in the beginning

This commit is contained in:
Peter Cottle 2012-08-13 12:40:14 -07:00
commit a817cec5f5
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//
// atoms.js
//
// particle system- or physics-related datatypes
//
var Node = function(data){
this._id = _nextNodeId++; // simple ints to allow the Kernel & ParticleSystem to chat
this.data = data || {}; // the user-serviceable parts
this._mass = (data.mass!==undefined) ? data.mass : 1
this._fixed = (data.fixed===true) ? true : false
this._p = new Point((typeof(data.x)=='number') ? data.x : null,
(typeof(data.y)=='number') ? data.y : null)
delete this.data.x
delete this.data.y
delete this.data.mass
delete this.data.fixed
};
var _nextNodeId = 1
var Edge = function(source, target, data){
this._id = _nextEdgeId--;
this.source = source;
this.target = target;
this.length = (data.length!==undefined) ? data.length : 1
this.data = (data!==undefined) ? data : {};
delete this.data.length
};
var _nextEdgeId = -1
var Particle = function(position, mass){
this.p = position;
this.m = mass;
this.v = new Point(0, 0); // velocity
this.f = new Point(0, 0); // force
};
Particle.prototype.applyForce = function(force){
this.f = this.f.add(force.divide(this.m));
};
var Spring = function(point1, point2, length, k)
{
this.point1 = point1; // a particle
this.point2 = point2; // another particle
this.length = length; // spring length at rest
this.k = k; // stiffness
};
Spring.prototype.distanceToParticle = function(point)
{
// see http://stackoverflow.com/questions/849211/shortest-distance-between-a-point-and-a-line-segment/865080#865080
var n = that.point2.p.subtract(that.point1.p).normalize().normal();
var ac = point.p.subtract(that.point1.p);
return Math.abs(ac.x * n.x + ac.y * n.y);
};
var Point = function(x, y){
if (x && x.hasOwnProperty('y')){
y = x.y; x=x.x;
}
this.x = x;
this.y = y;
}
Point.random = function(radius){
radius = (radius!==undefined) ? radius : 5
return new Point(2*radius * (Math.random() - 0.5), 2*radius* (Math.random() - 0.5));
}
Point.prototype = {
exploded:function(){
return ( isNaN(this.x) || isNaN(this.y) )
},
add:function(v2){
return new Point(this.x + v2.x, this.y + v2.y);
},
subtract:function(v2){
return new Point(this.x - v2.x, this.y - v2.y);
},
multiply:function(n){
return new Point(this.x * n, this.y * n);
},
divide:function(n){
return new Point(this.x / n, this.y / n);
},
magnitude:function(){
return Math.sqrt(this.x*this.x + this.y*this.y);
},
normal:function(){
return new Point(-this.y, this.x);
},
normalize:function(){
return this.divide(this.magnitude());
}
}

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//
// barnes-hut.js
//
// implementation of the barnes-hut quadtree algorithm for n-body repulsion
// http://www.cs.princeton.edu/courses/archive/fall03/cs126/assignments/barnes-hut.html
//
// Created by Christian Swinehart on 2011-01-14.
// Copyright (c) 2011 Samizdat Drafting Co. All rights reserved.
//
var BarnesHutTree = function(){
var _branches = []
var _branchCtr = 0
var _root = null
var _theta = .5
var that = {
init:function(topleft, bottomright, theta){
_theta = theta
// create a fresh root node for these spatial bounds
_branchCtr = 0
_root = that._newBranch()
_root.origin = topleft
_root.size = bottomright.subtract(topleft)
},
insert:function(newParticle){
// add a particle to the tree, starting at the current _root and working down
var node = _root
var queue = [newParticle]
while (queue.length){
var particle = queue.shift()
var p_mass = particle._m || particle.m
var p_quad = that._whichQuad(particle, node)
if (node[p_quad]===undefined){
// slot is empty, just drop this node in and update the mass/c.o.m.
node[p_quad] = particle
node.mass += p_mass
if (node.p){
node.p = node.p.add(particle.p.multiply(p_mass))
}else{
node.p = particle.p.multiply(p_mass)
}
}else if ('origin' in node[p_quad]){
// slot conatins a branch node, keep iterating with the branch
// as our new root
node.mass += (p_mass)
if (node.p) node.p = node.p.add(particle.p.multiply(p_mass))
else node.p = particle.p.multiply(p_mass)
node = node[p_quad]
queue.unshift(particle)
}else{
// slot contains a particle, create a new branch and recurse with
// both points in the queue now
var branch_size = node.size.divide(2)
var branch_origin = new Point(node.origin)
if (p_quad[0]=='s') branch_origin.y += branch_size.y
if (p_quad[1]=='e') branch_origin.x += branch_size.x
// replace the previously particle-occupied quad with a new internal branch node
var oldParticle = node[p_quad]
node[p_quad] = that._newBranch()
node[p_quad].origin = branch_origin
node[p_quad].size = branch_size
node.mass = p_mass
node.p = particle.p.multiply(p_mass)
node = node[p_quad]
if (oldParticle.p.x===particle.p.x && oldParticle.p.y===particle.p.y){
// prevent infinite bisection in the case where two particles
// have identical coordinates by jostling one of them slightly
var x_spread = branch_size.x*.08
var y_spread = branch_size.y*.08
oldParticle.p.x = Math.min(branch_origin.x+branch_size.x,
Math.max(branch_origin.x,
oldParticle.p.x - x_spread/2 +
Math.random()*x_spread))
oldParticle.p.y = Math.min(branch_origin.y+branch_size.y,
Math.max(branch_origin.y,
oldParticle.p.y - y_spread/2 +
Math.random()*y_spread))
}
// keep iterating but now having to place both the current particle and the
// one we just replaced with the branch node
queue.push(oldParticle)
queue.unshift(particle)
}
}
},
applyForces:function(particle, repulsion){
// find all particles/branch nodes this particle interacts with and apply
// the specified repulsion to the particle
var queue = [_root]
while (queue.length){
node = queue.shift()
if (node===undefined) continue
if (particle===node) continue
if ('f' in node){
// this is a particle leafnode, so just apply the force directly
var d = particle.p.subtract(node.p);
var distance = Math.max(1.0, d.magnitude());
var direction = ((d.magnitude()>0) ? d : Point.random(1)).normalize()
particle.applyForce(direction.multiply(repulsion*(node._m||node.m))
.divide(distance * distance) );
}else{
// it's a branch node so decide if it's cluster-y and distant enough
// to summarize as a single point. if it's too complex, open it and deal
// with its quadrants in turn
var dist = particle.p.subtract(node.p.divide(node.mass)).magnitude()
var size = Math.sqrt(node.size.x * node.size.y)
if (size/dist > _theta){ // i.e., s/d > Θ
// open the quad and recurse
queue.push(node.ne)
queue.push(node.nw)
queue.push(node.se)
queue.push(node.sw)
}else{
// treat the quad as a single body
var d = particle.p.subtract(node.p.divide(node.mass));
var distance = Math.max(1.0, d.magnitude());
var direction = ((d.magnitude()>0) ? d : Point.random(1)).normalize()
particle.applyForce(direction.multiply(repulsion*(node.mass))
.divide(distance * distance) );
}
}
}
},
_whichQuad:function(particle, node){
// sort the particle into one of the quadrants of this node
if (particle.p.exploded()) return null
var particle_p = particle.p.subtract(node.origin)
var halfsize = node.size.divide(2)
if (particle_p.y < halfsize.y){
if (particle_p.x < halfsize.x) return 'nw'
else return 'ne'
}else{
if (particle_p.x < halfsize.x) return 'sw'
else return 'se'
}
},
_newBranch:function(){
// to prevent a gc horrorshow, recycle the tree nodes between iterations
if (_branches[_branchCtr]){
var branch = _branches[_branchCtr]
branch.ne = branch.nw = branch.se = branch.sw = undefined
branch.mass = 0
delete branch.p
}else{
branch = {origin:null, size:null,
nw:undefined, ne:undefined, sw:undefined, se:undefined, mass:0}
_branches[_branchCtr] = branch
}
_branchCtr++
return branch
}
}
return that
}

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//
// physics.js
//
// the particle system itself. either run inline or in a worker (see worker.js)
//
var Physics = function(dt, stiffness, repulsion, friction, updateFn, integrator){
var bhTree = BarnesHutTree() // for computing particle repulsion
var active = {particles:{}, springs:{}}
var free = {particles:{}}
var particles = []
var springs = []
var _epoch=0
var _energy = {sum:0, max:0, mean:0}
var _bounds = {topleft:new Point(-1,-1), bottomright:new Point(1,1)}
var SPEED_LIMIT = 1000 // the max particle velocity per tick
var that = {
integrator:['verlet','euler'].indexOf(integrator)>=0 ? integrator : 'verlet',
stiffness:(stiffness!==undefined) ? stiffness : 1000,
repulsion:(repulsion!==undefined)? repulsion : 600,
friction:(friction!==undefined)? friction : .3,
gravity:false,
dt:(dt!==undefined)? dt : 0.02,
theta:.4, // the criterion value for the barnes-hut s/d calculation
init:function(){
return that
},
modifyPhysics:function(param){
$.each(['stiffness','repulsion','friction','gravity','dt','precision', 'integrator'], function(i, p){
if (param[p]!==undefined){
if (p=='precision'){
that.theta = 1-param[p]
return
}
that[p] = param[p]
if (p=='stiffness'){
var stiff=param[p]
$.each(active.springs, function(id, spring){
spring.k = stiff
})
}
}
})
},
addNode:function(c){
var id = c.id
var mass = c.m
var w = _bounds.bottomright.x - _bounds.topleft.x
var h = _bounds.bottomright.y - _bounds.topleft.y
var randomish_pt = new Point((c.x != null) ? c.x: _bounds.topleft.x + w*Math.random(),
(c.y != null) ? c.y: _bounds.topleft.y + h*Math.random())
active.particles[id] = new Particle(randomish_pt, mass);
active.particles[id].connections = 0
active.particles[id].fixed = (c.f===1)
free.particles[id] = active.particles[id]
particles.push(active.particles[id])
},
dropNode:function(c){
var id = c.id
var dropping = active.particles[id]
var idx = $.inArray(dropping, particles)
if (idx>-1) particles.splice(idx,1)
delete active.particles[id]
delete free.particles[id]
},
modifyNode:function(id, mods){
if (id in active.particles){
var pt = active.particles[id]
if ('x' in mods) pt.p.x = mods.x
if ('y' in mods) pt.p.y = mods.y
if ('m' in mods) pt.m = mods.m
if ('f' in mods) pt.fixed = (mods.f===1)
if ('_m' in mods){
if (pt._m===undefined) pt._m = pt.m
pt.m = mods._m
}
}
},
addSpring:function(c){
var id = c.id
var length = c.l
var from = active.particles[c.fm]
var to = active.particles[c.to]
if (from!==undefined && to!==undefined){
active.springs[id] = new Spring(from, to, length, that.stiffness)
springs.push(active.springs[id])
from.connections++
to.connections++
delete free.particles[c.fm]
delete free.particles[c.to]
}
},
dropSpring:function(c){
var id = c.id
var dropping = active.springs[id]
dropping.point1.connections--
dropping.point2.connections--
var idx = $.inArray(dropping, springs)
if (idx>-1){
springs.splice(idx,1)
}
delete active.springs[id]
},
_update:function(changes){
// batch changes phoned in (automatically) by a ParticleSystem
_epoch++
$.each(changes, function(i, c){
if (c.t in that) that[c.t](c)
})
return _epoch
},
tick:function(){
that.tendParticles()
if (that.integrator=='euler'){
that.updateForces()
that.updateVelocity(that.dt)
that.updatePosition(that.dt)
}else{
// default to verlet
that.updateForces();
that.cacheForces(); // snapshot f(t)
that.updatePosition(that.dt); // update position to x(t + 1)
that.updateForces(); // calculate f(t+1)
that.updateVelocity(that.dt); // update using f(t) and f(t+1)
}
that.tock()
},
tock:function(){
var coords = []
$.each(active.particles, function(id, pt){
coords.push(id)
coords.push(pt.p.x)
coords.push(pt.p.y)
})
if (updateFn) updateFn({geometry:coords, epoch:_epoch, energy:_energy, bounds:_bounds})
},
tendParticles:function(){
$.each(active.particles, function(id, pt){
// decay down any of the temporary mass increases that were passed along
// by using an {_m:} instead of an {m:} (which is to say via a Node having
// its .tempMass attr set)
if (pt._m!==undefined){
if (Math.abs(pt.m-pt._m)<1){
pt.m = pt._m
delete pt._m
}else{
pt.m *= .98
}
}
// zero out the velocity from one tick to the next
pt.v.x = pt.v.y = 0
})
},
// Physics stuff
updateForces:function() {
if (that.repulsion>0){
if (that.theta>0) that.applyBarnesHutRepulsion()
else that.applyBruteForceRepulsion()
}
if (that.stiffness>0) that.applySprings()
that.applyCenterDrift()
if (that.gravity) that.applyCenterGravity()
},
cacheForces:function() {
// keep a snapshot of the current forces for the verlet integrator
$.each(active.particles, function(id, point) {
point._F = point.f;
point._m = point.m;
});
},
applyBruteForceRepulsion:function(){
$.each(active.particles, function(id1, point1){
$.each(active.particles, function(id2, point2){
if (point1 !== point2){
var d = point1.p.subtract(point2.p);
var distance = Math.max(1.0, d.magnitude());
var direction = ((d.magnitude()>0) ? d : Point.random(1)).normalize()
// apply force to each end point
// (consult the cached `real' mass value if the mass is being poked to allow
// for repositioning. the poked mass will still be used in .applyforce() so
// all should be well)
point1.applyForce(direction.multiply(that.repulsion*(point2._m||point2.m)*.5)
.divide(distance * distance * 0.5) );
point2.applyForce(direction.multiply(that.repulsion*(point1._m||point1.m)*.5)
.divide(distance * distance * -0.5) );
}
})
})
},
applyBarnesHutRepulsion:function(){
if (!_bounds.topleft || !_bounds.bottomright) return
var bottomright = new Point(_bounds.bottomright)
var topleft = new Point(_bounds.topleft)
// build a barnes-hut tree...
bhTree.init(topleft, bottomright, that.theta)
$.each(active.particles, function(id, particle){
bhTree.insert(particle)
})
// ...and use it to approximate the repulsion forces
$.each(active.particles, function(id, particle){
bhTree.applyForces(particle, that.repulsion)
})
},
applySprings:function(){
$.each(active.springs, function(id, spring){
var d = spring.point2.p.subtract(spring.point1.p); // the direction of the spring
var displacement = spring.length - d.magnitude()//Math.max(.1, d.magnitude());
var direction = ( (d.magnitude()>0) ? d : Point.random(1) ).normalize()
// BUG:
// since things oscillate wildly for hub nodes, should probably normalize spring
// forces by the number of incoming edges for each node. naive normalization
// doesn't work very well though. what's the `right' way to do it?
// apply force to each end point
spring.point1.applyForce(direction.multiply(spring.k * displacement * -0.5))
spring.point2.applyForce(direction.multiply(spring.k * displacement * 0.5))
});
},
applyCenterDrift:function(){
// find the centroid of all the particles in the system and shift everything
// so the cloud is centered over the origin
var numParticles = 0
var centroid = new Point(0,0)
$.each(active.particles, function(id, point) {
centroid.add(point.p)
numParticles++
});
if (numParticles==0) return
var correction = centroid.divide(-numParticles)
$.each(active.particles, function(id, point) {
point.applyForce(correction)
})
},
applyCenterGravity:function(){
// attract each node to the origin
$.each(active.particles, function(id, point) {
var direction = point.p.multiply(-1.0);
point.applyForce(direction.multiply(that.repulsion / 100.0));
});
},
updateVelocity:function(timestep){
// translate forces to a new velocity for this particle
var sum=0, max=0, n = 0;
$.each(active.particles, function(id, point) {
if (point.fixed){
point.v = new Point(0,0)
point.f = new Point(0,0)
return
}
if (that.integrator=='euler'){
point.v = point.v.add(point.f.multiply(timestep)).multiply(1-that.friction);
}else{
point.v = point.v.add(point.f.add(point._F.divide(point._m)).multiply(timestep*0.5)).multiply(1-that.friction);
}
point.f.x = point.f.y = 0
var speed = point.v.magnitude()
if (speed>SPEED_LIMIT) point.v = point.v.divide(speed*speed)
var speed = point.v.magnitude();
var e = speed*speed
sum += e
max = Math.max(e,max)
n++
});
_energy = {sum:sum, max:max, mean:sum/n, n:n}
},
updatePosition:function(timestep){
// translate velocity to a position delta
var bottomright = null
var topleft = null
$.each(active.particles, function(i, point) {
// move the node to its new position
if (that.integrator=='euler'){
point.p = point.p.add(point.v.multiply(timestep));
}else{
//this should follow the equation
//x(t+1) = x(t) + v(t) * timestep + 1/2 * timestep^2 * a(t)
var accelPart = point.f.multiply(0.5 * timestep * timestep).divide(point.m);
point.p = point.p.add(point.v.multiply(timestep)).add(accelPart);
}
if (!bottomright){
bottomright = new Point(point.p.x, point.p.y)
topleft = new Point(point.p.x, point.p.y)
return
}
var pt = point.p
if (pt.x===null || pt.y===null) return
if (pt.x > bottomright.x) bottomright.x = pt.x;
if (pt.y > bottomright.y) bottomright.y = pt.y;
if (pt.x < topleft.x) topleft.x = pt.x;
if (pt.y < topleft.y) topleft.y = pt.y;
});
_bounds = {topleft:topleft||new Point(-1,-1), bottomright:bottomright||new Point(1,1)}
},
systemEnergy:function(timestep){
// system stats
return _energy
}
}
return that.init()
}
var _nearParticle = function(center_pt, r){
var r = r || .0
var x = center_pt.x
var y = center_pt.y
var d = r*2
return new Point(x-r+Math.random()*d, y-r+Math.random()*d)
}

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//
// system.js
//
// the main controller object for creating/modifying graphs
//
var ParticleSystem = function(repulsion, stiffness, friction, centerGravity, targetFps, dt, precision, integrator){
// also callable with ({integrator:, stiffness:, repulsion:, friction:, timestep:, fps:, dt:, gravity:})
var _changes=[]
var _notification=null
var _epoch = 0
var _screenSize = null
var _screenStep = .04
var _screenPadding = [20,20,20,20]
var _bounds = null
var _boundsTarget = null
if (typeof repulsion=='object'){
var _p = repulsion
friction = _p.friction
repulsion = _p.repulsion
targetFps = _p.fps
dt = _p.dt
stiffness = _p.stiffness
centerGravity = _p.gravity
precision = _p.precision
integrator = _p.integrator
}
// param validation and defaults
if (integrator!='verlet' && integrator!='euler') integrator='verlet'
friction = isNaN(friction) ? .5 : friction
repulsion = isNaN(repulsion) ? 1000 : repulsion
targetFps = isNaN(targetFps) ? 55 : targetFps
stiffness = isNaN(stiffness) ? 600 : stiffness
dt = isNaN(dt) ? 0.02 : dt
precision = isNaN(precision) ? .6 : precision
centerGravity = (centerGravity===true)
var _systemTimeout = (targetFps!==undefined) ? 1000/targetFps : 1000/50
var _parameters = {integrator:integrator, repulsion:repulsion, stiffness:stiffness, friction:friction, dt:dt, gravity:centerGravity, precision:precision, timeout:_systemTimeout}
var _energy
var state = {
renderer:null, // this is set by the library user
tween:null, // gets filled in by the Kernel
nodes:{}, // lookup based on node _id's from the worker
edges:{}, // likewise
adjacency:{}, // {name1:{name2:{}, name3:{}}}
names:{}, // lookup table based on 'name' field in data objects
kernel: null
}
var that={
parameters:function(newParams){
if (newParams!==undefined){
if (!isNaN(newParams.precision)){
newParams.precision = Math.max(0, Math.min(1, newParams.precision))
}
$.each(_parameters, function(p, v){
if (newParams[p]!==undefined) _parameters[p] = newParams[p]
})
state.kernel.physicsModified(newParams)
}
return _parameters
},
fps:function(newFPS){
if (newFPS===undefined) return state.kernel.fps()
else that.parameters({timeout:1000/(newFPS||50)})
},
start:function(){
state.kernel.start()
},
stop:function(){
state.kernel.stop()
},
addNode:function(name, data){
data = data || {}
var priorNode = state.names[name]
if (priorNode){
priorNode.data = data
return priorNode
}else if (name!=undefined){
// the data object has a few magic fields that are actually used
// by the simulation:
// 'mass' overrides the default of 1
// 'fixed' overrides the default of false
// 'x' & 'y' will set a starting position rather than
// defaulting to random placement
var x = (data.x!=undefined) ? data.x : null
var y = (data.y!=undefined) ? data.y : null
var fixed = (data.fixed) ? 1 : 0
var node = new Node(data)
node.name = name
state.names[name] = node
state.nodes[node._id] = node;
_changes.push({t:"addNode", id:node._id, m:node.mass, x:x, y:y, f:fixed})
that._notify();
return node;
}
},
// remove a node and its associated edges from the graph
pruneNode:function(nodeOrName) {
var node = that.getNode(nodeOrName)
if (typeof(state.nodes[node._id]) !== 'undefined'){
delete state.nodes[node._id]
delete state.names[node.name]
}
$.each(state.edges, function(id, e){
if (e.source._id === node._id || e.target._id === node._id){
that.pruneEdge(e);
}
})
_changes.push({t:"dropNode", id:node._id})
that._notify();
},
getNode:function(nodeOrName){
if (nodeOrName._id!==undefined){
return nodeOrName
}else if (typeof nodeOrName=='string' || typeof nodeOrName=='number'){
return state.names[nodeOrName]
}
// otherwise let it return undefined
},
eachNode:function(callback){
// callback should accept two arguments: Node, Point
$.each(state.nodes, function(id, n){
if (n._p.x==null || n._p.y==null) return
var pt = (_screenSize!==null) ? that.toScreen(n._p) : n._p
callback.call(that, n, pt);
})
},
addEdge:function(source, target, data){
source = that.getNode(source) || that.addNode(source)
target = that.getNode(target) || that.addNode(target)
data = data || {}
var edge = new Edge(source, target, data);
var src = source._id
var dst = target._id
state.adjacency[src] = state.adjacency[src] || {}
state.adjacency[src][dst] = state.adjacency[src][dst] || []
var exists = (state.adjacency[src][dst].length > 0)
if (exists){
// probably shouldn't allow multiple edges in same direction
// between same nodes? for now just overwriting the data...
$.extend(state.adjacency[src][dst].data, edge.data)
return
}else{
state.edges[edge._id] = edge
state.adjacency[src][dst].push(edge)
var len = (edge.length!==undefined) ? edge.length : 1
_changes.push({t:"addSpring", id:edge._id, fm:src, to:dst, l:len})
that._notify()
}
return edge;
},
// remove an edge and its associated lookup entries
pruneEdge:function(edge) {
_changes.push({t:"dropSpring", id:edge._id})
delete state.edges[edge._id]
for (var x in state.adjacency){
for (var y in state.adjacency[x]){
var edges = state.adjacency[x][y];
for (var j=edges.length - 1; j>=0; j--) {
if (state.adjacency[x][y][j]._id === edge._id){
state.adjacency[x][y].splice(j, 1);
}
}
}
}
that._notify();
},
// find the edges from node1 to node2
getEdges:function(node1, node2) {
node1 = that.getNode(node1)
node2 = that.getNode(node2)
if (!node1 || !node2) return []
if (typeof(state.adjacency[node1._id]) !== 'undefined'
&& typeof(state.adjacency[node1._id][node2._id]) !== 'undefined'){
return state.adjacency[node1._id][node2._id];
}
return [];
},
getEdgesFrom:function(node) {
node = that.getNode(node)
if (!node) return []
if (typeof(state.adjacency[node._id]) !== 'undefined'){
var nodeEdges = []
$.each(state.adjacency[node._id], function(id, subEdges){
nodeEdges = nodeEdges.concat(subEdges)
})
return nodeEdges
}
return [];
},
getEdgesTo:function(node) {
node = that.getNode(node)
if (!node) return []
var nodeEdges = []
$.each(state.edges, function(edgeId, edge){
if (edge.target == node) nodeEdges.push(edge)
})
return nodeEdges;
},
eachEdge:function(callback){
// callback should accept two arguments: Edge, Point
$.each(state.edges, function(id, e){
var p1 = state.nodes[e.source._id]._p
var p2 = state.nodes[e.target._id]._p
if (p1.x==null || p2.x==null) return
p1 = (_screenSize!==null) ? that.toScreen(p1) : p1
p2 = (_screenSize!==null) ? that.toScreen(p2) : p2
if (p1 && p2) callback.call(that, e, p1, p2);
})
},
prune:function(callback){
// callback should be of the form ƒ(node, {from:[],to:[]})
var changes = {dropped:{nodes:[], edges:[]}}
if (callback===undefined){
$.each(state.nodes, function(id, node){
changes.dropped.nodes.push(node)
that.pruneNode(node)
})
}else{
that.eachNode(function(node){
var drop = callback.call(that, node, {from:that.getEdgesFrom(node), to:that.getEdgesTo(node)})
if (drop){
changes.dropped.nodes.push(node)
that.pruneNode(node)
}
})
}
// trace('prune', changes.dropped)
return changes
},
graft:function(branch){
// branch is of the form: { nodes:{name1:{d}, name2:{d},...},
// edges:{fromNm:{toNm1:{d}, toNm2:{d}}, ...} }
var changes = {added:{nodes:[], edges:[]}}
if (branch.nodes) $.each(branch.nodes, function(name, nodeData){
var oldNode = that.getNode(name)
// should probably merge any x/y/m data as well...
// if (oldNode) $.extend(oldNode.data, nodeData)
if (oldNode) oldNode.data = nodeData
else changes.added.nodes.push( that.addNode(name, nodeData) )
state.kernel.start()
})
if (branch.edges) $.each(branch.edges, function(src, dsts){
var srcNode = that.getNode(src)
if (!srcNode) changes.added.nodes.push( that.addNode(src, {}) )
$.each(dsts, function(dst, edgeData){
// should probably merge any x/y/m data as well...
// if (srcNode) $.extend(srcNode.data, nodeData)
// i wonder if it should spawn any non-existant nodes that are part
// of one of these edge requests...
var dstNode = that.getNode(dst)
if (!dstNode) changes.added.nodes.push( that.addNode(dst, {}) )
var oldEdges = that.getEdges(src, dst)
if (oldEdges.length>0){
// trace("update",src,dst)
oldEdges[0].data = edgeData
}else{
// trace("new ->",src,dst)
changes.added.edges.push( that.addEdge(src, dst, edgeData) )
}
})
})
// trace('graft', changes.added)
return changes
},
merge:function(branch){
var changes = {added:{nodes:[], edges:[]}, dropped:{nodes:[], edges:[]}}
$.each(state.edges, function(id, edge){
// if ((branch.edges[edge.source.name]===undefined || branch.edges[edge.source.name][edge.target.name]===undefined) &&
// (branch.edges[edge.target.name]===undefined || branch.edges[edge.target.name][edge.source.name]===undefined)){
if ((branch.edges[edge.source.name]===undefined || branch.edges[edge.source.name][edge.target.name]===undefined)){
that.pruneEdge(edge)
changes.dropped.edges.push(edge)
}
})
var prune_changes = that.prune(function(node, edges){
if (branch.nodes[node.name] === undefined){
changes.dropped.nodes.push(node)
return true
}
})
var graft_changes = that.graft(branch)
changes.added.nodes = changes.added.nodes.concat(graft_changes.added.nodes)
changes.added.edges = changes.added.edges.concat(graft_changes.added.edges)
changes.dropped.nodes = changes.dropped.nodes.concat(prune_changes.dropped.nodes)
changes.dropped.edges = changes.dropped.edges.concat(prune_changes.dropped.edges)
// trace('changes', changes)
return changes
},
tweenNode:function(nodeOrName, dur, to){
var node = that.getNode(nodeOrName)
if (node) state.tween.to(node, dur, to)
},
tweenEdge:function(a,b,c,d){
if (d===undefined){
// called with (edge, dur, to)
that._tweenEdge(a,b,c)
}else{
// called with (node1, node2, dur, to)
var edges = that.getEdges(a,b)
$.each(edges, function(i, edge){
that._tweenEdge(edge, c, d)
})
}
},
_tweenEdge:function(edge, dur, to){
if (edge && edge._id!==undefined) state.tween.to(edge, dur, to)
},
_updateGeometry:function(e){
if (e != undefined){
var stale = (e.epoch<_epoch)
_energy = e.energy
var pts = e.geometry // an array of the form [id1,x1,y1, id2,x2,y2, ...]
if (pts!==undefined){
for (var i=0, j=pts.length/3; i<j; i++){
var id = pts[3*i]
// canary silencer...
if (stale && state.nodes[id]==undefined) continue
state.nodes[id]._p.x = pts[3*i + 1]
state.nodes[id]._p.y = pts[3*i + 2]
}
}
}
},
// convert to/from screen coordinates
screen:function(opts){
if (opts == undefined) return {size:(_screenSize)? objcopy(_screenSize) : undefined,
padding:_screenPadding.concat(),
step:_screenStep}
if (opts.size!==undefined) that.screenSize(opts.size.width, opts.size.height)
if (!isNaN(opts.step)) that.screenStep(opts.step)
if (opts.padding!==undefined) that.screenPadding(opts.padding)
},
screenSize:function(canvasWidth, canvasHeight){
_screenSize = {width:canvasWidth,height:canvasHeight}
that._updateBounds()
},
screenPadding:function(t,r,b,l){
if ($.isArray(t)) trbl = t
else trbl = [t,r,b,l]
var top = trbl[0]
var right = trbl[1]
var bot = trbl[2]
if (right===undefined) trbl = [top,top,top,top]
else if (bot==undefined) trbl = [top,right,top,right]
_screenPadding = trbl
},
screenStep:function(stepsize){
_screenStep = stepsize
},
toScreen:function(p) {
if (!_bounds || !_screenSize) return
// trace(p.x, p.y)
var _padding = _screenPadding || [0,0,0,0]
var size = _bounds.bottomright.subtract(_bounds.topleft)
var sx = _padding[3] + p.subtract(_bounds.topleft).divide(size.x).x * (_screenSize.width - (_padding[1] + _padding[3]))
var sy = _padding[0] + p.subtract(_bounds.topleft).divide(size.y).y * (_screenSize.height - (_padding[0] + _padding[2]))
// return arbor.Point(Math.floor(sx), Math.floor(sy))
return arbor.Point(sx, sy)
},
fromScreen:function(s) {
if (!_bounds || !_screenSize) return
var _padding = _screenPadding || [0,0,0,0]
var size = _bounds.bottomright.subtract(_bounds.topleft)
var px = (s.x-_padding[3]) / (_screenSize.width-(_padding[1]+_padding[3])) * size.x + _bounds.topleft.x
var py = (s.y-_padding[0]) / (_screenSize.height-(_padding[0]+_padding[2])) * size.y + _bounds.topleft.y
return arbor.Point(px, py);
},
_updateBounds:function(newBounds){
// step the renderer's current bounding box closer to the true box containing all
// the nodes. if _screenStep is set to 1 there will be no lag. if _screenStep is
// set to 0 the bounding box will remain stationary after being initially set
if (_screenSize===null) return
if (newBounds) _boundsTarget = newBounds
else _boundsTarget = that.bounds()
// _boundsTarget = newBounds || that.bounds()
// _boundsTarget.topleft = new Point(_boundsTarget.topleft.x,_boundsTarget.topleft.y)
// _boundsTarget.bottomright = new Point(_boundsTarget.bottomright.x,_boundsTarget.bottomright.y)
var bottomright = new Point(_boundsTarget.bottomright.x, _boundsTarget.bottomright.y)
var topleft = new Point(_boundsTarget.topleft.x, _boundsTarget.topleft.y)
var dims = bottomright.subtract(topleft)
var center = topleft.add(dims.divide(2))
var MINSIZE = 4 // perfect-fit scaling
// MINSIZE = Math.max(Math.max(MINSIZE,dims.y), dims.x) // proportional scaling
var size = new Point(Math.max(dims.x,MINSIZE), Math.max(dims.y,MINSIZE))
_boundsTarget.topleft = center.subtract(size.divide(2))
_boundsTarget.bottomright = center.add(size.divide(2))
if (!_bounds){
if ($.isEmptyObject(state.nodes)) return false
_bounds = _boundsTarget
return true
}
// var stepSize = (Math.max(dims.x,dims.y)<MINSIZE) ? .2 : _screenStep
var stepSize = _screenStep
_newBounds = {
bottomright: _bounds.bottomright.add( _boundsTarget.bottomright.subtract(_bounds.bottomright).multiply(stepSize) ),
topleft: _bounds.topleft.add( _boundsTarget.topleft.subtract(_bounds.topleft).multiply(stepSize) )
}
// return true if we're still approaching the target, false if we're close enough
var diff = new Point(_bounds.topleft.subtract(_newBounds.topleft).magnitude(), _bounds.bottomright.subtract(_newBounds.bottomright).magnitude())
if (diff.x*_screenSize.width>1 || diff.y*_screenSize.height>1){
_bounds = _newBounds
return true
}else{
return false
}
},
energy:function(){
return _energy
},
bounds:function(){
// TL -1
// -1 1
// 1 BR
var bottomright = null
var topleft = null
// find the true x/y range of the nodes
$.each(state.nodes, function(id, node){
if (!bottomright){
bottomright = new Point(node._p)
topleft = new Point(node._p)
return
}
var point = node._p
if (point.x===null || point.y===null) return
if (point.x > bottomright.x) bottomright.x = point.x;
if (point.y > bottomright.y) bottomright.y = point.y;
if (point.x < topleft.x) topleft.x = point.x;
if (point.y < topleft.y) topleft.y = point.y;
})
// return the true range then let to/fromScreen handle the padding
if (bottomright && topleft){
return {bottomright: bottomright, topleft: topleft}
}else{
return {topleft: new Point(-1,-1), bottomright: new Point(1,1)};
}
},
// Find the nearest node to a particular position
nearest:function(pos){
if (_screenSize!==null) pos = that.fromScreen(pos)
// if screen size has been specified, presume pos is in screen pixel
// units and convert it back to the particle system coordinates
var min = {node: null, point: null, distance: null};
var t = that;
$.each(state.nodes, function(id, node){
var pt = node._p
if (pt.x===null || pt.y===null) return
var distance = pt.subtract(pos).magnitude();
if (min.distance === null || distance < min.distance){
min = {node: node, point: pt, distance: distance};
if (_screenSize!==null) min.screenPoint = that.toScreen(pt)
}
})
if (min.node){
if (_screenSize!==null) min.distance = that.toScreen(min.node.p).subtract(that.toScreen(pos)).magnitude()
return min
}else{
return null
}
},
_notify:function() {
// pass on graph changes to the physics object in the worker thread
// (using a short timeout to batch changes)
if (_notification===null) _epoch++
else clearTimeout(_notification)
_notification = setTimeout(that._synchronize,20)
// that._synchronize()
},
_synchronize:function(){
if (_changes.length>0){
state.kernel.graphChanged(_changes)
_changes = []
_notification = null
}
},
}
state.kernel = Kernel(that)
state.tween = state.kernel.tween || null
// some magic attrs to make the Node objects phone-home their physics-relevant changes
Node.prototype.__defineGetter__("p", function() {
var self = this
var roboPoint = {}
roboPoint.__defineGetter__('x', function(){ return self._p.x; })
roboPoint.__defineSetter__('x', function(newX){ state.kernel.particleModified(self._id, {x:newX}) })
roboPoint.__defineGetter__('y', function(){ return self._p.y; })
roboPoint.__defineSetter__('y', function(newY){ state.kernel.particleModified(self._id, {y:newY}) })
roboPoint.__proto__ = Point.prototype
return roboPoint
})
Node.prototype.__defineSetter__("p", function(newP) {
this._p.x = newP.x
this._p.y = newP.y
state.kernel.particleModified(this._id, {x:newP.x, y:newP.y})
})
Node.prototype.__defineGetter__("mass", function() { return this._mass; });
Node.prototype.__defineSetter__("mass", function(newM) {
this._mass = newM
state.kernel.particleModified(this._id, {m:newM})
})
Node.prototype.__defineSetter__("tempMass", function(newM) {
state.kernel.particleModified(this._id, {_m:newM})
})
Node.prototype.__defineGetter__("fixed", function() { return this._fixed; });
Node.prototype.__defineSetter__("fixed", function(isFixed) {
this._fixed = isFixed
state.kernel.particleModified(this._id, {f:isFixed?1:0})
})
return that
}

157
arbor_src/physics/worker.js Normal file
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@ -0,0 +1,157 @@
//
// worker.js
//
// wraps physics.js in an onMessage/postMessage protocol that the
// Kernel object can deal with
//
importScripts('atoms.js');
importScripts('barnes-hut.js');
importScripts('physics.js');
// alias over the missing jquery utils so we can run in a worker
$ = {
each:function(obj, callback){
if ($.isArray(obj)){
for (var i=0, j=obj.length; i<j; i++) callback(i, obj[i])
}else{
for (var k in obj) callback(k, obj[k])
}
},
map:function(arr, fn){
var out = []
$.each(arr, function(i, elt){
var result = fn(elt, i)
if (result!==undefined) out.push(result)
})
return out
},
isArray:function(obj){
return (obj.constructor.toString().indexOf("Array") != -1)
},
inArray:function(elt, arr){
for (var i=0, j=arr.length; i<j; i++) if (arr[i]===elt) return i;
return -1
}
}
// endalias
var PhysicsWorker = function(){
var _timeout = 20
var _physics = null
var _physicsInterval = null
var _lastTick = null
var times = []
var last = new Date().valueOf()
var that = {
init:function(param){
that.timeout(param.timeout)
_physics = Physics(param.dt, param.stiffness, param.repulsion, param.friction, that.tock)
return that
},
timeout:function(newTimeout){
if (newTimeout!=_timeout){
_timeout = newTimeout
if (_physicsInterval!==null){
that.stop()
that.go()
}
}
},
go:function(){
if (_physicsInterval!==null) return
// postMessage('starting')
_lastTick=null
_physicsInterval = setInterval(that.tick, _timeout)
},
stop:function(){
if (_physicsInterval===null) return
clearInterval(_physicsInterval);
_physicsInterval = null;
// postMessage('stopping')
},
tick:function(){
// iterate the system
_physics.tick()
// but stop the simulation when energy of the system goes below a threshold
var sysEnergy = _physics.systemEnergy()
if ((sysEnergy.mean + sysEnergy.max)/2 < 0.05){
if (_lastTick===null) _lastTick=new Date().valueOf()
if (new Date().valueOf()-_lastTick>1000){
that.stop()
}else{
// postMessage('pausing')
}
}else{
_lastTick = null
}
},
tock:function(sysData){
sysData.type = "geometry"
postMessage(sysData)
},
modifyNode:function(id, mods){
_physics.modifyNode(id, mods)
that.go()
},
modifyPhysics:function(param){
_physics.modifyPhysics(param)
},
update:function(changes){
var epoch = _physics._update(changes)
}
}
return that
}
var physics = PhysicsWorker()
onmessage = function(e){
if (!e.data.type){
postMessage("¿kérnèl?")
return
}
if (e.data.type=='physics'){
var param = e.data.physics
physics.init(e.data.physics)
return
}
switch(e.data.type){
case "modify":
physics.modifyNode(e.data.id, e.data.mods)
break
case "changes":
physics.update(e.data.changes)
physics.go()
break
case "start":
physics.go()
break
case "stop":
physics.stop()
break
case "sys":
var param = e.data.param || {}
if (!isNaN(param.timeout)) physics.timeout(param.timeout)
physics.modifyPhysics(param)
physics.go()
break
}
}