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<!DOCTYPE html>
<html lang="en">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<title>BioWeb3D</title>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
<style>
body {
background-color: #000000;
margin: 0px;
overflow: hidden;
font-family:arial,sans-serif;
}
a {
color:#0078ff;
text-decoration:none;
}
a:hover {
text-decoration:underline;
}
h3 {
font-size : 12px;
}
.UI {
z-index:99;
}
.UIControl {
position:absolute;
left:5px;
bottom:-5px;
height:20px;
border: 5px solid transparent;
-moz-border-radius: 15px;
border-radius: 5px;
font-size:0.8em;
background:#fff;
padding : 5px 5px;
cursor: pointer;
opacity:0.6;
text-align:center;
filter:alpha(opacity=60);
}
.heightLimited {
max-height:450px;
}
</style>
<script type="text/javascript">
var _gaq = _gaq || [];
_gaq.push(['_setAccount', 'UA-21852728-12']);
_gaq.push(['_trackPageview']);
(function() {
var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
})();
</script>
</head>
<body>
<script src="build/json2.js"></script>
<script src="build/jquery-1.8.0.min.js"></script>
<script src="build/jquery-ui-1.9.0.custom.min.js"></script>
<link type="text/css" href="css/jquery-ui-1.8.24.custom.css" rel="Stylesheet" />
<script src="build/three.min.js"></script>
<script src="build/underscore.js"></script>
<script src="build/backbone.js"></script>
<script src="build/backbone-localstorage.js"></script>
<script src="build/Stats.js"></script>
<script src="build/Detector.js"></script>
<script src="build/TrackballControls.js"></script>
<script src="build/jscolor/jscolor.js"></script>
<script src="build/jquery.csv-0.71.min.js"></script>
<script>
//Checking for WebGL
if ( ! Detector.webgl ) Detector.addGetWebGLMessage();
//Defining application global variables
var KeyDown=false,axisLength=10000,renderer,container,worlds=new Array(),winHeight=window.innerHeight,winWidth=window.innerWidth,datasets=new Array(),numWorlds,timeout,alphaClust=1,alphaRaw=0.1,partSize=2,centerPoints=true;
</script>
<!-- creating the UI -->
<div class="UIControl">
Show/Hide UI
</div>
<div id='console' style="position:absolute;width:30%;padding:15px;text-align:center;font-weight:bold;background:#fff;display:none;font-color:#66A3FF;top:50%;left:35%"></div>
<div class="UI">
<div class="session" style="position:absolute;left:0px;top:0px;;width:100%;height:30px;border:1px solid #000;background:#fff;padding-top:5px;opacity:0.6;filter:alpha(opacity=60);">
<div id="current" style="display:inline"><b>BioWeb3D-1.0</b></div>
<div style="float:right;display:inline;margin-right:25px;">
<a href='http://www.ebi.ac.uk/~jbpettit/bioWeb3D/?dataset=examples/platynereis.json&cluster0=examples/20Clustbeta0Rand.json' target='_self'>See an example</a>    
<a href='https://github.com/jbogp/bioWeb3D/wiki/Getting-started' target='_blank'>Getting started</a>    
<a href='https://github.com/jbogp/bioWeb3D' target='_blank'>See project on Github</a>
</div>
</div>
<div class="controls" style="position:absolute;right:0px;top:36px;overflow: auto;width:400px;border:1px solid #000;background:#000;opacity:0.6;filter:alpha(opacity=60);">
<div id="accordion">
<h3><a href="#">Datasets</a></h3>
<div class="heightLimited">
<input type="file" id="newDataSet">
<div id="accordionData">
</div>
</div>
<h3><a href="#">View</a></h3>
<div>
<div id='worldAccordion' style="text-align:center">
<input type='checkbox' checked class="checkWorld" id='worldAccordion1' value=0 /><label for='worldAccordion1'>world 1</label>
<input type='checkbox' class="checkWorld" id='worldAccordion2' value=1 /><label for='worldAccordion2'>world 2</label><br />
<input type='checkbox' class="checkWorld" id='worldAccordion3' value=2 /><label for='worldAccordion3'>world 3</label>
<input type='checkbox' class="checkWorld" id='worldAccordion4' value=3 /><label for='worldAccordion4'>world 4</label>
</div>
</div>
<h3><a href="#">Settings</a></h3>
<div>
<div class="coefs" style="padding:10px !important;">
<input type='checkbox' checked class="checkCenter" id='checkCenter' value=1 /><label for='checkCenter'>Center points</label>
</div>
<div class="coefs" style="padding:10px !important;">
Axis Coefficients :</br>
X axis<div class="sliderCoord" id="sliderX"></div>
Y axis<div class="sliderCoord" id="sliderY"></div>
Z axis<div class="sliderCoord" id="sliderZ"></div>
</div>
<div class="coefs" style="padding:10px !important;">
Raw data transparency : </br>
<div class="alphaRaw" id="alphaRaw"></div>
</div>
<div class="coefs" style="padding:10px !important;">
Classes transparency : </br>
<div class="alphaClust" id="alphaClust"></div>
</div>
<div class="coefs" style="padding:10px !important;">
Particles size : </br>
<div class="sliderPartSize" id="sliderPartSize"></div>
</div>
</div>
</div>
</div>
</div>
<!-- importing application scripts -->
<script src="js/utils.js"></script>
<script src="js/materials.js"></script>
<script src="js/labelClasses.js"></script>
<script src="js/dataUpload.js"></script>
<script src="js/clusterUpload.js"></script>
<script>
//defining world model
function World(id,innerWidth,innerHeight,x,y,visible,labelsToUse){
//Initialisation
this.id = id;
this.visible = visible;
this.numDataSet = 0;
this.camera = new THREE.PerspectiveCamera( 75, innerWidth / innerHeight, 1, 100000 );
this.scene = new THREE.Scene();
this.controls = new THREE.TrackballControls( this.camera );
this.x = x;
this.y = y;
this.innerWidth = innerWidth;
this.innerHeight = innerHeight;
//Attached visualizations
this.datasets = new Array();
this.clusters = new Array();
//Setting camera position
this.camera.position.z = 100;
this.camera.position.x = 100;
this.camera.position.y = 100;
//Adding camera to the scene
this.scene.add( this.camera );
//Create axis (point1, point2, colour)
this.createAxis = function(p1, p2, color){
var line, lineGeometry = new THREE.Geometry(),lineMat = new THREE.LineBasicMaterial({color: color, lineWidth: 1});
lineGeometry.vertices.push(p1, p2);
line = new THREE.Line(lineGeometry, lineMat);
this.scene.add(line);
}
//Creating 3 axis
this.createAxis(v(-axisLength, 0, 0), v(axisLength, 0, 0), 0xffffff);
this.createAxis(v(0, -axisLength, 0), v(0, axisLength, 0), 0xffffff);
this.createAxis(v(0, 0, -axisLength), v(0, 0, axisLength), 0xffffff);
//Creating Axis labels
this.labelSet = new WorldLabelSet(this,labelsToUse);
//Turn off controls
this.disableControls = function () {
this.controls.enabled = false;
}
//Turn on controls
this.enableControls = function () {
this.controls.enabled = true;
}
//Change world size and localization
this.changeSize = function(innerWidth,innerHeight,x,y) {
this.innerWidth = innerWidth;
this.innerHeight = innerHeight;
this.x = x;
this.y = y;
}
//toggle visibility
this.toggle = function() {
if(this.visible) {
this.visible = false;
this.labelSet.hideAll();
}
else{
this.visible = true;
this.labelSet.worldLabel.show();
}
}
//attach a DataSet to the world
this.attachDataSet = function(dataSet,setNum,cluster) {
cluster = typeof cluster !== 'undefined' ? cluster : -1;
//Check if the dataset has been loaded
if(!dataSet.loaded) {
alert("loading is not finished");
}
else{
//Removing same already attached dataset (even if different cluster) if any
if(typeof this.datasets[""+setNum+""] !== 'undefined'){
this.detachDataSet(setNum);
}
//registering new PaticuleSystem
try{
this.datasets[""+setNum+""] = [dataSet.createParticuleSystem(cluster),setNum,cluster];
ret = this.datasetID;
//Adding particule Systems to the scene
for( var i=0; i<this.datasets[""+setNum+""][0].length ; i++ ) {
this.scene.add(this.datasets[""+setNum+""][0][i]);
}
//adding numDataSet
this.numDataSet++;
}
catch(e) {
console.log("particule system creation failed");
throw new Error("ParticleSystem error");
}
}
}
//Is a dataset attached ?
this.isAttached = function(setNum) {
return(typeof this.datasets[""+setNum+""] !== 'undefined')
}
//Is a dataset showing raw or cluster data ?
this.isRaw = function(setNum) {
return(this.isAttached(setNum) && this.datasets[""+setNum+""][2] == -1)
}
//Is the world empty ?
this.empty = function() {
return(this.numDataSet == 0)
}
//detach a DataSet from the world
this.detachDataSet = function(numDataset) {
//Catching eventual error
try{
//deleting ParticuleSystem
for( var i=0; i<this.datasets[""+numDataset+""][0].length ; i++ ) {
this.scene.remove(this.datasets[""+numDataset+""][0][i]);
if(typeof this.datasets[""+numDataset+""][0][i] !== 'undefined') {
this.datasets[""+numDataset+""][0][i].traverse( function ( object ) {
renderer.deallocateObject( object );
object.geometry.deallocate();
object.material.deallocate();
object.deallocate();
} );
}
}
delete this.datasets[""+numDataset+""];
//Removing numDataSet
this.numDataSet--;
}
catch(e) {
console.log("Deleting non-existing dataset... Just moving on with loading: "+e.message);
}
}
//Refresh DataSets
this.refreshDataSets = function() {
var numDataset;
var numClust;
var self = this;
$.each(this.datasets, function(key, value) {
if(typeof value !== 'undefined') {
numDataSet = value[1];
numClust = value[2];
self.detachDataSet(key);
self.attachDataSet(datasets[numDataSet],numDataSet,numClust);
}
});
}
//Creating the Render function
this.render = function () {
//Updating controls
this.controls.update();
if(this.visible) {
//Updating labels
this.labelSet.render();
renderer.setViewport(this.x, this.y, this.innerWidth, this.innerHeight);
renderer.render( this.scene, this.camera );
}
}
};
//defining dataset Model
function DataSet(data){
this.points;
this.name;
this.centered = new Array();
this.nonCentered = new Array();
this.clusterSets = new Array();
this.loaded = false;
this.chain;
this.mean = new Array();
this.loadMaterials = function() {
//Dataset Material
this.dataSetMaterial = new THREE.ParticleBasicMaterial({
color: 0xffffff,
size: 2,
opacity:alphaRaw,
blending: THREE.NormalBlending,
transparent: true
});
//Line Material
this.lineMaterial = new THREE.LineBasicMaterial({
color: 0xffffff,
linewidth: 4,
transparent : true,
opacity : 0.8,
});
}
//Create Three.js particle system for new dataset
this.createParticuleSystem = function(cluster){
var error = false;
var pX,pY,pZ;
this.loadMaterials();
cluster = typeof cluster !== 'undefined' ? cluster : -1;
//Take centered points if center is selected or let normal points otherwise
var points;
if(centerPoints) {
points = this.centered;
}
else {
points = this.nonCentered;
}
if(this.loaded) {
var geometry=new Array(),particles, particle,particleSystem=new Array();
//For chain
var geometryLine=new THREE.Geometry();
//Create particule system for raw data
if(cluster == -1) {
//create DataSet geometry
geometry[0] = new THREE.Geometry();
for (var i = 0; i < this.centered.length; i++) {
pX = points[i][0],
pY = points[i][1],
pZ = points[i][2],
particle = new THREE.Vector3(pX, pY, pZ);
geometry[0].vertices.push( particle );
}
if(!this.chain) {
// create the particle systems
particleSystem[0] = new THREE.ParticleSystem(geometry[0],this.dataSetMaterial);
}
else {
particleSystem[0] = new THREE.Line(geometry[0], this.lineMaterial);
}
particleSystem[0].dynamic = true;
particleSystem[0].sortParticles = true;
}
//Create particule Systems for cluster sets
else {
//Creating geometries
for( var i=0; i<this.clusterSets[cluster].numClust; i++ ) {
geometry[i] = new THREE.Geometry();
}
for (var i = 0; i < this.centered.length && !error; i++) {
var pX = points[i][0],
pY = points[i][1],
pZ = points[i][2],
particle = new THREE.Vector3(pX, pY, pZ);
if(this.chain) {
geometryLine.vertices.push( particle );
}
//Handling error in case of mismatching dataset and clusterset
try{
geometry[this.clusterSets[cluster].set[i]-1].vertices.push( particle );
}
catch(e) {
error = true;
//Zeros or negative values as class
if(this.clusterSets[cluster].set[i] <= 0) {
consoleMess("Error, the information layer contains 0s or negative values");
}
else {
consoleMess("Error, the information layer could not be read properly. Check :"
+"<ul><li> that you define a class for every point in the dataset</li><li>that the file is <a href=\"https://github.com/jibooo/bioWeb3D/wiki/Getting-started\" target='_blank'>well formated</a></li></ul>");
}
throw "bad info layer error";
}
}
for( var i=0; i<this.clusterSets[cluster].numClust && !error; i++ ) {
if(this.clusterSets[cluster].visible[i]) {
particleSystem[i] = new THREE.ParticleSystem(geometry[i],this.clusterSets[cluster].materials[i]);
}
else{
particleSystem[i] = new THREE.ParticleSystem(geometry[i],this.dataSetMaterial);
}
particleSystem[i].dynamic = true;
particleSystem[i].sortParticles = true;
}
if(this.chain && !error) {
particleSystem[i+1] = new THREE.Line(geometryLine, this.lineMaterial);
particleSystem[i+1].dynamic = true;
particleSystem[i+1].sortParticles = true;
}
}
return particleSystem;
}
}
//Setter for loaded points
this.setPoints = function(points) {
this.points = points;
//Making sure everything is numbers
for (var i = 0; i < this.points.length; i++) {
for(var j = 0; j < 3; j++) {
this.points[i][j] = Number(this.points[i][j]);
}
}
this.computeMeans();
this.center([1,1,1]);
}
//Setter for dataset Name
this.setName = function(name) {
this.name = name;
}
//Add clusterset to this dataset
this.addClusterSet = function(clusterSet) {
return this.clusterSets.push(clusterSet);
}
//Refresh clustersets to this dataset
this.refreshClusterSets = function() {
this.clusterSets.forEach(function(clusterSet) {
clusterSet.refreshSet();
});
}
//Computing mean of raw data to center on 0
this.computeMeans = function() {
var mean = new Array();
for (var i = 0; i < this.points.length; i++) {
if(i == 0) {
this.mean = [this.points[i][0],this.points[i][1],this.points[i][2]];
}
else {
this.mean[0] += this.points[i][0];
this.mean[1] += this.points[i][1];
this.mean[2] += this.points[i][2];
}
}
this.mean[0] = this.mean[0]/this.points.length;
this.mean[1] = this.mean[1]/this.points.length;
this.mean[2] = this.mean[2]/this.points.length;
}
//Centering data on 0 accounting for the axis respective coeficients
this.center = function(coef) {
for (var i = 0; i < this.points.length; i++) {
this.centered[i] = new Array();
this.nonCentered[i] = new Array();
for(var j = 0; j < 3; j++) {
this.centered[i][j] = (((this.points[i][j])-this.mean[j])*coef[j]);
this.nonCentered[i][j] = (this.points[i][j]*coef[j]);
}
}
}
//Constructor
this.setPoints(data.points);
//Setting name
if(typeof data.name !== 'undefined' && data.name !== '') {
this.setName(data.name);
}
else {
this.setName("Unamed dataset");
}
//Setting Chain
if(typeof data.chain !== 'undefined' && data.chain !== '') {
this.chain = data.chain;
}
else {
this.chain = false;
}
//Setting loaded
this.loaded = true;
}
//defining cluster Model
function ClusterSet(jsonObj){
this.set=jsonObj.values;
this.numClust = jsonObj.numClass;
this.name = jsonObj.name;
this.visible = new Array();
this.materials = new Array();
this.labels = new Array();
//Initialize visibility
for(var i=0;i<this.numClust;i++){
this.visible[i] = true;
}
//Initialize materials
for(var i=0;i<this.numClust;i++){
this.materials[i] = new THREE.ParticleBasicMaterial({
size: partSize,
opacity:1,
blending: THREE.NoBlending,
transparent: false
});
this.materials[i].color.setHex(colors[i]);
if(typeof jsonObj.labels !== 'undefined') {
this.labels[i] = jsonObj.labels[i];
}
else{
this.labels[i] = "cluster "+(i+1);
}
}
this.refreshSet = function() {
this.materials.forEach(function(material) {
material.opacity = alphaClust;
material.size = partSize;
});
}
//setter for cluster color
this.setColor = function(numClust, color) {
this.materials[numClust].color.setHex(color);
}
}
//Request Animation Frame
function animate() {
requestAnimationFrame( animate );
renderWorlds();
}
/********************************************************
LAUNCHING APPLICATION
*********************************************************/
$(function(){
//Initializing Renderer
initRenderer(window.innerWidth,window.innerHeight);
//Initializing UI
initUI();
//How many worlds
if(typeof getUrlVars()["numW"] !== 'undefined'){
numWorlds = getUrlVars()["numW"];
for(var i=1;i<=numWorlds;i++) {
$('#worldAccordion'+i+'').prop('checked',true);
$("#worldAccordion").buttonset();
}
}
else {
numWorlds = 1;
}
//Change labels ?
var i=0;
var labelsToUse = [];
if(getUrlVars()["labelset"] == 'bio'){
labelsToUse = ["lateral","medial","versal","dorsal","anterior","posterior"]
}
//Default Labels
else{
labelsToUse = ["x","x","z","z","y","y"];
}
console.log(labelsToUse);
//Starting 4 world
worlds[0] = new World(1,(window.innerWidth), (window.innerHeight),0,0,numWorlds>=1,labelsToUse);
worlds[1] = new World(2,(window.innerWidth), (window.innerHeight),0,0,numWorlds>=2,labelsToUse);
worlds[2] = new World(3,(window.innerWidth), (window.innerHeight),0,0,numWorlds>=3,labelsToUse);
worlds[3] = new World(4,(window.innerWidth), (window.innerHeight),0,0,numWorlds>=4,labelsToUse);
setWorlds();
var i=0;
if(typeof getUrlVars()["dataset"] !== 'undefined'){
setFactory(getUrlVars()["dataset"]);
while(typeof getUrlVars()["cluster"+i] !== 'undefined'){
setTimeout('clusterSetFactory(getUrlVars()["cluster'+i+'"],1)',(i+1)*2000);
i++;
}
}
animate();
});
</script>
</body>