1341 lines
259 KiB
Plaintext
1341 lines
259 KiB
Plaintext
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{
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"cells": [
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"attachments": {},
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# How to read data from HFD5 files"
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]
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},
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"attachments": {},
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"This is an example to read the data from those HDF5 files generated by LabScript.\n",
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"\n",
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"The idea is that one just need to give\n",
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"\n",
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"+ The path where data is stored\n",
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"+ The date of the data\n",
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"+ The shot number\n",
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"+ The path of data in HDF5 file (i.e. the name of group)\n",
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"\n",
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"It can automatically find the scan axes, and package all of them into an object of DataSet() in xarray package.\n",
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"\n",
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"Let us start with importing the supporting packages. In order to keep things ealier, here we will import all the packages, but not all of them will be used."
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]
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},
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{
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"attachments": {},
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Import supporting packages"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 1,
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"metadata": {},
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"outputs": [],
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"source": [
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"import copy\n",
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"import glob\n",
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"from datetime import datetime\n",
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"\n",
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"# The package for data structure\n",
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"import xarray as xr\n",
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"import pandas as pd\n",
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"import numpy as np\n",
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"\n",
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"# The packages for working with uncertainties\n",
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"from uncertainties import ufloat\n",
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"from uncertainties import unumpy as unp\n",
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"from uncertainties import umath\n",
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"\n",
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"# The package for plotting\n",
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"import matplotlib.pyplot as plt\n",
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"plt.rcParams['font.size'] = 18 # Set the global font size\n",
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"\n",
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"# -------------- The modules written by us --------------\n",
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"\n",
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"# The packages for read data\n",
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"from DataContainer.ReadData import read_hdf5_file, read_hdf5_global, read_hdf5_run_time, read_csv_file\n",
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"\n",
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"# The packages for data analysis\n",
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"from Analyser.ImagingAnalyser import ImageAnalyser\n",
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"from Analyser.FitAnalyser import FitAnalyser\n",
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"from Analyser.FitAnalyser import ThomasFermi2dModel, DensityProfileBEC2dModel, Polylog22dModel\n",
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"from Analyser.FFTAnalyser import fft, ifft, fft_nutou\n",
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"from ToolFunction.ToolFunction import *\n",
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"\n",
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"# Add errorbar plot to xarray package\n",
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"from ToolFunction.HomeMadeXarrayFunction import errorbar, dataarray_plot_errorbar\n",
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"xr.plot.dataarray_plot.errorbar = errorbar\n",
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"xr.plot.accessor.DataArrayPlotAccessor.errorbar = dataarray_plot_errorbar"
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]
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},
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{
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"attachments": {},
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"If one wants to read tens or few hundreds files, a normal script can finish in several minutes."
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]
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},
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{
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"attachments": {},
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Start a client for parallel computing"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/html": [
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"<div>\n",
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" <div style=\"width: 24px; height: 24px; background-color: #e1e1e1; border: 3px solid #9D9D9D; border-radius: 5px; position: absolute;\"> </div>\n",
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" <div style=\"margin-left: 48px;\">\n",
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" <h3 style=\"margin-bottom: 0px;\">Client</h3>\n",
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" <p style=\"color: #9D9D9D; margin-bottom: 0px;\">Client-f3431762-0b91-11ee-bc80-80e82ce2fa8e</p>\n",
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" <table style=\"width: 100%; text-align: left;\">\n",
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"\n",
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" <tr>\n",
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" \n",
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" <td style=\"text-align: left;\"><strong>Connection method:</strong> Cluster object</td>\n",
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" <td style=\"text-align: left;\"><strong>Cluster type:</strong> distributed.LocalCluster</td>\n",
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" \n",
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" </tr>\n",
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"\n",
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" \n",
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" <tr>\n",
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" <td style=\"text-align: left;\">\n",
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" <strong>Dashboard: </strong> <a href=\"http://127.0.0.1:8787/status\" target=\"_blank\">http://127.0.0.1:8787/status</a>\n",
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" </td>\n",
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" <td style=\"text-align: left;\"></td>\n",
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" </tr>\n",
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" \n",
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"\n",
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" </table>\n",
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"\n",
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" \n",
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"\n",
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" \n",
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" <details>\n",
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" <summary style=\"margin-bottom: 20px;\"><h3 style=\"display: inline;\">Cluster Info</h3></summary>\n",
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" <div class=\"jp-RenderedHTMLCommon jp-RenderedHTML jp-mod-trusted jp-OutputArea-output\">\n",
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" <div style=\"width: 24px; height: 24px; background-color: #e1e1e1; border: 3px solid #9D9D9D; border-radius: 5px; position: absolute;\">\n",
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" </div>\n",
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" <div style=\"margin-left: 48px;\">\n",
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" <h3 style=\"margin-bottom: 0px; margin-top: 0px;\">LocalCluster</h3>\n",
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" <p style=\"color: #9D9D9D; margin-bottom: 0px;\">6e648e73</p>\n",
|
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" <table style=\"width: 100%; text-align: left;\">\n",
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" <tr>\n",
|
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" <td style=\"text-align: left;\">\n",
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" <strong>Dashboard:</strong> <a href=\"http://127.0.0.1:8787/status\" target=\"_blank\">http://127.0.0.1:8787/status</a>\n",
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" </td>\n",
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" <td style=\"text-align: left;\">\n",
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" <strong>Workers:</strong> 6\n",
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" </td>\n",
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" </tr>\n",
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" <tr>\n",
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" <td style=\"text-align: left;\">\n",
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" <strong>Total threads:</strong> 60\n",
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" </td>\n",
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" <td style=\"text-align: left;\">\n",
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" <strong>Total memory:</strong> 55.88 GiB\n",
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" </td>\n",
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" </tr>\n",
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" \n",
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" <tr>\n",
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" <td style=\"text-align: left;\"><strong>Status:</strong> running</td>\n",
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" <td style=\"text-align: left;\"><strong>Using processes:</strong> True</td>\n",
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"</tr>\n",
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"\n",
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" \n",
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" </table>\n",
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"\n",
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" <details>\n",
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" <summary style=\"margin-bottom: 20px;\">\n",
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" <h3 style=\"display: inline;\">Scheduler Info</h3>\n",
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" </summary>\n",
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"\n",
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" <div style=\"\">\n",
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" <div>\n",
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" <div style=\"width: 24px; height: 24px; background-color: #FFF7E5; border: 3px solid #FF6132; border-radius: 5px; position: absolute;\"> </div>\n",
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" <div style=\"margin-left: 48px;\">\n",
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" <h3 style=\"margin-bottom: 0px;\">Scheduler</h3>\n",
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" <p style=\"color: #9D9D9D; margin-bottom: 0px;\">Scheduler-669a9b65-bae9-4798-96b7-f5d552eb72f9</p>\n",
|
||
|
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" <table style=\"width: 100%; text-align: left;\">\n",
|
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|
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" <tr>\n",
|
||
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" <td style=\"text-align: left;\">\n",
|
||
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" <strong>Comm:</strong> tcp://127.0.0.1:51057\n",
|
||
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" </td>\n",
|
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" <td style=\"text-align: left;\">\n",
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" <strong>Workers:</strong> 6\n",
|
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|
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" </td>\n",
|
||
|
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" </tr>\n",
|
||
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" <tr>\n",
|
||
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" <td style=\"text-align: left;\">\n",
|
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" <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",
|
||
|
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" <td style=\"text-align: left;\">\n",
|
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" <strong>Total threads:</strong> 60\n",
|
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" </td>\n",
|
||
|
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" </tr>\n",
|
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" <tr>\n",
|
||
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" <td style=\"text-align: left;\">\n",
|
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" <strong>Started:</strong> Just now\n",
|
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" </td>\n",
|
||
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" <td style=\"text-align: left;\">\n",
|
||
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" <strong>Total memory:</strong> 55.88 GiB\n",
|
||
|
|
" </td>\n",
|
||
|
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" </tr>\n",
|
||
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" </table>\n",
|
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" </div>\n",
|
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|
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" </div>\n",
|
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"\n",
|
||
|
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" <details style=\"margin-left: 48px;\">\n",
|
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" <summary style=\"margin-bottom: 20px;\">\n",
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" <h3 style=\"display: inline;\">Workers</h3>\n",
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" </summary>\n",
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"\n",
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" \n",
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" <div style=\"margin-bottom: 20px;\">\n",
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" <div style=\"width: 24px; height: 24px; background-color: #DBF5FF; border: 3px solid #4CC9FF; border-radius: 5px; position: absolute;\"> </div>\n",
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" <div style=\"margin-left: 48px;\">\n",
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" <details>\n",
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" <summary>\n",
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" <h4 style=\"margin-bottom: 0px; display: inline;\">Worker: 0</h4>\n",
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" </summary>\n",
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" <table style=\"width: 100%; text-align: left;\">\n",
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" <tr>\n",
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" <td style=\"text-align: left;\">\n",
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" <strong>Comm: </strong> tcp://127.0.0.1:51088\n",
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" </td>\n",
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" <td style=\"text-align: left;\">\n",
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" <strong>Total threads: </strong> 10\n",
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" </td>\n",
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" </tr>\n",
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" <tr>\n",
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" <td style=\"text-align: left;\">\n",
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" <strong>Dashboard: </strong> <a href=\"http://127.0.0.1:51093/status\" target=\"_blank\">http://127.0.0.1:51093/status</a>\n",
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" </td>\n",
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" <td style=\"text-align: left;\">\n",
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" <strong>Memory: </strong> 9.31 GiB\n",
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" </td>\n",
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" </tr>\n",
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" <tr>\n",
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" <td style=\"text-align: left;\">\n",
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" <strong>Nanny: </strong> tcp://127.0.0.1:51060\n",
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" </td>\n",
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" <td style=\"text-align: left;\"></td>\n",
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" </tr>\n",
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" <tr>\n",
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" <td colspan=\"2\" style=\"text-align: left;\">\n",
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" <strong>Local directory: </strong> C:\\Users\\data\\AppData\\Local\\Temp\\dask-worker-space\\worker-9s507mc2\n",
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" </td>\n",
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" </tr>\n",
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"\n",
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" \n",
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"\n",
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" \n",
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"\n",
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" </table>\n",
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" </details>\n",
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" </div>\n",
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" </div>\n",
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" \n",
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" <div style=\"margin-bottom: 20px;\">\n",
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" <div style=\"width: 24px; height: 24px; background-color: #DBF5FF; border: 3px solid #4CC9FF; border-radius: 5px; position: absolute;\"> </div>\n",
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" <div style=\"margin-left: 48px;\">\n",
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" <details>\n",
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|
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" <summary>\n",
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" <h4 style=\"margin-bottom: 0px; display: inline;\">Worker: 1</h4>\n",
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" </summary>\n",
|
||
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" <table style=\"width: 100%; text-align: left;\">\n",
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" <tr>\n",
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" <td style=\"text-align: left;\">\n",
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" <strong>Comm: </strong> tcp://127.0.0.1:51084\n",
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" </td>\n",
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" <td style=\"text-align: left;\">\n",
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" <strong>Total threads: </strong> 10\n",
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" </td>\n",
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" </tr>\n",
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" <tr>\n",
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" <td style=\"text-align: left;\">\n",
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" <strong>Dashboard: </strong> <a href=\"http://127.0.0.1:51085/status\" target=\"_blank\">http://127.0.0.1:51085/status</a>\n",
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" </td>\n",
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" <td style=\"text-align: left;\">\n",
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" <strong>Memory: </strong> 9.31 GiB\n",
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" </td>\n",
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" </tr>\n",
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" <tr>\n",
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" <td style=\"text-align: left;\">\n",
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" <strong>Nanny: </strong> tcp://127.0.0.1:51061\n",
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||
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" </td>\n",
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||
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" <td style=\"text-align: left;\"></td>\n",
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" </tr>\n",
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" <tr>\n",
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" <td colspan=\"2\" style=\"text-align: left;\">\n",
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" <strong>Local directory: </strong> C:\\Users\\data\\AppData\\Local\\Temp\\dask-worker-space\\worker-y5skkt4c\n",
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" </td>\n",
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" </tr>\n",
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"\n",
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" \n",
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"\n",
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" \n",
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"\n",
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" </table>\n",
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" </details>\n",
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" </div>\n",
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" </div>\n",
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" \n",
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" <div style=\"margin-bottom: 20px;\">\n",
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" <div style=\"width: 24px; height: 24px; background-color: #DBF5FF; border: 3px solid #4CC9FF; border-radius: 5px; position: absolute;\"> </div>\n",
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" <div style=\"margin-left: 48px;\">\n",
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" <details>\n",
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||
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" <summary>\n",
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" <h4 style=\"margin-bottom: 0px; display: inline;\">Worker: 2</h4>\n",
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" </summary>\n",
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" <table style=\"width: 100%; text-align: left;\">\n",
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" <tr>\n",
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" <td style=\"text-align: left;\">\n",
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" <strong>Comm: </strong> tcp://127.0.0.1:51098\n",
|
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" </td>\n",
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" <td style=\"text-align: left;\">\n",
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" <strong>Total threads: </strong> 10\n",
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" </td>\n",
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" </tr>\n",
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|
|
" <tr>\n",
|
||
|
|
" <td style=\"text-align: left;\">\n",
|
||
|
|
" <strong>Dashboard: </strong> <a href=\"http://127.0.0.1:51100/status\" target=\"_blank\">http://127.0.0.1:51100/status</a>\n",
|
||
|
|
" </td>\n",
|
||
|
|
" <td style=\"text-align: left;\">\n",
|
||
|
|
" <strong>Memory: </strong> 9.31 GiB\n",
|
||
|
|
" </td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <td style=\"text-align: left;\">\n",
|
||
|
|
" <strong>Nanny: </strong> tcp://127.0.0.1:51062\n",
|
||
|
|
" </td>\n",
|
||
|
|
" <td style=\"text-align: left;\"></td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <td colspan=\"2\" style=\"text-align: left;\">\n",
|
||
|
|
" <strong>Local directory: </strong> C:\\Users\\data\\AppData\\Local\\Temp\\dask-worker-space\\worker-gmddkxg0\n",
|
||
|
|
" </td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
"\n",
|
||
|
|
" \n",
|
||
|
|
"\n",
|
||
|
|
" \n",
|
||
|
|
"\n",
|
||
|
|
" </table>\n",
|
||
|
|
" </details>\n",
|
||
|
|
" </div>\n",
|
||
|
|
" </div>\n",
|
||
|
|
" \n",
|
||
|
|
" <div style=\"margin-bottom: 20px;\">\n",
|
||
|
|
" <div style=\"width: 24px; height: 24px; background-color: #DBF5FF; border: 3px solid #4CC9FF; border-radius: 5px; position: absolute;\"> </div>\n",
|
||
|
|
" <div style=\"margin-left: 48px;\">\n",
|
||
|
|
" <details>\n",
|
||
|
|
" <summary>\n",
|
||
|
|
" <h4 style=\"margin-bottom: 0px; display: inline;\">Worker: 3</h4>\n",
|
||
|
|
" </summary>\n",
|
||
|
|
" <table style=\"width: 100%; text-align: left;\">\n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <td style=\"text-align: left;\">\n",
|
||
|
|
" <strong>Comm: </strong> tcp://127.0.0.1:51095\n",
|
||
|
|
" </td>\n",
|
||
|
|
" <td style=\"text-align: left;\">\n",
|
||
|
|
" <strong>Total threads: </strong> 10\n",
|
||
|
|
" </td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <td style=\"text-align: left;\">\n",
|
||
|
|
" <strong>Dashboard: </strong> <a href=\"http://127.0.0.1:51096/status\" target=\"_blank\">http://127.0.0.1:51096/status</a>\n",
|
||
|
|
" </td>\n",
|
||
|
|
" <td style=\"text-align: left;\">\n",
|
||
|
|
" <strong>Memory: </strong> 9.31 GiB\n",
|
||
|
|
" </td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <td style=\"text-align: left;\">\n",
|
||
|
|
" <strong>Nanny: </strong> tcp://127.0.0.1:51063\n",
|
||
|
|
" </td>\n",
|
||
|
|
" <td style=\"text-align: left;\"></td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <td colspan=\"2\" style=\"text-align: left;\">\n",
|
||
|
|
" <strong>Local directory: </strong> C:\\Users\\data\\AppData\\Local\\Temp\\dask-worker-space\\worker-oycines6\n",
|
||
|
|
" </td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
"\n",
|
||
|
|
" \n",
|
||
|
|
"\n",
|
||
|
|
" \n",
|
||
|
|
"\n",
|
||
|
|
" </table>\n",
|
||
|
|
" </details>\n",
|
||
|
|
" </div>\n",
|
||
|
|
" </div>\n",
|
||
|
|
" \n",
|
||
|
|
" <div style=\"margin-bottom: 20px;\">\n",
|
||
|
|
" <div style=\"width: 24px; height: 24px; background-color: #DBF5FF; border: 3px solid #4CC9FF; border-radius: 5px; position: absolute;\"> </div>\n",
|
||
|
|
" <div style=\"margin-left: 48px;\">\n",
|
||
|
|
" <details>\n",
|
||
|
|
" <summary>\n",
|
||
|
|
" <h4 style=\"margin-bottom: 0px; display: inline;\">Worker: 4</h4>\n",
|
||
|
|
" </summary>\n",
|
||
|
|
" <table style=\"width: 100%; text-align: left;\">\n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <td style=\"text-align: left;\">\n",
|
||
|
|
" <strong>Comm: </strong> tcp://127.0.0.1:51087\n",
|
||
|
|
" </td>\n",
|
||
|
|
" <td style=\"text-align: left;\">\n",
|
||
|
|
" <strong>Total threads: </strong> 10\n",
|
||
|
|
" </td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <td style=\"text-align: left;\">\n",
|
||
|
|
" <strong>Dashboard: </strong> <a href=\"http://127.0.0.1:51091/status\" target=\"_blank\">http://127.0.0.1:51091/status</a>\n",
|
||
|
|
" </td>\n",
|
||
|
|
" <td style=\"text-align: left;\">\n",
|
||
|
|
" <strong>Memory: </strong> 9.31 GiB\n",
|
||
|
|
" </td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <td style=\"text-align: left;\">\n",
|
||
|
|
" <strong>Nanny: </strong> tcp://127.0.0.1:51064\n",
|
||
|
|
" </td>\n",
|
||
|
|
" <td style=\"text-align: left;\"></td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <td colspan=\"2\" style=\"text-align: left;\">\n",
|
||
|
|
" <strong>Local directory: </strong> C:\\Users\\data\\AppData\\Local\\Temp\\dask-worker-space\\worker-a8kpxp6o\n",
|
||
|
|
" </td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
"\n",
|
||
|
|
" \n",
|
||
|
|
"\n",
|
||
|
|
" \n",
|
||
|
|
"\n",
|
||
|
|
" </table>\n",
|
||
|
|
" </details>\n",
|
||
|
|
" </div>\n",
|
||
|
|
" </div>\n",
|
||
|
|
" \n",
|
||
|
|
" <div style=\"margin-bottom: 20px;\">\n",
|
||
|
|
" <div style=\"width: 24px; height: 24px; background-color: #DBF5FF; border: 3px solid #4CC9FF; border-radius: 5px; position: absolute;\"> </div>\n",
|
||
|
|
" <div style=\"margin-left: 48px;\">\n",
|
||
|
|
" <details>\n",
|
||
|
|
" <summary>\n",
|
||
|
|
" <h4 style=\"margin-bottom: 0px; display: inline;\">Worker: 5</h4>\n",
|
||
|
|
" </summary>\n",
|
||
|
|
" <table style=\"width: 100%; text-align: left;\">\n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <td style=\"text-align: left;\">\n",
|
||
|
|
" <strong>Comm: </strong> tcp://127.0.0.1:51099\n",
|
||
|
|
" </td>\n",
|
||
|
|
" <td style=\"text-align: left;\">\n",
|
||
|
|
" <strong>Total threads: </strong> 10\n",
|
||
|
|
" </td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <td style=\"text-align: left;\">\n",
|
||
|
|
" <strong>Dashboard: </strong> <a href=\"http://127.0.0.1:51101/status\" target=\"_blank\">http://127.0.0.1:51101/status</a>\n",
|
||
|
|
" </td>\n",
|
||
|
|
" <td style=\"text-align: left;\">\n",
|
||
|
|
" <strong>Memory: </strong> 9.31 GiB\n",
|
||
|
|
" </td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <td style=\"text-align: left;\">\n",
|
||
|
|
" <strong>Nanny: </strong> tcp://127.0.0.1:51065\n",
|
||
|
|
" </td>\n",
|
||
|
|
" <td style=\"text-align: left;\"></td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <td colspan=\"2\" style=\"text-align: left;\">\n",
|
||
|
|
" <strong>Local directory: </strong> C:\\Users\\data\\AppData\\Local\\Temp\\dask-worker-space\\worker-thoxr07z\n",
|
||
|
|
" </td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
"\n",
|
||
|
|
" \n",
|
||
|
|
"\n",
|
||
|
|
" \n",
|
||
|
|
"\n",
|
||
|
|
" </table>\n",
|
||
|
|
" </details>\n",
|
||
|
|
" </div>\n",
|
||
|
|
" </div>\n",
|
||
|
|
" \n",
|
||
|
|
"\n",
|
||
|
|
" </details>\n",
|
||
|
|
"</div>\n",
|
||
|
|
"\n",
|
||
|
|
" </details>\n",
|
||
|
|
" </div>\n",
|
||
|
|
"</div>\n",
|
||
|
|
" </details>\n",
|
||
|
|
" \n",
|
||
|
|
"\n",
|
||
|
|
" </div>\n",
|
||
|
|
"</div>"
|
||
|
|
],
|
||
|
|
"text/plain": [
|
||
|
|
"<Client: 'tcp://127.0.0.1:51057' processes=6 threads=60, memory=55.88 GiB>"
|
||
|
|
]
|
||
|
|
},
|
||
|
|
"metadata": {},
|
||
|
|
"output_type": "display_data"
|
||
|
|
}
|
||
|
|
],
|
||
|
|
"source": [
|
||
|
|
"from dask.distributed import Client\n",
|
||
|
|
"client = Client(n_workers=6, threads_per_worker=10, processes=True, memory_limit='10GB')\n",
|
||
|
|
"client"
|
||
|
|
]
|
||
|
|
},
|
||
|
|
{
|
||
|
|
"cell_type": "code",
|
||
|
|
"execution_count": null,
|
||
|
|
"metadata": {},
|
||
|
|
"outputs": [],
|
||
|
|
"source": [
|
||
|
|
"imageAnalyser = ImageAnalyser()"
|
||
|
|
]
|
||
|
|
},
|
||
|
|
{
|
||
|
|
"attachments": {},
|
||
|
|
"cell_type": "markdown",
|
||
|
|
"metadata": {},
|
||
|
|
"source": [
|
||
|
|
"## Set global path for experiment"
|
||
|
|
]
|
||
|
|
},
|
||
|
|
{
|
||
|
|
"cell_type": "code",
|
||
|
|
"execution_count": 68,
|
||
|
|
"metadata": {},
|
||
|
|
"outputs": [],
|
||
|
|
"source": [
|
||
|
|
"# filepath = \"//DyLabNAS/Data/Evaporative_Cooling/2023/05/03/0043/*.h5\"\n",
|
||
|
|
"# filepath = \"//DyLabNAS/Data/Evaporative_Cooling/2023/04/18/0003/2023-04-18_0003_Evaporative_Cooling_000.h5\"\n",
|
||
|
|
"\n",
|
||
|
|
"# filepath = \"//DyLabNAS/Data/Repetition_scan/2023/04/21/0002/*.h5\"\n",
|
||
|
|
"\n",
|
||
|
|
"# filepath = r\"./testData/0002/*.h5\"\n",
|
||
|
|
"\n",
|
||
|
|
"# filepath = r\"./testData/0002/2023-04-21_0002_Evaporative_Cooling_0.h5\"\n",
|
||
|
|
"\n",
|
||
|
|
"# filepath = r'd:/Jianshun Gao/Simulations/analyseScripts/testData/0002/2023-04-21_0002_Evaporative_Cooling_0.h5'\n",
|
||
|
|
"\n",
|
||
|
|
"# filepath = \"//DyLabNAS/Data/Evaporative_Cooling/2023/04/18/0003/*.h5\"\n",
|
||
|
|
"\n",
|
||
|
|
"filepath = \"//DyLabNAS/Data/Evaporative_Cooling/2023/05/04/0000/*.h5\"\n",
|
||
|
|
"\n",
|
||
|
|
"# filepath = './result_from_experiment/2023-04-24/0013/2023-04-24_0013_Evaporative_Cooling_13.h5'"
|
||
|
|
]
|
||
|
|
},
|
||
|
|
{
|
||
|
|
"cell_type": "code",
|
||
|
|
"execution_count": 69,
|
||
|
|
"metadata": {},
|
||
|
|
"outputs": [],
|
||
|
|
"source": [
|
||
|
|
"groupList = [\n",
|
||
|
|
" \"images/MOT_3D_Camera/in_situ_absorption\",\n",
|
||
|
|
" \"images/ODT_1_Axis_Camera/in_situ_absorption\",\n",
|
||
|
|
" \"images/ODT_2_Axis_Camera/in_situ_absorption\",\n",
|
||
|
|
"]\n",
|
||
|
|
"\n",
|
||
|
|
"dskey = {\n",
|
||
|
|
" \"images/MOT_3D_Camera/in_situ_absorption\": \"camera_1\",\n",
|
||
|
|
" \"images/ODT_1_Axis_Camera/in_situ_absorption\": \"camera_2\",\n",
|
||
|
|
" \"images/ODT_2_Axis_Camera/in_situ_absorption\": \"camera_3\",\n",
|
||
|
|
"}\n"
|
||
|
|
]
|
||
|
|
},
|
||
|
|
{
|
||
|
|
"cell_type": "code",
|
||
|
|
"execution_count": 70,
|
||
|
|
"metadata": {},
|
||
|
|
"outputs": [],
|
||
|
|
"source": [
|
||
|
|
"img_dir = '//DyLabNAS/Data/'\n",
|
||
|
|
"SequenceName = \"Evaporative_Cooling\" + \"/\"\n",
|
||
|
|
"folderPath = img_dir + SequenceName + '2023/05/23'# get_date()"
|
||
|
|
]
|
||
|
|
},
|
||
|
|
{
|
||
|
|
"attachments": {},
|
||
|
|
"cell_type": "markdown",
|
||
|
|
"metadata": {},
|
||
|
|
"source": [
|
||
|
|
"# An example for one experimental run"
|
||
|
|
]
|
||
|
|
},
|
||
|
|
{
|
||
|
|
"attachments": {},
|
||
|
|
"cell_type": "markdown",
|
||
|
|
"metadata": {},
|
||
|
|
"source": [
|
||
|
|
"## Load the data"
|
||
|
|
]
|
||
|
|
},
|
||
|
|
{
|
||
|
|
"cell_type": "code",
|
||
|
|
"execution_count": 75,
|
||
|
|
"metadata": {},
|
||
|
|
"outputs": [
|
||
|
|
{
|
||
|
|
"name": "stderr",
|
||
|
|
"output_type": "stream",
|
||
|
|
"text": [
|
||
|
|
"f:\\Jianshun\\analyseScript\\DataContainer\\ReadData.py:178: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison\n",
|
||
|
|
" if not key in datesetOfGlobal.scanAxis\n"
|
||
|
|
]
|
||
|
|
},
|
||
|
|
{
|
||
|
|
"data": {
|
||
|
|
"text/html": [
|
||
|
|
"<div><svg style=\"position: absolute; width: 0; height: 0; overflow: hidden\">\n",
|
||
|
|
"<defs>\n",
|
||
|
|
"<symbol id=\"icon-database\" viewBox=\"0 0 32 32\">\n",
|
||
|
|
"<path d=\"M16 0c-8.837 0-16 2.239-16 5v4c0 2.761 7.163 5 16 5s16-2.239 16-5v-4c0-2.761-7.163-5-16-5z\"></path>\n",
|
||
|
|
"<path d=\"M16 17c-8.837 0-16-2.239-16-5v6c0 2.761 7.163 5 16 5s16-2.239 16-5v-6c0 2.761-7.163 5-16 5z\"></path>\n",
|
||
|
|
"<path d=\"M16 26c-8.837 0-16-2.239-16-5v6c0 2.761 7.163 5 16 5s16-2.239 16-5v-6c0 2.761-7.163 5-16 5z\"></path>\n",
|
||
|
|
"</symbol>\n",
|
||
|
|
"<symbol id=\"icon-file-text2\" viewBox=\"0 0 32 32\">\n",
|
||
|
|
"<path d=\"M28.681 7.159c-0.694-0.947-1.662-2.053-2.724-3.116s-2.169-2.030-3.116-2.724c-1.612-1.182-2.393-1.319-2.841-1.319h-15.5c-1.378 0-2.5 1.121-2.5 2.5v27c0 1.378 1.122 2.5 2.5 2.5h23c1.378 0 2.5-1.122 2.5-2.5v-19.5c0-0.448-0.137-1.23-1.319-2.841zM24.543 5.457c0.959 0.959 1.712 1.825 2.268 2.543h-4.811v-4.811c0.718 0.556 1.584 1.309 2.543 2.268zM28 29.5c0 0.271-0.229 0.5-0.5 0.5h-23c-0.271 0-0.5-0.229-0.5-0.5v-27c0-0.271 0.229-0.5 0.5-0.5 0 0 15.499-0 15.5 0v7c0 0.552 0.448 1 1 1h7v19.5z\"></path>\n",
|
||
|
|
"<path d=\"M23 26h-14c-0.552 0-1-0.448-1-1s0.448-1 1-1h14c0.552 0 1 0.448 1 1s-0.448 1-1 1z\"></path>\n",
|
||
|
|
"<path d=\"M23 22h-14c-0.552 0-1-0.448-1-1s0.448-1 1-1h14c0.552 0 1 0.448 1 1s-0.448 1-1 1z\"></path>\n",
|
||
|
|
"<path d=\"M23 18h-14c-0.552 0-1-0.448-1-1s0.448-1 1-1h14c0.552 0 1 0.448 1 1s-0.448 1-1 1z\"></path>\n",
|
||
|
|
"</symbol>\n",
|
||
|
|
"</defs>\n",
|
||
|
|
"</svg>\n",
|
||
|
|
"<style>/* CSS stylesheet for displaying xarray objects in jupyterlab.\n",
|
||
|
|
" *\n",
|
||
|
|
" */\n",
|
||
|
|
"\n",
|
||
|
|
":root {\n",
|
||
|
|
" --xr-font-color0: var(--jp-content-font-color0, rgba(0, 0, 0, 1));\n",
|
||
|
|
" --xr-font-color2: var(--jp-content-font-color2, rgba(0, 0, 0, 0.54));\n",
|
||
|
|
" --xr-font-color3: var(--jp-content-font-color3, rgba(0, 0, 0, 0.38));\n",
|
||
|
|
" --xr-border-color: var(--jp-border-color2, #e0e0e0);\n",
|
||
|
|
" --xr-disabled-color: var(--jp-layout-color3, #bdbdbd);\n",
|
||
|
|
" --xr-background-color: var(--jp-layout-color0, white);\n",
|
||
|
|
" --xr-background-color-row-even: var(--jp-layout-color1, white);\n",
|
||
|
|
" --xr-background-color-row-odd: var(--jp-layout-color2, #eeeeee);\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
"html[theme=dark],\n",
|
||
|
|
"body[data-theme=dark],\n",
|
||
|
|
"body.vscode-dark {\n",
|
||
|
|
" --xr-font-color0: rgba(255, 255, 255, 1);\n",
|
||
|
|
" --xr-font-color2: rgba(255, 255, 255, 0.54);\n",
|
||
|
|
" --xr-font-color3: rgba(255, 255, 255, 0.38);\n",
|
||
|
|
" --xr-border-color: #1F1F1F;\n",
|
||
|
|
" --xr-disabled-color: #515151;\n",
|
||
|
|
" --xr-background-color: #111111;\n",
|
||
|
|
" --xr-background-color-row-even: #111111;\n",
|
||
|
|
" --xr-background-color-row-odd: #313131;\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-wrap {\n",
|
||
|
|
" display: block !important;\n",
|
||
|
|
" min-width: 300px;\n",
|
||
|
|
" max-width: 700px;\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-text-repr-fallback {\n",
|
||
|
|
" /* fallback to plain text repr when CSS is not injected (untrusted notebook) */\n",
|
||
|
|
" display: none;\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-header {\n",
|
||
|
|
" padding-top: 6px;\n",
|
||
|
|
" padding-bottom: 6px;\n",
|
||
|
|
" margin-bottom: 4px;\n",
|
||
|
|
" border-bottom: solid 1px var(--xr-border-color);\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-header > div,\n",
|
||
|
|
".xr-header > ul {\n",
|
||
|
|
" display: inline;\n",
|
||
|
|
" margin-top: 0;\n",
|
||
|
|
" margin-bottom: 0;\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-obj-type,\n",
|
||
|
|
".xr-array-name {\n",
|
||
|
|
" margin-left: 2px;\n",
|
||
|
|
" margin-right: 10px;\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-obj-type {\n",
|
||
|
|
" color: var(--xr-font-color2);\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-sections {\n",
|
||
|
|
" padding-left: 0 !important;\n",
|
||
|
|
" display: grid;\n",
|
||
|
|
" grid-template-columns: 150px auto auto 1fr 20px 20px;\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-section-item {\n",
|
||
|
|
" display: contents;\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-section-item input {\n",
|
||
|
|
" display: none;\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-section-item input + label {\n",
|
||
|
|
" color: var(--xr-disabled-color);\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-section-item input:enabled + label {\n",
|
||
|
|
" cursor: pointer;\n",
|
||
|
|
" color: var(--xr-font-color2);\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-section-item input:enabled + label:hover {\n",
|
||
|
|
" color: var(--xr-font-color0);\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-section-summary {\n",
|
||
|
|
" grid-column: 1;\n",
|
||
|
|
" color: var(--xr-font-color2);\n",
|
||
|
|
" font-weight: 500;\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-section-summary > span {\n",
|
||
|
|
" display: inline-block;\n",
|
||
|
|
" padding-left: 0.5em;\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-section-summary-in:disabled + label {\n",
|
||
|
|
" color: var(--xr-font-color2);\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-section-summary-in + label:before {\n",
|
||
|
|
" display: inline-block;\n",
|
||
|
|
" content: 'â–º';\n",
|
||
|
|
" font-size: 11px;\n",
|
||
|
|
" width: 15px;\n",
|
||
|
|
" text-align: center;\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-section-summary-in:disabled + label:before {\n",
|
||
|
|
" color: var(--xr-disabled-color);\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-section-summary-in:checked + label:before {\n",
|
||
|
|
" content: 'â–¼';\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-section-summary-in:checked + label > span {\n",
|
||
|
|
" display: none;\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-section-summary,\n",
|
||
|
|
".xr-section-inline-details {\n",
|
||
|
|
" padding-top: 4px;\n",
|
||
|
|
" padding-bottom: 4px;\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-section-inline-details {\n",
|
||
|
|
" grid-column: 2 / -1;\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-section-details {\n",
|
||
|
|
" display: none;\n",
|
||
|
|
" grid-column: 1 / -1;\n",
|
||
|
|
" margin-bottom: 5px;\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-section-summary-in:checked ~ .xr-section-details {\n",
|
||
|
|
" display: contents;\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-array-wrap {\n",
|
||
|
|
" grid-column: 1 / -1;\n",
|
||
|
|
" display: grid;\n",
|
||
|
|
" grid-template-columns: 20px auto;\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-array-wrap > label {\n",
|
||
|
|
" grid-column: 1;\n",
|
||
|
|
" vertical-align: top;\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-preview {\n",
|
||
|
|
" color: var(--xr-font-color3);\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-array-preview,\n",
|
||
|
|
".xr-array-data {\n",
|
||
|
|
" padding: 0 5px !important;\n",
|
||
|
|
" grid-column: 2;\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-array-data,\n",
|
||
|
|
".xr-array-in:checked ~ .xr-array-preview {\n",
|
||
|
|
" display: none;\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-array-in:checked ~ .xr-array-data,\n",
|
||
|
|
".xr-array-preview {\n",
|
||
|
|
" display: inline-block;\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-dim-list {\n",
|
||
|
|
" display: inline-block !important;\n",
|
||
|
|
" list-style: none;\n",
|
||
|
|
" padding: 0 !important;\n",
|
||
|
|
" margin: 0;\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-dim-list li {\n",
|
||
|
|
" display: inline-block;\n",
|
||
|
|
" padding: 0;\n",
|
||
|
|
" margin: 0;\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-dim-list:before {\n",
|
||
|
|
" content: '(';\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-dim-list:after {\n",
|
||
|
|
" content: ')';\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-dim-list li:not(:last-child):after {\n",
|
||
|
|
" content: ',';\n",
|
||
|
|
" padding-right: 5px;\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-has-index {\n",
|
||
|
|
" font-weight: bold;\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-var-list,\n",
|
||
|
|
".xr-var-item {\n",
|
||
|
|
" display: contents;\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-var-item > div,\n",
|
||
|
|
".xr-var-item label,\n",
|
||
|
|
".xr-var-item > .xr-var-name span {\n",
|
||
|
|
" background-color: var(--xr-background-color-row-even);\n",
|
||
|
|
" margin-bottom: 0;\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-var-item > .xr-var-name:hover span {\n",
|
||
|
|
" padding-right: 5px;\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-var-list > li:nth-child(odd) > div,\n",
|
||
|
|
".xr-var-list > li:nth-child(odd) > label,\n",
|
||
|
|
".xr-var-list > li:nth-child(odd) > .xr-var-name span {\n",
|
||
|
|
" background-color: var(--xr-background-color-row-odd);\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-var-name {\n",
|
||
|
|
" grid-column: 1;\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-var-dims {\n",
|
||
|
|
" grid-column: 2;\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-var-dtype {\n",
|
||
|
|
" grid-column: 3;\n",
|
||
|
|
" text-align: right;\n",
|
||
|
|
" color: var(--xr-font-color2);\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-var-preview {\n",
|
||
|
|
" grid-column: 4;\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-index-preview {\n",
|
||
|
|
" grid-column: 2 / 5;\n",
|
||
|
|
" color: var(--xr-font-color2);\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-var-name,\n",
|
||
|
|
".xr-var-dims,\n",
|
||
|
|
".xr-var-dtype,\n",
|
||
|
|
".xr-preview,\n",
|
||
|
|
".xr-attrs dt {\n",
|
||
|
|
" white-space: nowrap;\n",
|
||
|
|
" overflow: hidden;\n",
|
||
|
|
" text-overflow: ellipsis;\n",
|
||
|
|
" padding-right: 10px;\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-var-name:hover,\n",
|
||
|
|
".xr-var-dims:hover,\n",
|
||
|
|
".xr-var-dtype:hover,\n",
|
||
|
|
".xr-attrs dt:hover {\n",
|
||
|
|
" overflow: visible;\n",
|
||
|
|
" width: auto;\n",
|
||
|
|
" z-index: 1;\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-var-attrs,\n",
|
||
|
|
".xr-var-data,\n",
|
||
|
|
".xr-index-data {\n",
|
||
|
|
" display: none;\n",
|
||
|
|
" background-color: var(--xr-background-color) !important;\n",
|
||
|
|
" padding-bottom: 5px !important;\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-var-attrs-in:checked ~ .xr-var-attrs,\n",
|
||
|
|
".xr-var-data-in:checked ~ .xr-var-data,\n",
|
||
|
|
".xr-index-data-in:checked ~ .xr-index-data {\n",
|
||
|
|
" display: block;\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-var-data > table {\n",
|
||
|
|
" float: right;\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-var-name span,\n",
|
||
|
|
".xr-var-data,\n",
|
||
|
|
".xr-index-name div,\n",
|
||
|
|
".xr-index-data,\n",
|
||
|
|
".xr-attrs {\n",
|
||
|
|
" padding-left: 25px !important;\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-attrs,\n",
|
||
|
|
".xr-var-attrs,\n",
|
||
|
|
".xr-var-data,\n",
|
||
|
|
".xr-index-data {\n",
|
||
|
|
" grid-column: 1 / -1;\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
"dl.xr-attrs {\n",
|
||
|
|
" padding: 0;\n",
|
||
|
|
" margin: 0;\n",
|
||
|
|
" display: grid;\n",
|
||
|
|
" grid-template-columns: 125px auto;\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-attrs dt,\n",
|
||
|
|
".xr-attrs dd {\n",
|
||
|
|
" padding: 0;\n",
|
||
|
|
" margin: 0;\n",
|
||
|
|
" float: left;\n",
|
||
|
|
" padding-right: 10px;\n",
|
||
|
|
" width: auto;\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-attrs dt {\n",
|
||
|
|
" font-weight: normal;\n",
|
||
|
|
" grid-column: 1;\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-attrs dt:hover span {\n",
|
||
|
|
" display: inline-block;\n",
|
||
|
|
" background: var(--xr-background-color);\n",
|
||
|
|
" padding-right: 10px;\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-attrs dd {\n",
|
||
|
|
" grid-column: 2;\n",
|
||
|
|
" white-space: pre-wrap;\n",
|
||
|
|
" word-break: break-all;\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
".xr-icon-database,\n",
|
||
|
|
".xr-icon-file-text2,\n",
|
||
|
|
".xr-no-icon {\n",
|
||
|
|
" display: inline-block;\n",
|
||
|
|
" vertical-align: middle;\n",
|
||
|
|
" width: 1em;\n",
|
||
|
|
" height: 1.5em !important;\n",
|
||
|
|
" stroke-width: 0;\n",
|
||
|
|
" stroke: currentColor;\n",
|
||
|
|
" fill: currentColor;\n",
|
||
|
|
"}\n",
|
||
|
|
"</style><pre class='xr-text-repr-fallback'><xarray.Dataset>\n",
|
||
|
|
"Dimensions: (y: 1200, x: 1920)\n",
|
||
|
|
"Dimensions without coordinates: y, x\n",
|
||
|
|
"Data variables:\n",
|
||
|
|
" atoms (y, x) uint16 dask.array<chunksize=(1200, 1920), meta=np.ndarray>\n",
|
||
|
|
" background (y, x) uint16 dask.array<chunksize=(1200, 1920), meta=np.ndarray>\n",
|
||
|
|
" dark (y, x) uint16 dask.array<chunksize=(1200, 1920), meta=np.ndarray>\n",
|
||
|
|
" shotNum <U2 '11'\n",
|
||
|
|
" OD (y, x) float64 dask.array<chunksize=(1200, 1920), meta=np.ndarray>\n",
|
||
|
|
"Attributes: (12/96)\n",
|
||
|
|
" TOF_free: 0.02\n",
|
||
|
|
" abs_img_freq: 110.858\n",
|
||
|
|
" absorption_imaging_flag: True\n",
|
||
|
|
" backup_data: True\n",
|
||
|
|
" blink_off_time: nan\n",
|
||
|
|
" blink_on_time: nan\n",
|
||
|
|
" ... ...\n",
|
||
|
|
" y_offset: 0\n",
|
||
|
|
" y_offset_img: 0\n",
|
||
|
|
" z_offset: 0.189\n",
|
||
|
|
" z_offset_img: 0.189\n",
|
||
|
|
" scanAxis: []\n",
|
||
|
|
" scanAxisLength: []</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-3f6a2152-ef01-4819-91f5-a47fe1a85483' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-3f6a2152-ef01-4819-91f5-a47fe1a85483' class='xr-section-summary' title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span>y</span>: 1200</li><li><span>x</span>: 1920</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-71114a49-5445-43f4-a531-d6bdc6ba83e9' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-71114a49-5445-43f4-a531-d6bdc6ba83e9' class='xr-section-summary' title='Expand/collapse section'>Coordinates: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-87511f20-517f-4220-90f4-f268366d6d73' class='xr-section-summary-in' type='checkbox' checked><label for='section-87511f20-517f-4220-90f4-f268366d6d73' class='xr-section-summary' >Data variables: <span>(5)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>atoms</span></div><div class='xr-var-dims'>(y, x)</div><div class='xr-var-dtype'>uint16</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(1200, 1920), meta=np.ndarray></div><input id='attrs-81526946-1703-4ca5-8e13-3fc13c175996' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-81526946-1703-4ca5-8e13-3fc13c175996' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-77f2b9fc-57a9-4fc9-bcb9-7283191c0038' class='xr-var-data-in' type='checkbox'><label for='data-77f2b9fc-57a9-4fc9-bcb9-7283191c0038' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>IMAGE_SUBCLASS :</span></dt><dd>IMAGE_GRAYSCALE</dd><dt><span>IMAGE_VERSION :</span></dt><dd>1.2</dd><dt><span>IMAGE_WHITE_IS_ZERO :</span></dt><dd>0</dd></dl></div><div class='xr-var-data'><table>\n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <td>\n",
|
||
|
|
" <table style=\"border-collapse: collapse;\">\n",
|
||
|
|
" <thead>\n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <td> </td>\n",
|
||
|
|
" <th> Array </th>\n",
|
||
|
|
" <th> Chunk </th>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" </thead>\n",
|
||
|
|
" <tbody>\n",
|
||
|
|
" \n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <th> Bytes </th>\n",
|
||
|
|
" <td> 4.39 MiB </td>\n",
|
||
|
|
" <td> 4.39 MiB </td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" \n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <th> Shape </th>\n",
|
||
|
|
" <td> (1200, 1920) </td>\n",
|
||
|
|
" <td> (1200, 1920) </td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <th> Dask graph </th>\n",
|
||
|
|
" <td colspan=\"2\"> 1 chunks in 2 graph layers </td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <th> Data type </th>\n",
|
||
|
|
" <td colspan=\"2\"> uint16 numpy.ndarray </td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" </tbody>\n",
|
||
|
|
" </table>\n",
|
||
|
|
" </td>\n",
|
||
|
|
" <td>\n",
|
||
|
|
" <svg width=\"170\" height=\"125\" style=\"stroke:rgb(0,0,0);stroke-width:1\" >\n",
|
||
|
|
"\n",
|
||
|
|
" <!-- Horizontal lines -->\n",
|
||
|
|
" <line x1=\"0\" y1=\"0\" x2=\"120\" y2=\"0\" style=\"stroke-width:2\" />\n",
|
||
|
|
" <line x1=\"0\" y1=\"75\" x2=\"120\" y2=\"75\" style=\"stroke-width:2\" />\n",
|
||
|
|
"\n",
|
||
|
|
" <!-- Vertical lines -->\n",
|
||
|
|
" <line x1=\"0\" y1=\"0\" x2=\"0\" y2=\"75\" style=\"stroke-width:2\" />\n",
|
||
|
|
" <line x1=\"120\" y1=\"0\" x2=\"120\" y2=\"75\" style=\"stroke-width:2\" />\n",
|
||
|
|
"\n",
|
||
|
|
" <!-- Colored Rectangle -->\n",
|
||
|
|
" <polygon points=\"0.0,0.0 120.0,0.0 120.0,75.0 0.0,75.0\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n",
|
||
|
|
"\n",
|
||
|
|
" <!-- Text -->\n",
|
||
|
|
" <text x=\"60.000000\" y=\"95.000000\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" >1920</text>\n",
|
||
|
|
" <text x=\"140.000000\" y=\"37.500000\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(-90,140.000000,37.500000)\">1200</text>\n",
|
||
|
|
"</svg>\n",
|
||
|
|
" </td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
"</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>background</span></div><div class='xr-var-dims'>(y, x)</div><div class='xr-var-dtype'>uint16</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(1200, 1920), meta=np.ndarray></div><input id='attrs-cf0352d3-81af-4aa1-8a4b-d510a6d9ed9f' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-cf0352d3-81af-4aa1-8a4b-d510a6d9ed9f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-7cebfcb4-0749-41e1-a9df-8a3ca0e9cd57' class='xr-var-data-in' type='checkbox'><label for='data-7cebfcb4-0749-41e1-a9df-8a3ca0e9cd57' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>IMAGE_SUBCLASS :</span></dt><dd>IMAGE_GRAYSCALE</dd><dt><span>IMAGE_VERSION :</span></dt><dd>1.2</dd><dt><span>IMAGE_WHITE_IS_ZERO :</span></dt><dd>0</dd></dl></div><div class='xr-var-data'><table>\n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <td>\n",
|
||
|
|
" <table style=\"border-collapse: collapse;\">\n",
|
||
|
|
" <thead>\n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <td> </td>\n",
|
||
|
|
" <th> Array </th>\n",
|
||
|
|
" <th> Chunk </th>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" </thead>\n",
|
||
|
|
" <tbody>\n",
|
||
|
|
" \n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <th> Bytes </th>\n",
|
||
|
|
" <td> 4.39 MiB </td>\n",
|
||
|
|
" <td> 4.39 MiB </td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" \n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <th> Shape </th>\n",
|
||
|
|
" <td> (1200, 1920) </td>\n",
|
||
|
|
" <td> (1200, 1920) </td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <th> Dask graph </th>\n",
|
||
|
|
" <td colspan=\"2\"> 1 chunks in 2 graph layers </td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <th> Data type </th>\n",
|
||
|
|
" <td colspan=\"2\"> uint16 numpy.ndarray </td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" </tbody>\n",
|
||
|
|
" </table>\n",
|
||
|
|
" </td>\n",
|
||
|
|
" <td>\n",
|
||
|
|
" <svg width=\"170\" height=\"125\" style=\"stroke:rgb(0,0,0);stroke-width:1\" >\n",
|
||
|
|
"\n",
|
||
|
|
" <!-- Horizontal lines -->\n",
|
||
|
|
" <line x1=\"0\" y1=\"0\" x2=\"120\" y2=\"0\" style=\"stroke-width:2\" />\n",
|
||
|
|
" <line x1=\"0\" y1=\"75\" x2=\"120\" y2=\"75\" style=\"stroke-width:2\" />\n",
|
||
|
|
"\n",
|
||
|
|
" <!-- Vertical lines -->\n",
|
||
|
|
" <line x1=\"0\" y1=\"0\" x2=\"0\" y2=\"75\" style=\"stroke-width:2\" />\n",
|
||
|
|
" <line x1=\"120\" y1=\"0\" x2=\"120\" y2=\"75\" style=\"stroke-width:2\" />\n",
|
||
|
|
"\n",
|
||
|
|
" <!-- Colored Rectangle -->\n",
|
||
|
|
" <polygon points=\"0.0,0.0 120.0,0.0 120.0,75.0 0.0,75.0\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n",
|
||
|
|
"\n",
|
||
|
|
" <!-- Text -->\n",
|
||
|
|
" <text x=\"60.000000\" y=\"95.000000\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" >1920</text>\n",
|
||
|
|
" <text x=\"140.000000\" y=\"37.500000\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(-90,140.000000,37.500000)\">1200</text>\n",
|
||
|
|
"</svg>\n",
|
||
|
|
" </td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
"</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>dark</span></div><div class='xr-var-dims'>(y, x)</div><div class='xr-var-dtype'>uint16</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(1200, 1920), meta=np.ndarray></div><input id='attrs-ea5ca203-117f-4d7f-a382-5ea49ef757fe' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-ea5ca203-117f-4d7f-a382-5ea49ef757fe' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1c46121e-396f-4c19-b720-5bfd85d3db08' class='xr-var-data-in' type='checkbox'><label for='data-1c46121e-396f-4c19-b720-5bfd85d3db08' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>IMAGE_SUBCLASS :</span></dt><dd>IMAGE_GRAYSCALE</dd><dt><span>IMAGE_VERSION :</span></dt><dd>1.2</dd><dt><span>IMAGE_WHITE_IS_ZERO :</span></dt><dd>0</dd></dl></div><div class='xr-var-data'><table>\n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <td>\n",
|
||
|
|
" <table style=\"border-collapse: collapse;\">\n",
|
||
|
|
" <thead>\n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <td> </td>\n",
|
||
|
|
" <th> Array </th>\n",
|
||
|
|
" <th> Chunk </th>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" </thead>\n",
|
||
|
|
" <tbody>\n",
|
||
|
|
" \n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <th> Bytes </th>\n",
|
||
|
|
" <td> 4.39 MiB </td>\n",
|
||
|
|
" <td> 4.39 MiB </td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" \n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <th> Shape </th>\n",
|
||
|
|
" <td> (1200, 1920) </td>\n",
|
||
|
|
" <td> (1200, 1920) </td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <th> Dask graph </th>\n",
|
||
|
|
" <td colspan=\"2\"> 1 chunks in 2 graph layers </td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <th> Data type </th>\n",
|
||
|
|
" <td colspan=\"2\"> uint16 numpy.ndarray </td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" </tbody>\n",
|
||
|
|
" </table>\n",
|
||
|
|
" </td>\n",
|
||
|
|
" <td>\n",
|
||
|
|
" <svg width=\"170\" height=\"125\" style=\"stroke:rgb(0,0,0);stroke-width:1\" >\n",
|
||
|
|
"\n",
|
||
|
|
" <!-- Horizontal lines -->\n",
|
||
|
|
" <line x1=\"0\" y1=\"0\" x2=\"120\" y2=\"0\" style=\"stroke-width:2\" />\n",
|
||
|
|
" <line x1=\"0\" y1=\"75\" x2=\"120\" y2=\"75\" style=\"stroke-width:2\" />\n",
|
||
|
|
"\n",
|
||
|
|
" <!-- Vertical lines -->\n",
|
||
|
|
" <line x1=\"0\" y1=\"0\" x2=\"0\" y2=\"75\" style=\"stroke-width:2\" />\n",
|
||
|
|
" <line x1=\"120\" y1=\"0\" x2=\"120\" y2=\"75\" style=\"stroke-width:2\" />\n",
|
||
|
|
"\n",
|
||
|
|
" <!-- Colored Rectangle -->\n",
|
||
|
|
" <polygon points=\"0.0,0.0 120.0,0.0 120.0,75.0 0.0,75.0\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n",
|
||
|
|
"\n",
|
||
|
|
" <!-- Text -->\n",
|
||
|
|
" <text x=\"60.000000\" y=\"95.000000\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" >1920</text>\n",
|
||
|
|
" <text x=\"140.000000\" y=\"37.500000\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(-90,140.000000,37.500000)\">1200</text>\n",
|
||
|
|
"</svg>\n",
|
||
|
|
" </td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
"</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>shotNum</span></div><div class='xr-var-dims'>()</div><div class='xr-var-dtype'><U2</div><div class='xr-var-preview xr-preview'>'11'</div><input id='attrs-931dff3b-9054-49ae-a9a3-af23a3abe9d2' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-931dff3b-9054-49ae-a9a3-af23a3abe9d2' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-16b7a2e7-307c-45ef-8fd7-4961a352c6cd' class='xr-var-data-in' type='checkbox'><label for='data-16b7a2e7-307c-45ef-8fd7-4961a352c6cd' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array('11', dtype='<U2')</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>OD</span></div><div class='xr-var-dims'>(y, x)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(1200, 1920), meta=np.ndarray></div><input id='attrs-c45c4a1c-0006-43c9-be36-4e3d40196cf6' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-c45c4a1c-0006-43c9-be36-4e3d40196cf6' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-81f04315-1fc1-4433-9b5f-8dbcef03d3d4' class='xr-var-data-in' type='checkbox'><label for='data-81f04315-1fc1-4433-9b5f-8dbcef03d3d4' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>IMAGE_SUBCLASS :</span></dt><dd>IMAGE_GRAYSCALE</dd><dt><span>IMAGE_VERSION :</span></dt><dd>1.2</dd><dt><span>IMAGE_WHITE_IS_ZERO :</span></dt><dd>0</dd></dl></div><div class='xr-var-data'><table>\n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <td>\n",
|
||
|
|
" <table style=\"border-collapse: collapse;\">\n",
|
||
|
|
" <thead>\n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <td> </td>\n",
|
||
|
|
" <th> Array </th>\n",
|
||
|
|
" <th> Chunk </th>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" </thead>\n",
|
||
|
|
" <tbody>\n",
|
||
|
|
" \n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <th> Bytes </th>\n",
|
||
|
|
" <td> 17.58 MiB </td>\n",
|
||
|
|
" <td> 17.58 MiB </td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" \n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <th> Shape </th>\n",
|
||
|
|
" <td> (1200, 1920) </td>\n",
|
||
|
|
" <td> (1200, 1920) </td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <th> Dask graph </th>\n",
|
||
|
|
" <td colspan=\"2\"> 1 chunks in 16 graph layers </td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" <tr>\n",
|
||
|
|
" <th> Data type </th>\n",
|
||
|
|
" <td colspan=\"2\"> float64 numpy.ndarray </td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
" </tbody>\n",
|
||
|
|
" </table>\n",
|
||
|
|
" </td>\n",
|
||
|
|
" <td>\n",
|
||
|
|
" <svg width=\"170\" height=\"125\" style=\"stroke:rgb(0,0,0);stroke-width:1\" >\n",
|
||
|
|
"\n",
|
||
|
|
" <!-- Horizontal lines -->\n",
|
||
|
|
" <line x1=\"0\" y1=\"0\" x2=\"120\" y2=\"0\" style=\"stroke-width:2\" />\n",
|
||
|
|
" <line x1=\"0\" y1=\"75\" x2=\"120\" y2=\"75\" style=\"stroke-width:2\" />\n",
|
||
|
|
"\n",
|
||
|
|
" <!-- Vertical lines -->\n",
|
||
|
|
" <line x1=\"0\" y1=\"0\" x2=\"0\" y2=\"75\" style=\"stroke-width:2\" />\n",
|
||
|
|
" <line x1=\"120\" y1=\"0\" x2=\"120\" y2=\"75\" style=\"stroke-width:2\" />\n",
|
||
|
|
"\n",
|
||
|
|
" <!-- Colored Rectangle -->\n",
|
||
|
|
" <polygon points=\"0.0,0.0 120.0,0.0 120.0,75.0 0.0,75.0\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n",
|
||
|
|
"\n",
|
||
|
|
" <!-- Text -->\n",
|
||
|
|
" <text x=\"60.000000\" y=\"95.000000\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" >1920</text>\n",
|
||
|
|
" <text x=\"140.000000\" y=\"37.500000\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(-90,140.000000,37.500000)\">1200</text>\n",
|
||
|
|
"</svg>\n",
|
||
|
|
" </td>\n",
|
||
|
|
" </tr>\n",
|
||
|
|
"</table></div></li></ul></div></li><li class='xr-section-item'><input id='section-c33811d7-8cf5-4e35-8e55-5bc202a3ba60' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-c33811d7-8cf5-4e35-8e55-5bc202a3ba60' class='xr-section-summary' title='Expand/collapse section'>Indexes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-47715f26-a2f1-48c1-9cd1-23dbb2fa5488' class='xr-section-summary-in' type='checkbox' ><label for='section-47715f26-a2f1-48c1-9cd1-23dbb2fa5488' class='xr-section-summary' >Attributes: <span>(96)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>TOF_free :</span></dt><dd>0.02</dd><dt><span>abs_img_freq :</span></dt><dd>110.858</dd><dt><span>absorption_imaging_flag :</span></dt><dd>True</dd><dt><span>backup_data :</span></dt><dd>True</dd><dt><span>blink_off_time :</span></dt><dd>nan</dd><dt><span>blink_on_time :</span></dt><dd>nan</dd><dt><span>c_duration :</span></dt><dd>0.2</dd><dt><span>cmot_final_current :</span></dt><dd>0.65</dd><dt><span>cmot_hold :</span></dt><dd>0.06</dd><dt><span>cmot_initial_current :</span></dt><dd>0.18</dd><dt><span>compX_current :</span></dt><dd>0.005</dd><dt><span>compX_current_sg :</span></dt><dd>0</dd><dt><span>compX_final_current :</span></dt><dd>0.005</dd><dt><span>compX_initial_current :</span></dt><dd>0.005</dd><dt><span>compY_current :</span></dt><dd>0</dd><dt><span>compY_current_sg :</span></dt><dd>0</dd><dt><span>compY_final_current :</span></dt><dd>0.0</dd><dt><span>compY_initial_current :</span></dt><dd>0</dd><dt><span>compZ_current :</span></dt><dd>0</dd><dt><span>compZ_current_sg :</span></dt><dd>0.189</dd><dt><span>compZ_final_current :</span></dt><dd>0.2812</dd><dt><span>compZ_initial_current :</span></dt><dd>0</dd><dt><span>default_camera :</span></dt><dd>0</dd><dt><span>evap_1_arm_1_final_pow :</span></dt><dd>0.35</dd><dt><span>evap_1_arm_1_mod_depth_final :</span></dt><dd>0</dd><dt><span>evap_1_arm_1_mod_depth_initial :</span></dt><dd>1.0</dd><dt><span>evap_1_arm_1_mod_ramp_duration :</span></dt><dd>1.15</dd><dt><span>evap_1_arm_1_pow_ramp_duration :</span></dt><dd>1.65</dd><dt><span>evap_1_arm_1_start_pow :</span></dt><dd>7</dd><dt><span>evap_1_arm_2_final_pow :</span></dt><dd>5</dd><dt><span>evap_1_arm_2_ramp_duration :</span></dt><dd>0.5</dd><dt><span>evap_1_arm_2_start_pow :</span></dt><dd>0</dd><dt><span>evap_1_mod_ramp_trunc_value :</span></dt><dd>1</dd><dt><span>evap_1_pow_ramp_trunc_value :</span></dt><dd>1.0</dd><dt><span>evap_1_rate_constant_1 :</span></dt><dd>0.525</dd><dt><span>evap_1_rate_constant_2 :</span></dt><dd>0.51</dd><dt><span>evap_2_arm_1_final_pow :</span></dt><dd>0.037</dd><dt><span>evap_2_arm_1_start_pow :</span></dt><dd>0.35</dd><dt><span>evap_2_arm_2_final_pow :</span></dt><dd>0.09</dd><dt><span>evap_2_arm_2_start_pow :</span></dt><dd>5</dd><dt><span>evap_2_ramp_duration :</span></dt><dd>1.0</dd><dt><span>evap_2_ramp_trunc_value :</span></dt><dd>1</dd><dt><span>evap_2_rate_constant_1 :</span></dt><dd>0.37</dd><dt><span>evap_2_rate_constant_2 :</span></dt><dd>0.71</dd><dt><span>evap_3_arm_1_final_pow :</span></dt><dd>0.1038</dd><dt><span>evap_3_arm_1_mod_depth_final :</span></dt><dd>0.43</dd><dt><span>evap_3_arm_1_mod_depth_initial :</span></dt><dd>0</dd><dt><span>evap_3_arm_1_start_pow :</span></dt><dd>0.037</dd><dt><span>evap_3_ramp_duration :</span></dt><dd>0.1</dd><dt><span>evap_3_ramp_trunc_value :</span></dt><dd>1</dd><dt><span>evap_3_rate_constant_1 :</span></dt><dd>-0.879</dd><dt><span>evap_3_rate_constant_2 :</span></dt><dd>-0.297</dd><dt><span>final_amp :</span></dt><dd>8e-05</dd><dt><span>final_freq :</span></dt><dd>104.0</dd><dt><span>gradCoil_current :</span></dt><dd>0.18</dd><dt><span>gradCoil_current_sg :</span></dt><dd>0</dd><dt><span>imaging_method :</span></dt><dd>in_situ_absorption</dd><dt><span>imaging_pulse_duration :</span></dt><dd>2.5e-05</dd><dt><span>imaging_wavel
|
||
|
|
],
|
||
|
|
"text/plain": [
|
||
|
|
"<xarray.Dataset>\n",
|
||
|
|
"Dimensions: (y: 1200, x: 1920)\n",
|
||
|
|
"Dimensions without coordinates: y, x\n",
|
||
|
|
"Data variables:\n",
|
||
|
|
" atoms (y, x) uint16 dask.array<chunksize=(1200, 1920), meta=np.ndarray>\n",
|
||
|
|
" background (y, x) uint16 dask.array<chunksize=(1200, 1920), meta=np.ndarray>\n",
|
||
|
|
" dark (y, x) uint16 dask.array<chunksize=(1200, 1920), meta=np.ndarray>\n",
|
||
|
|
" shotNum <U2 '11'\n",
|
||
|
|
" OD (y, x) float64 dask.array<chunksize=(1200, 1920), meta=np.ndarray>\n",
|
||
|
|
"Attributes: (12/96)\n",
|
||
|
|
" TOF_free: 0.02\n",
|
||
|
|
" abs_img_freq: 110.858\n",
|
||
|
|
" absorption_imaging_flag: True\n",
|
||
|
|
" backup_data: True\n",
|
||
|
|
" blink_off_time: nan\n",
|
||
|
|
" blink_on_time: nan\n",
|
||
|
|
" ... ...\n",
|
||
|
|
" y_offset: 0\n",
|
||
|
|
" y_offset_img: 0\n",
|
||
|
|
" z_offset: 0.189\n",
|
||
|
|
" z_offset_img: 0.189\n",
|
||
|
|
" scanAxis: []\n",
|
||
|
|
" scanAxisLength: []"
|
||
|
|
]
|
||
|
|
},
|
||
|
|
"execution_count": 75,
|
||
|
|
"metadata": {},
|
||
|
|
"output_type": "execute_result"
|
||
|
|
}
|
||
|
|
],
|
||
|
|
"source": [
|
||
|
|
"shotNum = \"0069\"\n",
|
||
|
|
"filePath = folderPath + \"/\" + shotNum + \"/*.h5\"\n",
|
||
|
|
"# filePath = \"//DyLabNAS/Data/Evaporative_Cooling/2023/05/12/0065/*.h5\"\n",
|
||
|
|
"filePath = './result_from_experiment/2023-04-24/0013/2023-04-24_0013_Evaporative_Cooling_11.h5'\n",
|
||
|
|
"\n",
|
||
|
|
"dataSetDict = {\n",
|
||
|
|
" dskey[groupList[i]]: read_hdf5_file(filePath, groupList[i])\n",
|
||
|
|
" for i in [0] # range(len(groupList))\n",
|
||
|
|
"}\n",
|
||
|
|
"\n",
|
||
|
|
"dataSet = dataSetDict[\"camera_1\"]\n",
|
||
|
|
"dataSet = swap_xy(dataSet)\n",
|
||
|
|
"\n",
|
||
|
|
"scanAxis = get_scanAxis(dataSet)\n",
|
||
|
|
"\n",
|
||
|
|
"dataSet = auto_rechunk(dataSet)\n",
|
||
|
|
"\n",
|
||
|
|
"dataSet = imageAnalyser.get_absorption_images(dataSet)\n",
|
||
|
|
"\n",
|
||
|
|
"dataSet"
|
||
|
|
]
|
||
|
|
},
|
||
|
|
{
|
||
|
|
"attachments": {},
|
||
|
|
"cell_type": "markdown",
|
||
|
|
"metadata": {},
|
||
|
|
"source": [
|
||
|
|
"## Calculate an plot OD images"
|
||
|
|
]
|
||
|
|
},
|
||
|
|
{
|
||
|
|
"cell_type": "code",
|
||
|
|
"execution_count": 76,
|
||
|
|
"metadata": {},
|
||
|
|
"outputs": [
|
||
|
|
{
|
||
|
|
"data": {
|
||
|
|
"image/png": "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
|
||
|
|
"text/plain": [
|
||
|
|
"<Figure size 640x480 with 2 Axes>"
|
||
|
|
]
|
||
|
|
},
|
||
|
|
"metadata": {},
|
||
|
|
"output_type": "display_data"
|
||
|
|
}
|
||
|
|
],
|
||
|
|
"source": [
|
||
|
|
"# imageAnalyser.center = (960, 1040)\n",
|
||
|
|
"# imageAnalyser.span = (100, 100)\n",
|
||
|
|
"# imageAnalyser.fraction = (0.1, 0.1)\n",
|
||
|
|
"\n",
|
||
|
|
"imageAnalyser.center = (960, 875)\n",
|
||
|
|
"imageAnalyser.span = (300, 300)\n",
|
||
|
|
"imageAnalyser.fraction = (0.1, 0.1)\n",
|
||
|
|
"\n",
|
||
|
|
"dataSet_cropOD = imageAnalyser.crop_image(dataSet.OD)\n",
|
||
|
|
"dataSet_cropOD = imageAnalyser.substract_offset(dataSet_cropOD).load()\n",
|
||
|
|
"\n",
|
||
|
|
"dataSet_cropOD.plot.pcolormesh(cmap='jet', vmin=0, col=scanAxis[0], row=scanAxis[1])\n",
|
||
|
|
"plt.show()"
|
||
|
|
]
|
||
|
|
}
|
||
|
|
],
|
||
|
|
"metadata": {
|
||
|
|
"kernelspec": {
|
||
|
|
"display_name": "env",
|
||
|
|
"language": "python",
|
||
|
|
"name": "python3"
|
||
|
|
},
|
||
|
|
"language_info": {
|
||
|
|
"codemirror_mode": {
|
||
|
|
"name": "ipython",
|
||
|
|
"version": 3
|
||
|
|
},
|
||
|
|
"file_extension": ".py",
|
||
|
|
"mimetype": "text/x-python",
|
||
|
|
"name": "python",
|
||
|
|
"nbconvert_exporter": "python",
|
||
|
|
"pygments_lexer": "ipython3",
|
||
|
|
"version": "3.9.12"
|
||
|
|
},
|
||
|
|
"vscode": {
|
||
|
|
"interpreter": {
|
||
|
|
"hash": "c05913ad4f24fdc6b2418069394dc5835b1981849b107c9ba6df693aafd66650"
|
||
|
|
}
|
||
|
|
}
|
||
|
|
},
|
||
|
|
"nbformat": 4,
|
||
|
|
"nbformat_minor": 2
|
||
|
|
}
|