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finish reading from hdf5
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{
"cells": [
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{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
"# Import supporting package"
]
},
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{
"cell_type": "code",
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"execution_count": 1,
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"metadata": {},
"outputs": [],
"source": [
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"import xarray as xr\n",
"import numpy as np\n",
"\n",
not finished
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"from uncertainties import ufloat\n",
"from uncertainties import unumpy as unp\n",
"from uncertainties import umath\n",
"\n",
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"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",
not finished
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"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",
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"\n",
"imageAnalyser = ImageAnalyser()"
]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
"## Start a client for parallel computing"
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]
},
{
"cell_type": "code",
add tool function
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"execution_count": 2,
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"metadata": {},
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"outputs": [
debug and nwe functions
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{
"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 51109 instead\n",
" warnings.warn(\n"
]
},
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{
"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",
debug and nwe functions
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" <p style=\"color: #9D9D9D; margin-bottom: 0px;\">Client-224091e0-ec5e-11ed-addc-9c7bef43b4fb</p>\n",
add tool function
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" <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",
debug and nwe functions
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" <strong>Dashboard: </strong> <a href=\"http://127.0.0.1:51109/status\" target=\"_blank\">http://127.0.0.1:51109/status</a>\n",
add tool function
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" </td>\n",
" <td style=\"text-align: left;\"></td>\n",
" </tr>\n",
" \n",
"\n",
" </table>\n",
"\n",
" \n",
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" <button style=\"margin-bottom: 12px;\" data-commandlinker-command=\"dask:populate-and-launch-layout\" data-commandlinker-args='{\"url\": \"http://127.0.0.1:51109/status\" }'>\n",
" Launch dashboard in JupyterLab\n",
" </button>\n",
" \n",
add tool function
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"\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",
debug and nwe functions
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" <p style=\"color: #9D9D9D; margin-bottom: 0px;\">f360131e</p>\n",
add tool function
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" <table style=\"width: 100%; text-align: left;\">\n",
" <tr>\n",
" <td style=\"text-align: left;\">\n",
debug and nwe functions
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" <strong>Dashboard:</strong> <a href=\"http://127.0.0.1:51109/status\" target=\"_blank\">http://127.0.0.1:51109/status</a>\n",
add tool function
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" </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",
debug and nwe functions
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" <p style=\"color: #9D9D9D; margin-bottom: 0px;\">Scheduler-0e581a89-0733-49c5-8d25-60e26c6ac0bf</p>\n",
add tool function
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" <table style=\"width: 100%; text-align: left;\">\n",
" <tr>\n",
" <td style=\"text-align: left;\">\n",
debug and nwe functions
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" <strong>Comm:</strong> tcp://127.0.0.1:51110\n",
add tool function
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" </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",
debug and nwe functions
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" <strong>Dashboard:</strong> <a href=\"http://127.0.0.1:51109/status\" target=\"_blank\">http://127.0.0.1:51109/status</a>\n",
add tool function
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" </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",
debug and nwe functions
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" <strong>Comm: </strong> tcp://127.0.0.1:51150\n",
add tool function
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" </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",
debug and nwe functions
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" <strong>Dashboard: </strong> <a href=\"http://127.0.0.1:51155/status\" target=\"_blank\">http://127.0.0.1:51155/status</a>\n",
add tool function
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" </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",
debug and nwe functions
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" <strong>Nanny: </strong> tcp://127.0.0.1:51113\n",
add tool function
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" </td>\n",
" <td style=\"text-align: left;\"></td>\n",
" </tr>\n",
" <tr>\n",
" <td colspan=\"2\" style=\"text-align: left;\">\n",
debug and nwe functions
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" <strong>Local directory: </strong> C:\\Users\\Jianshun Gao\\AppData\\Local\\Temp\\dask-worker-space\\worker-2b8gvagb\n",
add tool function
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" </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",
debug and nwe functions
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" <strong>Comm: </strong> tcp://127.0.0.1:51141\n",
add tool function
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" </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",
debug and nwe functions
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" <strong>Dashboard: </strong> <a href=\"http://127.0.0.1:51148/status\" target=\"_blank\">http://127.0.0.1:51148/status</a>\n",
add tool function
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" </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",
debug and nwe functions
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" <strong>Nanny: </strong> tcp://127.0.0.1:51114\n",
add tool function
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" </td>\n",
" <td style=\"text-align: left;\"></td>\n",
" </tr>\n",
" <tr>\n",
" <td colspan=\"2\" style=\"text-align: left;\">\n",
debug and nwe functions
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" <strong>Local directory: </strong> C:\\Users\\Jianshun Gao\\AppData\\Local\\Temp\\dask-worker-space\\worker-a2ff372r\n",
add tool function
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" </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",
debug and nwe functions
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" <strong>Comm: </strong> tcp://127.0.0.1:51139\n",
add tool function
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" </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",
debug and nwe functions
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" <strong>Dashboard: </strong> <a href=\"http://127.0.0.1:51145/status\" target=\"_blank\">http://127.0.0.1:51145/status</a>\n",
add tool function
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" </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",
debug and nwe functions
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" <strong>Nanny: </strong> tcp://127.0.0.1:51115\n",
add tool function
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" </td>\n",
" <td style=\"text-align: left;\"></td>\n",
" </tr>\n",
" <tr>\n",
" <td colspan=\"2\" style=\"text-align: left;\">\n",
debug and nwe functions
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" <strong>Local directory: </strong> C:\\Users\\Jianshun Gao\\AppData\\Local\\Temp\\dask-worker-space\\worker-r4y9shfe\n",
add tool function
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" </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",
debug and nwe functions
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" <strong>Comm: </strong> tcp://127.0.0.1:51140\n",
add tool function
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" </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",
debug and nwe functions
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" <strong>Dashboard: </strong> <a href=\"http://127.0.0.1:51144/status\" target=\"_blank\">http://127.0.0.1:51144/status</a>\n",
add tool function
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" </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",
debug and nwe functions
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" <strong>Nanny: </strong> tcp://127.0.0.1:51116\n",
add tool function
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" </td>\n",
" <td style=\"text-align: left;\"></td>\n",
" </tr>\n",
" <tr>\n",
" <td colspan=\"2\" style=\"text-align: left;\">\n",
debug and nwe functions
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" <strong>Local directory: </strong> C:\\Users\\Jianshun Gao\\AppData\\Local\\Temp\\dask-worker-space\\worker-jcbj2z99\n",
add tool function
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" </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",
debug and nwe functions
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" <strong>Comm: </strong> tcp://127.0.0.1:51143\n",
add tool function
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" </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",
debug and nwe functions
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" <strong>Dashboard: </strong> <a href=\"http://127.0.0.1:51153/status\" target=\"_blank\">http://127.0.0.1:51153/status</a>\n",
add tool function
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" </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",
debug and nwe functions
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" <strong>Nanny: </strong> tcp://127.0.0.1:51117\n",
add tool function
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" </td>\n",
" <td style=\"text-align: left;\"></td>\n",
" </tr>\n",
" <tr>\n",
" <td colspan=\"2\" style=\"text-align: left;\">\n",
debug and nwe functions
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" <strong>Local directory: </strong> C:\\Users\\Jianshun Gao\\AppData\\Local\\Temp\\dask-worker-space\\worker-3ol5ipx3\n",
add tool function
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" </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",
debug and nwe functions
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" <strong>Comm: </strong> tcp://127.0.0.1:51142\n",
add tool function
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" </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",
debug and nwe functions
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" <strong>Dashboard: </strong> <a href=\"http://127.0.0.1:51151/status\" target=\"_blank\">http://127.0.0.1:51151/status</a>\n",
add tool function
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" </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",
debug and nwe functions
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" <strong>Nanny: </strong> tcp://127.0.0.1:51118\n",
add tool function
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" </td>\n",
" <td style=\"text-align: left;\"></td>\n",
" </tr>\n",
" <tr>\n",
" <td colspan=\"2\" style=\"text-align: left;\">\n",
debug and nwe functions
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" <strong>Local directory: </strong> C:\\Users\\Jianshun Gao\\AppData\\Local\\Temp\\dask-worker-space\\worker-0u_6_n9d\n",
add tool function
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" </td>\n",
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"\n",
" \n",
"\n",
" \n",
"\n",
" </table>\n",
" </details>\n",
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" \n",
"\n",
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"\n",
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" \n",
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],
"text/plain": [
debug and nwe functions
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"<Client: 'tcp://127.0.0.1:51110' processes=6 threads=60, memory=55.88 GiB>"
add tool function
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]
},
"execution_count": 2,
"metadata": {},
"output_type": "execute_result"
}
],
finish of fitting
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"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",
add tool function
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"execution_count": 3,
finish reading from hdf5
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"metadata": {},
"outputs": [],
"source": [
first working version
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"# filepath = \"//DyLabNAS/Data/Evaporative_Cooling/2023/05/03/0043/*.h5\"\n",
finish reading from hdf5
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"# filepath = \"//DyLabNAS/Data/Evaporative_Cooling/2023/04/18/0003/2023-04-18_0003_Evaporative_Cooling_000.h5\"\n",
"\n",
not finished
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"# filepath = \"//DyLabNAS/Data/Repetition_scan/2023/04/21/0002/*.h5\"\n",
finish of fitting
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"\n",
not finish get_fit_result
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"filepath = r\"./testData/0002/*.h5\"\n",
finish reading from hdf5
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"\n",
debug and nwe functions
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"# 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",
not finished
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"# filepath = \"//DyLabNAS/Data/Evaporative_Cooling/2023/04/18/0003/*.h5\"\n",
"\n",
not finish get_fit_result
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"# filepath = \"//DyLabNAS/Data/Evaporative_Cooling/2023/05/04/0000/*.h5\""
finish of fitting
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]
},
{
"cell_type": "code",
add tool function
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"execution_count": 4,
finish of fitting
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"metadata": {},
debug and nwe functions
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"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"{'unlimited_dims': set(), 'source': 'd:\\\\Jianshun Gao\\\\Simulations\\\\analyseScripts\\\\testData\\\\0002\\\\2023-04-21_0002_Evaporative_Cooling_0.h5'}\n"
]
}
],
finish of fitting
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"source": [
finish reading from hdf5
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"groupList = [\n",
" \"images/MOT_3D_Camera/in_situ_absorption\",\n",
finish of fitting
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" # \"images/ODT_1_Axis_Camera/in_situ_absorption\",\n",
finish reading from hdf5
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"]\n",
"\n",
"dskey = {\n",
" \"images/MOT_3D_Camera/in_situ_absorption\": \"camera_1\",\n",
finish of fitting
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" # \"images/ODT_1_Axis_Camera/in_situ_absorption\": \"camera_2\",\n",
finish reading from hdf5
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"}\n",
"\n",
add tool function
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"dataSetDict = {\n",
finish reading from hdf5
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" dskey[groupList[i]]: read_hdf5_file(filepath, groupList[i])\n",
" for i in range(len(groupList))\n",
"}"
]
},
finish of fitting
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{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
"## Rechunk the data for parallel computing"
]
},
finish reading from hdf5
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{
"cell_type": "code",
add tool function
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"execution_count": 5,
finish of fitting
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"metadata": {},
"outputs": [],
"source": [
add tool function
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"dataSet = dataSetDict[\"camera_1\"]\n",
finish of fitting
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"\n",
add tool function
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"scanAxis = dataSet.scanAxis\n",
finish of fitting
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"\n",
add tool function
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"# dataSet = dataSet.chunk(\n",
first working version
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"# {\n",
"# # \"compZ_current_sg\": \"auto\",\n",
"# \"sin_mod_freq\": \"auto\",\n",
"# \"runs\": 2,\n",
"# \"x\": \"auto\",\n",
"# \"y\": \"auto\",\n",
"# }\n",
"# )"
finish of fitting
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]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
"# Calculate absorption imaging"
]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
"## get OD images"
]
},
{
"cell_type": "code",
not finished
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"execution_count": 6,
finish reading from hdf5
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"metadata": {},
add tool function
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"outputs": [
{
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"</style><pre class='xr-text-repr-fallback'>&lt;xarray.Dataset&gt;\n",
not finished
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"Dimensions: (runs: 3, x: 1200, y: 1920)\n",
add tool function
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"Coordinates:\n",
" * runs (runs) float64 0.0 1.0 2.0\n",
"Dimensions without coordinates: x, y\n",
"Data variables:\n",
not finished
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" atoms (runs, x, y) uint16 dask.array&lt;chunksize=(1, 1200, 1920), meta=np.ndarray&gt;\n",
" background (runs, x, y) uint16 dask.array&lt;chunksize=(1, 1200, 1920), meta=np.ndarray&gt;\n",
" dark (runs, x, y) uint16 dask.array&lt;chunksize=(1, 1200, 1920), meta=np.ndarray&gt;\n",
debug and nwe functions
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" shotNum (runs) int64 0 1 2\n",
not finished
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" OD (runs, x, y) float64 dask.array&lt;chunksize=(1, 1200, 1920), meta=np.ndarray&gt;\n",
not finish get_fit_result
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"Attributes: (12/96)\n",
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add tool function
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" abs_img_freq: 110.858\n",
" absorption_imaging_flag: True\n",
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" ... ...\n",
not finished
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" y_offset_img: 0\n",
add tool function
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" z_offset: 0.189\n",
" z_offset_img: 0.189\n",
not finished
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" runs: [0. 1. 2.]\n",
" scanAxis: [&#x27;runs&#x27;]\n",
debug and nwe functions
2023-05-07 00:38:52 +02:00
" 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-562506ba-5de6-455a-868a-eb6a8fd249fd' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-562506ba-5de6-455a-868a-eb6a8fd249fd' 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-f0c323de-b626-49c2-a725-b9d6ebfcc6ea' class='xr-section-summary-in' type='checkbox' checked><label for='section-f0c323de-b626-49c2-a725-b9d6ebfcc6ea' 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-b3cad557-e427-4ac5-814c-f06ff668fe16' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-b3cad557-e427-4ac5-814c-f06ff668fe16' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-22ea35b3-1774-4e1e-8471-6be1acf96d7a' class='xr-var-data-in' type='checkbox'><label for='data-22ea35b3-1774-4e1e-8471-6be1acf96d7a' 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-e632acb3-d149-4033-a241-5a8d01e14622' class='xr-section-summary-in' type='checkbox' checked><label for='section-e632acb3-d149-4033-a241-5a8d01e14622' 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&lt;chunksize=(1, 1200, 1920), meta=np.ndarray&gt;</div><input id='attrs-934b2987-a0aa-436c-94b9-7830e49b89a2' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-934b2987-a0aa-436c-94b9-7830e49b89a2' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e8edce64-be70-4419-9721-78491f3a2f58' class='xr-var-data-in' type='checkbox'><label for='data-e8edce64-be70-4419-9721-78491f3a2f58' 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",
add tool function
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" <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",
not finished
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" <td> 13.18 MiB </td>\n",
add tool function
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" <td> 4.39 MiB </td>\n",
" </tr>\n",
" \n",
" <tr>\n",
" <th> Shape </th>\n",
not finished
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" <td> (3, 1200, 1920) </td>\n",
" <td> (1, 1200, 1920) </td>\n",
add tool function
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" </tr>\n",
" <tr>\n",
" <th> Dask graph </th>\n",
not finished
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" <td colspan=\"2\"> 3 chunks in 10 graph layers </td>\n",
add tool function
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" </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",
not finished
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" <svg width=\"194\" height=\"139\" style=\"stroke:rgb(0,0,0);stroke-width:1\" >\n",
add tool function
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"\n",
" <!-- Horizontal lines -->\n",
not finished
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" <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",
add tool function
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"\n",
" <!-- Vertical lines -->\n",
not finished
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" <line x1=\"10\" y1=\"0\" x2=\"10\" y2=\"75\" style=\"stroke-width:2\" />\n",
" <line x1=\"14\" y1=\"4\" x2=\"14\" y2=\"79\" />\n",
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" <line x1=\"24\" y1=\"14\" x2=\"24\" y2=\"89\" style=\"stroke-width:2\" />\n",
add tool function
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"\n",
" <!-- Colored Rectangle -->\n",
not finished
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" <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",
add tool function
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"\n",
" <!-- Horizontal lines -->\n",
not finished
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" <line x1=\"10\" y1=\"0\" x2=\"130\" y2=\"0\" style=\"stroke-width:2\" />\n",
" <line x1=\"14\" y1=\"4\" x2=\"134\" y2=\"4\" />\n",
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" <line x1=\"24\" y1=\"14\" x2=\"144\" y2=\"14\" style=\"stroke-width:2\" />\n",
add tool function
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"\n",
" <!-- Vertical lines -->\n",
not finished
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" <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",
add tool function
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"\n",
" <!-- Colored Rectangle -->\n",
not finished
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" <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",
add tool function
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"\n",
" <!-- Horizontal lines -->\n",
not finished
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" <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",
add tool function
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"\n",
" <!-- Vertical lines -->\n",
not finished
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" <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",
add tool function
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"\n",
" <!-- Colored Rectangle -->\n",
not finished
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" <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",
add tool function
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"\n",
" <!-- Text -->\n",
not finished
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" <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",
add tool function
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"</svg>\n",
" </td>\n",
" </tr>\n",
debug and nwe functions
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"</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>background</span></div><div class='xr-var-dims'>(runs, x, y)</div><div class='xr-var-dtype'>uint16</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(1, 1200, 1920), meta=np.ndarray&gt;</div><input id='attrs-07d4d7cc-da37-4ae1-a441-45f3fad38a94' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-07d4d7cc-da37-4ae1-a441-45f3fad38a94' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-215a7593-22c0-40da-aa4d-26c86f328ecb' class='xr-var-data-in' type='checkbox'><label for='data-215a7593-22c0-40da-aa4d-26c86f328ecb' 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",
add tool function
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" <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",
not finished
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" <td> 13.18 MiB </td>\n",
add tool function
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" <td> 4.39 MiB </td>\n",
" </tr>\n",
" \n",
" <tr>\n",
" <th> Shape </th>\n",
not finished
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" <td> (3, 1200, 1920) </td>\n",
" <td> (1, 1200, 1920) </td>\n",
add tool function
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" </tr>\n",
" <tr>\n",
" <th> Dask graph </th>\n",
not finished
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" <td colspan=\"2\"> 3 chunks in 10 graph layers </td>\n",
add tool function
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" </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",
not finished
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" <svg width=\"194\" height=\"139\" style=\"stroke:rgb(0,0,0);stroke-width:1\" >\n",
add tool function
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"\n",
" <!-- Horizontal lines -->\n",
not finished
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" <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",
add tool function
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"\n",
" <!-- Vertical lines -->\n",
not finished
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" <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",
add tool function
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"\n",
" <!-- Colored Rectangle -->\n",
not finished
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" <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",
add tool function
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"\n",
" <!-- Horizontal lines -->\n",
not finished
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" <line x1=\"10\" y1=\"0\" x2=\"130\" y2=\"0\" style=\"stroke-width:2\" />\n",
" <line x1=\"14\" y1=\"4\" x2=\"134\" y2=\"4\" />\n",
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" <line x1=\"24\" y1=\"14\" x2=\"144\" y2=\"14\" style=\"stroke-width:2\" />\n",
add tool function
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"\n",
" <!-- Vertical lines -->\n",
not finished
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" <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",
add tool function
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"\n",
" <!-- Colored Rectangle -->\n",
not finished
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" <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",
add tool function
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"\n",
" <!-- Horizontal lines -->\n",
not finished
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" <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",
add tool function
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"\n",
" <!-- Vertical lines -->\n",
not finished
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" <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",
add tool function
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"\n",
" <!-- Colored Rectangle -->\n",
not finished
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" <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",
add tool function
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"\n",
" <!-- Text -->\n",
not finished
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" <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",
add tool function
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"</svg>\n",
" </td>\n",
" </tr>\n",
debug and nwe functions
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"</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>dark</span></div><div class='xr-var-dims'>(runs, x, y)</div><div class='xr-var-dtype'>uint16</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(1, 1200, 1920), meta=np.ndarray&gt;</div><input id='attrs-35b57504-4fcd-4871-a3f2-3e90e75c41a4' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-35b57504-4fcd-4871-a3f2-3e90e75c41a4' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-19b83311-9d82-4eff-b47a-c280a871a909' class='xr-var-data-in' type='checkbox'><label for='data-19b83311-9d82-4eff-b47a-c280a871a909' 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",
add tool function
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" <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",
not finished
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" <td> 13.18 MiB </td>\n",
add tool function
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" <td> 4.39 MiB </td>\n",
" </tr>\n",
" \n",
" <tr>\n",
" <th> Shape </th>\n",
not finished
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" <td> (3, 1200, 1920) </td>\n",
" <td> (1, 1200, 1920) </td>\n",
add tool function
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" </tr>\n",
" <tr>\n",
" <th> Dask graph </th>\n",
not finished
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" <td colspan=\"2\"> 3 chunks in 10 graph layers </td>\n",
add tool function
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" </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",
not finished
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" <svg width=\"194\" height=\"139\" style=\"stroke:rgb(0,0,0);stroke-width:1\" >\n",
add tool function
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"\n",
" <!-- Horizontal lines -->\n",
not finished
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" <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",
add tool function
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"\n",
" <!-- Vertical lines -->\n",
not finished
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" <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",
add tool function
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"\n",
" <!-- Colored Rectangle -->\n",
not finished
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" <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",
add tool function
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"\n",
" <!-- Horizontal lines -->\n",
not finished
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" <line x1=\"10\" y1=\"0\" x2=\"130\" y2=\"0\" style=\"stroke-width:2\" />\n",
" <line x1=\"14\" y1=\"4\" x2=\"134\" y2=\"4\" />\n",
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" <line x1=\"24\" y1=\"14\" x2=\"144\" y2=\"14\" style=\"stroke-width:2\" />\n",
add tool function
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"\n",
" <!-- Vertical lines -->\n",
not finished
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" <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",
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"\n",
" <!-- Colored Rectangle -->\n",
not finished
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" <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",
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"\n",
" <!-- Horizontal lines -->\n",
not finished
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" <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",
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"\n",
" <!-- Vertical lines -->\n",
not finished
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" <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",
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"\n",
" <!-- Colored Rectangle -->\n",
not finished
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" <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",
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"\n",
" <!-- Text -->\n",
not finished
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" <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",
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"</svg>\n",
" </td>\n",
" </tr>\n",
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"</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>shotNum</span></div><div class='xr-var-dims'>(runs)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>0 1 2</div><input id='attrs-ebbdac90-8f1c-4e10-92d4-918979563e58' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ebbdac90-8f1c-4e10-92d4-918979563e58' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c447a455-2cb8-4f89-affd-5c72e71fbd58' class='xr-var-data-in' type='checkbox'><label for='data-c447a455-2cb8-4f89-affd-5c72e71fbd58' 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&lt;chunksize=(1, 1200, 1920), meta=np.ndarray&gt;</div><input id='attrs-6a481dde-c013-4bc6-afab-441110ae80bb' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-6a481dde-c013-4bc6-afab-441110ae80bb' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d538438c-c886-4f97-9401-b4026ba0a3e2' class='xr-var-data-in' type='checkbox'><label for='data-d538438c-c886-4f97-9401-b4026ba0a3e2' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>IMAGE_SUBCLASS :</span></dt><dd>IMAGE_GRAYSCALE</dd><dt><span>IMAGE_VERSION :</span></dt><dd>1.2</dd><dt><span>IMAGE_WHITE_IS_ZERO :</span></dt><dd>0</dd></dl></div><div class='xr-var-data'><table>\n",
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" <tr>\n",
" <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",
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" <td> 52.73 MiB </td>\n",
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" <td> 17.58 MiB </td>\n",
" </tr>\n",
" \n",
" <tr>\n",
" <th> Shape </th>\n",
not finished
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" <td> (3, 1200, 1920) </td>\n",
" <td> (1, 1200, 1920) </td>\n",
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" </tr>\n",
" <tr>\n",
" <th> Dask graph </th>\n",
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" <td colspan=\"2\"> 3 chunks in 40 graph layers </td>\n",
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" </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",
not finished
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" <svg width=\"194\" height=\"139\" style=\"stroke:rgb(0,0,0);stroke-width:1\" >\n",
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"\n",
" <!-- Horizontal lines -->\n",
not finished
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" <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",
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"\n",
" <!-- Vertical lines -->\n",
not finished
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" <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",
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"\n",
" <!-- Colored Rectangle -->\n",
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" <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",
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"\n",
" <!-- Horizontal lines -->\n",
not finished
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" <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",
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"\n",
" <!-- Vertical lines -->\n",
not finished
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" <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",
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"\n",
" <!-- Colored Rectangle -->\n",
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" <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",
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"\n",
" <!-- Horizontal lines -->\n",
not finished
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" <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",
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"\n",
" <!-- Vertical lines -->\n",
not finished
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" <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",
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"\n",
" <!-- Colored Rectangle -->\n",
not finished
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" <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",
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"\n",
" <!-- Text -->\n",
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" <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",
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"</svg>\n",
" </td>\n",
" </tr>\n",
debug and nwe functions
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"</table></div></li></ul></div></li><li class='xr-section-item'><input id='section-17ebeb8c-a7a0-4037-ac44-fe69655ac6ed' class='xr-section-summary-in' type='checkbox' ><label for='section-17ebeb8c-a7a0-4037-ac44-fe69655ac6ed' 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-f41ec41f-2dea-477e-b07f-a7cfde093ae5' class='xr-index-data-in' type='checkbox'/><label for='index-f41ec41f-2dea-477e-b07f-a7cfde093ae5' 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=&#x27;float64&#x27;, name=&#x27;runs&#x27;))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-3e608210-b9a0-4e86-8bbc-ae7b8780226b' class='xr-section-summary-in' type='checkbox' ><label for='section-3e608210-b9a0-4e86-8bbc-ae7b8780226b' 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
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],
"text/plain": [
"<xarray.Dataset>\n",
not finished
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"Dimensions: (runs: 3, x: 1200, y: 1920)\n",
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"Coordinates:\n",
" * runs (runs) float64 0.0 1.0 2.0\n",
"Dimensions without coordinates: x, y\n",
"Data variables:\n",
not finished
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" 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",
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" shotNum (runs) int64 0 1 2\n",
not finished
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" OD (runs, x, y) float64 dask.array<chunksize=(1, 1200, 1920), meta=np.ndarray>\n",
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"Attributes: (12/96)\n",
" TOF_free: 0.02\n",
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" 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",
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" y_offset_img: 0\n",
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" z_offset: 0.189\n",
" z_offset_img: 0.189\n",
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" runs: [0. 1. 2.]\n",
" scanAxis: ['runs']\n",
" scanAxisLength: [3.]"
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]
},
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"execution_count": 6,
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"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"dataSet = imageAnalyser.get_absorption_images(dataSet)\n",
"\n",
"dataSet"
]
},
not finished
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{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
"## Select region of interests"
]
},
{
"cell_type": "code",
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"execution_count": 8,
not finished
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"metadata": {},
"outputs": [],
"source": [
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"# imageAnalyser.center = (529, 962)\n",
"# imageAnalyser.span = (100,100)\n",
"# imageAnalyser.fraction = (0.1, 0.1)\n",
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"\n",
"# imageAnalyser.center = (890, 1150)\n",
"# imageAnalyser.span = (600,600)\n",
"# imageAnalyser.fraction = (0.1, 0.1)\n",
"\n",
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"imageAnalyser.center = (890, 950)\n",
"imageAnalyser.span = (100,100)\n",
"imageAnalyser.fraction = (0.1, 0.1)\n",
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"\n",
"dataSet_crop = imageAnalyser.crop_image(dataSet)"
]
},
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{
"cell_type": "code",
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"execution_count": 9,
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"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
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"<xarray.plot.facetgrid.FacetGrid at 0x274c65832e0>"
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]
},
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"execution_count": 9,
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"metadata": {},
"output_type": "execute_result"
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},
{
"data": {
not finish get_fit_result
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"image/png": "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
not finished
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"text/plain": [
not finish get_fit_result
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"<Figure size 720x216 with 4 Axes>"
not finished
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]
},
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"metadata": {
"needs_background": "light"
},
not finished
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"output_type": "display_data"
add tool function
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}
],
finish of fitting
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"source": [
not finished
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"# 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])"
finish of fitting
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]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
not finished
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"## Remove the background"
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]
},
{
"cell_type": "code",
debug and nwe functions
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"execution_count": 10,
finish of fitting
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"metadata": {},
"outputs": [],
"source": [
not finished
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"dataSet_crop['OD'] = dataSet_crop['OD'] + 500"
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]
},
{
"cell_type": "code",
debug and nwe functions
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"execution_count": 11,
finish of fitting
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"metadata": {},
first working version
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"outputs": [],
finish reading from hdf5
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"source": [
not finished
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"dataSet_crop['OD'] = imageAnalyser.substract_offset(dataSet_crop['OD'])"
finish of fitting
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]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
not finished
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"# Test Fit"
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]
},
{
"cell_type": "code",
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"execution_count": 12,
finish reading from hdf5
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"metadata": {},
"outputs": [],
"source": [
not finished
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"fitAnalyser = FitAnalyser(\"Two Gaussian-2D\", fitDim=2)\n",
"\n",
"params = fitAnalyser.guess(dataSet_crop.OD, dask=\"parallelized\")"
]
},
{
"cell_type": "code",
debug and nwe functions
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"execution_count": 13,
not finished
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"metadata": {},
"outputs": [],
"source": [
debug and nwe functions
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"fitResult = fitAnalyser.fit(dataSet_crop.OD, params).load()"
not finished
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]
},
{
"cell_type": "code",
debug and nwe functions
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"execution_count": 14,
not finished
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"metadata": {},
"outputs": [],
"source": [
"fitCurve = fitAnalyser.eval(fitResult, x=np.arange(100), y=np.arange(100), dask=\"parallelized\").load()"
finish of fitting
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]
},
{
"cell_type": "code",
debug and nwe functions
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"execution_count": 15,
finish of fitting
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"metadata": {},
not finish get_fit_result
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"outputs": [
{
"data": {
"text/plain": [
debug and nwe functions
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"<xarray.plot.facetgrid.FacetGrid at 0x274c888b340>"
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]
},
debug and nwe functions
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"execution_count": 15,
not finish get_fit_result
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"metadata": {},
"output_type": "execute_result"
},
{
"data": {
"image/png": "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
"text/plain": [
"<Figure size 720x216 with 4 Axes>"
]
},
"metadata": {
"needs_background": "light"
},
"output_type": "display_data"
}
],
"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",
debug and nwe functions
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"execution_count": 16,
"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": 17,
"metadata": {},
"outputs": [],
"source": [
"Ncount = dataSet_crop.OD.sum(dim=(scanAxis[0], 'x', 'y'))"
]
},
{
"cell_type": "code",
"execution_count": 18,
not finish get_fit_result
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"metadata": {},
bug fixing
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"outputs": [
debug and nwe functions
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{
"ename": "TypeError",
"evalue": "No numeric data to plot.",
"output_type": "error",
"traceback": [
"\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[1;31mTypeError\u001b[0m Traceback (most recent call last)",
"\u001b[1;32md:\\Jianshun Gao\\Simulations\\analyseScripts\\test.ipynb Cell 29\u001b[0m in \u001b[0;36m<cell line: 5>\u001b[1;34m()\u001b[0m\n\u001b[0;32m <a href='vscode-notebook-cell://127.0.0.1:8080/d%3A/Jianshun%20Gao/Simulations/analyseScripts/test.ipynb#X40sdnNjb2RlLXJlbW90ZQ%3D%3D?line=2'>3</a>\u001b[0m fig \u001b[39m=\u001b[39m plt\u001b[39m.\u001b[39mfigure()\n\u001b[0;32m <a href='vscode-notebook-cell://127.0.0.1:8080/d%3A/Jianshun%20Gao/Simulations/analyseScripts/test.ipynb#X40sdnNjb2RlLXJlbW90ZQ%3D%3D?line=3'>4</a>\u001b[0m ax \u001b[39m=\u001b[39m fig\u001b[39m.\u001b[39mgca()\n\u001b[1;32m----> <a href='vscode-notebook-cell://127.0.0.1:8080/d%3A/Jianshun%20Gao/Simulations/analyseScripts/test.ipynb#X40sdnNjb2RlLXJlbW90ZQ%3D%3D?line=4'>5</a>\u001b[0m Ncount\u001b[39m.\u001b[39;49mplot(ax\u001b[39m=\u001b[39;49max)\n",
"File \u001b[1;32mD:\\Program Files\\Python\\Python38\\Lib\\site-packages\\xarray\\plot\\accessor.py:46\u001b[0m, in \u001b[0;36mDataArrayPlotAccessor.__call__\u001b[1;34m(self, **kwargs)\u001b[0m\n\u001b[0;32m 44\u001b[0m \u001b[39m@functools\u001b[39m\u001b[39m.\u001b[39mwraps(dataarray_plot\u001b[39m.\u001b[39mplot, assigned\u001b[39m=\u001b[39m(\u001b[39m\"\u001b[39m\u001b[39m__doc__\u001b[39m\u001b[39m\"\u001b[39m, \u001b[39m\"\u001b[39m\u001b[39m__annotations__\u001b[39m\u001b[39m\"\u001b[39m))\n\u001b[0;32m 45\u001b[0m \u001b[39mdef\u001b[39;00m \u001b[39m__call__\u001b[39m(\u001b[39mself\u001b[39m, \u001b[39m*\u001b[39m\u001b[39m*\u001b[39mkwargs) \u001b[39m-\u001b[39m\u001b[39m>\u001b[39m Any:\n\u001b[1;32m---> 46\u001b[0m \u001b[39mreturn\u001b[39;00m dataarray_plot\u001b[39m.\u001b[39;49mplot(\u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49m_da, \u001b[39m*\u001b[39;49m\u001b[39m*\u001b[39;49mkwargs)\n",
"File \u001b[1;32mD:\\Program Files\\Python\\Python38\\Lib\\site-packages\\xarray\\plot\\dataarray_plot.py:285\u001b[0m, in \u001b[0;36mplot\u001b[1;34m(darray, row, col, col_wrap, ax, hue, subplot_kws, **kwargs)\u001b[0m\n\u001b[0;32m 282\u001b[0m plotfunc: Callable\n\u001b[0;32m 284\u001b[0m \u001b[39mif\u001b[39;00m ndims \u001b[39m==\u001b[39m \u001b[39m0\u001b[39m \u001b[39mor\u001b[39;00m darray\u001b[39m.\u001b[39msize \u001b[39m==\u001b[39m \u001b[39m0\u001b[39m:\n\u001b[1;32m--> 285\u001b[0m \u001b[39mraise\u001b[39;00m \u001b[39mTypeError\u001b[39;00m(\u001b[39m\"\u001b[39m\u001b[39mNo numeric data to plot.\u001b[39m\u001b[39m\"\u001b[39m)\n\u001b[0;32m 286\u001b[0m \u001b[39mif\u001b[39;00m ndims \u001b[39min\u001b[39;00m (\u001b[39m1\u001b[39m, \u001b[39m2\u001b[39m):\n\u001b[0;32m 287\u001b[0m \u001b[39mif\u001b[39;00m row \u001b[39mor\u001b[39;00m col:\n",
"\u001b[1;31mTypeError\u001b[0m: No numeric data to plot."
]
},
bug fixing
2023-05-05 18:30:53 +02:00
{
"data": {
debug and nwe functions
2023-05-07 00:38:52 +02:00
"image/png": "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
not finish get_fit_result
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"text/plain": [
debug and nwe functions
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"<Figure size 432x288 with 1 Axes>"
not finish get_fit_result
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]
},
debug and nwe functions
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"metadata": {
"needs_background": "light"
},
"output_type": "display_data"
not finish get_fit_result
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}
],
finish of fitting
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"source": [
not finished
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"Ncount.load()\n",
"\n",
first working version
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"fig = plt.figure()\n",
not finished
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"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)"
finish reading from hdf5
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]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
finish of fitting
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"display_name": "env",
finish reading from hdf5
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"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",
not finish get_fit_result
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"version": "3.8.10"
finish reading from hdf5
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},
finish of fitting
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"orig_nbformat": 4,
"vscode": {
"interpreter": {
"hash": "c05913ad4f24fdc6b2418069394dc5835b1981849b107c9ba6df693aafd66650"
}
}
finish reading from hdf5
2023-04-24 13:03:23 +02:00
},
"nbformat": 4,
"nbformat_minor": 2
}
Reference in New Issue Copy Permalink