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{ "cells": [ { "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ "# How to read data from HFD5 files" ] }, { "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ "This is an example to read the data from those HDF5 files generated by LabScript.\n", "\n", "The idea is that one just need to give\n", "\n", "+ The path where data is stored\n", "+ The date of the data\n", "+ The shot number\n", "+ The path of data in HDF5 file (i.e. the name of group)\n", "\n", "It can automatically find the scan axes, and package all of them into an object of DataSet() in xarray package.\n", "\n", "Let us start with importing the supporting packages. In order to keep things ealier, here we will import all the packages, but not all of them will be used." ] }, { "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ "## Import supporting packages" ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "import copy\n", "import glob\n", "from datetime import datetime\n", "\n", "# The package for data structure\n", "import xarray as xr\n", "import pandas as pd\n", "import numpy as np\n", "\n", "# The packages for working with uncertainties\n", "from uncertainties import ufloat\n", "from uncertainties import unumpy as unp\n", "from uncertainties import umath\n", "\n", "# The package for plotting\n", "import matplotlib.pyplot as plt\n", "plt.rcParams['font.size'] = 18 # Set the global font size\n", "\n", "# -------------- The modules written by us --------------\n", "\n", "# The packages for read data\n", "from DataContainer.ReadData import read_hdf5_file, read_hdf5_global, read_hdf5_run_time, read_csv_file\n", "\n", "# The packages for data analysis\n", "from Analyser.ImagingAnalyser import ImageAnalyser\n", "from Analyser.FitAnalyser import FitAnalyser\n", "from Analyser.FitAnalyser import ThomasFermi2dModel, DensityProfileBEC2dModel, Polylog22dModel\n", "from Analyser.FFTAnalyser import fft, ifft, fft_nutou\n", "from ToolFunction.ToolFunction import *\n", "\n", "# Add errorbar plot to xarray package\n", "from ToolFunction.HomeMadeXarrayFunction import errorbar, dataarray_plot_errorbar\n", "xr.plot.dataarray_plot.errorbar = errorbar\n", "xr.plot.accessor.DataArrayPlotAccessor.errorbar = dataarray_plot_errorbar" ] }, { "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ "If one wants to read tens or few hundreds files, a normal script can finish in several minutes." ] }, { "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ "## Start a client for parallel computing" ] }, { "cell_type": "code", "execution_count": null, "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-f3431762-0b91-11ee-bc80-80e82ce2fa8e</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;\">6e648e73</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-669a9b65-bae9-4798-96b7-f5d552eb72f9</p>\n", " <table style=\"width: 100%; text-align: left;\">\n", " <tr>\n", " <td style=\"text-align: left;\">\n", " <strong>Comm:</strong> tcp://127.0.0.1:51057\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://127.0.0.1:51088\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://127.0.0.1:51093/status\" target=\"_blank\">http://127.0.0.1:51093/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://127.0.0.1:51060\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-9s507mc2\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://127.0.0.1:51084\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://127.0.0.1:51085/status\" target=\"_blank\">http://127.0.0.1:51085/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://127.0.0.1:51061\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-y5skkt4c\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://127.0.0.1:51098\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://127.0.0.1:51100/status\" target=\"_blank\">http://127.0.0.1:51100/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://127.0.0.1:51062\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-gmddkxg0\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://127.0.0.1:51095\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://127.0.0.1:51096/status\" target=\"_blank\">http://127.0.0.1:51096/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://127.0.0.1:51063\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-oycines6\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://127.0.0.1:51087\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://127.0.0.1:51091/status\" target=\"_blank\">http://127.0.0.1:51091/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://127.0.0.1:51064\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-a8kpxp6o\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://127.0.0.1:51099\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://127.0.0.1:51101/status\" target=\"_blank\">http://127.0.0.1:51101/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://127.0.0.1:51065\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-thoxr07z\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://127.0.0.1:51057' processes=6 threads=60, memory=55.88 GiB>" ] }, "metadata": {}, "output_type": "display_data" } ], "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": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "imageAnalyser = ImageAnalyser()" ] }, { "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ "## Set global path for experiment" ] }, { "cell_type": "code", "execution_count": 68, "metadata": {}, "outputs": [], "source": [ "# filepath = \"//DyLabNAS/Data/Evaporative_Cooling/2023/05/03/0043/*.h5\"\n", "# filepath = \"//DyLabNAS/Data/Evaporative_Cooling/2023/04/18/0003/2023-04-18_0003_Evaporative_Cooling_000.h5\"\n", "\n", "# filepath = \"//DyLabNAS/Data/Repetition_scan/2023/04/21/0002/*.h5\"\n", "\n", "# filepath = r\"./testData/0002/*.h5\"\n", "\n", "# filepath = r\"./testData/0002/2023-04-21_0002_Evaporative_Cooling_0.h5\"\n", "\n", "# filepath = r'd:/Jianshun Gao/Simulations/analyseScripts/testData/0002/2023-04-21_0002_Evaporative_Cooling_0.h5'\n", "\n", "# filepath = \"//DyLabNAS/Data/Evaporative_Cooling/2023/04/18/0003/*.h5\"\n", "\n", "filepath = \"//DyLabNAS/Data/Evaporative_Cooling/2023/05/04/0000/*.h5\"\n", "\n", "# filepath = './result_from_experiment/2023-04-24/0013/2023-04-24_0013_Evaporative_Cooling_13.h5'" ] }, { "cell_type": "code", "execution_count": 69, "metadata": {}, "outputs": [], "source": [ "groupList = [\n", " \"images/MOT_3D_Camera/in_situ_absorption\",\n", " \"images/ODT_1_Axis_Camera/in_situ_absorption\",\n", " \"images/ODT_2_Axis_Camera/in_situ_absorption\",\n", "]\n", "\n", "dskey = {\n", " \"images/MOT_3D_Camera/in_situ_absorption\": \"camera_1\",\n", " \"images/ODT_1_Axis_Camera/in_situ_absorption\": \"camera_2\",\n", " \"images/ODT_2_Axis_Camera/in_situ_absorption\": \"camera_3\",\n", "}\n" ] }, { "cell_type": "code", "execution_count": 70, "metadata": {}, "outputs": [], "source": [ "img_dir = '//DyLabNAS/Data/'\n", "SequenceName = \"Evaporative_Cooling\" + \"/\"\n", "folderPath = img_dir + SequenceName + '2023/05/23'# get_date()" ] }, { "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ "# An example for one experimental run" ] }, { "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ "## Load the data" ] }, { "cell_type": "code", "execution_count": 75, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "f:\\Jianshun\\analyseScript\\DataContainer\\ReadData.py:178: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison\n", " if not key in datesetOfGlobal.scanAxis\n" ] }, { "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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".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: (y: 1200, x: 1920)\n", "Dimensions without coordinates: y, x\n", "Data variables:\n", " atoms (y, x) uint16 dask.array<chunksize=(1200, 1920), meta=np.ndarray>\n", " background (y, x) uint16 dask.array<chunksize=(1200, 1920), meta=np.ndarray>\n", " dark (y, x) uint16 dask.array<chunksize=(1200, 1920), meta=np.ndarray>\n", " shotNum <U2 '11'\n", " OD (y, x) float64 dask.array<chunksize=(1200, 1920), meta=np.ndarray>\n", "Attributes: (12/96)\n", " TOF_free: 0.02\n", " abs_img_freq: 110.858\n", " absorption_imaging_flag: True\n", " backup_data: True\n", " blink_off_time: nan\n", " blink_on_time: nan\n", " ... ...\n", " y_offset: 0\n", " y_offset_img: 0\n", " z_offset: 0.189\n", " z_offset_img: 0.189\n", " scanAxis: []\n", " scanAxisLength: []</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-3f6a2152-ef01-4819-91f5-a47fe1a85483' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-3f6a2152-ef01-4819-91f5-a47fe1a85483' class='xr-section-summary' title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><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-71114a49-5445-43f4-a531-d6bdc6ba83e9' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-71114a49-5445-43f4-a531-d6bdc6ba83e9' class='xr-section-summary' title='Expand/collapse section'>Coordinates: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-87511f20-517f-4220-90f4-f268366d6d73' class='xr-section-summary-in' type='checkbox' checked><label for='section-87511f20-517f-4220-90f4-f268366d6d73' 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'>(y, x)</div><div class='xr-var-dtype'>uint16</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(1200, 1920), meta=np.ndarray></div><input id='attrs-81526946-1703-4ca5-8e13-3fc13c175996' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-81526946-1703-4ca5-8e13-3fc13c175996' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-77f2b9fc-57a9-4fc9-bcb9-7283191c0038' class='xr-var-data-in' type='checkbox'><label for='data-77f2b9fc-57a9-4fc9-bcb9-7283191c0038' 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> 4.39 MiB </td>\n", " <td> 4.39 MiB </td>\n", " </tr>\n", " \n", " <tr>\n", " <th> Shape </th>\n", " <td> (1200, 1920) </td>\n", " <td> (1200, 1920) </td>\n", " </tr>\n", " <tr>\n", " <th> Dask graph </th>\n", " <td colspan=\"2\"> 1 chunks in 2 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=\"170\" height=\"125\" 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=\"75\" x2=\"120\" y2=\"75\" style=\"stroke-width:2\" />\n", "\n", " <!-- Vertical lines -->\n", " <line x1=\"0\" y1=\"0\" x2=\"0\" y2=\"75\" style=\"stroke-width:2\" />\n", " <line x1=\"120\" y1=\"0\" x2=\"120\" y2=\"75\" style=\"stroke-width:2\" />\n", "\n", " <!-- Colored Rectangle -->\n", " <polygon points=\"0.0,0.0 120.0,0.0 120.0,75.0 0.0,75.0\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n", "\n", " <!-- Text -->\n", " <text x=\"60.000000\" y=\"95.000000\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" >1920</text>\n", " <text x=\"140.000000\" y=\"37.500000\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(-90,140.000000,37.500000)\">1200</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'>(y, x)</div><div class='xr-var-dtype'>uint16</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(1200, 1920), meta=np.ndarray></div><input id='attrs-cf0352d3-81af-4aa1-8a4b-d510a6d9ed9f' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-cf0352d3-81af-4aa1-8a4b-d510a6d9ed9f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-7cebfcb4-0749-41e1-a9df-8a3ca0e9cd57' class='xr-var-data-in' type='checkbox'><label for='data-7cebfcb4-0749-41e1-a9df-8a3ca0e9cd57' 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> 4.39 MiB </td>\n", " <td> 4.39 MiB </td>\n", " </tr>\n", " \n", " <tr>\n", " <th> Shape </th>\n", " <td> (1200, 1920) </td>\n", " <td> (1200, 1920) </td>\n", " </tr>\n", " <tr>\n", " <th> Dask graph </th>\n", " <td colspan=\"2\"> 1 chunks in 2 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=\"170\" height=\"125\" 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=\"75\" x2=\"120\" y2=\"75\" style=\"stroke-width:2\" />\n", "\n", " <!-- Vertical lines -->\n", " <line x1=\"0\" y1=\"0\" x2=\"0\" y2=\"75\" style=\"stroke-width:2\" />\n", " <line x1=\"120\" y1=\"0\" x2=\"120\" y2=\"75\" style=\"stroke-width:2\" />\n", "\n", " <!-- Colored Rectangle -->\n", " <polygon points=\"0.0,0.0 120.0,0.0 120.0,75.0 0.0,75.0\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n", "\n", " <!-- Text -->\n", " <text x=\"60.000000\" y=\"95.000000\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" >1920</text>\n", " <text x=\"140.000000\" y=\"37.500000\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(-90,140.000000,37.500000)\">1200</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'>(y, x)</div><div class='xr-var-dtype'>uint16</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(1200, 1920), meta=np.ndarray></div><input id='attrs-ea5ca203-117f-4d7f-a382-5ea49ef757fe' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-ea5ca203-117f-4d7f-a382-5ea49ef757fe' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1c46121e-396f-4c19-b720-5bfd85d3db08' class='xr-var-data-in' type='checkbox'><label for='data-1c46121e-396f-4c19-b720-5bfd85d3db08' 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> 4.39 MiB </td>\n", " <td> 4.39 MiB </td>\n", " </tr>\n", " \n", " <tr>\n", " <th> Shape </th>\n", " <td> (1200, 1920) </td>\n", " <td> (1200, 1920) </td>\n", " </tr>\n", " <tr>\n", " <th> Dask graph </th>\n", " <td colspan=\"2\"> 1 chunks in 2 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=\"170\" height=\"125\" 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=\"75\" x2=\"120\" y2=\"75\" style=\"stroke-width:2\" />\n", "\n", " <!-- Vertical lines -->\n", " <line x1=\"0\" y1=\"0\" x2=\"0\" y2=\"75\" style=\"stroke-width:2\" />\n", " <line x1=\"120\" y1=\"0\" x2=\"120\" y2=\"75\" style=\"stroke-width:2\" />\n", "\n", " <!-- Colored Rectangle -->\n", " <polygon points=\"0.0,0.0 120.0,0.0 120.0,75.0 0.0,75.0\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n", "\n", " <!-- Text -->\n", " <text x=\"60.000000\" y=\"95.000000\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" >1920</text>\n", " <text x=\"140.000000\" y=\"37.500000\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(-90,140.000000,37.500000)\">1200</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'>()</div><div class='xr-var-dtype'><U2</div><div class='xr-var-preview xr-preview'>'11'</div><input id='attrs-931dff3b-9054-49ae-a9a3-af23a3abe9d2' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-931dff3b-9054-49ae-a9a3-af23a3abe9d2' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-16b7a2e7-307c-45ef-8fd7-4961a352c6cd' class='xr-var-data-in' type='checkbox'><label for='data-16b7a2e7-307c-45ef-8fd7-4961a352c6cd' 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('11', dtype='<U2')</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>OD</span></div><div class='xr-var-dims'>(y, x)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(1200, 1920), meta=np.ndarray></div><input id='attrs-c45c4a1c-0006-43c9-be36-4e3d40196cf6' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-c45c4a1c-0006-43c9-be36-4e3d40196cf6' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-81f04315-1fc1-4433-9b5f-8dbcef03d3d4' class='xr-var-data-in' type='checkbox'><label for='data-81f04315-1fc1-4433-9b5f-8dbcef03d3d4' 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> 17.58 MiB </td>\n", " <td> 17.58 MiB </td>\n", " </tr>\n", " \n", " <tr>\n", " <th> Shape </th>\n", " <td> (1200, 1920) </td>\n", " <td> (1200, 1920) </td>\n", " </tr>\n", " <tr>\n", " <th> Dask graph </th>\n", " <td colspan=\"2\"> 1 chunks in 16 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=\"170\" height=\"125\" 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=\"75\" x2=\"120\" y2=\"75\" style=\"stroke-width:2\" />\n", "\n", " <!-- Vertical lines -->\n", " <line x1=\"0\" y1=\"0\" x2=\"0\" y2=\"75\" style=\"stroke-width:2\" />\n", " <line x1=\"120\" y1=\"0\" x2=\"120\" y2=\"75\" style=\"stroke-width:2\" />\n", "\n", " <!-- Colored Rectangle -->\n", " <polygon points=\"0.0,0.0 120.0,0.0 120.0,75.0 0.0,75.0\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n", "\n", " <!-- Text -->\n", " <text x=\"60.000000\" y=\"95.000000\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" >1920</text>\n", " <text x=\"140.000000\" y=\"37.500000\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(-90,140.000000,37.500000)\">1200</text>\n", "</svg>\n", " </td>\n", " </tr>\n", "</table></div></li></ul></div></li><li class='xr-section-item'><input id='section-c33811d7-8cf5-4e35-8e55-5bc202a3ba60' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-c33811d7-8cf5-4e35-8e55-5bc202a3ba60' class='xr-section-summary' title='Expand/collapse section'>Indexes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-47715f26-a2f1-48c1-9cd1-23dbb2fa5488' class='xr-section-summary-in' type='checkbox' ><label for='section-47715f26-a2f1-48c1-9cd1-23dbb2fa5488' class='xr-section-summary' >Attributes: <span>(96)</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>110.858</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>0.005</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>0.0</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>0.189</dd><dt><span>compZ_final_current :</span></dt><dd>0.2812</dd><dt><span>compZ_initial_current :</span></dt><dd>0</dd><dt><span>default_camera :</span></dt><dd>0</dd><dt><span>evap_1_arm_1_final_pow :</span></dt><dd>0.35</dd><dt><span>evap_1_arm_1_mod_depth_final :</span></dt><dd>0</dd><dt><span>evap_1_arm_1_mod_depth_initial :</span></dt><dd>1.0</dd><dt><span>evap_1_arm_1_mod_ramp_duration :</span></dt><dd>1.15</dd><dt><span>evap_1_arm_1_pow_ramp_duration :</span></dt><dd>1.65</dd><dt><span>evap_1_arm_1_start_pow :</span></dt><dd>7</dd><dt><span>evap_1_arm_2_final_pow :</span></dt><dd>5</dd><dt><span>evap_1_arm_2_ramp_duration :</span></dt><dd>0.5</dd><dt><span>evap_1_arm_2_start_pow :</span></dt><dd>0</dd><dt><span>evap_1_mod_ramp_trunc_value :</span></dt><dd>1</dd><dt><span>evap_1_pow_ramp_trunc_value :</span></dt><dd>1.0</dd><dt><span>evap_1_rate_constant_1 :</span></dt><dd>0.525</dd><dt><span>evap_1_rate_constant_2 :</span></dt><dd>0.51</dd><dt><span>evap_2_arm_1_final_pow :</span></dt><dd>0.037</dd><dt><span>evap_2_arm_1_start_pow :</span></dt><dd>0.35</dd><dt><span>evap_2_arm_2_final_pow :</span></dt><dd>0.09</dd><dt><span>evap_2_arm_2_start_pow :</span></dt><dd>5</dd><dt><span>evap_2_ramp_duration :</span></dt><dd>1.0</dd><dt><span>evap_2_ramp_trunc_value :</span></dt><dd>1</dd><dt><span>evap_2_rate_constant_1 :</span></dt><dd>0.37</dd><dt><span>evap_2_rate_constant_2 :</span></dt><dd>0.71</dd><dt><span>evap_3_arm_1_final_pow :</span></dt><dd>0.1038</dd><dt><span>evap_3_arm_1_mod_depth_final :</span></dt><dd>0.43</dd><dt><span>evap_3_arm_1_mod_depth_initial :</span></dt><dd>0</dd><dt><span>evap_3_arm_1_start_pow :</span></dt><dd>0.037</dd><dt><span>evap_3_ramp_duration :</span></dt><dd>0.1</dd><dt><span>evap_3_ramp_trunc_value :</span></dt><dd>1</dd><dt><span>evap_3_rate_constant_1 :</span></dt><dd>-0.879</dd><dt><span>evap_3_rate_constant_2 :</span></dt><dd>-0.297</dd><dt><span>final_amp :</span></dt><dd>8e-05</dd><dt><span>final_freq :</span></dt><dd>104.0</dd><dt><span>gradCoil_current :</span></dt><dd>0.18</dd><dt><span>gradCoil_current_sg :</span></dt><dd>0</dd><dt><span>imaging_method :</span></dt><dd>in_situ_absorption</dd><dt><span>imaging_pulse_duration :</span></dt><dd>2.5e-05</dd><dt><span>imaging_wavel ], "text/plain": [ "<xarray.Dataset>\n", "Dimensions: (y: 1200, x: 1920)\n", "Dimensions without coordinates: y, x\n", "Data variables:\n", " atoms (y, x) uint16 dask.array<chunksize=(1200, 1920), meta=np.ndarray>\n", " background (y, x) uint16 dask.array<chunksize=(1200, 1920), meta=np.ndarray>\n", " dark (y, x) uint16 dask.array<chunksize=(1200, 1920), meta=np.ndarray>\n", " shotNum <U2 '11'\n", " OD (y, x) float64 dask.array<chunksize=(1200, 1920), meta=np.ndarray>\n", "Attributes: (12/96)\n", " TOF_free: 0.02\n", " abs_img_freq: 110.858\n", " absorption_imaging_flag: True\n", " backup_data: True\n", " blink_off_time: nan\n", " blink_on_time: nan\n", " ... ...\n", " y_offset: 0\n", " y_offset_img: 0\n", " z_offset: 0.189\n", " z_offset_img: 0.189\n", " scanAxis: []\n", " scanAxisLength: []" ] }, "execution_count": 75, "metadata": {}, "output_type": "execute_result" } ], "source": [ "shotNum = \"0069\"\n", "filePath = folderPath + \"/\" + shotNum + \"/*.h5\"\n", "# filePath = \"//DyLabNAS/Data/Evaporative_Cooling/2023/05/12/0065/*.h5\"\n", "filePath = './result_from_experiment/2023-04-24/0013/2023-04-24_0013_Evaporative_Cooling_11.h5'\n", "\n", "dataSetDict = {\n", " dskey[groupList[i]]: read_hdf5_file(filePath, groupList[i])\n", " for i in [0] # range(len(groupList))\n", "}\n", "\n", "dataSet = dataSetDict[\"camera_1\"]\n", "dataSet = swap_xy(dataSet)\n", "\n", "scanAxis = get_scanAxis(dataSet)\n", "\n", "dataSet = auto_rechunk(dataSet)\n", "\n", "dataSet = imageAnalyser.get_absorption_images(dataSet)\n", "\n", "dataSet" ] }, { "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ "## Calculate an plot OD images" ] }, { "cell_type": "code", "execution_count": 76, "metadata": {}, "outputs": [ { "data": { "image/png": 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"text/plain": [ "<Figure size 640x480 with 2 Axes>" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "# imageAnalyser.center = (960, 1040)\n", "# imageAnalyser.span = (100, 100)\n", "# imageAnalyser.fraction = (0.1, 0.1)\n", "\n", "imageAnalyser.center = (960, 875)\n", "imageAnalyser.span = (300, 300)\n", "imageAnalyser.fraction = (0.1, 0.1)\n", "\n", "dataSet_cropOD = imageAnalyser.crop_image(dataSet.OD)\n", "dataSet_cropOD = imageAnalyser.substract_offset(dataSet_cropOD).load()\n", "\n", "dataSet_cropOD.plot.pcolormesh(cmap='jet', vmin=0, col=scanAxis[0], row=scanAxis[1])\n", "plt.show()" ] } ], "metadata": { "kernelspec": { "display_name": "env", "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" }, "vscode": { "interpreter": { "hash": "c05913ad4f24fdc6b2418069394dc5835b1981849b107c9ba6df693aafd66650" } } }, "nbformat": 4, "nbformat_minor": 2}
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