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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 pandas as pd\n", "import numpy as np\n", "import copy\n", "\n", "import glob\n", "\n", "import xrft\n", "import finufft\n", "\n", "from uncertainties import ufloat\n", "from uncertainties import unumpy as unp\n", "from uncertainties import umath\n", "\n", "from datetime import datetime\n", "\n", "import matplotlib.pyplot as plt\n", "plt.rcParams['font.size'] = 18\n", "\n", "from DataContainer.ReadData import read_hdf5_file, read_hdf5_global, read_hdf5_run_time, read_csv_file\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", "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": [ { "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-3951b95c-199b-11ee-a3f4-80e82ce2fa8e</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;\">5ab7f5f8</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> 24\n", " </td>\n", " <td style=\"text-align: left;\">\n", " <strong>Total memory:</strong> 44.70 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-88282cc2-009d-4d17-9e26-16dbc72dfd02</p>\n", " <table style=\"width: 100%; text-align: left;\">\n", " <tr>\n", " <td style=\"text-align: left;\">\n", " <strong>Comm:</strong> tcp://127.0.0.1:61384\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> 24\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> 44.70 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://127.0.0.1:61428\n", " </td>\n", " <td style=\"text-align: left;\">\n", " <strong>Total threads: </strong> 4\n", " </td>\n", " </tr>\n", " <tr>\n", " <td style=\"text-align: left;\">\n", " <strong>Dashboard: </strong> <a href=\"http://127.0.0.1:61429/status\" target=\"_blank\">http://127.0.0.1:61429/status</a>\n", " </td>\n", " <td style=\"text-align: left;\">\n", " <strong>Memory: </strong> 7.45 GiB\n", " </td>\n", " </tr>\n", " <tr>\n", " <td style=\"text-align: left;\">\n", " <strong>Nanny: </strong> tcp://127.0.0.1:61387\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-uqj3h8qd\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://127.0.0.1:61419\n", " </td>\n", " <td style=\"text-align: left;\">\n", " <strong>Total threads: </strong> 4\n", " </td>\n", " </tr>\n", " <tr>\n", " <td style=\"text-align: left;\">\n", " <strong>Dashboard: </strong> <a href=\"http://127.0.0.1:61421/status\" target=\"_blank\">http://127.0.0.1:61421/status</a>\n", " </td>\n", " <td style=\"text-align: left;\">\n", " <strong>Memory: </strong> 7.45 GiB\n", " </td>\n", " </tr>\n", " <tr>\n", " <td style=\"text-align: left;\">\n", " <strong>Nanny: </strong> tcp://127.0.0.1:61388\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-vzm9iito\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://127.0.0.1:61420\n", " </td>\n", " <td style=\"text-align: left;\">\n", " <strong>Total threads: </strong> 4\n", " </td>\n", " </tr>\n", " <tr>\n", " <td style=\"text-align: left;\">\n", " <strong>Dashboard: </strong> <a href=\"http://127.0.0.1:61423/status\" target=\"_blank\">http://127.0.0.1:61423/status</a>\n", " </td>\n", " <td style=\"text-align: left;\">\n", " <strong>Memory: </strong> 7.45 GiB\n", " </td>\n", " </tr>\n", " <tr>\n", " <td style=\"text-align: left;\">\n", " <strong>Nanny: </strong> tcp://127.0.0.1:61389\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-9xccpbw5\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://127.0.0.1:61425\n", " </td>\n", " <td style=\"text-align: left;\">\n", " <strong>Total threads: </strong> 4\n", " </td>\n", " </tr>\n", " <tr>\n", " <td style=\"text-align: left;\">\n", " <strong>Dashboard: </strong> <a href=\"http://127.0.0.1:61426/status\" target=\"_blank\">http://127.0.0.1:61426/status</a>\n", " </td>\n", " <td style=\"text-align: left;\">\n", " <strong>Memory: </strong> 7.45 GiB\n", " </td>\n", " </tr>\n", " <tr>\n", " <td style=\"text-align: left;\">\n", " <strong>Nanny: </strong> tcp://127.0.0.1:61390\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-m8eyzltj\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://127.0.0.1:61416\n", " </td>\n", " <td style=\"text-align: left;\">\n", " <strong>Total threads: </strong> 4\n", " </td>\n", " </tr>\n", " <tr>\n", " <td style=\"text-align: left;\">\n", " <strong>Dashboard: </strong> <a href=\"http://127.0.0.1:61417/status\" target=\"_blank\">http://127.0.0.1:61417/status</a>\n", " </td>\n", " <td style=\"text-align: left;\">\n", " <strong>Memory: </strong> 7.45 GiB\n", " </td>\n", " </tr>\n", " <tr>\n", " <td style=\"text-align: left;\">\n", " <strong>Nanny: </strong> tcp://127.0.0.1:61391\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-aun9_6pf\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://127.0.0.1:61413\n", " </td>\n", " <td style=\"text-align: left;\">\n", " <strong>Total threads: </strong> 4\n", " </td>\n", " </tr>\n", " <tr>\n", " <td style=\"text-align: left;\">\n", " <strong>Dashboard: </strong> <a href=\"http://127.0.0.1:61414/status\" target=\"_blank\">http://127.0.0.1:61414/status</a>\n", " </td>\n", " <td style=\"text-align: left;\">\n", " <strong>Memory: </strong> 7.45 GiB\n", " </td>\n", " </tr>\n", " <tr>\n", " <td style=\"text-align: left;\">\n", " <strong>Nanny: </strong> tcp://127.0.0.1:61392\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-led72bz4\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://127.0.0.1:61384' processes=6 threads=24, memory=44.70 GiB>" ] }, "execution_count": 2, "metadata": {}, "output_type": "execute_result" } ], "source": [ "from dask.distributed import Client\n", "client = Client(n_workers=6, threads_per_worker=4, processes=True, memory_limit='8GB')\n", "client" ] }, { "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ "## Set global path for experiment" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [], "source": [ "groupList = [\n", " \"images/MOT_3D_Camera/in_situ_absorption\",\n", " \"images/ODT_1_Axis_Camera/in_situ_absorption\",\n", " \"images/ODT_2_Axis_Camera/in_situ_absorption\",\n", "]\n", "\n", "dskey = {\n", " \"images/MOT_3D_Camera/in_situ_absorption\": \"camera_0\",\n", " \"images/ODT_1_Axis_Camera/in_situ_absorption\": \"camera_1\",\n", " \"images/ODT_2_Axis_Camera/in_situ_absorption\": \"camera_2\",\n", "}\n" ] }, { "cell_type": "code", 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display: block !important;\n", " min-width: 300px;\n", " max-width: 700px;\n", "}\n", "\n", ".xr-text-repr-fallback {\n", " /* fallback to plain text repr when CSS is not injected (untrusted notebook) */\n", " display: none;\n", "}\n", "\n", ".xr-header {\n", " padding-top: 6px;\n", " padding-bottom: 6px;\n", " margin-bottom: 4px;\n", " border-bottom: solid 1px var(--xr-border-color);\n", "}\n", "\n", ".xr-header > div,\n", ".xr-header > ul {\n", " display: inline;\n", " margin-top: 0;\n", " margin-bottom: 0;\n", "}\n", "\n", ".xr-obj-type,\n", ".xr-array-name {\n", " margin-left: 2px;\n", " margin-right: 10px;\n", "}\n", "\n", ".xr-obj-type {\n", " color: var(--xr-font-color2);\n", "}\n", "\n", ".xr-sections {\n", " padding-left: 0 !important;\n", " display: grid;\n", " grid-template-columns: 150px auto auto 1fr 20px 20px;\n", "}\n", "\n", ".xr-section-item {\n", " display: contents;\n", "}\n", "\n", ".xr-section-item input {\n", " display: none;\n", "}\n", "\n", ".xr-section-item input + label {\n", " color: var(--xr-disabled-color);\n", "}\n", "\n", ".xr-section-item input:enabled + label {\n", " cursor: pointer;\n", " color: var(--xr-font-color2);\n", "}\n", "\n", ".xr-section-item input:enabled + label:hover {\n", " color: var(--xr-font-color0);\n", "}\n", "\n", ".xr-section-summary {\n", " grid-column: 1;\n", " color: var(--xr-font-color2);\n", " font-weight: 500;\n", "}\n", "\n", ".xr-section-summary > span {\n", " display: inline-block;\n", " padding-left: 0.5em;\n", "}\n", "\n", ".xr-section-summary-in:disabled + label {\n", " color: var(--xr-font-color2);\n", "}\n", "\n", ".xr-section-summary-in + label:before {\n", " display: inline-block;\n", " content: 'â–º';\n", " font-size: 11px;\n", " width: 15px;\n", " text-align: center;\n", "}\n", "\n", ".xr-section-summary-in:disabled + label:before {\n", " color: var(--xr-disabled-color);\n", "}\n", "\n", ".xr-section-summary-in:checked + label:before {\n", " content: 'â–¼';\n", "}\n", "\n", ".xr-section-summary-in:checked + label > span {\n", " display: none;\n", "}\n", "\n", ".xr-section-summary,\n", ".xr-section-inline-details {\n", " padding-top: 4px;\n", " padding-bottom: 4px;\n", "}\n", "\n", ".xr-section-inline-details {\n", " grid-column: 2 / -1;\n", "}\n", "\n", ".xr-section-details {\n", " display: none;\n", " grid-column: 1 / -1;\n", " margin-bottom: 5px;\n", "}\n", "\n", ".xr-section-summary-in:checked ~ .xr-section-details {\n", " display: contents;\n", "}\n", "\n", ".xr-array-wrap {\n", " grid-column: 1 / -1;\n", " display: grid;\n", " grid-template-columns: 20px auto;\n", "}\n", "\n", ".xr-array-wrap > label {\n", " grid-column: 1;\n", " vertical-align: top;\n", "}\n", "\n", ".xr-preview {\n", " color: var(--xr-font-color3);\n", "}\n", "\n", ".xr-array-preview,\n", ".xr-array-data {\n", " padding: 0 5px !important;\n", " grid-column: 2;\n", "}\n", "\n", ".xr-array-data,\n", ".xr-array-in:checked ~ .xr-array-preview {\n", " display: none;\n", "}\n", "\n", ".xr-array-in:checked ~ .xr-array-data,\n", ".xr-array-preview {\n", " display: inline-block;\n", "}\n", "\n", ".xr-dim-list {\n", " display: inline-block !important;\n", " list-style: none;\n", " padding: 0 !important;\n", " margin: 0;\n", "}\n", "\n", ".xr-dim-list li {\n", " display: inline-block;\n", " padding: 0;\n", " margin: 0;\n", "}\n", "\n", ".xr-dim-list:before {\n", " content: '(';\n", "}\n", "\n", ".xr-dim-list:after {\n", " content: ')';\n", "}\n", "\n", ".xr-dim-list li:not(:last-child):after {\n", " content: ',';\n", " padding-right: 5px;\n", "}\n", "\n", ".xr-has-index {\n", " font-weight: bold;\n", "}\n", "\n", ".xr-var-list,\n", ".xr-var-item {\n", " display: contents;\n", "}\n", "\n", ".xr-var-item > div,\n", ".xr-var-item label,\n", ".xr-var-item > .xr-var-name span {\n", " background-color: var(--xr-background-color-row-even);\n", " margin-bottom: 0;\n", "}\n", "\n", ".xr-var-item > .xr-var-name:hover span {\n", " padding-right: 5px;\n", "}\n", "\n", ".xr-var-list > li:nth-child(odd) > div,\n", ".xr-var-list > li:nth-child(odd) > label,\n", ".xr-var-list > li:nth-child(odd) > .xr-var-name span {\n", " background-color: var(--xr-background-color-row-odd);\n", "}\n", "\n", ".xr-var-name {\n", " grid-column: 1;\n", "}\n", "\n", ".xr-var-dims {\n", " grid-column: 2;\n", "}\n", "\n", ".xr-var-dtype {\n", " grid-column: 3;\n", " text-align: right;\n", " color: var(--xr-font-color2);\n", "}\n", "\n", ".xr-var-preview {\n", " grid-column: 4;\n", "}\n", "\n", ".xr-index-preview {\n", " grid-column: 2 / 5;\n", " color: var(--xr-font-color2);\n", "}\n", "\n", ".xr-var-name,\n", ".xr-var-dims,\n", ".xr-var-dtype,\n", ".xr-preview,\n", ".xr-attrs dt {\n", " white-space: nowrap;\n", " overflow: hidden;\n", " text-overflow: ellipsis;\n", " padding-right: 10px;\n", "}\n", "\n", ".xr-var-name:hover,\n", ".xr-var-dims:hover,\n", ".xr-var-dtype:hover,\n", ".xr-attrs dt:hover {\n", " overflow: visible;\n", " width: auto;\n", " z-index: 1;\n", "}\n", "\n", ".xr-var-attrs,\n", ".xr-var-data,\n", ".xr-index-data {\n", " display: none;\n", " background-color: var(--xr-background-color) !important;\n", " padding-bottom: 5px !important;\n", "}\n", "\n", ".xr-var-attrs-in:checked ~ .xr-var-attrs,\n", ".xr-var-data-in:checked ~ .xr-var-data,\n", ".xr-index-data-in:checked ~ .xr-index-data {\n", " display: block;\n", "}\n", "\n", ".xr-var-data > table {\n", " float: right;\n", "}\n", "\n", ".xr-var-name span,\n", ".xr-var-data,\n", ".xr-index-name div,\n", ".xr-index-data,\n", ".xr-attrs {\n", " padding-left: 25px !important;\n", "}\n", "\n", ".xr-attrs,\n", ".xr-var-attrs,\n", ".xr-var-data,\n", ".xr-index-data {\n", " grid-column: 1 / -1;\n", "}\n", "\n", "dl.xr-attrs {\n", " padding: 0;\n", " margin: 0;\n", " display: grid;\n", " grid-template-columns: 125px auto;\n", "}\n", "\n", ".xr-attrs dt,\n", ".xr-attrs dd {\n", " padding: 0;\n", " margin: 0;\n", " float: left;\n", " padding-right: 10px;\n", " width: auto;\n", "}\n", "\n", ".xr-attrs dt {\n", " font-weight: normal;\n", " grid-column: 1;\n", "}\n", "\n", ".xr-attrs dt:hover span {\n", " display: inline-block;\n", " background: var(--xr-background-color);\n", " padding-right: 10px;\n", "}\n", "\n", ".xr-attrs dd {\n", " grid-column: 2;\n", " white-space: pre-wrap;\n", " word-break: break-all;\n", "}\n", "\n", ".xr-icon-database,\n", ".xr-icon-file-text2,\n", ".xr-no-icon {\n", " display: inline-block;\n", " vertical-align: middle;\n", " width: 1em;\n", " height: 1.5em !important;\n", " stroke-width: 0;\n", " stroke: currentColor;\n", " fill: currentColor;\n", "}\n", "</style><pre class='xr-text-repr-fallback'><xarray.Dataset>\n", "Dimensions: (sin_mod_freq: 37, y: 1200, x: 1920)\n", "Coordinates:\n", " * sin_mod_freq (sin_mod_freq) float64 65.0 66.0 67.0 ... 99.0 100.0 101.0\n", "Dimensions without coordinates: y, x\n", "Data variables:\n", " atoms (sin_mod_freq, y, x) uint16 dask.array<chunksize=(29, 1200, 1920), meta=np.ndarray>\n", " background (sin_mod_freq, y, x) uint16 dask.array<chunksize=(29, 1200, 1920), meta=np.ndarray>\n", " dark (sin_mod_freq, y, x) uint16 dask.array<chunksize=(29, 1200, 1920), meta=np.ndarray>\n", " shotNum (sin_mod_freq) <U2 dask.array<chunksize=(37,), meta=np.ndarray>\n", " OD (sin_mod_freq, y, x) float64 dask.array<chunksize=(29, 1200, 1920), meta=np.ndarray>\n", "Attributes: (12/109)\n", " TOF_free: 0.01\n", " abs_img_freq: 110.858\n", " absorption_imaging_flag: True\n", " backup_data: True\n", " blink_off_time: 0.001\n", " blink_on_time: 0.001\n", " ... ...\n", " y_offset_img: 0\n", " z_offset: 0.189\n", " z_offset_img: 0.189\n", " sin_mod_freq: [ 65. 66. 67. 68. 69. 70. 71. 7...\n", " scanAxis: ['sin_mod_freq']\n", " scanAxisLength: [37.]</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-e9e8209e-8ac6-4b77-9f1d-73edeb11ea6d' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-e9e8209e-8ac6-4b77-9f1d-73edeb11ea6d' 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'>sin_mod_freq</span>: 37</li><li><span>y</span>: 1200</li><li><span>x</span>: 1920</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-417885ee-6100-4a25-ac77-3188924f1706' class='xr-section-summary-in' type='checkbox' checked><label for='section-417885ee-6100-4a25-ac77-3188924f1706' 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'>sin_mod_freq</span></div><div class='xr-var-dims'>(sin_mod_freq)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>65.0 66.0 67.0 ... 99.0 100.0 101.0</div><input id='attrs-d1444090-98bc-4e52-b3e1-f72265109897' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-d1444090-98bc-4e52-b3e1-f72265109897' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-55ca4ceb-6ab4-434c-b93f-f2da9a1091cc' class='xr-var-data-in' type='checkbox'><label for='data-55ca4ceb-6ab4-434c-b93f-f2da9a1091cc' 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([ 65., 66., 67., 68., 69., 70., 71., 72., 73., 74., 75., 76.,\n", " 77., 78., 79., 80., 81., 82., 83., 84., 85., 86., 87., 88.,\n", " 89., 90., 91., 92., 93., 94., 95., 96., 97., 98., 99., 100.,\n", " 101.])</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-b8a760bd-af8b-48e6-b52e-fca5b647ef1c' class='xr-section-summary-in' type='checkbox' checked><label for='section-b8a760bd-af8b-48e6-b52e-fca5b647ef1c' 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'>(sin_mod_freq, y, x)</div><div class='xr-var-dtype'>uint16</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(29, 1200, 1920), meta=np.ndarray></div><input id='attrs-9911f45b-c8d5-435e-9b25-0c5c0840948a' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-9911f45b-c8d5-435e-9b25-0c5c0840948a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-776f8147-9d5f-4979-8d77-e1633c65ae52' class='xr-var-data-in' type='checkbox'><label for='data-776f8147-9d5f-4979-8d77-e1633c65ae52' 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> 162.60 MiB </td>\n", " <td> 127.44 MiB </td>\n", " </tr>\n", " \n", " <tr>\n", " <th> Shape </th>\n", " <td> (37, 1200, 1920) </td>\n", " <td> (29, 1200, 1920) </td>\n", " </tr>\n", " <tr>\n", " <th> Dask graph </th>\n", " <td colspan=\"2\"> 2 chunks in 113 graph layers </td>\n", " </tr>\n", " <tr>\n", " <th> Data type </th>\n", " <td colspan=\"2\"> uint16 numpy.ndarray </td>\n", " </tr>\n", " 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y2=\"16\" style=\"stroke-width:2\" />\n", "\n", " <!-- Vertical lines -->\n", " <line x1=\"10\" y1=\"0\" x2=\"26\" y2=\"16\" style=\"stroke-width:2\" />\n", " <line x1=\"130\" y1=\"0\" x2=\"146\" y2=\"16\" style=\"stroke-width:2\" />\n", "\n", " <!-- Colored Rectangle -->\n", " <polygon points=\"10.0,0.0 130.0,0.0 146.95433225175046,16.954332251750458 26.954332251750458,16.954332251750458\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n", "\n", " <!-- Horizontal lines -->\n", " <line x1=\"26\" y1=\"16\" x2=\"146\" y2=\"16\" style=\"stroke-width:2\" />\n", " <line x1=\"26\" y1=\"91\" x2=\"146\" y2=\"91\" style=\"stroke-width:2\" />\n", "\n", " <!-- Vertical lines -->\n", " <line x1=\"26\" y1=\"16\" x2=\"26\" y2=\"91\" style=\"stroke-width:2\" />\n", " <line x1=\"146\" y1=\"16\" x2=\"146\" y2=\"91\" style=\"stroke-width:2\" />\n", "\n", " <!-- Colored Rectangle -->\n", " <polygon points=\"26.954332251750458,16.954332251750458 146.95433225175046,16.954332251750458 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class='xr-var-attrs-in' type='checkbox' ><label for='attrs-c154fb06-a9e7-4d54-bc93-bf90465f7284' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-f0e9c8c7-6a18-48d7-a1ff-86d372b56fa3' class='xr-var-data-in' type='checkbox'><label for='data-f0e9c8c7-6a18-48d7-a1ff-86d372b56fa3' 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> 162.60 MiB </td>\n", " <td> 127.44 MiB </td>\n", " </tr>\n", " \n", " <tr>\n", " <th> Shape </th>\n", " <td> (37, 1200, 1920) </td>\n", " <td> (29, 1200, 1920) </td>\n", " </tr>\n", " <tr>\n", " <th> Dask graph </th>\n", " <td colspan=\"2\"> 2 chunks in 113 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=\"196\" height=\"141\" style=\"stroke:rgb(0,0,0);stroke-width:1\" >\n", "\n", " <!-- Horizontal lines -->\n", " <line x1=\"10\" y1=\"0\" x2=\"26\" y2=\"16\" style=\"stroke-width:2\" />\n", " <line x1=\"10\" y1=\"75\" x2=\"26\" y2=\"91\" 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=\"23\" y1=\"13\" x2=\"23\" y2=\"88\" />\n", " <line x1=\"26\" y1=\"16\" x2=\"26\" y2=\"91\" style=\"stroke-width:2\" />\n", "\n", " <!-- Colored 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</tr>\n", "</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>dark</span></div><div class='xr-var-dims'>(sin_mod_freq, y, x)</div><div class='xr-var-dtype'>uint16</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(29, 1200, 1920), meta=np.ndarray></div><input id='attrs-4e20577d-5ca6-446c-8495-7308123c71e7' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-4e20577d-5ca6-446c-8495-7308123c71e7' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6bc197f9-2081-472a-81c3-3fb2801df887' class='xr-var-data-in' type='checkbox'><label for='data-6bc197f9-2081-472a-81c3-3fb2801df887' 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> 162.60 MiB </td>\n", " <td> 127.44 MiB </td>\n", " </tr>\n", " \n", " <tr>\n", " <th> Shape </th>\n", " <td> (37, 1200, 1920) </td>\n", " <td> (29, 1200, 1920) </td>\n", " </tr>\n", " <tr>\n", " <th> Dask graph </th>\n", " <td colspan=\"2\"> 2 chunks in 113 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=\"196\" height=\"141\" style=\"stroke:rgb(0,0,0);stroke-width:1\" >\n", "\n", " <!-- Horizontal lines -->\n", " <line x1=\"10\" y1=\"0\" x2=\"26\" y2=\"16\" style=\"stroke-width:2\" />\n", " <line x1=\"10\" y1=\"75\" x2=\"26\" y2=\"91\" 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=\"23\" y1=\"13\" x2=\"23\" y2=\"88\" />\n", " <line x1=\"26\" y1=\"16\" x2=\"26\" y2=\"91\" style=\"stroke-width:2\" />\n", "\n", " <!-- Colored Rectangle -->\n", " <polygon points=\"10.0,0.0 26.954332251750458,16.954332251750458 26.954332251750458,91.95433225175046 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=\"23\" y1=\"13\" x2=\"143\" y2=\"13\" />\n", " <line x1=\"26\" y1=\"16\" x2=\"146\" y2=\"16\" style=\"stroke-width:2\" />\n", "\n", " <!-- Vertical lines -->\n", " <line x1=\"10\" y1=\"0\" x2=\"26\" y2=\"16\" style=\"stroke-width:2\" />\n", " <line x1=\"130\" y1=\"0\" x2=\"146\" y2=\"16\" 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text-anchor=\"middle\" >1920</text>\n", " <text x=\"166.954332\" y=\"54.454332\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(-90,166.954332,54.454332)\">1200</text>\n", " <text x=\"8.477166\" y=\"103.477166\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(45,8.477166,103.477166)\">37</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'>(sin_mod_freq)</div><div class='xr-var-dtype'><U2</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(37,), meta=np.ndarray></div><input id='attrs-c6cbff41-63d7-4214-a017-064a511f8ba6' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-c6cbff41-63d7-4214-a017-064a511f8ba6' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-86b931fe-e9c5-4d5c-893d-ec70ac96d8d3' class='xr-var-data-in' type='checkbox'><label for='data-86b931fe-e9c5-4d5c-893d-ec70ac96d8d3' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>\n", " <tr>\n", " <td>\n", " <table style=\"border-collapse: collapse;\">\n", " <thead>\n", " <tr>\n", " <td> </td>\n", " <th> Array </th>\n", " <th> Chunk </th>\n", " </tr>\n", " </thead>\n", " <tbody>\n", " \n", " <tr>\n", " <th> Bytes </th>\n", " <td> 296 B </td>\n", " <td> 296 B </td>\n", " </tr>\n", " \n", " <tr>\n", " <th> Shape </th>\n", " <td> (37,) </td>\n", " <td> (37,) </td>\n", " </tr>\n", " <tr>\n", " <th> Dask graph </th>\n", " <td colspan=\"2\"> 1 chunks in 1 graph layer </td>\n", " </tr>\n", " <tr>\n", " <th> Data type </th>\n", " <td colspan=\"2\"> <U2 numpy.ndarray </td>\n", " </tr>\n", " </tbody>\n", " </table>\n", " </td>\n", " <td>\n", " <svg width=\"170\" height=\"80\" 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=\"30\" x2=\"120\" y2=\"30\" style=\"stroke-width:2\" />\n", "\n", " <!-- Vertical lines -->\n", " <line x1=\"0\" y1=\"0\" x2=\"0\" y2=\"30\" style=\"stroke-width:2\" />\n", " <line x1=\"120\" y1=\"0\" x2=\"120\" y2=\"30\" style=\"stroke-width:2\" />\n", "\n", " <!-- Colored Rectangle -->\n", " <polygon points=\"0.0,0.0 120.0,0.0 120.0,30.769621904823087 0.0,30.769621904823087\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n", "\n", " <!-- Text -->\n", " <text x=\"60.000000\" y=\"50.769622\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" >37</text>\n", " <text x=\"140.000000\" y=\"15.384811\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(0,140.000000,15.384811)\">1</text>\n", "</svg>\n", " </td>\n", " </tr>\n", "</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>OD</span></div><div class='xr-var-dims'>(sin_mod_freq, y, x)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(29, 1200, 1920), meta=np.ndarray></div><input id='attrs-5f3479f7-3b42-4c65-ab5a-840978328d2a' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-5f3479f7-3b42-4c65-ab5a-840978328d2a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b41e5924-7c12-49d2-9150-bc059f217044' class='xr-var-data-in' type='checkbox'><label for='data-b41e5924-7c12-49d2-9150-bc059f217044' 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> 650.39 MiB </td>\n", " <td> 509.77 MiB </td>\n", " </tr>\n", " \n", " <tr>\n", " <th> Shape </th>\n", " <td> (37, 1200, 1920) </td>\n", " <td> (29, 1200, 1920) </td>\n", " </tr>\n", " <tr>\n", " <th> Dask graph </th>\n", " <td colspan=\"2\"> 2 chunks in 349 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=\"196\" height=\"141\" style=\"stroke:rgb(0,0,0);stroke-width:1\" >\n", "\n", " <!-- Horizontal lines -->\n", " <line x1=\"10\" y1=\"0\" x2=\"26\" y2=\"16\" style=\"stroke-width:2\" />\n", " <line x1=\"10\" y1=\"75\" x2=\"26\" y2=\"91\" 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=\"23\" y1=\"13\" x2=\"23\" y2=\"88\" />\n", " <line x1=\"26\" y1=\"16\" x2=\"26\" y2=\"91\" style=\"stroke-width:2\" />\n", "\n", " <!-- Colored Rectangle -->\n", " <polygon points=\"10.0,0.0 26.954332251750458,16.954332251750458 26.954332251750458,91.95433225175046 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=\"23\" y1=\"13\" x2=\"143\" y2=\"13\" />\n", " <line x1=\"26\" y1=\"16\" x2=\"146\" y2=\"16\" style=\"stroke-width:2\" />\n", "\n", " <!-- Vertical lines -->\n", " <line x1=\"10\" y1=\"0\" x2=\"26\" y2=\"16\" style=\"stroke-width:2\" />\n", " <line x1=\"130\" y1=\"0\" x2=\"146\" y2=\"16\" style=\"stroke-width:2\" />\n", "\n", " <!-- Colored Rectangle -->\n", " <polygon points=\"10.0,0.0 130.0,0.0 146.95433225175046,16.954332251750458 26.954332251750458,16.954332251750458\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n", "\n", " <!-- Horizontal lines -->\n", " <line x1=\"26\" y1=\"16\" x2=\"146\" y2=\"16\" style=\"stroke-width:2\" />\n", " <line x1=\"26\" y1=\"91\" x2=\"146\" y2=\"91\" style=\"stroke-width:2\" />\n", "\n", " <!-- Vertical lines -->\n", " <line x1=\"26\" y1=\"16\" x2=\"26\" y2=\"91\" style=\"stroke-width:2\" />\n", " <line x1=\"146\" y1=\"16\" x2=\"146\" y2=\"91\" style=\"stroke-width:2\" />\n", "\n", " <!-- Colored Rectangle -->\n", " <polygon points=\"26.954332251750458,16.954332251750458 146.95433225175046,16.954332251750458 146.95433225175046,91.95433225175046 26.954332251750458,91.95433225175046\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n", "\n", " <!-- Text -->\n", " <text x=\"86.954332\" y=\"111.954332\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" >1920</text>\n", " <text x=\"166.954332\" y=\"54.454332\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(-90,166.954332,54.454332)\">1200</text>\n", " <text x=\"8.477166\" y=\"103.477166\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(45,8.477166,103.477166)\">37</text>\n", "</svg>\n", " </td>\n", " </tr>\n", "</table></div></li></ul></div></li><li class='xr-section-item'><input id='section-99883402-0d89-40d5-897d-46773993331e' class='xr-section-summary-in' type='checkbox' ><label for='section-99883402-0d89-40d5-897d-46773993331e' 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>sin_mod_freq</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-8724f3f5-f544-4ef1-8303-5dc158ba0f0d' class='xr-index-data-in' type='checkbox'/><label for='index-8724f3f5-f544-4ef1-8303-5dc158ba0f0d' 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([ 65.0, 66.0, 67.0, 68.0, 69.0, 70.0, 71.0, 72.0, 73.0,\n", " 74.0, 75.0, 76.0, 77.0, 78.0, 79.0, 80.0, 81.0, 82.0,\n", " 83.0, 84.0, 85.0, 86.0, 87.0, 88.0, 89.0, 90.0, 91.0,\n", " 92.0, 93.0, 94.0, 95.0, 96.0, 97.0, 98.0, 99.0, 100.0,\n", " 101.0],\n", " dtype='float64', name='sin_mod_freq'))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-5816d034-00b7-4d1f-97fe-6ca868b9a7d3' class='xr-section-summary-in' type='checkbox' ><label for='section-5816d034-00b7-4d1f-97fe-6ca868b9a7d3' class='xr-section-summary' >Attributes: <span>(109)</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>0.01</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>0.001</dd><dt><span>blink_on_time :</span></dt><dd>0.001</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>0.271</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>0.1</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>1.71</dd><dt><span>evap_2_arm_2_start_pow :</span></dt><dd>5</dd><dt><span>evap_2_ramp_duration :</span></dt><dd>0.5</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>0.1</dd><dt><span>evap_3_ramp_duration :</span></dt><dd>0.1</dd><dt><span>evap_3_ramp_trunc_value :</span></dt><dd>1.0</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>0.0001</dd><dt><span>final_freq :</span></dt><dd>104.0</dd><dt><span>final_pow_1 :</span></dt><dd>0.1038</dd><dt><span>final_pow_2 :</span></dt><dd>1.71</dd><dt><span>gradCoil_current :</span></dt><dd>0.18</dd><dt><span>gradCoil_current_sg :</span></dt><dd>0</dd><dt><span>imaging_method :</span></dt><dd>in_situ_absorption</dd><dt><span>imaging_pulse_duration :</span></dt><dd>2.5e-05</dd><dt><span>imaging_wavelength :</span></dt><dd>4.21291e-07</dd><dt><span>initial_amp :</span></dt><dd>0.62</dd><dt><span>initial_freq :</span></dt><dd>102.13</dd><dt><span>mod_depth_fin :</span></dt><dd>0.43</dd><dt><span>mod_depth_ini :</span></dt><dd>0</dd><d " 79. 80. 81. 82. 83. 84. 85. 86. 87. 88. 89. 90. 91. 92.\n", " 93. 94. 95. 96. 97. 98. 99. 100. 101.]</dd><dt><span>scanAxis :</span></dt><dd>['sin_mod_freq']</dd><dt><span>scanAxisLength :</span></dt><dd>[37.]</dd></dl></div></li></ul></div></div>" ], "text/plain": [ "<xarray.Dataset>\n", "Dimensions: (sin_mod_freq: 37, y: 1200, x: 1920)\n", "Coordinates:\n", " * sin_mod_freq (sin_mod_freq) float64 65.0 66.0 67.0 ... 99.0 100.0 101.0\n", "Dimensions without coordinates: y, x\n", "Data variables:\n", " atoms (sin_mod_freq, y, x) uint16 dask.array<chunksize=(29, 1200, 1920), meta=np.ndarray>\n", " background (sin_mod_freq, y, x) uint16 dask.array<chunksize=(29, 1200, 1920), meta=np.ndarray>\n", " dark (sin_mod_freq, y, x) uint16 dask.array<chunksize=(29, 1200, 1920), meta=np.ndarray>\n", " shotNum (sin_mod_freq) <U2 dask.array<chunksize=(37,), meta=np.ndarray>\n", " OD (sin_mod_freq, y, x) float64 dask.array<chunksize=(29, 1200, 1920), meta=np.ndarray>\n", "Attributes: (12/109)\n", " TOF_free: 0.01\n", " abs_img_freq: 110.858\n", " absorption_imaging_flag: True\n", " backup_data: True\n", " blink_off_time: 0.001\n", " blink_on_time: 0.001\n", " ... ...\n", " y_offset_img: 0\n", " z_offset: 0.189\n", " z_offset_img: 0.189\n", " sin_mod_freq: [ 65. 66. 67. 68. 69. 70. 71. 7...\n", " scanAxis: ['sin_mod_freq']\n", " scanAxisLength: [37.]" ] }, "execution_count": 5, "metadata": {}, "output_type": "execute_result" } ], "source": [ "shotNum = \"0065\"\n", "filePath = folderPath + \"/\" + shotNum + \"/*.h5\"\n", "\n", "# load the data from HDF5 files\n", "dataSetDict = {\n", " dskey[groupList[i]]: read_hdf5_file(filePath, groupList[i])\n", " for i in [0] # range(len(groupList))\n", "}\n", "\n", "# selecte the data for centain camera\n", "dataSet = dataSetDict[\"camera_0\"]\n", "# flip the x and y axis\n", "dataSet = swap_xy(dataSet)\n", "\n", "# get the scan axis name of the shot\n", "scanAxis = get_scanAxis(dataSet)\n", "\n", "# rechunck the data for parallel computing\n", "dataSet = auto_rechunk(dataSet)\n", "\n", "# calculate the absorption imaging\n", "dataSet = imageAnalyser.get_absorption_images(dataSet)\n", "\n", "dataSet\n", "\n", "OD = dataSet[\"OD\"]\n", "\n", "OD_np = OD.to_numpy()\n", "\n", "dataSet" ] }, { "cell_type": "code", "execution_count": 17, "metadata": {}, "outputs": [ { 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"text/plain": [ "<Figure size 11200x300 with 38 Axes>" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "imageAnalyser.center = (950, 250)\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()" ] }, { "cell_type": "code", "execution_count": 18, "metadata": {}, "outputs": [ { "data": { "text/html": [ "<div><svg style=\"position: absolute; width: 0; height: 0; overflow: hidden\">\n", "<defs>\n", "<symbol id=\"icon-database\" viewBox=\"0 0 32 32\">\n", "<path d=\"M16 0c-8.837 0-16 2.239-16 5v4c0 2.761 7.163 5 16 5s16-2.239 16-5v-4c0-2.761-7.163-5-16-5z\"></path>\n", "<path d=\"M16 17c-8.837 0-16-2.239-16-5v6c0 2.761 7.163 5 16 5s16-2.239 16-5v-6c0 2.761-7.163 5-16 5z\"></path>\n", "<path d=\"M16 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".xr-array-data {\n", " padding: 0 5px !important;\n", " grid-column: 2;\n", "}\n", "\n", ".xr-array-data,\n", ".xr-array-in:checked ~ .xr-array-preview {\n", " display: none;\n", "}\n", "\n", ".xr-array-in:checked ~ .xr-array-data,\n", ".xr-array-preview {\n", " display: inline-block;\n", "}\n", "\n", ".xr-dim-list {\n", " display: inline-block !important;\n", " list-style: none;\n", " padding: 0 !important;\n", " margin: 0;\n", "}\n", "\n", ".xr-dim-list li {\n", " display: inline-block;\n", " padding: 0;\n", " margin: 0;\n", "}\n", "\n", ".xr-dim-list:before {\n", " content: '(';\n", "}\n", "\n", ".xr-dim-list:after {\n", " content: ')';\n", "}\n", "\n", ".xr-dim-list li:not(:last-child):after {\n", " content: ',';\n", " padding-right: 5px;\n", "}\n", "\n", ".xr-has-index {\n", " font-weight: bold;\n", "}\n", "\n", ".xr-var-list,\n", ".xr-var-item {\n", " display: contents;\n", "}\n", "\n", ".xr-var-item > div,\n", ".xr-var-item label,\n", ".xr-var-item > .xr-var-name span {\n", " background-color: var(--xr-background-color-row-even);\n", " margin-bottom: 0;\n", "}\n", "\n", ".xr-var-item > .xr-var-name:hover span {\n", " padding-right: 5px;\n", "}\n", "\n", ".xr-var-list > li:nth-child(odd) > div,\n", ".xr-var-list > li:nth-child(odd) > label,\n", ".xr-var-list > li:nth-child(odd) > .xr-var-name span {\n", " background-color: var(--xr-background-color-row-odd);\n", "}\n", "\n", ".xr-var-name {\n", " grid-column: 1;\n", "}\n", "\n", ".xr-var-dims {\n", " grid-column: 2;\n", "}\n", "\n", ".xr-var-dtype {\n", " grid-column: 3;\n", " text-align: right;\n", " color: var(--xr-font-color2);\n", "}\n", "\n", ".xr-var-preview {\n", " grid-column: 4;\n", "}\n", "\n", ".xr-index-preview {\n", " grid-column: 2 / 5;\n", " color: var(--xr-font-color2);\n", "}\n", "\n", ".xr-var-name,\n", ".xr-var-dims,\n", ".xr-var-dtype,\n", ".xr-preview,\n", ".xr-attrs dt {\n", " white-space: nowrap;\n", " overflow: hidden;\n", " text-overflow: ellipsis;\n", " padding-right: 10px;\n", "}\n", "\n", ".xr-var-name:hover,\n", ".xr-var-dims:hover,\n", ".xr-var-dtype:hover,\n", ".xr-attrs dt:hover {\n", " overflow: visible;\n", " width: auto;\n", " z-index: 1;\n", "}\n", "\n", ".xr-var-attrs,\n", ".xr-var-data,\n", ".xr-index-data {\n", " display: none;\n", " background-color: var(--xr-background-color) !important;\n", " padding-bottom: 5px !important;\n", "}\n", "\n", ".xr-var-attrs-in:checked ~ .xr-var-attrs,\n", ".xr-var-data-in:checked ~ .xr-var-data,\n", ".xr-index-data-in:checked ~ .xr-index-data {\n", " display: block;\n", "}\n", "\n", ".xr-var-data > table {\n", " float: right;\n", "}\n", "\n", ".xr-var-name span,\n", ".xr-var-data,\n", ".xr-index-name div,\n", ".xr-index-data,\n", ".xr-attrs {\n", " padding-left: 25px !important;\n", "}\n", "\n", ".xr-attrs,\n", ".xr-var-attrs,\n", ".xr-var-data,\n", ".xr-index-data {\n", " grid-column: 1 / -1;\n", "}\n", "\n", "dl.xr-attrs {\n", " padding: 0;\n", " margin: 0;\n", " display: grid;\n", " grid-template-columns: 125px auto;\n", "}\n", "\n", ".xr-attrs dt,\n", ".xr-attrs dd {\n", " padding: 0;\n", " margin: 0;\n", " float: left;\n", " padding-right: 10px;\n", " width: auto;\n", "}\n", "\n", ".xr-attrs dt {\n", " font-weight: normal;\n", " grid-column: 1;\n", "}\n", "\n", ".xr-attrs dt:hover span {\n", " display: inline-block;\n", " background: var(--xr-background-color);\n", " padding-right: 10px;\n", "}\n", "\n", ".xr-attrs dd {\n", " grid-column: 2;\n", " white-space: pre-wrap;\n", " word-break: break-all;\n", "}\n", "\n", ".xr-icon-database,\n", ".xr-icon-file-text2,\n", ".xr-no-icon {\n", " display: inline-block;\n", " vertical-align: middle;\n", " width: 1em;\n", " height: 1.5em !important;\n", " stroke-width: 0;\n", " stroke: currentColor;\n", " fill: currentColor;\n", "}\n", "</style><pre class='xr-text-repr-fallback'><xarray.DataArray 'OD' (sin_mod_freq: 37, y: 300, x: 300)>\n", "array([[[ 0.0020338 , 0.11597806, 0.01753798, ..., 0.03280546,\n", " 0.0020338 , -0.03570653],\n", " [-0.08497758, 0.02072593, -0.12425993, ..., 0.0020338 ,\n", " 0.21334289, -0.05405567],\n", " [-0.0865196 , 0.11123309, 0.06265842, ..., 0.21774237,\n", " 0.0903264 , -0.08373303],\n", " ...,\n", " [ 0.0020338 , 0.01803414, -0.15960755, ..., -0.04448622,\n", " -0.012565 , -0.03935142],\n", " [ 0.02038294, 0.18072559, 0.05246465, ..., 0.16367515,\n", " 0.0020338 , 0.05838673],\n", " [-0.07207418, 0.03712512, -0.04756314, ..., 0.01730127,\n", " 0.0020338 , -0.06465758]],\n", "\n", " [[-0.16688474, -0.04827899, -0.03207702, ..., 0.16731735,\n", " -0.03088725, 0.03810562],\n", " [-0.0855391 , -0.12560308, -0.03335334, ..., -0.04577586,\n", " 0.06861158, 0.05261124],\n", " [-0.0871368 , 0.10017805, 0.0030143 , ..., 0.06755282,\n", " 0.12079734, 0.0749878 ],\n", "...\n", " [-0.12844621, 0.19080233, -0.02825124, ..., 0.06307244,\n", " 0.03539053, -0.00930355],\n", " [ 0.02488781, 0.06014496, 0.10686788, ..., 0.00508518,\n", " 0.07919316, 0.00508518],\n", " [ 0.02217962, 0.09861124, 0.02247693, ..., 0.01990027,\n", " 0.05020562, -0.0421677 ]],\n", "\n", " [[-0.06362606, 0.08931324, -0.03830825, ..., -0.08509483,\n", " 0.02421211, 0.01016299],\n", " [ 0.01016299, -0.1559566 , -0.02523617, ..., 0.08483673,\n", " -0.00753659, 0.00927053],\n", " [-0.00753659, 0.15609283, 0.01266612, ..., -0.00753659,\n", " 0.0079676 , -0.02280406],\n", " ...,\n", " [-0.04527692, -0.06064642, 0.06266767, ..., -0.07652946,\n", " -0.03784194, 0.00553549],\n", " [-0.08164456, 0.01048191, -0.02492833, ..., 0.02063429,\n", " -0.05478948, -0.07848833],\n", " [-0.00753659, -0.09608999, 0.08261451, ..., 0.02276876,\n", " 0.1259948 , -0.08056173]]])\n", "Coordinates:\n", " * sin_mod_freq (sin_mod_freq) float64 65.0 66.0 67.0 ... 99.0 100.0 101.0\n", "Dimensions without coordinates: y, x\n", "Attributes:\n", " IMAGE_SUBCLASS: IMAGE_GRAYSCALE\n", " IMAGE_VERSION: 1.2\n", " IMAGE_WHITE_IS_ZERO: 0\n", " x_start: 800\n", " x_end: 1100\n", " y_end: 400\n", " y_start: 100\n", " x_center: 950\n", " y_center: 250\n", " x_span: 300\n", " y_span: 300</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.DataArray</div><div class='xr-array-name'>'OD'</div><ul class='xr-dim-list'><li><span class='xr-has-index'>sin_mod_freq</span>: 37</li><li><span>y</span>: 300</li><li><span>x</span>: 300</li></ul></div><ul class='xr-sections'><li class='xr-section-item'><div class='xr-array-wrap'><input id='section-0e4133bb-76ac-46d4-aab5-73edaf57cfe7' class='xr-array-in' type='checkbox' checked><label for='section-0e4133bb-76ac-46d4-aab5-73edaf57cfe7' title='Show/hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-array-preview xr-preview'><span>0.002034 0.116 0.01754 -0.05108 ... -0.03929 0.02277 0.126 -0.08056</span></div><div class='xr-array-data'><pre>array([[[ 0.0020338 , 0.11597806, 0.01753798, ..., 0.03280546,\n", " 0.0020338 , -0.03570653],\n", " [-0.08497758, 0.02072593, -0.12425993, ..., 0.0020338 ,\n", " 0.21334289, -0.05405567],\n", " [-0.0865196 , 0.11123309, 0.06265842, ..., 0.21774237,\n", " 0.0903264 , -0.08373303],\n", " ...,\n", " [ 0.0020338 , 0.01803414, -0.15960755, ..., -0.04448622,\n", " -0.012565 , -0.03935142],\n", " [ 0.02038294, 0.18072559, 0.05246465, ..., 0.16367515,\n", " 0.0020338 , 0.05838673],\n", " [-0.07207418, 0.03712512, -0.04756314, ..., 0.01730127,\n", " 0.0020338 , -0.06465758]],\n", "\n", " [[-0.16688474, -0.04827899, -0.03207702, ..., 0.16731735,\n", " -0.03088725, 0.03810562],\n", " [-0.0855391 , -0.12560308, -0.03335334, ..., -0.04577586,\n", " 0.06861158, 0.05261124],\n", " [-0.0871368 , 0.10017805, 0.0030143 , ..., 0.06755282,\n", " 0.12079734, 0.0749878 ],\n", "...\n", " [-0.12844621, 0.19080233, -0.02825124, ..., 0.06307244,\n", " 0.03539053, -0.00930355],\n", " [ 0.02488781, 0.06014496, 0.10686788, ..., 0.00508518,\n", " 0.07919316, 0.00508518],\n", " [ 0.02217962, 0.09861124, 0.02247693, ..., 0.01990027,\n", " 0.05020562, -0.0421677 ]],\n", "\n", " [[-0.06362606, 0.08931324, -0.03830825, ..., -0.08509483,\n", " 0.02421211, 0.01016299],\n", " [ 0.01016299, -0.1559566 , -0.02523617, ..., 0.08483673,\n", " -0.00753659, 0.00927053],\n", " [-0.00753659, 0.15609283, 0.01266612, ..., -0.00753659,\n", " 0.0079676 , -0.02280406],\n", " ...,\n", " [-0.04527692, -0.06064642, 0.06266767, ..., -0.07652946,\n", " -0.03784194, 0.00553549],\n", " [-0.08164456, 0.01048191, -0.02492833, ..., 0.02063429,\n", " -0.05478948, -0.07848833],\n", " [-0.00753659, -0.09608999, 0.08261451, ..., 0.02276876,\n", " 0.1259948 , -0.08056173]]])</pre></div></div></li><li class='xr-section-item'><input id='section-def02fb1-6419-434d-8a6d-a1b7b7440783' class='xr-section-summary-in' type='checkbox' checked><label for='section-def02fb1-6419-434d-8a6d-a1b7b7440783' 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'>sin_mod_freq</span></div><div class='xr-var-dims'>(sin_mod_freq)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>65.0 66.0 67.0 ... 99.0 100.0 101.0</div><input id='attrs-2a660019-c652-42be-a4f0-501b33b35ca1' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-2a660019-c652-42be-a4f0-501b33b35ca1' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6d2ea97e-619a-4664-95cf-ecafb962ccf2' class='xr-var-data-in' type='checkbox'><label for='data-6d2ea97e-619a-4664-95cf-ecafb962ccf2' 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([ 65., 66., 67., 68., 69., 70., 71., 72., 73., 74., 75., 76.,\n", " 77., 78., 79., 80., 81., 82., 83., 84., 85., 86., 87., 88.,\n", " 89., 90., 91., 92., 93., 94., 95., 96., 97., 98., 99., 100.,\n", " 101.])</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-b02b99fa-20ca-41e0-9675-550269d1c088' class='xr-section-summary-in' type='checkbox' ><label for='section-b02b99fa-20ca-41e0-9675-550269d1c088' 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>sin_mod_freq</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-ed459eef-a562-4b1a-92ae-65933232625f' class='xr-index-data-in' type='checkbox'/><label for='index-ed459eef-a562-4b1a-92ae-65933232625f' 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([ 65.0, 66.0, 67.0, 68.0, 69.0, 70.0, 71.0, 72.0, 73.0,\n", " 74.0, 75.0, 76.0, 77.0, 78.0, 79.0, 80.0, 81.0, 82.0,\n", " 83.0, 84.0, 85.0, 86.0, 87.0, 88.0, 89.0, 90.0, 91.0,\n", " 92.0, 93.0, 94.0, 95.0, 96.0, 97.0, 98.0, 99.0, 100.0,\n", " 101.0],\n", " dtype='float64', name='sin_mod_freq'))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-2411aff5-d5b4-4aec-a24b-ce540656b031' class='xr-section-summary-in' type='checkbox' ><label for='section-2411aff5-d5b4-4aec-a24b-ce540656b031' class='xr-section-summary' >Attributes: <span>(11)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>IMAGE_SUBCLASS :</span></dt><dd>IMAGE_GRAYSCALE</dd><dt><span>IMAGE_VERSION :</span></dt><dd>1.2</dd><dt><span>IMAGE_WHITE_IS_ZERO :</span></dt><dd>0</dd><dt><span>x_start :</span></dt><dd>800</dd><dt><span>x_end :</span></dt><dd>1100</dd><dt><span>y_end :</span></dt><dd>400</dd><dt><span>y_start :</span></dt><dd>100</dd><dt><span>x_center :</span></dt><dd>950</dd><dt><span>y_center :</span></dt><dd>250</dd><dt><span>x_span :</span></dt><dd>300</dd><dt><span>y_span :</span></dt><dd>300</dd></dl></div></li></ul></div></div>" ], "text/plain": [ "<xarray.DataArray 'OD' (sin_mod_freq: 37, y: 300, x: 300)>\n", "array([[[ 0.0020338 , 0.11597806, 0.01753798, ..., 0.03280546,\n", " 0.0020338 , -0.03570653],\n", " [-0.08497758, 0.02072593, -0.12425993, ..., 0.0020338 ,\n", " 0.21334289, -0.05405567],\n", " [-0.0865196 , 0.11123309, 0.06265842, ..., 0.21774237,\n", " 0.0903264 , -0.08373303],\n", " ...,\n", " [ 0.0020338 , 0.01803414, -0.15960755, ..., -0.04448622,\n", " -0.012565 , -0.03935142],\n", " [ 0.02038294, 0.18072559, 0.05246465, ..., 0.16367515,\n", " 0.0020338 , 0.05838673],\n", " [-0.07207418, 0.03712512, -0.04756314, ..., 0.01730127,\n", " 0.0020338 , -0.06465758]],\n", "\n", " [[-0.16688474, -0.04827899, -0.03207702, ..., 0.16731735,\n", " -0.03088725, 0.03810562],\n", " [-0.0855391 , -0.12560308, -0.03335334, ..., -0.04577586,\n", " 0.06861158, 0.05261124],\n", " [-0.0871368 , 0.10017805, 0.0030143 , ..., 0.06755282,\n", " 0.12079734, 0.0749878 ],\n", "...\n", " [-0.12844621, 0.19080233, -0.02825124, ..., 0.06307244,\n", " 0.03539053, -0.00930355],\n", " [ 0.02488781, 0.06014496, 0.10686788, ..., 0.00508518,\n", " 0.07919316, 0.00508518],\n", " [ 0.02217962, 0.09861124, 0.02247693, ..., 0.01990027,\n", " 0.05020562, -0.0421677 ]],\n", "\n", " [[-0.06362606, 0.08931324, -0.03830825, ..., -0.08509483,\n", " 0.02421211, 0.01016299],\n", " [ 0.01016299, -0.1559566 , -0.02523617, ..., 0.08483673,\n", " -0.00753659, 0.00927053],\n", " [-0.00753659, 0.15609283, 0.01266612, ..., -0.00753659,\n", " 0.0079676 , -0.02280406],\n", " ...,\n", " [-0.04527692, -0.06064642, 0.06266767, ..., -0.07652946,\n", " -0.03784194, 0.00553549],\n", " [-0.08164456, 0.01048191, -0.02492833, ..., 0.02063429,\n", " -0.05478948, -0.07848833],\n", " [-0.00753659, -0.09608999, 0.08261451, ..., 0.02276876,\n", " 0.1259948 , -0.08056173]]])\n", "Coordinates:\n", " * sin_mod_freq (sin_mod_freq) float64 65.0 66.0 67.0 ... 99.0 100.0 101.0\n", "Dimensions without coordinates: y, x\n", "Attributes:\n", " IMAGE_SUBCLASS: IMAGE_GRAYSCALE\n", " IMAGE_VERSION: 1.2\n", " IMAGE_WHITE_IS_ZERO: 0\n", " x_start: 800\n", " x_end: 1100\n", " y_end: 400\n", " y_start: 100\n", " x_center: 950\n", " y_center: 250\n", " x_span: 300\n", " y_span: 300" ] }, "execution_count": 18, "metadata": {}, "output_type": "execute_result" } ], "source": [ "dataSet_cropOD" ] }, { "cell_type": "code", "execution_count": 19, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "array([[[ 0.0020338 , 0.11597806, 0.01753798, ..., 0.03280546,\n", " 0.0020338 , -0.03570653],\n", " [-0.08497758, 0.02072593, -0.12425993, ..., 0.0020338 ,\n", " 0.21334289, -0.05405567],\n", " [-0.0865196 , 0.11123309, 0.06265842, ..., 0.21774237,\n", " 0.0903264 , -0.08373303],\n", " ...,\n", " [ 0.0020338 , 0.01803414, -0.15960755, ..., -0.04448622,\n", " -0.012565 , -0.03935142],\n", " [ 0.02038294, 0.18072559, 0.05246465, ..., 0.16367515,\n", " 0.0020338 , 0.05838673],\n", " [-0.07207418, 0.03712512, -0.04756314, ..., 0.01730127,\n", " 0.0020338 , -0.06465758]],\n", "\n", " [[-0.16688474, -0.04827899, -0.03207702, ..., 0.16731735,\n", " -0.03088725, 0.03810562],\n", " [-0.0855391 , -0.12560308, -0.03335334, ..., -0.04577586,\n", " 0.06861158, 0.05261124],\n", " [-0.0871368 , 0.10017805, 0.0030143 , ..., 0.06755282,\n", " 0.12079734, 0.0749878 ],\n", " ...,\n", " [-0.03402697, -0.03270378, -0.03207702, ..., 0.04882384,\n", " -0.10395782, 0.10099471],\n", " [-0.0960766 , 0.0030143 , 0.0030143 , ..., -0.01225317,\n", " -0.07833134, -0.04143746],\n", " [-0.05414411, -0.0150042 , 0.13654569, ..., 0.0030143 ,\n", " -0.02775736, -0.01298604]],\n", "\n", " [[ 0.08257612, -0.06604552, 0.08946478, ..., 0.08946478,\n", " -0.06819837, 0.05256022],\n", " [-0.06932959, -0.09006039, 0.01651151, ..., 0.0497863 ,\n", " 0.03128283, -0.20035786],\n", " [-0.11070629, -0.001507 , -0.04151233, ..., -0.001507 ,\n", " 0.07486598, 0.04294477],\n", " ...,\n", " [-0.02092508, 0.06518438, 0.01718514, ..., 0.04501302,\n", " 0.18081456, -0.02748248],\n", " [-0.001507 , -0.05461682, -0.01889874, ..., 0.11985386,\n", " 0.01530012, 0.01376048],\n", " [-0.13503839, -0.01889874, 0.03421109, ..., -0.06122623,\n", " -0.0332557 , 0.08946478]],\n", "\n", " ...,\n", "\n", " [[-0.03833677, -0.05668591, 0.06356322, ..., 0.08146443,\n", " -0.0991712 , -0.00261868],\n", " [-0.0554312 , -0.0579863 , 0.0331222 , ..., -0.0174878 ,\n", " -0.00232137, -0.06931006],\n", " [-0.09058746, -0.00502957, 0.01477306, ..., -0.04494618,\n", " 0.10178444, 0.10574484],\n", " ...,\n", " [-0.07703449, 0.01477306, -0.07537804, ..., -0.04238536,\n", " 0.04334643, -0.07925589],\n", " [-0.0579863 , -0.04585156, 0.14339044, ..., -0.01553229,\n", " 0.05794523, 0.05794523],\n", " [-0.06369856, -0.00175624, -0.02031826, ..., 0.07633095,\n", " -0.03174696, 0.06058259]],\n", "\n", " [[-0.06511907, 0.07068247, -0.01066317, ..., -0.0421677 ,\n", " 0.08512789, -0.03128246],\n", " [-0.01326395, -0.1736066 , 0.04080327, ..., -0.04451176,\n", " -0.01144412, -0.15655617],\n", " [-0.04710057, 0.15350519, -0.1104277 , ..., -0.09176464,\n", " -0.14009683, -0.0243287 ],\n", " ...,\n", " [-0.12844621, 0.19080233, -0.02825124, ..., 0.06307244,\n", " 0.03539053, -0.00930355],\n", " [ 0.02488781, 0.06014496, 0.10686788, ..., 0.00508518,\n", " 0.07919316, 0.00508518],\n", " [ 0.02217962, 0.09861124, 0.02247693, ..., 0.01990027,\n", " 0.05020562, -0.0421677 ]],\n", "\n", " [[-0.06362606, 0.08931324, -0.03830825, ..., -0.08509483,\n", " 0.02421211, 0.01016299],\n", " [ 0.01016299, -0.1559566 , -0.02523617, ..., 0.08483673,\n", " -0.00753659, 0.00927053],\n", " [-0.00753659, 0.15609283, 0.01266612, ..., -0.00753659,\n", " 0.0079676 , -0.02280406],\n", " ...,\n", " [-0.04527692, -0.06064642, 0.06266767, ..., -0.07652946,\n", " -0.03784194, 0.00553549],\n", " [-0.08164456, 0.01048191, -0.02492833, ..., 0.02063429,\n", " -0.05478948, -0.07848833],\n", " [-0.00753659, -0.09608999, 0.08261451, ..., 0.02276876,\n", " 0.1259948 , -0.08056173]]])" ] }, "execution_count": 19, "metadata": {}, "output_type": "execute_result" } ], "source": [ "dataSet_cropOD.to_numpy()" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "from Analyser.FitAnalyser import ThomasFermi2dModel, DensityProfileBEC2dModel, polylog2_2d\n", "\n", "fitModel = DensityProfileBEC2dModel()\n", "# fitModel = ThomasFermi2dModel()\n", "\n", "fitAnalyser = FitAnalyser(fitModel, fitDim=2)\n", "\n", "# fitAnalyser = FitAnalyser(\"Gaussian-2D\", fitDim=2)\n", "\n", "# dataSet_cropOD = dataSet_cropOD.chunk((1,1,100,100))\n", "\n", "params = fitAnalyser.guess(dataSet_cropOD, guess_kwargs=dict(pureBECThreshold=0.3), dask=\"parallelized\")\n", "fitResult = fitAnalyser.fit(dataSet_cropOD, params).load()" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] } ], "metadata": { "kernelspec": { "display_name": "base", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.9.12" }, "orig_nbformat": 4 }, "nbformat": 4, "nbformat_minor": 2}
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