{
 "cells": [
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# How to read data from HFD5 files"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This is an example to read the data from those HDF5 files generated by LabScript.\n",
    "\n",
    "The idea is that one just need to give\n",
    "\n",
    "+ The path where data is stored\n",
    "+ The date of the data\n",
    "+ The shot number\n",
    "+ The path of data in HDF5 file (i.e. the name of group)\n",
    "\n",
    "It can automatically find the scan axes, and package all of them into an object of DataSet() in xarray package.\n",
    "\n",
    "Let us start with importing the supporting packages. In order to keep things ealier, here we will import all the packages, but not all of them will be used."
   ]
  },
  {
   "attachments": {},
   "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"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Start a client for parallel computing"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "If one wants to read tens or few hundreds files, a normal script can finish in several minutes. However, very likely, we have load and analyse thousands or even more shots, which is going to take much longer time. Therefore, it is necessary to use some other technics to accelerate the script. One solution is to do parallel loading and computing by using the dask package."
   ]
  },
  {
   "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-836bc314-1f0a-11ee-9fac-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;\">78c63c01</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-7b91ae15-611f-4967-a585-347a12dbf884</p>\n",
       "            <table style=\"width: 100%; text-align: left;\">\n",
       "                <tr>\n",
       "                    <td style=\"text-align: left;\">\n",
       "                        <strong>Comm:</strong> tcp://127.0.0.1:60497\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://127.0.0.1:60537\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://127.0.0.1:60539/status\" target=\"_blank\">http://127.0.0.1:60539/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://127.0.0.1:60500\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-hgh81x58\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://127.0.0.1:60536\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://127.0.0.1:60538/status\" target=\"_blank\">http://127.0.0.1:60538/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://127.0.0.1:60501\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-l6g2y451\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://127.0.0.1:60527\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://127.0.0.1:60528/status\" target=\"_blank\">http://127.0.0.1:60528/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://127.0.0.1:60502\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-2ecklsip\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://127.0.0.1:60524\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://127.0.0.1:60525/status\" target=\"_blank\">http://127.0.0.1:60525/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://127.0.0.1:60503\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-_bx_rrx9\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://127.0.0.1:60531\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://127.0.0.1:60534/status\" target=\"_blank\">http://127.0.0.1:60534/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://127.0.0.1:60504\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-gi8gzg2l\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://127.0.0.1:60530\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://127.0.0.1:60532/status\" target=\"_blank\">http://127.0.0.1:60532/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://127.0.0.1:60505\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-oy_0wm2p\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://127.0.0.1:60497' 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"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Set the path for different cameras"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "In our current experiment configuration (06.07.2023), the images of absorption imaging from different camera are stored in the following structure:\n",
    "\n",
    "        |       - images\n",
    "        |       |       - The name of the camera #1\n",
    "        |       |       |       - in_situ_absorption\n",
    "        |       |       |       |       - atoms\n",
    "        |       |       |       |       - background\n",
    "        |       |       |       |       - dard\n",
    "        |       |       |       \n",
    "        |       |       - The name of the camera #2\n",
    "        |       |       |       - in_situ_absorption\n",
    "        |       |       |       |       - atoms\n",
    "        |       |       |       |       - background\n",
    "        |       |       |       |       - dard\n",
    "\n",
    "Here we do not need to specify the name of the data we want to load. The programe only needs to know the group where the data are stored. Due to the way HDF5 file storing the data, going through and loading all the data under the same group won't significantly increase the time consumption.\n",
    "\n",
    "Therefore, in this example, the path of our absorption imaging data taken by the side-imaging camera is\n",
    "        \n",
    "        \"images/MOT_3D_Camera/in_situ_absorption\"\n",
    "\n",
    "Then we can create a dictionary for all three 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",
    "}"
   ]
  },
  {
   "attachments": {},
   "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()"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Here we will load the data from our NAS servers, taken by sequence 'Evaporative_Cooling', on 17.04.2023.\n",
    "\n",
    "The get_date() funciton in ToolFunction.ToolFunction module can return the date of today in a format of 'YYYY/MM/DD'."
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Load shot 0058"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
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       "    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-52a2826f-78a1-4723-b61e-fc303baeb0a5' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-52a2826f-78a1-4723-b61e-fc303baeb0a5' 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-624f54d2-c088-46c9-84dd-c2c785678ac1' class='xr-section-summary-in' type='checkbox'  checked><label for='section-624f54d2-c088-46c9-84dd-c2c785678ac1' 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-aa739bb0-d908-406d-ad58-7797fa93cc70' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-aa739bb0-d908-406d-ad58-7797fa93cc70' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-f53a9642-1ee0-4049-92ea-05a19f5a8b2f' class='xr-var-data-in' type='checkbox'><label for='data-f53a9642-1ee0-4049-92ea-05a19f5a8b2f' 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-e7279b66-2f51-40e7-9d62-907562076764' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-e7279b66-2f51-40e7-9d62-907562076764' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-54cb0760-919d-42c2-ba0a-4a9bb01f0524' class='xr-var-data-in' type='checkbox'><label for='data-54cb0760-919d-42c2-ba0a-4a9bb01f0524' 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-34e44800-f311-4aa3-a5b4-1c4dd37fc02a' class='xr-section-summary-in' type='checkbox'  checked><label for='section-34e44800-f311-4aa3-a5b4-1c4dd37fc02a' 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'>dask.array&lt;chunksize=(1, 1, 1200, 1920), meta=np.ndarray&gt;</div><input id='attrs-ff28fbfc-ba73-43df-8afe-c4183ed91183' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-ff28fbfc-ba73-43df-8afe-c4183ed91183' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-8e05466c-a52b-425a-a3e9-ec3b882b122a' class='xr-var-data-in' type='checkbox'><label for='data-8e05466c-a52b-425a-a3e9-ec3b882b122a' 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'><table>\n",
       "    <tr>\n",
       "        <td>\n",
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       "                        <td> </td>\n",
       "                        <th> Array </th>\n",
       "                        <th> Chunk </th>\n",
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       "                </thead>\n",
       "                <tbody>\n",
       "                    \n",
       "                    <tr>\n",
       "                        <th> Bytes </th>\n",
       "                        <td> 241.70 MiB </td>\n",
       "                        <td> 4.39 MiB </td>\n",
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       "                        <th> Shape </th>\n",
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       "                        <td> (1, 1, 1200, 1920) </td>\n",
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       "                    <tr>\n",
       "                        <th> Dask graph </th>\n",
       "                        <td colspan=\"2\"> 55 chunks in 177 graph layers </td>\n",
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       "                    <tr>\n",
       "                        <th> Data type </th>\n",
       "                        <td colspan=\"2\"> uint16 numpy.ndarray </td>\n",
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       "</table></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'>dask.array&lt;chunksize=(1, 1, 1200, 1920), meta=np.ndarray&gt;</div><input id='attrs-573cf8d8-6ef0-40b5-b1d8-2320952509f7' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-573cf8d8-6ef0-40b5-b1d8-2320952509f7' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-948e2b79-02fd-405c-80d6-0ea6679a17fa' class='xr-var-data-in' type='checkbox'><label for='data-948e2b79-02fd-405c-80d6-0ea6679a17fa' 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'><table>\n",
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       "                <tbody>\n",
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       "                    <tr>\n",
       "                        <th> Bytes </th>\n",
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       "                        <td> 4.39 MiB </td>\n",
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       "</table></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-ee4a563b-d565-4262-a2e6-fa3814412fbe' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ee4a563b-d565-4262-a2e6-fa3814412fbe' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-931c6eec-5a93-453f-a84b-fd5d02a7c1ea' class='xr-var-data-in' type='checkbox'><label for='data-931c6eec-5a93-453f-a84b-fd5d02a7c1ea' 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-f8963280-0317-4a2a-b8c4-3be8d82d74f1' class='xr-section-summary-in' type='checkbox'  ><label for='section-f8963280-0317-4a2a-b8c4-3be8d82d74f1' 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-567a94b5-c76d-42ca-81d2-9689871778c4' class='xr-index-data-in' type='checkbox'/><label for='index-567a94b5-c76d-42ca-81d2-9689871778c4' 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-1e3e3e87-7fd6-49e0-9f34-482bec9200ac' class='xr-index-data-in' type='checkbox'/><label for='index-1e3e3e87-7fd6-49e0-9f34-482bec9200ac' 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-f9b9880d-2cd4-427b-aed4-02ee83d56013' class='xr-section-summary-in' type='checkbox'  ><label for='section-f9b9880d-2cd4-427b-aed4-02ee83d56013' 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 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       " 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",
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       "Dimensions without coordinates: y, x\n",
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       "    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"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The above script reads the three images of 'camera_0', the side imaging camera, as an object of Datase() in xarray package. It has several key properties:\n",
    "\n",
    "- values: a numpy.ndarray holding the array’s values\n",
    "\n",
    "- dims: dimension names for each axis (e.g., ('x', 'y', 'z'))\n",
    "\n",
    "- coords: a dict-like container of arrays (coordinates) that label each point (e.g., 1-dimensional arrays of numbers, datetime objects or strings)\n",
    "\n",
    "- attrs: dict to hold arbitrary metadata (attributes)\n",
    "\n",
    "Xarray uses dims and coords to enable its core metadata aware operations. Dimensions provide names that xarray uses instead of the axis argument found in many numpy functions. Coordinates enable fast label based indexing and alignment, building on the functionality of the index found on a pandas DataFrame or Series.\n",
    "\n",
    "For more details about the data strcuture, please read the following link\n",
    "\n",
    "https://docs.xarray.dev/en/stable/user-guide/data-structures.html\n",
    "\n",
    "In our case, the coordinates are the scan axes of the sequence, which will be automatically recognized by going through all the global parameters among all HDF5 files.\n",
    "\n",
    "`If there are other parameters, who have the same value as the scanned one, the script will randomly return one of their name (depends on the storing order in HDF5 file).`\n",
    "\n",
    "`If there are other parameters, who have different values and change as the scanning parameters changing. the script can not tell which is the scan axes and raise an error message.`\n",
    "\n",
    "`In order to prevent the above two situations, please use the argument 'excludeAxis' to exclude those axes.`\n",
    "\n",
    "By put data into the xarray data structure, the data will automatically sorted by the coordinates (scan axes). In order to reach the original HDF5 file, it also return the shot number of each data point.\n",
    "\n",
    "The attributes records all the global parameters from HDF5 file.\n",
    "\n",
    "However, you may notice that now all the data values are 'Chunk', instead of any numbers. This is because we use the dask package for parallel reading and computing. Now the script does NOT read any thing from the disk, but it associates the data with the location in hard disk. Once you call or use the data, it then will start to really read them from hard disk. \n",
    "\n",
    "And please read more in the following link to get an idea how to work with parallel computing.\n",
    "\n",
    "https://docs.dask.org/en/stable/10-minutes-to-dask.html\n",
    "\n",
    "In one sentance, the basic idea of parallel computing is\n",
    "\n",
    "- In the very beginning, we draw a map for the computing, but the computer does not really do any calculation. Then it will return the results in 'chunks', which tells us the structure of data after calculation and how it will be distributed to different CPUs and threads.\n",
    "\n",
    "- After that, we can call .computer() method to let the computer do calculation once.\n",
    "\n",
    "- Or call .load() method to load the result into RAM."
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Use .compute() method to calculate once  \n",
    "\n",
    "We can call the .compute() method to let the computer calculate once."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
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       "    TOF_free:                          0.02\n",
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       "    backup_data:                       True\n",
       "    blink_off_time:                    nan\n",
       "    blink_on_time:                     nan\n",
       "    ...                                ...\n",
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       "    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-2cbd3c31-d9b4-41eb-8f8d-a2f10e630002' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-2cbd3c31-d9b4-41eb-8f8d-a2f10e630002' 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-80dd022c-2588-488d-b07b-40cbb246c054' class='xr-section-summary-in' type='checkbox'  checked><label for='section-80dd022c-2588-488d-b07b-40cbb246c054' 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-dd517d97-f908-49e1-8273-c87f01e6248a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-dd517d97-f908-49e1-8273-c87f01e6248a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-dac0ba8b-c9cb-430d-bb3b-def59776b913' class='xr-var-data-in' type='checkbox'><label for='data-dac0ba8b-c9cb-430d-bb3b-def59776b913' 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-88406b5d-b054-489f-9c02-8b9ac9e23646' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-88406b5d-b054-489f-9c02-8b9ac9e23646' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-13dcf4c6-1b5c-4022-9389-7c55dfd90713' class='xr-var-data-in' type='checkbox'><label for='data-13dcf4c6-1b5c-4022-9389-7c55dfd90713' 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-c2b89ea7-661b-4c97-86a2-b887c6f2098e' class='xr-section-summary-in' type='checkbox'  checked><label for='section-c2b89ea7-661b-4c97-86a2-b887c6f2098e' 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-b93deaae-8b3a-4313-8f0d-17f016c34974' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-b93deaae-8b3a-4313-8f0d-17f016c34974' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-95ec1bb5-36d9-4070-a954-d3a54e615bb9' class='xr-var-data-in' type='checkbox'><label for='data-95ec1bb5-36d9-4070-a954-d3a54e615bb9' 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-3ded8fcf-880a-4006-9aa1-337f9359c30c' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-3ded8fcf-880a-4006-9aa1-337f9359c30c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-311c13b3-9ecb-4b0e-864f-bc726e8884a6' class='xr-var-data-in' type='checkbox'><label for='data-311c13b3-9ecb-4b0e-864f-bc726e8884a6' 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-580f100e-1b77-4fa1-a73d-f44702aa8282' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-580f100e-1b77-4fa1-a73d-f44702aa8282' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c37d42f8-fe07-4cfe-b506-d18086456efa' class='xr-var-data-in' type='checkbox'><label for='data-c37d42f8-fe07-4cfe-b506-d18086456efa' 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-11895a4d-abb2-46e2-b813-c4b505fb6525' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-11895a4d-abb2-46e2-b813-c4b505fb6525' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b66e3650-6864-403f-887b-a192143c9845' class='xr-var-data-in' type='checkbox'><label for='data-b66e3650-6864-403f-887b-a192143c9845' 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-12d0628b-8b3a-4165-8eb6-3fb67af5031b' class='xr-section-summary-in' type='checkbox'  ><label for='section-12d0628b-8b3a-4165-8eb6-3fb67af5031b' 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-8f5f0325-8556-40c5-97c3-0baa332519a7' class='xr-index-data-in' type='checkbox'/><label for='index-8f5f0325-8556-40c5-97c3-0baa332519a7' 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-78da0206-026e-4348-b009-54082944ecdf' class='xr-index-data-in' type='checkbox'/><label for='index-78da0206-026e-4348-b009-54082944ecdf' 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-95c031b4-12c6-4933-afdf-a727e51b53f6' class='xr-section-summary-in' type='checkbox'  ><label for='section-95c031b4-12c6-4933-afdf-a727e51b53f6' 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": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dataSet.compute()"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Very important, .compute() method won't load the result to RAM. If we don't save the result, it will just be lost. We can now check what in dataSet again. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
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       "  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",
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       "  stroke-width: 0;\n",
       "  stroke: currentColor;\n",
       "  fill: currentColor;\n",
       "}\n",
       "</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 dask.array&lt;chunksize=(1, 1, 1200, 1920), meta=np.ndarray&gt;\n",
       "    background        (runs, truncation_value, y, x) uint16 dask.array&lt;chunksize=(1, 1, 1200, 1920), meta=np.ndarray&gt;\n",
       "    dark              (runs, truncation_value, y, x) uint16 dask.array&lt;chunksize=(1, 1, 1200, 1920), meta=np.ndarray&gt;\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-2e5715da-c2c9-486b-a04e-c5222fd3ecf6' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-2e5715da-c2c9-486b-a04e-c5222fd3ecf6' 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-91ed0f20-6e5a-4be2-948e-a5793660892a' class='xr-section-summary-in' type='checkbox'  checked><label for='section-91ed0f20-6e5a-4be2-948e-a5793660892a' 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-7c59185d-53fb-4d7a-a66b-f8b5ca563122' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-7c59185d-53fb-4d7a-a66b-f8b5ca563122' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-8e0ff7ad-b1cf-4e95-85be-71877ca9ec2e' class='xr-var-data-in' type='checkbox'><label for='data-8e0ff7ad-b1cf-4e95-85be-71877ca9ec2e' 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-d42b164d-7709-4555-98aa-860af01b57ae' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-d42b164d-7709-4555-98aa-860af01b57ae' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b6db2f37-43c8-4697-860e-d669c809f84b' class='xr-var-data-in' type='checkbox'><label for='data-b6db2f37-43c8-4697-860e-d669c809f84b' 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-68736520-79d7-4731-a204-85da92405c8a' class='xr-section-summary-in' type='checkbox'  checked><label for='section-68736520-79d7-4731-a204-85da92405c8a' 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'>dask.array&lt;chunksize=(1, 1, 1200, 1920), meta=np.ndarray&gt;</div><input id='attrs-2191cc41-f7b8-4092-a6f5-ac97c0c2c66d' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-2191cc41-f7b8-4092-a6f5-ac97c0c2c66d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-0e63d3f1-0685-4ec7-b3a6-089c858b6463' class='xr-var-data-in' type='checkbox'><label for='data-0e63d3f1-0685-4ec7-b3a6-089c858b6463' 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'><table>\n",
       "    <tr>\n",
       "        <td>\n",
       "            <table style=\"border-collapse: collapse;\">\n",
       "                <thead>\n",
       "                    <tr>\n",
       "                        <td> </td>\n",
       "                        <th> Array </th>\n",
       "                        <th> Chunk </th>\n",
       "                    </tr>\n",
       "                </thead>\n",
       "                <tbody>\n",
       "                    \n",
       "                    <tr>\n",
       "                        <th> Bytes </th>\n",
       "                        <td> 241.70 MiB </td>\n",
       "                        <td> 4.39 MiB </td>\n",
       "                    </tr>\n",
       "                    \n",
       "                    <tr>\n",
       "                        <th> Shape </th>\n",
       "                        <td> (5, 11, 1200, 1920) </td>\n",
       "                        <td> (1, 1, 1200, 1920) </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <th> Dask graph </th>\n",
       "                        <td colspan=\"2\"> 55 chunks in 177 graph layers </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <th> Data type </th>\n",
       "                        <td colspan=\"2\"> uint16 numpy.ndarray </td>\n",
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       "</table></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'>dask.array&lt;chunksize=(1, 1, 1200, 1920), meta=np.ndarray&gt;</div><input id='attrs-aa079dff-d7e1-4c80-99e8-a6fe69999434' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-aa079dff-d7e1-4c80-99e8-a6fe69999434' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-cca89f48-07da-42be-931a-73b8ae2f5ebd' class='xr-var-data-in' type='checkbox'><label for='data-cca89f48-07da-42be-931a-73b8ae2f5ebd' 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'><table>\n",
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       "    </tr>\n",
       "</table></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'>dask.array&lt;chunksize=(1, 1, 1200, 1920), meta=np.ndarray&gt;</div><input id='attrs-d6f7e456-0783-4032-a6f1-7ca8f3978e35' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-d6f7e456-0783-4032-a6f1-7ca8f3978e35' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d35c96cc-cd15-4181-b295-28440de0c66f' class='xr-var-data-in' type='checkbox'><label for='data-d35c96cc-cd15-4181-b295-28440de0c66f' 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'><table>\n",
       "    <tr>\n",
       "        <td>\n",
       "            <table style=\"border-collapse: collapse;\">\n",
       "                <thead>\n",
       "                    <tr>\n",
       "                        <td> </td>\n",
       "                        <th> Array </th>\n",
       "                        <th> Chunk </th>\n",
       "                    </tr>\n",
       "                </thead>\n",
       "                <tbody>\n",
       "                    \n",
       "                    <tr>\n",
       "                        <th> Bytes </th>\n",
       "                        <td> 241.70 MiB </td>\n",
       "                        <td> 4.39 MiB </td>\n",
       "                    </tr>\n",
       "                    \n",
       "                    <tr>\n",
       "                        <th> Shape </th>\n",
       "                        <td> (5, 11, 1200, 1920) </td>\n",
       "                        <td> (1, 1, 1200, 1920) </td>\n",
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       "                    <tr>\n",
       "                        <th> Dask graph </th>\n",
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       "                    </tr>\n",
       "                    <tr>\n",
       "                        <th> Data type </th>\n",
       "                        <td colspan=\"2\"> uint16 numpy.ndarray </td>\n",
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       "</table></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-ae5a7d8c-80b4-4b98-b84d-59c741a51e1a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ae5a7d8c-80b4-4b98-b84d-59c741a51e1a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a319e736-df11-4c80-a15b-f612428dac7b' class='xr-var-data-in' type='checkbox'><label for='data-a319e736-df11-4c80-a15b-f612428dac7b' 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-636eed61-0442-4397-9185-f0ee81f9616f' class='xr-section-summary-in' type='checkbox'  ><label for='section-636eed61-0442-4397-9185-f0ee81f9616f' 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-6b0064c5-859b-4713-92a0-500f61525828' class='xr-index-data-in' type='checkbox'/><label for='index-6b0064c5-859b-4713-92a0-500f61525828' 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-3dbfd26a-923d-4f22-9754-967fbde04d03' class='xr-index-data-in' type='checkbox'/><label for='index-3dbfd26a-923d-4f22-9754-967fbde04d03' 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-9f4b2906-b15f-4649-a95c-158efe65f704' class='xr-section-summary-in' type='checkbox'  ><label for='section-9f4b2906-b15f-4649-a95c-158efe65f704' 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 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:</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 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       " 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",
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      ],
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       "<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 dask.array<chunksize=(1, 1, 1200, 1920), meta=np.ndarray>\n",
       "    background        (runs, truncation_value, y, x) uint16 dask.array<chunksize=(1, 1, 1200, 1920), meta=np.ndarray>\n",
       "    dark              (runs, truncation_value, y, x) uint16 dask.array<chunksize=(1, 1, 1200, 1920), meta=np.ndarray>\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": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dataSet"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Use .load() method to calculate once  \n",
    "\n",
    "We can call the .load() method to let the computer calculate and load the data into RAM."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
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       "</style><pre class='xr-text-repr-fallback'>&lt;xarray.Dataset&gt;\n",
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       "    ...                                ...\n",
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       "    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-2420be20-0e49-46e7-b6b7-9612c548591a' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-2420be20-0e49-46e7-b6b7-9612c548591a' 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-05667ea5-377d-4ca7-95ea-47f7f92ed4b4' class='xr-section-summary-in' type='checkbox'  checked><label for='section-05667ea5-377d-4ca7-95ea-47f7f92ed4b4' 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-75429d10-4f16-4718-b257-a13fec7b41a7' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-75429d10-4f16-4718-b257-a13fec7b41a7' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-30fde803-edcf-4c08-8dcc-017e5bbf9d35' class='xr-var-data-in' type='checkbox'><label for='data-30fde803-edcf-4c08-8dcc-017e5bbf9d35' 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-bc6e4dbb-2219-4f6d-b869-ebec49ed0657' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-bc6e4dbb-2219-4f6d-b869-ebec49ed0657' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-217f38f2-5046-4398-903a-a7ce8d65bb4c' class='xr-var-data-in' type='checkbox'><label for='data-217f38f2-5046-4398-903a-a7ce8d65bb4c' 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-53e873ac-4631-44c4-ac39-54dfd0c39022' class='xr-section-summary-in' type='checkbox'  checked><label for='section-53e873ac-4631-44c4-ac39-54dfd0c39022' 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-7b86fa01-ecc3-4bc8-8750-409e2ac4c314' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-7b86fa01-ecc3-4bc8-8750-409e2ac4c314' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e1bd222c-c782-4d9a-a79d-83c5930d889a' class='xr-var-data-in' type='checkbox'><label for='data-e1bd222c-c782-4d9a-a79d-83c5930d889a' 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-823bca53-8d32-4dab-a39a-4a32b9f5d5ac' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-823bca53-8d32-4dab-a39a-4a32b9f5d5ac' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1281a183-1342-49cc-9615-c826259e44ed' class='xr-var-data-in' type='checkbox'><label for='data-1281a183-1342-49cc-9615-c826259e44ed' 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-beba7537-defa-4f09-8991-4342d67faa72' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-beba7537-defa-4f09-8991-4342d67faa72' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-f236731b-d74c-4849-a692-8b3ac2266f63' class='xr-var-data-in' type='checkbox'><label for='data-f236731b-d74c-4849-a692-8b3ac2266f63' 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-a467cb54-569e-4ea8-aa0a-4387c2024054' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-a467cb54-569e-4ea8-aa0a-4387c2024054' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d92eb643-4479-4ec1-a425-c19bed75ab07' class='xr-var-data-in' type='checkbox'><label for='data-d92eb643-4479-4ec1-a425-c19bed75ab07' 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-2f2854ad-0888-41be-a0f5-040d3db31856' class='xr-section-summary-in' type='checkbox'  ><label for='section-2f2854ad-0888-41be-a0f5-040d3db31856' 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-4f9e9c70-7721-4315-b917-7dffdff62326' class='xr-index-data-in' type='checkbox'/><label for='index-4f9e9c70-7721-4315-b917-7dffdff62326' 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-4d3a272d-3034-4b1b-8cf6-5d6cf23a0175' class='xr-index-data-in' type='checkbox'/><label for='index-4d3a272d-3034-4b1b-8cf6-5d6cf23a0175' 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-9265e595-965f-4937-88c9-933d2b9d058b' class='xr-section-summary-in' type='checkbox'  ><label for='section-9265e595-965f-4937-88c9-933d2b9d058b' 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 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:</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": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dataSet.load()"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We now check what in dataSet again."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
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       "}\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.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-2441a1c6-5b0d-4902-97ad-faf7e509791d' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-2441a1c6-5b0d-4902-97ad-faf7e509791d' 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-3df639b1-2be4-4200-b264-45e4fa3fed44' class='xr-section-summary-in' type='checkbox'  checked><label for='section-3df639b1-2be4-4200-b264-45e4fa3fed44' 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-649c70bb-91ed-45dc-9cd5-a44bfa43b261' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-649c70bb-91ed-45dc-9cd5-a44bfa43b261' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-602e179f-2fcf-4ad6-b1d1-826bc4ad06d8' class='xr-var-data-in' type='checkbox'><label for='data-602e179f-2fcf-4ad6-b1d1-826bc4ad06d8' 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-76b3d9fd-2e0e-4fc5-906f-1e440c523894' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-76b3d9fd-2e0e-4fc5-906f-1e440c523894' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-027dbf1c-1d30-4926-8352-e23103020bce' class='xr-var-data-in' type='checkbox'><label for='data-027dbf1c-1d30-4926-8352-e23103020bce' 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-f38f8f94-a576-4656-abe7-7f199b834f51' class='xr-section-summary-in' type='checkbox'  checked><label for='section-f38f8f94-a576-4656-abe7-7f199b834f51' 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-e8c90fb2-66fc-4cdb-9b90-da929f70fc26' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-e8c90fb2-66fc-4cdb-9b90-da929f70fc26' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ba64f770-c9e7-43e5-b231-b5b750332d74' class='xr-var-data-in' type='checkbox'><label for='data-ba64f770-c9e7-43e5-b231-b5b750332d74' 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-c065c653-5fa9-48f8-a5e5-56ffaa400440' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-c065c653-5fa9-48f8-a5e5-56ffaa400440' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-baf8a142-fd79-4333-a4de-e3fe74d9cf45' class='xr-var-data-in' type='checkbox'><label for='data-baf8a142-fd79-4333-a4de-e3fe74d9cf45' 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-91871308-d55f-4b05-a3e6-5f8d6fd3acc0' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-91871308-d55f-4b05-a3e6-5f8d6fd3acc0' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-34b912bf-1086-44ca-890e-528dcef61d77' class='xr-var-data-in' type='checkbox'><label for='data-34b912bf-1086-44ca-890e-528dcef61d77' 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-e45d1d16-6f05-4169-a7d9-2b1d7fad09c8' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-e45d1d16-6f05-4169-a7d9-2b1d7fad09c8' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e949eb9f-4c8c-4716-bac7-329d1bdf7ed5' class='xr-var-data-in' type='checkbox'><label for='data-e949eb9f-4c8c-4716-bac7-329d1bdf7ed5' 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-f30a3590-e3ed-4fd1-9be2-845fa7463330' class='xr-section-summary-in' type='checkbox'  ><label for='section-f30a3590-e3ed-4fd1-9be2-845fa7463330' 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-81d9deae-c6c3-4733-b1b1-3b1994c463a8' class='xr-index-data-in' type='checkbox'/><label for='index-81d9deae-c6c3-4733-b1b1-3b1994c463a8' 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-7be40e56-beea-4834-9316-bda6690b9288' class='xr-index-data-in' type='checkbox'/><label for='index-7be40e56-beea-4834-9316-bda6690b9288' 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-c1d2e157-7c83-47c6-a28f-d41040820a57' class='xr-section-summary-in' type='checkbox'  ><label for='section-c1d2e157-7c83-47c6-a28f-d41040820a57' 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>"
      ],
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       "<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": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dataSet"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Rechunk data to enable parallel computing"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "As we discussed before, the parallel computing needs a map. One of the earliest way to produce a map is to divide the data into chunks. And later the calculation taks with different chunks will be sent to different threads and CPUs.\n",
    "\n",
    "Therefore, after we load the data into RAM by calling .laod() method, without any other operation, all the furture calculation will NOT be finished parallelly. Because, there is no chunk!\n",
    "\n",
    "In order to enable the parallel computing, we have to rechunk our data."
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Use dataArray.chunk() or dataset.chunk() method to rechunk the data"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The dataArray.chunk() method can coerce this array’s data into a dask arrays with the given chunks. For more deltail please have a look of following link\n",
    "\n",
    "https://docs.xarray.dev/en/stable/generated/xarray.DataArray.chunk.html\n",
    "\n",
    "https://docs.xarray.dev/en/stable/generated/xarray.Dataset.chunk.html\n",
    "\n",
    "Here we rechunk the values of atoms in dataSet into a shape of (5, 1, 1200, 1920)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
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       "\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",
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       "\n",
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       ".xr-var-dims,\n",
       ".xr-var-dtype,\n",
       ".xr-preview,\n",
       ".xr-attrs dt {\n",
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       "\n",
       ".xr-var-name:hover,\n",
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       ".xr-attrs dt:hover {\n",
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       "\n",
       ".xr-var-attrs,\n",
       ".xr-var-data,\n",
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       "\n",
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       "\n",
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       "\n",
       ".xr-var-name span,\n",
       ".xr-var-data,\n",
       ".xr-index-name div,\n",
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       ".xr-attrs {\n",
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       "}\n",
       "\n",
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       ".xr-var-attrs,\n",
       ".xr-var-data,\n",
       ".xr-index-data {\n",
       "  grid-column: 1 / -1;\n",
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       "\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",
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       "  padding-right: 10px;\n",
       "  width: auto;\n",
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       "\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",
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       "  stroke-width: 0;\n",
       "  stroke: currentColor;\n",
       "  fill: currentColor;\n",
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       "</style><pre class='xr-text-repr-fallback'>&lt;xarray.DataArray &#x27;atoms&#x27; (runs: 5, truncation_value: 11, y: 1200, x: 1920)&gt;\n",
       "dask.array&lt;xarray-&lt;this-array&gt;, shape=(5, 11, 1200, 1920), dtype=uint16, chunksize=(5, 1, 1200, 1920), chunktype=numpy.ndarray&gt;\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-5151b7c3-ccb6-470f-aa8a-51a6cffb241c' class='xr-array-in' type='checkbox' checked><label for='section-5151b7c3-ccb6-470f-aa8a-51a6cffb241c' 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>dask.array&lt;chunksize=(5, 1, 1200, 1920), meta=np.ndarray&gt;</span></div><div class='xr-array-data'><table>\n",
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       "                    </tr>\n",
       "                </thead>\n",
       "                <tbody>\n",
       "                    \n",
       "                    <tr>\n",
       "                        <th> Bytes </th>\n",
       "                        <td> 241.70 MiB </td>\n",
       "                        <td> 21.97 MiB </td>\n",
       "                    </tr>\n",
       "                    \n",
       "                    <tr>\n",
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       "                        <td> (5, 1, 1200, 1920) </td>\n",
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       "                    <tr>\n",
       "                        <th> Dask graph </th>\n",
       "                        <td colspan=\"2\"> 11 chunks in 1 graph layer </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <th> Data type </th>\n",
       "                        <td colspan=\"2\"> uint16 numpy.ndarray </td>\n",
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       "</table></div></div></li><li class='xr-section-item'><input id='section-751cdac4-711b-4557-b047-30eff958ddba' class='xr-section-summary-in' type='checkbox'  checked><label for='section-751cdac4-711b-4557-b047-30eff958ddba' 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-818853ce-a4dc-42d6-a362-e51553eb533b' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-818853ce-a4dc-42d6-a362-e51553eb533b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-876fa2d9-0b59-42b5-8cf9-4d5c9db8e0aa' class='xr-var-data-in' type='checkbox'><label for='data-876fa2d9-0b59-42b5-8cf9-4d5c9db8e0aa' 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-bc341a4d-151e-4073-8a08-71c71664f744' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-bc341a4d-151e-4073-8a08-71c71664f744' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-76be006f-fb0f-4cbb-8349-f706d8592d49' class='xr-var-data-in' type='checkbox'><label for='data-76be006f-fb0f-4cbb-8349-f706d8592d49' 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-b262c212-8de0-4ab6-84b2-8d5c5372e816' class='xr-section-summary-in' type='checkbox'  ><label for='section-b262c212-8de0-4ab6-84b2-8d5c5372e816' 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-84e0084c-58f2-4318-8961-f984e403cead' class='xr-index-data-in' type='checkbox'/><label for='index-84e0084c-58f2-4318-8961-f984e403cead' 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-e3b1aa80-bf22-46e0-8283-29e6b134578c' class='xr-index-data-in' type='checkbox'/><label for='index-e3b1aa80-bf22-46e0-8283-29e6b134578c' 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-ba55e8ca-a4e6-4da6-85a6-a7330a820424' class='xr-section-summary-in' type='checkbox'  checked><label for='section-ba55e8ca-a4e6-4da6-85a6-a7330a820424' 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",
       "dask.array<xarray-<this-array>, shape=(5, 11, 1200, 1920), dtype=uint16, chunksize=(5, 1, 1200, 1920), chunktype=numpy.ndarray>\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": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dataSet.atoms.chunk((5,1,1200,1920))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Use our home-made auto_rechunk function"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We wrote a auto rechunk function to auto rechunk a xarrry DataSet. It works in the most time, but please check."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
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       "\n",
       ".xr-attrs dt,\n",
       ".xr-attrs dd {\n",
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       "\n",
       ".xr-attrs dt {\n",
       "  font-weight: normal;\n",
       "  grid-column: 1;\n",
       "}\n",
       "\n",
       ".xr-attrs dt:hover span {\n",
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       "\n",
       ".xr-attrs dd {\n",
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       "\n",
       ".xr-icon-database,\n",
       ".xr-icon-file-text2,\n",
       ".xr-no-icon {\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 dask.array&lt;chunksize=(5, 11, 1104, 1104), meta=np.ndarray&gt;\n",
       "    background        (runs, truncation_value, y, x) uint16 dask.array&lt;chunksize=(5, 11, 1104, 1104), meta=np.ndarray&gt;\n",
       "    dark              (runs, truncation_value, y, x) uint16 dask.array&lt;chunksize=(5, 11, 1104, 1104), meta=np.ndarray&gt;\n",
       "    shotNum           (runs, truncation_value) &lt;U2 dask.array&lt;chunksize=(5, 11), meta=np.ndarray&gt;\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-0dd83f68-af5b-419d-b3f8-a5cbc993a7f9' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-0dd83f68-af5b-419d-b3f8-a5cbc993a7f9' 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-580a2ca0-bdc1-4ffc-acd9-81155b0a9dfc' class='xr-section-summary-in' type='checkbox'  checked><label for='section-580a2ca0-bdc1-4ffc-acd9-81155b0a9dfc' 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-f365cbc7-c36f-4f3f-904c-c2bd418b81b9' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-f365cbc7-c36f-4f3f-904c-c2bd418b81b9' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-4dad7991-f189-4b0a-bf7a-d1bff5466c06' class='xr-var-data-in' type='checkbox'><label for='data-4dad7991-f189-4b0a-bf7a-d1bff5466c06' 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-72d4ec1b-5b21-4b63-87bd-4e1715ca431b' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-72d4ec1b-5b21-4b63-87bd-4e1715ca431b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-18be8e32-160d-41dd-b63b-e53250dd7517' class='xr-var-data-in' type='checkbox'><label for='data-18be8e32-160d-41dd-b63b-e53250dd7517' 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-f0c73af3-5ff3-4e07-aa1b-e320b3f5774d' class='xr-section-summary-in' type='checkbox'  checked><label for='section-f0c73af3-5ff3-4e07-aa1b-e320b3f5774d' 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'>dask.array&lt;chunksize=(5, 11, 1104, 1104), meta=np.ndarray&gt;</div><input id='attrs-131d3ea2-5190-4fd2-a64a-cd2802a078a5' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-131d3ea2-5190-4fd2-a64a-cd2802a078a5' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-7a21e7cf-48a7-4fc4-a9d5-c54d1187b908' class='xr-var-data-in' type='checkbox'><label for='data-7a21e7cf-48a7-4fc4-a9d5-c54d1187b908' 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'><table>\n",
       "    <tr>\n",
       "        <td>\n",
       "            <table style=\"border-collapse: collapse;\">\n",
       "                <thead>\n",
       "                    <tr>\n",
       "                        <td> </td>\n",
       "                        <th> Array </th>\n",
       "                        <th> Chunk </th>\n",
       "                    </tr>\n",
       "                </thead>\n",
       "                <tbody>\n",
       "                    \n",
       "                    <tr>\n",
       "                        <th> Bytes </th>\n",
       "                        <td> 241.70 MiB </td>\n",
       "                        <td> 127.86 MiB </td>\n",
       "                    </tr>\n",
       "                    \n",
       "                    <tr>\n",
       "                        <th> Shape </th>\n",
       "                        <td> (5, 11, 1200, 1920) </td>\n",
       "                        <td> (5, 11, 1104, 1104) </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <th> Dask graph </th>\n",
       "                        <td colspan=\"2\"> 4 chunks in 1 graph layer </td>\n",
       "                    </tr>\n",
       "                    <tr>\n",
       "                        <th> Data type </th>\n",
       "                        <td colspan=\"2\"> uint16 numpy.ndarray </td>\n",
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       "  <text x=\"140.000000\" y=\"27.272727\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(0,140.000000,27.272727)\">5</text>\n",
       "</svg>\n",
       "        </td>\n",
       "    </tr>\n",
       "</table></div></li></ul></div></li><li class='xr-section-item'><input id='section-e88c9e4a-beec-47a1-b450-03a1b427593e' class='xr-section-summary-in' type='checkbox'  ><label for='section-e88c9e4a-beec-47a1-b450-03a1b427593e' 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-d565c5e6-44c5-41d3-84da-98bd8a0e9d07' class='xr-index-data-in' type='checkbox'/><label for='index-d565c5e6-44c5-41d3-84da-98bd8a0e9d07' 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-fbee104d-3344-4353-86bc-6f68f70e69cc' class='xr-index-data-in' type='checkbox'/><label for='index-fbee104d-3344-4353-86bc-6f68f70e69cc' 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-69b9b259-7c9d-46b0-b4b8-00d79b630734' class='xr-section-summary-in' type='checkbox'  ><label for='section-69b9b259-7c9d-46b0-b4b8-00d79b630734' 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 dask.array<chunksize=(5, 11, 1104, 1104), meta=np.ndarray>\n",
       "    background        (runs, truncation_value, y, x) uint16 dask.array<chunksize=(5, 11, 1104, 1104), meta=np.ndarray>\n",
       "    dark              (runs, truncation_value, y, x) uint16 dask.array<chunksize=(5, 11, 1104, 1104), meta=np.ndarray>\n",
       "    shotNum           (runs, truncation_value) <U2 dask.array<chunksize=(5, 11), meta=np.ndarray>\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": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dataSet = auto_rechunk(dataSet)\n",
    "dataSet"
   ]
  }
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