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<!-- Import libraries-->
<script src="libraries/jquery-3.4.1.min.js"></script>
<script type="text/javascript" src="libraries/ngl.js"></script>
<script type="text/javascript" src="libraries/webGavrog/runtime.js"></script>
<script type="text/javascript" src="libraries/webGavrog/vendors.js"></script>
<script type="text/javascript" src="libraries/webGavrog/main.js"></script>
<script src="libraries/3Dmol-min.js"></script>
<script src="libraries/bootstrap.min.js"></script>
<script src="https://cdn.bokeh.org/bokeh/release/bokeh-2.3.1.min.js"></script>
<!-- Import CSS -->
<link rel="stylesheet" href="libraries/bootstrap.min.css">
<link rel="stylesheet" href="libraries/bootstrap_custom.min.css">
<!-- Custom CSS code is placed within the <style> tag -->
<style>
.round_button { /* For the round_button class */
border-radius: 25px;
font-size: 16px;
font-weight: bold;
min-width: 130px;
width: 33%;
background-color: #0000FF; /*blue*/
}
#plot_display { /* For anything with the plot_display ID */
display: block;
margin-left: auto;
margin-right: auto;
width: 100%;
}
#raw_data_figure {
display: block;
margin-left: auto;
margin-right: auto;
width: 50%;
}
.minibutton {
background: none;
border: none;
}
.round_minibutton {
background: none;
border-radius: 25px;
min-width: 130px;
width: 33%;
}
</style>
<head>
<!-- Global site tag (gtag.js) - Google Analytics -->
<script async src="https://www.googletagmanager.com/gtag/js?id=G-RP50QX41FS"></script>
<script>
window.dataLayer = window.dataLayer || [];
function gtag() { dataLayer.push(arguments); }
gtag('js', new Date());
gtag('config', 'G-RP50QX41FS');
</script>
<!-- End of Google Analytics stuff -->
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
<title>SESAMI Website</title>
</head>
<!-- Beginning of HTML section -->
<body>
<!-- This div contains a navbar. -->
<div class="navbar navbar-expand-lg fixed-top navbar-dark bg-primary">
<div class="container">
<a href="../" class="navbar-brand" style='font-size: 30px;'>A web interface for SESAMI analysis</a>
<div class="collapse navbar-collapse" id="navbarResponsive" style='font-size: 20px;'>
<ul class="navbar-nav">
<li class="nav-item" style='padding-left: 30px;'>
<a class="nav-link" href="/about_page">About</a>
</li>
<li class="nav-item" style='padding-left: 30px;'>
<a class="nav-link" href="https://github.com/hjkgrp/SESAMI_web">Source Code</a>
</li>
<li class="nav-item" style='padding-left: 30px;'>
<a class="nav-link" href="/how_to_cite">How to Cite</a>
</li>
</ul>
</div>
</div>
</div>
<!-- This div contains general information. -->
<div style='font-size:18px;' class="container">
<p>Tired of using an old excel spreadsheet from your co-workers?</p>
<p><b>On-the-fly</b>, this website performs <b>Brunauer-Emmett-Teller (BET)</b>, <b>BET+Excess Sorption Work (ESW)</b>, and <b>Machine Learning (ML)</b> analysis
to accurately estimate the surface area of nanoporous materials. You can upload your isotherm data in either <b>Comma Separated-Values (CSV)</b> or <b>Adsorption Information File (AIF)</b> file format.</p>
<p><b>Step 1 (optional): </b>Convert RAW output files from commercial equipment to AIF format using <a href="http://adsorptioninformationformat.com/raw2aif" target="_blank">this link.</a></p>
<p><b>Step 2: </b>Upload the converted data from Step 1 by clicking "Upload CSV or AIF"</p>
<p><b>Step 3: </b>Click "Run calculation"</p>
</div>
<div style='font-size:14px; background-color:#F6EFA6; border: solid black 2px;' class="container">
Default gas molecule for the analysis is <b>Nitrogen</b>, i.e. N<sub>2</sub>.<br><br>
Calculations assume the input data file contains an isotherm measured at one of the following conditions:<br>
• Nitrogen: T = 77 K <br>
• Argon: T = 87 K <br>
For both cases, p<sub>0</sub> = 1e5 Pa. The cross section of nitrogen used in the code is 16.2 Å<sup>2</sup> per molecule. The cross section of argon used is 14.2 Å<sup>2</sup> per molecule.<br><br>
If you want to analyze a simulated BET isotherm, <a href="/example_csv" download>download the example CSV file</a> and format your simulation data accordingly. Note the units and the column names in the first row!<br>
</div>
<div style='width:100%; text-align:center; margin-top:0.25cm;'>
<input type="checkbox" id="permission_checkbox" onclick='handleCheckbox(this)'>
<label for="permission_checkbox"> Share data with developers!</label><br>
</div>
<!-- This div displays figures and has a button that allows the user to download the figure pngs. -->
<div id='plot_div' style='font-size:16px; padding-top: 30px; width:100%;' class="container">
<!-- Figure type -->
<div class = 'row'>
<div class='col-lg-4'>
Figure type
</div>
<div class='col-lg-8'>
<input autocomplete="off" id='plottype_dropdown' style='font-size: 16px; width:100%' class='form-control locksMetrics' list='plottype_list' onmousedown="value = '';" onChange='switch_plot(this.value)'/>
<datalist id='plottype_list' style='font-size: 16px;'>
<!-- Set with option_generator function -->
</datalist>
</div>
</div>
<div style='text-align:center;'>
<img style='margin-top: 0.25cm;' id='plot_display' alt='SESAMI 1 plot'>
<button id='download_button' class='btn btn-primary round_button' style='font-size:16px;'>Download figure</button>
</div>
</div>
<!-- This div contains the print out of calculations run on the website. -->
<div style='font-size:16px; padding-top: 30px' id='print_out' class="container">
<p style='font-size:16px; margin-top:0.25cm;'>Any linear region selected by SESAMI 1.0 will fulfill Rouquerol criteria 1 and 2.</p>
<p style='font-size:16px; margin-top:0.25cm; font-weight:Bold' id='BET_readout_header'>SESAMI 1.0 (BET) results are:</p>
<p style='font-size:16px; margin-top:0.25cm;' id='BET_readout'></p>
<p style='font-size:16px; margin-top:0.25cm; font-weight:Bold' id='BETESW_readout_header'>SESAMI 1.0 (BET+ESW) results are:</p>
<p style='font-size:16px; margin-top:0.25cm;' id='BETESW_readout'></p>
<p style='font-size:16px; margin-top:0.25cm; font-weight:Bold' id='ML_prediction_header'>SESAMI 2.0 (LASSO) surface area prediction is:</p>
<p style='font-size:16px; margin-top:0.25cm;' id='ML_prediction'></p>
</div>
<!-- This div contains important buttons that run the pivotal commands on the website. -->
<div style='font-size:16px; padding-top: 30px' class="container">
<!-- Create a section containing buttons -->
<div class='col-lg-12'>
<div style='width:100%; text-align:center; margin-top:0.25cm;'>
<button id='example_isotherm' class='btn btn-primary round_button' style='font-size:16px;'>Example isotherm</button>
<button id='upload_button' class='btn btn-primary round_button' style='font-size:16px;'>Upload CSV or AIF</button>
<button id='run_button' class='btn btn-primary round_button' style='font-size:16px;'>Run calculation</button>
</div>
</div>
<div style='width:100%; text-align:center; margin-top:0.25cm;'>
<p id='calculation_status'></p> <!-- Will indicate whether a calculation is underway. -->
</div>
<div style='width:100%; text-align:center; margin-top:0.25cm;'>
<p id='calculation_hint'>Did you receive an empty error message? Try reloading the webpage and trying the calculation again.</p>
</div>
<div style='font-size:16px; margin-top:0.25cm;' id='upload_status'></div>
<!-- This div has links for the user to download the example input files. -->
<div class='col-lg-12'>
<div style='width:100%; text-align:center; margin-top:0.25cm;'>
<a href="/example_csv" download> Download the example CSV file </a>      
<a href="/example_aif" download> Download the example AIF file </a>
</div>
</div>
<!-- This div displays the data the user uploads. -->
<div id='raw_data_display'>
<img style='margin-top: 0.25cm;' id='raw_data_figure' alt='Your raw data'>
</div>
</div>
<!-- This div is a space for users to enter information about themselves so we can improve our services. -->
<div id='about_you_container' style='font-size:16px; padding-top: 30px; width:100%;' class="container">
<div style='text-align: center;'>
<button class='round_minibutton' id='about_you_button'>About you</button>
</div>
<div id='about_you_content'>
Name: <input type="text" id='user_name' class='form-control'><br>
Email: <input type="text" id='user_email' class='form-control'><br>
Institution: <input type="text" id='user_institution' class='form-control'><br>
Material type: <input type="text" id='user_material' class='form-control'><br>
</div>
</div>
<!-- This div contains general options. -->
<div style='font-size:16px; padding-top: 30px; text-align:center;' class="container">
<button class='round_minibutton' id='general_opt_button'>Show general options</button>
<div id='general_options'>
<!-- Adsorbate -->
<div class='row' id='gas_dropdown_section' style='margin-top: 0.5cm;'>
<div class='col-lg-4'>Type of gas</div>
<div class='col-lg-8'>
<input id='gas_dropdown' autocomplete="off" style='font-size: 16px; width:100%' class='form-control' list='gas_list' onmousedown="value = '';" />
<datalist id='gas_list' style='font-size: 16px;'>
<option value="Nitrogen">
<option value="Argon">
</datalist>
</div>
</div>
<!-- Custom adsorbate -->
<div class='row' style='margin-top: 0.5cm;'>
<div class='col-lg-4'>Custom adsorbate</div>
<div class='col-lg-8'>
<input id='custom_dropdown' autocomplete="off" style='font-size: 16px; width:100%' class='form-control' list='custom_list' onmousedown="value = '';" />
<datalist id='custom_list' style='font-size: 16px;'>
<option value="Yes">
<option value="No">
</datalist>
</div>
</div>
<div id='custom_options'>
<!-- Custom adsorbate cross section -->
<div class = 'row' style='margin-top: 0.25cm;'>
<div class='col-lg-4'>
Custom adsorbate cross section (Å<sup>2</sup>)
</div>
<div class='col-lg-8'>
<input type="text" id="custom_xsection_input" style='font-size: 16px; width:100%' class='form-control' placeholder="16.2">
</div>
</div>
<!-- Custom adsorbate temperature -->
<div class = 'row' style='margin-top: 0.25cm;'>
<div class='col-lg-4'>
Custom adsorbate temperature (K)
</div>
<div class='col-lg-8'>
<input type="text" id="custom_temperature_input" style='font-size: 16px; width:100%' class='form-control' placeholder="77">
</div>
</div>
<!-- Custom adsorbate saturation pressure -->
<div class = 'row' style='margin-top: 0.25cm;'>
<div class='col-lg-4'>
Custom adsorbate saturation pressure (Pa)
</div>
<div class='col-lg-8'>
<input type="text" id="custom_sat_p_input" style='font-size: 16px; width:100%' class='form-control' placeholder="100000">
</div>
</div>
</div>
<div class='row'>
<div class='col-lg-4' style='margin-top: 1.5cm;'> <h5>SESAMI 1.0</h5> </div>
</div>
<!-- Scope -->
<div class='row' style='margin-top: 0.25cm;'>
<div class='col-lg-4'>Scope</div>
<div class='col-lg-8'>
<input id='scope_dropdown' autocomplete="off" style='font-size: 16px; width:100%' class='form-control' list='scope_list' onmousedown="value = '';" />
<datalist id='scope_list' style='font-size: 16px;'>
<option value="BET and BET+ESW">
<option value="BET">
</datalist>
</div>
</div>
<!-- R^2 cutoff -->
<div class = 'row' style='margin-top: 0.25cm;'>
<div class='col-lg-4'>
R<sup>2</sup> cutoff
</div>
<div class='col-lg-8'>
<input type="text" id="r2cutoff_input" style='font-size: 16px; width:100%' class='form-control' placeholder="0.9995">
</div>
</div>
<!-- R^2 min -->
<div class = 'row' style='margin-top: 0.25cm;'>
<div class='col-lg-4'>
R<sup>2</sup> min
</div>
<div class='col-lg-8'>
<input type="text" id="r2min_input" style='font-size: 16px; width:100%' class='form-control' placeholder="0.998">
</div>
</div>
<div id='ml_section'>
<div class='row' style='margin-top: 1.5cm;'>
<div class='col-lg-4'> <h5>SESAMI 2.0</h5> </div>
</div>
<!-- ML -->
<div class='row' style='margin-top: 0.25cm;'>
<div class='col-lg-4'>Include ML prediction?</div>
<div class='col-lg-8'>
<input id='ML_dropdown' autocomplete="off" style='font-size: 16px; width:100%' class='form-control' list='ML_list' onmousedown="value = '';" />
<datalist id='ML_list' style='font-size: 16px;'>
<option value="Yes">
<option value="No">
</datalist>
</div>
<p style='margin-top: 0.25cm;'>
Note: The Lasso ML model prediction is automatically multiplied by 1.148 if Nitrogen gas is the adsorbate. See the SESAMI 2 paper for more details.
</p>
</div>
</div>
</div>
</div>
<!-- This div contains plotting options. -->
<div style='font-size:16px; padding-top: 30px; text-align:center;' class="container">
<button class='round_minibutton' id='plotting_opt_button'>Show plotting options (SESAMI 1.0)</button>
<div id='plotting_options'>
<!-- Figure legend -->
<div class = 'row' style='margin-top: 0.25cm;'>
<div class='col-lg-4'>
Figure legend
</div>
<div class='col-lg-8'>
<input autocomplete="off" id='legend_dropdown' style='font-size: 16px; width:100%' class='form-control' placeholder="Yes" list='legend_list' onmousedown="value = '';" />
<datalist id='legend_list' style='font-size: 16px;'>
<option value="Yes">
<option value="No">
</datalist>
</div>
</div>
<!-- Figure font size -->
<div class = 'row' style='margin-top: 0.25cm;'>
<div class='col-lg-4'>
Figure font size
</div>
<div class='col-lg-8'>
<input autocomplete="off" id='fontsize_dropdown' style='font-size: 16px; width:100%' class='form-control' placeholder="10" list='fontsize_list' onmousedown="value = '';" />
<datalist id='fontsize_list' style='font-size: 16px;'>
<option value="6">
<option value="8">
<option value="10">
<option value="12">
<option value="14">
<option value="16">
<option value="18">
<option value="20">
</datalist>
</div>
</div>
<!-- Figure font type -->
<div class = 'row' style='margin-top: 0.25cm;'>
<div class='col-lg-4'>
Figure font type
</div>
<div class='col-lg-8'>
<input autocomplete="off" id='fonttype_dropdown' style='font-size: 16px; width:100%' class='form-control' placeholder="sans-serif" list='fonttype_list' onmousedown="value = '';" />
<datalist id='fonttype_list' style='font-size: 16px;'>
<option value="sans-serif">
<option value="serif">
<option value="monospace">
</datalist>
</div>
</div>
<!-- Figure dpi -->
<div class = 'row' style='margin-top: 0.25cm;'>
<div class='col-lg-4'>
Figure dpi
</div>
<div class='col-lg-8'>
<input autocomplete="off" id='dpi_dropdown' style='font-size: 16px; width:100%' class='form-control' placeholder="300" list='dpi_list' onmousedown="value = '';" />
<datalist id='dpi_list' style='font-size: 16px;'>
<option value="300">
<option value="600">
</datalist>
</div>
</div>
</div>
</div>
<!-- This div contains a bottom bar. -->
<div class="navbar navbar-expand-lg relative navbar-light bg-light" style="margin-top: 50px; font-size: 18px;">
<div class="container">
<ul class="navbar-nav">
<li class="nav-item">
<a class="nav-link disabled">Site developed and maintained by Gianmarco Terrones (Kulik Group @ MIT) and Dr. Yongchul G. Chung (Pusan National
University)</a>
</li>
</ul>
</div>
</div>
<!-- This html element stores any uploaded CSV files. Does not display. -->
<input id="file_input" type="file" name="file_input" style="display:none" />
</body>
<!-- End of HTML section -->
<!-- Beginning of JavaScript section -->
<script>
// Global variables
let FIGURE_PATH = null
let OUTPUT_NAME = null
let PLOT_NUMBER = null
// A helper function that clears text out, hides elements, and sets default values.
function clean_slate() {
clean_slate_partial()
// setting default values
$('#permission_checkbox').prop('checked', true)
$('#gas_dropdown').val('Nitrogen')
$('#custom_dropdown').val('No')
$('#custom_xsection_input').val('16.2')
$('#custom_temperature_input').val('77')
$('#custom_sat_p_input').val('100000')
$('#scope_dropdown').val('BET and BET+ESW')
$('#r2cutoff_input').val('0.9995')
$('#r2min_input').val('0.998')
$('#ML_dropdown').val('No')
$('#legend_dropdown').val('Yes')
$('#fontsize_dropdown').val('10')
$('#fonttype_dropdown').val('sans-serif')
$('#dpi_dropdown').val('300')
$("#custom_options").hide()
}
// This function only clears and hides elements but does not reset the general and plotting options.
function clean_slate_partial() {
$('#BET_readout').text('')
$('#BETESW_readout').text('')
$('#ML_prediction').text('')
$('#plottype_dropdown').val('Multiplot')
$('#plot_div').hide()
$('#print_out').hide()
$('#general_options').hide()
$('#general_opt_button').text('Show general options')
$('#plotting_options').hide()
$('#plotting_opt_button').text('Show plotting options (SESAMI 1.0)')
$('#about_you_content').hide()
$('#raw_data_display').hide()
$('#calculation_hint').hide()
}
// This next function is used to parse a CSV to an array.
// ref: http://stackoverflow.com/a/1293163/2343
// This will parse a delimited string into an array of
// arrays. The default delimiter is the comma, but this
// can be overridden in the second argument.
function CSVToArray( strData, strDelimiter ){
// Check to see if the delimiter is defined. If not,
// then default to comma.
strDelimiter = (strDelimiter || ",");
// Create a regular expression to parse the CSV values.
var objPattern = new RegExp(
(
// Delimiters.
"(\\" + strDelimiter + "|\\r?\\n|\\r|^)" +
// Quoted fields.
"(?:\"([^\"]*(?:\"\"[^\"]*)*)\"|" +
// Standard fields.
"([^\"\\" + strDelimiter + "\\r\\n]*))"
),
"gi"
);
// Create an array to hold our data. Give the array
// a default empty first row.
var arrData = [[]];
// Create an array to hold our individual pattern
// matching groups.
var arrMatches = null;
// Keep looping over the regular expression matches
// until we can no longer find a match.
while (arrMatches = objPattern.exec( strData )){
// Get the delimiter that was found.
var strMatchedDelimiter = arrMatches[ 1 ];
// Check to see if the given delimiter has a length
// (is not the start of string) and if it matches
// field delimiter. If it does not, then we know
// that this delimiter is a row delimiter.
if (
strMatchedDelimiter.length &&
strMatchedDelimiter !== strDelimiter
){
// Since we have reached a new row of data,
// add an empty row to our data array.
arrData.push( [] );
}
var strMatchedValue;
// Now that we have our delimiter out of the way,
// let's check to see which kind of value we
// captured (quoted or unquoted).
if (arrMatches[ 2 ]){
// We found a quoted value. When we capture
// this value, unescape any double quotes.
strMatchedValue = arrMatches[ 2 ].replace(
new RegExp( "\"\"", "g" ),
"\""
);
} else {
// We found a non-quoted value.
strMatchedValue = arrMatches[ 3 ];
}
// Now that we have our value string, let's add
// it to the data array.
arrData[ arrData.length - 1 ].push( strMatchedValue );
}
// Return the parsed data.
return( arrData );
}
// Used for ensuring that only .csv and .aif files are uploaded.
function getExtension(filename) {
var parts = filename.split('.');
return parts[parts.length - 1];
}
function isCSV(filename) {
var ext = getExtension(filename);
return ext == 'csv';
}
function isAIF(filename) {
var ext = getExtension(filename);
return (ext == 'aif' || ext == 'aiff');
}
// Helper function that displays the isotherm data the user has selected in a semilogx plot.
function show_data(){
$('#raw_data_display').show()
$.get("/show_data").done(
function (response) {
FIGURE_PATH = 'generated_plots/raw_data_' + response + '.png'
$("#raw_data_figure").attr("src",FIGURE_PATH); // Setting the source of the image element appropriately
}
).fail(function(xhr, textStatus, errorThrown) { // for timeout error; triggers after 1 minute
alert(errorThrown)
return // doesn't continue
})
}
// Runs when the "Example isotherm" button is clicked.
$('#example_isotherm').click(function () {
clean_slate_partial()
$('#upload_status').text('Example isotherm loaded.');
$.get("/copy_example").done( // Copy the example input's txt file into the user's folder.
function (response) {
show_data()
})
})
// Runs when the Custom adsorbate dropdown is changed.
$("#custom_dropdown").change(function () {
custom = $('#custom_dropdown').val()
if (custom == 'Yes'){
$("#gas_dropdown_section").hide()
$("#custom_options").show()
// Disable ML approach for a custom gas, since the ML approach expects a P0 of 1e5 Pa
$("#ml_section").hide()
$('#ML_dropdown').val('No')
} else if (custom == 'No'){
$("#gas_dropdown_section").show()
$("#custom_options").hide()
$("#ml_section").show()
}
});
// Runs when the "Upload CSV or AIF" button is clicked.
$('#upload_button').on('click', function () { // button triggers upload
clean_slate_partial()
$('#file_input').val(null) // clears file_input
$('#file_input').trigger('click'); // OS file selection
});
$("#file_input").change(function () {
// Check if uploaded file is a CSV or AIF
if (!isCSV(this.value) && !isAIF(this.value)) { // if the uploaded file is not a CSV nor an AIF
this.value = null; // clear the non-CSV and non-AIF file
$('#upload_status').text('')
alert("The uploaded file must be a csv or AIF file.");
return; // If not a CSV nor an AIF, doesn't continue.
}
let myFile = document.getElementById('file_input').files[0]; // the uploaded file
if (isCSV(this.value)) {
$('#upload_status').text('Selected CSV: ' + myFile.name);
} else {
$('#upload_status').text('Selected AIF: ' + myFile.name);
}
if (this.files[0].size == 0) { // check if file is empty
this.value = null; // clear the file
$('#upload_status').text('')
alert("The uploaded file cannot be empty.");
return; // If the user uploaded an empty file, doesn't continue.
}
// Converting the uploaded file to a TXT, and checking its formatting
if (isCSV(this.value)) { // CSV case
myFile.text().then(function (my_content) {
// my_content is the content of the loaded CSV
my_content = CSVToArray(my_content, ',')
myDict = {'my_content': my_content}
$.post("/save_csv_txt", JSON.stringify(myDict)).done( // Saves the uploaded CSV as a CSV and TXT file in the user's folder.
function (response) {
// Check if the uploaded CSV is of the right format. If not, clear the file_input and upload_status elements.
$.get("/check_csv").done(
function (response) {
if (response.startsWith('Warning: Lacking data at low pressure region.')) {
alert(response) // Gives the user the warning message
} else if (response != 'All good!') { // The all good message indicates no errors were found in the input.
this.value = null; // clear the bad CSV file
$('#upload_status').text('')
alert(response) // Gives the user the error message
return // doesn't continue
}
show_data()
})
})
.fail(function(xhr, textStatus, errorThrown) { // for timeout error; triggers after 1 minute
alert(errorThrown)
return // doesn't continue
})
})
} else { // AIF case
myFile.text().then(function (my_content) {
myDict = {'my_content': my_content}
$.post("/save_aif_txt", JSON.stringify(myDict)).done( // Saves the uploaded AIF as an AIF and TXT file in the user's folder.
function (response) {
// Check if the uploaded AIF is of the right format. If not, clear the file_input and upload_status elements.
if (response != 'All good!') {
this.value = null; // clear the bad CSV file
$('#upload_status').text('')
alert(response)
return // doesn't continue
}
show_data()
})
.fail(function(xhr, textStatus, errorThrown) { // for timeout error; triggers after 1 minute
alert(errorThrown)
return // doesn't continue
})
})
}
});
// Function for formatting SESAMI 1 output. Replaces \n with breaks. Also adds some superscript and subscript.
// Source: https://stackoverflow.com/questions/4535888/jquery-text-and-newlines
$.fn.multiline = function(text){
this.text(text);
this.html(this.html().replace(/\n/g,'<br/>'));
this.html(this.html().replace(/2sup/g,'<sup>2</sup>'));
this.html(this.html().replace(/msub/g,'<sub>m</sub>'));
return this;
}
// Function for populating the plot dropdown based on whether BET+ESW plots are made or not.
var option_generator = function(scope) {
if (scope == 'BET and BET+ESW') {
options_list = ["Multiplot", "Isotherm", "BET", "ESW", "BET Linear Region", "BET+ESW Linear Region"]
} else if(scope == 'BET') {
options_list = ["Multiplot", "Isotherm", "BET", "BET Linear Region"]
}
else{
console.log("Error. Scope is " + scope)
}
var options = ''
for (var i = 0; i < options_list.length; i++) {
options += '<option value="' + options_list[i] + '" />';
}
return options
}
// Runs when the "Run calculation" button is clicked.
$('#run_button').click(function () {
clean_slate_partial()
// Check if the user has uploaded an isotherm or if they have selected the example isotherm.
let myFile = document.getElementById('file_input').files[0]; // the uploaded file
if (myFile == undefined && $('#upload_status').text() != 'Example isotherm loaded.') { // The user has neither uploaded an isotherm nor selected the example.
alert("Must select an isotherm for analysis first. Please either use the example isotherm or upload your own isotherm.");
return;
}
dpi = $('#dpi_dropdown').val() // Check which dpi is selected in the dpi dropdown.
font_size = $('#fontsize_dropdown').val()
font_type = $('#fonttype_dropdown').val()
legend = $('#legend_dropdown').val()
R2cutoff = $('#r2cutoff_input').val()
R2min = $('#r2min_input').val()
gas = $('#gas_dropdown').val()
scope = $('#scope_dropdown').val()
ML_boolean = $('#ML_dropdown').val()
// Account for if custom adsorbate settings are used.
custom_boolean = $('#custom_dropdown').val()
custom_xsection = $('#custom_xsection_input').val()
custom_temperature = $('#custom_temperature_input').val()
custom_sat_p_input = $('#custom_sat_p_input').val()
// Ensuring that no dropdowns options are empty.
const var_names = ["Type of gas", "Custom adsorbate", "Scope", "Include ML prediction?", "Figure legend", "Figure font size", "Figure font type", "Figure dpi"]
const vars = [gas, custom_boolean, scope, ML_boolean, legend, font_size, font_type, dpi]
// If we are using the custom adsorbate, don't care if type of gas is empty.
if (custom_boolean == 'Yes') {
var_names.shift() // Remove first element.
vars.shift()
}
for (let i=0; i<= vars.length; i++){
if (vars[i] == ''){
error_message = var_names[i].concat(" dropdown is empty. Please select an option.")
alert(error_message)
return; // Quit the function
}
}
// Ensuring the user put in numbers for R2 cutoff and R2min
if (isNaN(R2cutoff) || isNaN(R2min)) {
alert("R2cutoff and R2min must be numbers.");
return;
}
if (R2cutoff >= 1 || R2min >= 1 || R2cutoff <= 0 || R2min <= 0) {
alert("R2cutoff and R2min must be between zero and one."); // Values outside this range don't make sense.
return;
}
// Ensuring the user put in numbers for custom_xsection, custom_temperature, custom_sat_p_input
if (custom_boolean == 'Yes'){ // Only need to check this if the user is using the custom adsorbate option.
if (isNaN(custom_xsection) || isNaN(custom_temperature) || isNaN(custom_sat_p_input)) {
alert("Custom adsorbate cross section, temperature, and saturation pressure must be numbers.");
return;
}
if (custom_xsection <=0 || custom_temperature <=0 || custom_sat_p_input <=0) {
alert("Custom adsorbate cross section, temperature, and saturation pressure must be greater than zero.");
return;
}
}
// If the user used the font size drop down but never clicked anything, need to prevent this error of an empty field.
if (font_size == '') {
font_size = '10'
}
if (dpi == '') {
dpi = '300'
}
// User options
myDict = {
'dpi': dpi,
'font size': font_size,
'font type': font_type,
'legend': legend,
'R2 cutoff': R2cutoff,
'R2 min': R2min,
'gas': gas,
'scope': scope,
'ML': ML_boolean,
'custom adsorbate': custom_boolean,
'custom cross section': custom_xsection,
'custom temperature': custom_temperature,
'custom saturation pressure': custom_sat_p_input
}
// Setting the options of plottype_dropdown based on the scope
document.getElementById('plottype_list').innerHTML = option_generator(scope)
$('#calculation_status').text('Calculating...') // Gives the user peace of mind that their button click actually did something :)
$('#calculation_hint').show()
$.post("/run_SESAMI", JSON.stringify(myDict)).done( // Runs the SESAMI 1 and SESAMI 2 code
function (response) {
// Failure handling
if (response == 'No eswminima') {
alert("No ESW minima was found. Change scope (general options) to BET.")
$('#calculation_status').text('')
return; // Does not continue if this failure occurs.
}
if (response == 'BET linear failure') {
alert("No suitable BET linear region has been found. Try lowering R2min.")
$('#calculation_status').text('')
return; // Does not continue if this failure occurs.
}
if (response == 'BET+ESW linear failure') {
alert("No suitable BET+ESW linear region has been found. Try lowering R2min, or change scope (general options) to BET.")
$('#calculation_status').text('')
return; // Does not continue if this failure occurs.
}
BET_analysis = response['BET_analysis']
PLOT_NUMBER = response['plot_number']
$('#BET_readout').multiline(BET_analysis)
if (scope == 'BET and BET+ESW') {
BETESW_analysis = response['BETESW_analysis']
$('#BETESW_readout_header').show()
$('#BETESW_readout').multiline(BETESW_analysis)
} else {
// The user asked for no BET+ESW. So no BET+ESW is shown.
$('#BETESW_readout_header').hide()
}
if (ML_boolean == 'Yes') {
// The user requested a ML (SESAMI 2.0) prediction.
ML_prediction = response['ML_prediction']
if (ML_prediction.startsWith("Missing data in a pressure bin")) {
// This means the ML code could not be run. See SESAMI_2.py.
$('#ML_prediction_header').hide()
alert(ML_prediction)
}
else {
// The ML code ran. Display the ML prediction.
$('#ML_prediction_header').show()
$('#ML_prediction').multiline(ML_prediction + ' m2sup/g') // The multiline function from earlier formats things nicely.
}
} else {
// The user asked for no ML. So no ML is shown.
$('#ML_prediction_header').hide()
}
$('#plot_div').show()
$('#print_out').show()
FIGURE_PATH = 'generated_plots/multiplot_' + PLOT_NUMBER + '.png'
document.getElementById("plot_display").style.width = '100%' // Allow for larger figure for multiplot.
$("#plot_display").attr("src",FIGURE_PATH); // Setting the source of the image element appropriately.
OUTPUT_NAME = 'multiplot.png'
$('#calculation_status').text('')
})
.fail(function(xhr, textStatus, errorThrown) { // for timeout error; triggers after 1 minute
console.log('run_SESAMI failed!')
console.log(xhr)
console.log(textStatus)
console.log(errorThrown)
alert(errorThrown)
$('#calculation_status').text('')
})
info_dict = {
'name': $('#user_name').val(),
'email': $('#user_email').val(),
'institution': $('#user_institution').val(),
'adsorbent': $('#user_material').val(),
'adsorbate': gas,
'custom_adsorbate': custom_boolean,
'custom_cross_section': custom_xsection,
'custom_temperature': custom_temperature,
'custom_saturation_pressure': custom_sat_p_input
}
$.post('/process_info', JSON.stringify(info_dict)).done( // Pushing information to the MongoDB.
)
.fail(function(xhr, textStatus, errorThrown) { // for timeout error; triggers after 1 minute
alert(errorThrown)
$('#calculation_status').text('')
})
})
// Runs when the "Download figure" button is clicked.
$('#download_button').click(function () {
var a = document.createElement('a');
a.href = FIGURE_PATH // The download's location.
a.download = OUTPUT_NAME // The download's name.
document.body.appendChild(a);
a.click();
document.body.removeChild(a); // Downloads the currently displayed figure.
})
// Runs when the "Show general options"/"Hide general options" button is clicked.
$('#general_opt_button').click(function () {
if ($('#general_opt_button').text() == 'Show general options') { // In this case, need to show the section.
$('#general_options').show()
$('#general_opt_button').text('Hide general options')
} else { // In this case, need to hide the section.
$('#general_options').hide()
$('#general_opt_button').text('Show general options')
}
})
// Runs when the "Show plotting options (SESAMI 1.0)" button is clicked.
$('#plotting_opt_button').click(function () {
if ($('#plotting_opt_button').text() == 'Show plotting options (SESAMI 1.0)') { // In this case, need to show the section.
$('#plotting_options').show()
$('#plotting_opt_button').text('Hide plotting options (SESAMI 1.0)')
} else { // In this case, need to hide the section.
$('#plotting_options').hide()
$('#plotting_opt_button').text('Show plotting options (SESAMI 1.0)')
}
})
// Runs when the "About you" button is clicked.
$('#about_you_button').click(function () {
if ($('#about_you_content').is(':visible')) { // In this case, need to hide the section.
$('#about_you_content').hide()
} else {
$('#about_you_content').show() // In this case, need to show the section.
}
})
function switch_plot(plot_type) {
document.getElementById("plot_display").style.width = '50%' // For most cases, enforce a smaller figure.
switch (plot_type){
case 'Multiplot':
FIGURE_PATH = 'generated_plots/multiplot_' + PLOT_NUMBER + '.png'
OUTPUT_NAME = 'multiplot.png'
document.getElementById("plot_display").style.width = '100%' // Allow for larger figure for multiplot.
break
case 'Isotherm':
FIGURE_PATH = 'generated_plots/isotherm_' + PLOT_NUMBER + '.png'
OUTPUT_NAME = 'isotherm.png'
break
case 'BET':
FIGURE_PATH = 'generated_plots/BETPlot_' + PLOT_NUMBER + '.png'
OUTPUT_NAME = 'BET.png'
break
case 'ESW':
FIGURE_PATH = 'generated_plots/ESWPlot_' + PLOT_NUMBER + '.png'
OUTPUT_NAME = 'ESW.png'
break
case 'BET Linear Region':
FIGURE_PATH = 'generated_plots/BETPlotLinear_' + PLOT_NUMBER + '.png'
OUTPUT_NAME = 'BET_linear.png'
break
case 'BET+ESW Linear Region':
FIGURE_PATH = 'generated_plots/BETESWPlot_' + PLOT_NUMBER + '.png'
OUTPUT_NAME = 'BET+ESW.png'
break