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neu3d.js
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neu3d.js
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import * as Stats from 'stats.js';
import { PropertyManager } from './propertymanager';
import { FFBOLightsHelper } from './lightshelper';
// add FontAwesome
import fontawesome from '@fortawesome/fontawesome';
import solid from '@fortawesome/fontawesome-free-solid';
import regular from '@fortawesome/fontawesome-free-regular';
fontawesome.library.add(regular);
fontawesome.library.add(solid);
const Detector = require("three/examples/js/Detector");
const THREE = require('../etc/three');
import dat from '../etc/dat.gui';
import '../style/neu3d.css';
var isOnMobile = checkOnMobile();
function checkOnMobile() {
if( /Android|webOS|iPhone|iPad|iPod|BlackBerry|IEMobile|Opera Mini/i.test(navigator.userAgent) )
return true;
else
return false;
}
function getAttr(obj, key, val) {
if (key in obj)
val = obj[key];
return val;
}
function setAttrIfNotDefined(obj, key, val) {
if (!(key in obj))
obj[key] = val;
}
function getRandomIntInclusive(min, max) {
min = Math.ceil(min);
max = Math.floor(max);
return Math.floor(Math.random() * (max - min + 1)) + min;
}
if ( ! Detector.webgl ) Detector.addGetWebGLMessage();
/**
* Function taken from THREE.SceneUtils
*
* @param geometry
* @param materials
*
* ### Note
* reason for extracting this method is that loading THREE.SceneUtils
* always returns `module has been moved to ...` error.
*/
function createMultiMaterialObject(geometry, materials) {
var group = new THREE.Group();
for (var i = 0, l = materials.length; i < l; i++) {
group.add(new THREE.Mesh(geometry, materials[i]));
}
return group;
}
export default class Neu3D {
/**
*
* @param {HTMLDivElement} container : parent div element
* @param {JSON | undefined } data : optionally add initalization data
* @param {JSON | undefined } metadata : optional metadata
* @param {Object} [options={}] : additional options
*/
constructor(container, data, metadata, options={}) {
this.container = container;
/* default metadata */
this._metadata = {
"colormap": "rainbow_gist",
"maxColorNum": 1747591,
"allowPin": true,
"allowHighlight": true,
};
if (metadata !== undefined)
for (var key in this._metadata)
if ((key in metadata) && (metadata[key] !== undefined))
this._metadata[key] = metadata[key];
this.settings = new PropertyManager({
defaultOpacity: 0.7,
synapseOpacity: 1.0,
meshOscAmp: 0.0,
nonHighlightableOpacity: 0.1,
lowOpacity: 0.1,
pinOpacity: 0.9,
pinLowOpacity: 0.15,
highlightedObjectOpacity: 1.0,
defaultRadius: 0.5,
defaultSomaRadius: 3.0,
defaultSynapseRadius: 0.2,
backgroundOpacity: 1.0,
backgroundWireframeOpacity: 0.07,
neuron3d: false,
neuron3dMode: 1,
synapseMode: true,
meshWireframe: true,
backgroundColor: "#260226"
});
this.settings.toneMappingPass = new PropertyManager({ brightness: 0.95 });
this.settings.bloomPass = new PropertyManager({ radius: 0.2, strength: 0.2, threshold: 0.3 });
this.settings.effectFXAA = new PropertyManager({ enabled: true });
this.settings.backrenderSSAO = new PropertyManager({ enabled: true });
this.states = new PropertyManager({
mouseOver: false,
pinned: false,
highlight: false,
animate: false
});
this.meshDict = new PropertyManager();
this.uiVars = new PropertyManager({
pinnedObjects: new Set(),
toolTipPosition: new THREE.Vector2(),
highlightedObjects: null,
currentIntersected: undefined,
cursorPosition: new THREE.Vector2(-100000, -100000),
meshNum: 0,
frontNum: 0,
backNum: 0,
tooltip: undefined,
selected: undefined
});
// In case of non-unique labels, will hold the rid for the last object
// added with that label
this._labelToRid = {};
this.raycaster = new THREE.Raycaster();
this.raycaster.linePrecision = 3;
if (options['stats']) {
this.stats = new Stats();
this.stats.showPanel(0); // 0: fps, 1: ms, 2: mb, 3+: custom
this.stats.dom.style.position = "relative";
this.container.appendChild(this.stats.dom);
}
this.camera = this.initCamera();
this.renderer = this.initRenderer();
this.groups = {
front: new THREE.Group(),
back: new THREE.Group()
};
this.scenes = this.initScenes();
this.controls = this.initControls();
this.lightsHelper = this.initLights();
this.lut = this.initLut();
this.loadingManager = this.initLoadingManager();
let controlPanelDiv = document.createElement('div');
controlPanelDiv.id = 'vis-3d-settings';
this.controlPanel = this.initControlPanel(options['datGUI']);
controlPanelDiv.appendChild(this.controlPanel.domElement);
this.container.appendChild(controlPanelDiv);
this.container.addEventListener('click', this.onDocumentMouseClick.bind(this), false);
this.container.addEventListener('dblclick', this.onDocumentMouseDBLClick.bind(this), false);
if (isOnMobile) {
this.container.addEventListener('taphold', this.onDocumentMouseDBLClickMobile.bind(this));
document.body.addEventListener('contextmenu', function () { return false; });
}
this.container.addEventListener('mouseenter', this.onDocumentMouseEnter.bind(this), false);
this.container.addEventListener('mousemove', this.onDocumentMouseMove.bind(this), false);
this.container.addEventListener('mouseleave', this.onDocumentMouseLeave.bind(this), false);
this.container.addEventListener('resize', this.onWindowResize.bind(this), false);
this.animOpacity = {};
this.defaultBoundingBox = { 'maxY': -100000, 'minY': 100000, 'maxX': -100000, 'minX': 100000, 'maxZ': -100000, 'minZ': 100000 };
this.boundingBox = Object.assign({}, this.defaultBoundingBox);
this.visibleBoundingBox = Object.assign({}, this.defaultBoundingBox);
//this.createInfoPanel();
this.createToolTip();
this._take_screenshot = false;
this.initPostProcessing();
//this.composer.addPass( this.gammaCorrectionPass );
// this.UIBtns = {};
this.dispatch = {
click: undefined,
dblclick: undefined,
getInfo: this._getInfo,
syncControls: undefined,
resize: undefined
/*'showInfo': undefined,
'removeUnpin': undefined,
'hideAll': undefined,
'showAll': undefined,*/
};
this.commandDispatcher = {
'show': this.show,
'showall': this.showAll,
'hide': this.hide,
'hideall': this.hideAll,
'pin': this.pin,
'unpin': this.unpin,
'unpinall': this.unpinAll,
'remove': this.remove,
'setcolor': this.setColor,
'resetview': this.resetView,
};
this.callbackRegistry = {
'add': (function (func) { this.meshDict.on('add', func); }).bind(this),
'remove': (function (func) { this.meshDict.on('remove', func); }).bind(this),
'pinned': (function (func) { this.meshDict.on('change', func, 'pinned'); }).bind(this),
'visibility': (function (func) { this.meshDict.on('change', func, 'visibility'); }).bind(this),
'num': (function (func) { this.uiVars.on('change', func, 'frontNum'); }).bind(this),
'highlight': (function (func) { this.states.on('change', func, 'highlight'); }).bind(this),
'click': (function (func) { this.uiVars.on('change', func, 'selected'); }).bind(this)
};
this.on('add', (function (e) { this.onAddMesh(e); }).bind(this));
this.on('remove', (function (e) { this.onRemoveMesh(e); }).bind(this));
this.on('pinned', (function (e) { this.updatePinned(e); this.updateOpacity(e); }).bind(this));
this.on('visibility', (function (e) { this.onUpdateVisibility(e.path[0]); }).bind(this));
//this.on('num', (function () { this.updateInfoPanel(); }).bind(this));
this.on('num', ()=>{ this.controlPanel.__controllers[0].setValue(this.uiVars.frontNum); });
this.on('highlight', (function (e) { this.updateOpacity(e); this.onUpdateHighlight(e); }).bind(this));
this.settings.on("change", (function (e) {
this.updateOpacity(e);
}).bind(this), [
"pinLowOpacity", "pinOpacity", "defaultOpacity", "backgroundOpacity",
"backgroundWireframeOpacity", "synapseOpacity",
"highlightedObjectOpacity", "nonHighlightableOpacity", "lowOpacity"
]);
this.settings.on('change', (function (e) {
this[e.path[0]][e.prop] = e.value;
}).bind(this), ['radius', 'strength', 'threshold', 'enabled']);
this.settings.toneMappingPass.on('change', (function (e) {
this.toneMappingPass.setMinLuminance(1 - this.settings.toneMappingPass.brightness);
}).bind(this), 'brightness');
this.settings.on('change', (function (e) {
this.setBackgroundColor(e.value);
}).bind(this), 'backgroundColor');
if (data != undefined && Object.keys(data).length > 0)
this.addJson(data);
this.animate();
this._defaultSettings = this.export_settings();
// setup drag-drop functionality
$('#' + this.container.id).on({
'dragover dragenter': function (e) {
e.preventDefault();
e.stopPropagation();
},
'drop': function (e) {
var dataTransfer = e.originalEvent.dataTransfer;
if (dataTransfer && dataTransfer.files.length) {
e.preventDefault();
e.stopPropagation();
$.each(dataTransfer.files, function (i, file) {
var reader = new FileReader();
reader.onload = $.proxy(function (file, event) {
if (file.name.match('.+(\.swc)$')) {
var name = file.name.split('.')[0];
var json = {};
json[name] = {
label: name,
dataStr: event.target.result,
filetype: 'swc'
};
ffbomesh.addJson({ ffbo_json: json });
}
}, this, file);
reader.readAsText(file);
});
}
}
});
// add file input
let fileUploadInput = document.createElement('input');
fileUploadInput.id = "neu3d-file-upload";
fileUploadInput.setAttribute("type", "file");
fileUploadInput.style.visibility = 'hidden';
fileUploadInput.onchange = (evt) => {
$.each(evt.target.files, function (i, file) {
let reader = new FileReader();
reader.onload = $.proxy(function (file, event) {
if (file.name.match('.+(\.swc)$')) {
var name = file.name.split('.')[0];
var json = {};
json[name] = {
label: name,
dataStr: event.target.result,
filetype: 'swc'
};
ffbomesh.addJson({ ffbo_json: json });
}
}, this, file);
reader.readAsText(file);
});
}
// this input has to be added as siblinig of vis-3d
// becuase vis-3d blocks click event propagation.
this.container.insertAdjacentElement('afterend',fileUploadInput);
// <DEBUG>: this resize event is not working right now
this.container.addEventListener('resize',()=>{
console.log('div resize');
this.onWindowResize();
})
window.onresize = this.onWindowResize.bind(this);
} // ENDOF Constructor
on(key, func) {
if (typeof (func) !== "function") {
console.log("not a function");
return;
}
if (key in this.callbackRegistry) {
var register = this.callbackRegistry[key];
register(func);
}
else {
console.log("callback keyword '" + key + "' not recognized.");
}
}
initControlPanel(options={}){
let GUIOptions = {
autoPlace: (options.autoPlace) ? options.autoPlace : false,
resizable: (options.resizable) ? options.resizable : true,
scrollable: (options.scrollable) ? options.scrollable : true,
closeOnTop: (options.closeOnTop) ? options.closeOnTop : true,
load: datGuiPresets
};
for (let key in options){
if (!(key in GUIOptions)){
GUIOptions[key] = options[key];
}
}
let controlPanel = new dat.GUI(GUIOptions);
window.panel = controlPanel;
let neuronNum = controlPanel.add(this.uiVars, 'frontNum').name('Neuron Number');
neuronNum.domElement.style["pointerEvents"] = "None";
function _createBtn (name, icon, iconAttrs, tooltip, func) {
let newButton = function () {
this[name] = func;
};
let btn = new newButton();
controlPanel.add(btn, name).title(tooltip).icon(icon,"strip",iconAttrs);
}
_createBtn("uploadFile", "fa fa-upload", {}, "Upload SWC File", () => { document.getElementById('neu3d-file-upload').click(); });
_createBtn("resetView", "fa fa-sync", { "aria-hidden": "true" }, "Reset View", () => { this.resetView() });
_createBtn("resetVisibleView", "fa fa-align-justify",{}, "Center and zoom into visible Neurons/Synapses", () => { this.resetVisibleView() });
_createBtn("hideAll", "fa fa-eye-slash",{}, "Hide All", () => { this.hideAll() });
_createBtn("showAll", "fa fa-eye",{}, "Show All", () => { this.showAll() });
_createBtn("takeScreenshot", "fa fa-camera",{}, "Download Screenshot", () => { this._take_screenshot = true;});
_createBtn("removeUnpin", "fa fa-trash", {}, "Remove Unpinned Neurons", ()=> {this.removeUnpinned();})
_createBtn("removeUnpin", "fa fa-map-upin", {}, "Unpin All", () => { this.unpinAll(); })
// add settings
let f_vis = controlPanel.addFolder('Settings');
let f0 = f_vis.addFolder('Display Mode');
f0.add(this.settings, 'neuron3d').name("Enable 3D Mode");
f0.add(this.settings, 'neuron3dMode', [1, 2, 3]);
f0.add(this.settings, 'synapseMode');
let f1 = f_vis.addFolder('Visualization');
f1.add(this.settings, 'meshWireframe').name("Display Wireframe");
f1.addColor(this.settings, 'backgroundColor').name("Background");
let f1_1 = f1.addFolder('Opacity');
f1_1.add(this.settings, 'defaultOpacity', 0.0, 1.0);
f1_1.add(this.settings, 'synapseOpacity', 0.0, 1.0);
f1_1.add(this.settings, 'nonHighlightableOpacity', 0.0, 1.0);
f1_1.add(this.settings, 'lowOpacity', 0.0, 1.0);
f1_1.add(this.settings, 'pinOpacity', 0.0, 1.0);
f1_1.add(this.settings, 'pinLowOpacity', 0.0, 1.0);
f1_1.add(this.settings, 'highlightedObjectOpacity', 0.0, 1.0);
f1_1.add(this.settings, 'backgroundOpacity', 0.0, 1.0);
f1_1.add(this.settings, 'backgroundWireframeOpacity', 0.0, 1.0);
let f1_2 = f1.addFolder('Advanced');
f1_2.add(this.settings.toneMappingPass, 'brightness').name("ToneMap Brightness");
f1_2.add(this.settings.bloomPass, 'radius', 0.0, 10.0).name("BloomPass Radius");;
f1_2.add(this.settings.bloomPass, 'strength', 0.0, 1.0).name("BloomPass Strength");;
f1_2.add(this.settings.bloomPass, 'threshold', 0.0, 2.0).name("BloomPass Threshold");;
f1_2.add(this.settings.effectFXAA, 'enabled').name("FXAA");
f1_2.add(this.settings.backrenderSSAO, 'enabled').name("SSAO");
let f2 = f_vis.addFolder('Size');
f2.add(this.settings, 'defaultRadius');
f2.add(this.settings, 'defaultSomaRadius');
f2.add(this.settings, 'defaultSynapseRadius');
// let f3 = f_vis.addFolder('Animation');
// f3.add(this.states, 'animate');
// f3.add(this.settings, 'meshOscAmp', 0.0, 1.0);
controlPanel.remember(this.settings);
controlPanel.remember(this.settings.toneMappingPass);
controlPanel.remember(this.settings.bloomPass);
controlPanel.remember(this.settings.effectFXAA);
controlPanel.remember(this.settings.backrenderSSAO);
controlPanel.open();
return controlPanel;
}
initCamera() {
var height = this.container.clientHeight;
var width = this.container.clientWidth;
this.fov = 20;
this.prevhfov = 2 * Math.atan(Math.tan(Math.PI * this.fov / 2 / 180) * width / height);
let camera = new THREE.PerspectiveCamera(this.fov, width / height, 0.1, 20000);
camera.position.z = 1800;
if (width < 768 && width / height < 1)
camera.position.z = 3800;
if (width < 768 && width / height >= 1)
camera.position.z = 2600;
return camera;
}
initRenderer() {
let renderer = new THREE.WebGLRenderer({ 'logarithmicDepthBuffer': true });
renderer.setPixelRatio(window.devicePixelRatio);
renderer.setSize(this.container.clientWidth, this.container.clientHeight);
this.container.appendChild(renderer.domElement);
return renderer;
}
initControls() {
let controls = new THREE.TrackballControls(this.camera, this.renderer.domElement);
controls.rotateSpeed = 2.0;
controls.zoomSpeed = 1.0;
controls.panSpeed = 2.0;
controls.staticMoving = true;
controls.dynamicDampingFactor = 0.3;
controls.addEventListener('change', this.render.bind(this));
return controls;
}
initPostProcessing() {
var height = this.container.clientHeight;
var width = this.container.clientWidth;
this.renderScene = new THREE.RenderPass(this.scenes.front, this.camera);
this.renderScene.clear = false;
this.renderScene.clearDepth = true;
this.backrenderScene = new THREE.RenderPass(this.scenes.back, this.camera);
this.backrenderSSAO = new THREE.SSAOPass(this.scenes.back, this.camera, width, height);
this.effectFXAA = new THREE.ShaderPass(THREE.FXAAShader);
this.effectFXAA.uniforms['resolution'].value.set(1 / Math.max(width, 1440), 1 / Math.max(height, 900));
this.bloomPass = new THREE.UnrealBloomPass(new THREE.Vector2(width, height), this.settings.bloomPass.strength, this.settings.bloomPass.radius, this.settings.bloomPass.threshold);
this.bloomPass.renderToScreen = true;
this.toneMappingPass = new THREE.AdaptiveToneMappingPass(true, width);
this.toneMappingPass.setMinLuminance(1. - this.settings.toneMappingPass.brightness);
this.renderer.gammaInput = true;
this.renderer.gammaOutput = true;
this.composer = new THREE.EffectComposer(this.renderer);
this.composer.addPass(this.backrenderScene);
this.composer.addPass(this.backrenderSSAO);
this.composer.addPass(this.renderScene);
this.composer.addPass(this.effectFXAA);
this.composer.addPass(this.toneMappingPass);
this.composer.addPass(this.bloomPass);
this.composer.setSize(width * window.devicePixelRatio, height * window.devicePixelRatio);
}
initScenes() {
let scenes = {
front: new THREE.Scene(),
back: new THREE.Scene()
};
scenes.front.background = null;
scenes.front.add(this.camera);
scenes.back.background = new THREE.Color(0x030305);
scenes.back.add(this.camera);
scenes.front.add(this.groups.front);
scenes.back.add(this.groups.back);
return scenes;
}
initLut() {
this.maxColorNum = this._metadata.maxColorNum;
let lut = new THREE.Lut(this._metadata.colormap, this.maxColorNum);
lut.setMin(0);
lut.setMax(1);
return lut;
}
initLights() {
let lightsHelper = new FFBOLightsHelper(this.camera, this.controls, this.scenes.front);
lightsHelper.addAmbientLight({
intensity: 0.1,
key: 'frontAmbient'
});
lightsHelper.addAmbientLight({
intensity: 0.4,
scene: this.scenes.back,
key: 'backAmbient'
});
lightsHelper.addDirectionalLight({
intensity: 0.1,
position: new THREE.Vector3(0, 0, 5000),
key: 'frontDirectional_1'
});
lightsHelper.addDirectionalLight({
intensity: 0.55,
position: new THREE.Vector3(0, 0, 5000),
scene: this.scenes.back,
key: 'backDirectional_1'
});
lightsHelper.addDirectionalLight({
intensity: 0.1,
position: new THREE.Vector3(0, 0, -5000),
key: 'frontDirectional_2'
});
lightsHelper.addDirectionalLight({
intensity: 0.55,
position: new THREE.Vector3(0, 0, -5000),
scene: this.scenes.back,
key: 'backDirectional_2'
});
lightsHelper.addSpotLight({
posAngle1: 80,
posAngle2: 80,
key: 'frontSpot_1'
});
lightsHelper.addSpotLight({
posAngle1: 80,
posAngle2: 80,
intensity: 5.5,
scene: this.scenes.back,
key: 'backSpot_1'
});
lightsHelper.addSpotLight({
posAngle1: -80,
posAngle2: 80,
key: 'frontSpot_2'
});
lightsHelper.addSpotLight({
posAngle1: -80,
posAngle2: 80,
intensity: 5.5,
scene: this.scenes.back,
key: 'backSpot_2'
});
return lightsHelper;
}
initLoadingManager() {
let loadingManager = new THREE.LoadingManager();
loadingManager.onLoad = function () {
this.controls.target0.x = 0.5 * (this.boundingBox.minX + this.boundingBox.maxX);
this.controls.target0.y = 0.5 * (this.boundingBox.minY + this.boundingBox.maxY);
this.controls.reset();
this.groups.front.visible = true;
}.bind(this);
return loadingManager;
}
select(id) {
this.uiVars.selected = id;
}
reset(resetBackground = false) {
//resetBackground = resetBackground || false;
for (var key of Object.keys(this.meshDict)) {
if (!resetBackground && this.meshDict[key].background) {
continue;
}
if (this.meshDict[key]['pinned'])
this.meshDict[key]['pinned'] = false;
var meshobj = this.meshDict[key].object;
for (var i = 0; i < meshobj.children.length; i++) {
meshobj.children[i].geometry.dispose();
meshobj.children[i].material.dispose();
}
--this.uiVars.meshNum;
this.groups.front.remove(meshobj);
meshobj = null;
delete this.meshDict[key];
}
this.uiVars.frontNum = 0;
this.states.highlight = false;
// this.uiVars.pinnedObjects.clear()
if (resetBackground) {
this.controls.target0.set(0, 0, 0);
this.boundingBox = { 'maxY': -100000, 'minY': 100000, 'maxX': -100000, 'minX': 100000, 'maxZ': -100000, 'minZ': 100000 };
}
//this.controls.reset();
}
_configureCallbacks() {
this.settings.on("change", function (e) {
for (i = 0; i < this.groups.back.children.length; i++)
this.groups.back.children[i].children[1].visible = e["value"];
}.bind(this), "meshWireframe");
}
execCommand(json) {
var neuList = json['neurons'] || [];
var commandList = json['commands'] || [];
var args = json['args'] || undefined;
neuList = this.asarray(neuList);
commandList = this.asarray(commandList);
for (var i = 0; i < commandList.length; ++i) {
var c = commandList[i].toLowerCase();
this.commandDispatcher[c].call(this, neuList, args);
}
}
addJson(json) {
return new Promise((function (resolve) {
if ((json === undefined) || !("ffbo_json" in json)) {
console.log('mesh json is undefined');
return;
}
var metadata = {
"type": undefined,
"visibility": true,
"colormap": this._metadata.colormap,
"colororder": "random",
"showAfterLoadAll": false,
};
for (var key in metadata)
if ((key in json) && (json[key] !== undefined))
metadata[key] = json[key];
if (('reset' in json) && json.reset)
this.reset();
/* set colormap */
var keyList = Object.keys(json.ffbo_json);
var colorNum, id2float, lut;
if (metadata.colororder === "order") {
colorNum = keyList.length;
id2float = function (i) { return i / colorNum; };
}
else {
colorNum = this.maxColorNum;
id2float = function (i) { return getRandomIntInclusive(1, colorNum) / colorNum; };
}
if (metadata.colororder === "order" && (colorNum !== this.maxColorNum || metadata.colormap !== "rainbow_gist")) {
colorNum = keyList.length;
lut = new THREE.Lut(metadata.colormap, colorNum);
lut.setMin(0);
lut.setMax(1);
}
else
lut = this.lut;
if (metadata.showAfterLoadAll)
this.groups.front.visible = false;
for (var i = 0; i < keyList.length; ++i) {
var key = keyList[i];
if (key in this.meshDict) {
console.log('mesh object already exists... skip rendering...');
continue;
}
var unit = new PropertyManager(json.ffbo_json[key]);
unit.boundingBox = Object.assign({}, this.defaultBoundingBox);
setAttrIfNotDefined(unit, 'highlight', true);
setAttrIfNotDefined(unit, 'visibility', true);
setAttrIfNotDefined(unit, 'background', false);
setAttrIfNotDefined(unit, 'color', lut.getColor(id2float(i)));
setAttrIfNotDefined(unit, 'label', getAttr(unit, 'uname', key));
if (Array.isArray(unit.color))
unit.color = new THREE.Color(...unit.color);
/* read mesh */
if (metadata.type === "morphology_json") {
this.loadMorphJSONCallBack(key, unit, metadata.visibility).bind(this)();
}
else if (('dataStr' in unit) && ('filename' in unit)) {
console.log('mesh object has both data string and filename... should only have one... skip rendering');
continue;
}
else if ('filename' in unit) {
unit['filetype'] = unit.filename.split('.').pop();
var loader = new THREE.FileLoader(this.loadingManager);
if (unit['filetype'] == "json")
loader.load(unit.filename, this.loadMeshCallBack(key, unit, metadata.visibility).bind(this));
else if (unit['filetype'] == "swc")
loader.load(unit.filename, this.loadSWCCallBack(key, unit, metadata.visibility).bind(this));
else {
console.log('mesh object has unrecognized data format... skip rendering');
continue;
}
}
else if ('dataStr' in unit) {
if (unit['filetype'] == "json")
this.ladMeshCallBack(key, unit, metadata.visibility).bind(this)(unit['dataStr']);
else if (unit['filetype'] == "swc")
this.loadSWCCallBack(key, unit, metadata.visibility).bind(this)(unit['dataStr']);
else {
console.log('mesh object has unrecognized data format... skip rendering');
continue;
}
}
else {
console.log('mesh object has neither filename nor data string... skip rendering');
continue;
}
}
resolve();
}).bind(this));
}
computeVisibleBoundingBox(includeBackground = false) {
this.visibleBoundingBox = Object.assign({}, this.defaultBoundingBox);
let updated = false;
for (var key in this.meshDict) {
if (this.meshDict[key].background)
continue;
if (this.meshDict[key].visibility) {
updated = true;
if (this.meshDict[key].boundingBox.minX < this.visibleBoundingBox.minX)
this.visibleBoundingBox.minX = this.meshDict[key].boundingBox.minX;
if (this.meshDict[key].boundingBox.maxX > this.visibleBoundingBox.maxX)
this.visibleBoundingBox.maxX = this.meshDict[key].boundingBox.maxX;
if (this.meshDict[key].boundingBox.minY < this.visibleBoundingBox.minY)
this.visibleBoundingBox.minY = this.meshDict[key].boundingBox.minY;
if (this.meshDict[key].boundingBox.maxY > this.visibleBoundingBox.maxY)
this.visibleBoundingBox.maxY = this.meshDict[key].boundingBox.maxY;
if (this.meshDict[key].boundingBox.maxZ < this.visibleBoundingBox.minZ)
this.visibleBoundingBox.minZ = this.meshDict[key].boundingBox.minZ;
if (this.meshDict[key].boundingBox.maxZ > this.visibleBoundingBox.maxZ)
this.visibleBoundingBox.maxZ = this.meshDict[key].boundingBox.maxZ;
}
}
if (!updated)
Object.assign(this.visibleBoundingBox, this.boundingBox);
}
updateObjectBoundingBox(obj, x, y, z) {
if (x < obj.boundingBox.minX)
obj.boundingBox.minX = x;
if (x > obj.boundingBox.maxX)
obj.boundingBox.maxX = x;
if (y < obj.boundingBox.minY)
obj.boundingBox.minY = y;
if (y > obj.boundingBox.maxY)
obj.boundingBox.maxY = y;
if (z < obj.boundingBox.minZ)
obj.boundingBox.minZ = z;
if (z > obj.boundingBox.maxZ)
obj.boundingBox.maxZ = z;
}
updateBoundingBox(x, y, z) {
if (x < this.boundingBox.minX)
this.boundingBox.minX = x;
if (x > this.boundingBox.maxX)
this.boundingBox.maxX = x;
if (y < this.boundingBox.minY)
this.boundingBox.minY = y;
if (y > this.boundingBox.maxY)
this.boundingBox.maxY = y;
if (z < this.boundingBox.minZ)
this.boundingBox.minZ = z;
if (z > this.boundingBox.maxZ)
this.boundingBox.maxZ = z;
}
setAnim(data) {
for (var key in data) {
if (this.meshDict[key].object === undefined)
continue;
this.animOpacity[key] = data[key];
}
this.states.animate = true;
}
stopAnim() {
this.states.animate = false;
}
animate() {
if (this.stats){
this.stats.begin();
}
this.controls.update(); // required if controls.enableDamping = true, or if controls.autoRotate = true
if (this.states.mouseOver && this.dispatch.syncControls)
this.dispatch.syncControls(this);
this.render();
if (this.stats){
this.stats.end();
}
requestAnimationFrame(this.animate.bind(this));
}
loadMeshCallBack(key, unit, visibility) {
return function (jsonString) {
var json = JSON.parse(jsonString);
var color = unit['color'];
var geometry = new THREE.Geometry();
var vtx = json['vertices'];
var idx = json['faces'];
for (var j = 0; j < vtx.length / 3; j++) {
var x = parseFloat(vtx[3 * j + 0]);
var y = parseFloat(vtx[3 * j + 1]);
var z = parseFloat(vtx[3 * j + 2]);
geometry.vertices.push(new THREE.Vector3(x, y, z));
this.updateObjectBoundingBox(unit, x, y, z);
this.updateBoundingBox(x, y, z);
}
for (var j = 0; j < idx.length / 3; j++) {
geometry.faces.push(new THREE.Face3(parseInt(idx[3 * j + 0]), parseInt(idx[3 * j + 1]), parseInt(idx[3 * j + 2])));
}
geometry.mergeVertices();
geometry.computeFaceNormals();
geometry.computeVertexNormals();
let materials = [
//new THREE.MeshPhongMaterial( { color: color, flatShading: true, shininess: 0, transparent: true } ),
new THREE.MeshLambertMaterial({ color: color, transparent: true, side: 2, flatShading: true }),
new THREE.MeshBasicMaterial({ color: color, wireframe: true, transparent: true })
];
var object = createMultiMaterialObject(geometry, materials);
if (!this.settings.meshWireframe)
object.children[1].visible = false;
object.visible = visibility;
this._registerObject(key, unit, object);
};
}
loadSWCCallBack(key, unit, visibility) {
return function (swcString) {
/*
* process string
*/
swcString = swcString.replace(/\r\n/g, "\n");
var swcLine = swcString.split("\n");
var len = swcLine.length;
var swcObj = {};
swcLine.forEach(function (e) {
var seg = e.split(' ');
if (seg.length == 7) {
swcObj[parseInt(seg[0])] = {
'type': parseInt(seg[1]),
'x': parseFloat(seg[2]),
'y': parseFloat(seg[3]),
'z': parseFloat(seg[4]),
'radius': parseFloat(seg[5]),
'parent': parseInt(seg[6]),
};
}
});
var color = unit['color']
var object = new THREE.Object3D();
var pointGeometry = undefined;
var mergedGeometry = undefined;
var geometry = undefined;
for (var idx in swcObj) {
var c = swcObj[idx];
if (idx == Math.round(len / 2) && unit.position == undefined)
unit.position = new THREE.Vector3(c.x, c.y, c.z);
this.updateObjectBoundingBox(unit, c.x, c.y, c.z);
this.updateBoundingBox(c.x, c.y, c.z);
if (c.parent != -1) {
var p = swcObj[c.parent];
if (this.settings.neuron3d) {
if (mergedGeometry == undefined)
mergedGeometry = new THREE.Geometry();
var d = new THREE.Vector3((p.x - c.x), (p.y - c.y), (p.z - c.z));
if (!p.radius || !c.radius)
var geometry = new THREE.CylinderGeometry(this.settings.defaultRadius, this.settings.defaultRadius, d.length(), 4, 1, 0);
else
var geometry = new THREE.CylinderGeometry(p.radius, c.radius, d.length(), 8, 1, 0);
geometry.translate(0, 0.5 * d.length(), 0);
geometry.applyMatrix(new THREE.Matrix4().makeRotationX(Math.PI / 2));
geometry.lookAt(d.clone());
geometry.translate((c.x + c.x) / 2, -0.0 * d.length() + (c.y + c.y) / 2, (c.z + c.z) / 2);
mergedGeometry.merge(geometry);
geometry = null;
if (this.settings.neuron3dMode == 2) {
var geometry = new THREE.SphereGeometry(c.radius, 8, 8);
geometry.applyMatrix(new THREE.Matrix4().makeRotationX(Math.PI / 2));
geometry.lookAt(d);
geometry.translate((c.x + c.x) / 2, (c.y + c.y) / 2, (c.z + c.z) / 2);
mergedGeometry.merge(geometry);
geometry = null;
}
else if (this.settings.neuron3dMode == 3) {
if (p.parent != -1) {
let p2 = swcObj[p.parent];
var a = new THREE.Vector3(0.9 * p.x + 0.1 * p2.x, 0.9 * p.y + 0.1 * p2.y, 0.9 * p.z + 0.1 * p2.z);
var b = new THREE.Vector3(0.9 * p.x + 0.1 * c.x, 0.9 * p.y + 0.1 * c.y, 0.9 * p.z + 0.1 * c.z);
var curve = new THREE.QuadraticBezierCurve3(a, new THREE.Vector3(p.x, p.y, p.z), b);
var geometry = new THREE.TubeGeometry(curve, 8, p.radius, 4, false);
mergedGeometry.merge(geometry);
geometry = null;
}
}
}
else {
if (geometry == undefined)
geometry = new THREE.Geometry();
geometry.vertices.push(new THREE.Vector3(c.x, c.y, c.z));
geometry.vertices.push(new THREE.Vector3(p.x, p.y, p.z));
geometry.colors.push(color);
geometry.colors.push(color);
}
}
if (c.type == 1) {
if (c.radius)
var sphereGeometry = new THREE.SphereGeometry(c.radius, 8, 8);
else
var sphereGeometry = new THREE.SphereGeometry(this.settings.defaultSomaRadius, 8, 8);
sphereGeometry.translate(c.x, c.y, c.z);
var sphereMaterial = new THREE.MeshLambertMaterial({ color: color, transparent: true });
object.add(new THREE.Mesh(sphereGeometry, sphereMaterial));
unit['position'] = new THREE.Vector3(c.x, c.y, c.z);
}
if (c.type == -1) {
if (this.settings.synapseMode == true) {
if (mergedGeometry == undefined)
mergedGeometry = new THREE.Geometry();
if (c.radius)
var sphereGeometry = new THREE.SphereGeometry(c.radius, 8, 8);
else
var sphereGeometry = new THREE.SphereGeometry(this.settings.defaultSynapseRadius, 8, 8);
sphereGeometry.translate(c.x, c.y, c.z);
//var sphereMaterial = new THREE.MeshLambertMaterial( {color: color, transparent: true} );
//object.add(new THREE.Mesh( sphereGeometry, sphereMaterial));
mergedGeometry.merge(sphereGeometry);
unit['position'] = new THREE.Vector3(c.x, c.y, c.z);
}
else {
if (pointGeometry == undefined)
pointGeometry = new THREE.Geometry();
pointGeometry.vertices.push(new THREE.Vector3(c.x, c.y, c.z));
}
}
}
if (pointGeometry) {
var pointMaterial = new THREE.PointsMaterial({ color: color, size: this.settings.defaultSynapseRadius, lights: true });
var points = new THREE.Points(pointGeometry, pointMaterial);
object.add(points);
}
if (mergedGeometry) {
var material = new THREE.MeshLambertMaterial({ color: color, transparent: true });
//var modifier = new THREE.SimplifyModifier();
//simplified = modifier.modify( mergedGeometry, geometry.vertices.length * 0.25 | 0 )
var mesh = new THREE.Mesh(mergedGeometry, material);
//var mesh = new THREE.Mesh(simplified, material);
object.add(mesh);
}
if (geometry) {
var material = new THREE.LineBasicMaterial({ vertexColors: THREE.VertexColors, transparent: true, color: color });
object.add(new THREE.LineSegments(geometry, material));
}
object.visible = visibility;
this._registerObject(key, unit, object);
};
}
loadMorphJSONCallBack(key, unit, visibility) {
return function () {
/*
* process string
*/
var swcObj = {};
var len = unit['sample'].length;
for (var j = 0; j < len; j++) {
swcObj[parseInt(unit['sample'][j])] = {
'type': parseInt(unit['identifier'][j]),
'x': parseFloat(unit['x'][j]),
'y': parseFloat(unit['y'][j]),
'z': parseFloat(unit['z'][j]),
'radius': parseFloat(unit['r'][j]),
'parent': parseInt(unit['parent'][j]),
};
}
var color = unit['color'];
var object = new THREE.Object3D();
var pointGeometry = undefined;
var mergedGeometry = undefined;
var geometry = undefined;
for (var idx in swcObj) {
var c = swcObj[idx];
if (idx == Math.round(len / 2) && unit.position == undefined)
unit.position = new THREE.Vector3(c.x, c.y, c.z);
this.updateObjectBoundingBox(unit, c.x, c.y, c.z);
this.updateBoundingBox(c.x, c.y, c.z);
if (c.parent != -1) {
var p = swcObj[c.parent];
if (this.settings.neuron3d) {
if (mergedGeometry == undefined)
mergedGeometry = new THREE.Geometry();
var d = new THREE.Vector3((p.x - c.x), (p.y - c.y), (p.z - c.z));
if (!p.radius || !c.radius)
var geometry = new THREE.CylinderGeometry(this.settings.defaultRadius, this.settings.defaultRadius, d.length(), 4, 1, 0);
else
var geometry = new THREE.CylinderGeometry(p.radius, c.radius, d.length(), 8, 1, 0);
geometry.translate(0, 0.5 * d.length(), 0);
geometry.applyMatrix(new THREE.Matrix4().makeRotationX(Math.PI / 2));
geometry.lookAt(d.clone());
geometry.translate((c.x + c.x) / 2, -0.0 * d.length() + (c.y + c.y) / 2, (c.z + c.z) / 2);
mergedGeometry.merge(geometry);
geometry = null;
if (this.settings.neuron3dMode == 2) {
var geometry = new THREE.SphereGeometry(c.radius, 8, 8);
geometry.applyMatrix(new THREE.Matrix4().makeRotationX(Math.PI / 2));
geometry.lookAt(d);
geometry.translate((c.x + c.x) / 2, (c.y + c.y) / 2, (c.z + c.z) / 2);
mergedGeometry.merge(geometry);
geometry = null;
}
else if (this.settings.neuron3dMode == 3) {
if (p.parent != -1) {
p2 = swcObj[p.parent];
var a = new THREE.Vector3(0.9 * p.x + 0.1 * p2.x, 0.9 * p.y + 0.1 * p2.y, 0.9 * p.z + 0.1 * p2.z);
var b = new THREE.Vector3(0.9 * p.x + 0.1 * c.x, 0.9 * p.y + 0.1 * c.y, 0.9 * p.z + 0.1 * c.z);
var curve = new THREE.QuadraticBezierCurve3(a, new THREE.Vector3(p.x, p.y, p.z), b);
var geometry = new THREE.TubeGeometry(curve, 8, p.radius, 4, false);