Simplified Octree/Quadtree Partitioning in THREE.js

example.js

// Create the tree
var box = new THREE.Box3(new THREE.Vector3(-25, -25, -25), new THREE.Vector3(25, 25, 25));
var tree = new Octree(box, {
   maxDepth: 10,
   splitThreshold: 5,
   joinThreshold: 3
});
scene.add(tree);

// Add children the same way you would any other regular object.
var myObject = new THREE.Object3D();
myObject.position.set(10, 20, -15);
tree.add(myObject);

// The tree will update and subdivide itself automatically
for(var i = 0, obj; i < 100; i++) {
    obj = new THREE.Object3D();
    obj.position.set(Math.random() - 0.5, Math.random() - 0.5, Math.random() - 0.5);
    obj.position.multiplyScalar(50);
    tree.add(obj);
}

// To find the subdivision of a particular object
obj.parent;

// To remove an object (either way works)
tree.remove(obj);
obj.parent.remove(obj);

// To get the objects that all belong to a subdivision
obj.parent.children;

// To update an object after it has moved (either way works)
tree.updateObject(obj);
obj.parent.updateObject(obj);

// To get the bounding box of a subdivision
tree.box;
obj.parent.box;

// To find the subdivision that would hold a certain point
var subtree = tree.point(new THREE.Vector3(15, 20, -5));

// To split and join a subdivision manually
tree.split();
tree.join();

// To update manually
tree.update();

// To prevent automatic updating whenever objects are added/removed
tree.add(obj, false);
tree.remove(obj, false);

// To generate a visualization mesh for the tree
var mesh = tree.generateGeometry();
scene.add(mesh);

three.octree.js

/**
 * A special scenegraph object to implement octree division for its children. 
 * This works for quadtrees and binary trees as well, just set the boundary box 
 * coordinates `-Infinity` and `Infinity`  for the dimension(s) you want to 
 * ignore.
 * 
 * @class Octree
 * @constructor
 * @extends THREE.Object3D
 * 
 * @author Monty Thibault
**/
function Octree(box, config) {
    THREE.Object3D.call(this);

    this.divided = false;
    this.box = box || new THREE.Box3();
    
    this.config = config || {};
    this.config.maxDepth = this.config.maxDepth || 5;
    this.config.splitThreshold = this.config.splitThreshold || 10;
    this.config.joinThreshold =  this.config.joinThreshold || 5;
}

Octree.prototype = Object.create(THREE.Object3D.prototype);
Octree.prototype.constructor = Octree;

/**
 * Emulates the standard `object.add` API found in THREE.js. Automatically sorts
 * the object into the appropriate region of the tree.
 * 
 * @returns true on success, false if the object is not within bounds
**/
Octree.prototype.add = function(object, update) {
    if(this.box.containsPoint(object.position)) {
        if(this.divided) {
            var region;
            for(var i = 0; i < this.children.length; i++) {
                region = this.children[i];
                
                if(region.add(object, update)) {
                    return true;
                }
            }
        } else {
            THREE.Object3D.prototype.add.call(this, object);
            (update !== false) && this.update();
            return true;
        }
    }
    
    return false;
};

/**
 * Emulates the standard `object.remove` API found in THREE.js.
**/
Octree.prototype.remove = function(object, update) {
    if(object.parent !== this) {
        object.parent.remove(object, update);
        return;
    }
    
    THREE.Object3D.prototype.remove.call(this, object);
    if(this.parent instanceof Octree) {
        (update !== false) && this.parent.update();
    }
};

/**
 * Returns the region that the given point belongs to, without adding it as an 
 * object
**/
Octree.prototype.point = function(vec) {
    if(this.box.containsPoint(vec)) {
        if(this.divided) {
            var region;
            for(var i = 0; i < this.children.length; i++) {
                region = this.children[i].point(vec);
                if(region) {
                    return region;
                }
            }
        } else {
            return this;
        }
    }
    
    return false;
};

/**
 * Splits this object into several smaller regions and sorts children
 * appropriately. This only performs the operation 1 level deep.
**/
Octree.prototype.split = function() {
    if(this.divided || (this.config.maxDepth <= 1)) return false;
    
    var config = {
        joinThreshold: this.config.joinThreshold,
        splitThreshold: this.config.splitThreshold,
        maxDepth: this.config.maxDepth - 1
    };
    
    var regions = this.generateRegions(),
        objects = this.children;
        
    this.children = [];
    for(var i = 0; i < regions.length; i++) {
        THREE.Object3D.prototype.add.call(this, new Octree(regions[i], config));
    } 
    
    this.divided = true;
    for(i = 0; i < objects.length; i++) {
        objects[i].parent = undefined;
        this.add(objects[i], false);
    }
    
    return true;
};

/**
 * Merges child regions back into this one.
**/
Octree.prototype.join = function() {
    if(!this.divided) return false;
    
    var newChildren = [];
    for(var i = 0; i < this.children.length; i++) {
        this.children[i].join();
        newChildren = newChildren.concat(this.children[i].children);
    }
    
    this.children = newChildren;
    this.divided = false;
};

/**
 * Determines the new bounding boxes when this will be split. (8 octants if 
 * using an octree and 4 quadrants if using a quadtree)
**/
Octree.prototype.generateRegions = function() {
    var regions = [this.box.clone()],
        center = this.box.center(), 
        i, l, boxA, boxB;
    
    if(isFinite(this.box.max.x)) {
        boxA = regions[0];
        boxB = boxA.clone();

        boxA.max.x = center.x;
        boxB.min.x = center.x;
        
        // The first box is already part of the array
        regions.push(boxB);
    }
    
    if(isFinite(this.box.max.y)) {
        for(i = 0, l = regions.length; i < l; i++) {
            boxA = regions[i];
            boxB = boxA.clone();
            
            boxA.max.y = center.y;
            boxB.min.y = center.y;
            
            regions.push(boxB);
        }
    }
    
    if(isFinite(this.box.max.z)) {
        for(i = 0, l = regions.length; i < l; i++) {
            boxA = regions[i];
            boxB = boxA.clone();
            
            boxA.max.z = center.z;
            boxB.min.z = center.z;
            
            regions.push(boxB);
        }
    }
    
    return regions;
};
/**
 * Splits or joins the tree if there are too many/few children in this region.
**/
Octree.prototype.update = function() {
    var totalChildren = 0;
    
    if(this.divided) {
        for(var i = 0; i < this.children.length; i++) {
            totalChildren += this.children[i].update();
        }
        
        if(totalChildren <= this.config.joinThreshold) {
            this.join();
        }
    } else {
        totalChildren = this.children.length;
        
        if(totalChildren >= this.config.splitThreshold) {
            if(this.split()) {
                // If it split successfully, see if we can do it again
                this.update();
            }
        }
    }
    
    return totalChildren;
};

/**
 * Sorts object into the correct region. This should be called on objects that 
 * may have moved out of their regions since the last update. Since it will be
 * called frequently, this method does not update the octree structure.
**/
Octree.prototype.updateObject = function(object) {
    // If object is no longer inside this region
    if(!object.parent.box.containsPoint(object.position)) {
        object.parent.remove(object, false);
        
        // Loop through parent regions until the object is added successfully
        var oct = object.parent.parent;
        
        while(oct instanceof Octree) {
            if(oct.add(object, false)) {
                break;
            }
            oct = oct.parent;
        }
    }
};

/** 
 * Generates a wireframe object to visualize the tree.
**/
Octree.prototype.generateGeometry = function() {
    var container = new THREE.Object3D();
    var material = new THREE.MeshBasicMaterial({ 
        color: 0x000000, 
        wireframe: true });
    
    this.traverse(function(object) {
        if(object instanceof Octree) {
            var size = object.box.size(),
                center = object.box.center();
            
            var geo = new THREE.CubeGeometry(
                isFinite(size.x) ? size.x : 0, 
                isFinite(size.y) ? size.y : 0, 
                isFinite(size.z) ? size.z : 0, 
                1, 1, 1);
            
            var mesh = new THREE.Mesh(geo, material);
            mesh.position.set(
                isFinite(center.x) ? center.x : 0, 
                isFinite(center.y) ? center.y : 0, 
                isFinite(center.z) ? center.z : 0);
            
            container.add(mesh);
        } 
    });
    
    return container;
};

I've also added this.matrixAutoUpdate = false; at the end of the constructor, for performance reasons, considering the position of the Octree itself doesn't really change.

The following change was made because three.js now checks against null with triple equals.

// ... in split method
    for(i = 0; i < objects.length; i++) {
-        objects[i].parent = undefined;
+        objects[i].parent = null;
        this.add(objects[i], false);
    }