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brainTractography-----Tracing_task.html
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<!DOCTYPE html>
<html lang="en">
<head>
<title>three.js DMRI brain tractography</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 {
font-family: Monospace;
background-color: #000;
color: #fff;
margin: 0px;
overflow: hidden;
}
#info {
color: #fff;
position: absolute;
top: 15px;
width: 100%;
text-align: center;
z-index: 100;
display:block;
}
#info a, .button { color: #f00; font-weight: bold; text-decoration: underline; cursor: pointer }
#progress {
color:red;
top:7em;
width: 100%;
font-size:3em;
font-variant:small-caps;
font-weight:bold;
position:absolute;
z-index:100;
text-align: center;
text-shadow: #000 0px 0px 10px;
display:none;
}
#start {
color:#fff;
text-shadow: #000 0px 0px 2px;
padding:0.1em 0.3em;
width:3em;
text-align: center;
display:none;
}
.shadow {
-moz-box-shadow: 0px 0px 5px #000;
-webkit-box-shadow: 0px 0px 5px #000;
box-shadow: 0px 0px 5px #000;
}
#progressbar {
text-align: center;
background: white;
width: 250px;
height: 10px;
}
#bar {
background:#d00;
width:50px;
height:10px;
}
.enabled {
color: lime!important;
cursor:pointer;
}
.enabled:hover {
text-shadow: #0f0 0px 0px 5px !important;
}
.disabled {
background:gray;
cursor:default;
}
a { color:red }
canvas { pointer-events:none; z-index:10; }
#scene_explorer {
background:transparent;
color:#fff;
width:200px;
position:absolute;
text-align:left;
top:0px;
z-index:200;
overflow:auto;
}
</style>
</head>
<body>
<div id="progress">
<span id="message">Loading ...</span>
<center>
<div id="progressbar" class="shadow"><div id="bar" class="shadow"></div></div>
<div id="start" class="disabled">Start</div>
</center>
</div>
<script src="./js/three.js"></script>
<script src="./js/FidxTubeGeometry.js"></script>
<script src="./js/FiberIdxLoader.js"></script>
<script src="./js/FiberGeoLoader.js"></script>
<script src="./js/MinmaxBoxGeometry.js"></script>
<script src="./js/BoxLoader.js"></script>
<script src="./js/Detector.js"></script>
<script>
if ( ! Detector.webgl ) Detector.addGetWebGLMessage();
var container; //remove stats ./js/stats.min.js
var camera, scene, renderer;
var group;
var mainGroup;
var loadedCount =0;
//for trackball
var mouseDown = false;
var rotateStartP = new THREE.Vector3(0,0,1);
var rotateEndP = new THREE.Vector3(0,0,1);
var quater;
var zoomValue =0;
init();
animate();
function $( id ) {
return document.getElementById( id );
}
function init() {
container = document.createElement( 'div' );
document.body.appendChild( container );
var info = document.createElement( 'div' );
info.style.position = 'absolute';
info.style.top = '15px';
info.style.width = '100%';
info.style.textAlign = 'center';
info.innerHTML = 'DMRI brain tractography-----Tracing for Fiber Orientation';
container.appendChild( info );
camera = new THREE.PerspectiveCamera( 45, window.innerWidth / window.innerHeight, 1, 1000 );
camera.position.z = 220;
// scene
scene = new THREE.Scene();
var light;
light = new THREE.DirectionalLight( 0xffeedd );
light.position.set( 0, 0, 200 );
scene.add( light );
light = new THREE.DirectionalLight( 0xffeedd );
light.position.set( -200, 0, 0 );
scene.add( light );
light = new THREE.DirectionalLight( 0xffeedd );
light.position.set( 0, 200, 0 );
scene.add( light );
// FLOOR
/*
var floorTexture = new THREE.ImageUtils.loadTexture( './images/checkerboard.jpg' );
floorTexture.wrapS = floorTexture.wrapT = THREE.RepeatWrapping;
floorTexture.repeat.set( 10, 10 );
var floorMaterial = new THREE.MeshBasicMaterial( { map: floorTexture, side: THREE.DoubleSide } );
var floorGeometry = new THREE.PlaneGeometry(1000, 1000, 10, 10);
var floor = new THREE.Mesh(floorGeometry, floorMaterial);
floor.position.y = -100;
floor.rotation.x = Math.PI / 2;
scene.add(floor);
*/
var helper = new THREE.GridHelper( 200, 10 );
helper.setColors( 0x808080, 0x808080 );
helper.position.y = -100;
scene.add( helper );
$( "progress" ).style.display = "block";
group = new THREE.Object3D(); //scene -> group(mainGroup, plane, bar) ->mainGroup(model, box, sphere)
mainGroup = new THREE.Object3D();
function setProgressBar(loaded, total)
{
var bar = 250;
if ( total )
bar = Math.floor( bar * loaded / total );
$( "bar" ).style.width = bar + "px";
if(loaded === total)
{
Finished();
}
}
function Finished() {
$( "message" ).style.display = "none";
$( "progressbar" ).style.display = "none";
$( "progress" ).style.display = "none";//from start click
scene.add(group);
}
//Generate the data file
var fiberBundle =[];
fiberBundle.push('cc');
//fiberBundle.push('cg');
fiberBundle.push('cst');
fiberBundle.push('ifo');
fiberBundle.push('ilf');
var modelPath = './data/combine/s3.data';
var boxPath1 = './data/Tracing/s3/';
var boxPath2 = './data/Tracing/s3/';
var boxPath3 = './data/Tracing/s3/';
var fiberIdx = './data/Tracing/s3/';
//var post ='.data';
var postBox1='/tumorbox_0_region_s3.data';
var postBox2='/tumorbox_1_region_s3.data';
var postBox3='/tumorbox_2_region_s3.data';
var postFiberIdx ='/fiberidx_2000002_region_s3.data';
var bundleType = fiberBundle[THREE.Math.randInt(0,3)];// if has cg (0,4)
if(bundleType != null)
{
boxPath1 +=bundleType;
boxPath1 += postBox1;
boxPath2 +=bundleType;
boxPath2 += postBox2;
boxPath3 +=bundleType;
boxPath3 += postBox3;
fiberIdx +=bundleType;
fiberIdx += postFiberIdx;
}
//objectvar
var manager = new THREE.LoadingManager();
manager.onProgress = function ( item, loaded, total ) {
console.log( item, loaded, total );
};
var loadIdx = new FiberIdxLoader(manager);
loadIdx.load( fiberIdx, function ( fiberIdx )
{
if(fiberIdx.length!==0 && loadIdx.center !== null)
{
var loader = new GeometryLoader(manager,fiberIdx );
loader.load( modelPath, function ( object ) {
object.position.x = -loader.center.x;
object.position.y = -loader.center.y;
object.position.z = -loader.center.z;
//group.add( object );
mainGroup.add(object);
loadedCount++;
setProgressBar(loadedCount, 4);
} );
}
});
/*var material = new THREE.MeshBasicMaterial({
color: 'yellow',wireframe: true,
wireframeLinewidth: 3
});*/
var loaderbox = new BoxLoader(manager );
loaderbox.load( boxPath1, function ( geometry ) {
if(geometry !== undefined && loaderbox.center !== null)
{
var material = new THREE.MeshBasicMaterial({
transparent: true,
opacity: 0.5,
color: 'silver',
side: THREE.BackSide
});
//var mesh = THREE.SceneUtils.createMultiMaterialObject(geometry, [material, material1]);
var mesh = new THREE.Mesh( geometry, material );
mesh.position.x = loaderbox.center.x;
mesh.position.y = loaderbox.center.y;
mesh.position.z = loaderbox.center.z ;
{//create the wireframe
var verticeGeo = new THREE.Geometry();
var vertices = geometry.vertices;
for(var i =0;i<4;++i)
{
verticeGeo.vertices.push(vertices[2*i]);
verticeGeo.vertices.push(vertices[2*i+1]);
}
{
verticeGeo.vertices.push(vertices[0]);
verticeGeo.vertices.push(vertices[5]);
verticeGeo.vertices.push(vertices[1]);
verticeGeo.vertices.push(vertices[4]);
verticeGeo.vertices.push(vertices[2]);
verticeGeo.vertices.push(vertices[7]);
verticeGeo.vertices.push(vertices[3]);
verticeGeo.vertices.push(vertices[6]);
}
for(i =0;i<2;++i)
{
verticeGeo.vertices.push(vertices[i]);
verticeGeo.vertices.push(vertices[i+2]);
verticeGeo.vertices.push(vertices[4+i]);
verticeGeo.vertices.push(vertices[4+i+2]);
}
var materialLine = new THREE.LineBasicMaterial({ color: 'yellow' });
var line = new THREE.Line( verticeGeo, materialLine,THREE.LinePieces );
line.position.x = loaderbox.center.x;
line.position.y = loaderbox.center.y;
line.position.z = loaderbox.center.z ;
mainGroup.add( line );
}
var spritey = makeTextSprite( " 1 ",
{ fontsize:12, borderColor: {r:255, g:0, b:0, a:1.0}, backgroundColor: {r:255, g:100, b:100, a:0.8} } );
spritey.position.set(loaderbox.center.x,loaderbox.center.y ,loaderbox.center.z );
//group.add( spritey );
mainGroup.add(spritey);
//group.add(mesh);
mainGroup.add(mesh);
loadedCount++;
setProgressBar(loadedCount, 4);
}
} );
var loaderbox2 = new BoxLoader(manager );
loaderbox2.load( boxPath2, function ( geometry ) {
if(geometry !== undefined && loaderbox2.center !== null)
{
var material = new THREE.MeshBasicMaterial({
transparent: true,
opacity: 0.5,
color: 'silver',
side: THREE.BackSide
});
var mesh = new THREE.Mesh(geometry, material);
//var mesh = THREE.SceneUtils.createMultiMaterialObject(geometry, [material, material1]);
mesh.position.x = loaderbox2.center.x;
mesh.position.y = loaderbox2.center.y;
mesh.position.z = loaderbox2.center.z ;
//group.add(mesh);
mainGroup.add(mesh);
{//create the wireframe
var verticeGeo = new THREE.Geometry();
var vertices = geometry.vertices;
for(var i =0;i<4;++i)
{
verticeGeo.vertices.push(vertices[2*i]);
verticeGeo.vertices.push(vertices[2*i+1]);
}
{
verticeGeo.vertices.push(vertices[0]);
verticeGeo.vertices.push(vertices[5]);
verticeGeo.vertices.push(vertices[1]);
verticeGeo.vertices.push(vertices[4]);
verticeGeo.vertices.push(vertices[2]);
verticeGeo.vertices.push(vertices[7]);
verticeGeo.vertices.push(vertices[3]);
verticeGeo.vertices.push(vertices[6]);
}
for(i =0;i<2;++i)
{
verticeGeo.vertices.push(vertices[i]);
verticeGeo.vertices.push(vertices[i+2]);
verticeGeo.vertices.push(vertices[4+i]);
verticeGeo.vertices.push(vertices[4+i+2]);
}
var materialLine = new THREE.LineBasicMaterial({ color: 'yellow' });
var line = new THREE.Line( verticeGeo, materialLine,THREE.LinePieces );
line.position.x = loaderbox2.center.x;
line.position.y = loaderbox2.center.y;
line.position.z = loaderbox2.center.z ;
mainGroup.add( line );
}
var spritey = makeTextSprite( "2 ",
{ fontsize:12, borderColor: {r:255, g:0, b:0, a:1.0}, backgroundColor: {r:255, g:100, b:100, a:0.8} } );
spritey.position.set(loaderbox2.center.x,loaderbox2.center.y ,loaderbox2.center.z );
//group.add( spritey );
mainGroup.add(spritey);
loadedCount++;
setProgressBar(loadedCount, 4);
}
} );
var loaderbox3 = new BoxLoader(manager );
loaderbox3.load( boxPath3, function ( geometry ) {
if(geometry !== undefined && loaderbox3.center !== null)
{
var material = new THREE.MeshBasicMaterial({
transparent: true,
opacity: 0.5,
color: 'silver',
side: THREE.BackSide
});
var mesh = new THREE.Mesh(geometry, material);
//var mesh = THREE.SceneUtils.createMultiMaterialObject(geometry, [material, material1]);
mesh.position.x = loaderbox3.center.x;
mesh.position.y = loaderbox3.center.y;
mesh.position.z = loaderbox3.center.z ;
//group.add(mesh);
mainGroup.add(mesh);
mainGroup.add(mesh);
{//create the wireframe
var verticeGeo = new THREE.Geometry();
var vertices = geometry.vertices;
for(var i =0;i<4;++i)
{
verticeGeo.vertices.push(vertices[2*i]);
verticeGeo.vertices.push(vertices[2*i+1]);
}
{
verticeGeo.vertices.push(vertices[0]);
verticeGeo.vertices.push(vertices[5]);
verticeGeo.vertices.push(vertices[1]);
verticeGeo.vertices.push(vertices[4]);
verticeGeo.vertices.push(vertices[2]);
verticeGeo.vertices.push(vertices[7]);
verticeGeo.vertices.push(vertices[3]);
verticeGeo.vertices.push(vertices[6]);
}
for(i =0;i<2;++i)
{
verticeGeo.vertices.push(vertices[i]);
verticeGeo.vertices.push(vertices[i+2]);
verticeGeo.vertices.push(vertices[4+i]);
verticeGeo.vertices.push(vertices[4+i+2]);
}
var materialLine = new THREE.LineBasicMaterial({ color: 'yellow' });
var line = new THREE.Line( verticeGeo, materialLine,THREE.LinePieces );
line.position.x = loaderbox3.center.x;
line.position.y = loaderbox3.center.y;
line.position.z = loaderbox3.center.z ;
mainGroup.add( line );
}
var spritey = makeTextSprite( "3 ",
{ fontsize:12, borderColor: {r:255, g:0, b:0, a:1.0}, backgroundColor: {r:255, g:100, b:100, a:0.8} } );
spritey.position.set(loaderbox3.center.x,loaderbox3.center.y ,loaderbox3.center.z );
//group.add( spritey );
mainGroup.add(spritey);
loadedCount++;
setProgressBar(loadedCount, 4);
}
} );
//scene.add(group);
group.add(mainGroup);
//render
renderer = new THREE.WebGLRenderer({antialias:true});
renderer.setSize( window.innerWidth, window.innerHeight );
container.appendChild( renderer.domElement );
document.addEventListener( 'mousedown', onDocumentMouseDown, false );
document.addEventListener( 'mousewheel', onMouseWheel, false );
document.addEventListener( 'DOMMouseScroll', onMouseWheel, false ); // firefox
window.addEventListener( 'resize', onWindowResize, false );
}
function onWindowResize() {
camera.aspect = window.innerWidth / window.innerHeight;
camera.updateProjectionMatrix();
renderer.setSize( window.innerWidth, window.innerHeight );
controls.handleResize();
render();
}
function onDocumentMouseDown( event ) {
event.preventDefault();
document.addEventListener( 'mousemove', onDocumentMouseMove, false );
document.addEventListener( 'mouseup', onDocumentMouseUp, false );
document.addEventListener( 'mouseout', onDocumentMouseOut, false );
mouseDown = true;
rotateStartP = projectOnTrackball(event.clientX, event.clientY);
}
function onDocumentMouseMove( event ) {
if(!mouseDown)
{
return;
}
rotateEndP = projectOnTrackball(event.clientX, event.clientY);
}
function getMouseOnScreen( pageX, pageY) {
return new THREE.Vector2.set(pageX / window.innerWidth ,pageY / window.innerHeight);
}
function projectOnTrackball(pageX, pageY) // The screen coordinate[(0,0)on the left-top] convert to the
//trackball coordinate [(0,0) on the center of the page]
{
var mouseOnBall = new THREE.Vector3();
mouseOnBall.set(
( pageX - window.innerWidth * 0.5 ) / (window.innerWidth * .5),
( window.innerHeight * 0.5 - pageY ) / ( window.innerHeight * .5),
0.0
);
var length = mouseOnBall.length();
if (length > 1.0) {
mouseOnBall.normalize();
}
else {
mouseOnBall.z = Math.sqrt(1.0 - length * length);
}
return mouseOnBall;
}
function rotateMatrix(rotateStart, rotateEnd)
{
var axis = new THREE.Vector3(),
quaternion = new THREE.Quaternion();
var angle = Math.acos( rotateStart.dot( rotateEnd ) / rotateStart.length() / rotateEnd.length() );
if ( angle )
{
axis.crossVectors( rotateStart, rotateEnd ).normalize();
angle *= 0.01; //Here we could define rotate speed
quaternion.setFromAxisAngle( axis, angle );
}
return quaternion;
}
function onDocumentMouseUp( event ) {
document.removeEventListener( 'mousemove', onDocumentMouseMove, false );
document.removeEventListener( 'mouseup', onDocumentMouseUp, false );
document.removeEventListener( 'mouseout', onDocumentMouseOut, false );
mouseDown = false;
rotateStartP = rotateEndP;
}
function onDocumentMouseOut( event ) {
document.removeEventListener( 'mousemove', onDocumentMouseMove, false );
document.removeEventListener( 'mouseup', onDocumentMouseUp, false );
document.removeEventListener( 'mouseout', onDocumentMouseOut, false );
}
function onMouseWheel( event ) {
event.preventDefault();
event.stopPropagation();
var delta = 0;
if ( event.wheelDelta ) { // WebKit / Opera / Explorer 9
delta = event.wheelDelta / 40;
} else if ( event.detail ) { // Firefox
delta = - event.detail / 3;
}
zoomValue += delta /10;
}
function makeTextSprite( message, parameters )
{
if ( parameters === undefined ) parameters = {};
var fontface = parameters.hasOwnProperty("fontface") ?
parameters["fontface"] : "Arial";
var fontsize = parameters.hasOwnProperty("fontsize") ?
parameters["fontsize"] : 12;
var borderThickness = parameters.hasOwnProperty("borderThickness") ?
parameters["borderThickness"] : 1;
var borderColor = parameters.hasOwnProperty("borderColor") ?
parameters["borderColor"] : { r:0, g:0, b:0, a:1.0 };
var backgroundColor = parameters.hasOwnProperty("backgroundColor") ?
parameters["backgroundColor"] : { r:255, g:255, b:255, a:1.0 };
var canvas = document.createElement('canvas');
var context = canvas.getContext('2d');
context.font = "Bold " + fontsize + "px " + fontface;
// get size data (height depends only on font size)
var metrics = context.measureText( message );
var textWidth = metrics.width;
// background color
context.fillStyle = "rgba(" + backgroundColor.r + "," + backgroundColor.g + ","
+ backgroundColor.b + "," + backgroundColor.a + ")";
// border color
context.strokeStyle = "rgba(" + borderColor.r + "," + borderColor.g + ","
+ borderColor.b + "," + borderColor.a + ")";
context.lineWidth = borderThickness;
roundRect(context, borderThickness/2, borderThickness/2, textWidth + borderThickness, fontsize * 1.2 + borderThickness, 2);
// 1.4 is extra height factor for text below baseline: g,j,p,q.
// text color
context.fillStyle = "rgba(255, 255, 255, 1.0)";
context.fillText( message, borderThickness, fontsize + borderThickness);
// canvas contents will be used for a texture
var texture = new THREE.Texture(canvas);
texture.needsUpdate = true;
var spriteMaterial = new THREE.SpriteMaterial(
{ map: texture, useScreenCoordinates: false} );
var sprite = new THREE.Sprite( spriteMaterial );
sprite.scale.set(35,35,35.0);
return sprite;
}
// function for drawing rounded rectangles
function roundRect(ctx, x, y, w, h, r)
{
ctx.beginPath();
ctx.moveTo(x+r, y);
ctx.lineTo(x+w-r, y);
ctx.quadraticCurveTo(x+w, y, x+w, y+r);
ctx.lineTo(x+w, y+h-r);
ctx.quadraticCurveTo(x+w, y+h, x+w-r, y+h);
ctx.lineTo(x+r, y+h);
ctx.quadraticCurveTo(x, y+h, x, y+h-r);
ctx.lineTo(x, y+r);
ctx.quadraticCurveTo(x, y, x+r, y);
ctx.closePath();
ctx.fill();
ctx.stroke();
}
//
function animate() {
requestAnimationFrame( animate );
update();
render();
}
function update(){
var rotateQuaternion = rotateMatrix(rotateStartP, rotateEndP);
quater = mainGroup.quaternion;
quater.multiplyQuaternions(rotateQuaternion,quater);
quater.normalize();
mainGroup.setRotationFromQuaternion(quater);
mainGroup.position.z += zoomValue;
zoomValue = 0;
}
function render() {
renderer.render( scene, camera );
}
</script>
</body>
</html>