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{ "cells": [ { "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ "# Import supporting package" ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "import xarray as xr\n", "import numpy as np\n", "\n", "from uncertainties import ufloat\n", "from uncertainties import unumpy as unp\n", "from uncertainties import umath\n", "\n", "import matplotlib.pyplot as plt\n", "\n", "from DataContainer.ReadData import read_hdf5_file\n", "from Analyser.ImagingAnalyser import ImageAnalyser\n", "from Analyser.FitAnalyser import FitAnalyser\n", "from ToolFunction.ToolFunction import *\n", "\n", "from ToolFunction.HomeMadeXarrayFunction import errorbar, dataarray_plot_errorbar\n", "xr.plot.dataarray_plot.errorbar = errorbar\n", "xr.plot.accessor.DataArrayPlotAccessor.errorbar = dataarray_plot_errorbar\n", "\n", "imageAnalyser = ImageAnalyser()" ] }, { "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ "## Start a client for parallel computing" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "D:\\Program Files\\Python\\Python38\\Lib\\site-packages\\distributed\\node.py:182: UserWarning: Port 8787 is already in use.\n", "Perhaps you already have a cluster running?\n", "Hosting the HTTP server on port 59390 instead\n", " warnings.warn(\n" ] }, { "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-9a0ca19d-ecb4-11ed-af18-9c7bef43b4fb</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://127.0.0.1:59390/status\" target=\"_blank\">http://127.0.0.1:59390/status</a>\n", " </td>\n", " <td style=\"text-align: left;\"></td>\n", " </tr>\n", " \n", "\n", " </table>\n", "\n", " \n", " <button style=\"margin-bottom: 12px;\" data-commandlinker-command=\"dask:populate-and-launch-layout\" data-commandlinker-args='{\"url\": \"http://127.0.0.1:59390/status\" }'>\n", " Launch dashboard in JupyterLab\n", " </button>\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;\">40e09024</p>\n", " <table style=\"width: 100%; text-align: left;\">\n", " <tr>\n", " <td style=\"text-align: left;\">\n", " <strong>Dashboard:</strong> <a href=\"http://127.0.0.1:59390/status\" target=\"_blank\">http://127.0.0.1:59390/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-616be11d-c546-4d58-ad88-3bacd53b13c0</p>\n", " <table style=\"width: 100%; text-align: left;\">\n", " <tr>\n", " <td style=\"text-align: left;\">\n", " <strong>Comm:</strong> tcp://127.0.0.1:59391\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://127.0.0.1:59390/status\" target=\"_blank\">http://127.0.0.1:59390/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://127.0.0.1:59424\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://127.0.0.1:59428/status\" target=\"_blank\">http://127.0.0.1:59428/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://127.0.0.1:59394\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\\Jianshun Gao\\AppData\\Local\\Temp\\dask-worker-space\\worker-ybrgy95q\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://127.0.0.1:59422\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://127.0.0.1:59427/status\" target=\"_blank\">http://127.0.0.1:59427/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://127.0.0.1:59395\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\\Jianshun Gao\\AppData\\Local\\Temp\\dask-worker-space\\worker-ms_3izxs\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://127.0.0.1:59434\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://127.0.0.1:59437/status\" target=\"_blank\">http://127.0.0.1:59437/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://127.0.0.1:59396\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\\Jianshun Gao\\AppData\\Local\\Temp\\dask-worker-space\\worker-qteiamcm\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://127.0.0.1:59421\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://127.0.0.1:59426/status\" target=\"_blank\">http://127.0.0.1:59426/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://127.0.0.1:59397\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\\Jianshun Gao\\AppData\\Local\\Temp\\dask-worker-space\\worker-r2y5vxh3\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://127.0.0.1:59425\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://127.0.0.1:59435/status\" target=\"_blank\">http://127.0.0.1:59435/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://127.0.0.1:59398\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\\Jianshun Gao\\AppData\\Local\\Temp\\dask-worker-space\\worker-3ykst_31\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://127.0.0.1:59423\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://127.0.0.1:59429/status\" target=\"_blank\">http://127.0.0.1:59429/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://127.0.0.1:59399\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\\Jianshun Gao\\AppData\\Local\\Temp\\dask-worker-space\\worker-egpqiwk3\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://127.0.0.1:59391' processes=6 threads=60, memory=55.88 GiB>" ] }, "execution_count": 2, "metadata": {}, "output_type": "execute_result" } ], "source": [ "from dask.distributed import Client\n", "client = Client(n_workers=6, threads_per_worker=10, processes=True, memory_limit='10GB')\n", "client" ] }, { "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ "# Read data" ] }, { "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ "## Set file path" ] }, { "cell_type": "code", "execution_count": 3, "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\"" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [], "source": [ "groupList = [\n", " \"images/MOT_3D_Camera/in_situ_absorption\",\n", " # \"images/ODT_1_Axis_Camera/in_situ_absorption\",\n", "]\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", "}\n", "\n", "dataSetDict = {\n", " dskey[groupList[i]]: read_hdf5_file(filepath, groupList[i])\n", " for i in range(len(groupList))\n", "}" ] }, { "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ "## Rechunk the data for parallel computing" ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [], "source": [ "dataSet = dataSetDict[\"camera_1\"]\n", "\n", "scanAxis = dataSet.scanAxis\n", "\n", "# dataSet = dataSet.chunk(\n", "# {\n", "# # \"compZ_current_sg\": \"auto\",\n", "# \"sin_mod_freq\": \"auto\",\n", "# \"runs\": 2,\n", "# \"x\": \"auto\",\n", "# \"y\": \"auto\",\n", "# }\n", "# )" ] }, { "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ "# Calculate absorption imaging" ] }, { "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ "## get OD images" ] }, { "cell_type": "code", "execution_count": 6, "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 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{\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: 3, x: 1200, y: 1920)\n", "Coordinates:\n", " * runs (runs) float64 0.0 1.0 2.0\n", "Dimensions without coordinates: x, y\n", "Data variables:\n", " atoms (runs, x, y) uint16 dask.array<chunksize=(1, 1200, 1920), meta=np.ndarray>\n", " background (runs, x, y) uint16 dask.array<chunksize=(1, 1200, 1920), meta=np.ndarray>\n", " dark (runs, x, y) uint16 dask.array<chunksize=(1, 1200, 1920), meta=np.ndarray>\n", " shotNum (runs) int64 0 1 2\n", " OD (runs, x, y) float64 dask.array<chunksize=(1, 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_img: 0\n", " z_offset: 0.189\n", " z_offset_img: 0.189\n", " runs: [0. 1. 2.]\n", " scanAxis: ['runs']\n", " scanAxisLength: [3.]</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-f93fede0-0ffa-4c21-b9ba-c80d42838e9a' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-f93fede0-0ffa-4c21-b9ba-c80d42838e9a' 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>: 3</li><li><span>x</span>: 1200</li><li><span>y</span>: 1920</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-3dec71c4-b180-4438-934e-50bc3c02d447' class='xr-section-summary-in' type='checkbox' checked><label for='section-3dec71c4-b180-4438-934e-50bc3c02d447' class='xr-section-summary' >Coordinates: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>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</div><input id='attrs-35d0177d-948f-4b66-b45d-edfed01c339f' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-35d0177d-948f-4b66-b45d-edfed01c339f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6995abb3-bf0c-4aa7-9aa2-0c4082d0d6b1' class='xr-var-data-in' type='checkbox'><label for='data-6995abb3-bf0c-4aa7-9aa2-0c4082d0d6b1' 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.])</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-6b5f08a3-382c-44dd-ac4e-312cf9dc366e' class='xr-section-summary-in' type='checkbox' checked><label for='section-6b5f08a3-382c-44dd-ac4e-312cf9dc366e' 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, x, y)</div><div class='xr-var-dtype'>uint16</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(1, 1200, 1920), meta=np.ndarray></div><input id='attrs-18c85580-860b-4be5-be6c-dfab7bdaa4b7' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-18c85580-860b-4be5-be6c-dfab7bdaa4b7' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-0801c4a5-fd40-4956-924d-5871de1976c4' class='xr-var-data-in' type='checkbox'><label for='data-0801c4a5-fd40-4956-924d-5871de1976c4' 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> 13.18 MiB </td>\n", " <td> 4.39 MiB </td>\n", " </tr>\n", " \n", " <tr>\n", " <th> Shape </th>\n", " <td> (3, 1200, 1920) </td>\n", " <td> (1, 1200, 1920) </td>\n", " </tr>\n", " <tr>\n", " <th> Dask graph </th>\n", " <td colspan=\"2\"> 3 chunks in 10 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=\"194\" height=\"139\" style=\"stroke:rgb(0,0,0);stroke-width:1\" >\n", "\n", " <!-- Horizontal lines -->\n", " <line x1=\"10\" y1=\"0\" x2=\"24\" y2=\"14\" style=\"stroke-width:2\" />\n", " <line x1=\"10\" y1=\"75\" x2=\"24\" y2=\"89\" style=\"stroke-width:2\" />\n", "\n", " <!-- Vertical lines -->\n", " <line x1=\"10\" y1=\"0\" x2=\"10\" y2=\"75\" style=\"stroke-width:2\" />\n", " <line x1=\"14\" y1=\"4\" x2=\"14\" y2=\"79\" />\n", " <line x1=\"19\" y1=\"9\" x2=\"19\" y2=\"84\" />\n", " <line x1=\"24\" y1=\"14\" x2=\"24\" y2=\"89\" style=\"stroke-width:2\" />\n", "\n", " <!-- Colored Rectangle -->\n", " <polygon points=\"10.0,0.0 24.9485979497544,14.948597949754403 24.9485979497544,89.9485979497544 10.0,75.0\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n", "\n", " <!-- Horizontal lines -->\n", " <line x1=\"10\" y1=\"0\" x2=\"130\" y2=\"0\" style=\"stroke-width:2\" />\n", " <line x1=\"14\" y1=\"4\" x2=\"134\" y2=\"4\" />\n", " <line x1=\"19\" y1=\"9\" x2=\"139\" y2=\"9\" />\n", " <line x1=\"24\" y1=\"14\" x2=\"144\" y2=\"14\" style=\"stroke-width:2\" />\n", "\n", " <!-- Vertical lines -->\n", " <line x1=\"10\" y1=\"0\" x2=\"24\" y2=\"14\" style=\"stroke-width:2\" />\n", " <line x1=\"130\" y1=\"0\" x2=\"144\" y2=\"14\" style=\"stroke-width:2\" />\n", "\n", " <!-- Colored Rectangle -->\n", " <polygon points=\"10.0,0.0 130.0,0.0 144.9485979497544,14.948597949754403 24.9485979497544,14.948597949754403\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n", "\n", " <!-- Horizontal lines -->\n", " <line x1=\"24\" y1=\"14\" x2=\"144\" y2=\"14\" style=\"stroke-width:2\" />\n", " <line x1=\"24\" y1=\"89\" x2=\"144\" y2=\"89\" style=\"stroke-width:2\" />\n", "\n", " <!-- Vertical lines -->\n", " <line x1=\"24\" y1=\"14\" x2=\"24\" y2=\"89\" style=\"stroke-width:2\" />\n", " <line x1=\"144\" y1=\"14\" x2=\"144\" y2=\"89\" style=\"stroke-width:2\" />\n", "\n", " <!-- Colored Rectangle -->\n", " <polygon points=\"24.9485979497544,14.948597949754403 144.9485979497544,14.948597949754403 144.9485979497544,89.9485979497544 24.9485979497544,89.9485979497544\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n", "\n", " <!-- Text -->\n", " <text x=\"84.948598\" y=\"109.948598\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" >1920</text>\n", " <text x=\"164.948598\" y=\"52.448598\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(-90,164.948598,52.448598)\">1200</text>\n", " <text x=\"7.474299\" y=\"102.474299\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(45,7.474299,102.474299)\">3</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, x, y)</div><div class='xr-var-dtype'>uint16</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(1, 1200, 1920), meta=np.ndarray></div><input id='attrs-48a73fd3-7731-4eb6-bcb7-d35cef143851' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-48a73fd3-7731-4eb6-bcb7-d35cef143851' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6d9bb466-2ed5-48b2-8991-b812f0633673' class='xr-var-data-in' type='checkbox'><label for='data-6d9bb466-2ed5-48b2-8991-b812f0633673' 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> 13.18 MiB </td>\n", " <td> 4.39 MiB </td>\n", " </tr>\n", " \n", " <tr>\n", " <th> Shape </th>\n", " <td> (3, 1200, 1920) </td>\n", " <td> (1, 1200, 1920) </td>\n", " </tr>\n", " <tr>\n", " <th> Dask graph </th>\n", " <td colspan=\"2\"> 3 chunks in 10 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=\"194\" height=\"139\" style=\"stroke:rgb(0,0,0);stroke-width:1\" >\n", "\n", " <!-- Horizontal lines -->\n", " <line x1=\"10\" y1=\"0\" x2=\"24\" y2=\"14\" style=\"stroke-width:2\" />\n", " <line x1=\"10\" y1=\"75\" x2=\"24\" y2=\"89\" style=\"stroke-width:2\" />\n", "\n", " <!-- Vertical lines -->\n", " <line x1=\"10\" y1=\"0\" x2=\"10\" y2=\"75\" style=\"stroke-width:2\" />\n", " <line x1=\"14\" y1=\"4\" x2=\"14\" 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transform=\"rotate(-90,164.948598,52.448598)\">1200</text>\n", " <text x=\"7.474299\" y=\"102.474299\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(45,7.474299,102.474299)\">3</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, x, y)</div><div class='xr-var-dtype'>uint16</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(1, 1200, 1920), meta=np.ndarray></div><input id='attrs-ced29619-3399-44f1-af13-2104035019ad' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-ced29619-3399-44f1-af13-2104035019ad' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-55f03d0d-eeed-4a0c-8a02-ad327d3b47ef' class='xr-var-data-in' type='checkbox'><label for='data-55f03d0d-eeed-4a0c-8a02-ad327d3b47ef' 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> 13.18 MiB </td>\n", " <td> 4.39 MiB </td>\n", " </tr>\n", " \n", " <tr>\n", " <th> Shape </th>\n", " <td> (3, 1200, 1920) </td>\n", " <td> (1, 1200, 1920) </td>\n", " </tr>\n", " <tr>\n", " <th> Dask graph </th>\n", " <td colspan=\"2\"> 3 chunks in 10 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=\"194\" height=\"139\" style=\"stroke:rgb(0,0,0);stroke-width:1\" >\n", "\n", " <!-- Horizontal lines -->\n", " <line x1=\"10\" y1=\"0\" x2=\"24\" y2=\"14\" style=\"stroke-width:2\" />\n", " <line x1=\"10\" y1=\"75\" x2=\"24\" y2=\"89\" style=\"stroke-width:2\" />\n", "\n", " <!-- Vertical lines -->\n", " <line x1=\"10\" y1=\"0\" x2=\"10\" y2=\"75\" style=\"stroke-width:2\" />\n", " <line x1=\"14\" y1=\"4\" x2=\"14\" y2=\"79\" />\n", " <line x1=\"19\" y1=\"9\" x2=\"19\" y2=\"84\" />\n", " <line x1=\"24\" y1=\"14\" x2=\"24\" y2=\"89\" style=\"stroke-width:2\" />\n", "\n", " <!-- Colored Rectangle -->\n", " <polygon points=\"10.0,0.0 24.9485979497544,14.948597949754403 24.9485979497544,89.9485979497544 10.0,75.0\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n", "\n", " <!-- Horizontal lines -->\n", " <line x1=\"10\" y1=\"0\" x2=\"130\" y2=\"0\" style=\"stroke-width:2\" />\n", " <line x1=\"14\" y1=\"4\" x2=\"134\" y2=\"4\" />\n", " <line x1=\"19\" y1=\"9\" x2=\"139\" y2=\"9\" />\n", " <line x1=\"24\" y1=\"14\" x2=\"144\" y2=\"14\" style=\"stroke-width:2\" />\n", "\n", " <!-- Vertical lines -->\n", " <line x1=\"10\" y1=\"0\" x2=\"24\" y2=\"14\" style=\"stroke-width:2\" />\n", " <line x1=\"130\" y1=\"0\" x2=\"144\" y2=\"14\" style=\"stroke-width:2\" />\n", "\n", " <!-- Colored Rectangle -->\n", " <polygon points=\"10.0,0.0 130.0,0.0 144.9485979497544,14.948597949754403 24.9485979497544,14.948597949754403\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n", "\n", " <!-- Horizontal lines -->\n", " <line x1=\"24\" y1=\"14\" x2=\"144\" y2=\"14\" style=\"stroke-width:2\" />\n", " <line x1=\"24\" y1=\"89\" x2=\"144\" y2=\"89\" style=\"stroke-width:2\" />\n", "\n", " <!-- Vertical lines -->\n", " <line x1=\"24\" y1=\"14\" x2=\"24\" y2=\"89\" style=\"stroke-width:2\" />\n", " <line x1=\"144\" y1=\"14\" x2=\"144\" y2=\"89\" style=\"stroke-width:2\" />\n", "\n", " <!-- Colored Rectangle -->\n", " <polygon points=\"24.9485979497544,14.948597949754403 144.9485979497544,14.948597949754403 144.9485979497544,89.9485979497544 24.9485979497544,89.9485979497544\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n", "\n", " <!-- Text -->\n", " <text x=\"84.948598\" y=\"109.948598\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" >1920</text>\n", " <text x=\"164.948598\" y=\"52.448598\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(-90,164.948598,52.448598)\">1200</text>\n", " <text x=\"7.474299\" y=\"102.474299\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(45,7.474299,102.474299)\">3</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)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>0 1 2</div><input id='attrs-06cd93c4-61f2-4562-8ba6-4c20d452e78b' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-06cd93c4-61f2-4562-8ba6-4c20d452e78b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-5ee97d7b-66bd-4c48-b1a3-53571521fef4' class='xr-var-data-in' type='checkbox'><label for='data-5ee97d7b-66bd-4c48-b1a3-53571521fef4' 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], dtype=int64)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>OD</span></div><div class='xr-var-dims'>(runs, x, y)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(1, 1200, 1920), meta=np.ndarray></div><input id='attrs-c68900f2-6164-4204-843b-aa719b3b7b70' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-c68900f2-6164-4204-843b-aa719b3b7b70' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-f16fbad2-1a80-444c-bad8-56e3457eb05f' class='xr-var-data-in' type='checkbox'><label for='data-f16fbad2-1a80-444c-bad8-56e3457eb05f' 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> 52.73 MiB </td>\n", " <td> 17.58 MiB </td>\n", " </tr>\n", " \n", " <tr>\n", " <th> Shape </th>\n", " <td> (3, 1200, 1920) </td>\n", " <td> (1, 1200, 1920) </td>\n", " </tr>\n", " <tr>\n", " <th> Dask graph </th>\n", " <td colspan=\"2\"> 3 chunks in 40 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=\"194\" height=\"139\" style=\"stroke:rgb(0,0,0);stroke-width:1\" >\n", "\n", " <!-- Horizontal lines -->\n", " <line x1=\"10\" y1=\"0\" x2=\"24\" y2=\"14\" style=\"stroke-width:2\" />\n", " <line x1=\"10\" y1=\"75\" x2=\"24\" y2=\"89\" style=\"stroke-width:2\" />\n", "\n", " <!-- Vertical lines -->\n", " <line x1=\"10\" y1=\"0\" x2=\"10\" y2=\"75\" style=\"stroke-width:2\" />\n", " <line x1=\"14\" y1=\"4\" x2=\"14\" y2=\"79\" />\n", " <line x1=\"19\" y1=\"9\" x2=\"19\" y2=\"84\" />\n", " <line x1=\"24\" y1=\"14\" x2=\"24\" y2=\"89\" style=\"stroke-width:2\" />\n", "\n", " <!-- Colored Rectangle -->\n", " <polygon points=\"10.0,0.0 24.9485979497544,14.948597949754403 24.9485979497544,89.9485979497544 10.0,75.0\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n", "\n", " <!-- Horizontal lines -->\n", " <line x1=\"10\" y1=\"0\" x2=\"130\" y2=\"0\" style=\"stroke-width:2\" />\n", " <line x1=\"14\" y1=\"4\" x2=\"134\" y2=\"4\" />\n", " <line x1=\"19\" y1=\"9\" x2=\"139\" y2=\"9\" />\n", " <line x1=\"24\" y1=\"14\" x2=\"144\" y2=\"14\" style=\"stroke-width:2\" />\n", "\n", " <!-- Vertical lines -->\n", " <line x1=\"10\" y1=\"0\" x2=\"24\" y2=\"14\" style=\"stroke-width:2\" />\n", " <line x1=\"130\" y1=\"0\" x2=\"144\" y2=\"14\" style=\"stroke-width:2\" />\n", "\n", " <!-- Colored Rectangle -->\n", " <polygon points=\"10.0,0.0 130.0,0.0 144.9485979497544,14.948597949754403 24.9485979497544,14.948597949754403\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n", "\n", " <!-- Horizontal lines -->\n", " <line x1=\"24\" y1=\"14\" x2=\"144\" y2=\"14\" style=\"stroke-width:2\" />\n", " <line x1=\"24\" y1=\"89\" x2=\"144\" y2=\"89\" style=\"stroke-width:2\" />\n", "\n", " <!-- Vertical lines -->\n", " <line x1=\"24\" y1=\"14\" x2=\"24\" y2=\"89\" style=\"stroke-width:2\" />\n", " <line x1=\"144\" y1=\"14\" x2=\"144\" y2=\"89\" style=\"stroke-width:2\" />\n", "\n", " <!-- Colored Rectangle -->\n", " <polygon points=\"24.9485979497544,14.948597949754403 144.9485979497544,14.948597949754403 144.9485979497544,89.9485979497544 24.9485979497544,89.9485979497544\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n", "\n", " <!-- Text -->\n", " <text x=\"84.948598\" y=\"109.948598\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" >1920</text>\n", " <text x=\"164.948598\" y=\"52.448598\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(-90,164.948598,52.448598)\">1200</text>\n", " <text x=\"7.474299\" y=\"102.474299\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(45,7.474299,102.474299)\">3</text>\n", "</svg>\n", " </td>\n", " </tr>\n", "</table></div></li></ul></div></li><li class='xr-section-item'><input id='section-5c3d2d31-aba4-4f09-afe5-e28bb74a7c71' class='xr-section-summary-in' type='checkbox' ><label for='section-5c3d2d31-aba4-4f09-afe5-e28bb74a7c71' class='xr-section-summary' >Indexes: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-index-name'><div>runs</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-decca0b6-3468-41ab-9850-a5b69dadce82' class='xr-index-data-in' type='checkbox'/><label for='index-decca0b6-3468-41ab-9850-a5b69dadce82' 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], dtype='float64', name='runs'))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-f1e5c163-3f1f-4b5e-8a9d-be23047482a2' class='xr-section-summary-in' type='checkbox' ><label for='section-f1e5c163-3f1f-4b5e-8a9d-be23047482a2' 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>0.002</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>0.189</dd><dt><span>compZ_final_current :</span></dt><dd>0.283</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>1.0</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_va ], "text/plain": [ "<xarray.Dataset>\n", "Dimensions: (runs: 3, x: 1200, y: 1920)\n", "Coordinates:\n", " * runs (runs) float64 0.0 1.0 2.0\n", "Dimensions without coordinates: x, y\n", "Data variables:\n", " atoms (runs, x, y) uint16 dask.array<chunksize=(1, 1200, 1920), meta=np.ndarray>\n", " background (runs, x, y) uint16 dask.array<chunksize=(1, 1200, 1920), meta=np.ndarray>\n", " dark (runs, x, y) uint16 dask.array<chunksize=(1, 1200, 1920), meta=np.ndarray>\n", " shotNum (runs) int64 0 1 2\n", " OD (runs, x, y) float64 dask.array<chunksize=(1, 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_img: 0\n", " z_offset: 0.189\n", " z_offset_img: 0.189\n", " runs: [0. 1. 2.]\n", " scanAxis: ['runs']\n", " scanAxisLength: [3.]" ] }, "execution_count": 6, "metadata": {}, "output_type": "execute_result" } ], "source": [ "dataSet = imageAnalyser.get_absorption_images(dataSet)\n", "\n", "dataSet" ] }, { "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ "## Select region of interests" ] }, { "cell_type": "code", "execution_count": 9, "metadata": {}, "outputs": [], "source": [ "# imageAnalyser.center = (529, 962)\n", "# imageAnalyser.span = (100,100)\n", "# imageAnalyser.fraction = (0.1, 0.1)\n", "\n", "# imageAnalyser.center = (890, 1150)\n", "# imageAnalyser.span = (600,600)\n", "# imageAnalyser.fraction = (0.1, 0.1)\n", "\n", "imageAnalyser.center = (890, 950)\n", "imageAnalyser.span = (100,100)\n", "imageAnalyser.fraction = (0.1, 0.1)\n", "\n", "dataSet_crop = imageAnalyser.crop_image(dataSet)" ] }, { "cell_type": "code", "execution_count": 10, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "<xarray.plot.facetgrid.FacetGrid at 0x274b90445e0>" ] }, "execution_count": 10, "metadata": {}, "output_type": "execute_result" }, { "data": { "image/png": "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 "text/plain": [ "<Figure size 288x216 with 2 Axes>" ] }, "metadata": { "needs_background": "light" }, "output_type": "display_data" } ], "source": [ "dataSet_crop.OD.isel(runs=[0]).plot.pcolormesh(cmap='jet', vmin=0, col=scanAxis[0], row=scanAxis[1])\n", "# dataSet_crop.OD.plot.pcolormesh(cmap='jet', vmin=0, col=scanAxis[0])" ] }, { "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ "## Remove the background" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "dataSet_crop['OD'] = dataSet_crop['OD'] + 500" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "dataSet_crop['OD'] = imageAnalyser.substract_offset(dataSet_crop['OD'])" ] }, { "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ "# Test Fit" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "fitAnalyser = FitAnalyser(\"Two Gaussian-2D\", fitDim=2)\n", "\n", "params = fitAnalyser.guess(dataSet_crop.OD, dask=\"parallelized\")" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "fitResult = fitAnalyser.fit(dataSet_crop.OD, params).load()" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "fitCurve = fitAnalyser.eval(fitResult, x=np.arange(100), y=np.arange(100), dask=\"parallelized\").load()" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "# fitCurve.isel(**{scanAxis[0]:np.arange(30), 'runs':range(dataSet_crop.OD['runs'].size)}).plot.pcolormesh(cmap='jet', vmin=0, col=scanAxis[0], row=scanAxis[1])\n", "\n", "fitCurve.plot.pcolormesh(cmap='jet', vmin=0, col=scanAxis[0])" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "a = fitAnalyser.get_fit_value(fitResult)\n", "b = fitAnalyser.get_fit_std(fitResult)\n", "data = combine_uncertainty(a, b)" ] }, { "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ "# Get the Ncount" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "Ncount = dataSet_crop.OD.sum(dim=(scanAxis[0], 'x', 'y'))" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "Ncount.load()\n", "\n", "fig = plt.figure()\n", "ax = fig.gca()\n", "Ncount.plot(ax=ax)" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "fitAnalyser = FitAnalyser(\"Lorentzian With Offset\")\n", "params = fitAnalyser.guess(Ncount, x='sin_mod_freq', dask=\"parallelized\", guess_kwargs=dict(negative=True))" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "fitResult = fitAnalyser.fit(Ncount, params, x='sin_mod_freq', dask=\"parallelized\")\n", "fitCurve = fitAnalyser.eval(fitResult, x=np.arange(40), dask=\"parallelized\").load()" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "fig = plt.figure()\n", "ax = fig.gca()\n", "plt.errorbar([1], [1], yerr=[1])" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "fitCurve.plot.errorbar(yerr=fitCurve)" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "np.ufunc(fitCurve)" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] } ], "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": "3.8.10 (tags/v3.8.10:3d8993a, May 3 2021, 11:48:03) [MSC v.1928 64 bit (AMD64)]" }, "orig_nbformat": 4, "vscode": { "interpreter": { "hash": "c05913ad4f24fdc6b2418069394dc5835b1981849b107c9ba6df693aafd66650" } } }, "nbformat": 4, "nbformat_minor": 2}
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