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feat: optimization of forceAtlas2

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This commit is contained in:
Yanyan-Wang 2018-08-20 17:10:57 +08:00
parent f2b98a0cec
commit 551701be01
2 changed files with 167 additions and 51 deletions
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197
plugins/layout.forceAtlas2/forceCalculator.js
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@ -8,54 +8,138 @@ class ForceCalculator {
let { let {
nodes, nodes,
edges, edges,
maxIteration,
barnesHut,
prune
} = data;
const size = nodes.length;
const esize = edges.length;
const degrees = [];
const idMap = {};
const edgeEndsIdMap = {};
const Es = [];
for (let i = 0; i < size; i += 1) {
idMap[nodes[i].id] = i;
degrees[i] = 0;
if (nodes[i].x === undefined || isNaN(nodes[i].x)) { nodes[i].x = Math.random() * 1000; }
if (nodes[i].y === undefined || isNaN(nodes[i].y)) { nodes[i].y = Math.random() * 1000; }
Es.push({ x: nodes[i].x, y: nodes[i].y });
}
for (let i = 0; i < esize; i += 1) {
let node1;
let node2;
let sIdx = 0,
tIdx = 0;
for (let j = 0; j < size; j += 1) {
if (nodes[j].id === edges[i].source) {
node1 = nodes[j];
sIdx = j;
} else if (nodes[j].id === edges[i].target) {
node2 = nodes[j];
tIdx = j;
}
edgeEndsIdMap[i] = { sourceIdx: sIdx, targetIdx: tIdx };
}
degrees[idMap[node1.id]] += 1;
degrees[idMap[node2.id]] += 1;
}
// page rank
// const alpha = 0.9;
// const pageRankIter = 200;
// const reNodeIds = [];
// for (let i = 0; i < size; i++) {
// const ren = [];
// for (let j = 0; j < esize; j++) {
// if (edges[j].source === nodes[i].id) ren.push(idMap[edges[j].target]);
// if (edges[j].target === nodes[i].id) ren.push(idMap[edges[j].source]);
// }
// reNodeIds.push(ren);
// }
// let it = 0;
// do {
// for (let i = 0; i < size; i += 1) {
// let xsum = 0,
// ysum = 0;
// for (let j = 0; j < degrees[i]; j += 1) {
// xsum += 1 / degrees[i] * Es[reNodeIds[i][j]].x;
// ysum += 1 / degrees[i] * Es[reNodeIds[i][j]].y;
// }
// if (isNaN(xsum)) xsum = 0;
// if (isNaN(ysum)) ysum = 0;
// Es[i].x = nodes[i].x + alpha * xsum;
// Es[i].y = nodes[i].y + alpha * ysum;
// }
// it++;
// } while (it < pageRankIter);
// for (let i = 0; i < size; i += 1) {
// nodes[i].x = Es[i].x - nodes[i].x;
// nodes[i].y = Es[i].y - nodes[i].y;
// }
// const pIndicates = [];
// if (prune) {
// for (let i = 0; i < degrees.length; i += 1) {
// if (degrees[i] === 1) {
// pIndicates[i] = true;
// } else {
// pIndicates[i] = false;
// }
// }
// }
nodes = this.iterate(data, size, esize, idMap, degrees, maxIteration, prune, barnesHut);
// if prune, place the leaves around their parents, and then re-layout for several iterations.
if (prune) {
for (let i = 0; i < degrees.length; i += 1) {
if (degrees[i] === 1) {
for (let j = 0; j < edges.length; j += 1) {
if (edges[j].source === nodes[i].id) {
nodes[i].x = nodes[edgeEndsIdMap[j].targetIdx].x;
nodes[i].y = nodes[edgeEndsIdMap[j].targetIdx].y;
} else if (edges[j].target === nodes[i].id) {
nodes[i].x = nodes[edgeEndsIdMap[j].sourceIdx].x;
nodes[i].y = nodes[edgeEndsIdMap[j].sourceIdx].y;
}
}
}
}
prune = false;
barnesHut = false;
nodes = this.iterate(data, size, esize, idMap, degrees, 50, prune, barnesHut);
}
return nodes;
}
iterate(data, size, esize, idMap, degrees, maxIteration, prune, barnesHut) {
let {
nodes,
edges,
ks,
kr, kr,
kg, kg,
mode, mode,
prevOverlapping, prevOverlapping,
dissuadeHubs, dissuadeHubs,
barnesHut,
maxIteration,
ks,
ksmax, ksmax,
tao, tao,
center, center,
widths widths
} = data; } = data;
const size = nodes.length;
const esize = edges.length;
let SG = 0; let SG = 0;
const bodies = [];
const degrees = [];
const idmap = {};
for (let i = 0; i < size; i += 1) {
idmap[nodes[i].id] = i;
degrees[i] = 0;
if (nodes[i].x === undefined || isNaN(nodes[i].x)) { nodes[i].x = Math.random() * 1000; }
if (nodes[i].y === undefined || isNaN(nodes[i].y)) { nodes[i].y = Math.random() * 1000; }
}
for (let i = 0; i < esize; i += 1) {
let node1;
let node2;
for (let j = 0; j < size; j += 1) {
if (nodes[j].id === edges[i].source) {
node1 = nodes[j];
} else if (nodes[j].id === edges[i].target) {
node2 = nodes[j];
}
}
degrees[idmap[node1.id]] += 1;
degrees[idmap[node2.id]] += 1;
}
const krPrime = 100; const krPrime = 100;
let iter = maxIteration; let iter = maxIteration;
const prevoIter = 50; const prevoIter = 50;
let Forces = []; let Forces = [];
const preForces = []; const preForces = [];
const bodies = [];
for (let i = 0; i < size; i += 1) { for (let i = 0; i < size; i += 1) {
Forces[2 * i] = 0; Forces[2 * i] = 0;
Forces[2 * i + 1] = 0; Forces[2 * i + 1] = 0;
@ -81,27 +165,25 @@ class ForceCalculator {
Forces[2 * i] = 0; Forces[2 * i] = 0;
Forces[2 * i + 1] = 0; Forces[2 * i + 1] = 0;
} }
// // attractive forces, existing on every actual edge // attractive forces, existing on every actual edge
Forces = this.getAttrForces(nodes, edges, size, esize, prevOverlapping, dissuadeHubs, mode, iter, prevoIter, Forces, widths, idmap, degrees); Forces = this.getAttrForces(nodes, edges, size, esize, prevOverlapping, dissuadeHubs, mode, iter, prevoIter, Forces, widths, idMap, degrees, prune);
// // // repulsive forces and Gravity, existing on every node pair // repulsive forces and Gravity, existing on every node pair
// // // if prevOverlapping, using the no-optimized method in the last prevoIter instead. // if prevOverlapping, using the no-optimized method in the last prevoIter instead.
if (barnesHut && ((prevOverlapping && iter > prevoIter) || !prevOverlapping)) { if (barnesHut && ((prevOverlapping && iter > prevoIter) || !prevOverlapping)) {
Forces = this.getOptRepGraForces(nodes, edges, size, esize, prevOverlapping, dissuadeHubs, mode, iter, prevoIter, Forces, kr, krPrime, kg, center, bodies, degrees); Forces = this.getOptRepGraForces(nodes, edges, size, esize, prevOverlapping, dissuadeHubs, mode, iter, prevoIter, Forces, kr, krPrime, kg, center, bodies, degrees, prune);
} else { } else {
Forces = this.getRepGraForces(nodes, edges, size, esize, prevOverlapping, dissuadeHubs, mode, iter, prevoIter, Forces, kr, krPrime, kg, center, widths, degrees); Forces = this.getRepGraForces(nodes, edges, size, esize, prevOverlapping, dissuadeHubs, mode, iter, prevoIter, Forces, kr, krPrime, kg, center, widths, degrees, prune);
} }
// // update the positions // // update the positions
const res = this.updatePos(size, nodes, Forces, preForces, SG, ks, ksmax, tao, degrees); const res = this.updatePos(size, nodes, Forces, preForces, SG, ks, ksmax, tao, degrees, prune);
nodes = res[0]; nodes = res[0];
SG = res[1]; SG = res[1];
iter -= 1; iter -= 1;
} while (iter > 0); } while (iter > 0);
return nodes; return nodes;
} }
getAttrForces(nodes, edges, size, esize, prevOverlapping, dissuadeHubs, mode, iter, prevoIter, Forces, widths, idmap, degrees) { getAttrForces(nodes, edges, size, esize, prevOverlapping, dissuadeHubs, mode, iter, prevoIter, Forces, widths, idMap, degrees, prune) {
for (let i = 0; i < esize; i += 1) { for (let i = 0; i < esize; i += 1) {
// const sourceNode = graph.find(edges[i].source).getModel();
// const targetNode = graph.find(edges[i].target).getModel();
let sourceNode; let sourceNode;
let targetNode; let targetNode;
let sourceIdx; let sourceIdx;
@ -115,6 +197,9 @@ class ForceCalculator {
targetIdx = j; targetIdx = j;
} }
} }
if (prune && (degrees[sourceIdx] === 1 || degrees[targetIdx] === 1)) continue;
let dir = [ targetNode.x - sourceNode.x, targetNode.y - sourceNode.y ]; let dir = [ targetNode.x - sourceNode.x, targetNode.y - sourceNode.y ];
let eucliDis = Math.hypot(dir[0], dir[1]); let eucliDis = Math.hypot(dir[0], dir[1]);
eucliDis = eucliDis < 0.0001 ? 0.0001 : eucliDis; eucliDis = eucliDis < 0.0001 ? 0.0001 : eucliDis;
@ -139,17 +224,20 @@ class ForceCalculator {
Fa1 = eucliDis; Fa1 = eucliDis;
Fa2 = eucliDis; Fa2 = eucliDis;
} }
Forces[2 * idmap[sourceNode.id]] += Fa1 * dir[0]; Forces[2 * idMap[sourceNode.id]] += Fa1 * dir[0];
Forces[2 * idmap[targetNode.id]] -= Fa2 * dir[0]; Forces[2 * idMap[targetNode.id]] -= Fa2 * dir[0];
Forces[2 * idmap[sourceNode.id] + 1] += Fa1 * dir[1]; Forces[2 * idMap[sourceNode.id] + 1] += Fa1 * dir[1];
Forces[2 * idmap[targetNode.id] + 1] -= Fa2 * dir[1]; Forces[2 * idMap[targetNode.id] + 1] -= Fa2 * dir[1];
dir = null; dir = null;
} }
return Forces; return Forces;
} }
getRepGraForces(nodes, edges, size, esize, prevOverlapping, dissuadeHubs, mode, iter, prevoIter, Forces, kr, krPrime, kg, center, widths, degrees) { getRepGraForces(nodes, edges, size, esize, prevOverlapping, dissuadeHubs, mode, iter, prevoIter, Forces, kr, krPrime, kg, center, widths, degrees, prune) {
for (let i = 0; i < size; i += 1) { for (let i = 0; i < size; i += 1) {
for (let j = i + 1; j < size; j += 1) { for (let j = i + 1; j < size; j += 1) {
if (prune && (degrees[i] === 1 || degrees[j] === 1)) continue;
let dir = [ nodes[j].x - nodes[i].x, nodes[j].y - nodes[i].y ]; let dir = [ nodes[j].x - nodes[i].x, nodes[j].y - nodes[i].y ];
let eucliDis = Math.hypot(dir[0], dir[1]); let eucliDis = Math.hypot(dir[0], dir[1]);
eucliDis = eucliDis < 0.0001 ? 0.0001 : eucliDis; eucliDis = eucliDis < 0.0001 ? 0.0001 : eucliDis;
@ -187,12 +275,13 @@ class ForceCalculator {
return Forces; return Forces;
} }
getOptRepGraForces(nodes, edges, size, esize, prevOverlapping, dissuadeHubs, mode, iter, prevoIter, Forces, kr, krPrime, kg, ct, bodies, degrees) { getOptRepGraForces(nodes, edges, size, esize, prevOverlapping, dissuadeHubs, mode, iter, prevoIter, Forces, kr, krPrime, kg, ct, bodies, degrees, prune) {
let minx = 9e10, let minx = 9e10,
maxx = -9e10, maxx = -9e10,
miny = 9e10, miny = 9e10,
maxy = -9e10; maxy = -9e10;
for (let i = 0; i < size; i += 1) { for (let i = 0; i < size; i += 1) {
if (prune && (degrees[i] === 1)) continue;
bodies[i].setPos(nodes[i].x, nodes[i].y); bodies[i].setPos(nodes[i].x, nodes[i].y);
if (nodes[i].x >= maxx) maxx = nodes[i].x; if (nodes[i].x >= maxx) maxx = nodes[i].x;
if (nodes[i].x <= minx) minx = nodes[i].x; if (nodes[i].x <= minx) minx = nodes[i].x;
@ -214,10 +303,16 @@ class ForceCalculator {
// build the tree, insert the nodes(quads) into the tree // build the tree, insert the nodes(quads) into the tree
for (let i = 0; i < size; i += 1) { for (let i = 0; i < size; i += 1) {
if (prune && (degrees[i] === 1)) continue;
if (bodies[i].in(quad)) quadTree.insert(bodies[i]); if (bodies[i].in(quad)) quadTree.insert(bodies[i]);
} }
// update the repulsive forces and the gravity. // update the repulsive forces and the gravity.
for (let i = 0; i < size; i += 1) { for (let i = 0; i < size; i += 1) {
if (prune && (degrees[i] === 1)) continue;
bodies[i].resetForce(); bodies[i].resetForce();
quadTree.updateForce(bodies[i]); quadTree.updateForce(bodies[i]);
Forces[2 * i] -= bodies[i].fx; Forces[2 * i] -= bodies[i].fx;
@ -244,13 +339,16 @@ class ForceCalculator {
return Forces; return Forces;
} }
updatePos(size, nodes, Forces, preForces, SG, ks, ksmax, tao, degrees) { updatePos(size, nodes, Forces, preForces, SG, ks, ksmax, tao, degrees, prune) {
let swgns = []; let swgns = [];
let trans = []; let trans = [];
// swg(G) and tra(G) // swg(G) and tra(G)
let swgG = 0; let swgG = 0;
let traG = 0; let traG = 0;
for (let i = 0; i < size; i += 1) { for (let i = 0; i < size; i += 1) {
if (prune && (degrees[i] === 1)) continue;
const minus = [ Forces[2 * i] - preForces[2 * i], const minus = [ Forces[2 * i] - preForces[2 * i],
Forces[2 * i + 1] - preForces[2 * i + 1] Forces[2 * i + 1] - preForces[2 * i + 1]
]; ];
@ -274,6 +372,9 @@ class ForceCalculator {
} }
// update the node positions // update the node positions
for (let i = 0; i < size; i += 1) { for (let i = 0; i < size; i += 1) {
if (prune && (degrees[i] === 1)) continue;
let Sn = ks * SG / (1 + SG * Math.sqrt(swgns[i])); let Sn = ks * SG / (1 + SG * Math.sqrt(swgns[i]));
let absForce = Math.hypot(Forces[2 * i], Forces[2 * i + 1]); let absForce = Math.hypot(Forces[2 * i], Forces[2 * i + 1]);
absForce = absForce < 0.0001 ? 0.0001 : absForce; absForce = absForce < 0.0001 ? 0.0001 : absForce;

21
plugins/layout.forceAtlas2/layout.js
View File

@ -106,7 +106,16 @@ class Layout {
* activate the webworker for this algorithm or not * activate the webworker for this algorithm or not
* @type {boolean} * @type {boolean}
*/ */
useWorker: true useWorker: true,
/**
* activate prune or not.
* prune the leaves during most iterations, layout the leaves in the last 50 iteraitons.
* if prune === '', it will be activated when the nodes number > 100
* note that it will reduce the quality of the layout
* @type {boolean}
*/
prune: ''
}, options); }, options);
} }
// execute the layout // execute the layout
@ -125,7 +134,8 @@ class Layout {
ks, ks,
ksmax, ksmax,
tao, tao,
onLayoutComplete onLayoutComplete,
prune
} = this; } = this;
const width = this.width ? this.width : graph.getWidth(); const width = this.width ? this.width : graph.getWidth();
@ -164,6 +174,10 @@ class Layout {
if (size > 100 && size <= 500) kg = 10; if (size > 100 && size <= 500) kg = 10;
else if (size > 500) kg = 1; else if (size > 500) kg = 1;
} }
if (prune === '') {
if (size > 100) prune = true;
else prune = false;
}
const obj = { const obj = {
nodes, nodes,
edges, edges,
@ -178,7 +192,8 @@ class Layout {
ksmax, ksmax,
tao, tao,
center, center,
widths widths,
prune
}; };
if (this.useWorker) { if (this.useWorker) {