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{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# How to get and plot the absorption imaging" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "This is an example to calculate OD from absorption imaging from the loaded data.\n", "\n", "Let us start with importing the supporting packages and loading the data. In order to keep things ealier, here we will import all the packages, but not all of them will be used." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Load some example data" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Import supporting packages" ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "# Set the system path for importing packages\n", "# This is just because I put all example scripts in another folder\n", "# You DO NOT need to do this \n", "# -------------- You do NOT need following part --------------\n", "import sys\n", "import os\n", "sys.path.insert(0, os.path.abspath('..'))\n", "# -------------- You do NOT need above part --------------\n", "\n", "import copy\n", "import glob\n", "from datetime import datetime\n", "\n", "# The package for data structure\n", "import xarray as xr\n", "import pandas as pd\n", "import numpy as np\n", "\n", "# The packages for working with uncertainties\n", "from uncertainties import ufloat\n", "from uncertainties import unumpy as unp\n", "from uncertainties import umath\n", "\n", "# The package for plotting\n", "import matplotlib.pyplot as plt\n", "plt.rcParams['font.size'] = 18 # Set the global font size\n", "\n", "# -------------- The modules written by us --------------\n", "\n", "# The packages for read data\n", "from DataContainer.ReadData import read_hdf5_file, read_hdf5_global, read_hdf5_run_time, read_csv_file\n", "\n", "# The packages for data analysis\n", "from Analyser.ImagingAnalyser import ImageAnalyser\n", "from Analyser.FitAnalyser import FitAnalyser\n", "from Analyser.FitAnalyser import ThomasFermi2dModel, DensityProfileBEC2dModel, Polylog22dModel\n", "from Analyser.FFTAnalyser import fft, ifft, fft_nutou\n", "from ToolFunction.ToolFunction import *\n", "\n", "# Add errorbar plot to xarray package\n", "from ToolFunction.HomeMadeXarrayFunction import errorbar, dataarray_plot_errorbar\n", "xr.plot.dataarray_plot.errorbar = errorbar\n", "xr.plot.accessor.DataArrayPlotAccessor.errorbar = dataarray_plot_errorbar" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Start a client for parallel computing" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "data": { "text/html": [ "<div>\n", " <div style=\"width: 24px; height: 24px; background-color: #e1e1e1; border: 3px solid #9D9D9D; border-radius: 5px; position: absolute;\"> </div>\n", " <div style=\"margin-left: 48px;\">\n", " <h3 style=\"margin-bottom: 0px;\">Client</h3>\n", " <p style=\"color: #9D9D9D; margin-bottom: 0px;\">Client-6c49ef74-1f18-11ee-a568-80e82ce2fa8e</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;\">64b816fb</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-1686989d-dc22-4ca9-bbed-200c9a09b8e2</p>\n", " <table style=\"width: 100%; text-align: left;\">\n", " <tr>\n", " <td style=\"text-align: left;\">\n", " <strong>Comm:</strong> tcp://127.0.0.1:62024\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://127.0.0.1:62055\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://127.0.0.1:62058/status\" target=\"_blank\">http://127.0.0.1:62058/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://127.0.0.1:62027\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-z3ariy1d\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://127.0.0.1:62049\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://127.0.0.1:62052/status\" target=\"_blank\">http://127.0.0.1:62052/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://127.0.0.1:62028\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-froctrq_\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://127.0.0.1:62061\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://127.0.0.1:62063/status\" target=\"_blank\">http://127.0.0.1:62063/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://127.0.0.1:62029\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-aidgx9kg\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://127.0.0.1:62060\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://127.0.0.1:62062/status\" target=\"_blank\">http://127.0.0.1:62062/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://127.0.0.1:62030\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-_dx16v2n\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://127.0.0.1:62066\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://127.0.0.1:62067/status\" target=\"_blank\">http://127.0.0.1:62067/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://127.0.0.1:62031\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-cuvxixxp\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://127.0.0.1:62054\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://127.0.0.1:62056/status\" target=\"_blank\">http://127.0.0.1:62056/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://127.0.0.1:62032\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-jublykr0\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://127.0.0.1:62024' processes=6 threads=60, memory=55.88 GiB>" ] }, "execution_count": 2, "metadata": {}, "output_type": "execute_result" } ], "source": [ "from dask.distributed import Client\n", "client = Client(n_workers=6, threads_per_worker=10, processes=True, memory_limit='10GB')\n", "client" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Set the path for different cameras" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [], "source": [ "groupList = [\n", " \"images/MOT_3D_Camera/in_situ_absorption\",\n", " \"images/ODT_1_Axis_Camera/in_situ_absorption\",\n", " \"images/ODT_2_Axis_Camera/in_situ_absorption\",\n", "]\n", "\n", "# give a short name to each path (or let's say each camera)\n", "dskey = {\n", " \"images/MOT_3D_Camera/in_situ_absorption\": \"camera_0\",\n", " \"images/ODT_1_Axis_Camera/in_situ_absorption\": \"camera_1\",\n", " \"images/ODT_2_Axis_Camera/in_situ_absorption\": \"camera_2\",\n", "}" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Set global path for experiment" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [], "source": [ "img_dir = '//DyLabNAS/Data/'\n", "SequenceName = \"Evaporative_Cooling\" + \"/\"\n", "folderPath = img_dir + SequenceName + '2023/04/17'# get_date()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Load shot 0058" ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [ { "data": { "text/html": [ "<div><svg style=\"position: absolute; width: 0; height: 0; overflow: hidden\">\n", "<defs>\n", "<symbol id=\"icon-database\" viewBox=\"0 0 32 32\">\n", "<path d=\"M16 0c-8.837 0-16 2.239-16 5v4c0 2.761 7.163 5 16 5s16-2.239 16-5v-4c0-2.761-7.163-5-16-5z\"></path>\n", "<path d=\"M16 17c-8.837 0-16-2.239-16-5v6c0 2.761 7.163 5 16 5s16-2.239 16-5v-6c0 2.761-7.163 5-16 5z\"></path>\n", "<path d=\"M16 26c-8.837 0-16-2.239-16-5v6c0 2.761 7.163 5 16 5s16-2.239 16-5v-6c0 2.761-7.163 5-16 5z\"></path>\n", "</symbol>\n", "<symbol id=\"icon-file-text2\" viewBox=\"0 0 32 32\">\n", "<path d=\"M28.681 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var(--jp-content-font-color0, rgba(0, 0, 0, 1));\n", " --xr-font-color2: var(--jp-content-font-color2, rgba(0, 0, 0, 0.54));\n", " --xr-font-color3: var(--jp-content-font-color3, rgba(0, 0, 0, 0.38));\n", " --xr-border-color: var(--jp-border-color2, #e0e0e0);\n", " --xr-disabled-color: var(--jp-layout-color3, #bdbdbd);\n", " --xr-background-color: var(--jp-layout-color0, white);\n", " --xr-background-color-row-even: var(--jp-layout-color1, white);\n", " --xr-background-color-row-odd: var(--jp-layout-color2, #eeeeee);\n", "}\n", "\n", "html[theme=dark],\n", "body[data-theme=dark],\n", "body.vscode-dark {\n", " --xr-font-color0: rgba(255, 255, 255, 1);\n", " --xr-font-color2: rgba(255, 255, 255, 0.54);\n", " --xr-font-color3: rgba(255, 255, 255, 0.38);\n", " --xr-border-color: #1F1F1F;\n", " --xr-disabled-color: #515151;\n", " --xr-background-color: #111111;\n", " --xr-background-color-row-even: #111111;\n", " --xr-background-color-row-odd: #313131;\n", "}\n", "\n", ".xr-wrap {\n", " display: block !important;\n", " min-width: 300px;\n", " max-width: 700px;\n", "}\n", "\n", ".xr-text-repr-fallback {\n", " /* fallback to plain text repr when CSS is not injected (untrusted notebook) */\n", " display: none;\n", "}\n", "\n", ".xr-header {\n", " padding-top: 6px;\n", " padding-bottom: 6px;\n", " margin-bottom: 4px;\n", " border-bottom: solid 1px var(--xr-border-color);\n", "}\n", "\n", ".xr-header > div,\n", ".xr-header > ul {\n", " display: inline;\n", " margin-top: 0;\n", " margin-bottom: 0;\n", "}\n", "\n", ".xr-obj-type,\n", ".xr-array-name {\n", " margin-left: 2px;\n", " margin-right: 10px;\n", "}\n", "\n", ".xr-obj-type {\n", " color: var(--xr-font-color2);\n", "}\n", "\n", ".xr-sections {\n", " padding-left: 0 !important;\n", " display: grid;\n", " grid-template-columns: 150px auto auto 1fr 20px 20px;\n", "}\n", "\n", ".xr-section-item {\n", " display: contents;\n", "}\n", "\n", ".xr-section-item input {\n", " display: none;\n", "}\n", "\n", ".xr-section-item input + label {\n", " color: var(--xr-disabled-color);\n", "}\n", "\n", ".xr-section-item input:enabled + label {\n", " cursor: pointer;\n", " color: var(--xr-font-color2);\n", "}\n", "\n", ".xr-section-item input:enabled + label:hover {\n", " color: var(--xr-font-color0);\n", "}\n", "\n", ".xr-section-summary {\n", " grid-column: 1;\n", " color: var(--xr-font-color2);\n", " font-weight: 500;\n", "}\n", "\n", ".xr-section-summary > span {\n", " display: inline-block;\n", " padding-left: 0.5em;\n", "}\n", "\n", ".xr-section-summary-in:disabled + label {\n", " color: var(--xr-font-color2);\n", "}\n", "\n", ".xr-section-summary-in + label:before {\n", " display: inline-block;\n", " content: 'â–º';\n", " font-size: 11px;\n", " width: 15px;\n", " text-align: center;\n", "}\n", "\n", ".xr-section-summary-in:disabled + label:before {\n", " color: var(--xr-disabled-color);\n", "}\n", "\n", ".xr-section-summary-in:checked + label:before {\n", " content: 'â–¼';\n", "}\n", "\n", ".xr-section-summary-in:checked + label > span {\n", " display: none;\n", "}\n", "\n", ".xr-section-summary,\n", ".xr-section-inline-details {\n", " padding-top: 4px;\n", " padding-bottom: 4px;\n", "}\n", "\n", ".xr-section-inline-details {\n", " grid-column: 2 / -1;\n", "}\n", "\n", ".xr-section-details {\n", " display: none;\n", " grid-column: 1 / -1;\n", " margin-bottom: 5px;\n", "}\n", "\n", ".xr-section-summary-in:checked ~ .xr-section-details {\n", " display: contents;\n", "}\n", "\n", ".xr-array-wrap {\n", " grid-column: 1 / -1;\n", " display: grid;\n", " grid-template-columns: 20px auto;\n", "}\n", "\n", ".xr-array-wrap > label {\n", " grid-column: 1;\n", " vertical-align: top;\n", "}\n", "\n", ".xr-preview {\n", " color: var(--xr-font-color3);\n", "}\n", "\n", ".xr-array-preview,\n", ".xr-array-data {\n", " padding: 0 5px !important;\n", " grid-column: 2;\n", "}\n", "\n", ".xr-array-data,\n", ".xr-array-in:checked ~ .xr-array-preview {\n", " display: none;\n", "}\n", "\n", ".xr-array-in:checked ~ .xr-array-data,\n", ".xr-array-preview {\n", " display: inline-block;\n", "}\n", "\n", ".xr-dim-list {\n", " display: inline-block !important;\n", " list-style: none;\n", " padding: 0 !important;\n", " margin: 0;\n", "}\n", "\n", ".xr-dim-list li {\n", " display: inline-block;\n", " padding: 0;\n", " margin: 0;\n", "}\n", "\n", ".xr-dim-list:before {\n", " content: '(';\n", "}\n", "\n", ".xr-dim-list:after {\n", " content: ')';\n", "}\n", "\n", ".xr-dim-list li:not(:last-child):after {\n", " content: ',';\n", " padding-right: 5px;\n", "}\n", "\n", ".xr-has-index {\n", " font-weight: bold;\n", "}\n", "\n", ".xr-var-list,\n", ".xr-var-item {\n", " display: contents;\n", "}\n", "\n", ".xr-var-item > div,\n", ".xr-var-item label,\n", ".xr-var-item > .xr-var-name span {\n", " background-color: var(--xr-background-color-row-even);\n", " margin-bottom: 0;\n", "}\n", "\n", ".xr-var-item > .xr-var-name:hover span {\n", " padding-right: 5px;\n", "}\n", "\n", ".xr-var-list > li:nth-child(odd) > div,\n", ".xr-var-list > li:nth-child(odd) > label,\n", ".xr-var-list > li:nth-child(odd) > .xr-var-name span {\n", " background-color: var(--xr-background-color-row-odd);\n", "}\n", "\n", ".xr-var-name {\n", " grid-column: 1;\n", "}\n", "\n", ".xr-var-dims {\n", " grid-column: 2;\n", "}\n", "\n", ".xr-var-dtype {\n", " grid-column: 3;\n", " text-align: right;\n", " color: var(--xr-font-color2);\n", "}\n", "\n", ".xr-var-preview {\n", " grid-column: 4;\n", "}\n", "\n", ".xr-index-preview {\n", " grid-column: 2 / 5;\n", " color: var(--xr-font-color2);\n", "}\n", "\n", ".xr-var-name,\n", ".xr-var-dims,\n", ".xr-var-dtype,\n", ".xr-preview,\n", ".xr-attrs dt {\n", " white-space: nowrap;\n", " overflow: hidden;\n", " text-overflow: ellipsis;\n", " padding-right: 10px;\n", "}\n", "\n", ".xr-var-name:hover,\n", ".xr-var-dims:hover,\n", ".xr-var-dtype:hover,\n", ".xr-attrs dt:hover {\n", " overflow: visible;\n", " width: auto;\n", " z-index: 1;\n", "}\n", "\n", ".xr-var-attrs,\n", ".xr-var-data,\n", ".xr-index-data {\n", " display: none;\n", " background-color: var(--xr-background-color) !important;\n", " padding-bottom: 5px !important;\n", "}\n", "\n", ".xr-var-attrs-in:checked ~ .xr-var-attrs,\n", ".xr-var-data-in:checked ~ .xr-var-data,\n", ".xr-index-data-in:checked ~ .xr-index-data {\n", " display: block;\n", "}\n", "\n", ".xr-var-data > table {\n", " float: right;\n", "}\n", "\n", ".xr-var-name span,\n", ".xr-var-data,\n", ".xr-index-name div,\n", ".xr-index-data,\n", ".xr-attrs {\n", " padding-left: 25px !important;\n", "}\n", "\n", ".xr-attrs,\n", ".xr-var-attrs,\n", ".xr-var-data,\n", ".xr-index-data {\n", " grid-column: 1 / -1;\n", "}\n", "\n", "dl.xr-attrs {\n", " padding: 0;\n", " margin: 0;\n", " display: grid;\n", " grid-template-columns: 125px auto;\n", "}\n", "\n", ".xr-attrs dt,\n", ".xr-attrs dd {\n", " padding: 0;\n", " margin: 0;\n", " float: left;\n", " padding-right: 10px;\n", " width: auto;\n", "}\n", "\n", ".xr-attrs dt {\n", " font-weight: normal;\n", " grid-column: 1;\n", "}\n", "\n", ".xr-attrs dt:hover span {\n", " display: inline-block;\n", " background: var(--xr-background-color);\n", " padding-right: 10px;\n", "}\n", "\n", ".xr-attrs dd {\n", " grid-column: 2;\n", " white-space: pre-wrap;\n", " word-break: break-all;\n", "}\n", "\n", ".xr-icon-database,\n", ".xr-icon-file-text2,\n", ".xr-no-icon {\n", " display: inline-block;\n", " vertical-align: middle;\n", " width: 1em;\n", " height: 1.5em !important;\n", " stroke-width: 0;\n", " stroke: currentColor;\n", " fill: currentColor;\n", "}\n", "</style><pre class='xr-text-repr-fallback'><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, 1200, 1920), meta=np.ndarray>\n", " background (runs, truncation_value, y, x) uint16 dask.array<chunksize=(5, 11, 1200, 1920), meta=np.ndarray>\n", " dark (runs, truncation_value, y, x) uint16 dask.array<chunksize=(5, 11, 1200, 1920), 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.]</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-60ad284d-6c17-4de5-87e8-9c5041954e24' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-60ad284d-6c17-4de5-87e8-9c5041954e24' 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-e7a8e751-ef52-4ef4-bfed-3fab473997ce' class='xr-section-summary-in' type='checkbox' checked><label for='section-e7a8e751-ef52-4ef4-bfed-3fab473997ce' 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-751d2c4f-1dc9-4e14-8fd4-2ae10c9866e4' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-751d2c4f-1dc9-4e14-8fd4-2ae10c9866e4' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6cab3602-978c-45c5-b385-2e6bf83d40a4' class='xr-var-data-in' type='checkbox'><label for='data-6cab3602-978c-45c5-b385-2e6bf83d40a4' 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-710393a6-211c-43a0-ac23-2e056a6ba52d' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-710393a6-211c-43a0-ac23-2e056a6ba52d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-2faceeac-ee11-47c9-ba9b-36f14b75a120' class='xr-var-data-in' type='checkbox'><label for='data-2faceeac-ee11-47c9-ba9b-36f14b75a120' 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-04b9fe0f-fd01-417a-bcbb-0418bc3369a5' class='xr-section-summary-in' type='checkbox' checked><label for='section-04b9fe0f-fd01-417a-bcbb-0418bc3369a5' 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<chunksize=(5, 11, 1200, 1920), meta=np.ndarray></div><input id='attrs-8bde07a1-4cfe-4ae2-a785-84a25ee9286b' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-8bde07a1-4cfe-4ae2-a785-84a25ee9286b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-9f7ad42b-ab6a-445f-af3a-e491ceeb1082' class='xr-var-data-in' type='checkbox'><label for='data-9f7ad42b-ab6a- " <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> 241.70 MiB </td>\n", " </tr>\n", " \n", " <tr>\n", " <th> Shape </th>\n", " <td> (5, 11, 1200, 1920) </td>\n", " <td> (5, 11, 1200, 1920) </td>\n", " </tr>\n", " <tr>\n", " <th> Dask graph </th>\n", " <td colspan=\"2\"> 1 chunks in 178 graph layers </td>\n", " </tr>\n", " <tr>\n", " <th> Data type </th>\n", " <td colspan=\"2\"> uint16 numpy.ndarray </td>\n", " </tr>\n", " </tbody>\n", " </table>\n", " </td>\n", " <td>\n", " <svg width=\"374\" height=\"139\" style=\"stroke:rgb(0,0,0);stroke-width:1\" >\n", "\n", " <!-- Horizontal lines -->\n", " <line x1=\"0\" y1=\"0\" x2=\"25\" y2=\"0\" style=\"stroke-width:2\" />\n", " <line x1=\"0\" y1=\"25\" x2=\"25\" y2=\"25\" style=\"stroke-width:2\" />\n", "\n", " <!-- Vertical lines -->\n", " <line x1=\"0\" y1=\"0\" x2=\"0\" y2=\"25\" style=\"stroke-width:2\" />\n", " <line x1=\"25\" y1=\"0\" x2=\"25\" y2=\"25\" style=\"stroke-width:2\" />\n", "\n", " <!-- Colored Rectangle -->\n", " <polygon points=\"0.0,0.0 25.412616514582485,0.0 25.412616514582485,25.412616514582485 0.0,25.412616514582485\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n", "\n", " <!-- Text -->\n", " <text x=\"12.706308\" y=\"45.412617\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" >5</text>\n", " <text x=\"45.412617\" y=\"12.706308\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(0,45.412617,12.706308)\">1</text>\n", "\n", "\n", " <!-- Horizontal lines -->\n", " <line x1=\"95\" y1=\"0\" x2=\"109\" y2=\"14\" style=\"stroke-width:2\" />\n", " <line x1=\"95\" y1=\"75\" x2=\"109\" y2=\"89\" style=\"stroke-width:2\" />\n", "\n", " <!-- Vertical lines -->\n", " <line x1=\"95\" y1=\"0\" x2=\"95\" y2=\"75\" style=\"stroke-width:2\" />\n", " <line x1=\"109\" y1=\"14\" x2=\"109\" y2=\"89\" style=\"stroke-width:2\" />\n", "\n", " <!-- Colored Rectangle -->\n", " <polygon points=\"95.0,0.0 109.9485979497544,14.948597949754403 109.9485979497544,89.9485979497544 95.0,75.0\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n", "\n", " <!-- Horizontal lines -->\n", " <line x1=\"95\" y1=\"0\" x2=\"215\" y2=\"0\" style=\"stroke-width:2\" />\n", " <line x1=\"109\" y1=\"14\" x2=\"229\" y2=\"14\" style=\"stroke-width:2\" />\n", "\n", " <!-- Vertical lines -->\n", " <line x1=\"95\" y1=\"0\" x2=\"109\" y2=\"14\" style=\"stroke-width:2\" />\n", " <line x1=\"215\" y1=\"0\" x2=\"229\" y2=\"14\" style=\"stroke-width:2\" />\n", "\n", " <!-- Colored Rectangle -->\n", " <polygon points=\"95.0,0.0 215.0,0.0 229.9485979497544,14.948597949754403 109.9485979497544,14.948597949754403\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n", "\n", " <!-- Horizontal lines -->\n", " <line x1=\"109\" y1=\"14\" x2=\"229\" y2=\"14\" style=\"stroke-width:2\" />\n", " <line x1=\"109\" y1=\"89\" x2=\"229\" y2=\"89\" style=\"stroke-width:2\" />\n", "\n", " <!-- Vertical lines -->\n", " <line x1=\"109\" y1=\"14\" x2=\"109\" y2=\"89\" style=\"stroke-width:2\" />\n", " <line x1=\"229\" y1=\"14\" x2=\"229\" y2=\"89\" style=\"stroke-width:2\" />\n", "\n", " <!-- Colored Rectangle -->\n", " <polygon points=\"109.9485979497544,14.948597949754403 229.9485979497544,14.948597949754403 229.9485979497544,89.9485979497544 109.9485979497544,89.9485979497544\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n", "\n", " <!-- Text -->\n", " <text x=\"169.948598\" y=\"109.948598\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" >1920</text>\n", " <text x=\"249.948598\" y=\"52.448598\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(-90,249.948598,52.448598)\">1200</text>\n", " <text x=\"92.474299\" y=\"102.474299\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(45,92.474299,102.474299)\">11</text>\n", "</svg>\n", " </td>\n", " </tr>\n", "</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<chunksize=(5, 11, 1200, 1920), meta=np.ndarray></div><input id='attrs-4110b8fd-4de3-449e-849a-41f04d803fc4' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-4110b8fd-4de3-449e-849a-41f04d803fc4' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1acc979b-7a34-4452-8886-b3ba2303436c' class='xr-var-data-in' type='checkbox'><label for='data-1acc979b-7a34-4452-8886-b3ba2303436c' 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> 241.70 MiB </td>\n", " </tr>\n", " \n", " <tr>\n", " <th> Shape </th>\n", " <td> (5, 11, 1200, 1920) </td>\n", " <td> (5, 11, 1200, 1920) </td>\n", " </tr>\n", " <tr>\n", " <th> Dask graph </th>\n", " <td colspan=\"2\"> 1 chunks in 178 graph layers </td>\n", " </tr>\n", " <tr>\n", " <th> Data type </th>\n", " <td colspan=\"2\"> uint16 numpy.ndarray </td>\n", " </tr>\n", " </tbody>\n", " </table>\n", " </td>\n", " <td>\n", " <svg width=\"374\" height=\"139\" style=\"stroke:rgb(0,0,0);stroke-width:1\" >\n", "\n", " <!-- Horizontal lines -->\n", " <line x1=\"0\" y1=\"0\" x2=\"25\" y2=\"0\" style=\"stroke-width:2\" />\n", " <line x1=\"0\" y1=\"25\" x2=\"25\" y2=\"25\" style=\"stroke-width:2\" />\n", "\n", " <!-- Vertical lines -->\n", " <line x1=\"0\" y1=\"0\" x2=\"0\" y2=\"25\" style=\"stroke-width:2\" />\n", " <line x1=\"25\" y1=\"0\" x2=\"25\" y2=\"25\" style=\"stroke-width:2\" />\n", "\n", " <!-- Colored Rectangle -->\n", " <polygon points=\"0.0,0.0 25.412616514582485,0.0 25.412616514582485,25.412616514582485 0.0,25.412616514582485\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n", "\n", " <!-- Text -->\n", " <text x=\"12.706308\" y=\"45.412617\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" >5</text>\n", " <text x=\"45.412617\" y=\"12.706308\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(0,45.412617,12.706308)\">1</text>\n", "\n", "\n", " <!-- Horizontal lines -->\n", " <line x1=\"95\" y1=\"0\" x2=\"109\" y2=\"14\" style=\"stroke-width:2\" />\n", " <line x1=\"95\" y1=\"75\" x2=\"109\" y2=\"89\" style=\"stroke-width:2\" />\n", "\n", " <!-- Vertical lines -->\n", " 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font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(45,92.474299,102.474299)\">11</text>\n", "</svg>\n", " </td>\n", " </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<chunksize=(5, 11, 1200, 1920), meta=np.ndarray></div><input id='attrs-cc001339-3532-4597-91ff-9c6f778b56a0' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-cc001339-3532-4597-91ff-9c6f778b56a0' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-88d17b84-ca9b-45ad-9080-9c4f9c722cad' class='xr-var-data-in' type='checkbox'><label for='data-88d17b84-ca9b-45ad-9080-9c4f9c722cad' 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> 241.70 MiB </td>\n", " </tr>\n", " \n", " <tr>\n", " <th> Shape </th>\n", " <td> (5, 11, 1200, 1920) </td>\n", " <td> (5, 11, 1200, 1920) </td>\n", " </tr>\n", " <tr>\n", " <th> Dask graph </th>\n", " <td colspan=\"2\"> 1 chunks in 178 graph layers </td>\n", " </tr>\n", " <tr>\n", " <th> Data type </th>\n", " <td colspan=\"2\"> uint16 numpy.ndarray </td>\n", " </tr>\n", " </tbody>\n", " </table>\n", " </td>\n", " <td>\n", " <svg width=\"374\" height=\"139\" style=\"stroke:rgb(0,0,0);stroke-width:1\" >\n", "\n", " <!-- Horizontal lines -->\n", " <line x1=\"0\" y1=\"0\" x2=\"25\" y2=\"0\" style=\"stroke-width:2\" />\n", " <line x1=\"0\" y1=\"25\" x2=\"25\" y2=\"25\" style=\"stroke-width:2\" />\n", "\n", " <!-- Vertical lines -->\n", " <line x1=\"0\" y1=\"0\" x2=\"0\" y2=\"25\" style=\"stroke-width:2\" />\n", " <line x1=\"25\" y1=\"0\" x2=\"25\" y2=\"25\" style=\"stroke-width:2\" />\n", "\n", " <!-- Colored Rectangle -->\n", " <polygon points=\"0.0,0.0 25.412616514582485,0.0 25.412616514582485,25.412616514582485 0.0,25.412616514582485\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n", "\n", " <!-- Text -->\n", " <text x=\"12.706308\" y=\"45.412617\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" >5</text>\n", " <text x=\"45.412617\" y=\"12.706308\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(0,45.412617,12.706308)\">1</text>\n", "\n", "\n", " <!-- Horizontal lines -->\n", " <line x1=\"95\" y1=\"0\" x2=\"109\" y2=\"14\" style=\"stroke-width:2\" />\n", " <line x1=\"95\" y1=\"75\" x2=\"109\" y2=\"89\" style=\"stroke-width:2\" />\n", "\n", " <!-- Vertical lines -->\n", " <line x1=\"95\" y1=\"0\" x2=\"95\" y2=\"75\" style=\"stroke-width:2\" />\n", " <line x1=\"109\" y1=\"14\" x2=\"109\" y2=\"89\" style=\"stroke-width:2\" />\n", "\n", " <!-- Colored Rectangle -->\n", " <polygon points=\"95.0,0.0 109.9485979497544,14.948597949754403 109.9485979497544,89.9485979497544 95.0,75.0\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n", "\n", " <!-- Horizontal lines -->\n", " <line x1=\"95\" y1=\"0\" x2=\"215\" y2=\"0\" style=\"stroke-width:2\" />\n", " <line x1=\"109\" y1=\"14\" x2=\"229\" y2=\"14\" style=\"stroke-width:2\" />\n", "\n", " <!-- Vertical lines -->\n", " <line x1=\"95\" y1=\"0\" x2=\"109\" y2=\"14\" style=\"stroke-width:2\" />\n", " <line x1=\"215\" y1=\"0\" x2=\"229\" y2=\"14\" style=\"stroke-width:2\" />\n", "\n", " <!-- Colored Rectangle -->\n", " <polygon points=\"95.0,0.0 215.0,0.0 229.9485979497544,14.948597949754403 109.9485979497544,14.948597949754403\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n", "\n", " <!-- Horizontal lines -->\n", " <line x1=\"109\" y1=\"14\" x2=\"229\" y2=\"14\" style=\"stroke-width:2\" />\n", " <line x1=\"109\" y1=\"89\" x2=\"229\" y2=\"89\" style=\"stroke-width:2\" />\n", "\n", " <!-- Vertical lines -->\n", " <line x1=\"109\" y1=\"14\" x2=\"109\" y2=\"89\" style=\"stroke-width:2\" />\n", " <line x1=\"229\" y1=\"14\" x2=\"229\" y2=\"89\" style=\"stroke-width:2\" />\n", "\n", " <!-- Colored Rectangle -->\n", " <polygon points=\"109.9485979497544,14.948597949754403 229.9485979497544,14.948597949754403 229.9485979497544,89.9485979497544 109.9485979497544,89.9485979497544\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n", "\n", " <!-- Text -->\n", " <text x=\"169.948598\" y=\"109.948598\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" >1920</text>\n", " <text x=\"249.948598\" y=\"52.448598\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(-90,249.948598,52.448598)\">1200</text>\n", " <text x=\"92.474299\" y=\"102.474299\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(45,92.474299,102.474299)\">11</text>\n", "</svg>\n", " </td>\n", " </tr>\n", "</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'><U2</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(5, 11), meta=np.ndarray></div><input id='attrs-6b8c8483-a6a5-4167-aeab-8346b01c5eab' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-6b8c8483-a6a5-4167-aeab-8346b01c5eab' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-530badb7-3994-4e40-af3d-87dbf61ad701' class='xr-var-data-in' type='checkbox'><label for='data-530badb7-3994-4e40-af3d-87dbf61ad701' 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'><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> 440 B </td>\n", " <td> 440 B </td>\n", " </tr>\n", " \n", " <tr>\n", " <th> Shape </th>\n", " <td> (5, 11) </td>\n", " <td> (5, 11) </td>\n", " </tr>\n", " <tr>\n", " <th> Dask graph </th>\n", " <td colspan=\"2\"> 1 chunks in 1 graph layer </td>\n", " </tr>\n", " <tr>\n", " <th> Data type </th>\n", " <td colspan=\"2\"> <U2 numpy.ndarray </td>\n", " </tr>\n", " </tbody>\n", " </table>\n", " </td>\n", " <td>\n", " <svg width=\"170\" height=\"104\" style=\"stroke:rgb(0,0,0);stroke-width:1\" >\n", "\n", " <!-- Horizontal lines -->\n", " <line x1=\"0\" y1=\"0\" x2=\"120\" y2=\"0\" style=\"stroke-width:2\" />\n", " <line x1=\"0\" y1=\"54\" x2=\"120\" y2=\"54\" style=\"stroke-width:2\" />\n", "\n", " <!-- Vertical lines -->\n", " <line x1=\"0\" y1=\"0\" x2=\"0\" y2=\"54\" style=\"stroke-width:2\" />\n", " <line x1=\"120\" y1=\"0\" x2=\"120\" y2=\"54\" style=\"stroke-width:2\" />\n", "\n", " <!-- Colored Rectangle -->\n", " <polygon points=\"0.0,0.0 120.0,0.0 120.0,54.54545454545454 0.0,54.54545454545454\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n", "\n", " <!-- Text -->\n", " <text x=\"60.000000\" y=\"74.545455\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" >11</text>\n", " <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-2de491bf-fa24-4cb3-80ef-cb2101d97450' class='xr-section-summary-in' type='checkbox' ><label for='section-2de491bf-fa24-4cb3-80ef-cb2101d97450' 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-41a901d2-1225-4e0c-8c6d-b4d1e2b187e9' class='xr-index-data-in' type='checkbox'/><label for='index-41a901d2-1225-4e0c-8c6d-b4d1e2b187e9' 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='float64', name='runs'))</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-371f1d73-9852-402f-9120-554525577ebc' class='xr-index-data-in' type='checkbox'/><label for='index-371f1d73-9852-402f-9120-554525577ebc' 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='float64', name='truncation_value'))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-a0ecb7b8-dc8e-47f3-bb45-e06e06c147ef' class='xr-section-summary-in' type='checkbox' ><label for='section-a0ecb7b8-dc8e-47f3-bb45-e06e06c147ef' 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_ar " 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>['runs' 'truncation_value']</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, 1200, 1920), meta=np.ndarray>\n", " background (runs, truncation_value, y, x) uint16 dask.array<chunksize=(5, 11, 1200, 1920), meta=np.ndarray>\n", " dark (runs, truncation_value, y, x) uint16 dask.array<chunksize=(5, 11, 1200, 1920), 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": 5, "metadata": {}, "output_type": "execute_result" } ], "source": [ "shotNum = \"0058\"\n", "filePath = folderPath + \"/\" + shotNum + \"/*.h5\"\n", "\n", "dataSetDict = {\n", " dskey[groupList[i]]: read_hdf5_file(filePath, groupList[i])\n", " for i in [0] # range(len(groupList)) # uncommont to load data for all three cameras\n", "}\n", "dataSet = dataSetDict[\"camera_0\"]\n", "\n", "dataSet = swap_xy(dataSet)\n", "\n", "scanAxis = get_scanAxis(dataSet)\n", "\n", "dataSet = auto_rechunk(dataSet)\n", "\n", "dataSet" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Creat an object of imaging analyser " ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "The idea is to package all imaging related analysis funciton into a clasee, the 'ImageAnalyser'. The advantage is that it record our last settings, i.e. the region of interest, and thus we don't need to set it again.\n", "\n", "Therefore, first we need to create an object of the 'ImageAnalyser' class." ] }, { "cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [], "source": [ "imageAnalyser = ImageAnalyser()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Calculate OD of absorption imaging" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "A brief introduction to the absorption iamging can be found in following link\n", "\n", "https://arxiv.org/pdf/1209.3408.pdf\n", "\n", "You now can directly call the function ImageAnalyser.get_absorption_images() to get the OD of aborption imging from the loaded data. It will return a copy of the data and add the calculation result with a name 'OD'." ] }, { "cell_type": "code", "execution_count": 7, "metadata": {}, "outputs": [ { "data": { "text/html": [ "<div><svg style=\"position: absolute; width: 0; height: 0; overflow: hidden\">\n", "<defs>\n", "<symbol id=\"icon-database\" viewBox=\"0 0 32 32\">\n", "<path d=\"M16 0c-8.837 0-16 2.239-16 5v4c0 2.761 7.163 5 16 5s16-2.239 16-5v-4c0-2.761-7.163-5-16-5z\"></path>\n", "<path d=\"M16 17c-8.837 0-16-2.239-16-5v6c0 2.761 7.163 5 16 5s16-2.239 16-5v-6c0 2.761-7.163 5-16 5z\"></path>\n", "<path d=\"M16 26c-8.837 0-16-2.239-16-5v6c0 2.761 7.163 5 16 5s16-2.239 16-5v-6c0 2.761-7.163 5-16 5z\"></path>\n", "</symbol>\n", "<symbol id=\"icon-file-text2\" viewBox=\"0 0 32 32\">\n", "<path d=\"M28.681 7.159c-0.694-0.947-1.662-2.053-2.724-3.116s-2.169-2.030-3.116-2.724c-1.612-1.182-2.393-1.319-2.841-1.319h-15.5c-1.378 0-2.5 1.121-2.5 2.5v27c0 1.378 1.122 2.5 2.5 2.5h23c1.378 0 2.5-1.122 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".xr-var-attrs-in:checked ~ .xr-var-attrs,\n", ".xr-var-data-in:checked ~ .xr-var-data,\n", ".xr-index-data-in:checked ~ .xr-index-data {\n", " display: block;\n", "}\n", "\n", ".xr-var-data > table {\n", " float: right;\n", "}\n", "\n", ".xr-var-name span,\n", ".xr-var-data,\n", ".xr-index-name div,\n", ".xr-index-data,\n", ".xr-attrs {\n", " padding-left: 25px !important;\n", "}\n", "\n", ".xr-attrs,\n", ".xr-var-attrs,\n", ".xr-var-data,\n", ".xr-index-data {\n", " grid-column: 1 / -1;\n", "}\n", "\n", "dl.xr-attrs {\n", " padding: 0;\n", " margin: 0;\n", " display: grid;\n", " grid-template-columns: 125px auto;\n", "}\n", "\n", ".xr-attrs dt,\n", ".xr-attrs dd {\n", " padding: 0;\n", " margin: 0;\n", " float: left;\n", " padding-right: 10px;\n", " width: auto;\n", "}\n", "\n", ".xr-attrs dt {\n", " font-weight: normal;\n", " grid-column: 1;\n", "}\n", "\n", ".xr-attrs dt:hover span {\n", " display: inline-block;\n", " background: var(--xr-background-color);\n", " padding-right: 10px;\n", "}\n", "\n", ".xr-attrs dd {\n", " grid-column: 2;\n", " white-space: pre-wrap;\n", " word-break: break-all;\n", "}\n", "\n", ".xr-icon-database,\n", ".xr-icon-file-text2,\n", ".xr-no-icon {\n", " display: inline-block;\n", " vertical-align: middle;\n", " width: 1em;\n", " height: 1.5em !important;\n", " stroke-width: 0;\n", " stroke: currentColor;\n", " fill: currentColor;\n", "}\n", "</style><pre class='xr-text-repr-fallback'><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, 1200, 1920), meta=np.ndarray>\n", " background (runs, truncation_value, y, x) uint16 dask.array<chunksize=(5, 11, 1200, 1920), meta=np.ndarray>\n", " dark (runs, truncation_value, y, x) uint16 dask.array<chunksize=(5, 11, 1200, 1920), meta=np.ndarray>\n", " shotNum (runs, truncation_value) <U2 dask.array<chunksize=(5, 11), meta=np.ndarray>\n", " OD (runs, truncation_value, y, x) float64 dask.array<chunksize=(5, 11, 1200, 1920), 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.]</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-0ab3933f-2d21-4231-b90b-f7798daf5712' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-0ab3933f-2d21-4231-b90b-f7798daf5712' 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-b9380d46-c8d8-4b12-9a04-bb4c64792478' class='xr-section-summary-in' type='checkbox' checked><label for='section-b9380d46-c8d8-4b12-9a04-bb4c64792478' 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-9522b1ba-399e-414d-a4a1-1c360237d1af' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-9522b1ba-399e-414d-a4a1-1c360237d1af' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-9670235c-abd9-47be-b6a9-cf1c2de2a57b' class='xr-var-data-in' type='checkbox'><label for='data-9670235c-abd9-47be-b6a9-cf1c2de2a57b' 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-3e2ab95c-15fb-4ad6-806a-05f92ea4c580' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-3e2ab95c-15fb-4ad6-806a-05f92ea4c580' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-04344353-cb2a-4fd2-8795-d7d35ef4e5aa' class='xr-var-data-in' type='checkbox'><label for='data-04344353-cb2a-4fd2-8795-d7d35ef4e5aa' 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-442581b4-cf7c-4cb8-9c2e-897a64a9989d' class='xr-section-summary-in' type='checkbox' checked><label for='section-442581b4-cf7c-4cb8-9c2e-897a64a9989d' class='xr-section-summary' >Data variables: <span>(5)</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<chunksize=(5, 11, 1200, 1920), meta=np.ndarray></div><input id='attrs-2e1ef343-deb4-42b2-af95-f3ee865eb158' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-2e1ef343-deb4-42b2-af95-f3ee865eb158' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e57683ca-a01e-4368-ba45-7b991468a9e4' class='xr-var-data-in' type='checkbox'><label for='data-e57683ca-a01e- " <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> 241.70 MiB </td>\n", " </tr>\n", " \n", " <tr>\n", " <th> Shape </th>\n", " <td> (5, 11, 1200, 1920) </td>\n", " <td> (5, 11, 1200, 1920) </td>\n", " </tr>\n", " <tr>\n", " <th> Dask graph </th>\n", " <td colspan=\"2\"> 1 chunks in 178 graph layers </td>\n", " </tr>\n", " <tr>\n", " <th> Data type </th>\n", " <td colspan=\"2\"> uint16 numpy.ndarray </td>\n", " </tr>\n", " </tbody>\n", " </table>\n", " </td>\n", " <td>\n", " <svg width=\"374\" height=\"139\" style=\"stroke:rgb(0,0,0);stroke-width:1\" >\n", "\n", " <!-- Horizontal lines -->\n", " <line x1=\"0\" y1=\"0\" x2=\"25\" y2=\"0\" style=\"stroke-width:2\" />\n", " <line x1=\"0\" y1=\"25\" x2=\"25\" y2=\"25\" style=\"stroke-width:2\" />\n", "\n", " <!-- Vertical lines -->\n", " <line x1=\"0\" y1=\"0\" x2=\"0\" y2=\"25\" style=\"stroke-width:2\" />\n", " <line x1=\"25\" y1=\"0\" x2=\"25\" y2=\"25\" style=\"stroke-width:2\" />\n", "\n", " <!-- Colored Rectangle -->\n", " <polygon points=\"0.0,0.0 25.412616514582485,0.0 25.412616514582485,25.412616514582485 0.0,25.412616514582485\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n", "\n", " <!-- Text -->\n", " <text x=\"12.706308\" y=\"45.412617\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" >5</text>\n", " <text x=\"45.412617\" y=\"12.706308\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(0,45.412617,12.706308)\">1</text>\n", "\n", "\n", " <!-- Horizontal lines -->\n", " <line x1=\"95\" y1=\"0\" x2=\"109\" y2=\"14\" style=\"stroke-width:2\" />\n", " <line x1=\"95\" y1=\"75\" x2=\"109\" y2=\"89\" style=\"stroke-width:2\" />\n", "\n", " <!-- Vertical lines -->\n", " <line x1=\"95\" y1=\"0\" x2=\"95\" y2=\"75\" style=\"stroke-width:2\" />\n", " <line x1=\"109\" y1=\"14\" x2=\"109\" y2=\"89\" style=\"stroke-width:2\" />\n", "\n", " <!-- Colored Rectangle -->\n", " <polygon points=\"95.0,0.0 109.9485979497544,14.948597949754403 109.9485979497544,89.9485979497544 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y1=\"14\" x2=\"229\" y2=\"89\" style=\"stroke-width:2\" />\n", "\n", " <!-- Colored Rectangle -->\n", " <polygon points=\"109.9485979497544,14.948597949754403 229.9485979497544,14.948597949754403 229.9485979497544,89.9485979497544 109.9485979497544,89.9485979497544\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n", "\n", " <!-- Text -->\n", " <text x=\"169.948598\" y=\"109.948598\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" >1920</text>\n", " <text x=\"249.948598\" y=\"52.448598\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(-90,249.948598,52.448598)\">1200</text>\n", " <text x=\"92.474299\" y=\"102.474299\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(45,92.474299,102.474299)\">11</text>\n", "</svg>\n", " </td>\n", " </tr>\n", "</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<chunksize=(5, 11, 1200, 1920), meta=np.ndarray></div><input id='attrs-7ffcb26e-62be-4a7f-8d78-9744ac86c88d' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-7ffcb26e-62be-4a7f-8d78-9744ac86c88d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-4613a65b-2fa1-4d6c-9c06-216e23c6c1ec' class='xr-var-data-in' type='checkbox'><label for='data-4613a65b-2fa1-4d6c-9c06-216e23c6c1ec' 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> 241.70 MiB </td>\n", " </tr>\n", " \n", " <tr>\n", " <th> Shape </th>\n", " <td> (5, 11, 1200, 1920) </td>\n", " <td> (5, 11, 1200, 1920) </td>\n", " </tr>\n", " <tr>\n", " <th> Dask graph </th>\n", " <td colspan=\"2\"> 1 chunks in 178 graph layers </td>\n", " </tr>\n", " <tr>\n", " <th> Data type </th>\n", " <td colspan=\"2\"> uint16 numpy.ndarray </td>\n", " </tr>\n", " </tbody>\n", " </table>\n", " </td>\n", " <td>\n", " <svg width=\"374\" height=\"139\" style=\"stroke:rgb(0,0,0);stroke-width:1\" >\n", "\n", " <!-- Horizontal lines -->\n", " <line x1=\"0\" y1=\"0\" x2=\"25\" y2=\"0\" style=\"stroke-width:2\" />\n", " <line x1=\"0\" y1=\"25\" x2=\"25\" y2=\"25\" style=\"stroke-width:2\" />\n", "\n", " <!-- Vertical lines -->\n", " <line x1=\"0\" y1=\"0\" x2=\"0\" y2=\"25\" style=\"stroke-width:2\" />\n", " <line x1=\"25\" y1=\"0\" x2=\"25\" y2=\"25\" style=\"stroke-width:2\" />\n", "\n", " <!-- Colored Rectangle -->\n", " <polygon points=\"0.0,0.0 25.412616514582485,0.0 25.412616514582485,25.412616514582485 0.0,25.412616514582485\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n", "\n", " <!-- Text -->\n", " <text x=\"12.706308\" y=\"45.412617\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" >5</text>\n", " <text x=\"45.412617\" y=\"12.706308\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(0,45.412617,12.706308)\">1</text>\n", "\n", "\n", " <!-- Horizontal lines -->\n", " <line x1=\"95\" y1=\"0\" x2=\"109\" y2=\"14\" style=\"stroke-width:2\" />\n", " <line x1=\"95\" y1=\"75\" x2=\"109\" y2=\"89\" style=\"stroke-width:2\" />\n", "\n", " <!-- Vertical lines -->\n", " <line x1=\"95\" y1=\"0\" x2=\"95\" y2=\"75\" style=\"stroke-width:2\" />\n", " <line x1=\"109\" y1=\"14\" x2=\"109\" y2=\"89\" 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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<chunksize=(5, 11, 1200, 1920), meta=np.ndarray></div><input id='attrs-ed551fc4-9b5f-403c-b486-f93c50d456ff' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-ed551fc4-9b5f-403c-b486-f93c50d456ff' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-eeabd647-76f0-45ba-90a1-acca47380af6' class='xr-var-data-in' type='checkbox'><label for='data-eeabd647-76f0-45ba-90a1-acca47380af6' 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> 241.70 MiB </td>\n", " </tr>\n", " \n", " <tr>\n", " <th> Shape </th>\n", " <td> (5, 11, 1200, 1920) </td>\n", " <td> (5, 11, 1200, 1920) </td>\n", " </tr>\n", " <tr>\n", " <th> Dask graph </th>\n", " <td colspan=\"2\"> 1 chunks in 178 graph layers </td>\n", " </tr>\n", " <tr>\n", " <th> Data type </th>\n", " <td colspan=\"2\"> uint16 numpy.ndarray </td>\n", " </tr>\n", " </tbody>\n", " </table>\n", " </td>\n", " <td>\n", " <svg width=\"374\" height=\"139\" style=\"stroke:rgb(0,0,0);stroke-width:1\" >\n", "\n", " <!-- Horizontal lines -->\n", " <line x1=\"0\" y1=\"0\" x2=\"25\" y2=\"0\" style=\"stroke-width:2\" />\n", " <line x1=\"0\" y1=\"25\" x2=\"25\" y2=\"25\" style=\"stroke-width:2\" />\n", "\n", " <!-- Vertical lines -->\n", " <line x1=\"0\" y1=\"0\" x2=\"0\" y2=\"25\" style=\"stroke-width:2\" />\n", " <line x1=\"25\" y1=\"0\" x2=\"25\" y2=\"25\" style=\"stroke-width:2\" />\n", "\n", " <!-- Colored Rectangle -->\n", " <polygon points=\"0.0,0.0 25.412616514582485,0.0 25.412616514582485,25.412616514582485 0.0,25.412616514582485\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n", "\n", " <!-- Text -->\n", " <text x=\"12.706308\" y=\"45.412617\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" >5</text>\n", " <text x=\"45.412617\" y=\"12.706308\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(0,45.412617,12.706308)\">1</text>\n", "\n", "\n", " <!-- Horizontal lines -->\n", " <line x1=\"95\" y1=\"0\" x2=\"109\" y2=\"14\" style=\"stroke-width:2\" />\n", " <line x1=\"95\" y1=\"75\" x2=\"109\" y2=\"89\" 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transform=\"rotate(-90,249.948598,52.448598)\">1200</text>\n", " <text x=\"92.474299\" y=\"102.474299\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(45,92.474299,102.474299)\">11</text>\n", "</svg>\n", " </td>\n", " </tr>\n", "</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'><U2</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(5, 11), meta=np.ndarray></div><input id='attrs-793954e4-7ce3-4451-9c07-3b02bf13626d' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-793954e4-7ce3-4451-9c07-3b02bf13626d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-30d37d87-c0e2-470a-8030-8cea4afdd53b' class='xr-var-data-in' type='checkbox'><label for='data-30d37d87-c0e2-470a-8030-8cea4afdd53b' 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'><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> 440 B </td>\n", " <td> 440 B </td>\n", " </tr>\n", " \n", " <tr>\n", " <th> Shape </th>\n", " <td> (5, 11) </td>\n", " <td> (5, 11) </td>\n", " </tr>\n", " <tr>\n", " <th> Dask graph </th>\n", " <td colspan=\"2\"> 1 chunks in 1 graph layer </td>\n", " </tr>\n", " <tr>\n", " <th> Data type </th>\n", " <td colspan=\"2\"> <U2 numpy.ndarray </td>\n", " </tr>\n", " </tbody>\n", " </table>\n", " </td>\n", " <td>\n", " <svg width=\"170\" height=\"104\" style=\"stroke:rgb(0,0,0);stroke-width:1\" >\n", "\n", " <!-- Horizontal lines -->\n", " <line x1=\"0\" y1=\"0\" x2=\"120\" y2=\"0\" style=\"stroke-width:2\" />\n", " <line x1=\"0\" y1=\"54\" x2=\"120\" y2=\"54\" style=\"stroke-width:2\" />\n", "\n", " <!-- Vertical lines -->\n", " <line x1=\"0\" y1=\"0\" x2=\"0\" y2=\"54\" style=\"stroke-width:2\" />\n", " <line x1=\"120\" y1=\"0\" x2=\"120\" y2=\"54\" style=\"stroke-width:2\" />\n", "\n", " <!-- Colored Rectangle -->\n", " <polygon points=\"0.0,0.0 120.0,0.0 120.0,54.54545454545454 0.0,54.54545454545454\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n", "\n", " <!-- Text -->\n", " <text x=\"60.000000\" y=\"74.545455\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" >11</text>\n", " <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><li class='xr-var-item'><div class='xr-var-name'><span>OD</span></div><div class='xr-var-dims'>(runs, truncation_value, y, x)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(5, 11, 1200, 1920), meta=np.ndarray></div><input id='attrs-72a71814-5d06-4a6e-862b-dd849fd92028' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-72a71814-5d06-4a6e-862b-dd849fd92028' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c26495be-4776-4c0f-8229-28e455687e7e' class='xr-var-data-in' type='checkbox'><label for='data-c26495be-4776-4c0f-8229-28e455687e7e' 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> 0.94 GiB </td>\n", " <td> 0.94 GiB </td>\n", " </tr>\n", " \n", " <tr>\n", " <th> Shape </th>\n", " <td> (5, 11, 1200, 1920) </td>\n", " <td> (5, 11, 1200, 1920) </td>\n", " </tr>\n", " <tr>\n", " <th> Dask graph </th>\n", " <td colspan=\"2\"> 1 chunks in 544 graph layers </td>\n", " </tr>\n", " <tr>\n", " <th> Data type </th>\n", " <td colspan=\"2\"> float64 numpy.ndarray </td>\n", " </tr>\n", " </tbody>\n", " </table>\n", " </td>\n", " <td>\n", " <svg width=\"374\" height=\"139\" style=\"stroke:rgb(0,0,0);stroke-width:1\" >\n", "\n", " <!-- Horizontal lines -->\n", " <line x1=\"0\" y1=\"0\" x2=\"25\" y2=\"0\" style=\"stroke-width:2\" />\n", " <line x1=\"0\" y1=\"25\" x2=\"25\" y2=\"25\" style=\"stroke-width:2\" />\n", "\n", " <!-- Vertical lines -->\n", " <line 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x2=\"229\" y2=\"89\" style=\"stroke-width:2\" />\n", "\n", " <!-- Vertical lines -->\n", " <line x1=\"109\" y1=\"14\" x2=\"109\" y2=\"89\" style=\"stroke-width:2\" />\n", " <line x1=\"229\" y1=\"14\" x2=\"229\" y2=\"89\" style=\"stroke-width:2\" />\n", "\n", " <!-- Colored Rectangle -->\n", " <polygon points=\"109.9485979497544,14.948597949754403 229.9485979497544,14.948597949754403 229.9485979497544,89.9485979497544 109.9485979497544,89.9485979497544\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n", "\n", " <!-- Text -->\n", " <text x=\"169.948598\" y=\"109.948598\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" >1920</text>\n", " <text x=\"249.948598\" y=\"52.448598\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(-90,249.948598,52.448598)\">1200</text>\n", " <text x=\"92.474299\" y=\"102.474299\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(45,92.474299,102.474299)\">11</text>\n", "</svg>\n", " </td>\n", " </tr>\n", "</table></div></li></ul></div></li><li class='xr-section-item'><input id='section-ce10879d-b52f-433a-a19a-9307c838abd9' class='xr-section-summary-in' type='checkbox' ><label for='section-ce10879d-b52f-433a-a19a-9307c838abd9' 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-b2884047-a233-42be-8016-4fa7222abd55' class='xr-index-data-in' type='checkbox'/><label for='index-b2884047-a233-42be-8016-4fa7222abd55' 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='float64', name='runs'))</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-4bf4fac9-78c3-4539-b00f-385715808b89' class='xr-index-data-in' type='checkbox'/><label for='index-4bf4fac9-78c3-4539-b00f-385715808b89' 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='float64', name='truncation_value'))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-2f0d32ed-8375-4d0f-aedf-7af6c0bd70ae' class='xr-section-summary-in' type='checkbox' ><label for='section-2f0d32ed-8375-4d0f-aedf-7af6c0bd70ae' 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_ar " 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>['runs' 'truncation_value']</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, 1200, 1920), meta=np.ndarray>\n", " background (runs, truncation_value, y, x) uint16 dask.array<chunksize=(5, 11, 1200, 1920), meta=np.ndarray>\n", " dark (runs, truncation_value, y, x) uint16 dask.array<chunksize=(5, 11, 1200, 1920), meta=np.ndarray>\n", " shotNum (runs, truncation_value) <U2 dask.array<chunksize=(5, 11), meta=np.ndarray>\n", " OD (runs, truncation_value, y, x) float64 dask.array<chunksize=(5, 11, 1200, 1920), 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": 7, "metadata": {}, "output_type": "execute_result" } ], "source": [ "dataSet = imageAnalyser.get_absorption_images(dataSet)\n", "dataSet" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Crop the region of interest" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "The next thing we usually need to do is to select the region of interest (ROI)." ] }, { "cell_type": "code", "execution_count": 8, "metadata": {}, "outputs": [], "source": [ "imageAnalyser.center = (960, 875)\n", "imageAnalyser.span = (300, 300)\n", "imageAnalyser.fraction = (0.1, 0.1)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "The object of the ImageAnalyser will save the information until we change it, so we don't need to tell it again and again.\n", "\n", "Here the \n", "- center: the center of the ROI as a tuple (center of x, center of y)\n", "- span: the span of the ROI as a tuple (span of x, span of y)\n", "- fraction: the fraction of the region at the conner of ROI to calculate the background. It is in a format of a tuple (fraction of x, fraction of y)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Then we can crop the images and remove the background." ] }, { "cell_type": "code", "execution_count": 9, "metadata": {}, "outputs": [ { "data": { "text/html": [ "<div><svg style=\"position: absolute; width: 0; height: 0; overflow: hidden\">\n", "<defs>\n", "<symbol id=\"icon-database\" viewBox=\"0 0 32 32\">\n", "<path d=\"M16 0c-8.837 0-16 2.239-16 5v4c0 2.761 7.163 5 16 5s16-2.239 16-5v-4c0-2.761-7.163-5-16-5z\"></path>\n", "<path d=\"M16 17c-8.837 0-16-2.239-16-5v6c0 2.761 7.163 5 16 5s16-2.239 16-5v-6c0 2.761-7.163 5-16 5z\"></path>\n", "<path d=\"M16 26c-8.837 0-16-2.239-16-5v6c0 2.761 7.163 5 16 5s16-2.239 16-5v-6c0 2.761-7.163 5-16 5z\"></path>\n", "</symbol>\n", "<symbol id=\"icon-file-text2\" viewBox=\"0 0 32 32\">\n", "<path d=\"M28.681 7.159c-0.694-0.947-1.662-2.053-2.724-3.116s-2.169-2.030-3.116-2.724c-1.612-1.182-2.393-1.319-2.841-1.319h-15.5c-1.378 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fallback to plain text repr when CSS is not injected (untrusted notebook) */\n", " display: none;\n", "}\n", "\n", ".xr-header {\n", " padding-top: 6px;\n", " padding-bottom: 6px;\n", " margin-bottom: 4px;\n", " border-bottom: solid 1px var(--xr-border-color);\n", "}\n", "\n", ".xr-header > div,\n", ".xr-header > ul {\n", " display: inline;\n", " margin-top: 0;\n", " margin-bottom: 0;\n", "}\n", "\n", ".xr-obj-type,\n", ".xr-array-name {\n", " margin-left: 2px;\n", " margin-right: 10px;\n", "}\n", "\n", ".xr-obj-type {\n", " color: var(--xr-font-color2);\n", "}\n", "\n", ".xr-sections {\n", " padding-left: 0 !important;\n", " display: grid;\n", " grid-template-columns: 150px auto auto 1fr 20px 20px;\n", "}\n", "\n", ".xr-section-item {\n", " display: contents;\n", "}\n", "\n", ".xr-section-item input {\n", " display: none;\n", "}\n", "\n", ".xr-section-item input + label {\n", " color: var(--xr-disabled-color);\n", "}\n", "\n", ".xr-section-item input:enabled + label {\n", " cursor: pointer;\n", " color: var(--xr-font-color2);\n", "}\n", "\n", ".xr-section-item input:enabled + label:hover {\n", " color: var(--xr-font-color0);\n", "}\n", "\n", ".xr-section-summary {\n", " grid-column: 1;\n", " color: var(--xr-font-color2);\n", " font-weight: 500;\n", "}\n", "\n", ".xr-section-summary > span {\n", " display: inline-block;\n", " padding-left: 0.5em;\n", "}\n", "\n", ".xr-section-summary-in:disabled + label {\n", " color: var(--xr-font-color2);\n", "}\n", "\n", ".xr-section-summary-in + label:before {\n", " display: inline-block;\n", " content: 'â–º';\n", " font-size: 11px;\n", " width: 15px;\n", " text-align: center;\n", "}\n", "\n", ".xr-section-summary-in:disabled + label:before {\n", " color: var(--xr-disabled-color);\n", "}\n", "\n", ".xr-section-summary-in:checked + label:before {\n", " content: 'â–¼';\n", "}\n", "\n", ".xr-section-summary-in:checked + label > span {\n", " display: none;\n", "}\n", "\n", ".xr-section-summary,\n", ".xr-section-inline-details {\n", " padding-top: 4px;\n", " padding-bottom: 4px;\n", "}\n", "\n", ".xr-section-inline-details {\n", " grid-column: 2 / -1;\n", "}\n", "\n", ".xr-section-details {\n", " display: none;\n", " grid-column: 1 / -1;\n", " margin-bottom: 5px;\n", "}\n", "\n", ".xr-section-summary-in:checked ~ .xr-section-details {\n", " display: contents;\n", "}\n", "\n", ".xr-array-wrap {\n", " grid-column: 1 / -1;\n", " display: grid;\n", " grid-template-columns: 20px auto;\n", "}\n", "\n", ".xr-array-wrap > label {\n", " grid-column: 1;\n", " vertical-align: top;\n", "}\n", "\n", ".xr-preview {\n", " color: var(--xr-font-color3);\n", "}\n", "\n", ".xr-array-preview,\n", ".xr-array-data {\n", " padding: 0 5px !important;\n", " grid-column: 2;\n", "}\n", "\n", ".xr-array-data,\n", ".xr-array-in:checked ~ .xr-array-preview {\n", " display: none;\n", "}\n", "\n", ".xr-array-in:checked ~ .xr-array-data,\n", ".xr-array-preview {\n", " display: inline-block;\n", "}\n", "\n", ".xr-dim-list {\n", " display: inline-block !important;\n", " list-style: none;\n", " padding: 0 !important;\n", " margin: 0;\n", "}\n", "\n", ".xr-dim-list li {\n", " display: inline-block;\n", " padding: 0;\n", " margin: 0;\n", "}\n", "\n", ".xr-dim-list:before {\n", " content: '(';\n", "}\n", "\n", ".xr-dim-list:after {\n", " content: ')';\n", "}\n", "\n", ".xr-dim-list li:not(:last-child):after {\n", " content: ',';\n", " padding-right: 5px;\n", "}\n", "\n", ".xr-has-index {\n", " font-weight: bold;\n", "}\n", "\n", ".xr-var-list,\n", ".xr-var-item {\n", " display: contents;\n", "}\n", "\n", ".xr-var-item > div,\n", ".xr-var-item label,\n", ".xr-var-item > .xr-var-name span {\n", " background-color: var(--xr-background-color-row-even);\n", " margin-bottom: 0;\n", "}\n", "\n", ".xr-var-item > .xr-var-name:hover span {\n", " padding-right: 5px;\n", "}\n", "\n", ".xr-var-list > li:nth-child(odd) > div,\n", ".xr-var-list > li:nth-child(odd) > label,\n", ".xr-var-list > li:nth-child(odd) > .xr-var-name span {\n", " background-color: var(--xr-background-color-row-odd);\n", "}\n", "\n", ".xr-var-name {\n", " grid-column: 1;\n", "}\n", "\n", ".xr-var-dims {\n", " grid-column: 2;\n", "}\n", "\n", ".xr-var-dtype {\n", " grid-column: 3;\n", " text-align: right;\n", " color: var(--xr-font-color2);\n", "}\n", "\n", ".xr-var-preview {\n", " grid-column: 4;\n", "}\n", "\n", ".xr-index-preview {\n", " grid-column: 2 / 5;\n", " color: var(--xr-font-color2);\n", "}\n", "\n", ".xr-var-name,\n", ".xr-var-dims,\n", ".xr-var-dtype,\n", ".xr-preview,\n", ".xr-attrs dt {\n", " white-space: nowrap;\n", " overflow: hidden;\n", " text-overflow: ellipsis;\n", " padding-right: 10px;\n", "}\n", "\n", ".xr-var-name:hover,\n", ".xr-var-dims:hover,\n", ".xr-var-dtype:hover,\n", ".xr-attrs dt:hover {\n", " overflow: visible;\n", " width: auto;\n", " z-index: 1;\n", "}\n", "\n", ".xr-var-attrs,\n", ".xr-var-data,\n", ".xr-index-data {\n", " display: none;\n", " background-color: var(--xr-background-color) !important;\n", " padding-bottom: 5px !important;\n", "}\n", "\n", ".xr-var-attrs-in:checked ~ .xr-var-attrs,\n", ".xr-var-data-in:checked ~ .xr-var-data,\n", ".xr-index-data-in:checked ~ .xr-index-data {\n", " display: block;\n", "}\n", "\n", ".xr-var-data > table {\n", " float: right;\n", "}\n", "\n", ".xr-var-name span,\n", ".xr-var-data,\n", ".xr-index-name div,\n", ".xr-index-data,\n", ".xr-attrs {\n", " padding-left: 25px !important;\n", "}\n", "\n", ".xr-attrs,\n", ".xr-var-attrs,\n", ".xr-var-data,\n", ".xr-index-data {\n", " grid-column: 1 / -1;\n", "}\n", "\n", "dl.xr-attrs {\n", " padding: 0;\n", " margin: 0;\n", " display: grid;\n", " grid-template-columns: 125px auto;\n", "}\n", "\n", ".xr-attrs dt,\n", ".xr-attrs dd {\n", " padding: 0;\n", " margin: 0;\n", " float: left;\n", " padding-right: 10px;\n", " width: auto;\n", "}\n", "\n", ".xr-attrs dt {\n", " font-weight: normal;\n", " grid-column: 1;\n", "}\n", "\n", ".xr-attrs dt:hover span {\n", " display: inline-block;\n", " background: var(--xr-background-color);\n", " padding-right: 10px;\n", "}\n", "\n", ".xr-attrs dd {\n", " grid-column: 2;\n", " white-space: pre-wrap;\n", " word-break: break-all;\n", "}\n", "\n", ".xr-icon-database,\n", ".xr-icon-file-text2,\n", ".xr-no-icon {\n", " display: inline-block;\n", " vertical-align: middle;\n", " width: 1em;\n", " height: 1.5em !important;\n", " stroke-width: 0;\n", " stroke: currentColor;\n", " fill: currentColor;\n", "}\n", "</style><pre class='xr-text-repr-fallback'><xarray.DataArray 'OD' (runs: 5, truncation_value: 11, y: 300, x: 300)>\n", "array([[[[ 0.10089884, 0.0696463 , 0.05767011, ..., 0.01963588,\n", " -0.0650863 , -0.00446167],\n", " [ 0.10342729, 0.04260584, 0.02118076, ..., 0.11194868,\n", " 0.00723437, -0.0801735 ],\n", " [ 0.00780842, 0.00827735, -0.02827232, ..., -0.02693453,\n", " -0.00446167, 0.0622297 ],\n", " ...,\n", " [-0.1117072 , -0.0575715 , -0.03836323, ..., -0.05152918,\n", " -0.02529576, 0.00751452],\n", " [ 0.12183205, 0.03190597, 0.01355683, ..., -0.02573907,\n", " -0.05682966, -0.00446167],\n", " [ 0.03475904, 0.0325796 , 0.07721636, ..., 0.02662891,\n", " -0.05738408, 0.00751452]],\n", "\n", " [[ 0.05613155, -0.10849043, 0.05082337, ..., 0.09902547,\n", " 0.01710835, 0.03692657],\n", " [-0.08110418, -0.09280022, 0.01710835, ..., -0.04168176,\n", " -0.15458948, 0.00483825],\n", " [-0.07212279, -0.00743184, -0.05653069, ..., -0.18356235,\n", " -0.01621516, -0.07006305],\n", "...\n", " [ 0.15678264, 0.09630046, 0.1255301 , ..., -0.00355249,\n", " 0.01855798, -0.00499196],\n", " [ 0.00774706, -0.07926432, 0.0260962 , ..., -0.01447608,\n", " -0.03527032, 0.04126975],\n", " [-0.01094507, -0.16745703, -0.0624572 , ..., 0.07159853,\n", " 0.01769739, -0.06124581]],\n", "\n", " [[ 0.05950001, 0.0086876 , -0.02921711, ..., 0.04073558,\n", " -0.00421581, -0.04723319],\n", " [-0.0555091 , -0.11475768, -0.05360856, ..., -0.01551536,\n", " 0.03087551, -0.00421581],\n", " [ 0.03352452, -0.01663833, 0.01931469, ..., 0.01752418,\n", " -0.02504989, 0.04815218],\n", " ...,\n", " [ 0.03087551, 0.05294261, -0.13050953, ..., -0.0277463 ,\n", " -0.05020092, -0.04014782],\n", " [ 0.03352452, -0.04422114, -0.06030527, ..., -0.06009626,\n", " -0.03467501, 0.09642772],\n", " [-0.04125708, 0.01447633, 0.07129175, ..., 0.06247557,\n", " -0.05947848, -0.01538911]]]])\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\n", " x_start: 810\n", " x_end: 1110\n", " y_end: 1025\n", " y_start: 725\n", " x_center: 960\n", " y_center: 875\n", " x_span: 300\n", " y_span: 300</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.DataArray</div><div class='xr-array-name'>'OD'</div><ul class='xr-dim-list'><li><span class='xr-has-index'>runs</span>: 5</li><li><span class='xr-has-index'>truncation_value</span>: 11</li><li><span>y</span>: 300</li><li><span>x</span>: 300</li></ul></div><ul class='xr-sections'><li class='xr-section-item'><div class='xr-array-wrap'><input id='section-adbe2e42-433a-40bc-a9d2-a58217889ae1' class='xr-array-in' type='checkbox' checked><label for='section-adbe2e42-433a-40bc-a9d2-a58217889ae1' 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>0.1009 0.06965 0.05767 0.08365 ... -0.05714 0.06248 -0.05948 -0.01539</span></div><div class='xr-array-data'><pre>array([[[[ 0.10089884, 0.0696463 , 0.05767011, ..., 0.01963588,\n", " -0.0650863 , -0.00446167],\n", " [ 0.10342729, 0.04260584, 0.02118076, ..., 0.11194868,\n", " 0.00723437, -0.0801735 ],\n", " [ 0.00780842, 0.00827735, -0.02827232, ..., -0.02693453,\n", " -0.00446167, 0.0622297 ],\n", " ...,\n", " [-0.1117072 , -0.0575715 , -0.03836323, ..., -0.05152918,\n", " -0.02529576, 0.00751452],\n", " [ 0.12183205, 0.03190597, 0.01355683, ..., -0.02573907,\n", " -0.05682966, -0.00446167],\n", " [ 0.03475904, 0.0325796 , 0.07721636, ..., 0.02662891,\n", " -0.05738408, 0.00751452]],\n", "\n", " [[ 0.05613155, -0.10849043, 0.05082337, ..., 0.09902547,\n", " 0.01710835, 0.03692657],\n", " [-0.08110418, -0.09280022, 0.01710835, ..., -0.04168176,\n", " -0.15458948, 0.00483825],\n", " [-0.07212279, -0.00743184, -0.05653069, ..., -0.18356235,\n", " -0.01621516, -0.07006305],\n", "...\n", " [ 0.15678264, 0.09630046, 0.1255301 , ..., -0.00355249,\n", " 0.01855798, -0.00499196],\n", " [ 0.00774706, -0.07926432, 0.0260962 , ..., -0.01447608,\n", " -0.03527032, 0.04126975],\n", " [-0.01094507, -0.16745703, -0.0624572 , ..., 0.07159853,\n", " 0.01769739, -0.06124581]],\n", "\n", " [[ 0.05950001, 0.0086876 , -0.02921711, ..., 0.04073558,\n", " -0.00421581, -0.04723319],\n", " [-0.0555091 , -0.11475768, -0.05360856, ..., -0.01551536,\n", " 0.03087551, -0.00421581],\n", " [ 0.03352452, -0.01663833, 0.01931469, ..., 0.01752418,\n", " -0.02504989, 0.04815218],\n", " ...,\n", " [ 0.03087551, 0.05294261, -0.13050953, ..., -0.0277463 ,\n", " -0.05020092, -0.04014782],\n", " [ 0.03352452, -0.04422114, -0.06030527, ..., -0.06009626,\n", " -0.03467501, 0.09642772],\n", " [-0.04125708, 0.01447633, 0.07129175, ..., 0.06247557,\n", " -0.05947848, -0.01538911]]]])</pre></div></div></li><li class='xr-section-item'><input id='section-4635c4ee-c74e-4658-95dc-e2745349464f' class='xr-section-summary-in' type='checkbox' checked><label for='section-4635c4ee-c74e-4658-95dc-e2745349464f' 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-da6a31a2-c6ec-4bf0-9ff7-be7714114867' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-da6a31a2-c6ec-4bf0-9ff7-be7714114867' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-de1006a8-ddd1-4a29-be28-f5465527e40c' class='xr-var-data-in' type='checkbox'><label for='data-de1006a8-ddd1-4a29-be28-f5465527e40c' 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-31bcc169-67ea-4227-8ab8-34ebcca8a285' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-31bcc169-67ea-4227-8ab8-34ebcca8a285' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b5ad171b-7705-4110-9829-db4cc2236742' class='xr-var-data-in' type='checkbox'><label for='data-b5ad171b-7705-4110-9829-db4cc2236742' 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-fb430d9e-e84c-4b4c-99f1-43b7225fe27f' class='xr-section-summary-in' type='checkbox' ><label for='section-fb430d9e-e84c-4b4c-99f1-43b7225fe27f' 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-e8fcba79-cc16-4d51-914d-118980c3eb06' class='xr-index-data-in' type='checkbox'/><label for='index-e8fcba79-cc16-4d51-914d-118980c3eb06' 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='float64', name='runs'))</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-dd1575a7-7894-4781-9b26-e626eaabfcd7' class='xr-index-data-in' type='checkbox'/><label for='index-dd1575a7-7894-4781-9b26-e626eaabfcd7' 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='float64', name='truncation_value'))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-015e05bd-5334-4b84-a32b-a329055598b6' class='xr-section-summary-in' type='checkbox' ><label for='section-015e05bd-5334-4b84-a32b-a329055598b6' class='xr-section- ], "text/plain": [ "<xarray.DataArray 'OD' (runs: 5, truncation_value: 11, y: 300, x: 300)>\n", "array([[[[ 0.10089884, 0.0696463 , 0.05767011, ..., 0.01963588,\n", " -0.0650863 , -0.00446167],\n", " [ 0.10342729, 0.04260584, 0.02118076, ..., 0.11194868,\n", " 0.00723437, -0.0801735 ],\n", " [ 0.00780842, 0.00827735, -0.02827232, ..., -0.02693453,\n", " -0.00446167, 0.0622297 ],\n", " ...,\n", " [-0.1117072 , -0.0575715 , -0.03836323, ..., -0.05152918,\n", " -0.02529576, 0.00751452],\n", " [ 0.12183205, 0.03190597, 0.01355683, ..., -0.02573907,\n", " -0.05682966, -0.00446167],\n", " [ 0.03475904, 0.0325796 , 0.07721636, ..., 0.02662891,\n", " -0.05738408, 0.00751452]],\n", "\n", " [[ 0.05613155, -0.10849043, 0.05082337, ..., 0.09902547,\n", " 0.01710835, 0.03692657],\n", " [-0.08110418, -0.09280022, 0.01710835, ..., -0.04168176,\n", " -0.15458948, 0.00483825],\n", " [-0.07212279, -0.00743184, -0.05653069, ..., -0.18356235,\n", " -0.01621516, -0.07006305],\n", "...\n", " [ 0.15678264, 0.09630046, 0.1255301 , ..., -0.00355249,\n", " 0.01855798, -0.00499196],\n", " [ 0.00774706, -0.07926432, 0.0260962 , ..., -0.01447608,\n", " -0.03527032, 0.04126975],\n", " [-0.01094507, -0.16745703, -0.0624572 , ..., 0.07159853,\n", " 0.01769739, -0.06124581]],\n", "\n", " [[ 0.05950001, 0.0086876 , -0.02921711, ..., 0.04073558,\n", " -0.00421581, -0.04723319],\n", " [-0.0555091 , -0.11475768, -0.05360856, ..., -0.01551536,\n", " 0.03087551, -0.00421581],\n", " [ 0.03352452, -0.01663833, 0.01931469, ..., 0.01752418,\n", " -0.02504989, 0.04815218],\n", " ...,\n", " [ 0.03087551, 0.05294261, -0.13050953, ..., -0.0277463 ,\n", " -0.05020092, -0.04014782],\n", " [ 0.03352452, -0.04422114, -0.06030527, ..., -0.06009626,\n", " -0.03467501, 0.09642772],\n", " [-0.04125708, 0.01447633, 0.07129175, ..., 0.06247557,\n", " -0.05947848, -0.01538911]]]])\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\n", " x_start: 810\n", " x_end: 1110\n", " y_end: 1025\n", " y_start: 725\n", " x_center: 960\n", " y_center: 875\n", " x_span: 300\n", " y_span: 300" ] }, "execution_count": 9, "metadata": {}, "output_type": "execute_result" } ], "source": [ "dataSet_cropOD = imageAnalyser.crop_image(dataSet.OD)\n", "dataSet_cropOD = imageAnalyser.substract_offset(dataSet_cropOD).load()\n", "dataSet_cropOD" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "The information of ROI will be written to the attributes of the images." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Plot the OD images" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Like panadas package, xarray also provide a easy function to plot the results. Here is an link ot the introduction\n", "\n", "https://docs.xarray.dev/en/stable/user-guide/plotting.html\n", "\n", "`The original xarray plotting function doesn't support to do an errorbar plot, but we implement it by ourselves.`\n", "\n", "If you do not have any patient to read it, you can always copy and paste the following sentance, but with some different settings." ] }, { "cell_type": "code", "execution_count": 10, "metadata": {}, "outputs": [ { "data": { "image/png": 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"text/plain": [ "<Figure size 3400x1500 with 56 Axes>" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "# first get the scan axes\n", "scanAxis = get_scanAxis(dataSet)\n", "\n", "# Name_of_varibale.plot.name_of_plot_type(col=scanAxis[0], row=scanAxis[1], **kwargs)\n", "# The name of the plot type has the same name as it in the matplotlib package\n", "# The **kwargs to adjust the plot also as same as the matplotlib package\n", "dataSet_cropOD.plot.pcolormesh(col=scanAxis[0], row=scanAxis[1], cmap='jet', vmin=0, vmax=2)\n", "\n", "plt.show()" ] } ], "metadata": { "kernelspec": { "display_name": "base", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.9.12" }, "orig_nbformat": 4 }, "nbformat": 4, "nbformat_minor": 2}
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