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index.html
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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<link rel="stylesheet" href="https://fonts.googleapis.com/css2?family=Josefin+Sans:wght@300;400;600&family=Josefin+Sans:wght@700&display=swap">
<title>NP Ultra Viewer</title>
<style>
body {
display: flex;
flex-direction: column;
align-items: center;
justify-content: center;
height: 100vh;
margin: 0;
background-color: white;
}
p {
font-family: 'Josefin Sans', sans-serif;
font-size: small;
font-weight: 300; /* Make it bold */
}
.container {
display: flex;
height: 100%;
width: 100%;
max-width: 1900px;
max-height: 1200px;
justify-content: center;
align-items: center;
}
/* Left column */
.left-col {
flex: 0 0 10%; /* 10% width, does not grow or shrink */
}
/* Middle column */
.mid-col {
flex: 0 0 50%; /* 50% width, does not grow or shrink */
height: 100%;
display: flex;
flex-direction: column;
text-align: center;
margin-top:20px
}
.mid-col-top-row {
flex: 0 0 10%; /* 10% height, does not grow or shrink */
max-height: 10vh;
display:flex;
flex-direction: row;
}
.mid-col-top-row-left {
flex: 0 0 50%;
}
.mid-col-top-row-right {
flex: 0 0 50%;
}
.mid-col-mid-row {
flex: 0 0 80%; /* 80% height, takes remaining space */
max-height: 80vh;
}
.mid-col-bot-row {
flex: 0 0 10%; /* 10% height, does not grow or shrink */
display: flex; /* Use flexbox to arrange items */
align-items: center; /* Align items vertically */
justify-content: center; /* Center items horizontally */
text-align: center;
max-height: 10vh;
}
/* Right column */
.right-col {
flex: 0 0 40%; /* 40% width, does not grow or shrink */
max-width: 40vw;
display: flex;
flex-direction: row;
}
.right-col-left {
flex: 0 0 50%;
max-width: 20vw;
}
.right-col-right {
flex: 1 0 50%;
display: flex;
flex-direction: column;
max-width: 20vw;
}
.right-col-right-top-row {
flex: 0 0 80%; /* 80% height, does not grow or shrink */
max-width: 20vw;
}
.right-col-right-bot-row {
display: flex;
flex: 1 0 ; /* Take remaining space */
align-items: flex-end; /* Align items to the bottom */
justify-content: center; /* Center items horizontally */
}
.bottom-content {
width: 100%;
bottom: 0;
left: 0;
right: 0;
text-align: center;
}
#probeGraphic {
margin-top: 20px;
margin-bottom: 20px;
width:100%;
background-color: #ffffff00;
}
#unity-container {
width:100%;
height: 100%;
}
#unity-canvas {
width: 95%;
height: 95%;
}
#probeImage {
height: 100%;
max-height: 100vh;
}
#pngImage {
max-width: 20vw;
max-height: 80vh;
}
#gifImage {
width: auto;
height: 100%;
max-height: 100vh;
max-width: 20vw;
object-fit: contain; /* Ensure the aspect ratio is preserved */
}
#logo-brain {
width: 30%;
max-width: 12vw;
margin-left: 2.5%;
margin-right: 2.5%;
}
#logo {
width: 50%;
max-width: 12vw;
margin-left: 2.5%;
margin-right: 2.5%;
}
.table-container {
max-width: 80%; /* Adjust the max-width as needed */
min-width: 30vw; /* Set minimum width */
table-layout: fixed; /* Ensure fixed column width */
margin-bottom: 20px;
margin-right: 10px; /* Add margin to separate the table and the button */
}
#dataTable {
width: 100%; /* Ensure the table takes full width of its container */
table-layout: fixed; /* Ensure fixed column width */
}
#dataTable th {
font-family: 'Josefin Sans', sans-serif;
font-weight: 500; /* Make it bold */
}
#dataTable td {
font-family: 'Josefin Sans', sans-serif;
font-weight: 300; /* Make it thin */
}
.area-button {
width: 11%;
margin: 3px;
padding: 5px;
background-color: white; /* Placeholder color */
color:white;
font-size: smaller;
border:none;
border-radius: 5px;
cursor: pointer;
}
#areaContainer {
max-width: 100%;
}
.button {
background-color: #add8e6;
color: white;
padding: 10px 20px;
margin: 5px;
border: none;
border-radius: 5px;
cursor: pointer;
}
.overlay {
display: block;
position: fixed;
top: 0;
left: 0;
width: 100%;
height: 100%;
background-color: rgba(255, 255, 255, 0.8); /* Transparent white */
z-index: 9999;
}
.overlay-content {
position: absolute;
top: 50%;
left: 50%;
transform: translate(-50%, -50%);
text-align: center;
}
.loader {
border: 8px solid #f3f3f3; /* Light grey */
border-top: 8px solid #3498db; /* Blue */
border-radius: 50%;
width: 50px;
height: 50px;
animation: spin 1s linear infinite;
}
@keyframes spin {
0% { transform: rotate(0deg); }
100% { transform: rotate(360deg); }
}
</style>
</head>
<body>
<div id="loadingOverlay" class="overlay">
<div class="overlay-content">
<div class="loader"></div>
<p>Loading...</p>
</div>
</div>
<div class="container">
<!-- Left column -->
<div class="left-col">
<div id="probeGraphic">
<img id="probeImage" src="images/ultra_probe.svg" alt="Ultra Probe">
</div>
</div>
<!-- Middle column -->
<div class="mid-col">
<div class="mid-col-top-row">
<div class="mid-col-top-row-left">
<div id="areaContainer">
<div id="areas"></div>
</div>
</div>
<div class="mid-col-top-row-right">
<div>
<button class="button" id="smallFootprintButton" onclick="footprint(true);">Small footprint</button>
<button class="button" id="largeFootprintButton" onclick="footprint(false);">Large footprint</button>
</div>
<div>
<button class="button" id="shortDurationButton" onclick="duration(true);">Short duration</button>
<button class="button" id="longDurationButton" onclick="duration(false);">Long duration</button>
</div>
</div>
</div>
<div class="mid-col-mid-row">
<div id="unity-container">
<canvas id="unity-canvas"></canvas>
</div>
</div>
<div class="mid-col-bot-row">
<div class="table-container">
<table id="dataTable">
<thead>
<tr>
</tr>
</thead>
<tbody>
<tr>
</tr>
</tbody>
</table>
</div>
<button class="button" onclick="updateState();">Share URL to this neuron</button>
</div>
</div>
<!-- Right column -->
<div class="right-col">
<div class="right-col-left">
<img id="gifImage" src="./images/loading_gif.png" alt="GIF Image">
</div>
<div class="right-col-right">
<div class="right-col-right-top-row">
<img id="pngImage" src="./images/loading_png.png" alt="PNG Image">
</div>
<div class="right-col-right-bot-row">
<div class="bottom-content">
<a href="http://www.steinmetzlab.net"><img id="logo" src="./images/lablogo.png"></a>
<img id="logo-brain" src="./images/BI_logo1.jpg">
<p style="font-size: 8pt; margin:5%">Code by <a href="https://danbirman.com">Daniel Birman</a>; data
collection and figures by <a href="https://www.yezhiwen.com/">Zhiwen Ye</a>. Read the <a href="https://www.biorxiv.org/content/10.1101/2023.08.23.554527">Paper</a> or access the <a href="https://figshare.com/articles/dataset/Detailed_neuronal_waveforms_across_brain_regions_recorded_with_Neuropixels_Ultra_/19493588">Data</a>. Thanks to support from the NIH BRAIN Initiative (U01NS113252)</p>
</div>
</div>
</div>
</div>
</div>
<script>
var state = {
selected: -1, // 1 to N
search: '', // area acronym
footprint_small: true, // -1 short, 1 long, 0 both
footprint_large: true, // -1 small, 1 big, 0 both
duration_short: true,
duration_long: true,
};
var defaultState = state;
var N;
var myGameInstance;
// Button labels
const buttonLabels = [
'MO', 'ORB', 'VIS', 'PIR', 'CTXsp', 'CA1', 'SUB', 'CA3',
'DG', 'cc', 'VPM', 'VPL', 'PO', 'CP', 'ACB', 'MB'
];
const buttonColors = ['#1f9d5a',
'#248a5e',
'#08858c',
'#6acbba',
'#8ada87',
'#7ed04b',
'#4fc244',
'#7ed04b',
'#7ed04b',
'#cccccc',
'#ff8084',
'#ff8084',
'#ff909f',
'#98d6f9',
'#80cdf8',
'#ff64ff']
let buttons = []
let pngLoading = new Image();
let gifLoading = new Image();
function setup() {
pngLoading.src = "./images/loading_png.png";
gifLoading.src = "./images/loading_gif.png";
setupButtons();
// Add event listener for keydown event
document.addEventListener('keydown', function(event) {
// Check if left arrow key was pressed
if (event.keyCode === 39) {
// Decrement the selected value
myGameInstance.SendMessage('main', 'SelectDirection', 1);
}
// Check if right arrow key was pressed
else if (event.keyCode === 37) {
// Increment the selected value
myGameInstance.SendMessage('main', 'SelectDirection', -1);
}
});
var urlParams = new URLSearchParams(window.location.search);
if (urlParams.get('state')) {
console.log('Found state in URL');
readState(urlParams.get('state'));
}
else if (urlParams.get('selected')) {
console.log('Found query strings in URL');
readQuery();
}
}
////////////////////////////////
// BUTTONS //////////
////////////////////////////////
// window.addEventListener('resize', resizeButtons); // Listen for window resize events
function setupButtons() {
// Get reference to the top container
let topContainer = document.getElementById('areas');
// Create and append buttons
for (var i = 0; i < buttonLabels.length; i++) {
let label = buttonLabels[i];
let color = buttonColors[i];
let button = document.createElement('button');
buttons.push(button);
button.textContent = label;
button.className = 'area-button';
button.style.backgroundColor = color;
if (label == 'Clear') {
button.onclick = function() {
search('');
};
}
else {
button.onclick = function() {
search(label);
};
}
topContainer.appendChild(button);
}
}
// Function to resize buttons
function resizeButtons() {
// var container = document.getElementById('areaContainer');
// var containerWidth = container.offsetWidth;
// var containerHeight = container.offsetHeight;
// var buttons = container.getElementsByClassName('button');
// var totalButtonWidth = 0;
// var totalButtonHeight = 0;
// console.log(containerWidth);
// console.log(containerHeight);
// console.log(totalButtonWidth);
// console.log(totalButtonHeight);
// // Calculate total width and height of buttons
// for (var i = 0; i < buttons.length; i++) {
// totalButtonWidth += buttons[i].offsetWidth;
// totalButtonHeight += buttons[i].offsetHeight;
// }
// // Check if total button width exceeds container width or total button height exceeds container height
// if (totalButtonWidth > containerWidth || totalButtonHeight > containerHeight) {
// var scaleFactor = Math.min(containerWidth / totalButtonWidth, containerHeight / totalButtonHeight) * 3;
// // Resize each button
// for (var i = 0; i < buttons.length; i++) {
// buttons[i].style.transform = 'scale(' + scaleFactor + ')';
// }
// } else {
// // Reset button sizes if they fit within the container
// for (var i = 0; i < buttons.length; i++) {
// buttons[i].style.transform = 'scale(1)';
// }
// }
}
////////////////////////////////
// STATE //////////
////////////////////////////////
function updateState() {
encodeQueryState();
}
function readQuery() {
decodeQueryState();
updateStateDefaults();
}
function readState(inputStr) {
decodeJSONState(inputStr);
updateStateDefaults();
}
function updateStateDefaults() {
// Check for duplicates in the state, replace with the real ID
if (dupMapping[state.selected] > 0) {
state.selected = dupMapping[state.selected];
}
// check if there are missing fields in state, copy from default
for (var key in defaultState) {
if (!(key in state)) {
state[key] = defaultState[key];
}
}
}
// QUERY STRING STATE
function encodeQueryState() {
var queryStr = Object.keys(state)
.map(key => `${encodeURIComponent(key)}=${encodeURIComponent(state[key])}`)
.join('&');
var url = window.location.href.split('?')[0] + '?' + queryStr;
window.history.replaceState({}, '', url); // Update URL with encoded state
navigator.clipboard.writeText(url);
}
function decodeQueryState() {
const params = new URLSearchParams(window.location.search);
const decodedData = {};
for (const [key, value] of params) {
decodedData[decodeURIComponent(key)] = decodeURIComponent(value);
}
state = decodedData;
}
// JSON STATE
function encodeJSONState() {
var stateJson = JSON.stringify(state);
var stateBase64 = btoa(stateJson); // Encode JSON to base64
var url = window.location.href.split('?')[0] + '?state=' + encodeURIComponent(stateBase64);
window.history.replaceState({}, '', url); // Update URL with encoded state
navigator.clipboard.writeText(url);
}
function decodeJSONState(stateBase64) {
var decodedStateJson = atob(stateBase64); // Decode base64 to JSON
state = JSON.parse(decodedStateJson);
}
const length = 5896;
const initialValue = -1;
var dupMapping = Array(length).fill(initialValue);
var dupLoaded = false;
// Function to load the CSV file and cache the data
async function loadDupFile() {
try {
const response = await fetch('./duplicate_mapping.csv');
const dupText = await response.text();
parseDup(dupText);
} catch (error) {
console.error('Error loading CSV file:', error);
}
}
function parseDup(dupText) {
const lines = dupText.trim().split('\n');
const headers = lines[0].split(',');
for (let i = 1; i < lines.length; i++) {
const values = lines[i].split(',');
dupMapping[parseInt(values[0])] = parseInt(values[1]);
}
}
loadDupFile();
////////////////////////////////
// SELECTION / SEARCH //////////
////////////////////////////////
function searchOnEnter(event) {
if (event.key == 'Enter') {
search(area);
}
}
function search(area) {
if (state.search == area) {
state.search = '';
}
else {
state.search = area;
}
console.log(`Search set to ${state.search}`);
update();
}
////////////////////////////////
// FOOTPRINT / DURATION //////////
////////////////////////////////
var default_button_color = '#add8e6'
var small_fp_button = document.getElementById('smallFootprintButton');
var large_fp_button = document.getElementById('largeFootprintButton');
var short_dur_button = document.getElementById('shortDurationButton');
var long_dur_button = document.getElementById('longDurationButton');
function footprint(small) {
if (small) {
state.footprint_small = !state.footprint_small;
}
else {
state.footprint_large = !state.footprint_large;
}
myGameInstance.SendMessage('main', 'Search', JSON.stringify(state));
updateFPDurButtons();
}
function duration(short) {
if (short) {
state.duration_short = !state.duration_short;
}
else {
state.duration_long = !state.duration_long;
}
myGameInstance.SendMessage('main', 'Search', JSON.stringify(state));
updateFPDurButtons();
}
function updateFPDurButtons() {
if (state.footprint_small) {
small_fp_button.style.backgroundColor = default_button_color;
}
else {
small_fp_button.style.backgroundColor = '#808080';
}
if (state.footprint_large) {
large_fp_button.style.backgroundColor = default_button_color;
}
else {
large_fp_button.style.backgroundColor = '#808080';
}
if (state.duration_long) {
long_dur_button.style.backgroundColor = default_button_color;
}
else {
long_dur_button.style.backgroundColor = '#808080';
}
if (state.duration_short) {
short_dur_button.style.backgroundColor = default_button_color;
}
else {
short_dur_button.style.backgroundColor = '#808080';
}
}
////////////////////////////////
// UPDATE //////////
////////////////////////////////
// CALLED FROM UNITY
function updateSelection(idx) {
// Note that the data row is idx-1 but the images are idx (MATLAB people...
state.selected = idx;
// Tell Unity that we selected something new, and update the table
update();
}
let prevSearch = '';
let prevSelected = -1;
function update() {
if (state.selected == -1) {
state.selected = 9
}
document.getElementById('loadingOverlay').style.display = 'none';
if (state.search != prevSearch) {
myGameInstance.SendMessage('main', 'Search', JSON.stringify(state));
prevSearch = state.search;
if (state.search == '') {
for (var i = 0; i < buttonLabels.length; i++) {
let label = buttonLabels[i];
let color = buttonColors[i];
let button = buttons[i];
button.style.backgroundColor = color;
}
}
else {
for (var i = 0; i < buttonLabels.length; i++) {
let label = buttonLabels[i];
let color = buttonColors[i];
let button = buttons[i];
if (label == state.search) {
button.style.backgroundColor = color;
}
else {
button.style.backgroundColor = '#808080';
}
}
}
}
if (state.selected != prevSelected) {
myGameInstance.SendMessage('main', 'Select', String(state.selected));
updateTable();
prevSelected = state.selected;
}
}
////////////////////////////////
// METADATA ////////////////////
////////////////////////////////
let csvData = null;
// Function to load the CSV file and cache the data
async function loadCSVFile() {
try {
const response = await fetch('./metadata_stripped.csv');
const csvText = await response.text();
csvData = parseCSV(csvText);
} catch (error) {
console.error('Error loading CSV file:', error);
}
setup();
}
function parseCSV(csvText) {
const lines = csvText.trim().split('\n');
const headers = lines[0].split(',');
const data = [];
for (let i = 1; i < lines.length; i++) {
const values = lines[i].split(',');
const entry = {};
for (let j = 0; j < headers.length; j++) {
entry[headers[j]] = values[j];
}
data.push(entry);
}
N = data.length;
return data;
}
function updateTableHeaders() {
if (!csvData || csvData.length === 0) {
console.error('CSV data not loaded or empty.');
return;
}
const table = document.getElementById('dataTable');
const thead = table.querySelector('thead');
// Clear existing headers in the thead
thead.innerHTML = '';
// Create a new row for the headers
const headerRow = thead.insertRow();
// Add headers based on the first row of the CSV data
const headers = Object.keys(csvData[0]);
headers.forEach(header => {
const th = document.createElement('th');
th.textContent = header;
headerRow.appendChild(th);
});
}
function updateTable() {
if (!csvData) {
console.error('CSV data not loaded yet.');
return;
}
let idx = state.selected;
if (idx < 0 || idx >= csvData.length) {
console.error('Invalid row index:', idx);
return;
}
const selectedRow = csvData[idx-1];
// Update table
const table = document.getElementById('dataTable');
const tbody = table.querySelector('tbody');
// Clear existing rows in the tbody
tbody.innerHTML = '';
// Create a new row and cells for the selected data
const newRow = tbody.insertRow();
for (const key in selectedRow) {
const cell = newRow.insertCell();
cell.textContent = selectedRow[key];
}
// Change the image lement sources
document.getElementById('gifImage').src = gifLoading.src;
document.getElementById('pngImage').src = pngLoading.src;
document.getElementById('gifImage').src = `https://data.virtualbrainlab.org/NPUltra/gif/neuron${idx}.gif`;
document.getElementById('pngImage').src = `https://data.virtualbrainlab.org/NPUltra/png/neuron${idx}.png`;
}
////////////////////////////////
// UNITY ///////////////////////
////////////////////////////////
const hideFullScreenButton = "";
const buildUrl = "build/Build";
const loaderUrl = buildUrl + "/build.loader.js";
const config = {
dataUrl: buildUrl + "/build.data.unityweb",
frameworkUrl: buildUrl + "/build.framework.js.unityweb",
codeUrl: buildUrl + "/build.wasm.unityweb",
streamingAssetsUrl: "build/StreamingAssets",
companyName: "VirtualBrainLab",
productName: "NPUltra",
productVersion: "0.1.0",
// matchWebGLToCanvasSize:false,
};
// const container = document.querySelector("#unity-container");
const canvas = document.querySelector("#unity-canvas");
// const loadingCover = document.querySelector("#loading-cover");
// const progressBarEmpty = document.querySelector("#unity-progress-bar-empty");
// const progressBarFull = document.querySelector("#unity-progress-bar-full");
// const fullscreenButton = document.querySelector("#unity-fullscreen-button");
// const spinner = document.querySelector('.spinner');
// const canFullscreen = (function() {
// for (const key of [
// 'exitFullscreen',
// 'webkitExitFullscreen',
// 'webkitCancelFullScreen',
// 'mozCancelFullScreen',
// 'msExitFullscreen',
// ]) {
// if (key in document) {
// return true;
// }
// }
// return false;
// }());
// if (/iPhone|iPad|iPod|Android/i.test(navigator.userAgent)) {
// container.className = "unity-mobile";
// config.devicePixelRatio = 1;
// }
// loadingCover.style.display = "";
const script = document.createElement("script");
script.src = loaderUrl;
script.onload = () => {
createUnityInstance(canvas, config, (progress) => {
// spinner.style.display = "none";
// progressBarEmpty.style.display = "";
// progressBarFull.style.width = `${100 * progress}%`;
}).then((unityInstance) => {
myGameInstance = unityInstance;
}).catch((message) => {
alert(message);
});
};
loadCSVFile().then(() => {
updateTableHeaders();
});
document.body.appendChild(script);
</script>
</body>
</html>