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{
"cells": [
{
"cell_type": "markdown",
"id": "6a764d92",
"metadata": {},
"source": [
"# Gaussian Processes\n",
"\n",
"If one is ready to assume the data available is such that the variable being fit is Gaussian for any pair of samples taken, one can use fit the data and obtain a reliable uncertainty with a very small set of assumptions.\n",
"\n",
"For this example, we will use the dataset collected in Mauna Loa showing the amount of CO2 present in the atmosphere. This data may be downloaded from https://gml.noaa.gov/ccgg/trends/data.html\n",
"\n",
"If you have Linux or MacOS with standard tools installed, just run the next line of the notebook to download it with wget. If you are use Windows, download the dataset at: https://gml.noaa.gov/webdata/ccgg/trends/co2/co2_weekly_mlo.txt"
]
},
{
"cell_type": "code",
"execution_count": 1,
"id": "8337a15a",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
Danilo Ferreira de Lima
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"--2021-12-17 16:04:48-- https://gml.noaa.gov/webdata/ccgg/trends/co2/co2_weekly_mlo.txt\n",
"Resolving gml.noaa.gov (gml.noaa.gov)... 140.172.200.41, 2610:20:8800:6101::29\n",
"Connecting to gml.noaa.gov (gml.noaa.gov)|140.172.200.41|:443... connected.\n",
"HTTP request sent, awaiting response... 200 OK\n",
Danilo Ferreira de Lima
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"Length: 191093 (187K) [text/plain]\n",
"Saving to: ‘co2_weekly_mlo.txt.4’\n",
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"co2_weekly_mlo.txt. 100%[===================>] 186,61K 67,4KB/s in 2,8s \n",
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"2021-12-17 16:04:52 (67,4 KB/s) - ‘co2_weekly_mlo.txt.4’ saved [191093/191093]\n",
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"\n"
]
}
],
"source": [
"!wget --no-check-certificate https://gml.noaa.gov/webdata/ccgg/trends/co2/co2_weekly_mlo.txt"
]
},
{
"cell_type": "markdown",
"id": "c8131588",
"metadata": {},
"source": [
"We can take a quick look at the file to see what is inside:"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "07ecc0d3",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"# --------------------------------------------------------------------\n",
"# USE OF NOAA GML DATA\n",
"# \n",
"# These data are made freely available to the public and the\n",
"# scientific community in the belief that their wide dissemination\n",
"# will lead to greater understanding and new scientific insights.\n",
"# The availability of these data does not constitute publication\n",
"# of the data. NOAA relies on the ethics and integrity of the user to\n",
"# ensure that GML receives fair credit for their work. If the data \n",
"# are obtained for potential use in a publication or presentation, \n",
"# GML should be informed at the outset of the nature of this work. \n",
"# If the GML data are essential to the work, or if an important \n",
"# result or conclusion depends on the GML data, co-authorship\n",
"# may be appropriate. This should be discussed at an early stage in\n",
"# the work. Manuscripts using the GML data should be sent to GML\n",
"# for review before they are submitted for publication so we can\n",
"# ensure that the quality and limitations of the data are accurately\n",
"# represented.\n",
"# \n",
"# Contact: Pieter Tans (303 497 6678; pieter.tans@noaa.gov)\n",
"# \n",
Danilo Ferreira de Lima
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"# File Creation: Fri Dec 17 05:00:13 2021\n",
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"# \n",
"# RECIPROCITY\n",
"# \n",
"# Use of these data implies an agreement to reciprocate.\n",
"# Laboratories making similar measurements agree to make their\n",
"# own data available to the general public and to the scientific\n",
"# community in an equally complete and easily accessible form.\n",
"# Modelers are encouraged to make available to the community,\n",
"# upon request, their own tools used in the interpretation\n",
"# of the GML data, namely well documented model code, transport\n",
"# fields, and additional information necessary for other\n",
"# scientists to repeat the work and to run modified versions.\n",
"# Model availability includes collaborative support for new\n",
"# users of the models.\n",
"# --------------------------------------------------------------------\n",
"# \n",
"# \n",
"# See www.esrl.noaa.gov/gmd/ccgg/trends/ for additional details.\n",
"# \n",
"# NOTE: DATA FOR THE LAST SEVERAL MONTHS ARE PRELIMINARY, ARE STILL SUBJECT\n",
"# TO QUALITY CONTROL PROCEDURES.\n",
"# NOTE: The week \"1 yr ago\" is exactly 365 days ago, and thus does not run from\n",
"# Sunday through Saturday. 365 also ignores the possibility of a leap year.\n",
"# The week \"10 yr ago\" is exactly 10*365 days +3 days (for leap years) ago.\n",
"# \n",
"# Start of week CO2 molfrac (-999.99 = no data) increase\n",
"# (yr, mon, day, decimal) (ppm) #days 1 yr ago 10 yr ago since 1800\n",
" 1974 5 19 1974.3795 333.37 5 -999.99 -999.99 50.40\n",
" 1974 5 26 1974.3986 332.95 6 -999.99 -999.99 50.06\n",
" 1974 6 2 1974.4178 332.35 5 -999.99 -999.99 49.60\n",
" 1974 6 9 1974.4370 332.20 7 -999.99 -999.99 49.65\n",
" 1974 6 16 1974.4562 332.37 7 -999.99 -999.99 50.06\n",
" 1974 6 23 1974.4753 331.73 5 -999.99 -999.99 49.72\n",
" 1974 6 30 1974.4945 331.68 6 -999.99 -999.99 50.02\n",
" 1974 7 7 1974.5137 331.46 6 -999.99 -999.99 50.20\n",
" 1974 7 14 1974.5329 330.83 5 -999.99 -999.99 50.01\n",
" 1974 7 21 1974.5521 330.76 7 -999.99 -999.99 50.41\n",
" 1974 7 28 1974.5712 329.80 4 -999.99 -999.99 49.97\n",
" 1974 8 4 1974.5904 329.85 5 -999.99 -999.99 50.54\n"
]
}
],
"source": [
"with open(\"co2_weekly_mlo.txt\", \"r\") as f:\n",
" for i, line in enumerate(f.readlines()):\n",
" if i > 60: # let's print only the first 60 lines only\n",
" break\n",
" print(line[:-1])"
]
},
{
"cell_type": "markdown",
"id": "fce4d8e8",
"metadata": {},
"source": [
"We start by loading the necessary Python modules. If you have not yet installed them, run the following cell to install them with pip:"
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "44ca341e",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
Danilo Ferreira de Lima
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"Requirement already satisfied: numpy in /home/daniloefl/miniconda3/envs/mltut/lib/python3.6/site-packages (1.19.2)\n",
"Requirement already satisfied: scikit-learn in /home/daniloefl/miniconda3/envs/mltut/lib/python3.6/site-packages (0.24.2)\n",
"Requirement already satisfied: pandas in /home/daniloefl/miniconda3/envs/mltut/lib/python3.6/site-packages (1.1.5)\n",
"Requirement already satisfied: matplotlib in /home/daniloefl/miniconda3/envs/mltut/lib/python3.6/site-packages (3.3.4)\n",
"Requirement already satisfied: threadpoolctl>=2.0.0 in /home/daniloefl/miniconda3/envs/mltut/lib/python3.6/site-packages (from scikit-learn) (2.2.0)\n",
"Requirement already satisfied: joblib>=0.11 in /home/daniloefl/miniconda3/envs/mltut/lib/python3.6/site-packages (from scikit-learn) (1.0.1)\n",
"Requirement already satisfied: scipy>=0.19.1 in /home/daniloefl/miniconda3/envs/mltut/lib/python3.6/site-packages (from scikit-learn) (1.5.2)\n",
"Requirement already satisfied: python-dateutil>=2.7.3 in /home/daniloefl/miniconda3/envs/mltut/lib/python3.6/site-packages (from pandas) (2.8.2)\n",
"Requirement already satisfied: pytz>=2017.2 in /home/daniloefl/miniconda3/envs/mltut/lib/python3.6/site-packages (from pandas) (2021.3)\n",
"Requirement already satisfied: pillow>=6.2.0 in /home/daniloefl/miniconda3/envs/mltut/lib/python3.6/site-packages (from matplotlib) (8.3.1)\n",
"Requirement already satisfied: cycler>=0.10 in /home/daniloefl/miniconda3/envs/mltut/lib/python3.6/site-packages (from matplotlib) (0.11.0)\n",
"Requirement already satisfied: kiwisolver>=1.0.1 in /home/daniloefl/miniconda3/envs/mltut/lib/python3.6/site-packages (from matplotlib) (1.3.1)\n",
"Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.3 in /home/daniloefl/miniconda3/envs/mltut/lib/python3.6/site-packages (from matplotlib) (3.0.4)\n",
"Requirement already satisfied: six>=1.5 in /home/daniloefl/miniconda3/envs/mltut/lib/python3.6/site-packages (from python-dateutil>=2.7.3->pandas) (1.16.0)\n"
]
}
],
"source": [
"!pip install numpy scikit-learn pandas matplotlib"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "300cf8d3",
"metadata": {},
"outputs": [],
"source": [
Danilo Ferreira de Lima
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"%matplotlib notebook\n",
"\n",
"import matplotlib.pyplot as plt\n",
"\n",
"import pandas as pd\n",
"import numpy as np\n",
"from sklearn.gaussian_process import GaussianProcessRegressor\n",
Danilo Ferreira de Lima
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"from sklearn.gaussian_process.kernels import RBF, ExpSineSquared, WhiteKernel, RationalQuadratic"
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},
{
"cell_type": "markdown",
"id": "0ecd6a69",
"metadata": {},
"source": [
"Let us now load the data downloaded using pandas. If you are not familiar with Pandas, take a look at the documentation for a quick introduction at https://pandas.pydata.org/docs/user_guide/10min.html\n",
"\n",
"We can easily parse the data file using Pandas' read_csv function. It would require some coding to do it manually. As Pandas does not detect the column names, we have to specify it manually in the names parameter below."
]
},
{
"cell_type": "code",
"execution_count": 5,
"id": "4959a292",
"metadata": {},
"outputs": [],
"source": [
"data = pd.read_csv(\"co2_weekly_mlo.txt\",\n",
" delim_whitespace=True,\n",
" comment='#',\n",
" header=None,\n",
" names=[\"year\", \"month\", \"day\", \"decimal\",\n",
" \"co2\",\n",
" \"ndays\",\n",
" \"last_year\", \"last_decade\",\n",
" \"increase\"])"
]
},
{
"cell_type": "markdown",
"id": "d8295e8a",
"metadata": {},
"source": [
"Let's print out the dataset read first."
]
},
{
"cell_type": "code",
"execution_count": 6,
"id": "024fb65a",
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<style scoped>\n",
" .dataframe tbody tr th:only-of-type {\n",
" vertical-align: middle;\n",
" }\n",
"\n",
" .dataframe tbody tr th {\n",
" vertical-align: top;\n",
" }\n",
"\n",
" .dataframe thead th {\n",
" text-align: right;\n",
" }\n",
"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>year</th>\n",
" <th>month</th>\n",
" <th>day</th>\n",
" <th>decimal</th>\n",
" <th>co2</th>\n",
" <th>ndays</th>\n",
" <th>last_year</th>\n",
" <th>last_decade</th>\n",
" <th>increase</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>1974</td>\n",
" <td>5</td>\n",
" <td>19</td>\n",
" <td>1974.3795</td>\n",
" <td>333.37</td>\n",
" <td>5</td>\n",
" <td>-999.99</td>\n",
" <td>-999.99</td>\n",
" <td>50.40</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>1974</td>\n",
" <td>5</td>\n",
" <td>26</td>\n",
" <td>1974.3986</td>\n",
" <td>332.95</td>\n",
" <td>6</td>\n",
" <td>-999.99</td>\n",
" <td>-999.99</td>\n",
" <td>50.06</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>1974</td>\n",
" <td>6</td>\n",
" <td>2</td>\n",
" <td>1974.4178</td>\n",
" <td>332.35</td>\n",
" <td>5</td>\n",
" <td>-999.99</td>\n",
" <td>-999.99</td>\n",
" <td>49.60</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>1974</td>\n",
" <td>6</td>\n",
" <td>9</td>\n",
" <td>1974.4370</td>\n",
" <td>332.20</td>\n",
" <td>7</td>\n",
" <td>-999.99</td>\n",
" <td>-999.99</td>\n",
" <td>49.65</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>1974</td>\n",
" <td>6</td>\n",
" <td>16</td>\n",
" <td>1974.4562</td>\n",
" <td>332.37</td>\n",
" <td>7</td>\n",
" <td>-999.99</td>\n",
" <td>-999.99</td>\n",
" <td>50.06</td>\n",
" </tr>\n",
" <tr>\n",
" <th>...</th>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2477</th>\n",
" <td>2021</td>\n",
" <td>11</td>\n",
" <td>7</td>\n",
" <td>2021.8507</td>\n",
" <td>414.97</td>\n",
" <td>7</td>\n",
" <td>412.97</td>\n",
" <td>390.09</td>\n",
Danilo Ferreira de Lima
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" <td>137.30</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2478</th>\n",
" <td>2021</td>\n",
" <td>11</td>\n",
" <td>14</td>\n",
" <td>2021.8699</td>\n",
" <td>414.88</td>\n",
" <td>7</td>\n",
" <td>412.80</td>\n",
" <td>390.71</td>\n",
Danilo Ferreira de Lima
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" <td>136.86</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2479</th>\n",
" <td>2021</td>\n",
" <td>11</td>\n",
" <td>21</td>\n",
" <td>2021.8890</td>\n",
" <td>415.36</td>\n",
" <td>7</td>\n",
" <td>413.55</td>\n",
" <td>390.78</td>\n",
Danilo Ferreira de Lima
committed
" <td>136.99</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2480</th>\n",
" <td>2021</td>\n",
" <td>11</td>\n",
" <td>28</td>\n",
" <td>2021.9082</td>\n",
" <td>416.16</td>\n",
" <td>7</td>\n",
" <td>414.36</td>\n",
" <td>391.33</td>\n",
" <td>137.45</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2481</th>\n",
" <td>2021</td>\n",
" <td>12</td>\n",
" <td>5</td>\n",
" <td>2021.9274</td>\n",
" <td>415.86</td>\n",
" <td>5</td>\n",
" <td>413.50</td>\n",
" <td>391.72</td>\n",
" <td>136.84</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
Danilo Ferreira de Lima
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"<p>2482 rows × 9 columns</p>\n",
"</div>"
],
"text/plain": [
" year month day decimal co2 ndays last_year last_decade \\\n",
"0 1974 5 19 1974.3795 333.37 5 -999.99 -999.99 \n",
"1 1974 5 26 1974.3986 332.95 6 -999.99 -999.99 \n",
"2 1974 6 2 1974.4178 332.35 5 -999.99 -999.99 \n",
"3 1974 6 9 1974.4370 332.20 7 -999.99 -999.99 \n",
"4 1974 6 16 1974.4562 332.37 7 -999.99 -999.99 \n",
"... ... ... ... ... ... ... ... ... \n",
"2477 2021 11 7 2021.8507 414.97 7 412.97 390.09 \n",
"2478 2021 11 14 2021.8699 414.88 7 412.80 390.71 \n",
"2479 2021 11 21 2021.8890 415.36 7 413.55 390.78 \n",
Danilo Ferreira de Lima
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"2480 2021 11 28 2021.9082 416.16 7 414.36 391.33 \n",
"2481 2021 12 5 2021.9274 415.86 5 413.50 391.72 \n",
"\n",
" increase \n",
"0 50.40 \n",
"1 50.06 \n",
"2 49.60 \n",
"3 49.65 \n",
"4 50.06 \n",
"... ... \n",
Danilo Ferreira de Lima
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"2477 137.30 \n",
"2478 136.86 \n",
"2479 136.99 \n",
"2480 137.45 \n",
"2481 136.84 \n",
Danilo Ferreira de Lima
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"[2482 rows x 9 columns]"
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},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"data"
]
},
{
"cell_type": "markdown",
"id": "1c178424",
"metadata": {},
"source": [
"We can plot this fairly easily using Matplotlib."
]
},
{
"cell_type": "code",
"execution_count": 7,
"id": "e63b38c5",
"metadata": {},
"outputs": [
{
"data": {
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"application/javascript": [
"/* Put everything inside the global mpl namespace */\n",
"/* global mpl */\n",
"window.mpl = {};\n",
"\n",
"mpl.get_websocket_type = function () {\n",
" if (typeof WebSocket !== 'undefined') {\n",
" return WebSocket;\n",
" } else if (typeof MozWebSocket !== 'undefined') {\n",
" return MozWebSocket;\n",
" } else {\n",
" alert(\n",
" 'Your browser does not have WebSocket support. ' +\n",
" 'Please try Chrome, Safari or Firefox ≥ 6. ' +\n",
" 'Firefox 4 and 5 are also supported but you ' +\n",
" 'have to enable WebSockets in about:config.'\n",
" );\n",
" }\n",
"};\n",
"\n",
"mpl.figure = function (figure_id, websocket, ondownload, parent_element) {\n",
" this.id = figure_id;\n",
"\n",
" this.ws = websocket;\n",
"\n",
" this.supports_binary = this.ws.binaryType !== undefined;\n",
"\n",
" if (!this.supports_binary) {\n",
" var warnings = document.getElementById('mpl-warnings');\n",
" if (warnings) {\n",
" warnings.style.display = 'block';\n",
" warnings.textContent =\n",
" 'This browser does not support binary websocket messages. ' +\n",
" 'Performance may be slow.';\n",
" }\n",
" }\n",
"\n",
" this.imageObj = new Image();\n",
"\n",
" this.context = undefined;\n",
" this.message = undefined;\n",
" this.canvas = undefined;\n",
" this.rubberband_canvas = undefined;\n",
" this.rubberband_context = undefined;\n",
" this.format_dropdown = undefined;\n",
"\n",
" this.image_mode = 'full';\n",
"\n",
" this.root = document.createElement('div');\n",
" this.root.setAttribute('style', 'display: inline-block');\n",
" this._root_extra_style(this.root);\n",
"\n",
" parent_element.appendChild(this.root);\n",
"\n",
" this._init_header(this);\n",
" this._init_canvas(this);\n",
" this._init_toolbar(this);\n",
"\n",
" var fig = this;\n",
"\n",
" this.waiting = false;\n",
"\n",
" this.ws.onopen = function () {\n",
" fig.send_message('supports_binary', { value: fig.supports_binary });\n",
" fig.send_message('send_image_mode', {});\n",
" if (fig.ratio !== 1) {\n",
" fig.send_message('set_dpi_ratio', { dpi_ratio: fig.ratio });\n",
" }\n",
" fig.send_message('refresh', {});\n",
" };\n",
"\n",
" this.imageObj.onload = function () {\n",
" if (fig.image_mode === 'full') {\n",
" // Full images could contain transparency (where diff images\n",
" // almost always do), so we need to clear the canvas so that\n",
" // there is no ghosting.\n",
" fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n",
" }\n",
" fig.context.drawImage(fig.imageObj, 0, 0);\n",
" };\n",
"\n",
" this.imageObj.onunload = function () {\n",
" fig.ws.close();\n",
" };\n",
"\n",
" this.ws.onmessage = this._make_on_message_function(this);\n",
"\n",
" this.ondownload = ondownload;\n",
"};\n",
"\n",
"mpl.figure.prototype._init_header = function () {\n",
" var titlebar = document.createElement('div');\n",
" titlebar.classList =\n",
" 'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n",
" var titletext = document.createElement('div');\n",
" titletext.classList = 'ui-dialog-title';\n",
" titletext.setAttribute(\n",
" 'style',\n",
" 'width: 100%; text-align: center; padding: 3px;'\n",
" );\n",
" titlebar.appendChild(titletext);\n",
" this.root.appendChild(titlebar);\n",
" this.header = titletext;\n",
"};\n",
"\n",
"mpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n",
"\n",
"mpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n",
"\n",
"mpl.figure.prototype._init_canvas = function () {\n",
" var fig = this;\n",
"\n",
" var canvas_div = (this.canvas_div = document.createElement('div'));\n",
" canvas_div.setAttribute(\n",
" 'style',\n",
" 'border: 1px solid #ddd;' +\n",
" 'box-sizing: content-box;' +\n",
" 'clear: both;' +\n",
" 'min-height: 1px;' +\n",
" 'min-width: 1px;' +\n",
" 'outline: 0;' +\n",
" 'overflow: hidden;' +\n",
" 'position: relative;' +\n",
" 'resize: both;'\n",
" );\n",
"\n",
" function on_keyboard_event_closure(name) {\n",
" return function (event) {\n",
" return fig.key_event(event, name);\n",
" };\n",
" }\n",
"\n",
" canvas_div.addEventListener(\n",
" 'keydown',\n",
" on_keyboard_event_closure('key_press')\n",
" );\n",
" canvas_div.addEventListener(\n",
" 'keyup',\n",
" on_keyboard_event_closure('key_release')\n",
" );\n",
"\n",
" this._canvas_extra_style(canvas_div);\n",
" this.root.appendChild(canvas_div);\n",
"\n",
" var canvas = (this.canvas = document.createElement('canvas'));\n",
" canvas.classList.add('mpl-canvas');\n",
" canvas.setAttribute('style', 'box-sizing: content-box;');\n",
"\n",
" this.context = canvas.getContext('2d');\n",
"\n",
" var backingStore =\n",
" this.context.backingStorePixelRatio ||\n",
" this.context.webkitBackingStorePixelRatio ||\n",
" this.context.mozBackingStorePixelRatio ||\n",
" this.context.msBackingStorePixelRatio ||\n",
" this.context.oBackingStorePixelRatio ||\n",
" this.context.backingStorePixelRatio ||\n",
" 1;\n",
"\n",
" this.ratio = (window.devicePixelRatio || 1) / backingStore;\n",
"\n",
" var rubberband_canvas = (this.rubberband_canvas = document.createElement(\n",
" 'canvas'\n",
" ));\n",
" rubberband_canvas.setAttribute(\n",
" 'style',\n",
" 'box-sizing: content-box; position: absolute; left: 0; top: 0; z-index: 1;'\n",
" );\n",
"\n",
" // Apply a ponyfill if ResizeObserver is not implemented by browser.\n",
" if (this.ResizeObserver === undefined) {\n",
" if (window.ResizeObserver !== undefined) {\n",
" this.ResizeObserver = window.ResizeObserver;\n",
" } else {\n",
" var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n",
" this.ResizeObserver = obs.ResizeObserver;\n",
" }\n",
" }\n",
"\n",
" this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n",
" var nentries = entries.length;\n",
" for (var i = 0; i < nentries; i++) {\n",
" var entry = entries[i];\n",
" var width, height;\n",
" if (entry.contentBoxSize) {\n",
" if (entry.contentBoxSize instanceof Array) {\n",
" // Chrome 84 implements new version of spec.\n",
" width = entry.contentBoxSize[0].inlineSize;\n",
" height = entry.contentBoxSize[0].blockSize;\n",
" } else {\n",
" // Firefox implements old version of spec.\n",
" width = entry.contentBoxSize.inlineSize;\n",
" height = entry.contentBoxSize.blockSize;\n",
" }\n",
" } else {\n",
" // Chrome <84 implements even older version of spec.\n",
" width = entry.contentRect.width;\n",
" height = entry.contentRect.height;\n",
" }\n",
"\n",
" // Keep the size of the canvas and rubber band canvas in sync with\n",
" // the canvas container.\n",
" if (entry.devicePixelContentBoxSize) {\n",
" // Chrome 84 implements new version of spec.\n",
" canvas.setAttribute(\n",
" 'width',\n",
" entry.devicePixelContentBoxSize[0].inlineSize\n",
" );\n",
" canvas.setAttribute(\n",
" 'height',\n",
" entry.devicePixelContentBoxSize[0].blockSize\n",
" );\n",
" } else {\n",
" canvas.setAttribute('width', width * fig.ratio);\n",
" canvas.setAttribute('height', height * fig.ratio);\n",
" }\n",
" canvas.setAttribute(\n",
" 'style',\n",
" 'width: ' + width + 'px; height: ' + height + 'px;'\n",
" );\n",
"\n",
" rubberband_canvas.setAttribute('width', width);\n",
" rubberband_canvas.setAttribute('height', height);\n",
"\n",
" // And update the size in Python. We ignore the initial 0/0 size\n",
" // that occurs as the element is placed into the DOM, which should\n",
" // otherwise not happen due to the minimum size styling.\n",
" if (fig.ws.readyState == 1 && width != 0 && height != 0) {\n",
" fig.request_resize(width, height);\n",
" }\n",
" }\n",
" });\n",
" this.resizeObserverInstance.observe(canvas_div);\n",
"\n",
" function on_mouse_event_closure(name) {\n",
" return function (event) {\n",
" return fig.mouse_event(event, name);\n",
" };\n",
" }\n",
"\n",
" rubberband_canvas.addEventListener(\n",
" 'mousedown',\n",
" on_mouse_event_closure('button_press')\n",
" );\n",
" rubberband_canvas.addEventListener(\n",
" 'mouseup',\n",
" on_mouse_event_closure('button_release')\n",
" );\n",
" // Throttle sequential mouse events to 1 every 20ms.\n",
" rubberband_canvas.addEventListener(\n",
" 'mousemove',\n",
" on_mouse_event_closure('motion_notify')\n",
" );\n",
"\n",
" rubberband_canvas.addEventListener(\n",
" 'mouseenter',\n",
" on_mouse_event_closure('figure_enter')\n",
" );\n",
" rubberband_canvas.addEventListener(\n",
" 'mouseleave',\n",
" on_mouse_event_closure('figure_leave')\n",
" );\n",
"\n",
" canvas_div.addEventListener('wheel', function (event) {\n",
" if (event.deltaY < 0) {\n",
" event.step = 1;\n",
" } else {\n",
" event.step = -1;\n",
" }\n",
" on_mouse_event_closure('scroll')(event);\n",
" });\n",
"\n",
" canvas_div.appendChild(canvas);\n",
" canvas_div.appendChild(rubberband_canvas);\n",
"\n",
" this.rubberband_context = rubberband_canvas.getContext('2d');\n",
" this.rubberband_context.strokeStyle = '#000000';\n",
"\n",
" this._resize_canvas = function (width, height, forward) {\n",
" if (forward) {\n",
" canvas_div.style.width = width + 'px';\n",
" canvas_div.style.height = height + 'px';\n",
" }\n",
" };\n",
"\n",
" // Disable right mouse context menu.\n",
" this.rubberband_canvas.addEventListener('contextmenu', function (_e) {\n",
" event.preventDefault();\n",
" return false;\n",
" });\n",
"\n",
" function set_focus() {\n",
" canvas.focus();\n",
" canvas_div.focus();\n",
" }\n",
"\n",
" window.setTimeout(set_focus, 100);\n",
"};\n",
"\n",
"mpl.figure.prototype._init_toolbar = function () {\n",
" var fig = this;\n",
"\n",
" var toolbar = document.createElement('div');\n",
" toolbar.classList = 'mpl-toolbar';\n",
" this.root.appendChild(toolbar);\n",
"\n",
" function on_click_closure(name) {\n",
" return function (_event) {\n",
" return fig.toolbar_button_onclick(name);\n",
" };\n",
" }\n",
"\n",
" function on_mouseover_closure(tooltip) {\n",
" return function (event) {\n",
" if (!event.currentTarget.disabled) {\n",
" return fig.toolbar_button_onmouseover(tooltip);\n",
" }\n",
" };\n",
" }\n",
"\n",
" fig.buttons = {};\n",
" var buttonGroup = document.createElement('div');\n",
" buttonGroup.classList = 'mpl-button-group';\n",
" for (var toolbar_ind in mpl.toolbar_items) {\n",
" var name = mpl.toolbar_items[toolbar_ind][0];\n",
" var tooltip = mpl.toolbar_items[toolbar_ind][1];\n",
" var image = mpl.toolbar_items[toolbar_ind][2];\n",
" var method_name = mpl.toolbar_items[toolbar_ind][3];\n",
"\n",
" if (!name) {\n",
" /* Instead of a spacer, we start a new button group. */\n",
" if (buttonGroup.hasChildNodes()) {\n",
" toolbar.appendChild(buttonGroup);\n",
" }\n",
" buttonGroup = document.createElement('div');\n",
" buttonGroup.classList = 'mpl-button-group';\n",
" continue;\n",
" }\n",
"\n",
" var button = (fig.buttons[name] = document.createElement('button'));\n",
" button.classList = 'mpl-widget';\n",
" button.setAttribute('role', 'button');\n",
" button.setAttribute('aria-disabled', 'false');\n",
" button.addEventListener('click', on_click_closure(method_name));\n",
" button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n",
"\n",
" var icon_img = document.createElement('img');\n",
" icon_img.src = '_images/' + image + '.png';\n",
" icon_img.srcset = '_images/' + image + '_large.png 2x';\n",
" icon_img.alt = tooltip;\n",
" button.appendChild(icon_img);\n",
"\n",
" buttonGroup.appendChild(button);\n",
" }\n",
"\n",
" if (buttonGroup.hasChildNodes()) {\n",
" toolbar.appendChild(buttonGroup);\n",
" }\n",
"\n",
" var fmt_picker = document.createElement('select');\n",
" fmt_picker.classList = 'mpl-widget';\n",
" toolbar.appendChild(fmt_picker);\n",
" this.format_dropdown = fmt_picker;\n",
"\n",
" for (var ind in mpl.extensions) {\n",
" var fmt = mpl.extensions[ind];\n",
" var option = document.createElement('option');\n",
" option.selected = fmt === mpl.default_extension;\n",
" option.innerHTML = fmt;\n",
" fmt_picker.appendChild(option);\n",
" }\n",
"\n",
" var status_bar = document.createElement('span');\n",
" status_bar.classList = 'mpl-message';\n",
" toolbar.appendChild(status_bar);\n",
" this.message = status_bar;\n",
"};\n",
"\n",
"mpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n",
" // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n",
" // which will in turn request a refresh of the image.\n",
" this.send_message('resize', { width: x_pixels, height: y_pixels });\n",
"};\n",
"\n",
"mpl.figure.prototype.send_message = function (type, properties) {\n",
" properties['type'] = type;\n",
" properties['figure_id'] = this.id;\n",
" this.ws.send(JSON.stringify(properties));\n",
"};\n",
"\n",
"mpl.figure.prototype.send_draw_message = function () {\n",
" if (!this.waiting) {\n",
" this.waiting = true;\n",
" this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n",
" }\n",
"};\n",
"\n",
"mpl.figure.prototype.handle_save = function (fig, _msg) {\n",
" var format_dropdown = fig.format_dropdown;\n",
" var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n",
" fig.ondownload(fig, format);\n",
"};\n",
"\n",
"mpl.figure.prototype.handle_resize = function (fig, msg) {\n",
" var size = msg['size'];\n",
" if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n",
" fig._resize_canvas(size[0], size[1], msg['forward']);\n",
" fig.send_message('refresh', {});\n",
" }\n",
"};\n",
"\n",
"mpl.figure.prototype.handle_rubberband = function (fig, msg) {\n",
" var x0 = msg['x0'] / fig.ratio;\n",
" var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n",
" var x1 = msg['x1'] / fig.ratio;\n",
" var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n",
" x0 = Math.floor(x0) + 0.5;\n",
" y0 = Math.floor(y0) + 0.5;\n",
" x1 = Math.floor(x1) + 0.5;\n",
" y1 = Math.floor(y1) + 0.5;\n",
" var min_x = Math.min(x0, x1);\n",
" var min_y = Math.min(y0, y1);\n",
" var width = Math.abs(x1 - x0);\n",
" var height = Math.abs(y1 - y0);\n",
"\n",
" fig.rubberband_context.clearRect(\n",
" 0,\n",
" 0,\n",
" fig.canvas.width / fig.ratio,\n",
" fig.canvas.height / fig.ratio\n",
" );\n",
"\n",
" fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n",
"};\n",
"\n",
"mpl.figure.prototype.handle_figure_label = function (fig, msg) {\n",
" // Updates the figure title.\n",
" fig.header.textContent = msg['label'];\n",
"};\n",
"\n",
"mpl.figure.prototype.handle_cursor = function (fig, msg) {\n",
" var cursor = msg['cursor'];\n",
" switch (cursor) {\n",
" case 0:\n",
" cursor = 'pointer';\n",
" break;\n",
" case 1:\n",
" cursor = 'default';\n",
" break;\n",
" case 2:\n",
" cursor = 'crosshair';\n",
" break;\n",
" case 3:\n",
" cursor = 'move';\n",
" break;\n",
" }\n",
" fig.rubberband_canvas.style.cursor = cursor;\n",
"};\n",
"\n",
"mpl.figure.prototype.handle_message = function (fig, msg) {\n",
" fig.message.textContent = msg['message'];\n",
"};\n",
"\n",
"mpl.figure.prototype.handle_draw = function (fig, _msg) {\n",
" // Request the server to send over a new figure.\n",
" fig.send_draw_message();\n",
"};\n",
"\n",
"mpl.figure.prototype.handle_image_mode = function (fig, msg) {\n",
" fig.image_mode = msg['mode'];\n",
"};\n",
"\n",
"mpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n",
" for (var key in msg) {\n",
" if (!(key in fig.buttons)) {\n",
" continue;\n",
" }\n",
" fig.buttons[key].disabled = !msg[key];\n",
" fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n",
" }\n",
"};\n",
"\n",
"mpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n",
" if (msg['mode'] === 'PAN') {\n",
" fig.buttons['Pan'].classList.add('active');\n",
" fig.buttons['Zoom'].classList.remove('active');\n",
" } else if (msg['mode'] === 'ZOOM') {\n",
" fig.buttons['Pan'].classList.remove('active');\n",
" fig.buttons['Zoom'].classList.add('active');\n",
" } else {\n",
" fig.buttons['Pan'].classList.remove('active');\n",
" fig.buttons['Zoom'].classList.remove('active');\n",
" }\n",
"};\n",
"\n",
"mpl.figure.prototype.updated_canvas_event = function () {\n",
" // Called whenever the canvas gets updated.\n",
" this.send_message('ack', {});\n",
"};\n",
"\n",
"// A function to construct a web socket function for onmessage handling.\n",
"// Called in the figure constructor.\n",
"mpl.figure.prototype._make_on_message_function = function (fig) {\n",
" return function socket_on_message(evt) {\n",
" if (evt.data instanceof Blob) {\n",
" /* FIXME: We get \"Resource interpreted as Image but\n",
" * transferred with MIME type text/plain:\" errors on\n",
" * Chrome. But how to set the MIME type? It doesn't seem\n",
" * to be part of the websocket stream */\n",
" evt.data.type = 'image/png';\n",
"\n",
" /* Free the memory for the previous frames */\n",
" if (fig.imageObj.src) {\n",
" (window.URL || window.webkitURL).revokeObjectURL(\n",
" fig.imageObj.src\n",
" );\n",
" }\n",
"\n",
" fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n",
" evt.data\n",
" );\n",
" fig.updated_canvas_event();\n",
" fig.waiting = false;\n",
" return;\n",
" } else if (\n",
" typeof evt.data === 'string' &&\n",
" evt.data.slice(0, 21) === 'data:image/png;base64'\n",
" ) {\n",
" fig.imageObj.src = evt.data;\n",
" fig.updated_canvas_event();\n",
" fig.waiting = false;\n",
" return;\n",
" }\n",
"\n",
" var msg = JSON.parse(evt.data);\n",
" var msg_type = msg['type'];\n",
"\n",
" // Call the \"handle_{type}\" callback, which takes\n",
" // the figure and JSON message as its only arguments.\n",
" try {\n",
" var callback = fig['handle_' + msg_type];\n",
" } catch (e) {\n",
" console.log(\n",