ind in mpl.extensions) {\n        var fmt = mpl.extensions[ind];\n        var option = document.createElement('option');\n        option.selected = fmt === mpl.default_extension;\n        option.innerHTML = fmt;\n        fmt_picker.appendChild(option);\n    }\n\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n};\n\nmpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n    // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n    // which will in turn request a refresh of the image.\n    this.send_message('resize', { width: x_pixels, height: y_pixels });\n};\n\nmpl.figure.prototype.send_message = function (type, properties) {\n    properties['type'] = type;\n    properties['figure_id'] = this.id;\n    this.ws.send(JSON.stringify(properties));\n};\n\nmpl.figure.prototype.send_draw_message = function () {\n    if (!this.waiting) {\n        this.waiting = true;\n        this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    var format_dropdown = fig.format_dropdown;\n    var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n    fig.ondownload(fig, format);\n};\n\nmpl.figure.prototype.handle_resize = function (fig, msg) {\n    var size = msg['size'];\n    if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n        fig._resize_canvas(size[0], size[1], msg['forward']);\n        fig.send_message('refresh', {});\n    }\n};\n\nmpl.figure.prototype.handle_rubberband = function (fig, msg) {\n    var x0 = msg['x0'] / fig.ratio;\n    var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n    var x1 = msg['x1'] / fig.ratio;\n    var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n    x0 = Math.floor(x0) + 0.5;\n    y0 = Math.floor(y0) + 0.5;\n    x1 = Math.floor(x1) + 0.5;\n    y1 = Math.floor(y1) + 0.5;\n    var min_x = Math.min(x0, x1);\n    var min_y = Math.min(y0, y1);\n    var width = Math.abs(x1 - x0);\n    var height = Math.abs(y1 - y0);\n\n    fig.rubberband_context.clearRect(\n        0,\n        0,\n        fig.canvas.width / fig.ratio,\n        fig.canvas.height / fig.ratio\n    );\n\n    fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n};\n\nmpl.figure.prototype.handle_figure_label = function (fig, msg) {\n    // Updates the figure title.\n    fig.header.textContent = msg['label'];\n};\n\nmpl.figure.prototype.handle_cursor = function (fig, msg) {\n    fig.rubberband_canvas.style.cursor = msg['cursor'];\n};\n\nmpl.figure.prototype.handle_message = function (fig, msg) {\n    fig.message.textContent = msg['message'];\n};\n\nmpl.figure.prototype.handle_draw = function (fig, _msg) {\n    // Request the server to send over a new figure.\n    fig.send_draw_message();\n};\n\nmpl.figure.prototype.handle_image_mode = function (fig, msg) {\n    fig.image_mode = msg['mode'];\n};\n\nmpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n    for (var key in msg) {\n        if (!(key in fig.buttons)) {\n            continue;\n        }\n        fig.buttons[key].disabled = !msg[key];\n        fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n    }\n};\n\nmpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n    if (msg['mode'] === 'PAN') {\n        fig.buttons['Pan'].classList.add('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    } else if (msg['mode'] === 'ZOOM') {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.add('active');\n    } else {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    }\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Called whenever the canvas gets updated.\n    this.send_message('ack', {});\n};\n\n// A function to construct a web socket function for onmessage handling.\n// Called in the figure constructor.\nmpl.figure.prototype._make_on_message_function = function (fig) {\n    return function socket_on_message(evt) {\n        if (evt.data instanceof Blob) {\n            var img = evt.data;\n            if (img.type !== 'image/png') {\n                /* FIXME: We get \"Resource interpreted as Image but\n                 * transferred with MIME type text/plain:\" errors on\n                 * Chrome.  But how to set the MIME type?  It doesn't seem\n                 * to be part of the websocket stream */\n                img.type = 'image/png';\n            }\n\n            /* Free the memory for the previous frames */\n            if (fig.imageObj.src) {\n                (window.URL || window.webkitURL).revokeObjectURL(\n                    fig.imageObj.src\n                );\n            }\n\n            fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n                img\n            );\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        } else if (\n            typeof evt.data === 'string' &&\n            evt.data.slice(0, 21) === 'data:image/png;base64'\n        ) {\n            fig.imageObj.src = evt.data;\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        }\n\n        var msg = JSON.parse(evt.data);\n        var msg_type = msg['type'];\n\n        // Call the  \"handle_{type}\" callback, which takes\n        // the figure and JSON message as its only arguments.\n        try {\n            var callback = fig['handle_' + msg_type];\n        } catch (e) {\n            console.log(\n                \"No handler for the '\" + msg_type + \"' message type: \",\n                msg\n            );\n            return;\n        }\n\n        if (callback) {\n            try {\n                // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n                callback(fig, msg);\n            } catch (e) {\n                console.log(\n                    \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n                    e,\n                    e.stack,\n                    msg\n                );\n            }\n        }\n    };\n};\n\n// from https://stackoverflow.com/questions/1114465/getting-mouse-location-in-canvas\nmpl.findpos = function (e) {\n    //this section is from http://www.quirksmode.org/js/events_properties.html\n    var targ;\n    if (!e) {\n        e = window.event;\n    }\n    if (e.target) {\n        targ = e.target;\n    } else if (e.srcElement) {\n        targ = e.srcElement;\n    }\n    if (targ.nodeType === 3) {\n        // defeat Safari bug\n        targ = targ.parentNode;\n    }\n\n    // pageX,Y are the mouse positions relative to the document\n    var boundingRect = targ.getBoundingClientRect();\n    var x = e.pageX - (boundingRect.left + document.body.scrollLeft);\n    var y = e.pageY - (boundingRect.top + document.body.scrollTop);\n\n    return { x: x, y: y };\n};\n\n/*\n * return a copy of an object with only non-object keys\n * we need this to avoid circular references\n * https://stackoverflow.com/a/24161582/3208463\n */\nfunction simpleKeys(original) {\n    return Object.keys(original).reduce(function (obj, key) {\n        if (typeof original[key] !== 'object') {\n            obj[key] = original[key];\n        }\n        return obj;\n    }, {});\n}\n\nmpl.figure.prototype.mouse_event = function (event, name) {\n    var canvas_pos = mpl.findpos(event);\n\n    if (name === 'button_press') {\n        this.canvas.focus();\n        this.canvas_div.focus();\n    }\n\n    var x = canvas_pos.x * this.ratio;\n    var y = canvas_pos.y * this.ratio;\n\n    this.send_message(name, {\n        x: x,\n        y: y,\n        button: event.button,\n        step: event.step,\n        guiEvent: simpleKeys(event),\n    });\n\n    /* This prevents the web browser from automatically changing to\n     * the text insertion cursor when the button is pressed.  We want\n     * to control all of the cursor setting manually through the\n     * 'cursor' event from matplotlib */\n    event.preventDefault();\n    return false;\n};\n\nmpl.figure.prototype._key_event_extra = function (_event, _name) {\n    // Handle any extra behaviour associated with a key event\n};\n\nmpl.figure.prototype.key_event = function (event, name) {\n    // Prevent repeat events\n    if (name === 'key_press') {\n        if (event.key === this._key) {\n            return;\n        } else {\n            this._key = event.key;\n        }\n    }\n    if (name === 'key_release') {\n        this._key = null;\n    }\n\n    var value = '';\n    if (event.ctrlKey && event.key !== 'Control') {\n        value += 'ctrl+';\n    }\n    else if (event.altKey && event.key !== 'Alt') {\n        value += 'alt+';\n    }\n    else if (event.shiftKey && event.key !== 'Shift') {\n        value += 'shift+';\n    }\n\n    value += 'k' + event.key;\n\n    this._key_event_extra(event, name);\n\n    this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n    return false;\n};\n\nmpl.figure.prototype.toolbar_button_onclick = function (name) {\n    if (name === 'download') {\n        this.handle_save(this, null);\n    } else {\n        this.send_message('toolbar_button', { name: name });\n    }\n};\n\nmpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n    this.message.textContent = tooltip;\n};\n\n///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n// prettier-ignore\nvar _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\nmpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home icon-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left icon-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right icon-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows icon-move\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis\", \"fa fa-square-o icon-check-empty\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o icon-save\", \"download\"]];\n\nmpl.extensions = [\"eps\", \"jpeg\", \"pgf\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\"];\n\nmpl.default_extension = \"png\";/* global mpl */\n\nvar comm_websocket_adapter = function (comm) {\n    // Create a \"websocket\"-like object which calls the given IPython comm\n    // object with the appropriate methods. Currently this is a non binary\n    // socket, so there is still some room for performance tuning.\n    var ws = {};\n\n    ws.binaryType = comm.kernel.ws.binaryType;\n    ws.readyState = comm.kernel.ws.readyState;\n    function updateReadyState(_event) {\n        if (comm.kernel.ws) {\n            ws.readyState = comm.kernel.ws.readyState;\n        } else {\n            ws.readyState = 3; // Closed state.\n        }\n    }\n    comm.kernel.ws.addEventListener('open', updateReadyState);\n    comm.kernel.ws.addEventListener('close', updateReadyState);\n    comm.kernel.ws.addEventListener('error', updateReadyState);\n\n    ws.close = function () {\n        comm.close();\n    };\n    ws.send = function (m) {\n        //console.log('sending', m);\n        comm.send(m);\n    };\n    // Register the callback with on_msg.\n    comm.on_msg(function (msg) {\n        //console.log('receiving', msg['content']['data'], msg);\n        var data = msg['content']['data'];\n        if (data['blob'] !== undefined) {\n            data = {\n                data: new Blob(msg['buffers'], { type: data['blob'] }),\n            };\n        }\n        // Pass the mpl event to the overridden (by mpl) onmessage function.\n        ws.onmessage(data);\n    });\n    return ws;\n};\n\nmpl.mpl_figure_comm = function (comm, msg) {\n    // This is the function which gets called when the mpl process\n    // starts-up an IPython Comm through the \"matplotlib\" channel.\n\n    var id = msg.content.data.id;\n    // Get hold of the div created by the display call when the Comm\n    // socket was opened in Python.\n    var element = document.getElementById(id);\n    var ws_proxy = comm_websocket_adapter(comm);\n\n    function ondownload(figure, _format) {\n        window.open(figure.canvas.toDataURL());\n    }\n\n    var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n\n    // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n    // web socket which is closed, not our websocket->open comm proxy.\n    ws_proxy.onopen();\n\n    fig.parent_element = element;\n    fig.cell_info = mpl.find_output_cell(\"<div id='\" + id + \"'></div>\");\n    if (!fig.cell_info) {\n        console.error('Failed to find cell for figure', id, fig);\n        return;\n    }\n    fig.cell_info[0].output_area.element.on(\n        'cleared',\n        { fig: fig },\n        fig._remove_fig_handler\n    );\n};\n\nmpl.figure.prototype.handle_close = function (fig, msg) {\n    var width = fig.canvas.width / fig.ratio;\n    fig.cell_info[0].output_area.element.off(\n        'cleared',\n        fig._remove_fig_handler\n    );\n    fig.resizeObserverInstance.unobserve(fig.canvas_div);\n\n    // Update the output cell to use the data from the current canvas.\n    fig.push_to_output();\n    var dataURL = fig.canvas.toDataURL();\n    // Re-enable the keyboard manager in IPython - without this line, in FF,\n    // the notebook keyboard shortcuts fail.\n    IPython.keyboard_manager.enable();\n    fig.parent_element.innerHTML =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n    fig.close_ws(fig, msg);\n};\n\nmpl.figure.prototype.close_ws = function (fig, msg) {\n    fig.send_message('closing', msg);\n    // fig.ws.close()\n};\n\nmpl.figure.prototype.push_to_output = function (_remove_interactive) {\n    // Turn the data on the canvas into data in the output cell.\n    var width = this.canvas.width / this.ratio;\n    var dataURL = this.canvas.toDataURL();\n    this.cell_info[1]['text/html'] =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Tell IPython that the notebook contents must change.\n    IPython.notebook.set_dirty(true);\n    this.send_message('ack', {});\n    var fig = this;\n    // Wait a second, then push the new image to the DOM so\n    // that it is saved nicely (might be nice to debounce this).\n    setTimeout(function () {\n        fig.push_to_output();\n    }, 1000);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'btn-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'btn-group';\n    var button;\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'btn-group';\n            continue;\n        }\n\n        button = fig.buttons[name] = document.createElement('button');\n        button.classList = 'btn btn-default';\n        button.href = '#';\n        button.title = name;\n        button.innerHTML = '<i class=\"fa ' + image + ' fa-lg\"></i>';\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    // Add the status bar.\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message pull-right';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n\n    // Add the close button to the window.\n    var buttongrp = document.createElement('div');\n    buttongrp.classList = 'btn-group inline pull-right';\n    button = document.createElement('button');\n    button.classList = 'btn btn-mini btn-primary';\n    button.href = '#';\n    button.title = 'Stop Interaction';\n    button.innerHTML = '<i class=\"fa fa-power-off icon-remove icon-large\"></i>';\n    button.addEventListener('click', function (_evt) {\n        fig.handle_close(fig, {});\n    });\n    button.addEventListener(\n        'mouseover',\n        on_mouseover_closure('Stop Interaction')\n    );\n    buttongrp.appendChild(button);\n    var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n    titlebar.insertBefore(buttongrp, titlebar.firstChild);\n};\n\nmpl.figure.prototype._remove_fig_handler = function (event) {\n    var fig = event.data.fig;\n    if (event.target !== this) {\n        // Ignore bubbled events from children.\n        return;\n    }\n    fig.close_ws(fig, {});\n};\n\nmpl.figure.prototype._root_extra_style = function (el) {\n    el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n};\n\nmpl.figure.prototype._canvas_extra_style = function (el) {\n    // this is important to make the div 'focusable\n    el.setAttribute('tabindex', 0);\n    // reach out to IPython and tell the keyboard manager to turn it's self\n    // off when our div gets focus\n\n    // location in version 3\n    if (IPython.notebook.keyboard_manager) {\n        IPython.notebook.keyboard_manager.register_events(el);\n    } else {\n        // location in version 2\n        IPython.keyboard_manager.register_events(el);\n    }\n};\n\nmpl.figure.prototype._key_event_extra = function (event, _name) {\n    // Check for shift+enter\n    if (event.shiftKey && event.which === 13) {\n        this.canvas_div.blur();\n        // select the cell after this one\n        var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n        IPython.notebook.select(index + 1);\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    fig.ondownload(fig, null);\n};\n\nmpl.find_output_cell = function (html_output) {\n    // Return the cell and output element which can be found *uniquely* in the notebook.\n    // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n    // IPython event is triggered only after the cells have been serialised, which for\n    // our purposes (turning an active figure into a static one), is too late.\n    var cells = IPython.notebook.get_cells();\n    var ncells = cells.length;\n    for (var i = 0; i < ncells; i++) {\n        var cell = cells[i];\n        if (cell.cell_type === 'code') {\n            for (var j = 0; j < cell.output_area.outputs.length; j++) {\n                var data = cell.output_area.outputs[j];\n                if (data.data) {\n                    // IPython >= 3 moved mimebundle to data attribute of output\n                    data = data.data;\n                }\n                if (data['text/html'] === html_output) {\n                    return [cell, data, j];\n                }\n            }\n        }\n    }\n};\n\n// Register the function which deals with the matplotlib target/channel.\n// The kernel may be null if the page has been refreshed.\nif (IPython.notebook.kernel !== null) {\n    IPython.notebook.kernel.comm_manager.register_target(\n        'matplotlib',\n        mpl.mpl_figure_comm\n    );\n}\n",
      "text/plain": [
       "<IPython.core.display.Javascript object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<img src=\"data:image/png;base64,[encoded data, 81832 characters]\" width=\"640\">"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "f = 224.9906 ± 0.4995 Hz\n"
     ]
    }
   ],
   "source": [
    "def damp_osci(t, t0, A, B, nu, gamma):\n",
    "    return A * np.exp(-gamma*t)*np.sin(2*np.pi*nu*(t-t0)) + B\n",
    "\n",
    "yvals     = val_mean#.sel(blink_on_time=slice(0.005, 0.025))\n",
    "yvals_std = std_mean#.sel(blink_on_time=slice(0.005, 0.025))\n",
    "xvals     = dataSet_cropOD[scanAxis[0]]#.sel(blink_on_time=slice(0.005, 0.025))\n",
    "\n",
    "fitted_qtys_1 = yvals.to_numpy()\n",
    "scan_para = xvals.to_numpy()\n",
    "fitted_qtys_err_1 = yvals_std.to_numpy()\n",
    "\n",
    "\n",
    "plt.figure()\n",
    "popt_x, pcov_x = curve_fit(damp_osci, scan_para, fitted_qtys_1, np.array([0, 3, 147, 3e2, 0.1]))\n",
    "freqdata = np.linspace(0.005, 20e-3, 500)\n",
    "plt.plot(freqdata, damp_osci(freqdata, *popt_x), 'g--',label='fit: t0=%5.3f, A=%5.3f, B=%5.3f, nu=%5.3f, Gamma=%5.3f' % tuple(popt_x))\n",
    "plt.errorbar(scan_para, fitted_qtys_1, yerr=fitted_qtys_err_1, fmt='or')\n",
    "plt.xlabel('hold time after switch on the trap (s)')\n",
    "plt.ylabel('Center along gravity direction (pixels)')\n",
    "plt.tight_layout()\n",
    "plt.grid(visible=1)\n",
    "#plt.ylim([0,750])\n",
    "#plt.xlim([0.004, 0.025])\n",
    "#plt.legend(prop={'size': 14})\n",
    "plt.show()\n",
    "\n",
    "f_x = popt_x[3]\n",
    "df_x = pcov_x[3][3]**0.5\n",
    "\n",
    "print('f = %.4f \\u00B1 %.4f Hz'% tuple([np.abs(f_x),df_x]))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Truncation: 0.775"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 128,
   "metadata": {},
   "outputs": [
    {
     "ename": "OSError",
     "evalue": "[Errno group not found: images] 'images'",
     "output_type": "error",
     "traceback": [
      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[1;31mOSError\u001b[0m                                   Traceback (most recent call last)",
      "Input \u001b[1;32mIn [128]\u001b[0m, in \u001b[0;36m<cell line: 5>\u001b[1;34m()\u001b[0m\n\u001b[0;32m      2\u001b[0m shotNum \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m0013\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[0;32m      3\u001b[0m filePath \u001b[38;5;241m=\u001b[39m folderPath \u001b[38;5;241m+\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m/\u001b[39m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;241m+\u001b[39m shotNum \u001b[38;5;241m+\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m/*.h5\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m----> 5\u001b[0m dataSetDict \u001b[38;5;241m=\u001b[39m {\n\u001b[0;32m      6\u001b[0m     dskey[groupList[i]]: read_hdf5_file(filePath, groupList[i], excludeAxis \u001b[38;5;241m=\u001b[39m [\u001b[38;5;124m'\u001b[39m\u001b[38;5;124msweep_start_freq\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124msweep_stop_freq\u001b[39m\u001b[38;5;124m'\u001b[39m])\n\u001b[0;32m      7\u001b[0m     \u001b[38;5;28;01mfor\u001b[39;00m i \u001b[38;5;129;01min\u001b[39;00m [\u001b[38;5;241m0\u001b[39m]\n\u001b[0;32m      8\u001b[0m }\n\u001b[0;32m     10\u001b[0m dataSet \u001b[38;5;241m=\u001b[39m dataSetDict[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mcamera_0\u001b[39m\u001b[38;5;124m\"\u001b[39m]\n\u001b[0;32m     12\u001b[0m print_scanAxis(dataSet)\n",
      "Input \u001b[1;32mIn [128]\u001b[0m, in \u001b[0;36m<dictcomp>\u001b[1;34m(.0)\u001b[0m\n\u001b[0;32m      2\u001b[0m shotNum \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m0013\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[0;32m      3\u001b[0m filePath \u001b[38;5;241m=\u001b[39m folderPath \u001b[38;5;241m+\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m/\u001b[39m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;241m+\u001b[39m shotNum \u001b[38;5;241m+\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m/*.h5\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[0;32m      5\u001b[0m dataSetDict \u001b[38;5;241m=\u001b[39m {\n\u001b[1;32m----> 6\u001b[0m     dskey[groupList[i]]: \u001b[43mread_hdf5_file\u001b[49m\u001b[43m(\u001b[49m\u001b[43mfilePath\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mgroupList\u001b[49m\u001b[43m[\u001b[49m\u001b[43mi\u001b[49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mexcludeAxis\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43msweep_start_freq\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43msweep_stop_freq\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m)\u001b[49m\n\u001b[0;32m      7\u001b[0m     \u001b[38;5;28;01mfor\u001b[39;00m i \u001b[38;5;129;01min\u001b[39;00m [\u001b[38;5;241m0\u001b[39m]\n\u001b[0;32m      8\u001b[0m }\n\u001b[0;32m     10\u001b[0m dataSet \u001b[38;5;241m=\u001b[39m dataSetDict[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mcamera_0\u001b[39m\u001b[38;5;124m\"\u001b[39m]\n\u001b[0;32m     12\u001b[0m print_scanAxis(dataSet)\n",
      "File \u001b[1;32mZ:\\Dy_Lab\\Data\\Analysis\\2023\\07\\31\\DataContainer\\ReadData.py:170\u001b[0m, in \u001b[0;36mread_hdf5_file\u001b[1;34m(filePath, group, datesetOfGlobal, preprocess, join, parallel, engine, phony_dims, excludeAxis, maxFileNum, **kwargs)\u001b[0m\n\u001b[0;32m    167\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m    168\u001b[0m     kwargs\u001b[38;5;241m.\u001b[39mupdate({\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mpreprocess\u001b[39m\u001b[38;5;124m'\u001b[39m:preprocess})\n\u001b[1;32m--> 170\u001b[0m ds \u001b[38;5;241m=\u001b[39m xr\u001b[38;5;241m.\u001b[39mopen_mfdataset(fullFilePath, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n\u001b[0;32m    172\u001b[0m newDimKey \u001b[38;5;241m=\u001b[39m np\u001b[38;5;241m.\u001b[39mappend([\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mx\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124my\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mz\u001b[39m\u001b[38;5;124m'\u001b[39m], [ \u001b[38;5;28mchr\u001b[39m(i) \u001b[38;5;28;01mfor\u001b[39;00m i \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mrange\u001b[39m(\u001b[38;5;241m97\u001b[39m, \u001b[38;5;241m97\u001b[39m\u001b[38;5;241m+\u001b[39m\u001b[38;5;241m23\u001b[39m)])\n\u001b[0;32m    174\u001b[0m oldDimKey \u001b[38;5;241m=\u001b[39m np\u001b[38;5;241m.\u001b[39msort(\n\u001b[0;32m    175\u001b[0m     [\n\u001b[0;32m    176\u001b[0m         key \n\u001b[1;32m   (...)\u001b[0m\n\u001b[0;32m    179\u001b[0m     ]\n\u001b[0;32m    180\u001b[0m )\n",
      "File \u001b[1;32m~\\anaconda3\\envs\\py39\\lib\\site-packages\\xarray\\backends\\api.py:990\u001b[0m, in \u001b[0;36mopen_mfdataset\u001b[1;34m(paths, chunks, concat_dim, compat, preprocess, engine, data_vars, coords, combine, parallel, join, attrs_file, combine_attrs, **kwargs)\u001b[0m\n\u001b[0;32m    985\u001b[0m     datasets \u001b[38;5;241m=\u001b[39m [preprocess(ds) \u001b[38;5;28;01mfor\u001b[39;00m ds \u001b[38;5;129;01min\u001b[39;00m datasets]\n\u001b[0;32m    987\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m parallel:\n\u001b[0;32m    988\u001b[0m     \u001b[38;5;66;03m# calling compute here will return the datasets/file_objs lists,\u001b[39;00m\n\u001b[0;32m    989\u001b[0m     \u001b[38;5;66;03m# the underlying datasets will still be stored as dask arrays\u001b[39;00m\n\u001b[1;32m--> 990\u001b[0m     datasets, closers \u001b[38;5;241m=\u001b[39m \u001b[43mdask\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcompute\u001b[49m\u001b[43m(\u001b[49m\u001b[43mdatasets\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mclosers\u001b[49m\u001b[43m)\u001b[49m\n\u001b[0;32m    992\u001b[0m \u001b[38;5;66;03m# Combine all datasets, closing them in case of a ValueError\u001b[39;00m\n\u001b[0;32m    993\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n",
      "File \u001b[1;32m~\\anaconda3\\envs\\py39\\lib\\site-packages\\dask\\base.py:599\u001b[0m, in \u001b[0;36mcompute\u001b[1;34m(traverse, optimize_graph, scheduler, get, *args, **kwargs)\u001b[0m\n\u001b[0;32m    596\u001b[0m     keys\u001b[38;5;241m.\u001b[39mappend(x\u001b[38;5;241m.\u001b[39m__dask_keys__())\n\u001b[0;32m    597\u001b[0m     postcomputes\u001b[38;5;241m.\u001b[39mappend(x\u001b[38;5;241m.\u001b[39m__dask_postcompute__())\n\u001b[1;32m--> 599\u001b[0m results \u001b[38;5;241m=\u001b[39m schedule(dsk, keys, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n\u001b[0;32m    600\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m repack([f(r, \u001b[38;5;241m*\u001b[39ma) \u001b[38;5;28;01mfor\u001b[39;00m r, (f, a) \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mzip\u001b[39m(results, postcomputes)])\n",
      "File \u001b[1;32m~\\anaconda3\\envs\\py39\\lib\\site-packages\\distributed\\client.py:3224\u001b[0m, in \u001b[0;36mClient.get\u001b[1;34m(self, dsk, keys, workers, allow_other_workers, resources, sync, asynchronous, direct, retries, priority, fifo_timeout, actors, **kwargs)\u001b[0m\n\u001b[0;32m   3222\u001b[0m         should_rejoin \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mFalse\u001b[39;00m\n\u001b[0;32m   3223\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[1;32m-> 3224\u001b[0m     results \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mgather\u001b[49m\u001b[43m(\u001b[49m\u001b[43mpacked\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43masynchronous\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43masynchronous\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mdirect\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mdirect\u001b[49m\u001b[43m)\u001b[49m\n\u001b[0;32m   3225\u001b[0m \u001b[38;5;28;01mfinally\u001b[39;00m:\n\u001b[0;32m   3226\u001b[0m     \u001b[38;5;28;01mfor\u001b[39;00m f \u001b[38;5;129;01min\u001b[39;00m futures\u001b[38;5;241m.\u001b[39mvalues():\n",
      "File \u001b[1;32m~\\anaconda3\\envs\\py39\\lib\\site-packages\\distributed\\client.py:2359\u001b[0m, in \u001b[0;36mClient.gather\u001b[1;34m(self, futures, errors, direct, asynchronous)\u001b[0m\n\u001b[0;32m   2357\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m   2358\u001b[0m     local_worker \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[1;32m-> 2359\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msync\u001b[49m\u001b[43m(\u001b[49m\n\u001b[0;32m   2360\u001b[0m \u001b[43m    \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_gather\u001b[49m\u001b[43m,\u001b[49m\n\u001b[0;32m   2361\u001b[0m \u001b[43m    \u001b[49m\u001b[43mfutures\u001b[49m\u001b[43m,\u001b[49m\n\u001b[0;32m   2362\u001b[0m \u001b[43m    \u001b[49m\u001b[43merrors\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43merrors\u001b[49m\u001b[43m,\u001b[49m\n\u001b[0;32m   2363\u001b[0m \u001b[43m    \u001b[49m\u001b[43mdirect\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mdirect\u001b[49m\u001b[43m,\u001b[49m\n\u001b[0;32m   2364\u001b[0m \u001b[43m    \u001b[49m\u001b[43mlocal_worker\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mlocal_worker\u001b[49m\u001b[43m,\u001b[49m\n\u001b[0;32m   2365\u001b[0m \u001b[43m    \u001b[49m\u001b[43masynchronous\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43masynchronous\u001b[49m\u001b[43m,\u001b[49m\n\u001b[0;32m   2366\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n",
      "File \u001b[1;32m~\\anaconda3\\envs\\py39\\lib\\site-packages\\distributed\\utils.py:351\u001b[0m, in \u001b[0;36mSyncMethodMixin.sync\u001b[1;34m(self, func, asynchronous, callback_timeout, *args, **kwargs)\u001b[0m\n\u001b[0;32m    349\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m future\n\u001b[0;32m    350\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m--> 351\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m sync(\n\u001b[0;32m    352\u001b[0m         \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mloop, func, \u001b[38;5;241m*\u001b[39margs, callback_timeout\u001b[38;5;241m=\u001b[39mcallback_timeout, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs\n\u001b[0;32m    353\u001b[0m     )\n",
      "File \u001b[1;32m~\\anaconda3\\envs\\py39\\lib\\site-packages\\distributed\\utils.py:418\u001b[0m, in \u001b[0;36msync\u001b[1;34m(loop, func, callback_timeout, *args, **kwargs)\u001b[0m\n\u001b[0;32m    416\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m error:\n\u001b[0;32m    417\u001b[0m     typ, exc, tb \u001b[38;5;241m=\u001b[39m error\n\u001b[1;32m--> 418\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m exc\u001b[38;5;241m.\u001b[39mwith_traceback(tb)\n\u001b[0;32m    419\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m    420\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m result\n",
      "File \u001b[1;32m~\\anaconda3\\envs\\py39\\lib\\site-packages\\distributed\\utils.py:391\u001b[0m, in \u001b[0;36msync.<locals>.f\u001b[1;34m()\u001b[0m\n\u001b[0;32m    389\u001b[0m         future \u001b[38;5;241m=\u001b[39m wait_for(future, callback_timeout)\n\u001b[0;32m    390\u001b[0m     future \u001b[38;5;241m=\u001b[39m asyncio\u001b[38;5;241m.\u001b[39mensure_future(future)\n\u001b[1;32m--> 391\u001b[0m     result \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01myield\u001b[39;00m future\n\u001b[0;32m    392\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mException\u001b[39;00m:\n\u001b[0;32m    393\u001b[0m     error \u001b[38;5;241m=\u001b[39m sys\u001b[38;5;241m.\u001b[39mexc_info()\n",
      "File \u001b[1;32m~\\anaconda3\\envs\\py39\\lib\\site-packages\\tornado\\gen.py:762\u001b[0m, in \u001b[0;36mRunner.run\u001b[1;34m(self)\u001b[0m\n\u001b[0;32m    759\u001b[0m exc_info \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[0;32m    761\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[1;32m--> 762\u001b[0m     value \u001b[38;5;241m=\u001b[39m \u001b[43mfuture\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mresult\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[0;32m    763\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mException\u001b[39;00m:\n\u001b[0;32m    764\u001b[0m     exc_info \u001b[38;5;241m=\u001b[39m sys\u001b[38;5;241m.\u001b[39mexc_info()\n",
      "File \u001b[1;32m~\\anaconda3\\envs\\py39\\lib\\site-packages\\distributed\\client.py:2222\u001b[0m, in \u001b[0;36mClient._gather\u001b[1;34m(self, futures, errors, direct, local_worker)\u001b[0m\n\u001b[0;32m   2220\u001b[0m         exc \u001b[38;5;241m=\u001b[39m CancelledError(key)\n\u001b[0;32m   2221\u001b[0m     \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m-> 2222\u001b[0m         \u001b[38;5;28;01mraise\u001b[39;00m exception\u001b[38;5;241m.\u001b[39mwith_traceback(traceback)\n\u001b[0;32m   2223\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m exc\n\u001b[0;32m   2224\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m errors \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mskip\u001b[39m\u001b[38;5;124m\"\u001b[39m:\n",
      "File \u001b[1;32m~\\anaconda3\\envs\\py39\\lib\\site-packages\\dask\\utils.py:73\u001b[0m, in \u001b[0;36mapply\u001b[1;34m()\u001b[0m\n\u001b[0;32m     42\u001b[0m \u001b[38;5;124;03m\"\"\"Apply a function given its positional and keyword arguments.\u001b[39;00m\n\u001b[0;32m     43\u001b[0m \n\u001b[0;32m     44\u001b[0m \u001b[38;5;124;03mEquivalent to ``func(*args, **kwargs)``\u001b[39;00m\n\u001b[1;32m   (...)\u001b[0m\n\u001b[0;32m     70\u001b[0m \u001b[38;5;124;03m>>> dsk = {'task-name': task}  # adds the task to a low level Dask task graph\u001b[39;00m\n\u001b[0;32m     71\u001b[0m \u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[0;32m     72\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m kwargs:\n\u001b[1;32m---> 73\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m func(\u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n\u001b[0;32m     74\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m     75\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m func(\u001b[38;5;241m*\u001b[39margs)\n",
      "File \u001b[1;32m~\\anaconda3\\envs\\py39\\lib\\site-packages\\xarray\\backends\\api.py:525\u001b[0m, in \u001b[0;36mopen_dataset\u001b[1;34m()\u001b[0m\n\u001b[0;32m    513\u001b[0m decoders \u001b[38;5;241m=\u001b[39m _resolve_decoders_kwargs(\n\u001b[0;32m    514\u001b[0m     decode_cf,\n\u001b[0;32m    515\u001b[0m     open_backend_dataset_parameters\u001b[38;5;241m=\u001b[39mbackend\u001b[38;5;241m.\u001b[39mopen_dataset_parameters,\n\u001b[1;32m   (...)\u001b[0m\n\u001b[0;32m    521\u001b[0m     decode_coords\u001b[38;5;241m=\u001b[39mdecode_coords,\n\u001b[0;32m    522\u001b[0m )\n\u001b[0;32m    524\u001b[0m overwrite_encoded_chunks \u001b[38;5;241m=\u001b[39m kwargs\u001b[38;5;241m.\u001b[39mpop(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124moverwrite_encoded_chunks\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;28;01mNone\u001b[39;00m)\n\u001b[1;32m--> 525\u001b[0m backend_ds \u001b[38;5;241m=\u001b[39m backend\u001b[38;5;241m.\u001b[39mopen_dataset(\n\u001b[0;32m    526\u001b[0m     filename_or_obj,\n\u001b[0;32m    527\u001b[0m     drop_variables\u001b[38;5;241m=\u001b[39mdrop_variables,\n\u001b[0;32m    528\u001b[0m     \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mdecoders,\n\u001b[0;32m    529\u001b[0m     \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs,\n\u001b[0;32m    530\u001b[0m )\n\u001b[0;32m    531\u001b[0m ds \u001b[38;5;241m=\u001b[39m _dataset_from_backend_dataset(\n\u001b[0;32m    532\u001b[0m     backend_ds,\n\u001b[0;32m    533\u001b[0m     filename_or_obj,\n\u001b[1;32m   (...)\u001b[0m\n\u001b[0;32m    541\u001b[0m     \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs,\n\u001b[0;32m    542\u001b[0m )\n\u001b[0;32m    543\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m ds\n",
      "File \u001b[1;32m~\\anaconda3\\envs\\py39\\lib\\site-packages\\xarray\\backends\\h5netcdf_.py:413\u001b[0m, in \u001b[0;36mopen_dataset\u001b[1;34m()\u001b[0m\n\u001b[0;32m    394\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mopen_dataset\u001b[39m(  \u001b[38;5;66;03m# type: ignore[override]  # allow LSP violation, not supporting **kwargs\u001b[39;00m\n\u001b[0;32m    395\u001b[0m     \u001b[38;5;28mself\u001b[39m,\n\u001b[0;32m    396\u001b[0m     filename_or_obj: \u001b[38;5;28mstr\u001b[39m \u001b[38;5;241m|\u001b[39m os\u001b[38;5;241m.\u001b[39mPathLike[Any] \u001b[38;5;241m|\u001b[39m BufferedIOBase \u001b[38;5;241m|\u001b[39m AbstractDataStore,\n\u001b[1;32m   (...)\u001b[0m\n\u001b[0;32m    410\u001b[0m     decode_vlen_strings\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m,\n\u001b[0;32m    411\u001b[0m ) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m Dataset:\n\u001b[0;32m    412\u001b[0m     filename_or_obj \u001b[38;5;241m=\u001b[39m _normalize_path(filename_or_obj)\n\u001b[1;32m--> 413\u001b[0m     store \u001b[38;5;241m=\u001b[39m H5NetCDFStore\u001b[38;5;241m.\u001b[39mopen(\n\u001b[0;32m    414\u001b[0m         filename_or_obj,\n\u001b[0;32m    415\u001b[0m         \u001b[38;5;28mformat\u001b[39m\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mformat\u001b[39m,\n\u001b[0;32m    416\u001b[0m         group\u001b[38;5;241m=\u001b[39mgroup,\n\u001b[0;32m    417\u001b[0m         lock\u001b[38;5;241m=\u001b[39mlock,\n\u001b[0;32m    418\u001b[0m         invalid_netcdf\u001b[38;5;241m=\u001b[39minvalid_netcdf,\n\u001b[0;32m    419\u001b[0m         phony_dims\u001b[38;5;241m=\u001b[39mphony_dims,\n\u001b[0;32m    420\u001b[0m         decode_vlen_strings\u001b[38;5;241m=\u001b[39mdecode_vlen_strings,\n\u001b[0;32m    421\u001b[0m     )\n\u001b[0;32m    423\u001b[0m     store_entrypoint \u001b[38;5;241m=\u001b[39m StoreBackendEntrypoint()\n\u001b[0;32m    425\u001b[0m     ds \u001b[38;5;241m=\u001b[39m store_entrypoint\u001b[38;5;241m.\u001b[39mopen_dataset(\n\u001b[0;32m    426\u001b[0m         store,\n\u001b[0;32m    427\u001b[0m         mask_and_scale\u001b[38;5;241m=\u001b[39mmask_and_scale,\n\u001b[1;32m   (...)\u001b[0m\n\u001b[0;32m    433\u001b[0m         decode_timedelta\u001b[38;5;241m=\u001b[39mdecode_timedelta,\n\u001b[0;32m    434\u001b[0m     )\n",
      "File \u001b[1;32m~\\anaconda3\\envs\\py39\\lib\\site-packages\\xarray\\backends\\h5netcdf_.py:176\u001b[0m, in \u001b[0;36mopen\u001b[1;34m()\u001b[0m\n\u001b[0;32m    173\u001b[0m         lock \u001b[38;5;241m=\u001b[39m combine_locks([HDF5_LOCK, get_write_lock(filename)])\n\u001b[0;32m    175\u001b[0m manager \u001b[38;5;241m=\u001b[39m CachingFileManager(h5netcdf\u001b[38;5;241m.\u001b[39mFile, filename, mode\u001b[38;5;241m=\u001b[39mmode, kwargs\u001b[38;5;241m=\u001b[39mkwargs)\n\u001b[1;32m--> 176\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mcls\u001b[39m(manager, group\u001b[38;5;241m=\u001b[39mgroup, mode\u001b[38;5;241m=\u001b[39mmode, lock\u001b[38;5;241m=\u001b[39mlock, autoclose\u001b[38;5;241m=\u001b[39mautoclose)\n",
      "File \u001b[1;32m~\\anaconda3\\envs\\py39\\lib\\site-packages\\xarray\\backends\\h5netcdf_.py:127\u001b[0m, in \u001b[0;36m__init__\u001b[1;34m()\u001b[0m\n\u001b[0;32m    124\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mformat \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[0;32m    125\u001b[0m \u001b[38;5;66;03m# todo: utilizing find_root_and_group seems a bit clunky\u001b[39;00m\n\u001b[0;32m    126\u001b[0m \u001b[38;5;66;03m#  making filename available on h5netcdf.Group seems better\u001b[39;00m\n\u001b[1;32m--> 127\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_filename \u001b[38;5;241m=\u001b[39m find_root_and_group(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mds)[\u001b[38;5;241m0\u001b[39m]\u001b[38;5;241m.\u001b[39mfilename\n\u001b[0;32m    128\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mis_remote \u001b[38;5;241m=\u001b[39m is_remote_uri(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_filename)\n\u001b[0;32m    129\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mlock \u001b[38;5;241m=\u001b[39m ensure_lock(lock)\n",
      "File \u001b[1;32m~\\anaconda3\\envs\\py39\\lib\\site-packages\\xarray\\backends\\h5netcdf_.py:187\u001b[0m, in \u001b[0;36mds\u001b[1;34m()\u001b[0m\n\u001b[0;32m    185\u001b[0m \u001b[38;5;129m@property\u001b[39m\n\u001b[0;32m    186\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mds\u001b[39m(\u001b[38;5;28mself\u001b[39m):\n\u001b[1;32m--> 187\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_acquire()\n",
      "File \u001b[1;32m~\\anaconda3\\envs\\py39\\lib\\site-packages\\xarray\\backends\\h5netcdf_.py:180\u001b[0m, in \u001b[0;36m_acquire\u001b[1;34m()\u001b[0m\n\u001b[0;32m    178\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m_acquire\u001b[39m(\u001b[38;5;28mself\u001b[39m, needs_lock\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m):\n\u001b[0;32m    179\u001b[0m     \u001b[38;5;28;01mwith\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_manager\u001b[38;5;241m.\u001b[39macquire_context(needs_lock) \u001b[38;5;28;01mas\u001b[39;00m root:\n\u001b[1;32m--> 180\u001b[0m         ds \u001b[38;5;241m=\u001b[39m _nc4_require_group(\n\u001b[0;32m    181\u001b[0m             root, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_group, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_mode, create_group\u001b[38;5;241m=\u001b[39m_h5netcdf_create_group\n\u001b[0;32m    182\u001b[0m         )\n\u001b[0;32m    183\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m ds\n",
      "File \u001b[1;32m~\\anaconda3\\envs\\py39\\lib\\site-packages\\xarray\\backends\\netCDF4_.py:191\u001b[0m, in \u001b[0;36m_nc4_require_group\u001b[1;34m()\u001b[0m\n\u001b[0;32m    188\u001b[0m             ds \u001b[38;5;241m=\u001b[39m create_group(ds, key)\n\u001b[0;32m    189\u001b[0m         \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m    190\u001b[0m             \u001b[38;5;66;03m# wrap error to provide slightly more helpful message\u001b[39;00m\n\u001b[1;32m--> 191\u001b[0m             \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mOSError\u001b[39;00m(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mgroup not found: \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mkey\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m, e)\n\u001b[0;32m    192\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m ds\n",
      "\u001b[1;31mOSError\u001b[0m: [Errno group not found: images] 'images'"
     ]
    }
   ],
   "source": [
    "%matplotlib notebook\n",
    "shotNum = \"0013\"\n",
    "filePath = folderPath + \"/\" + shotNum + \"/*.h5\"\n",
    "\n",
    "dataSetDict = {\n",
    "    dskey[groupList[i]]: read_hdf5_file(filePath, groupList[i], excludeAxis = ['sweep_start_freq', 'sweep_stop_freq'])\n",
    "    for i in [0]\n",
    "}\n",
    "\n",
    "dataSet = dataSetDict[\"camera_0\"]\n",
    "\n",
    "print_scanAxis(dataSet)\n",
    "\n",
    "scanAxis = get_scanAxis(dataSet)\n",
    "\n",
    "dataSet = auto_rechunk(dataSet)\n",
    "\n",
    "dataSet = imageAnalyser.get_absorption_images(dataSet)\n",
    "\n",
    "imageAnalyser.center = (800, 900)\n",
    "imageAnalyser.span = (300, 300)\n",
    "imageAnalyser.fraction = (0.1, 0.1)\n",
    "\n",
    "dataSet_cropOD = imageAnalyser.crop_image(dataSet.OD)\n",
    "dataSet_cropOD = imageAnalyser.substract_offset(dataSet_cropOD).load()\n",
    "\n",
    "Ncount = imageAnalyser.get_Ncount(dataSet_cropOD)\n",
    "Ncount_mean = calculate_mean(Ncount)\n",
    "Ncount_std = calculate_std(Ncount)\n",
    "\n",
    "fig = plt.figure()\n",
    "ax = fig.gca()\n",
    "Ncount_mean.plot.errorbar(ax=ax, yerr = None, fmt='ob')\n",
    "plt.ylabel('NCount')\n",
    "plt.tight_layout()\n",
    "plt.grid(visible=1)\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "dataSet_cropOD_chunk = dataSet_cropOD.chunk((1, 1, 300, 300))\n",
    "fitAnalyser = FitAnalyser(\"Gaussian-2D\", fitDim=2)\n",
    "params = fitAnalyser.guess(dataSet_cropOD_chunk, dask=\"parallelized\")\n",
    "fitResult = fitAnalyser.fit(dataSet_cropOD_chunk, params, dask=\"parallelized\").load()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "val = fitAnalyser.get_fit_value(fitResult)\n",
    "std = fitAnalyser.get_fit_std(fitResult)\n",
    "\n",
    "fitCurve = fitAnalyser.eval(fitResult, x=np.arange(300), y=np.arange(300), dask=\"parallelized\").load()\n",
    "\n",
    "# dataKey = 'sigmax'\n",
    "# dataKey = 'centerx'\n",
    "# dataKey = 'sigmay'\n",
    "dataKey = 'centery'\n",
    "\n",
    "# val_mean = val[dataKey].mean(dim='runs')\n",
    "# std_mean = val[dataKey].std(dim='runs')\n",
    "\n",
    "val_mean = calculate_mean(val[dataKey])\n",
    "std_mean = calculate_std(val[dataKey])\n",
    "\n",
    "fig = plt.figure()\n",
    "ax = fig.gca()\n",
    "\n",
    "val_mean.plot.errorbar(yerr=std_mean, fmt='--ob')\n",
    "\n",
    "plt.grid()\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 129,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/javascript": "/* Put everything inside the global mpl namespace */\n/* global mpl */\nwindow.mpl = {};\n\nmpl.get_websocket_type = function () {\n    if (typeof WebSocket !== 'undefined') {\n        return WebSocket;\n    } else if (typeof MozWebSocket !== 'undefined') {\n        return MozWebSocket;\n    } else {\n        alert(\n            'Your browser does not have WebSocket support. ' +\n                'Please try Chrome, Safari or Firefox ≥ 6. ' +\n                'Firefox 4 and 5 are also supported but you ' +\n                'have to enable WebSockets in about:config.'\n        );\n    }\n};\n\nmpl.figure = function (figure_id, websocket, ondownload, parent_element) {\n    this.id = figure_id;\n\n    this.ws = websocket;\n\n    this.supports_binary = this.ws.binaryType !== undefined;\n\n    if (!this.supports_binary) {\n        var warnings = document.getElementById('mpl-warnings');\n        if (warnings) {\n            warnings.style.display = 'block';\n            warnings.textContent =\n                'This browser does not support binary websocket messages. ' +\n                'Performance may be slow.';\n        }\n    }\n\n    this.imageObj = new Image();\n\n    this.context = undefined;\n    this.message = undefined;\n    this.canvas = undefined;\n    this.rubberband_canvas = undefined;\n    this.rubberband_context = undefined;\n    this.format_dropdown = undefined;\n\n    this.image_mode = 'full';\n\n    this.root = document.createElement('div');\n    this.root.setAttribute('style', 'display: inline-block');\n    this._root_extra_style(this.root);\n\n    parent_element.appendChild(this.root);\n\n    this._init_header(this);\n    this._init_canvas(this);\n    this._init_toolbar(this);\n\n    var fig = this;\n\n    this.waiting = false;\n\n    this.ws.onopen = function () {\n        fig.send_message('supports_binary', { value: fig.supports_binary });\n        fig.send_message('send_image_mode', {});\n        if (fig.ratio !== 1) {\n            fig.send_message('set_device_pixel_ratio', {\n                device_pixel_ratio: fig.ratio,\n            });\n        }\n        fig.send_message('refresh', {});\n    };\n\n    this.imageObj.onload = function () {\n        if (fig.image_mode === 'full') {\n            // Full images could contain transparency (where diff images\n            // almost always do), so we need to clear the canvas so that\n            // there is no ghosting.\n            fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n        }\n        fig.context.drawImage(fig.imageObj, 0, 0);\n    };\n\n    this.imageObj.onunload = function () {\n        fig.ws.close();\n    };\n\n    this.ws.onmessage = this._make_on_message_function(this);\n\n    this.ondownload = ondownload;\n};\n\nmpl.figure.prototype._init_header = function () {\n    var titlebar = document.createElement('div');\n    titlebar.classList =\n        'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n    var titletext = document.createElement('div');\n    titletext.classList = 'ui-dialog-title';\n    titletext.setAttribute(\n        'style',\n        'width: 100%; text-align: center; padding: 3px;'\n    );\n    titlebar.appendChild(titletext);\n    this.root.appendChild(titlebar);\n    this.header = titletext;\n};\n\nmpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n\nmpl.figure.prototype._init_canvas = function () {\n    var fig = this;\n\n    var canvas_div = (this.canvas_div = document.createElement('div'));\n    canvas_div.setAttribute(\n        'style',\n        'border: 1px solid #ddd;' +\n            'box-sizing: content-box;' +\n            'clear: both;' +\n            'min-height: 1px;' +\n            'min-width: 1px;' +\n            'outline: 0;' +\n            'overflow: hidden;' +\n            'position: relative;' +\n            'resize: both;'\n    );\n\n    function on_keyboard_event_closure(name) {\n        return function (event) {\n            return fig.key_event(event, name);\n        };\n    }\n\n    canvas_div.addEventListener(\n        'keydown',\n        on_keyboard_event_closure('key_press')\n    );\n    canvas_div.addEventListener(\n        'keyup',\n        on_keyboard_event_closure('key_release')\n    );\n\n    this._canvas_extra_style(canvas_div);\n    this.root.appendChild(canvas_div);\n\n    var canvas = (this.canvas = document.createElement('canvas'));\n    canvas.classList.add('mpl-canvas');\n    canvas.setAttribute('style', 'box-sizing: content-box;');\n\n    this.context = canvas.getContext('2d');\n\n    var backingStore =\n        this.context.backingStorePixelRatio ||\n        this.context.webkitBackingStorePixelRatio ||\n        this.context.mozBackingStorePixelRatio ||\n        this.context.msBackingStorePixelRatio ||\n        this.context.oBackingStorePixelRatio ||\n        this.context.backingStorePixelRatio ||\n        1;\n\n    this.ratio = (window.devicePixelRatio || 1) / backingStore;\n\n    var rubberband_canvas = (this.rubberband_canvas = document.createElement(\n        'canvas'\n    ));\n    rubberband_canvas.setAttribute(\n        'style',\n        'box-sizing: content-box; position: absolute; left: 0; top: 0; z-index: 1;'\n    );\n\n    // Apply a ponyfill if ResizeObserver is not implemented by browser.\n    if (this.ResizeObserver === undefined) {\n        if (window.ResizeObserver !== undefined) {\n            this.ResizeObserver = window.ResizeObserver;\n        } else {\n            var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n            this.ResizeObserver = obs.ResizeObserver;\n        }\n    }\n\n    this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n        var nentries = entries.length;\n        for (var i = 0; i < nentries; i++) {\n            var entry = entries[i];\n            var width, height;\n            if (entry.contentBoxSize) {\n                if (entry.contentBoxSize instanceof Array) {\n                    // Chrome 84 implements new version of spec.\n                    width = entry.contentBoxSize[0].inlineSize;\n                    height = entry.contentBoxSize[0].blockSize;\n                } else {\n                    // Firefox implements old version of spec.\n                    width = entry.contentBoxSize.inlineSize;\n                    height = entry.contentBoxSize.blockSize;\n                }\n            } else {\n                // Chrome <84 implements even older version of spec.\n                width = entry.contentRect.width;\n                height = entry.contentRect.height;\n            }\n\n            // Keep the size of the canvas and rubber band canvas in sync with\n            // the canvas container.\n            if (entry.devicePixelContentBoxSize) {\n                // Chrome 84 implements new version of spec.\n                canvas.setAttribute(\n                    'width',\n                    entry.devicePixelContentBoxSize[0].inlineSize\n                );\n                canvas.setAttribute(\n                    'height',\n                    entry.devicePixelContentBoxSize[0].blockSize\n                );\n            } else {\n                canvas.setAttribute('width', width * fig.ratio);\n                canvas.setAttribute('height', height * fig.ratio);\n            }\n            canvas.setAttribute(\n                'style',\n                'width: ' + width + 'px; height: ' + height + 'px;'\n            );\n\n            rubberband_canvas.setAttribute('width', width);\n            rubberband_canvas.setAttribute('height', height);\n\n            // And update the size in Python. We ignore the initial 0/0 size\n            // that occurs as the element is placed into the DOM, which should\n            // otherwise not happen due to the minimum size styling.\n            if (fig.ws.readyState == 1 && width != 0 && height != 0) {\n                fig.request_resize(width, height);\n            }\n        }\n    });\n    this.resizeObserverInstance.observe(canvas_div);\n\n    function on_mouse_event_closure(name) {\n        return function (event) {\n            return fig.mouse_event(event, name);\n        };\n    }\n\n    rubberband_canvas.addEventListener(\n        'mousedown',\n        on_mouse_event_closure('button_press')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseup',\n        on_mouse_event_closure('button_release')\n    );\n    rubberband_canvas.addEventListener(\n        'dblclick',\n        on_mouse_event_closure('dblclick')\n    );\n    // Throttle sequential mouse events to 1 every 20ms.\n    rubberband_canvas.addEventListener(\n        'mousemove',\n        on_mouse_event_closure('motion_notify')\n    );\n\n    rubberband_canvas.addEventListener(\n        'mouseenter',\n        on_mouse_event_closure('figure_enter')\n    );\n    rubberband_canvas.addEventListener(\n        'mouseleave',\n        on_mouse_event_closure('figure_leave')\n    );\n\n    canvas_div.addEventListener('wheel', function (event) {\n        if (event.deltaY < 0) {\n            event.step = 1;\n        } else {\n            event.step = -1;\n        }\n        on_mouse_event_closure('scroll')(event);\n    });\n\n    canvas_div.appendChild(canvas);\n    canvas_div.appendChild(rubberband_canvas);\n\n    this.rubberband_context = rubberband_canvas.getContext('2d');\n    this.rubberband_context.strokeStyle = '#000000';\n\n    this._resize_canvas = function (width, height, forward) {\n        if (forward) {\n            canvas_div.style.width = width + 'px';\n            canvas_div.style.height = height + 'px';\n        }\n    };\n\n    // Disable right mouse context menu.\n    this.rubberband_canvas.addEventListener('contextmenu', function (_e) {\n        event.preventDefault();\n        return false;\n    });\n\n    function set_focus() {\n        canvas.focus();\n        canvas_div.focus();\n    }\n\n    window.setTimeout(set_focus, 100);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'mpl-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'mpl-button-group';\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'mpl-button-group';\n            continue;\n        }\n\n        var button = (fig.buttons[name] = document.createElement('button'));\n        button.classList = 'mpl-widget';\n        button.setAttribute('role', 'button');\n        button.setAttribute('aria-disabled', 'false');\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n\n        var icon_img = document.createElement('img');\n        icon_img.src = '_images/' + image + '.png';\n        icon_img.srcset = '_images/' + image + '_large.png 2x';\n        icon_img.alt = tooltip;\n        button.appendChild(icon_img);\n\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    var fmt_picker = document.createElement('select');\n    fmt_picker.classList = 'mpl-widget';\n    toolbar.appendChild(fmt_picker);\n    this.format_dropdown = fmt_picker;\n\n    for (var ind in mpl.extensions) {\n        var fmt = mpl.extensions[ind];\n        var option = document.createElement('option');\n        option.selected = fmt === mpl.default_extension;\n        option.innerHTML = fmt;\n        fmt_picker.appendChild(option);\n    }\n\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n};\n\nmpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n    // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n    // which will in turn request a refresh of the image.\n    this.send_message('resize', { width: x_pixels, height: y_pixels });\n};\n\nmpl.figure.prototype.send_message = function (type, properties) {\n    properties['type'] = type;\n    properties['figure_id'] = this.id;\n    this.ws.send(JSON.stringify(properties));\n};\n\nmpl.figure.prototype.send_draw_message = function () {\n    if (!this.waiting) {\n        this.waiting = true;\n        this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    var format_dropdown = fig.format_dropdown;\n    var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n    fig.ondownload(fig, format);\n};\n\nmpl.figure.prototype.handle_resize = function (fig, msg) {\n    var size = msg['size'];\n    if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n        fig._resize_canvas(size[0], size[1], msg['forward']);\n        fig.send_message('refresh', {});\n    }\n};\n\nmpl.figure.prototype.handle_rubberband = function (fig, msg) {\n    var x0 = msg['x0'] / fig.ratio;\n    var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n    var x1 = msg['x1'] / fig.ratio;\n    var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n    x0 = Math.floor(x0) + 0.5;\n    y0 = Math.floor(y0) + 0.5;\n    x1 = Math.floor(x1) + 0.5;\n    y1 = Math.floor(y1) + 0.5;\n    var min_x = Math.min(x0, x1);\n    var min_y = Math.min(y0, y1);\n    var width = Math.abs(x1 - x0);\n    var height = Math.abs(y1 - y0);\n\n    fig.rubberband_context.clearRect(\n        0,\n        0,\n        fig.canvas.width / fig.ratio,\n        fig.canvas.height / fig.ratio\n    );\n\n    fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n};\n\nmpl.figure.prototype.handle_figure_label = function (fig, msg) {\n    // Updates the figure title.\n    fig.header.textContent = msg['label'];\n};\n\nmpl.figure.prototype.handle_cursor = function (fig, msg) {\n    fig.rubberband_canvas.style.cursor = msg['cursor'];\n};\n\nmpl.figure.prototype.handle_message = function (fig, msg) {\n    fig.message.textContent = msg['message'];\n};\n\nmpl.figure.prototype.handle_draw = function (fig, _msg) {\n    // Request the server to send over a new figure.\n    fig.send_draw_message();\n};\n\nmpl.figure.prototype.handle_image_mode = function (fig, msg) {\n    fig.image_mode = msg['mode'];\n};\n\nmpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n    for (var key in msg) {\n        if (!(key in fig.buttons)) {\n            continue;\n        }\n        fig.buttons[key].disabled = !msg[key];\n        fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n    }\n};\n\nmpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n    if (msg['mode'] === 'PAN') {\n        fig.buttons['Pan'].classList.add('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    } else if (msg['mode'] === 'ZOOM') {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.add('active');\n    } else {\n        fig.buttons['Pan'].classList.remove('active');\n        fig.buttons['Zoom'].classList.remove('active');\n    }\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Called whenever the canvas gets updated.\n    this.send_message('ack', {});\n};\n\n// A function to construct a web socket function for onmessage handling.\n// Called in the figure constructor.\nmpl.figure.prototype._make_on_message_function = function (fig) {\n    return function socket_on_message(evt) {\n        if (evt.data instanceof Blob) {\n            var img = evt.data;\n            if (img.type !== 'image/png') {\n                /* FIXME: We get \"Resource interpreted as Image but\n                 * transferred with MIME type text/plain:\" errors on\n                 * Chrome.  But how to set the MIME type?  It doesn't seem\n                 * to be part of the websocket stream */\n                img.type = 'image/png';\n            }\n\n            /* Free the memory for the previous frames */\n            if (fig.imageObj.src) {\n                (window.URL || window.webkitURL).revokeObjectURL(\n                    fig.imageObj.src\n                );\n            }\n\n            fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n                img\n            );\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        } else if (\n            typeof evt.data === 'string' &&\n            evt.data.slice(0, 21) === 'data:image/png;base64'\n        ) {\n            fig.imageObj.src = evt.data;\n            fig.updated_canvas_event();\n            fig.waiting = false;\n            return;\n        }\n\n        var msg = JSON.parse(evt.data);\n        var msg_type = msg['type'];\n\n        // Call the  \"handle_{type}\" callback, which takes\n        // the figure and JSON message as its only arguments.\n        try {\n            var callback = fig['handle_' + msg_type];\n        } catch (e) {\n            console.log(\n                \"No handler for the '\" + msg_type + \"' message type: \",\n                msg\n            );\n            return;\n        }\n\n        if (callback) {\n            try {\n                // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n                callback(fig, msg);\n            } catch (e) {\n                console.log(\n                    \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n                    e,\n                    e.stack,\n                    msg\n                );\n            }\n        }\n    };\n};\n\n// from https://stackoverflow.com/questions/1114465/getting-mouse-location-in-canvas\nmpl.findpos = function (e) {\n    //this section is from http://www.quirksmode.org/js/events_properties.html\n    var targ;\n    if (!e) {\n        e = window.event;\n    }\n    if (e.target) {\n        targ = e.target;\n    } else if (e.srcElement) {\n        targ = e.srcElement;\n    }\n    if (targ.nodeType === 3) {\n        // defeat Safari bug\n        targ = targ.parentNode;\n    }\n\n    // pageX,Y are the mouse positions relative to the document\n    var boundingRect = targ.getBoundingClientRect();\n    var x = e.pageX - (boundingRect.left + document.body.scrollLeft);\n    var y = e.pageY - (boundingRect.top + document.body.scrollTop);\n\n    return { x: x, y: y };\n};\n\n/*\n * return a copy of an object with only non-object keys\n * we need this to avoid circular references\n * https://stackoverflow.com/a/24161582/3208463\n */\nfunction simpleKeys(original) {\n    return Object.keys(original).reduce(function (obj, key) {\n        if (typeof original[key] !== 'object') {\n            obj[key] = original[key];\n        }\n        return obj;\n    }, {});\n}\n\nmpl.figure.prototype.mouse_event = function (event, name) {\n    var canvas_pos = mpl.findpos(event);\n\n    if (name === 'button_press') {\n        this.canvas.focus();\n        this.canvas_div.focus();\n    }\n\n    var x = canvas_pos.x * this.ratio;\n    var y = canvas_pos.y * this.ratio;\n\n    this.send_message(name, {\n        x: x,\n        y: y,\n        button: event.button,\n        step: event.step,\n        guiEvent: simpleKeys(event),\n    });\n\n    /* This prevents the web browser from automatically changing to\n     * the text insertion cursor when the button is pressed.  We want\n     * to control all of the cursor setting manually through the\n     * 'cursor' event from matplotlib */\n    event.preventDefault();\n    return false;\n};\n\nmpl.figure.prototype._key_event_extra = function (_event, _name) {\n    // Handle any extra behaviour associated with a key event\n};\n\nmpl.figure.prototype.key_event = function (event, name) {\n    // Prevent repeat events\n    if (name === 'key_press') {\n        if (event.key === this._key) {\n            return;\n        } else {\n            this._key = event.key;\n        }\n    }\n    if (name === 'key_release') {\n        this._key = null;\n    }\n\n    var value = '';\n    if (event.ctrlKey && event.key !== 'Control') {\n        value += 'ctrl+';\n    }\n    else if (event.altKey && event.key !== 'Alt') {\n        value += 'alt+';\n    }\n    else if (event.shiftKey && event.key !== 'Shift') {\n        value += 'shift+';\n    }\n\n    value += 'k' + event.key;\n\n    this._key_event_extra(event, name);\n\n    this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n    return false;\n};\n\nmpl.figure.prototype.toolbar_button_onclick = function (name) {\n    if (name === 'download') {\n        this.handle_save(this, null);\n    } else {\n        this.send_message('toolbar_button', { name: name });\n    }\n};\n\nmpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n    this.message.textContent = tooltip;\n};\n\n///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n// prettier-ignore\nvar _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\nmpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home icon-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left icon-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right icon-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows icon-move\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis\", \"fa fa-square-o icon-check-empty\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o icon-save\", \"download\"]];\n\nmpl.extensions = [\"eps\", \"jpeg\", \"pgf\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\"];\n\nmpl.default_extension = \"png\";/* global mpl */\n\nvar comm_websocket_adapter = function (comm) {\n    // Create a \"websocket\"-like object which calls the given IPython comm\n    // object with the appropriate methods. Currently this is a non binary\n    // socket, so there is still some room for performance tuning.\n    var ws = {};\n\n    ws.binaryType = comm.kernel.ws.binaryType;\n    ws.readyState = comm.kernel.ws.readyState;\n    function updateReadyState(_event) {\n        if (comm.kernel.ws) {\n            ws.readyState = comm.kernel.ws.readyState;\n        } else {\n            ws.readyState = 3; // Closed state.\n        }\n    }\n    comm.kernel.ws.addEventListener('open', updateReadyState);\n    comm.kernel.ws.addEventListener('close', updateReadyState);\n    comm.kernel.ws.addEventListener('error', updateReadyState);\n\n    ws.close = function () {\n        comm.close();\n    };\n    ws.send = function (m) {\n        //console.log('sending', m);\n        comm.send(m);\n    };\n    // Register the callback with on_msg.\n    comm.on_msg(function (msg) {\n        //console.log('receiving', msg['content']['data'], msg);\n        var data = msg['content']['data'];\n        if (data['blob'] !== undefined) {\n            data = {\n                data: new Blob(msg['buffers'], { type: data['blob'] }),\n            };\n        }\n        // Pass the mpl event to the overridden (by mpl) onmessage function.\n        ws.onmessage(data);\n    });\n    return ws;\n};\n\nmpl.mpl_figure_comm = function (comm, msg) {\n    // This is the function which gets called when the mpl process\n    // starts-up an IPython Comm through the \"matplotlib\" channel.\n\n    var id = msg.content.data.id;\n    // Get hold of the div created by the display call when the Comm\n    // socket was opened in Python.\n    var element = document.getElementById(id);\n    var ws_proxy = comm_websocket_adapter(comm);\n\n    function ondownload(figure, _format) {\n        window.open(figure.canvas.toDataURL());\n    }\n\n    var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n\n    // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n    // web socket which is closed, not our websocket->open comm proxy.\n    ws_proxy.onopen();\n\n    fig.parent_element = element;\n    fig.cell_info = mpl.find_output_cell(\"<div id='\" + id + \"'></div>\");\n    if (!fig.cell_info) {\n        console.error('Failed to find cell for figure', id, fig);\n        return;\n    }\n    fig.cell_info[0].output_area.element.on(\n        'cleared',\n        { fig: fig },\n        fig._remove_fig_handler\n    );\n};\n\nmpl.figure.prototype.handle_close = function (fig, msg) {\n    var width = fig.canvas.width / fig.ratio;\n    fig.cell_info[0].output_area.element.off(\n        'cleared',\n        fig._remove_fig_handler\n    );\n    fig.resizeObserverInstance.unobserve(fig.canvas_div);\n\n    // Update the output cell to use the data from the current canvas.\n    fig.push_to_output();\n    var dataURL = fig.canvas.toDataURL();\n    // Re-enable the keyboard manager in IPython - without this line, in FF,\n    // the notebook keyboard shortcuts fail.\n    IPython.keyboard_manager.enable();\n    fig.parent_element.innerHTML =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n    fig.close_ws(fig, msg);\n};\n\nmpl.figure.prototype.close_ws = function (fig, msg) {\n    fig.send_message('closing', msg);\n    // fig.ws.close()\n};\n\nmpl.figure.prototype.push_to_output = function (_remove_interactive) {\n    // Turn the data on the canvas into data in the output cell.\n    var width = this.canvas.width / this.ratio;\n    var dataURL = this.canvas.toDataURL();\n    this.cell_info[1]['text/html'] =\n        '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n    // Tell IPython that the notebook contents must change.\n    IPython.notebook.set_dirty(true);\n    this.send_message('ack', {});\n    var fig = this;\n    // Wait a second, then push the new image to the DOM so\n    // that it is saved nicely (might be nice to debounce this).\n    setTimeout(function () {\n        fig.push_to_output();\n    }, 1000);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n    var fig = this;\n\n    var toolbar = document.createElement('div');\n    toolbar.classList = 'btn-toolbar';\n    this.root.appendChild(toolbar);\n\n    function on_click_closure(name) {\n        return function (_event) {\n            return fig.toolbar_button_onclick(name);\n        };\n    }\n\n    function on_mouseover_closure(tooltip) {\n        return function (event) {\n            if (!event.currentTarget.disabled) {\n                return fig.toolbar_button_onmouseover(tooltip);\n            }\n        };\n    }\n\n    fig.buttons = {};\n    var buttonGroup = document.createElement('div');\n    buttonGroup.classList = 'btn-group';\n    var button;\n    for (var toolbar_ind in mpl.toolbar_items) {\n        var name = mpl.toolbar_items[toolbar_ind][0];\n        var tooltip = mpl.toolbar_items[toolbar_ind][1];\n        var image = mpl.toolbar_items[toolbar_ind][2];\n        var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n        if (!name) {\n            /* Instead of a spacer, we start a new button group. */\n            if (buttonGroup.hasChildNodes()) {\n                toolbar.appendChild(buttonGroup);\n            }\n            buttonGroup = document.createElement('div');\n            buttonGroup.classList = 'btn-group';\n            continue;\n        }\n\n        button = fig.buttons[name] = document.createElement('button');\n        button.classList = 'btn btn-default';\n        button.href = '#';\n        button.title = name;\n        button.innerHTML = '<i class=\"fa ' + image + ' fa-lg\"></i>';\n        button.addEventListener('click', on_click_closure(method_name));\n        button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n        buttonGroup.appendChild(button);\n    }\n\n    if (buttonGroup.hasChildNodes()) {\n        toolbar.appendChild(buttonGroup);\n    }\n\n    // Add the status bar.\n    var status_bar = document.createElement('span');\n    status_bar.classList = 'mpl-message pull-right';\n    toolbar.appendChild(status_bar);\n    this.message = status_bar;\n\n    // Add the close button to the window.\n    var buttongrp = document.createElement('div');\n    buttongrp.classList = 'btn-group inline pull-right';\n    button = document.createElement('button');\n    button.classList = 'btn btn-mini btn-primary';\n    button.href = '#';\n    button.title = 'Stop Interaction';\n    button.innerHTML = '<i class=\"fa fa-power-off icon-remove icon-large\"></i>';\n    button.addEventListener('click', function (_evt) {\n        fig.handle_close(fig, {});\n    });\n    button.addEventListener(\n        'mouseover',\n        on_mouseover_closure('Stop Interaction')\n    );\n    buttongrp.appendChild(button);\n    var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n    titlebar.insertBefore(buttongrp, titlebar.firstChild);\n};\n\nmpl.figure.prototype._remove_fig_handler = function (event) {\n    var fig = event.data.fig;\n    if (event.target !== this) {\n        // Ignore bubbled events from children.\n        return;\n    }\n    fig.close_ws(fig, {});\n};\n\nmpl.figure.prototype._root_extra_style = function (el) {\n    el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n};\n\nmpl.figure.prototype._canvas_extra_style = function (el) {\n    // this is important to make the div 'focusable\n    el.setAttribute('tabindex', 0);\n    // reach out to IPython and tell the keyboard manager to turn it's self\n    // off when our div gets focus\n\n    // location in version 3\n    if (IPython.notebook.keyboard_manager) {\n        IPython.notebook.keyboard_manager.register_events(el);\n    } else {\n        // location in version 2\n        IPython.keyboard_manager.register_events(el);\n    }\n};\n\nmpl.figure.prototype._key_event_extra = function (event, _name) {\n    // Check for shift+enter\n    if (event.shiftKey && event.which === 13) {\n        this.canvas_div.blur();\n        // select the cell after this one\n        var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n        IPython.notebook.select(index + 1);\n    }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n    fig.ondownload(fig, null);\n};\n\nmpl.find_output_cell = function (html_output) {\n    // Return the cell and output element which can be found *uniquely* in the notebook.\n    // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n    // IPython event is triggered only after the cells have been serialised, which for\n    // our purposes (turning an active figure into a static one), is too late.\n    var cells = IPython.notebook.get_cells();\n    var ncells = cells.length;\n    for (var i = 0; i < ncells; i++) {\n        var cell = cells[i];\n        if (cell.cell_type === 'code') {\n            for (var j = 0; j < cell.output_area.outputs.length; j++) {\n                var data = cell.output_area.outputs[j];\n                if (data.data) {\n                    // IPython >= 3 moved mimebundle to data attribute of output\n                    data = data.data;\n                }\n                if (data['text/html'] === html_output) {\n                    return [cell, data, j];\n                }\n            }\n        }\n    }\n};\n\n// Register the function which deals with the matplotlib target/channel.\n// The kernel may be null if the page has been refreshed.\nif (IPython.notebook.kernel !== null) {\n    IPython.notebook.kernel.comm_manager.register_target(\n        'matplotlib',\n        mpl.mpl_figure_comm\n    );\n}\n",
      "text/plain": [
       "<IPython.core.display.Javascript object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<img src=\"data:image/png;base64,[encoded data, 81016 characters]\" width=\"640\">"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "f = 224.9906 ± 0.4995 Hz\n"
     ]
    }
   ],
   "source": [
    "def damp_osci(t, t0, A, B, nu, gamma):\n",
    "    return A * np.exp(-gamma*t)*np.sin(2*np.pi*nu*(t-t0)) + B\n",
    "\n",
    "yvals     = val_mean#.sel(blink_on_time=slice(0.005, 0.025))\n",
    "yvals_std = std_mean#.sel(blink_on_time=slice(0.005, 0.025))\n",
    "xvals     = dataSet_cropOD[scanAxis[0]]#.sel(blink_on_time=slice(0.005, 0.025))\n",
    "\n",
    "fitted_qtys_1 = yvals.to_numpy()\n",
    "scan_para = xvals.to_numpy()\n",
    "fitted_qtys_err_1 = yvals_std.to_numpy()\n",
    "\n",
    "\n",
    "plt.figure()\n",
    "popt_x, pcov_x = curve_fit(damp_osci, scan_para, fitted_qtys_1, np.array([0, 3, 147, 3e2, 0.1]))\n",
    "freqdata = np.linspace(0.005, 19e-3, 500)\n",
    "plt.plot(freqdata, damp_osci(freqdata, *popt_x), 'g--',label='fit: t0=%5.3f, A=%5.3f, B=%5.3f, nu=%5.3f, Gamma=%5.3f' % tuple(popt_x))\n",
    "plt.errorbar(scan_para, fitted_qtys_1, yerr=fitted_qtys_err_1, fmt='or')\n",
    "plt.xlabel('hold time after switch on the trap (s)')\n",
    "plt.ylabel('Center along gravity direction (pixels)')\n",
    "plt.tight_layout()\n",
    "plt.grid(visible=1)\n",
    "#plt.ylim([0,750])\n",
    "#plt.xlim([0.004, 0.025])\n",
    "#plt.legend(prop={'size': 14})\n",
    "plt.show()\n",
    "\n",
    "f_x = popt_x[3]\n",
    "df_x = pcov_x[3][3]**0.5\n",
    "\n",
    "print('f = %.4f \\u00B1 %.4f Hz'% tuple([np.abs(f_x),df_x]))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Truncation: 0.8"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "%matplotlib notebook\n",
    "shotNum = \"0036\"\n",
    "filePath = folderPath + \"/\" + shotNum + \"/*.h5\"\n",
    "\n",
    "dataSetDict = {\n",
    "    dskey[groupList[i]]: read_hdf5_file(filePath, groupList[i], excludeAxis = ['sweep_start_freq', 'sweep_stop_freq'])\n",
    "    for i in [0]\n",
    "}\n",
    "\n",
    "dataSet = dataSetDict[\"camera_0\"]\n",
    "\n",
    "print_scanAxis(dataSet)\n",
    "\n",
    "scanAxis = get_scanAxis(dataSet)\n",
    "\n",
    "dataSet = auto_rechunk(dataSet)\n",
    "\n",
    "dataSet = imageAnalyser.get_absorption_images(dataSet)\n",
    "\n",
    "imageAnalyser.center = (800, 900)\n",
    "imageAnalyser.span = (300, 300)\n",
    "imageAnalyser.fraction = (0.1, 0.1)\n",
    "\n",
    "dataSet_cropOD = imageAnalyser.crop_image(dataSet.OD)\n",
    "dataSet_cropOD = imageAnalyser.substract_offset(dataSet_cropOD).load()\n",
    "\n",
    "Ncount = imageAnalyser.get_Ncount(dataSet_cropOD)\n",
    "Ncount_mean = calculate_mean(Ncount)\n",
    "Ncount_std = calculate_std(Ncount)\n",
    "\n",
    "fig = plt.figure()\n",
    "ax = fig.gca()\n",
    "Ncount_mean.plot.errorbar(ax=ax, yerr = None, fmt='ob')\n",
    "plt.ylabel('NCount')\n",
    "plt.tight_layout()\n",
    "plt.grid(visible=1)\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "dataSet_cropOD_chunk = dataSet_cropOD.chunk((1, 1, 300, 300))\n",
    "fitAnalyser = FitAnalyser(\"Gaussian-2D\", fitDim=2)\n",
    "params = fitAnalyser.guess(dataSet_cropOD_chunk, dask=\"parallelized\")\n",
    "fitResult = fitAnalyser.fit(dataSet_cropOD_chunk, params, dask=\"parallelized\").load()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "val = fitAnalyser.get_fit_value(fitResult)\n",
    "std = fitAnalyser.get_fit_std(fitResult)\n",
    "\n",
    "fitCurve = fitAnalyser.eval(fitResult, x=np.arange(300), y=np.arange(300), dask=\"parallelized\").load()\n",
    "\n",
    "# dataKey = 'sigmax'\n",
    "# dataKey = 'centerx'\n",
    "# dataKey = 'sigmay'\n",
    "dataKey = 'centery'\n",
    "\n",
    "# val_mean = val[dataKey].mean(dim='runs')\n",
    "# std_mean = val[dataKey].std(dim='runs')\n",
    "\n",
    "val_mean = calculate_mean(val[dataKey])\n",
    "std_mean = calculate_std(val[dataKey])\n",
    "\n",
    "fig = plt.figure()\n",
    "ax = fig.gca()\n",
    "\n",
    "val_mean.plot.errorbar(yerr=std_mean, fmt='--ob')\n",
    "\n",
    "plt.grid()\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "def damp_osci(t, t0, A, B, nu, gamma):\n",
    "    return A * np.exp(-gamma*t)*np.sin(2*np.pi*nu*(t-t0)) + B\n",
    "\n",
    "yvals     = val_mean#.sel(blink_on_time=slice(0.005, 0.025))\n",
    "yvals_std = std_mean#.sel(blink_on_time=slice(0.005, 0.025))\n",
    "xvals     = dataSet_cropOD[scanAxis[0]]#.sel(blink_on_time=slice(0.005, 0.025))\n",
    "\n",
    "fitted_qtys_1 = yvals.to_numpy()\n",
    "scan_para = xvals.to_numpy()\n",
    "fitted_qtys_err_1 = yvals_std.to_numpy()\n",
    "\n",
    "\n",
    "plt.figure()\n",
    "popt_x, pcov_x = curve_fit(damp_osci, scan_para, fitted_qtys_1, np.array([0, 3, 147, 2e2, 0.1]))\n",
    "freqdata = np.linspace(0.005, 19e-3, 500)\n",
    "plt.plot(freqdata, damp_osci(freqdata, *popt_x), 'g--',label='fit: t0=%5.3f, A=%5.3f, B=%5.3f, nu=%5.3f, Gamma=%5.3f' % tuple(popt_x))\n",
    "plt.errorbar(scan_para, fitted_qtys_1, yerr=fitted_qtys_err_1, fmt='or')\n",
    "plt.xlabel('hold time after switch on the trap (s)')\n",
    "plt.ylabel('Center along gravity direction (pixels)')\n",
    "plt.tight_layout()\n",
    "plt.grid(visible=1)\n",
    "#plt.ylim([0,750])\n",
    "#plt.xlim([0.004, 0.025])\n",
    "#plt.legend(prop={'size': 14})\n",
    "plt.show()\n",
    "\n",
    "f_x = popt_x[3]\n",
    "df_x = pcov_x[3][3]**0.5\n",
    "\n",
    "print('f = %.4f \\u00B1 %.4f Hz'% tuple([np.abs(f_x),df_x]))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Truncation: 0.85"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "%matplotlib notebook\n",
    "shotNum = \"0038\"\n",
    "filePath = folderPath + \"/\" + shotNum + \"/*.h5\"\n",
    "\n",
    "dataSetDict = {\n",
    "    dskey[groupList[i]]: read_hdf5_file(filePath, groupList[i], excludeAxis = ['sweep_start_freq', 'sweep_stop_freq'])\n",
    "    for i in [0]\n",
    "}\n",
    "\n",
    "dataSet = dataSetDict[\"camera_0\"]\n",
    "\n",
    "print_scanAxis(dataSet)\n",
    "\n",
    "scanAxis = get_scanAxis(dataSet)\n",
    "\n",
    "dataSet = auto_rechunk(dataSet)\n",
    "\n",
    "dataSet = imageAnalyser.get_absorption_images(dataSet)\n",
    "\n",
    "imageAnalyser.center = (800, 900)\n",
    "imageAnalyser.span = (300, 300)\n",
    "imageAnalyser.fraction = (0.1, 0.1)\n",
    "\n",
    "dataSet_cropOD = imageAnalyser.crop_image(dataSet.OD)\n",
    "dataSet_cropOD = imageAnalyser.substract_offset(dataSet_cropOD).load()\n",
    "\n",
    "Ncount = imageAnalyser.get_Ncount(dataSet_cropOD)\n",
    "Ncount_mean = calculate_mean(Ncount)\n",
    "Ncount_std = calculate_std(Ncount)\n",
    "\n",
    "fig = plt.figure()\n",
    "ax = fig.gca()\n",
    "Ncount_mean.plot.errorbar(ax=ax, yerr = None, fmt='ob')\n",
    "plt.ylabel('NCount')\n",
    "plt.tight_layout()\n",
    "plt.grid(visible=1)\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "dataSet_cropOD_chunk = dataSet_cropOD.chunk((1, 1, 300, 300))\n",
    "fitAnalyser = FitAnalyser(\"Gaussian-2D\", fitDim=2)\n",
    "params = fitAnalyser.guess(dataSet_cropOD_chunk, dask=\"parallelized\")\n",
    "fitResult = fitAnalyser.fit(dataSet_cropOD_chunk, params, dask=\"parallelized\").load()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "val = fitAnalyser.get_fit_value(fitResult)\n",
    "std = fitAnalyser.get_fit_std(fitResult)\n",
    "\n",
    "fitCurve = fitAnalyser.eval(fitResult, x=np.arange(300), y=np.arange(300), dask=\"parallelized\").load()\n",
    "\n",
    "# dataKey = 'sigmax'\n",
    "# dataKey = 'centerx'\n",
    "# dataKey = 'sigmay'\n",
    "dataKey = 'centery'\n",
    "\n",
    "# val_mean = val[dataKey].mean(dim='runs')\n",
    "# std_mean = val[dataKey].std(dim='runs')\n",
    "\n",
    "val_mean = calculate_mean(val[dataKey])\n",
    "std_mean = calculate_std(val[dataKey])\n",
    "\n",
    "fig = plt.figure()\n",
    "ax = fig.gca()\n",
    "\n",
    "val_mean.plot.errorbar(yerr=std_mean, fmt='--ob')\n",
    "\n",
    "plt.grid()\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "def damp_osci(t, t0, A, B, nu, gamma):\n",
    "    return A * np.exp(-gamma*t)*np.sin(2*np.pi*nu*(t-t0)) + B\n",
    "\n",
    "yvals     = val_mean#.sel(blink_on_time=slice(0.005, 0.025))\n",
    "yvals_std = std_mean#.sel(blink_on_time=slice(0.005, 0.025))\n",
    "xvals     = dataSet_cropOD[scanAxis[0]]#.sel(blink_on_time=slice(0.005, 0.025))\n",
    "\n",
    "fitted_qtys_1 = yvals.to_numpy()\n",
    "scan_para = xvals.to_numpy()\n",
    "fitted_qtys_err_1 = yvals_std.to_numpy()\n",
    "\n",
    "\n",
    "plt.figure()\n",
    "popt_x, pcov_x = curve_fit(damp_osci, scan_para, fitted_qtys_1, np.array([0, 3, 147, 2e2, 0.1]))\n",
    "freqdata = np.linspace(0.005, 19e-3, 500)\n",
    "plt.plot(freqdata, damp_osci(freqdata, *popt_x), 'g--',label='fit: t0=%5.3f, A=%5.3f, B=%5.3f, nu=%5.3f, Gamma=%5.3f' % tuple(popt_x))\n",
    "plt.errorbar(scan_para, fitted_qtys_1, yerr=fitted_qtys_err_1, fmt='or')\n",
    "plt.xlabel('hold time after switch on the trap (s)')\n",
    "plt.ylabel('Center along gravity direction (pixels)')\n",
    "plt.tight_layout()\n",
    "plt.grid(visible=1)\n",
    "#plt.ylim([0,750])\n",
    "#plt.xlim([0.004, 0.025])\n",
    "#plt.legend(prop={'size': 14})\n",
    "plt.show()\n",
    "\n",
    "f_x = popt_x[3]\n",
    "df_x = pcov_x[3][3]**0.5\n",
    "\n",
    "print('f = %.4f \\u00B1 %.4f Hz'% tuple([np.abs(f_x),df_x]))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Truncation: 0.9"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "%matplotlib notebook\n",
    "shotNum = \"0040\"\n",
    "filePath = folderPath + \"/\" + shotNum + \"/*.h5\"\n",
    "\n",
    "dataSetDict = {\n",
    "    dskey[groupList[i]]: read_hdf5_file(filePath, groupList[i], excludeAxis = ['sweep_start_freq', 'sweep_stop_freq'])\n",
    "    for i in [0]\n",
    "}\n",
    "\n",
    "dataSet = dataSetDict[\"camera_0\"]\n",
    "\n",
    "print_scanAxis(dataSet)\n",
    "\n",
    "scanAxis = get_scanAxis(dataSet)\n",
    "\n",
    "dataSet = auto_rechunk(dataSet)\n",
    "\n",
    "dataSet = imageAnalyser.get_absorption_images(dataSet)\n",
    "\n",
    "imageAnalyser.center = (800, 900)\n",
    "imageAnalyser.span = (300, 300)\n",
    "imageAnalyser.fraction = (0.1, 0.1)\n",
    "\n",
    "dataSet_cropOD = imageAnalyser.crop_image(dataSet.OD)\n",
    "dataSet_cropOD = imageAnalyser.substract_offset(dataSet_cropOD).load()\n",
    "\n",
    "Ncount = imageAnalyser.get_Ncount(dataSet_cropOD)\n",
    "Ncount_mean = calculate_mean(Ncount)\n",
    "Ncount_std = calculate_std(Ncount)\n",
    "\n",
    "fig = plt.figure()\n",
    "ax = fig.gca()\n",
    "Ncount_mean.plot.errorbar(ax=ax, yerr = None, fmt='ob')\n",
    "plt.ylabel('NCount')\n",
    "plt.tight_layout()\n",
    "plt.grid(visible=1)\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "dataSet_cropOD_chunk = dataSet_cropOD.chunk((1, 1, 300, 300))\n",
    "fitAnalyser = FitAnalyser(\"Gaussian-2D\", fitDim=2)\n",
    "params = fitAnalyser.guess(dataSet_cropOD_chunk, dask=\"parallelized\")\n",
    "fitResult = fitAnalyser.fit(dataSet_cropOD_chunk, params, dask=\"parallelized\").load()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "val = fitAnalyser.get_fit_value(fitResult)\n",
    "std = fitAnalyser.get_fit_std(fitResult)\n",
    "\n",
    "fitCurve = fitAnalyser.eval(fitResult, x=np.arange(300), y=np.arange(300), dask=\"parallelized\").load()\n",
    "\n",
    "# dataKey = 'sigmax'\n",
    "# dataKey = 'centerx'\n",
    "# dataKey = 'sigmay'\n",
    "dataKey = 'centery'\n",
    "\n",
    "# val_mean = val[dataKey].mean(dim='runs')\n",
    "# std_mean = val[dataKey].std(dim='runs')\n",
    "\n",
    "val_mean = calculate_mean(val[dataKey])\n",
    "std_mean = calculate_std(val[dataKey])\n",
    "\n",
    "fig = plt.figure()\n",
    "ax = fig.gca()\n",
    "\n",
    "val_mean.plot.errorbar(yerr=std_mean, fmt='--ob')\n",
    "\n",
    "plt.grid()\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "def damp_osci(t, t0, A, B, nu, gamma):\n",
    "    return A * np.exp(-gamma*t)*np.sin(2*np.pi*nu*(t-t0)) + B\n",
    "\n",
    "yvals     = val_mean#.sel(blink_on_time=slice(0.005, 0.025))\n",
    "yvals_std = std_mean#.sel(blink_on_time=slice(0.005, 0.025))\n",
    "xvals     = dataSet_cropOD[scanAxis[0]]#.sel(blink_on_time=slice(0.005, 0.025))\n",
    "\n",
    "fitted_qtys_1 = yvals.to_numpy()\n",
    "scan_para = xvals.to_numpy()\n",
    "fitted_qtys_err_1 = yvals_std.to_numpy()\n",
    "\n",
    "\n",
    "plt.figure()\n",
    "popt_x, pcov_x = curve_fit(damp_osci, scan_para, fitted_qtys_1, np.array([0, 3, 147, 2e2, 0.1]))\n",
    "freqdata = np.linspace(0.005, 19e-3, 500)\n",
    "plt.plot(freqdata, damp_osci(freqdata, *popt_x), 'g--',label='fit: t0=%5.3f, A=%5.3f, B=%5.3f, nu=%5.3f, Gamma=%5.3f' % tuple(popt_x))\n",
    "plt.errorbar(scan_para, fitted_qtys_1, yerr=fitted_qtys_err_1, fmt='or')\n",
    "plt.xlabel('hold time after switch on the trap (s)')\n",
    "plt.ylabel('Center along gravity direction (pixels)')\n",
    "plt.tight_layout()\n",
    "plt.grid(visible=1)\n",
    "#plt.ylim([0,750])\n",
    "#plt.xlim([0.004, 0.025])\n",
    "#plt.legend(prop={'size': 14})\n",
    "plt.show()\n",
    "\n",
    "f_x = popt_x[3]\n",
    "df_x = pcov_x[3][3]**0.5\n",
    "\n",
    "print('f = %.4f \\u00B1 %.4f Hz'% tuple([np.abs(f_x),df_x]))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": "[encoded data, 26364 characters]",
      "text/plain": [
       "<Figure size 640x480 with 1 Axes>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "image/png": "[encoded data, 22184 characters]",
      "text/plain": [
       "<Figure size 640x480 with 1 Axes>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "image/png": "[encoded data, 25972 characters]",
      "text/plain": [
       "<Figure size 640x480 with 1 Axes>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "tf_z = [299.3777,  288.1736, 272.4744, 259.5129, 241.8841, 233.8030, 229.2665, 219.5115, 211.4388, 199.3276, 184.9726]\n",
    "dtf_z = [3.7588, 3.5503,1.2193, 0.7946, 1.7848, 1.4811, 0.7289, 1.0038, 0.7646, 1.0321, 1.0431]\n",
    "trunc = [0.5, 0.55, 0.6, 0.65, 0.7, 0.725, 0.75, 0.775, 0.8, 0.85, 0.9]\n",
    "p_1 = [0.507, 0.449, 0.398, 0.354, 0.315, 0.298, 0.282, 0.266, 0.252, 0.226, 0.204]\n",
    "p_2 = [3.88, 3.38, 2.911, 2.474, 2.066, 1.873, 1.687, 1.507, 1.33, 1.003, 0.696]\n",
    "         \n",
    "plt.figure()\n",
    "plt.errorbar(p_1, tf_z, yerr = dtf_z, fmt = 'ob')\n",
    "plt.xlabel('Power of Arm 1')\n",
    "plt.ylabel('Vertical TF (Hz)')\n",
    "plt.tight_layout()\n",
    "plt.grid(visible=1)\n",
    "\n",
    "tf_y = [49.3970, 47.4535, 43.9127, 40.8258, 36.6638, 35.6111, 34.3650, 32.0196, 29.9294, 26.5413, 22.4257]\n",
    "dtf_y = [1.5574, 0.5536, 0.3721, 0.4734, 0.9428, 0.7725, 0.3264, 0.2862, 0.1988, 0.2477, 0.3690]\n",
    "trunc = [0.5, 0.55, 0.6, 0.65, 0.7, 0.725, 0.75, 0.775, 0.8, 0.85, 0.9]\n",
    "         \n",
    "plt.figure()\n",
    "plt.errorbar(p_2, tf_y, yerr = dtf_y, fmt = 'oy')\n",
    "plt.xlabel('Power of Arm 2')\n",
    "plt.ylabel('Axial TF (Hz)')\n",
    "plt.tight_layout()\n",
    "plt.grid(visible=1)\n",
    "\n",
    "tf_x = [303.5930, 286.0152, 272.6675, 253.6669, 238.8665, 232.4375, 224.9906, 218.7975, 210.9468, 196.7401, 180.0950]\n",
    "dtf_x = [6.9704, 2.5433, 0.6739, 0.5183, 0.3901, 0.3994, 0.4995, 0.3777, 0.3864, 0.3636, 0.4790]\n",
    "trunc = [0.5, 0.55, 0.6, 0.65, 0.7, 0.725, 0.75, 0.775, 0.8, 0.85, 0.9]\n",
    "         \n",
    "plt.figure()\n",
    "plt.errorbar(p_1, tf_x, yerr = dtf_x, fmt = 'og')\n",
    "plt.xlabel('Power of Arm 1')\n",
    "plt.ylabel('Horz TF (Hz)')\n",
    "plt.tight_layout()\n",
    "plt.grid(visible=1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "v_x = 27451.697 Hz\n"
     ]
    }
   ],
   "source": [
    "import numpy as np\n",
    "from astropy import units as u, constants as ac\n",
    "\n",
    "DY_POLARIZABILITY = 184.4 # in a.u, most precise measured value of Dy polarizability\n",
    "DY_MASS = 164*u.u\n",
    "\n",
    "def horz_tf(x, w_x, w_z):\n",
    "    w_x = w_x*u.um\n",
    "    w_z = w_z*u.um\n",
    "    x = x * u.W\n",
    "    alpha = DY_POLARIZABILITY\n",
    "    m = DY_MASS\n",
    "    TrapDepth = 2*x/(np.pi*w_x*w_z) * (1 / (2 * ac.eps0 * ac.c)) * alpha * (4 * np.pi * ac.eps0 * ac.a0**3)\n",
    "    ret = ((1/(2 * np.pi)) * np.sqrt(4 * TrapDepth / (m*w_x**2))).decompose()\n",
    "    return ret.value\n",
    "    \n",
    "def vert_tf(x, w_x, w_z):\n",
    "    w_x = w_x*u.um\n",
    "    w_z = w_z*u.um\n",
    "    x = x * u.W\n",
    "    alpha = DY_POLARIZABILITY\n",
    "    m = DY_MASS\n",
    "    TrapDepth = 2*x/(np.pi*w_x*w_z) * (1 / (2 * ac.eps0 * ac.c)) * alpha * (4 * np.pi * ac.eps0 * ac.a0**3)\n",
    "    ret = ((1/(2 * np.pi)) * np.sqrt(4 * TrapDepth / (m*w_z**2))).decompose()\n",
    "    return ret.value\n",
    "\n",
    "\n",
    "v = horz_tf(30, 30, 0.2)\n",
    "print('v_x = %.3f Hz' %(v))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 42,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<h2> Model</h2> Model(horz_tf) <h2>Fit Statistics</h2><table><tr><td>fitting method</td><td>leastsq</td><td></td></tr><tr><td># function evals</td><td>26</td><td></td></tr><tr><td># data points</td><td>9</td><td></td></tr><tr><td># variables</td><td>2</td><td></td></tr><tr><td>chi-square</td><td> 79.9011718</td><td></td></tr><tr><td>reduced chi-square</td><td> 11.4144531</td><td></td></tr><tr><td>Akaike info crit.</td><td> 23.6520935</td><td></td></tr><tr><td>Bayesian info crit.</td><td> 24.0465426</td><td></td></tr></table><h2>Variables</h2><table><tr><th> name </th><th> value </th><th> standard error </th><th> relative error </th><th> initial value </th><th> min </th><th> max </th><th> vary </th></tr><tr><td> w_x </td><td>  24.1519450 </td><td>  292150.064 </td><td> (1209633.69%) </td><td> 25 </td><td>  0.00000000 </td><td>  100.000000 </td><td> True </td></tr><tr><td> w_z </td><td>  52.4613985 </td><td>  1903772.36 </td><td> (3628901.28%) </td><td> 35 </td><td>  0.00000000 </td><td>  100.000000 </td><td> True </td></tr></table><h2>Correlations (unreported correlations are < 0.100)</h2><table><tr><td>w_x</td><td>w_z</td><td>-1.0000</td></tr></table>"
      ],
      "text/plain": [
       "<lmfit.model.ModelResult at 0x1b68d072d60>"
      ]
     },
     "execution_count": 42,
     "metadata": {},
     "output_type": "execute_result"
    },
    {
     "data": {
      "image/png": "[encoded data, 34200 characters]",
      "text/plain": [
       "<Figure size 640x480 with 1 Axes>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "from lmfit import Model\n",
    "\n",
    "fitModel = Model(horz_tf, independent_vars=['x'], param_names=['w_x', 'w_z'], nan_policy='raise')\n",
    "params = fitModel.make_params()\n",
    "params['w_x'].set(value=25, min=0, max=100)\n",
    "params['w_z'].set(value=35, min=0, max=100)\n",
    "fitResult = fitModel.fit(data=np.array(tf_z[:-2]), params=params, x=np.array(p_1[:-2]))\n",
    "\n",
    "plt.figure()\n",
    "plt.errorbar(p_1, tf_x, yerr = dtf_x, fmt = 'og')\n",
    "plt.errorbar(p_1[:-2], fitResult.best_fit, fmt = 'k--')\n",
    "plt.xlabel('Power of Arm 1')\n",
    "plt.ylabel('Horz TF (Hz)')\n",
    "plt.tight_layout()\n",
    "plt.grid(visible=1)\n",
    "\n",
    "fitResult"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 68,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[0.005, 0.0057, 0.0064, 0.0071, 0.0078, 0.0085, 0.0092, 0.0099, 0.0106, 0.0113, 0.012, 0.0127, 0.0134, 0.0141, 0.0148, 0.0155, 0.0162, 0.0169, 0.0176, 0.0183, 0.019, 0.0197]\n",
      "22\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "0.01235"
      ]
     },
     "execution_count": 68,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "l = list(np.arange(0.005, 0.02, 7e-4))\n",
    "# l = np.logspace(np.log10(250e-6), np.log10(500e-3), num=15)\n",
    "\n",
    "l = [round(item, 7) for item in l]\n",
    "#random.shuffle(l)\n",
    "\n",
    "print(l)\n",
    "print(len(l))\n",
    "np.mean(l)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "pixel = 5.86e-6\n",
    "M     = 0.6827\n",
    "F = (1/(0.3725*8.4743e-14)) * (pixel / M)**2\n",
    "NCount = 85000\n",
    "AtomNumber = NCount * F / 1e8\n",
    "print(AtomNumber)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "muB = 9.274e-24\n",
    "hbar = 6.626e-34 / (2 * np.pi)\n",
    "gJ = 1.24\n",
    "\n",
    "f = ufloat(10108.46982, 0.26282) \n",
    "Delta = 2 * np.pi *  f  * 1e3\n",
    "\n",
    "Bz = (Delta*hbar) / (muB*gJ)\n",
    "print(Bz * 1e4)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "muB = 9.274e-24\n",
    "hbar = 6.626e-34 / (2 * np.pi)\n",
    "gJ = 1.24\n",
    "Bz = 5.8854 * 1e-4\n",
    "(Bz*muB*gJ/hbar) / (2 * np.pi * 1e6)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## ODT 1 Calibration"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "v_high = 2.7\n",
    "\"\"\"High Power\"\"\"\n",
    "P_arm1_high = 5.776 * v_high - 0.683\n",
    "\n",
    "v_mid = 0.2076\n",
    "\"\"\"Intermediate Power\"\"\"\n",
    "P_arm1_mid = 5.815 * v_mid - 0.03651\n",
    "\n",
    "v_low = 0.062\n",
    "\"\"\"Low Power\"\"\"\n",
    "P_arm1_low = 5271 * v_low - 27.5\n",
    "\n",
    "print(round(P_arm1_high, 3))\n",
    "print(round(P_arm1_mid, 3))\n",
    "print(round(P_arm1_low, 3))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## ODT 2 Power Calibration"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "v = 0.842\n",
    "P_arm2 = 2.302 * v - 0.06452\n",
    "print(round(P_arm2, 3))"
   ]
  }
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