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https://gitee.com/antv/g6.git
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feat: optimization of forceAtlas2
This commit is contained in:
Yanyan-Wang
parent
f2b98a0cec
commit
551701be01
@ -8,54 +8,138 @@ class ForceCalculator {
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let {
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nodes,
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edges,
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maxIteration,
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barnesHut,
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prune
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} = data;
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const size = nodes.length;
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const esize = edges.length;
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const degrees = [];
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const idMap = {};
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const edgeEndsIdMap = {};
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const Es = [];
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for (let i = 0; i < size; i += 1) {
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idMap[nodes[i].id] = i;
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degrees[i] = 0;
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if (nodes[i].x === undefined || isNaN(nodes[i].x)) { nodes[i].x = Math.random() * 1000; }
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if (nodes[i].y === undefined || isNaN(nodes[i].y)) { nodes[i].y = Math.random() * 1000; }
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Es.push({ x: nodes[i].x, y: nodes[i].y });
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}
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for (let i = 0; i < esize; i += 1) {
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let node1;
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let node2;
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let sIdx = 0,
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tIdx = 0;
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for (let j = 0; j < size; j += 1) {
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if (nodes[j].id === edges[i].source) {
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node1 = nodes[j];
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sIdx = j;
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} else if (nodes[j].id === edges[i].target) {
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node2 = nodes[j];
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tIdx = j;
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}
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edgeEndsIdMap[i] = { sourceIdx: sIdx, targetIdx: tIdx };
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}
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degrees[idMap[node1.id]] += 1;
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degrees[idMap[node2.id]] += 1;
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}
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// page rank
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// const alpha = 0.9;
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// const pageRankIter = 200;
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// const reNodeIds = [];
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// for (let i = 0; i < size; i++) {
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// const ren = [];
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// for (let j = 0; j < esize; j++) {
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// if (edges[j].source === nodes[i].id) ren.push(idMap[edges[j].target]);
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// if (edges[j].target === nodes[i].id) ren.push(idMap[edges[j].source]);
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// }
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// reNodeIds.push(ren);
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// }
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// let it = 0;
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// do {
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// for (let i = 0; i < size; i += 1) {
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// let xsum = 0,
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// ysum = 0;
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// for (let j = 0; j < degrees[i]; j += 1) {
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// xsum += 1 / degrees[i] * Es[reNodeIds[i][j]].x;
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// ysum += 1 / degrees[i] * Es[reNodeIds[i][j]].y;
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// }
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// if (isNaN(xsum)) xsum = 0;
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// if (isNaN(ysum)) ysum = 0;
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// Es[i].x = nodes[i].x + alpha * xsum;
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// Es[i].y = nodes[i].y + alpha * ysum;
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// }
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// it++;
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// } while (it < pageRankIter);
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// for (let i = 0; i < size; i += 1) {
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// nodes[i].x = Es[i].x - nodes[i].x;
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// nodes[i].y = Es[i].y - nodes[i].y;
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// }
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// const pIndicates = [];
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// if (prune) {
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// for (let i = 0; i < degrees.length; i += 1) {
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// if (degrees[i] === 1) {
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// pIndicates[i] = true;
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// } else {
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// pIndicates[i] = false;
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// }
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// }
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// }
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nodes = this.iterate(data, size, esize, idMap, degrees, maxIteration, prune, barnesHut);
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// if prune, place the leaves around their parents, and then re-layout for several iterations.
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if (prune) {
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for (let i = 0; i < degrees.length; i += 1) {
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if (degrees[i] === 1) {
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for (let j = 0; j < edges.length; j += 1) {
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if (edges[j].source === nodes[i].id) {
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nodes[i].x = nodes[edgeEndsIdMap[j].targetIdx].x;
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nodes[i].y = nodes[edgeEndsIdMap[j].targetIdx].y;
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} else if (edges[j].target === nodes[i].id) {
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nodes[i].x = nodes[edgeEndsIdMap[j].sourceIdx].x;
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nodes[i].y = nodes[edgeEndsIdMap[j].sourceIdx].y;
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}
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}
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}
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}
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prune = false;
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barnesHut = false;
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nodes = this.iterate(data, size, esize, idMap, degrees, 50, prune, barnesHut);
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}
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return nodes;
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}
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iterate(data, size, esize, idMap, degrees, maxIteration, prune, barnesHut) {
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let {
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nodes,
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edges,
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ks,
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kr,
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kg,
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mode,
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prevOverlapping,
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dissuadeHubs,
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barnesHut,
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maxIteration,
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ks,
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ksmax,
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tao,
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center,
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widths
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} = data;
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const size = nodes.length;
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const esize = edges.length;
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let SG = 0;
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const bodies = [];
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const degrees = [];
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const idmap = {};
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for (let i = 0; i < size; i += 1) {
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idmap[nodes[i].id] = i;
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degrees[i] = 0;
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if (nodes[i].x === undefined || isNaN(nodes[i].x)) { nodes[i].x = Math.random() * 1000; }
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if (nodes[i].y === undefined || isNaN(nodes[i].y)) { nodes[i].y = Math.random() * 1000; }
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}
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for (let i = 0; i < esize; i += 1) {
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let node1;
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let node2;
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for (let j = 0; j < size; j += 1) {
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if (nodes[j].id === edges[i].source) {
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node1 = nodes[j];
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} else if (nodes[j].id === edges[i].target) {
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node2 = nodes[j];
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}
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}
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degrees[idmap[node1.id]] += 1;
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degrees[idmap[node2.id]] += 1;
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}
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const krPrime = 100;
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let iter = maxIteration;
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const prevoIter = 50;
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let Forces = [];
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const preForces = [];
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const bodies = [];
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for (let i = 0; i < size; i += 1) {
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Forces[2 * i] = 0;
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Forces[2 * i + 1] = 0;
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@ -81,27 +165,25 @@ class ForceCalculator {
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Forces[2 * i] = 0;
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Forces[2 * i + 1] = 0;
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}
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// // attractive forces, existing on every actual edge
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Forces = this.getAttrForces(nodes, edges, size, esize, prevOverlapping, dissuadeHubs, mode, iter, prevoIter, Forces, widths, idmap, degrees);
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// // // repulsive forces and Gravity, existing on every node pair
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// // // if prevOverlapping, using the no-optimized method in the last prevoIter instead.
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// attractive forces, existing on every actual edge
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Forces = this.getAttrForces(nodes, edges, size, esize, prevOverlapping, dissuadeHubs, mode, iter, prevoIter, Forces, widths, idMap, degrees, prune);
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// repulsive forces and Gravity, existing on every node pair
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// if prevOverlapping, using the no-optimized method in the last prevoIter instead.
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if (barnesHut && ((prevOverlapping && iter > prevoIter) || !prevOverlapping)) {
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Forces = this.getOptRepGraForces(nodes, edges, size, esize, prevOverlapping, dissuadeHubs, mode, iter, prevoIter, Forces, kr, krPrime, kg, center, bodies, degrees);
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Forces = this.getOptRepGraForces(nodes, edges, size, esize, prevOverlapping, dissuadeHubs, mode, iter, prevoIter, Forces, kr, krPrime, kg, center, bodies, degrees, prune);
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} else {
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Forces = this.getRepGraForces(nodes, edges, size, esize, prevOverlapping, dissuadeHubs, mode, iter, prevoIter, Forces, kr, krPrime, kg, center, widths, degrees);
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Forces = this.getRepGraForces(nodes, edges, size, esize, prevOverlapping, dissuadeHubs, mode, iter, prevoIter, Forces, kr, krPrime, kg, center, widths, degrees, prune);
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}
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// // update the positions
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const res = this.updatePos(size, nodes, Forces, preForces, SG, ks, ksmax, tao, degrees);
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const res = this.updatePos(size, nodes, Forces, preForces, SG, ks, ksmax, tao, degrees, prune);
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nodes = res[0];
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SG = res[1];
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iter -= 1;
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} while (iter > 0);
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return nodes;
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}
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getAttrForces(nodes, edges, size, esize, prevOverlapping, dissuadeHubs, mode, iter, prevoIter, Forces, widths, idmap, degrees) {
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getAttrForces(nodes, edges, size, esize, prevOverlapping, dissuadeHubs, mode, iter, prevoIter, Forces, widths, idMap, degrees, prune) {
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for (let i = 0; i < esize; i += 1) {
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// const sourceNode = graph.find(edges[i].source).getModel();
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// const targetNode = graph.find(edges[i].target).getModel();
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let sourceNode;
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let targetNode;
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let sourceIdx;
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@ -115,6 +197,9 @@ class ForceCalculator {
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targetIdx = j;
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}
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}
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if (prune && (degrees[sourceIdx] === 1 || degrees[targetIdx] === 1)) continue;
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let dir = [ targetNode.x - sourceNode.x, targetNode.y - sourceNode.y ];
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let eucliDis = Math.hypot(dir[0], dir[1]);
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eucliDis = eucliDis < 0.0001 ? 0.0001 : eucliDis;
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@ -139,17 +224,20 @@ class ForceCalculator {
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Fa1 = eucliDis;
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Fa2 = eucliDis;
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}
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Forces[2 * idmap[sourceNode.id]] += Fa1 * dir[0];
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Forces[2 * idmap[targetNode.id]] -= Fa2 * dir[0];
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Forces[2 * idmap[sourceNode.id] + 1] += Fa1 * dir[1];
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Forces[2 * idmap[targetNode.id] + 1] -= Fa2 * dir[1];
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Forces[2 * idMap[sourceNode.id]] += Fa1 * dir[0];
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Forces[2 * idMap[targetNode.id]] -= Fa2 * dir[0];
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Forces[2 * idMap[sourceNode.id] + 1] += Fa1 * dir[1];
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Forces[2 * idMap[targetNode.id] + 1] -= Fa2 * dir[1];
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dir = null;
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}
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return Forces;
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}
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getRepGraForces(nodes, edges, size, esize, prevOverlapping, dissuadeHubs, mode, iter, prevoIter, Forces, kr, krPrime, kg, center, widths, degrees) {
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getRepGraForces(nodes, edges, size, esize, prevOverlapping, dissuadeHubs, mode, iter, prevoIter, Forces, kr, krPrime, kg, center, widths, degrees, prune) {
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for (let i = 0; i < size; i += 1) {
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for (let j = i + 1; j < size; j += 1) {
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if (prune && (degrees[i] === 1 || degrees[j] === 1)) continue;
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let dir = [ nodes[j].x - nodes[i].x, nodes[j].y - nodes[i].y ];
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let eucliDis = Math.hypot(dir[0], dir[1]);
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eucliDis = eucliDis < 0.0001 ? 0.0001 : eucliDis;
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@ -187,12 +275,13 @@ class ForceCalculator {
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return Forces;
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}
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getOptRepGraForces(nodes, edges, size, esize, prevOverlapping, dissuadeHubs, mode, iter, prevoIter, Forces, kr, krPrime, kg, ct, bodies, degrees) {
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getOptRepGraForces(nodes, edges, size, esize, prevOverlapping, dissuadeHubs, mode, iter, prevoIter, Forces, kr, krPrime, kg, ct, bodies, degrees, prune) {
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let minx = 9e10,
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maxx = -9e10,
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miny = 9e10,
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maxy = -9e10;
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for (let i = 0; i < size; i += 1) {
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if (prune && (degrees[i] === 1)) continue;
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bodies[i].setPos(nodes[i].x, nodes[i].y);
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if (nodes[i].x >= maxx) maxx = nodes[i].x;
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if (nodes[i].x <= minx) minx = nodes[i].x;
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@ -214,10 +303,16 @@ class ForceCalculator {
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// build the tree, insert the nodes(quads) into the tree
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for (let i = 0; i < size; i += 1) {
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if (prune && (degrees[i] === 1)) continue;
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if (bodies[i].in(quad)) quadTree.insert(bodies[i]);
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}
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// update the repulsive forces and the gravity.
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for (let i = 0; i < size; i += 1) {
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if (prune && (degrees[i] === 1)) continue;
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bodies[i].resetForce();
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quadTree.updateForce(bodies[i]);
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Forces[2 * i] -= bodies[i].fx;
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@ -244,13 +339,16 @@ class ForceCalculator {
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return Forces;
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}
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updatePos(size, nodes, Forces, preForces, SG, ks, ksmax, tao, degrees) {
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updatePos(size, nodes, Forces, preForces, SG, ks, ksmax, tao, degrees, prune) {
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let swgns = [];
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let trans = [];
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// swg(G) and tra(G)
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let swgG = 0;
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let traG = 0;
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for (let i = 0; i < size; i += 1) {
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if (prune && (degrees[i] === 1)) continue;
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const minus = [ Forces[2 * i] - preForces[2 * i],
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Forces[2 * i + 1] - preForces[2 * i + 1]
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];
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@ -274,6 +372,9 @@ class ForceCalculator {
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}
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// update the node positions
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for (let i = 0; i < size; i += 1) {
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if (prune && (degrees[i] === 1)) continue;
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let Sn = ks * SG / (1 + SG * Math.sqrt(swgns[i]));
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let absForce = Math.hypot(Forces[2 * i], Forces[2 * i + 1]);
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absForce = absForce < 0.0001 ? 0.0001 : absForce;
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@ -106,7 +106,16 @@ class Layout {
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* activate the webworker for this algorithm or not
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* @type {boolean}
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*/
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useWorker: true
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useWorker: true,
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/**
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* activate prune or not.
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* prune the leaves during most iterations, layout the leaves in the last 50 iteraitons.
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* if prune === '', it will be activated when the nodes number > 100
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* note that it will reduce the quality of the layout
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* @type {boolean}
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*/
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prune: ''
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}, options);
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}
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// execute the layout
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@ -125,7 +134,8 @@ class Layout {
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ks,
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ksmax,
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tao,
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onLayoutComplete
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onLayoutComplete,
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prune
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} = this;
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const width = this.width ? this.width : graph.getWidth();
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@ -164,6 +174,10 @@ class Layout {
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if (size > 100 && size <= 500) kg = 10;
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else if (size > 500) kg = 1;
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}
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if (prune === '') {
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if (size > 100) prune = true;
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else prune = false;
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}
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const obj = {
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nodes,
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edges,
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@ -178,7 +192,8 @@ class Layout {
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ksmax,
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tao,
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center,
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widths
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widths,
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prune
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};
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if (this.useWorker) {
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