แก้ coding style ภาค 2
This commit is contained in:
38
.eslintrc
38
.eslintrc
@@ -1,15 +1,41 @@
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parserOptions:
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parserOptions:
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sourceType: module
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sourceType: module
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extends:
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extends:
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"eslint:recommended"
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"standard"
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rules:
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rules:
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no-cond-assign: 0
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no-cond-assign: 0
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no-console: 0
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no-console: 0
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semi:
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- error
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- always
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/*
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no-extra-parens: 1
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curly: 0
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block-scoped-var: 1
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no-tabs: 1
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no-negated-condition: 1
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block-spacing: 1
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brace-style: 1
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comma-spacing: 1
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comma-style: 1
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eol-last: 1
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func-call-spacing: 1
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indent:
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- error
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- 2
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key-spacing: 1
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linebreak-style: 1
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no-lonely-if: 1
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*/
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env:
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env:
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es6: true
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es6: true
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globals:
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globals:
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console: false
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console: false
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/*
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plugins:
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- import
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- node
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- promise
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*/
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12
index.js
12
index.js
@@ -1,17 +1,17 @@
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export {default as forceNeighbourSampling}
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export {default as forceNeighbourSampling}
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from "./src/neighbourSampling";
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from './src/neighbourSampling';
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export { default as forceBarnesHut}
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export { default as forceBarnesHut}
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from "./src/barnesHut";
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from './src/barnesHut';
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export { default as tSNE}
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export { default as tSNE}
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from "./src/t-sne";
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from './src/t-sne';
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export { default as forceLinkCompleteGraph}
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export { default as forceLinkCompleteGraph}
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from "./src/link";
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from './src/link';
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export { default as hybridSimulation}
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export { default as hybridSimulation}
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from "./src/hybridSimulation";
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from './src/hybridSimulation';
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export { getStress as calculateStress }
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export { getStress as calculateStress }
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from "./src/stress";
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from './src/stress';
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@@ -19,6 +19,11 @@
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},
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},
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"devDependencies": {
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"devDependencies": {
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"eslint": "4",
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"eslint": "4",
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"eslint-config-standard": "^11.0.0",
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"eslint-plugin-import": "^2.9.0",
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"eslint-plugin-node": "^6.0.1",
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"eslint-plugin-promise": "^3.7.0",
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"eslint-plugin-standard": "^3.0.1",
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"rollup": "0.36",
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"rollup": "0.36",
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"uglify-js": "git+https://github.com/mishoo/UglifyJS2.git#harmony"
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"uglify-js": "git+https://github.com/mishoo/UglifyJS2.git#harmony"
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},
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},
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@@ -1,7 +1,7 @@
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import constant from "./constant";
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import constant from './constant';
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import jiggle from "./jiggle";
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import jiggle from './jiggle';
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import {x, y} from "./xy";
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import {x, y} from './xy';
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import {quadtree} from "d3-quadtree";
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import {quadtree} from 'd3-quadtree';
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/**
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/**
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* The refinement of the existing Barnes-Hut implementation in D3
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* The refinement of the existing Barnes-Hut implementation in D3
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@@ -12,7 +12,7 @@ import {quadtree} from "d3-quadtree";
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* The check to see if the nodes are far away was also changed to the one described in original Barnes-Hut paper.
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* The check to see if the nodes are far away was also changed to the one described in original Barnes-Hut paper.
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* @return {force} calculated forces.
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* @return {force} calculated forces.
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*/
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*/
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export default function() {
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export default function () {
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var nodes,
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var nodes,
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node,
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node,
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alpha,
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alpha,
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@@ -25,7 +25,7 @@ export default function() {
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* @param {number} _ - controls the stopping of the
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* @param {number} _ - controls the stopping of the
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* particle simulations.
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* particle simulations.
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*/
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*/
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function force(_) {
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function force (_) {
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var i, n = nodes.length, tree = quadtree(nodes, x, y).visitAfter(accumulate);
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var i, n = nodes.length, tree = quadtree(nodes, x, y).visitAfter(accumulate);
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for (alpha = _, i = 0; i < n; ++i) {
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for (alpha = _, i = 0; i < n; ++i) {
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node = nodes[i], tree.visit(apply);
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node = nodes[i], tree.visit(apply);
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@@ -38,7 +38,7 @@ export default function() {
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* nodes accumulate forces from coincident quadrants.
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* nodes accumulate forces from coincident quadrants.
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* @param {quadrant} quad - node representing the quadrant in quadtree.
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* @param {quadrant} quad - node representing the quadrant in quadtree.
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*/
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*/
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function accumulate(quad) {
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function accumulate (quad) {
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var q, d, children = [];
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var q, d, children = [];
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// For internal nodes, accumulate forces from child quadrants.
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// For internal nodes, accumulate forces from child quadrants.
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@@ -69,8 +69,7 @@ export default function() {
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* @param {number} x2 - upper x bound of the node.
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* @param {number} x2 - upper x bound of the node.
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* @return {boolean} - true if the approximation was applied.
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* @return {boolean} - true if the approximation was applied.
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*/
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*/
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function apply(quad, x1, _, x2) {
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function apply (quad, x1, _, x2) {
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var x = quad.data.x + quad.data.vx - node.x - node.vx,
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var x = quad.data.x + quad.data.vx - node.x - node.vx,
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y = quad.data.y + quad.data.vy - node.y - node.vy,
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y = quad.data.y + quad.data.vy - node.y - node.vy,
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w = x2 - x1,
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w = x2 - x1,
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@@ -98,13 +97,15 @@ export default function() {
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if (y === 0) y = jiggle(), l += y * y;
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if (y === 0) y = jiggle(), l += y * y;
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}
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}
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do if (quad.data !== node) {
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do {
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l = (l - +distance(node, quad.data)) / l * alpha;
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if (quad.data !== node) {
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x *= l, y *= l;
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l = (l - +distance(node, quad.data)) / l * alpha;
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quad.data.vx -= x;
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x *= l, y *= l;
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quad.data.vy -= y;
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quad.data.vx -= x;
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node.vx += x;
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quad.data.vy -= y;
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node.vy += y;
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node.vx += x;
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node.vy += y;
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}
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} while (quad = quad.next);
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} while (quad = quad.next);
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}
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}
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@@ -114,37 +115,37 @@ export default function() {
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* the better layout.
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* the better layout.
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* @return {number} - stress of the layout.
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* @return {number} - stress of the layout.
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*/
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*/
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function getStress() {
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function getStress () {
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var totalDiffSq = 0, totalHighDistSq = 0;
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var totalDiffSq = 0, totalHighDistSq = 0;
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for (var i = 0, source, target, realDist, highDist; i < nodes.length; i++) {
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for (var i = 0, source, target, realDist, highDist; i < nodes.length; i++) {
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for (var j = 0; j < nodes.length; j++) {
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for (var j = 0; j < nodes.length; j++) {
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if (i !== j) {
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if (i !== j) {
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source = nodes[i], target = nodes[j];
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source = nodes[i], target = nodes[j];
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realDist = Math.hypot(target.x-source.x, target.y-source.y);
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realDist = Math.hypot(target.x - source.x, target.y - source.y);
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highDist = +distance(nodes[i], nodes[j]);
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highDist = +distance(nodes[i], nodes[j]);
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totalDiffSq += Math.pow(realDist-highDist, 2);
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totalDiffSq += Math.pow(realDist - highDist, 2);
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totalHighDistSq += highDist * highDist;
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totalHighDistSq += highDist * highDist;
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}
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}
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}
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}
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}
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}
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return Math.sqrt(totalDiffSq/totalHighDistSq);
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return Math.sqrt(totalDiffSq / totalHighDistSq);
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}
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}
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// API for initializing the algorithm, setting parameters and querying
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// API for initializing the algorithm, setting parameters and querying
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// metrics.
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// metrics.
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force.initialize = function(_) {
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force.initialize = function (_) {
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nodes = _;
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nodes = _;
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};
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};
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force.distance = function(_) {
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force.distance = function (_) {
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return arguments.length ? (distance = typeof _ === "function" ? _ : constant(+_), force) : distance;
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return arguments.length ? (distance = typeof _ === 'function' ? _ : constant(+_), force) : distance;
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};
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};
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force.theta = function(_) {
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force.theta = function (_) {
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return arguments.length ? (theta = _, force) : theta;
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return arguments.length ? (theta = _, force) : theta;
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};
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};
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force.stress = function() {
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force.stress = function () {
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return getStress();
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return getStress();
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};
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};
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@@ -1,8 +1,8 @@
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/**
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/**
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* @return a constant defined by x.
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* @return a constant defined by x.
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*/
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*/
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export default function(x) {
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export default function (x) {
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return function() {
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return function () {
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return x;
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return x;
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};
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};
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}
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}
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@@ -8,7 +8,7 @@
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sample is the list of selected objects while
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sample is the list of selected objects while
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remainder is the list of those unselected.
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remainder is the list of those unselected.
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*/
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*/
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export function takeSampleFrom(sourceList, amount) {
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export function takeSampleFrom (sourceList, amount) {
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let randElements = [],
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let randElements = [],
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max = sourceList.length,
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max = sourceList.length,
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swap = false;
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swap = false;
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@@ -18,7 +18,7 @@ export function takeSampleFrom(sourceList, amount) {
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}
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}
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// If picking more than half of the entire set, random to pick the remainder instead
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// If picking more than half of the entire set, random to pick the remainder instead
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if (amount > Math.ceil(max/2)){
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if (amount > Math.ceil(max / 2)) {
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amount = max - amount;
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amount = max - amount;
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swap = true;
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swap = true;
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}
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}
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@@ -35,7 +35,7 @@ export function takeSampleFrom(sourceList, amount) {
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return !randElements.includes(obj);
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return !randElements.includes(obj);
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});
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});
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if(swap) {
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if (swap) {
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return {
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return {
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sample: remainder,
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sample: remainder,
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remainder: randElements
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remainder: randElements
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@@ -57,14 +57,14 @@ export function takeSampleFrom(sourceList, amount) {
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* @param {number} r
|
* @param {number} r
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* @return {object} - coordinate {x: number, y: number} of the point
|
* @return {object} - coordinate {x: number, y: number} of the point
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*/
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*/
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export function pointOnCircle(h, k, angle, r) {
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export function pointOnCircle (h, k, angle, r) {
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return {
|
return {
|
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x: h + r*Math.cos(toRadians(angle)),
|
x: h + r * Math.cos(toRadians(angle)),
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y: k + r*Math.sin(toRadians(angle))
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y: k + r * Math.sin(toRadians(angle))
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};
|
};
|
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}
|
}
|
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|
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function toRadians(degrees) {
|
function toRadians (degrees) {
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return degrees * (Math.PI / 180);
|
return degrees * (Math.PI / 180);
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}
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}
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@@ -79,7 +79,7 @@ function toRadians(degrees) {
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that of samples.
|
that of samples.
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* @return {number} - Sum of distances differences
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* @return {number} - Sum of distances differences
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*/
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*/
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export function sumDistError(node, samples, realDistances) {
|
export function sumDistError (node, samples, realDistances) {
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let total = 0.0;
|
let total = 0.0;
|
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for (let i = 0; i < samples.length; i++) {
|
for (let i = 0; i < samples.length; i++) {
|
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let sample = samples[i];
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let sample = samples[i];
|
||||||
|
|||||||
@@ -1,7 +1,7 @@
|
|||||||
/**
|
/**
|
||||||
* @return {number} a very small non-zero random number.
|
* @return {number} a very small non-zero random number.
|
||||||
*/
|
*/
|
||||||
export default function() {
|
export default function () {
|
||||||
let rand;
|
let rand;
|
||||||
do {
|
do {
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rand = (Math.random() - 0.5) * 1e-6;
|
rand = (Math.random() - 0.5) * 1e-6;
|
||||||
|
|||||||
60
src/link.js
60
src/link.js
@@ -1,5 +1,5 @@
|
|||||||
import constant from "./constant";
|
import constant from './constant';
|
||||||
import jiggle from "./jiggle";
|
import jiggle from './jiggle';
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* Modified link force algorithm
|
* Modified link force algorithm
|
||||||
@@ -8,7 +8,7 @@ import jiggle from "./jiggle";
|
|||||||
* - removed other unused functions
|
* - removed other unused functions
|
||||||
* Alpha should be constant 1 for accurate simulation
|
* Alpha should be constant 1 for accurate simulation
|
||||||
*/
|
*/
|
||||||
export default function() {
|
export default function () {
|
||||||
var dataSizeFactor,
|
var dataSizeFactor,
|
||||||
distance = constant(30),
|
distance = constant(30),
|
||||||
distances = [],
|
distances = [],
|
||||||
@@ -18,11 +18,11 @@ export default function() {
|
|||||||
latestVelocityDiff = 0,
|
latestVelocityDiff = 0,
|
||||||
iterations = 1;
|
iterations = 1;
|
||||||
|
|
||||||
function force(alpha) {
|
function force (alpha) {
|
||||||
let n = nodes.length;
|
let n = nodes.length;
|
||||||
// Cache old velocity for comparison later
|
// Cache old velocity for comparison later
|
||||||
if (stableVeloHandler!==null && stableVelocity>=0) {
|
if (stableVeloHandler !== null && stableVelocity >= 0) {
|
||||||
for (let i = n-1, node; i>=0; i--) {
|
for (let i = n - 1, node; i >= 0; i--) {
|
||||||
node = nodes[i];
|
node = nodes[i];
|
||||||
node.oldvx = node.vx;
|
node.oldvx = node.vx;
|
||||||
node.oldvy = node.vy;
|
node.oldvy = node.vy;
|
||||||
@@ -32,46 +32,48 @@ export default function() {
|
|||||||
// Each iteration in a tick
|
// Each iteration in a tick
|
||||||
for (var k = 0, source, target, i, j, x, y, l; k < iterations; ++k) {
|
for (var k = 0, source, target, i, j, x, y, l; k < iterations; ++k) {
|
||||||
// For each link
|
// For each link
|
||||||
for (i = 1; i < n; i++) for (j = 0; j < i; j++) {
|
for (i = 1; i < n; i++) {
|
||||||
|
for (j = 0; j < i; j++) {
|
||||||
// jiggle so l won't be zero and divide by zero error after this
|
// jiggle so l won't be zero and divide by zero error after this
|
||||||
source = nodes[i];
|
source = nodes[i];
|
||||||
target = nodes[j];
|
target = nodes[j];
|
||||||
x = target.x + target.vx - source.x - source.vx || jiggle();
|
x = target.x + target.vx - source.x - source.vx || jiggle();
|
||||||
y = target.y + target.vy - source.y - source.vy || jiggle();
|
y = target.y + target.vy - source.y - source.vy || jiggle();
|
||||||
l = Math.sqrt(x * x + y * y);
|
l = Math.sqrt(x * x + y * y);
|
||||||
l = (l - distances[i*(i-1)/2+j]) / l * dataSizeFactor * alpha;
|
l = (l - distances[i * (i - 1) / 2 + j]) / l * dataSizeFactor * alpha;
|
||||||
x *= l, y *= l;
|
x *= l, y *= l;
|
||||||
target.vx -= x;
|
target.vx -= x;
|
||||||
target.vy -= y;
|
target.vy -= y;
|
||||||
source.vx += x;
|
source.vx += x;
|
||||||
source.vy += y;
|
source.vy += y;
|
||||||
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
// Calculate velocity changes, aka force applied.
|
// Calculate velocity changes, aka force applied.
|
||||||
if (stableVeloHandler!==null && stableVelocity>=0) {
|
if (stableVeloHandler !== null && stableVelocity >= 0) {
|
||||||
let velocityDiff = 0;
|
let velocityDiff = 0;
|
||||||
for (let i = n-1, node; i>=0; i--) {
|
for (let i = n - 1, node; i >= 0; i--) {
|
||||||
node = nodes[i];
|
node = nodes[i];
|
||||||
velocityDiff += Math.abs(Math.hypot(node.vx-node.oldvx, node.vy-node.oldvy));
|
velocityDiff += Math.abs(Math.hypot(node.vx - node.oldvx, node.vy - node.oldvy));
|
||||||
}
|
}
|
||||||
velocityDiff /= n;
|
velocityDiff /= n;
|
||||||
latestVelocityDiff = velocityDiff;
|
latestVelocityDiff = velocityDiff;
|
||||||
|
|
||||||
if(velocityDiff<stableVelocity){
|
if (velocityDiff < stableVelocity) {
|
||||||
stableVeloHandler();
|
stableVeloHandler();
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
function initialize() {
|
function initialize () {
|
||||||
if (!nodes) return;
|
if (!nodes) return;
|
||||||
// 0.5 to divide the force to two part for source and target node
|
// 0.5 to divide the force to two part for source and target node
|
||||||
dataSizeFactor = 0.5/(nodes.length-1);
|
dataSizeFactor = 0.5 / (nodes.length - 1);
|
||||||
initializeDistance();
|
initializeDistance();
|
||||||
}
|
}
|
||||||
|
|
||||||
function initializeDistance() {
|
function initializeDistance () {
|
||||||
if (!nodes) return;
|
if (!nodes) return;
|
||||||
for (let i = 1, n = nodes.length; i < n; i++) {
|
for (let i = 1, n = nodes.length; i < n; i++) {
|
||||||
for (let j = 0; j < i; j++) {
|
for (let j = 0; j < i; j++) {
|
||||||
@@ -80,17 +82,17 @@ export default function() {
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
force.initialize = function(_) {
|
force.initialize = function (_) {
|
||||||
nodes = _;
|
nodes = _;
|
||||||
initialize();
|
initialize();
|
||||||
};
|
};
|
||||||
|
|
||||||
force.iterations = function(_) {
|
force.iterations = function (_) {
|
||||||
return arguments.length ? (iterations = +_, force) : iterations;
|
return arguments.length ? (iterations = +_, force) : iterations;
|
||||||
};
|
};
|
||||||
|
|
||||||
force.distance = function(_) {
|
force.distance = function (_) {
|
||||||
return arguments.length ? (distance = typeof _ === "function" ? _ : constant(+_), initializeDistance(), force) : distance;
|
return arguments.length ? (distance = typeof _ === 'function' ? _ : constant(+_), initializeDistance(), force) : distance;
|
||||||
};
|
};
|
||||||
|
|
||||||
force.latestAccel = function () {
|
force.latestAccel = function () {
|
||||||
|
|||||||
@@ -1,12 +1,12 @@
|
|||||||
import constant from "./constant";
|
import constant from './constant';
|
||||||
import jiggle from "./jiggle";
|
import jiggle from './jiggle';
|
||||||
/**
|
/**
|
||||||
* An implementation of Chalmers' 1996 Neighbour and Sampling algorithm.
|
* An implementation of Chalmers' 1996 Neighbour and Sampling algorithm.
|
||||||
* It uses random sampling to find the most suited neighbours from the
|
* It uses random sampling to find the most suited neighbours from the
|
||||||
* data set.
|
* data set.
|
||||||
*/
|
*/
|
||||||
|
|
||||||
function sortDistances(a, b) {
|
function sortDistances (a, b) {
|
||||||
return b[1] - a[1];
|
return b[1] - a[1];
|
||||||
}
|
}
|
||||||
|
|
||||||
@@ -25,18 +25,18 @@ export default function () {
|
|||||||
* Apply spring forces at each simulation iteration.
|
* Apply spring forces at each simulation iteration.
|
||||||
* @param {number} alpha - multiplier for amount of force applied
|
* @param {number} alpha - multiplier for amount of force applied
|
||||||
*/
|
*/
|
||||||
function force(alpha) {
|
function force (alpha) {
|
||||||
let n = nodes.length;
|
let n = nodes.length;
|
||||||
// Cache old velocity for comparison later
|
// Cache old velocity for comparison later
|
||||||
if (stableVeloHandler!==null && stableVelocity>=0) {
|
if (stableVeloHandler !== null && stableVelocity >= 0) {
|
||||||
for (let i = n-1, node; i>=0; i--) {
|
for (let i = n - 1, node; i >= 0; i--) {
|
||||||
node = nodes[i];
|
node = nodes[i];
|
||||||
node.oldvx = node.vx;
|
node.oldvx = node.vx;
|
||||||
node.oldvy = node.vy;
|
node.oldvy = node.vy;
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
for (let i = n-1, node, samples; i>=0; i--) {
|
for (let i = n - 1, node, samples; i >= 0; i--) {
|
||||||
node = nodes[i];
|
node = nodes[i];
|
||||||
samples = createRandomSamples(i);
|
samples = createRandomSamples(i);
|
||||||
|
|
||||||
@@ -52,16 +52,16 @@ export default function () {
|
|||||||
}
|
}
|
||||||
|
|
||||||
// Calculate velocity changes, aka force applied.
|
// Calculate velocity changes, aka force applied.
|
||||||
if (stableVeloHandler!==null && stableVelocity>=0) {
|
if (stableVeloHandler !== null && stableVelocity >= 0) {
|
||||||
let velocityDiff = 0;
|
let velocityDiff = 0;
|
||||||
for (let i = n-1, node; i>=0; i--) {
|
for (let i = n - 1, node; i >= 0; i--) {
|
||||||
node = nodes[i];
|
node = nodes[i];
|
||||||
velocityDiff += Math.abs(Math.hypot(node.vx-node.oldvx, node.vy-node.oldvy));
|
velocityDiff += Math.abs(Math.hypot(node.vx - node.oldvx, node.vy - node.oldvy));
|
||||||
}
|
}
|
||||||
velocityDiff /= n;
|
velocityDiff /= n;
|
||||||
latestVelocityDiff = velocityDiff;
|
latestVelocityDiff = velocityDiff;
|
||||||
|
|
||||||
if(velocityDiff<stableVelocity){
|
if (velocityDiff < stableVelocity) {
|
||||||
stableVeloHandler();
|
stableVeloHandler();
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
@@ -74,7 +74,7 @@ export default function () {
|
|||||||
* @param {number} dist - high dimensional distance between the two nodes
|
* @param {number} dist - high dimensional distance between the two nodes
|
||||||
* @param {number} alpha - multiplier for the amount of force applied
|
* @param {number} alpha - multiplier for the amount of force applied
|
||||||
*/
|
*/
|
||||||
function setVelocity(source, target, dist, alpha) {
|
function setVelocity (source, target, dist, alpha) {
|
||||||
let x, y, l;
|
let x, y, l;
|
||||||
// jiggle so l won't be zero and divide by zero error after this
|
// jiggle so l won't be zero and divide by zero error after this
|
||||||
x = target.x + target.vx - source.x - source.vx || jiggle();
|
x = target.x + target.vx - source.x - source.vx || jiggle();
|
||||||
@@ -90,11 +90,11 @@ export default function () {
|
|||||||
}
|
}
|
||||||
|
|
||||||
// Called on nodes change and added to a simulation
|
// Called on nodes change and added to a simulation
|
||||||
function initialize() {
|
function initialize () {
|
||||||
if (!nodes) return;
|
if (!nodes) return;
|
||||||
|
|
||||||
// Initialize for each node some random neighbours.
|
// Initialize for each node some random neighbours.
|
||||||
for (let i = nodes.length-1; i>=0; i--) {
|
for (let i = nodes.length - 1; i >= 0; i--) {
|
||||||
let neighbs = pickRandomNodesFor(i, [i], neighbourSize);
|
let neighbs = pickRandomNodesFor(i, [i], neighbourSize);
|
||||||
// Sort the neighbour set by the distances.
|
// Sort the neighbour set by the distances.
|
||||||
neighbours[i] = new Map(neighbs.sort(sortDistances));
|
neighbours[i] = new Map(neighbs.sort(sortDistances));
|
||||||
@@ -103,8 +103,8 @@ export default function () {
|
|||||||
initDataSizeFactor();
|
initDataSizeFactor();
|
||||||
}
|
}
|
||||||
|
|
||||||
function initDataSizeFactor(){
|
function initDataSizeFactor () {
|
||||||
dataSizeFactor = 0.5/(neighbourSize+sampleSize);
|
dataSizeFactor = 0.5 / (neighbourSize + sampleSize);
|
||||||
}
|
}
|
||||||
|
|
||||||
/**
|
/**
|
||||||
@@ -116,7 +116,7 @@ export default function () {
|
|||||||
* @param {number} size - max number of elements in the map to return.
|
* @param {number} size - max number of elements in the map to return.
|
||||||
* @return {array}
|
* @return {array}
|
||||||
*/
|
*/
|
||||||
function pickRandomNodesFor(index, exclude, size) {
|
function pickRandomNodesFor (index, exclude, size) {
|
||||||
let randElements = [];
|
let randElements = [];
|
||||||
let max = nodes.length;
|
let max = nodes.length;
|
||||||
|
|
||||||
@@ -133,7 +133,7 @@ export default function () {
|
|||||||
}
|
}
|
||||||
randElements.push(rand);
|
randElements.push(rand);
|
||||||
}
|
}
|
||||||
for(let i=randElements.length-1, rand; i>=0; i--){
|
for (let i = randElements.length - 1, rand; i >= 0; i--) {
|
||||||
rand = randElements[i];
|
rand = randElements[i];
|
||||||
randElements[i] = [rand, distance(nodes[index], nodes[rand])];
|
randElements[i] = [rand, distance(nodes[index], nodes[rand])];
|
||||||
}
|
}
|
||||||
@@ -146,7 +146,7 @@ export default function () {
|
|||||||
* @param {number} index - index of the node to generate sample for
|
* @param {number} index - index of the node to generate sample for
|
||||||
* @return {map}
|
* @return {map}
|
||||||
*/
|
*/
|
||||||
function createRandomSamples(index) {
|
function createRandomSamples (index) {
|
||||||
// Ignore the current neighbours of the node and itself.
|
// Ignore the current neighbours of the node and itself.
|
||||||
let exclude = [index];
|
let exclude = [index];
|
||||||
exclude = exclude.concat(Array.from(neighbours[index].keys()));
|
exclude = exclude.concat(Array.from(neighbours[index].keys()));
|
||||||
@@ -160,13 +160,12 @@ export default function () {
|
|||||||
* @param {map} samples - map of samples
|
* @param {map} samples - map of samples
|
||||||
* @return {map} - new map of neighbours
|
* @return {map} - new map of neighbours
|
||||||
*/
|
*/
|
||||||
function findNewNeighbours(neighbours, samples) {
|
function findNewNeighbours (neighbours, samples) {
|
||||||
let combined = [...neighbours.entries()].concat([...samples.entries()]);
|
let combined = [...neighbours.entries()].concat([...samples.entries()]);
|
||||||
combined = combined.sort(sortDistances);
|
combined = combined.sort(sortDistances);
|
||||||
return new Map(combined.slice(0, neighbourSize));
|
return new Map(combined.slice(0, neighbourSize));
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
// API for initializing the algorithm and setting parameters
|
// API for initializing the algorithm and setting parameters
|
||||||
force.initialize = function (_) {
|
force.initialize = function (_) {
|
||||||
nodes = _;
|
nodes = _;
|
||||||
@@ -186,7 +185,7 @@ export default function () {
|
|||||||
};
|
};
|
||||||
|
|
||||||
force.distance = function (_) {
|
force.distance = function (_) {
|
||||||
return arguments.length ? (distance = typeof _ === "function" ? _ : constant(+_), force) : distance;
|
return arguments.length ? (distance = typeof _ === 'function' ? _ : constant(+_), force) : distance;
|
||||||
};
|
};
|
||||||
|
|
||||||
force.latestAccel = function () {
|
force.latestAccel = function () {
|
||||||
|
|||||||
@@ -4,10 +4,10 @@
|
|||||||
* to the better layout.
|
* to the better layout.
|
||||||
* @return {number} - stress of the layout.
|
* @return {number} - stress of the layout.
|
||||||
*/
|
*/
|
||||||
export function getStress(nodes, distance) {
|
export function getStress (nodes, distance) {
|
||||||
let sumDiffSq = 0
|
let sumDiffSq = 0;
|
||||||
let sumLowDDistSq = 0;
|
let sumLowDDistSq = 0;
|
||||||
for (let j = nodes.length-1; j >= 1; j--) {
|
for (let j = nodes.length - 1; j >= 1; j--) {
|
||||||
for (let i = 0; i < j; i++) {
|
for (let i = 0; i < j; i++) {
|
||||||
let source = nodes[i], target = nodes[j];
|
let source = nodes[i], target = nodes[j];
|
||||||
let lowDDist = Math.hypot(target.x - source.x, target.y - source.y);
|
let lowDDist = Math.hypot(target.x - source.x, target.y - source.y);
|
||||||
|
|||||||
47
src/t-sne.js
47
src/t-sne.js
@@ -1,5 +1,5 @@
|
|||||||
/* eslint-disable block-scoped-var */
|
/* eslint-disable block-scoped-var */
|
||||||
import constant from "./constant";
|
import constant from './constant';
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* Set the node id accessor to the specified i.
|
* Set the node id accessor to the specified i.
|
||||||
@@ -7,7 +7,7 @@ import constant from "./constant";
|
|||||||
* @param {accessor} i - id accessor.
|
* @param {accessor} i - id accessor.
|
||||||
* @return {accessor} - node id accessor.
|
* @return {accessor} - node id accessor.
|
||||||
*/
|
*/
|
||||||
function index(d, i) {
|
function index (d, i) {
|
||||||
return i;
|
return i;
|
||||||
}
|
}
|
||||||
|
|
||||||
@@ -15,7 +15,7 @@ function index(d, i) {
|
|||||||
* t-SNE implementation in D3 by using the code existing in tsnejs
|
* t-SNE implementation in D3 by using the code existing in tsnejs
|
||||||
* (https://github.com/karpathy/tsnejs) to compute the solution.
|
* (https://github.com/karpathy/tsnejs) to compute the solution.
|
||||||
*/
|
*/
|
||||||
export default function() {
|
export default function () {
|
||||||
var id = index,
|
var id = index,
|
||||||
distance = constant(300),
|
distance = constant(300),
|
||||||
nodes,
|
nodes,
|
||||||
@@ -33,7 +33,7 @@ export default function() {
|
|||||||
* Make a step in t-SNE algorithm and set the velocities for the nodes
|
* Make a step in t-SNE algorithm and set the velocities for the nodes
|
||||||
* to accumulate the values from solution.
|
* to accumulate the values from solution.
|
||||||
*/
|
*/
|
||||||
function force() {
|
function force () {
|
||||||
// Make a step at each iteration.
|
// Make a step at each iteration.
|
||||||
step();
|
step();
|
||||||
var solution = getSolution();
|
var solution = getSolution();
|
||||||
@@ -49,7 +49,7 @@ export default function() {
|
|||||||
* Calculates the random number from Gaussian distribution.
|
* Calculates the random number from Gaussian distribution.
|
||||||
* @return {number} random number.
|
* @return {number} random number.
|
||||||
*/
|
*/
|
||||||
function gaussRandom() {
|
function gaussRandom () {
|
||||||
let u = 2 * Math.random() - 1;
|
let u = 2 * Math.random() - 1;
|
||||||
let v = 2 * Math.random() - 1;
|
let v = 2 * Math.random() - 1;
|
||||||
let r = u * u + v * v;
|
let r = u * u + v * v;
|
||||||
@@ -63,11 +63,11 @@ export default function() {
|
|||||||
* Return the normalized number.
|
* Return the normalized number.
|
||||||
* @return {number} normalized random number from Gaussian distribution.
|
* @return {number} normalized random number from Gaussian distribution.
|
||||||
*/
|
*/
|
||||||
function randomN() {
|
function randomN () {
|
||||||
return gaussRandom() * 1e-4;
|
return gaussRandom() * 1e-4;
|
||||||
}
|
}
|
||||||
|
|
||||||
function sign(x) {
|
function sign (x) {
|
||||||
return x > 0 ? 1 : x < 0 ? -1 : 0;
|
return x > 0 ? 1 : x < 0 ? -1 : 0;
|
||||||
}
|
}
|
||||||
|
|
||||||
@@ -76,7 +76,7 @@ export default function() {
|
|||||||
* @param {number} n - length of array.
|
* @param {number} n - length of array.
|
||||||
* @return {Float64Array} - array of zeros with length n.
|
* @return {Float64Array} - array of zeros with length n.
|
||||||
*/
|
*/
|
||||||
function zeros(n) {
|
function zeros (n) {
|
||||||
if (typeof n === 'undefined' || isNaN(n)) {
|
if (typeof n === 'undefined' || isNaN(n)) {
|
||||||
return [];
|
return [];
|
||||||
}
|
}
|
||||||
@@ -90,7 +90,7 @@ export default function() {
|
|||||||
* @param {number} d - columns.
|
* @param {number} d - columns.
|
||||||
* @return {array} - 2d array
|
* @return {array} - 2d array
|
||||||
*/
|
*/
|
||||||
function random2d(n, d) {
|
function random2d (n, d) {
|
||||||
var x = [];
|
var x = [];
|
||||||
for (var i = 0; i < n; i++) {
|
for (var i = 0; i < n; i++) {
|
||||||
var y = [];
|
var y = [];
|
||||||
@@ -109,7 +109,7 @@ export default function() {
|
|||||||
* @param {number} tol - limit for entropy difference.
|
* @param {number} tol - limit for entropy difference.
|
||||||
* @return {2d array} - 2d matrix containing probabilities.
|
* @return {2d array} - 2d matrix containing probabilities.
|
||||||
*/
|
*/
|
||||||
function d2p(data, perplexity, tol) {
|
function d2p (data, perplexity, tol) {
|
||||||
N = Math.floor(data.length);
|
N = Math.floor(data.length);
|
||||||
var Htarget = Math.log(perplexity); // target entropy of distribution.
|
var Htarget = Math.log(perplexity); // target entropy of distribution.
|
||||||
var P1 = zeros(N * N); // temporary probability matrix.
|
var P1 = zeros(N * N); // temporary probability matrix.
|
||||||
@@ -161,7 +161,6 @@ export default function() {
|
|||||||
} else {
|
} else {
|
||||||
beta = (beta + betamax) / 2;
|
beta = (beta + betamax) / 2;
|
||||||
}
|
}
|
||||||
|
|
||||||
} else {
|
} else {
|
||||||
// Converse case. Make distrubtion less peaky.
|
// Converse case. Make distrubtion less peaky.
|
||||||
betamax = beta;
|
betamax = beta;
|
||||||
@@ -183,7 +182,6 @@ export default function() {
|
|||||||
for (j = 0; j < N; j++) {
|
for (j = 0; j < N; j++) {
|
||||||
P1[i * N + j] = prow[j];
|
P1[i * N + j] = prow[j];
|
||||||
}
|
}
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
// Symmetrize P and normalize it to sum to 1 over all ij
|
// Symmetrize P and normalize it to sum to 1 over all ij
|
||||||
@@ -200,7 +198,7 @@ export default function() {
|
|||||||
/**
|
/**
|
||||||
* Initialize a starting (random) solution.
|
* Initialize a starting (random) solution.
|
||||||
*/
|
*/
|
||||||
function initSolution() {
|
function initSolution () {
|
||||||
Y = random2d(N, dim);
|
Y = random2d(N, dim);
|
||||||
// Step gains to accelerate progress in unchanging directions.
|
// Step gains to accelerate progress in unchanging directions.
|
||||||
gains = random2d(N, dim, 1.0);
|
gains = random2d(N, dim, 1.0);
|
||||||
@@ -212,7 +210,7 @@ export default function() {
|
|||||||
/**
|
/**
|
||||||
* @return {2d array} the solution.
|
* @return {2d array} the solution.
|
||||||
*/
|
*/
|
||||||
function getSolution() {
|
function getSolution () {
|
||||||
return Y;
|
return Y;
|
||||||
}
|
}
|
||||||
|
|
||||||
@@ -220,7 +218,7 @@ export default function() {
|
|||||||
* Do a single step (iteration) for the layout.
|
* Do a single step (iteration) for the layout.
|
||||||
* @return {number} the current cost.
|
* @return {number} the current cost.
|
||||||
*/
|
*/
|
||||||
function step() {
|
function step () {
|
||||||
iteration += 1;
|
iteration += 1;
|
||||||
|
|
||||||
var cg = costGrad(Y); // Evaluate gradient.
|
var cg = costGrad(Y); // Evaluate gradient.
|
||||||
@@ -269,8 +267,7 @@ export default function() {
|
|||||||
* @param {2d array} Y - the current solution to evaluate.
|
* @param {2d array} Y - the current solution to evaluate.
|
||||||
* @return {object} that contains a cost and a gradient.
|
* @return {object} that contains a cost and a gradient.
|
||||||
*/
|
*/
|
||||||
function costGrad(Y) {
|
function costGrad (Y) {
|
||||||
|
|
||||||
var pmul = iteration < 100 ? 4 : 1;
|
var pmul = iteration < 100 ? 4 : 1;
|
||||||
|
|
||||||
// Compute current Q distribution, unnormalized first.
|
// Compute current Q distribution, unnormalized first.
|
||||||
@@ -326,7 +323,7 @@ export default function() {
|
|||||||
* the better layout.
|
* the better layout.
|
||||||
* @return {number} - stress of the layout.
|
* @return {number} - stress of the layout.
|
||||||
*/
|
*/
|
||||||
function getStress() {
|
function getStress () {
|
||||||
var totalDiffSq = 0,
|
var totalDiffSq = 0,
|
||||||
totalHighDistSq = 0;
|
totalHighDistSq = 0;
|
||||||
for (var i = 0, source, target, realDist, highDist; i < nodes.length; i++) {
|
for (var i = 0, source, target, realDist, highDist; i < nodes.length; i++) {
|
||||||
@@ -345,7 +342,7 @@ export default function() {
|
|||||||
|
|
||||||
// API for initializing the algorithm, setting parameters and querying
|
// API for initializing the algorithm, setting parameters and querying
|
||||||
// metrics.
|
// metrics.
|
||||||
force.initialize = function(_) {
|
force.initialize = function (_) {
|
||||||
nodes = _;
|
nodes = _;
|
||||||
N = nodes.length;
|
N = nodes.length;
|
||||||
// Initialize the probability matrix.
|
// Initialize the probability matrix.
|
||||||
@@ -353,23 +350,23 @@ export default function() {
|
|||||||
initSolution();
|
initSolution();
|
||||||
};
|
};
|
||||||
|
|
||||||
force.id = function(_) {
|
force.id = function (_) {
|
||||||
return arguments.length ? (id = _, force) : id;
|
return arguments.length ? (id = _, force) : id;
|
||||||
};
|
};
|
||||||
|
|
||||||
force.distance = function(_) {
|
force.distance = function (_) {
|
||||||
return arguments.length ? (distance = typeof _ === "function" ? _ : constant(+_), force) : distance;
|
return arguments.length ? (distance = typeof _ === 'function' ? _ : constant(+_), force) : distance;
|
||||||
};
|
};
|
||||||
|
|
||||||
force.stress = function() {
|
force.stress = function () {
|
||||||
return getStress();
|
return getStress();
|
||||||
};
|
};
|
||||||
|
|
||||||
force.learningRate = function(_) {
|
force.learningRate = function (_) {
|
||||||
return arguments.length ? (learningRate = +_, force) : learningRate;
|
return arguments.length ? (learningRate = +_, force) : learningRate;
|
||||||
};
|
};
|
||||||
|
|
||||||
force.perplexity = function(_) {
|
force.perplexity = function (_) {
|
||||||
return arguments.length ? (perplexity = +_, force) : perplexity;
|
return arguments.length ? (perplexity = +_, force) : perplexity;
|
||||||
};
|
};
|
||||||
|
|
||||||
|
|||||||
@@ -1,13 +1,13 @@
|
|||||||
/**
|
/**
|
||||||
* @return x value of a node
|
* @return x value of a node
|
||||||
*/
|
*/
|
||||||
export function x(d) {
|
export function x (d) {
|
||||||
return d.x;
|
return d.x;
|
||||||
}
|
}
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* @return y value of a node
|
* @return y value of a node
|
||||||
*/
|
*/
|
||||||
export function y(d) {
|
export function y (d) {
|
||||||
return d.y;
|
return d.y;
|
||||||
}
|
}
|
||||||
|
|||||||
Reference in New Issue
Block a user