{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# How to index, slice, modify, and delete data points"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Very usually, we need to select, modify and even delete the data of certain shots. Here there is a short introduction on how to do that.\n",
    "\n",
    "Let us start with importing the supporting packages and loading the data. In order to keep things ealier, here we will import all the packages, but not all of them will be us"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Load some example data"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Import supporting packages"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Set the system path for importing packages\n",
    "# This is just because I put all example scripts in another folder\n",
    "# You DO NOT need to do this \n",
    "# -------------- You do NOT need following part --------------\n",
    "import sys\n",
    "import os\n",
    "sys.path.insert(0, os.path.abspath('..'))\n",
    "# -------------- You do NOT need above part --------------\n",
    "\n",
    "import copy\n",
    "import glob\n",
    "from datetime import datetime\n",
    "\n",
    "# The package for data structure\n",
    "import xarray as xr\n",
    "import pandas as pd\n",
    "import numpy as np\n",
    "\n",
    "# The packages for working with uncertainties\n",
    "from uncertainties import ufloat\n",
    "from uncertainties import unumpy as unp\n",
    "from uncertainties import umath\n",
    "\n",
    "# The package for plotting\n",
    "import matplotlib.pyplot as plt\n",
    "plt.rcParams['font.size'] = 18 # Set the global font size\n",
    "\n",
    "# -------------- The modules written by us --------------\n",
    "\n",
    "# The packages for read data\n",
    "from DataContainer.ReadData import read_hdf5_file, read_hdf5_global, read_hdf5_run_time, read_csv_file\n",
    "\n",
    "# The packages for data analysis\n",
    "from Analyser.ImagingAnalyser import ImageAnalyser\n",
    "from Analyser.FitAnalyser import FitAnalyser\n",
    "from Analyser.FitAnalyser import ThomasFermi2dModel, DensityProfileBEC2dModel, Polylog22dModel\n",
    "from Analyser.FFTAnalyser import fft, ifft, fft_nutou\n",
    "from ToolFunction.ToolFunction import *\n",
    "\n",
    "# Add errorbar plot to xarray package\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"
   ]
  },
  {
   "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-b0e6c9ce-2097-11ee-9d7c-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;\">2c85baf6</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> 6\n",
       "                </td>\n",
       "            </tr>\n",
       "            <tr>\n",
       "                <td style=\"text-align: left;\">\n",
       "                    <strong>Total threads:</strong> 60\n",
       "                </td>\n",
       "                <td style=\"text-align: left;\">\n",
       "                    <strong>Total memory:</strong> 55.88 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-3edf5152-70c9-41bc-b2e3-dd1cacfc5ef2</p>\n",
       "            <table style=\"width: 100%; text-align: left;\">\n",
       "                <tr>\n",
       "                    <td style=\"text-align: left;\">\n",
       "                        <strong>Comm:</strong> tcp://127.0.0.1:62125\n",
       "                    </td>\n",
       "                    <td style=\"text-align: left;\">\n",
       "                        <strong>Workers:</strong> 6\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> 60\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> 55.88 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://127.0.0.1:62161\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Total threads: </strong> 10\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Dashboard: </strong> <a href=\"http://127.0.0.1:62163/status\" target=\"_blank\">http://127.0.0.1:62163/status</a>\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Memory: </strong> 9.31 GiB\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Nanny: </strong> tcp://127.0.0.1:62128\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-doscq09y\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://127.0.0.1:62167\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Total threads: </strong> 10\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Dashboard: </strong> <a href=\"http://127.0.0.1:62168/status\" target=\"_blank\">http://127.0.0.1:62168/status</a>\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Memory: </strong> 9.31 GiB\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Nanny: </strong> tcp://127.0.0.1:62129\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-7b8nhgmg\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://127.0.0.1:62156\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Total threads: </strong> 10\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Dashboard: </strong> <a href=\"http://127.0.0.1:62159/status\" target=\"_blank\">http://127.0.0.1:62159/status</a>\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Memory: </strong> 9.31 GiB\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Nanny: </strong> tcp://127.0.0.1:62130\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-y1tkfpfy\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://127.0.0.1:62162\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Total threads: </strong> 10\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Dashboard: </strong> <a href=\"http://127.0.0.1:62165/status\" target=\"_blank\">http://127.0.0.1:62165/status</a>\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Memory: </strong> 9.31 GiB\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Nanny: </strong> tcp://127.0.0.1:62131\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-613gqycm\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://127.0.0.1:62150\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Total threads: </strong> 10\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Dashboard: </strong> <a href=\"http://127.0.0.1:62153/status\" target=\"_blank\">http://127.0.0.1:62153/status</a>\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Memory: </strong> 9.31 GiB\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Nanny: </strong> tcp://127.0.0.1:62132\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-nf2w0fki\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://127.0.0.1:62155\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Total threads: </strong> 10\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Dashboard: </strong> <a href=\"http://127.0.0.1:62157/status\" target=\"_blank\">http://127.0.0.1:62157/status</a>\n",
       "                        </td>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Memory: </strong> 9.31 GiB\n",
       "                        </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <td style=\"text-align: left;\">\n",
       "                            <strong>Nanny: </strong> tcp://127.0.0.1:62133\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-xm8jsrrg\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://127.0.0.1:62125' processes=6 threads=60, memory=55.88 GiB>"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from dask.distributed import Client\n",
    "client = Client(n_workers=6, threads_per_worker=10, processes=True, memory_limit='10GB')\n",
    "client"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Set the path for different cameras"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "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",
    "# give a short name to each path (or let's say each camera)\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",
    "}"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Set global path for experiment"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "img_dir = '//DyLabNAS/Data/'\n",
    "SequenceName = \"Evaporative_Cooling\" + \"/\"\n",
    "folderPath = img_dir + SequenceName + '2023/04/17'# get_date()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Load shot 0058"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "\n",
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       ".xr-attrs dd {\n",
       "  padding: 0;\n",
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       "\n",
       ".xr-attrs dt {\n",
       "  font-weight: normal;\n",
       "  grid-column: 1;\n",
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       "\n",
       ".xr-attrs dt:hover span {\n",
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       "\n",
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       "\n",
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       "</style><pre class='xr-text-repr-fallback'>&lt;xarray.Dataset&gt;\n",
       "Dimensions:           (runs: 5, truncation_value: 11, y: 1200, x: 1920)\n",
       "Coordinates:\n",
       "  * runs              (runs) float64 0.0 1.0 2.0 3.0 4.0\n",
       "  * truncation_value  (truncation_value) float64 0.8 0.83 0.85 ... 0.97 0.99 1.0\n",
       "Dimensions without coordinates: y, x\n",
       "Data variables:\n",
       "    atoms             (runs, truncation_value, y, x) uint16 99 100 ... 126 129\n",
       "    background        (runs, truncation_value, y, x) uint16 103 100 ... 122 124\n",
       "    dark              (runs, truncation_value, y, x) uint16 51 52 52 ... 49 50\n",
       "    shotNum           (runs, truncation_value) &lt;U2 &#x27;00&#x27; &#x27;01&#x27; &#x27;02&#x27; ... &#x27;53&#x27; &#x27;54&#x27;\n",
       "Attributes: (12/100)\n",
       "    TOF_free:                          0.02\n",
       "    abs_img_freq:                      110.866\n",
       "    absorption_imaging_flag:           True\n",
       "    backup_data:                       True\n",
       "    blink_off_time:                    nan\n",
       "    blink_on_time:                     nan\n",
       "    ...                                ...\n",
       "    z_offset:                          0.195\n",
       "    z_offset_img:                      0.195\n",
       "    truncation_value:                  [0.8  0.83 0.85 0.87 0.89 0.91 0.93 0....\n",
       "    runs:                              [0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 1...\n",
       "    scanAxis:                          [&#x27;runs&#x27; &#x27;truncation_value&#x27;]\n",
       "    scanAxisLength:                    [55. 55.]</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-f6866415-13e6-4ceb-9e2b-bb7ccda03142' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-f6866415-13e6-4ceb-9e2b-bb7ccda03142' class='xr-section-summary'  title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span class='xr-has-index'>runs</span>: 5</li><li><span class='xr-has-index'>truncation_value</span>: 11</li><li><span>y</span>: 1200</li><li><span>x</span>: 1920</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-e5d20d4c-8cf2-4236-9189-e341a83a1b66' class='xr-section-summary-in' type='checkbox'  checked><label for='section-e5d20d4c-8cf2-4236-9189-e341a83a1b66' 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'>runs</span></div><div class='xr-var-dims'>(runs)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>0.0 1.0 2.0 3.0 4.0</div><input id='attrs-c9415d14-bf51-46e8-9859-e5bfddddc1dd' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-c9415d14-bf51-46e8-9859-e5bfddddc1dd' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-01eac335-7b56-462b-8231-7467bd19d7c0' class='xr-var-data-in' type='checkbox'><label for='data-01eac335-7b56-462b-8231-7467bd19d7c0' 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., 1., 2., 3., 4.])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>truncation_value</span></div><div class='xr-var-dims'>(truncation_value)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>0.8 0.83 0.85 ... 0.97 0.99 1.0</div><input id='attrs-dc9d5dc6-8fe5-4e0a-87ea-409689e906af' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-dc9d5dc6-8fe5-4e0a-87ea-409689e906af' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ca9ff513-98c4-4649-874e-dbd81877bbf1' class='xr-var-data-in' type='checkbox'><label for='data-ca9ff513-98c4-4649-874e-dbd81877bbf1' 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([0.8 , 0.83, 0.85, 0.87, 0.89, 0.91, 0.93, 0.95, 0.97, 0.99, 1.  ])</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-3d03f457-3b77-4a87-9eaa-8e130f0a616b' class='xr-section-summary-in' type='checkbox'  checked><label for='section-3d03f457-3b77-4a87-9eaa-8e130f0a616b' class='xr-section-summary' >Data variables: <span>(4)</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>atoms</span></div><div class='xr-var-dims'>(runs, truncation_value, y, x)</div><div class='xr-var-dtype'>uint16</div><div class='xr-var-preview xr-preview'>99 100 102 87 ... 130 125 126 129</div><input id='attrs-4309b054-d25d-4782-8642-c423c254d48c' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-4309b054-d25d-4782-8642-c423c254d48c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1616364a-d417-4fea-8bc5-96a6bafbf0f6' class='xr-var-data-in' type='checkbox'><label for='data-1616364a-d417-4fea-8bc5-96a6bafbf0f6' 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'><dt><span>IMAGE_SUBCLASS :</span></dt><dd>IMAGE_GRAYSCALE</dd><dt><span>IMAGE_VERSION :</span></dt><dd>1.2</dd><dt><span>IMAGE_WHITE_IS_ZERO :</span></dt><dd>0</dd></dl></div><div class='xr-var-data'><pre>array([[[[ 99, 100, 102, ..., 163, 153, 147],\n",
       "         [100, 106,  99, ..., 149, 148, 146],\n",
       "         [ 94,  95,  96, ..., 139, 144, 148],\n",
       "         ...,\n",
       "         [ 98, 106, 105, ..., 133, 142, 142],\n",
       "         [112, 109, 102, ..., 128, 136, 131],\n",
       "         [112, 113, 111, ..., 121, 122, 131]],\n",
       "\n",
       "        [[102, 103, 100, ..., 155, 154, 142],\n",
       "         [ 97, 100, 101, ..., 146, 146, 156],\n",
       "         [ 91,  93,  97, ..., 142, 136, 151],\n",
       "         ...,\n",
       "         [105, 103, 103, ..., 144, 134, 142],\n",
       "         [102, 104, 112, ..., 133, 134, 135],\n",
       "         [114, 115, 113, ..., 119, 126, 122]],\n",
       "\n",
       "        [[101, 105, 103, ..., 148, 152, 146],\n",
       "         [101, 102,  98, ..., 143, 146, 149],\n",
       "         [ 97,  98,  98, ..., 139, 137, 146],\n",
       "         ...,\n",
       "...\n",
       "         ...,\n",
       "         [100, 102, 109, ..., 135, 141, 140],\n",
       "         [106, 103, 105, ..., 128, 140, 132],\n",
       "         [114, 107, 108, ..., 121, 123, 126]],\n",
       "\n",
       "        [[101, 102, 101, ..., 153, 153, 146],\n",
       "         [101, 103, 100, ..., 148, 143, 149],\n",
       "         [ 96,  95,  98, ..., 145, 138, 144],\n",
       "         ...,\n",
       "         [ 98, 107, 103, ..., 140, 142, 145],\n",
       "         [106, 100, 103, ..., 133, 133, 136],\n",
       "         [115, 103, 102, ..., 123, 125, 128]],\n",
       "\n",
       "        [[103, 100, 102, ..., 154, 147, 153],\n",
       "         [ 96, 103,  97, ..., 150, 150, 152],\n",
       "         [ 96, 100,  96, ..., 141, 142, 144],\n",
       "         ...,\n",
       "         [101, 102, 101, ..., 139, 142, 140],\n",
       "         [105, 105,  98, ..., 132, 135, 131],\n",
       "         [109, 111, 107, ..., 125, 126, 129]]]], dtype=uint16)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>background</span></div><div class='xr-var-dims'>(runs, truncation_value, y, x)</div><div class='xr-var-dtype'>uint16</div><div class='xr-var-preview xr-preview'>103 100 101 92 ... 130 122 122 124</div><input id='attrs-f9914ab6-98a1-4a63-8217-da175587ca5e' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-f9914ab6-98a1-4a63-8217-da175587ca5e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-abec8df5-4e10-4673-ac41-49e32040b672' class='xr-var-data-in' type='checkbox'><label for='data-abec8df5-4e10-4673-ac41-49e32040b672' 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'><dt><span>IMAGE_SUBCLASS :</span></dt><dd>IMAGE_GRAYSCALE</dd><dt><span>IMAGE_VERSION :</span></dt><dd>1.2</dd><dt><span>IMAGE_WHITE_IS_ZERO :</span></dt><dd>0</dd></dl></div><div class='xr-var-data'><pre>array([[[[103, 100, 101, ..., 161, 147, 146],\n",
       "         [101,  96,  97, ..., 146, 144, 146],\n",
       "         [ 92,  95,  96, ..., 143, 134, 149],\n",
       "         ...,\n",
       "         [104, 103, 107, ..., 139, 142, 137],\n",
       "         [104, 105, 109, ..., 128, 133, 130],\n",
       "         [111, 111, 107, ..., 118, 120, 123]],\n",
       "\n",
       "        [[ 96, 100,  99, ..., 155, 149, 139],\n",
       "         [ 94, 101, 100, ..., 149, 143, 151],\n",
       "         [ 94,  90,  97, ..., 140, 143, 139],\n",
       "         ...,\n",
       "         [103, 105, 103, ..., 126, 139, 144],\n",
       "         [104, 111, 105, ..., 131, 136, 134],\n",
       "         [111, 112, 104, ..., 121, 126, 137]],\n",
       "\n",
       "        [[101,  99, 107, ..., 154, 146, 151],\n",
       "         [ 97, 101, 100, ..., 148, 148, 145],\n",
       "         [ 87, 102, 100, ..., 145, 133, 140],\n",
       "         ...,\n",
       "...\n",
       "         ...,\n",
       "         [105, 100,  99, ..., 132, 142, 137],\n",
       "         [ 96, 104, 102, ..., 133, 135, 133],\n",
       "         [110, 109, 103, ..., 123, 122, 119]],\n",
       "\n",
       "        [[101, 102, 101, ..., 156, 154, 149],\n",
       "         [ 95,  99,  99, ..., 140, 146, 153],\n",
       "         [ 91, 103,  97, ..., 142, 140, 147],\n",
       "         ...,\n",
       "         [ 98, 106, 106, ..., 132, 139, 147],\n",
       "         [102, 110, 108, ..., 127, 130, 131],\n",
       "         [110, 109, 106, ..., 127, 125, 127]],\n",
       "\n",
       "        [[103, 106, 105, ..., 146, 146, 147],\n",
       "         [ 99, 103, 102, ..., 152, 142, 152],\n",
       "         [ 97, 100,  92, ..., 143, 138, 156],\n",
       "         ...,\n",
       "         [104, 108, 105, ..., 142, 141, 139],\n",
       "         [107, 104, 104, ..., 131, 137, 128],\n",
       "         [110, 109, 107, ..., 122, 122, 124]]]], dtype=uint16)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>dark</span></div><div class='xr-var-dims'>(runs, truncation_value, y, x)</div><div class='xr-var-dtype'>uint16</div><div class='xr-var-preview xr-preview'>51 52 52 51 51 ... 52 50 53 49 50</div><input id='attrs-76370da3-3eeb-4ffc-8da7-38cfa32416fd' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-76370da3-3eeb-4ffc-8da7-38cfa32416fd' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-90342ed7-aa13-46bd-a2cb-f0f48910fe9d' class='xr-var-data-in' type='checkbox'><label for='data-90342ed7-aa13-46bd-a2cb-f0f48910fe9d' 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'><dt><span>IMAGE_SUBCLASS :</span></dt><dd>IMAGE_GRAYSCALE</dd><dt><span>IMAGE_VERSION :</span></dt><dd>1.2</dd><dt><span>IMAGE_WHITE_IS_ZERO :</span></dt><dd>0</dd></dl></div><div class='xr-var-data'><pre>array([[[[51, 52, 52, ..., 50, 51, 51],\n",
       "         [50, 50, 51, ..., 51, 51, 49],\n",
       "         [51, 51, 50, ..., 50, 50, 49],\n",
       "         ...,\n",
       "         [50, 51, 50, ..., 50, 50, 49],\n",
       "         [50, 50, 49, ..., 50, 50, 51],\n",
       "         [51, 50, 50, ..., 50, 50, 51]],\n",
       "\n",
       "        [[50, 52, 51, ..., 50, 50, 49],\n",
       "         [51, 50, 50, ..., 50, 50, 50],\n",
       "         [50, 51, 49, ..., 50, 50, 51],\n",
       "         ...,\n",
       "         [51, 50, 50, ..., 52, 50, 51],\n",
       "         [51, 50, 51, ..., 50, 52, 51],\n",
       "         [51, 52, 51, ..., 51, 50, 50]],\n",
       "\n",
       "        [[51, 51, 52, ..., 51, 51, 50],\n",
       "         [50, 50, 51, ..., 51, 51, 51],\n",
       "         [50, 50, 50, ..., 50, 50, 50],\n",
       "         ...,\n",
       "...\n",
       "         ...,\n",
       "         [51, 50, 51, ..., 51, 51, 51],\n",
       "         [50, 49, 50, ..., 49, 51, 51],\n",
       "         [50, 51, 50, ..., 50, 49, 51]],\n",
       "\n",
       "        [[50, 50, 50, ..., 51, 50, 51],\n",
       "         [51, 50, 51, ..., 51, 50, 49],\n",
       "         [52, 49, 50, ..., 52, 51, 51],\n",
       "         ...,\n",
       "         [50, 50, 50, ..., 49, 50, 49],\n",
       "         [50, 49, 51, ..., 51, 50, 51],\n",
       "         [52, 51, 52, ..., 50, 51, 51]],\n",
       "\n",
       "        [[50, 51, 49, ..., 50, 51, 51],\n",
       "         [51, 52, 51, ..., 51, 51, 50],\n",
       "         [52, 51, 51, ..., 49, 51, 51],\n",
       "         ...,\n",
       "         [52, 50, 51, ..., 52, 50, 51],\n",
       "         [50, 51, 50, ..., 51, 50, 50],\n",
       "         [50, 51, 51, ..., 53, 49, 50]]]], dtype=uint16)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>shotNum</span></div><div class='xr-var-dims'>(runs, truncation_value)</div><div class='xr-var-dtype'>&lt;U2</div><div class='xr-var-preview xr-preview'>&#x27;00&#x27; &#x27;01&#x27; &#x27;02&#x27; ... &#x27;52&#x27; &#x27;53&#x27; &#x27;54&#x27;</div><input id='attrs-d222e2e8-8564-45fc-91cc-6a8ef6b20bc2' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-d222e2e8-8564-45fc-91cc-6a8ef6b20bc2' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-82580c3f-c948-4675-a4fa-39d0c59b6cea' class='xr-var-data-in' type='checkbox'><label for='data-82580c3f-c948-4675-a4fa-39d0c59b6cea' 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([[&#x27;00&#x27;, &#x27;01&#x27;, &#x27;02&#x27;, &#x27;03&#x27;, &#x27;04&#x27;, &#x27;05&#x27;, &#x27;06&#x27;, &#x27;07&#x27;, &#x27;08&#x27;, &#x27;09&#x27;, &#x27;10&#x27;],\n",
       "       [&#x27;11&#x27;, &#x27;12&#x27;, &#x27;13&#x27;, &#x27;14&#x27;, &#x27;15&#x27;, &#x27;16&#x27;, &#x27;17&#x27;, &#x27;18&#x27;, &#x27;19&#x27;, &#x27;20&#x27;, &#x27;21&#x27;],\n",
       "       [&#x27;22&#x27;, &#x27;23&#x27;, &#x27;24&#x27;, &#x27;25&#x27;, &#x27;26&#x27;, &#x27;27&#x27;, &#x27;28&#x27;, &#x27;29&#x27;, &#x27;30&#x27;, &#x27;31&#x27;, &#x27;32&#x27;],\n",
       "       [&#x27;33&#x27;, &#x27;34&#x27;, &#x27;35&#x27;, &#x27;36&#x27;, &#x27;37&#x27;, &#x27;38&#x27;, &#x27;39&#x27;, &#x27;40&#x27;, &#x27;41&#x27;, &#x27;42&#x27;, &#x27;43&#x27;],\n",
       "       [&#x27;44&#x27;, &#x27;45&#x27;, &#x27;46&#x27;, &#x27;47&#x27;, &#x27;48&#x27;, &#x27;49&#x27;, &#x27;50&#x27;, &#x27;51&#x27;, &#x27;52&#x27;, &#x27;53&#x27;, &#x27;54&#x27;]],\n",
       "      dtype=&#x27;&lt;U2&#x27;)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-330a8433-d4b6-47ea-9e85-5fdc7612e0e9' class='xr-section-summary-in' type='checkbox'  ><label for='section-330a8433-d4b6-47ea-9e85-5fdc7612e0e9' 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>runs</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-3f3fae6c-3d6d-4507-a2c3-e03b55fa5052' class='xr-index-data-in' type='checkbox'/><label for='index-3f3fae6c-3d6d-4507-a2c3-e03b55fa5052' 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([0.0, 1.0, 2.0, 3.0, 4.0], dtype=&#x27;float64&#x27;, name=&#x27;runs&#x27;))</pre></div></li><li class='xr-var-item'><div class='xr-index-name'><div>truncation_value</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-de25337f-f532-44ee-abbc-badfdecb8ec4' class='xr-index-data-in' type='checkbox'/><label for='index-de25337f-f532-44ee-abbc-badfdecb8ec4' 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([0.8, 0.83, 0.85, 0.87, 0.89, 0.91, 0.93, 0.95, 0.97, 0.99, 1.0], dtype=&#x27;float64&#x27;, name=&#x27;truncation_value&#x27;))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-0e9068ec-5b28-4b91-999c-6fe2882e98ec' class='xr-section-summary-in' type='checkbox'  ><label for='section-0e9068ec-5b28-4b91-999c-6fe2882e98ec' class='xr-section-summary' >Attributes: <span>(100)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>TOF_free :</span></dt><dd>0.02</dd><dt><span>abs_img_freq :</span></dt><dd>110.866</dd><dt><span>absorption_imaging_flag :</span></dt><dd>True</dd><dt><span>backup_data :</span></dt><dd>True</dd><dt><span>blink_off_time :</span></dt><dd>nan</dd><dt><span>blink_on_time :</span></dt><dd>nan</dd><dt><span>c_duration :</span></dt><dd>0.2</dd><dt><span>cmot_final_current :</span></dt><dd>0.65</dd><dt><span>cmot_hold :</span></dt><dd>0.06</dd><dt><span>cmot_initial_current :</span></dt><dd>0.18</dd><dt><span>compX_current :</span></dt><dd>0.005</dd><dt><span>compX_current_sg :</span></dt><dd>0</dd><dt><span>compX_final_current :</span></dt><dd>0.002</dd><dt><span>compX_initial_current :</span></dt><dd>0.005</dd><dt><span>compY_current :</span></dt><dd>0</dd><dt><span>compY_current_sg :</span></dt><dd>0</dd><dt><span>compY_final_current :</span></dt><dd>0</dd><dt><span>compY_initial_current :</span></dt><dd>0</dd><dt><span>compZ_current :</span></dt><dd>0</dd><dt><span>compZ_current_sg :</span></dt><dd>0.195</dd><dt><span>compZ_final_current :</span></dt><dd>0.287</dd><dt><span>compZ_initial_current :</span></dt><dd>0</dd><dt><span>default_camera :</span></dt><dd>0</dd><dt><span>evap_1_final_pow_1 :</span></dt><dd>4.8</dd><dt><span>evap_1_final_pow_2 :</span></dt><dd>2.2</dd><dt><span>evap_1_final_pow_3 :</span></dt><dd>1.2</dd><dt><span>evap_1_final_pow_4 :</span></dt><dd>0.526</dd><dt><span>evap_1_ramp_duration_1 :</span></dt><dd>0.15</dd><dt><span>evap_1_ramp_duration_2 :</span></dt><dd>0.3</dd><dt><span>evap_1_ramp_duration_3 :</span></dt><dd>0.2</dd><dt><span>evap_1_ramp_duration_4 :</span></dt><dd>0.5</dd><dt><span>evap_1_start_pow_1 :</span></dt><dd>7</dd><dt><span>evap_1_start_pow_2 :</span></dt><dd>4.8</dd><dt><span>evap_1_start_pow_3 :</span></dt><dd>2.2</dd><dt><span>evap_1_start_pow_4 :</span></dt><dd>1.2</dd><dt><span>evap_2_final_pow_1 :</span></dt><dd>0.35</dd><dt><span>evap_2_ramp_duration_1 :</span></dt><dd>0.5</dd><dt><span>evap_2_start_pow_1 :</span></dt><dd>0.526</dd><dt><span>evap_3_arm_1_final_pow :</span></dt><dd>0.037</dd><dt><span>evap_3_arm_1_start_pow :</span></dt><dd>0.35</dd><dt><span>evap_3_arm_2_final_pow :</span></dt><dd>0.09</dd><dt><span>evap_3_arm_2_start_pow :</span></dt><dd>5</dd><dt><span>evap_3_ramp_duration :</span></dt><dd>1</dd><dt><span>evap_3_rate_constant_1 :</span></dt><dd>0.37</dd><dt><span>evap_3_rate_constant_2 :</span></dt><dd>0.71</dd><dt><span>evap_4_arm_1_final_pow :</span></dt><dd>0.085</dd><dt><span>evap_4_arm_1_start_pow :</span></dt><dd>0.037</dd><dt><span>evap_ramp_4_duration :</span></dt><dd>0.1</dd><dt><span>final_amp :</span></dt><dd>0.00018</dd><dt><span>final_freq :</span></dt><dd>104</dd><dt><span>gradCoil_current :</span></dt><dd>0.18</dd><dt><span>gradCoil_current_sg :</span></dt><dd>0</dd><dt><span>imaging_method :</span></dt><dd>in_situ_absorption</dd><dt><span>imaging_pulse_duration :</span></dt><dd>2.5e-05</dd><dt><span>imaging_wavelength :</span></dt><dd>4.21291e-07</dd><dt><span>initial_amp :</span></dt><dd>0.62</dd><dt><span>initial_freq :</span></dt><dd>101.9</dd><dt><span>mod_depth_1_fin :</span></dt><dd>0.5</dd><dt><span>mod_depth_1_ini :</span></dt><dd>1</dd><dt><span>mod_depth_2_fin :</span></dt><dd>0.2</dd><dt><span>mod_depth_2_ini :</span></dt><dd>0.5</dd><dt><span>mod_depth_3_fin :</span></dt><dd>0.15</dd><dt><span>mod_depth_3_ini :</span></dt><dd>0.2</dd><dt><span>mod_depth_4_fin :</span></dt><dd>0</dd><dt><span>mod_depth_4_ini :</span></dt><dd>0.15</dd><dt><span>mod_depth_ini :</span></dt><dd>1</dd><dt><span>mod_depth_on_final :</span></dt><dd>0.35</dd><dt><span>mod_depth_on_initial :</span></dt><dd>0</dd><dt><span>mot_3d_amp :</span></dt><dd>0.62</dd><dt><span>mot_3d_camera_exposure_time :</span></dt><dd>0.002</dd><dt><span>mot_3d_camera_trigger_duration :</span></dt><dd>0.00025</dd><dt><span>mot_3d_freq :</span></dt><dd>101.9</dd><dt><span>mot_load_duration :</span></dt><dd>2</dd><dt><span>odt_axis_camera_trigger_duration :</span></dt><dd>0.002</dd><dt><span>odt_hold_time_1 :</span></dt><dd>0.01</dd><dt><span>odt_hold_time_2 :</span></dt><dd>0.1</dd><dt><span>odt_hold_time_3 :</span></dt><dd>0.1</dd><dt><span>odt_hold_time_4 :</span></dt><dd>1</dd><dt><span>pow_arm_1 :</span></dt><dd>7</dd><dt><span>pow_arm_2 :</span></dt><dd>0</dd><dt><span>pow_fin_arm_2 :</span></dt><dd>5</dd><dt><span>pow_ini_arm_2 :</span></dt><dd>0</dd><dt><span>pulse_delay :</span></dt><dd>8e-05</dd><dt><span>push_amp :</span></dt><dd>0.16</dd><dt><span>push_freq :</span></dt><dd>102.6</dd><dt><span>ramp_duration :</span></dt><dd>1</dd><dt><span>save_results :</span></dt><dd>False</dd><dt><span>stern_gerlach_duration :</span></dt><dd>0.001</dd><dt><span>wait_after_2dmot_off :</span></dt><dd>0</dd><dt><span>wait_time_between_images :</span></dt><dd>0.22</dd><dt><span>x_offset :</span></dt><dd>0</dd><dt><span>x_offset_img :</span></dt><dd>0</dd><dt><span>y_offset :</span></dt><dd>0</dd><dt><span>y_offset_img :</span></dt><dd>0</dd><dt><span>z_offset :</span></dt><dd>0.195</dd><dt><span>z_offset_img :</span></dt><dd>0.195</dd><dt><span>truncation_value :</span></dt><dd>[0.8  0.83 0.85 0.87 0.89 0.91 0.93 0.95 0.97 0.99 1.   0.8  0.83 0.85\n",
       " 0.87 0.89 0.91 0.93 0.95 0.97 0.99 1.   0.8  0.83 0.85 0.87 0.89 0.91\n",
       " 0.93 0.95 0.97 0.99 1.   0.8  0.83 0.85 0.87 0.89 0.91 0.93 0.95 0.97\n",
       " 0.99 1.   0.8  0.83 0.85 0.87 0.89 0.91 0.93 0.95 0.97 0.99 1.  ]</dd><dt><span>runs :</span></dt><dd>[0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 2. 2.\n",
       " 2. 2. 2. 2. 2. 2. 2. 2. 2. 3. 3. 3. 3. 3. 3. 3. 3. 3. 3. 3. 4. 4. 4. 4.\n",
       " 4. 4. 4. 4. 4. 4. 4.]</dd><dt><span>scanAxis :</span></dt><dd>[&#x27;runs&#x27; &#x27;truncation_value&#x27;]</dd><dt><span>scanAxisLength :</span></dt><dd>[55. 55.]</dd></dl></div></li></ul></div></div>"
      ],
      "text/plain": [
       "<xarray.Dataset>\n",
       "Dimensions:           (runs: 5, truncation_value: 11, y: 1200, x: 1920)\n",
       "Coordinates:\n",
       "  * runs              (runs) float64 0.0 1.0 2.0 3.0 4.0\n",
       "  * truncation_value  (truncation_value) float64 0.8 0.83 0.85 ... 0.97 0.99 1.0\n",
       "Dimensions without coordinates: y, x\n",
       "Data variables:\n",
       "    atoms             (runs, truncation_value, y, x) uint16 99 100 ... 126 129\n",
       "    background        (runs, truncation_value, y, x) uint16 103 100 ... 122 124\n",
       "    dark              (runs, truncation_value, y, x) uint16 51 52 52 ... 49 50\n",
       "    shotNum           (runs, truncation_value) <U2 '00' '01' '02' ... '53' '54'\n",
       "Attributes: (12/100)\n",
       "    TOF_free:                          0.02\n",
       "    abs_img_freq:                      110.866\n",
       "    absorption_imaging_flag:           True\n",
       "    backup_data:                       True\n",
       "    blink_off_time:                    nan\n",
       "    blink_on_time:                     nan\n",
       "    ...                                ...\n",
       "    z_offset:                          0.195\n",
       "    z_offset_img:                      0.195\n",
       "    truncation_value:                  [0.8  0.83 0.85 0.87 0.89 0.91 0.93 0....\n",
       "    runs:                              [0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 1...\n",
       "    scanAxis:                          ['runs' 'truncation_value']\n",
       "    scanAxisLength:                    [55. 55.]"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "shotNum = \"0058\"\n",
    "filePath = folderPath + \"/\" + shotNum + \"/*.h5\"\n",
    "\n",
    "dataSetDict = {\n",
    "    dskey[groupList[i]]: read_hdf5_file(filePath, groupList[i])\n",
    "    for i in [0] # range(len(groupList)) # uncommont to load data for all three cameras\n",
    "}\n",
    "dataSet = dataSetDict[\"camera_0\"]\n",
    "\n",
    "dataSet = swap_xy(dataSet)\n",
    "\n",
    "scanAxis = get_scanAxis(dataSet)\n",
    "\n",
    "dataSet = auto_rechunk(dataSet)\n",
    "\n",
    "dataSet.load()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Index and select data"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Since we use the xarray package, in fact, it already has a well developed function to index and select the data. Therefore, have a look of the following link\n",
    "\n",
    "https://docs.xarray.dev/en/stable/user-guide/indexing.html"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Modify the data"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "There are two ways to select an element in xarray and modify the value of it."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Select by value"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The first method is to select it by the value of coordiante.\n",
    "\n",
    "Here is an emaxple of selecting the element in 'ShotNum' at 'runs'=0, truncation_value=0.8, and change it to '-1'."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
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       "</style><pre class='xr-text-repr-fallback'>&lt;xarray.DataArray &#x27;shotNum&#x27; (runs: 5, truncation_value: 11)&gt;\n",
       "array([[&#x27;-1&#x27;, &#x27;01&#x27;, &#x27;02&#x27;, &#x27;03&#x27;, &#x27;04&#x27;, &#x27;05&#x27;, &#x27;06&#x27;, &#x27;07&#x27;, &#x27;08&#x27;, &#x27;09&#x27;, &#x27;10&#x27;],\n",
       "       [&#x27;11&#x27;, &#x27;12&#x27;, &#x27;13&#x27;, &#x27;14&#x27;, &#x27;15&#x27;, &#x27;16&#x27;, &#x27;17&#x27;, &#x27;18&#x27;, &#x27;19&#x27;, &#x27;20&#x27;, &#x27;21&#x27;],\n",
       "       [&#x27;22&#x27;, &#x27;23&#x27;, &#x27;24&#x27;, &#x27;25&#x27;, &#x27;26&#x27;, &#x27;27&#x27;, &#x27;28&#x27;, &#x27;29&#x27;, &#x27;30&#x27;, &#x27;31&#x27;, &#x27;32&#x27;],\n",
       "       [&#x27;33&#x27;, &#x27;34&#x27;, &#x27;35&#x27;, &#x27;36&#x27;, &#x27;37&#x27;, &#x27;38&#x27;, &#x27;39&#x27;, &#x27;40&#x27;, &#x27;41&#x27;, &#x27;42&#x27;, &#x27;43&#x27;],\n",
       "       [&#x27;44&#x27;, &#x27;45&#x27;, &#x27;46&#x27;, &#x27;47&#x27;, &#x27;48&#x27;, &#x27;49&#x27;, &#x27;50&#x27;, &#x27;51&#x27;, &#x27;52&#x27;, &#x27;53&#x27;, &#x27;54&#x27;]],\n",
       "      dtype=&#x27;&lt;U2&#x27;)\n",
       "Coordinates:\n",
       "  * runs              (runs) float64 0.0 1.0 2.0 3.0 4.0\n",
       "  * truncation_value  (truncation_value) float64 0.8 0.83 0.85 ... 0.97 0.99 1.0</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'>'shotNum'</div><ul class='xr-dim-list'><li><span class='xr-has-index'>runs</span>: 5</li><li><span class='xr-has-index'>truncation_value</span>: 11</li></ul></div><ul class='xr-sections'><li class='xr-section-item'><div class='xr-array-wrap'><input id='section-d99314fe-ff17-44cb-b5f7-a182cc4128e0' class='xr-array-in' type='checkbox' checked><label for='section-d99314fe-ff17-44cb-b5f7-a182cc4128e0' 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>&#x27;-1&#x27; &#x27;01&#x27; &#x27;02&#x27; &#x27;03&#x27; &#x27;04&#x27; &#x27;05&#x27; &#x27;06&#x27; ... &#x27;49&#x27; &#x27;50&#x27; &#x27;51&#x27; &#x27;52&#x27; &#x27;53&#x27; &#x27;54&#x27;</span></div><div class='xr-array-data'><pre>array([[&#x27;-1&#x27;, &#x27;01&#x27;, &#x27;02&#x27;, &#x27;03&#x27;, &#x27;04&#x27;, &#x27;05&#x27;, &#x27;06&#x27;, &#x27;07&#x27;, &#x27;08&#x27;, &#x27;09&#x27;, &#x27;10&#x27;],\n",
       "       [&#x27;11&#x27;, &#x27;12&#x27;, &#x27;13&#x27;, &#x27;14&#x27;, &#x27;15&#x27;, &#x27;16&#x27;, &#x27;17&#x27;, &#x27;18&#x27;, &#x27;19&#x27;, &#x27;20&#x27;, &#x27;21&#x27;],\n",
       "       [&#x27;22&#x27;, &#x27;23&#x27;, &#x27;24&#x27;, &#x27;25&#x27;, &#x27;26&#x27;, &#x27;27&#x27;, &#x27;28&#x27;, &#x27;29&#x27;, &#x27;30&#x27;, &#x27;31&#x27;, &#x27;32&#x27;],\n",
       "       [&#x27;33&#x27;, &#x27;34&#x27;, &#x27;35&#x27;, &#x27;36&#x27;, &#x27;37&#x27;, &#x27;38&#x27;, &#x27;39&#x27;, &#x27;40&#x27;, &#x27;41&#x27;, &#x27;42&#x27;, &#x27;43&#x27;],\n",
       "       [&#x27;44&#x27;, &#x27;45&#x27;, &#x27;46&#x27;, &#x27;47&#x27;, &#x27;48&#x27;, &#x27;49&#x27;, &#x27;50&#x27;, &#x27;51&#x27;, &#x27;52&#x27;, &#x27;53&#x27;, &#x27;54&#x27;]],\n",
       "      dtype=&#x27;&lt;U2&#x27;)</pre></div></div></li><li class='xr-section-item'><input id='section-072c487d-d002-4259-a01b-c08c9f7ea79b' class='xr-section-summary-in' type='checkbox'  checked><label for='section-072c487d-d002-4259-a01b-c08c9f7ea79b' 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'>runs</span></div><div class='xr-var-dims'>(runs)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>0.0 1.0 2.0 3.0 4.0</div><input id='attrs-6385a017-4275-4e49-961d-e85d6ddf7cc7' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-6385a017-4275-4e49-961d-e85d6ddf7cc7' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-2d912bad-e388-4747-94fc-8e91e9ab1d65' class='xr-var-data-in' type='checkbox'><label for='data-2d912bad-e388-4747-94fc-8e91e9ab1d65' 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., 1., 2., 3., 4.])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>truncation_value</span></div><div class='xr-var-dims'>(truncation_value)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>0.8 0.83 0.85 ... 0.97 0.99 1.0</div><input id='attrs-09ed0bfd-14e3-4a30-adac-d71498309ce8' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-09ed0bfd-14e3-4a30-adac-d71498309ce8' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-62e5405a-da06-4a0f-bf31-e46024c03b81' class='xr-var-data-in' type='checkbox'><label for='data-62e5405a-da06-4a0f-bf31-e46024c03b81' 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([0.8 , 0.83, 0.85, 0.87, 0.89, 0.91, 0.93, 0.95, 0.97, 0.99, 1.  ])</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-e9b63c1f-c666-49cb-bdbb-1aa34bb6385e' class='xr-section-summary-in' type='checkbox'  ><label for='section-e9b63c1f-c666-49cb-bdbb-1aa34bb6385e' 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>runs</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-6d6ac887-feed-4441-bca4-a789b1f3b61d' class='xr-index-data-in' type='checkbox'/><label for='index-6d6ac887-feed-4441-bca4-a789b1f3b61d' 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([0.0, 1.0, 2.0, 3.0, 4.0], dtype=&#x27;float64&#x27;, name=&#x27;runs&#x27;))</pre></div></li><li class='xr-var-item'><div class='xr-index-name'><div>truncation_value</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-db91c79a-99fe-4316-b8ef-b3092bceb87b' class='xr-index-data-in' type='checkbox'/><label for='index-db91c79a-99fe-4316-b8ef-b3092bceb87b' 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([0.8, 0.83, 0.85, 0.87, 0.89, 0.91, 0.93, 0.95, 0.97, 0.99, 1.0], dtype=&#x27;float64&#x27;, name=&#x27;truncation_value&#x27;))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-c91e228a-d7cb-4584-8e9f-4435a2481da5' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-c91e228a-d7cb-4584-8e9f-4435a2481da5' 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 'shotNum' (runs: 5, truncation_value: 11)>\n",
       "array([['-1', '01', '02', '03', '04', '05', '06', '07', '08', '09', '10'],\n",
       "       ['11', '12', '13', '14', '15', '16', '17', '18', '19', '20', '21'],\n",
       "       ['22', '23', '24', '25', '26', '27', '28', '29', '30', '31', '32'],\n",
       "       ['33', '34', '35', '36', '37', '38', '39', '40', '41', '42', '43'],\n",
       "       ['44', '45', '46', '47', '48', '49', '50', '51', '52', '53', '54']],\n",
       "      dtype='<U2')\n",
       "Coordinates:\n",
       "  * runs              (runs) float64 0.0 1.0 2.0 3.0 4.0\n",
       "  * truncation_value  (truncation_value) float64 0.8 0.83 0.85 ... 0.97 0.99 1.0"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dataSet.shotNum.loc[\n",
    "        {\n",
    "            'runs': 0,\n",
    "            'truncation_value': 0.8,\n",
    "        }\n",
    "    ] = '-1'\n",
    "\n",
    "# Or wirte it in short\n",
    "dataSet.shotNum.loc[0, 0.8] = '-1'\n",
    "\n",
    "dataSet.shotNum"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Select by index"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The second method is to select it by index.\n",
    "\n",
    "Here is an emaxple of selecting the element in 'ShotNum' at (0, 1), and change it to '-2'."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
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       "</style><pre class='xr-text-repr-fallback'>&lt;xarray.DataArray &#x27;shotNum&#x27; (runs: 5, truncation_value: 11)&gt;\n",
       "array([[&#x27;-1&#x27;, &#x27;-2&#x27;, &#x27;02&#x27;, &#x27;03&#x27;, &#x27;04&#x27;, &#x27;05&#x27;, &#x27;06&#x27;, &#x27;07&#x27;, &#x27;08&#x27;, &#x27;09&#x27;, &#x27;10&#x27;],\n",
       "       [&#x27;11&#x27;, &#x27;12&#x27;, &#x27;13&#x27;, &#x27;14&#x27;, &#x27;15&#x27;, &#x27;16&#x27;, &#x27;17&#x27;, &#x27;18&#x27;, &#x27;19&#x27;, &#x27;20&#x27;, &#x27;21&#x27;],\n",
       "       [&#x27;22&#x27;, &#x27;23&#x27;, &#x27;24&#x27;, &#x27;25&#x27;, &#x27;26&#x27;, &#x27;27&#x27;, &#x27;28&#x27;, &#x27;29&#x27;, &#x27;30&#x27;, &#x27;31&#x27;, &#x27;32&#x27;],\n",
       "       [&#x27;33&#x27;, &#x27;34&#x27;, &#x27;35&#x27;, &#x27;36&#x27;, &#x27;37&#x27;, &#x27;38&#x27;, &#x27;39&#x27;, &#x27;40&#x27;, &#x27;41&#x27;, &#x27;42&#x27;, &#x27;43&#x27;],\n",
       "       [&#x27;44&#x27;, &#x27;45&#x27;, &#x27;46&#x27;, &#x27;47&#x27;, &#x27;48&#x27;, &#x27;49&#x27;, &#x27;50&#x27;, &#x27;51&#x27;, &#x27;52&#x27;, &#x27;53&#x27;, &#x27;54&#x27;]],\n",
       "      dtype=&#x27;&lt;U2&#x27;)\n",
       "Coordinates:\n",
       "  * runs              (runs) float64 0.0 1.0 2.0 3.0 4.0\n",
       "  * truncation_value  (truncation_value) float64 0.8 0.83 0.85 ... 0.97 0.99 1.0</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'>'shotNum'</div><ul class='xr-dim-list'><li><span class='xr-has-index'>runs</span>: 5</li><li><span class='xr-has-index'>truncation_value</span>: 11</li></ul></div><ul class='xr-sections'><li class='xr-section-item'><div class='xr-array-wrap'><input id='section-f8b88ce0-8467-4b1c-9e79-353a4f1ee8d2' class='xr-array-in' type='checkbox' checked><label for='section-f8b88ce0-8467-4b1c-9e79-353a4f1ee8d2' 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>&#x27;-1&#x27; &#x27;-2&#x27; &#x27;02&#x27; &#x27;03&#x27; &#x27;04&#x27; &#x27;05&#x27; &#x27;06&#x27; ... &#x27;49&#x27; &#x27;50&#x27; &#x27;51&#x27; &#x27;52&#x27; &#x27;53&#x27; &#x27;54&#x27;</span></div><div class='xr-array-data'><pre>array([[&#x27;-1&#x27;, &#x27;-2&#x27;, &#x27;02&#x27;, &#x27;03&#x27;, &#x27;04&#x27;, &#x27;05&#x27;, &#x27;06&#x27;, &#x27;07&#x27;, &#x27;08&#x27;, &#x27;09&#x27;, &#x27;10&#x27;],\n",
       "       [&#x27;11&#x27;, &#x27;12&#x27;, &#x27;13&#x27;, &#x27;14&#x27;, &#x27;15&#x27;, &#x27;16&#x27;, &#x27;17&#x27;, &#x27;18&#x27;, &#x27;19&#x27;, &#x27;20&#x27;, &#x27;21&#x27;],\n",
       "       [&#x27;22&#x27;, &#x27;23&#x27;, &#x27;24&#x27;, &#x27;25&#x27;, &#x27;26&#x27;, &#x27;27&#x27;, &#x27;28&#x27;, &#x27;29&#x27;, &#x27;30&#x27;, &#x27;31&#x27;, &#x27;32&#x27;],\n",
       "       [&#x27;33&#x27;, &#x27;34&#x27;, &#x27;35&#x27;, &#x27;36&#x27;, &#x27;37&#x27;, &#x27;38&#x27;, &#x27;39&#x27;, &#x27;40&#x27;, &#x27;41&#x27;, &#x27;42&#x27;, &#x27;43&#x27;],\n",
       "       [&#x27;44&#x27;, &#x27;45&#x27;, &#x27;46&#x27;, &#x27;47&#x27;, &#x27;48&#x27;, &#x27;49&#x27;, &#x27;50&#x27;, &#x27;51&#x27;, &#x27;52&#x27;, &#x27;53&#x27;, &#x27;54&#x27;]],\n",
       "      dtype=&#x27;&lt;U2&#x27;)</pre></div></div></li><li class='xr-section-item'><input id='section-6450436a-e28e-4f5a-8baa-2f7bea8f5d0e' class='xr-section-summary-in' type='checkbox'  checked><label for='section-6450436a-e28e-4f5a-8baa-2f7bea8f5d0e' 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'>runs</span></div><div class='xr-var-dims'>(runs)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>0.0 1.0 2.0 3.0 4.0</div><input id='attrs-2c6597d1-ed15-407e-877c-b36c0fc5da74' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-2c6597d1-ed15-407e-877c-b36c0fc5da74' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-57bee2cd-3e7d-405e-9d55-58166d8d9006' class='xr-var-data-in' type='checkbox'><label for='data-57bee2cd-3e7d-405e-9d55-58166d8d9006' 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., 1., 2., 3., 4.])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>truncation_value</span></div><div class='xr-var-dims'>(truncation_value)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>0.8 0.83 0.85 ... 0.97 0.99 1.0</div><input id='attrs-14c52d66-3e94-4752-9639-a044fae05baa' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-14c52d66-3e94-4752-9639-a044fae05baa' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b106cb39-4a89-40cc-92e7-7fd915f1dfb0' class='xr-var-data-in' type='checkbox'><label for='data-b106cb39-4a89-40cc-92e7-7fd915f1dfb0' 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([0.8 , 0.83, 0.85, 0.87, 0.89, 0.91, 0.93, 0.95, 0.97, 0.99, 1.  ])</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-46769c5f-0b89-4a91-a3af-775ee3df58b5' class='xr-section-summary-in' type='checkbox'  ><label for='section-46769c5f-0b89-4a91-a3af-775ee3df58b5' 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>runs</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-250befeb-cc4a-4ded-af8b-15fbfc6fcc50' class='xr-index-data-in' type='checkbox'/><label for='index-250befeb-cc4a-4ded-af8b-15fbfc6fcc50' 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([0.0, 1.0, 2.0, 3.0, 4.0], dtype=&#x27;float64&#x27;, name=&#x27;runs&#x27;))</pre></div></li><li class='xr-var-item'><div class='xr-index-name'><div>truncation_value</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-0bb02b75-8d25-4632-be0d-ecb9c68cac4a' class='xr-index-data-in' type='checkbox'/><label for='index-0bb02b75-8d25-4632-be0d-ecb9c68cac4a' 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([0.8, 0.83, 0.85, 0.87, 0.89, 0.91, 0.93, 0.95, 0.97, 0.99, 1.0], dtype=&#x27;float64&#x27;, name=&#x27;truncation_value&#x27;))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-f616ad52-3d9b-44a5-b060-bb4c419037d0' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-f616ad52-3d9b-44a5-b060-bb4c419037d0' 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 'shotNum' (runs: 5, truncation_value: 11)>\n",
       "array([['-1', '-2', '02', '03', '04', '05', '06', '07', '08', '09', '10'],\n",
       "       ['11', '12', '13', '14', '15', '16', '17', '18', '19', '20', '21'],\n",
       "       ['22', '23', '24', '25', '26', '27', '28', '29', '30', '31', '32'],\n",
       "       ['33', '34', '35', '36', '37', '38', '39', '40', '41', '42', '43'],\n",
       "       ['44', '45', '46', '47', '48', '49', '50', '51', '52', '53', '54']],\n",
       "      dtype='<U2')\n",
       "Coordinates:\n",
       "  * runs              (runs) float64 0.0 1.0 2.0 3.0 4.0\n",
       "  * truncation_value  (truncation_value) float64 0.8 0.83 0.85 ... 0.97 0.99 1.0"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dataSet.shotNum[0, 1] = '-2'\n",
    "dataSet.shotNum"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Remove the data"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Simply remove element or variables"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "For simply remove elements or variables in xarray, please read the introduction and examples from xarray package in the following link\n",
    "\n",
    "    https://docs.xarray.dev/en/stable/generated/xarray.Dataset.drop_vars.html\n",
    "    https://docs.xarray.dev/en/latest/generated/xarray.Dataset.drop_sel.html\n",
    "    https://docs.xarray.dev/en/latest/generated/xarray.Dataset.drop_isel.html"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Remove bad shot"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "However, if one wants to remove the bad shot, it is highly recommended to set the value to 'np.nan', instead of directly delete it.\n",
    "\n",
    "In order to do that, except the two ways we demenstrate in the section 'Modify the data', we also implent a function to do it."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
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       "\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;atoms&#x27; (runs: 5, truncation_value: 11, y: 1200, x: 1920)&gt;\n",
       "array([[[[ nan,  nan,  nan, ...,  nan,  nan,  nan],\n",
       "         [ nan,  nan,  nan, ...,  nan,  nan,  nan],\n",
       "         [ nan,  nan,  nan, ...,  nan,  nan,  nan],\n",
       "         ...,\n",
       "         [ nan,  nan,  nan, ...,  nan,  nan,  nan],\n",
       "         [ nan,  nan,  nan, ...,  nan,  nan,  nan],\n",
       "         [ nan,  nan,  nan, ...,  nan,  nan,  nan]],\n",
       "\n",
       "        [[102., 103., 100., ..., 155., 154., 142.],\n",
       "         [ 97., 100., 101., ..., 146., 146., 156.],\n",
       "         [ 91.,  93.,  97., ..., 142., 136., 151.],\n",
       "         ...,\n",
       "         [105., 103., 103., ..., 144., 134., 142.],\n",
       "         [102., 104., 112., ..., 133., 134., 135.],\n",
       "         [114., 115., 113., ..., 119., 126., 122.]],\n",
       "\n",
       "        [[101., 105., 103., ..., 148., 152., 146.],\n",
       "         [101., 102.,  98., ..., 143., 146., 149.],\n",
       "         [ 97.,  98.,  98., ..., 139., 137., 146.],\n",
       "         ...,\n",
       "...\n",
       "         ...,\n",
       "         [100., 102., 109., ..., 135., 141., 140.],\n",
       "         [106., 103., 105., ..., 128., 140., 132.],\n",
       "         [114., 107., 108., ..., 121., 123., 126.]],\n",
       "\n",
       "        [[101., 102., 101., ..., 153., 153., 146.],\n",
       "         [101., 103., 100., ..., 148., 143., 149.],\n",
       "         [ 96.,  95.,  98., ..., 145., 138., 144.],\n",
       "         ...,\n",
       "         [ 98., 107., 103., ..., 140., 142., 145.],\n",
       "         [106., 100., 103., ..., 133., 133., 136.],\n",
       "         [115., 103., 102., ..., 123., 125., 128.]],\n",
       "\n",
       "        [[103., 100., 102., ..., 154., 147., 153.],\n",
       "         [ 96., 103.,  97., ..., 150., 150., 152.],\n",
       "         [ 96., 100.,  96., ..., 141., 142., 144.],\n",
       "         ...,\n",
       "         [101., 102., 101., ..., 139., 142., 140.],\n",
       "         [105., 105.,  98., ..., 132., 135., 131.],\n",
       "         [109., 111., 107., ..., 125., 126., 129.]]]])\n",
       "Coordinates:\n",
       "  * runs              (runs) float64 0.0 1.0 2.0 3.0 4.0\n",
       "  * truncation_value  (truncation_value) float64 0.8 0.83 0.85 ... 0.97 0.99 1.0\n",
       "Dimensions without coordinates: y, x\n",
       "Attributes:\n",
       "    IMAGE_SUBCLASS:       IMAGE_GRAYSCALE\n",
       "    IMAGE_VERSION:        1.2\n",
       "    IMAGE_WHITE_IS_ZERO:  0</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'>'atoms'</div><ul class='xr-dim-list'><li><span class='xr-has-index'>runs</span>: 5</li><li><span class='xr-has-index'>truncation_value</span>: 11</li><li><span>y</span>: 1200</li><li><span>x</span>: 1920</li></ul></div><ul class='xr-sections'><li class='xr-section-item'><div class='xr-array-wrap'><input id='section-96fcd01b-3091-424c-960e-87b40148b49e' class='xr-array-in' type='checkbox' checked><label for='section-96fcd01b-3091-424c-960e-87b40148b49e' 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>nan nan nan nan nan nan nan ... 132.0 129.0 130.0 125.0 126.0 129.0</span></div><div class='xr-array-data'><pre>array([[[[ nan,  nan,  nan, ...,  nan,  nan,  nan],\n",
       "         [ nan,  nan,  nan, ...,  nan,  nan,  nan],\n",
       "         [ nan,  nan,  nan, ...,  nan,  nan,  nan],\n",
       "         ...,\n",
       "         [ nan,  nan,  nan, ...,  nan,  nan,  nan],\n",
       "         [ nan,  nan,  nan, ...,  nan,  nan,  nan],\n",
       "         [ nan,  nan,  nan, ...,  nan,  nan,  nan]],\n",
       "\n",
       "        [[102., 103., 100., ..., 155., 154., 142.],\n",
       "         [ 97., 100., 101., ..., 146., 146., 156.],\n",
       "         [ 91.,  93.,  97., ..., 142., 136., 151.],\n",
       "         ...,\n",
       "         [105., 103., 103., ..., 144., 134., 142.],\n",
       "         [102., 104., 112., ..., 133., 134., 135.],\n",
       "         [114., 115., 113., ..., 119., 126., 122.]],\n",
       "\n",
       "        [[101., 105., 103., ..., 148., 152., 146.],\n",
       "         [101., 102.,  98., ..., 143., 146., 149.],\n",
       "         [ 97.,  98.,  98., ..., 139., 137., 146.],\n",
       "         ...,\n",
       "...\n",
       "         ...,\n",
       "         [100., 102., 109., ..., 135., 141., 140.],\n",
       "         [106., 103., 105., ..., 128., 140., 132.],\n",
       "         [114., 107., 108., ..., 121., 123., 126.]],\n",
       "\n",
       "        [[101., 102., 101., ..., 153., 153., 146.],\n",
       "         [101., 103., 100., ..., 148., 143., 149.],\n",
       "         [ 96.,  95.,  98., ..., 145., 138., 144.],\n",
       "         ...,\n",
       "         [ 98., 107., 103., ..., 140., 142., 145.],\n",
       "         [106., 100., 103., ..., 133., 133., 136.],\n",
       "         [115., 103., 102., ..., 123., 125., 128.]],\n",
       "\n",
       "        [[103., 100., 102., ..., 154., 147., 153.],\n",
       "         [ 96., 103.,  97., ..., 150., 150., 152.],\n",
       "         [ 96., 100.,  96., ..., 141., 142., 144.],\n",
       "         ...,\n",
       "         [101., 102., 101., ..., 139., 142., 140.],\n",
       "         [105., 105.,  98., ..., 132., 135., 131.],\n",
       "         [109., 111., 107., ..., 125., 126., 129.]]]])</pre></div></div></li><li class='xr-section-item'><input id='section-eead7289-9142-4668-b985-10b192d24f32' class='xr-section-summary-in' type='checkbox'  checked><label for='section-eead7289-9142-4668-b985-10b192d24f32' 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'>runs</span></div><div class='xr-var-dims'>(runs)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>0.0 1.0 2.0 3.0 4.0</div><input id='attrs-5297672f-0b3f-404c-a9f3-3d450736770c' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-5297672f-0b3f-404c-a9f3-3d450736770c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-0b2f5a69-9f4e-4e01-b6a6-697a8cb9e145' class='xr-var-data-in' type='checkbox'><label for='data-0b2f5a69-9f4e-4e01-b6a6-697a8cb9e145' 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., 1., 2., 3., 4.])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>truncation_value</span></div><div class='xr-var-dims'>(truncation_value)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>0.8 0.83 0.85 ... 0.97 0.99 1.0</div><input id='attrs-62c03571-880f-4bc3-b4cc-760a0ea23177' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-62c03571-880f-4bc3-b4cc-760a0ea23177' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-f846df74-48be-4f5d-b406-33b1c7beae76' class='xr-var-data-in' type='checkbox'><label for='data-f846df74-48be-4f5d-b406-33b1c7beae76' 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([0.8 , 0.83, 0.85, 0.87, 0.89, 0.91, 0.93, 0.95, 0.97, 0.99, 1.  ])</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-39aa964f-5d61-486f-993a-cbd5937e2d40' class='xr-section-summary-in' type='checkbox'  ><label for='section-39aa964f-5d61-486f-993a-cbd5937e2d40' 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>runs</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-5a7cf4d5-d1c5-422b-a5a2-65901ab1a718' class='xr-index-data-in' type='checkbox'/><label for='index-5a7cf4d5-d1c5-422b-a5a2-65901ab1a718' 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([0.0, 1.0, 2.0, 3.0, 4.0], dtype=&#x27;float64&#x27;, name=&#x27;runs&#x27;))</pre></div></li><li class='xr-var-item'><div class='xr-index-name'><div>truncation_value</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-3e10ed60-13d7-40dc-893e-174d6b9a4a86' class='xr-index-data-in' type='checkbox'/><label for='index-3e10ed60-13d7-40dc-893e-174d6b9a4a86' 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([0.8, 0.83, 0.85, 0.87, 0.89, 0.91, 0.93, 0.95, 0.97, 0.99, 1.0], dtype=&#x27;float64&#x27;, name=&#x27;truncation_value&#x27;))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-e0bee93d-d684-4ff0-aeb6-6c44853eea65' class='xr-section-summary-in' type='checkbox'  checked><label for='section-e0bee93d-d684-4ff0-aeb6-6c44853eea65' class='xr-section-summary' >Attributes: <span>(3)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>IMAGE_SUBCLASS :</span></dt><dd>IMAGE_GRAYSCALE</dd><dt><span>IMAGE_VERSION :</span></dt><dd>1.2</dd><dt><span>IMAGE_WHITE_IS_ZERO :</span></dt><dd>0</dd></dl></div></li></ul></div></div>"
      ],
      "text/plain": [
       "<xarray.DataArray 'atoms' (runs: 5, truncation_value: 11, y: 1200, x: 1920)>\n",
       "array([[[[ nan,  nan,  nan, ...,  nan,  nan,  nan],\n",
       "         [ nan,  nan,  nan, ...,  nan,  nan,  nan],\n",
       "         [ nan,  nan,  nan, ...,  nan,  nan,  nan],\n",
       "         ...,\n",
       "         [ nan,  nan,  nan, ...,  nan,  nan,  nan],\n",
       "         [ nan,  nan,  nan, ...,  nan,  nan,  nan],\n",
       "         [ nan,  nan,  nan, ...,  nan,  nan,  nan]],\n",
       "\n",
       "        [[102., 103., 100., ..., 155., 154., 142.],\n",
       "         [ 97., 100., 101., ..., 146., 146., 156.],\n",
       "         [ 91.,  93.,  97., ..., 142., 136., 151.],\n",
       "         ...,\n",
       "         [105., 103., 103., ..., 144., 134., 142.],\n",
       "         [102., 104., 112., ..., 133., 134., 135.],\n",
       "         [114., 115., 113., ..., 119., 126., 122.]],\n",
       "\n",
       "        [[101., 105., 103., ..., 148., 152., 146.],\n",
       "         [101., 102.,  98., ..., 143., 146., 149.],\n",
       "         [ 97.,  98.,  98., ..., 139., 137., 146.],\n",
       "         ...,\n",
       "...\n",
       "         ...,\n",
       "         [100., 102., 109., ..., 135., 141., 140.],\n",
       "         [106., 103., 105., ..., 128., 140., 132.],\n",
       "         [114., 107., 108., ..., 121., 123., 126.]],\n",
       "\n",
       "        [[101., 102., 101., ..., 153., 153., 146.],\n",
       "         [101., 103., 100., ..., 148., 143., 149.],\n",
       "         [ 96.,  95.,  98., ..., 145., 138., 144.],\n",
       "         ...,\n",
       "         [ 98., 107., 103., ..., 140., 142., 145.],\n",
       "         [106., 100., 103., ..., 133., 133., 136.],\n",
       "         [115., 103., 102., ..., 123., 125., 128.]],\n",
       "\n",
       "        [[103., 100., 102., ..., 154., 147., 153.],\n",
       "         [ 96., 103.,  97., ..., 150., 150., 152.],\n",
       "         [ 96., 100.,  96., ..., 141., 142., 144.],\n",
       "         ...,\n",
       "         [101., 102., 101., ..., 139., 142., 140.],\n",
       "         [105., 105.,  98., ..., 132., 135., 131.],\n",
       "         [109., 111., 107., ..., 125., 126., 129.]]]])\n",
       "Coordinates:\n",
       "  * runs              (runs) float64 0.0 1.0 2.0 3.0 4.0\n",
       "  * truncation_value  (truncation_value) float64 0.8 0.83 0.85 ... 0.97 0.99 1.0\n",
       "Dimensions without coordinates: y, x\n",
       "Attributes:\n",
       "    IMAGE_SUBCLASS:       IMAGE_GRAYSCALE\n",
       "    IMAGE_VERSION:        1.2\n",
       "    IMAGE_WHITE_IS_ZERO:  0"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "data = copy.deepcopy(dataSet.atoms)\n",
    "# we first need to change the dtype from unsign 16-bit integer (uint16) to float, \n",
    "# since the uint16 doesn't support to store nan value.\n",
    "data = data.astype(float)\n",
    "data = remove_bad_shots(data, runs=0, truncation_value=0.8)\n",
    "data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
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