fix(rng)!: use better seedable RNG (#352)

* fix(rng)!: use better seedable RNG

BREAKING CHANGE: The layout for the same graph and seed is different
when compared to the previous version.

This replaces the Math.sin() based ones and Math.random() with Alea
based RNG from Vis Util.

* test(physics): add simple pinning tests

This simply runs some basic physics configurations on a few sets of data
and tests that the positions of the nodes after stabilization didn't
change from the last time.

* test(snapshots): remove only

I had to change Math.pow to **. No idea why but without this change it
didn't want to output the same values. I just hope this is not going to
break in CI or other people's machines.

examples/network/basic_usage/standalone.html

@@ -38,7 +38,7 @@
 
  <script
  type="text/javascript"
- src="../../../standalone/umd/vis-network.min.js"
+ src="../../../standalone/umd/vis-network.js"
  ></script>
  </head>
 

examples/network/data/importingFromGephi.html

@@ -7,10 +7,12 @@
 
  <meta name="example-screenshot-selector" content="body" />
 
+ <script
+ type="text/javascript"
+ src="../../../standalone/umd/vis-network.min.js"
+ ></script>
  <script type="text/javascript" src="../exampleUtil.js"></script>
 
- <script type="text/javascript" src="../../../standalone/umd/vis-network.min.js"></script>
-
  <style type="text/css">
  #mynetwork {
  width: 800px;

examples/network/exampleUtil.js

@@ -1,5 +1,9 @@
 /**
  * Created by Alex on 5/20/2015.
+ *
+ * @remarks
+ * This depends on Alea from Vis Util and therefore has to be loaded AFTER Vis
+ * Util or standalone Vis Network has already been loaded.
  */
 
 function loadJSON(path, success, error) {
@@ -69,11 +73,7 @@ function getScaleFreeNetwork(nodeCount) {
  return {nodes:nodes, edges:edges};
 }
 
-var randomSeed = 764; // Math.round(Math.random()*1000);
-function seededRandom() {
- var x = Math.sin(randomSeed++) * 10000;
- return x - Math.floor(x);
-}
+var seededRandom = vis.util.Alea('SEED')
 
 function getScaleFreeNetworkSeeded(nodeCount, seed) {
  if (seed) {

examples/network/layout/hierarchicalLayout.html

@@ -15,8 +15,11 @@
  }
  </style>
 
+ <script
+ type="text/javascript"
+ src="../../../standalone/umd/vis-network.min.js"
+ ></script>
  <script type="text/javascript" src="../exampleUtil.js"></script>
- <script type="text/javascript" src="../../../standalone/umd/vis-network.min.js"></script>
 
  <script type="text/javascript">
  var nodes = null;

examples/network/other/animationShowcase.html

@@ -34,8 +34,11 @@
  }
  </style>
 
+ <script
+ type="text/javascript"
+ src="../../../standalone/umd/vis-network.min.js"
+ ></script>
  <script type="text/javascript" src="../exampleUtil.js"></script>
- <script type="text/javascript" src="../../../standalone/umd/vis-network.min.js"></script>
 
  <script type="text/javascript">
  var nodes = null;

examples/network/other/configuration.html

@@ -26,9 +26,11 @@
  }
  </style>
 
-
+ <script
+ type="text/javascript"
+ src="../../../standalone/umd/vis-network.min.js"
+ ></script>
  <script type="text/javascript" src="../exampleUtil.js"></script>
- <script type="text/javascript" src="../../../standalone/umd/vis-network.min.js"></script>
 
  <script type="text/javascript">
  var nodes = null;

examples/network/other/manipulation.html

@@ -53,8 +53,12 @@
  text-align: center;
  }
  </style>
+
+ <script
+ type="text/javascript"
+ src="../../../standalone/umd/vis-network.min.js"
+ ></script>
  <script type="text/javascript" src="../exampleUtil.js"></script>
- <script type="text/javascript" src="../../../standalone/umd/vis-network.min.js"></script>
 
  <script type="text/javascript">
  var nodes = null;

examples/network/other/manipulationEditEdgeNoDrag.html

@@ -68,8 +68,12 @@
  text-align: center;
  }
  </style>
+
+ <script
+ type="text/javascript"
+ src="../../../standalone/umd/vis-network.min.js"
+ ></script>
  <script type="text/javascript" src="../exampleUtil.js"></script>
- <script type="text/javascript" src="../../../standalone/umd/vis-network.min.js"></script>
 
  <script type="text/javascript">
  var nodes = null;

examples/network/other/navigation.html

@@ -27,8 +27,11 @@
  }
  </style>
 
+ <script
+ type="text/javascript"
+ src="../../../standalone/umd/vis-network.min.js"
+ ></script>
  <script type="text/javascript" src="../exampleUtil.js"></script>
- <script type="text/javascript" src="../../../standalone/umd/vis-network.min.js"></script>
 
  <script type="text/javascript">
  var nodes = null;

examples/network/other/performance.html

@@ -22,8 +22,11 @@
  }
  </style>
 
+ <script
+ type="text/javascript"
+ src="../../../standalone/umd/vis-network.min.js"
+ ></script>
  <script type="text/javascript" src="../exampleUtil.js"></script>
- <script type="text/javascript" src="../../../standalone/umd/vis-network.min.js"></script>
 
  <script type="text/javascript">
  var nodes = null;

examples/network/other/saveAndLoad.html

@@ -32,8 +32,11 @@
  }
  </style>
 
+ <script
+ type="text/javascript"
+ src="../../../standalone/umd/vis-network.min.js"
+ ></script>
  <script type="text/javascript" src="../exampleUtil.js"></script>
- <script type="text/javascript" src="../../../standalone/umd/vis-network.min.js"></script>
  </head>
 
  <body>

examples/network/physics/physicsConfiguration.html

@@ -22,8 +22,11 @@
  </style>
 
 
+ <script
+ type="text/javascript"
+ src="../../../standalone/umd/vis-network.min.js"
+ ></script>
  <script type="text/javascript" src="../exampleUtil.js"></script>
- <script type="text/javascript" src="../../../standalone/umd/vis-network.min.js"></script>
 
  <script type="text/javascript">
  var nodes = null;

lib/network/modules/KamadaKawai.js

@@ -119,7 +119,7 @@ class KamadaKawai {
  */
  _getEnergy(m) {
  let [dE_dx,dE_dy] = this.E_sums[m];
- let delta_m = Math.sqrt(Math.pow(dE_dx, 2) + Math.pow(dE_dy, 2));
+ let delta_m = Math.sqrt((dE_dx ** 2) + (dE_dy ** 2));
  return [delta_m, dE_dx, dE_dy];
  }
 
@@ -150,10 +150,10 @@ class KamadaKawai {
  let y_i = nodes[i].y;
  let kmat = km[i];
  let lmat = lm[i];
- let denominator = 1.0 / Math.pow(Math.pow(x_m - x_i, 2) + Math.pow(y_m - y_i, 2), 1.5);
- d2E_dx2 += kmat * (1 - lmat * Math.pow(y_m - y_i, 2) * denominator);
+ let denominator = 1.0 / ((((x_m - x_i) ** 2) + ((y_m - y_i) ** 2)) ** 1.5);
+ d2E_dx2 += kmat * (1 - lmat * ((y_m - y_i) ** 2) * denominator);
  d2E_dxdy += kmat * (lmat * (x_m - x_i) * (y_m - y_i) * denominator);
- d2E_dy2 += kmat * (1 - lmat * Math.pow(x_m - x_i, 2) * denominator);
+ d2E_dy2 += kmat * (1 - lmat * ((x_m - x_i) ** 2) * denominator);
  }
  }
  // make the variable names easier to make the solving of the linear system easier to read
@@ -204,7 +204,7 @@ class KamadaKawai {
  for (let i = 0; i < nodesArray.length; i++) {
  this.K_matrix[nodesArray[i]] = {};
  for (let j = 0; j < nodesArray.length; j++) {
- this.K_matrix[nodesArray[i]][nodesArray[j]] = edgeStrength * Math.pow(D_matrix[nodesArray[i]][nodesArray[j]], -2);
+ this.K_matrix[nodesArray[i]][nodesArray[j]] = edgeStrength * (D_matrix[nodesArray[i]][nodesArray[j]] ** -2);
  }
  }
  }
@@ -232,7 +232,7 @@ class KamadaKawai {
  if (i !== m) {
  let x_i = nodes[i].x;
  let y_i = nodes[i].y;
- let denominator = 1.0 / Math.sqrt(Math.pow(x_m - x_i, 2) + Math.pow(y_m - y_i, 2));
+ let denominator = 1.0 / Math.sqrt(((x_m - x_i) ** 2) + ((y_m - y_i) ** 2));
  this.E_matrix[m][iIdx] = [
  this.K_matrix[m][i] * ((x_m - x_i) - this.L_matrix[m][i] * (x_m - x_i) * denominator),
  this.K_matrix[m][i] * ((y_m - y_i) - this.L_matrix[m][i] * (y_m - y_i) * denominator)
@@ -274,7 +274,7 @@ class KamadaKawai {
  //Calc new energy:
  let x_i = nodes[i].x;
  let y_i = nodes[i].y;
- let denominator = 1.0 / Math.sqrt(Math.pow(x_m - x_i, 2) + Math.pow(y_m - y_i, 2));
+ let denominator = 1.0 / Math.sqrt(((x_m - x_i) ** 2) + ((y_m - y_i) ** 2));
  let dx = kcolm[i] * ((x_m - x_i) - lcolm[i] * (x_m - x_i) * denominator);
  let dy = kcolm[i] * ((y_m - y_i) - lcolm[i] * (y_m - y_i) * denominator);
  colm[iIdx] = [dx, dy];
@@ -292,4 +292,4 @@ class KamadaKawai {
  }
 }
 
-export default KamadaKawai;
+export default KamadaKawai;

lib/network/modules/LayoutEngine.js

@@ -38,6 +38,7 @@ import {
  fillLevelsByDirectionLeaves,
  fillLevelsByDirectionRoots
 } from "./layout-engine";
+import { Alea } from "vis-util";
 
 
 /**
@@ -332,8 +333,10 @@ class LayoutEngine {
  constructor(body) {
  this.body = body;
 
- this.initialRandomSeed = Math.round(Math.random() * 1000000);
- this.randomSeed = this.initialRandomSeed;
+ // Make sure there always is some RNG because the setOptions method won't
+ // set it unless there's a seed for it.
+ this._resetRNG(Math.random() + ":" + Date.now());
+
  this.setPhysics = false;
  this.options = {};
  this.optionsBackup = {physics:{}};
@@ -395,7 +398,10 @@ class LayoutEngine {
  let prevHierarchicalState = hierarchical.enabled;
  util.selectiveDeepExtend(["randomSeed", "improvedLayout", "clusterThreshold"],this.options, options);
  util.mergeOptions(this.options, options, 'hierarchical');
- if (options.randomSeed !== undefined) {this.initialRandomSeed = options.randomSeed;}
+
+ if (options.randomSeed !== undefined) {
+ this._resetRNG(options.randomSeed);
+ }
 
  if (hierarchical.enabled === true) {
  if (prevHierarchicalState === true) {
@@ -433,6 +439,16 @@ class LayoutEngine {
  return allOptions;
  }
 
+ /**
+ * Reset the random number generator with given seed.
+ *
+ * @param {any} seed - The seed that will be forwarded the the RNG.
+ */
+ _resetRNG(seed) {
+ this.initialRandomSeed = seed;
+ this._rng = Alea(this.initialRandomSeed);
+ }
+
  /**
  *
  * @param {Object} allOptions
@@ -514,26 +530,17 @@ class LayoutEngine {
  return allOptions;
  }
 
- /**
- *
- * @returns {number}
- */
- seededRandom() {
- let x = Math.sin(this.randomSeed++) * 10000;
- return x - Math.floor(x);
- }
-
  /**
  *
  * @param {Array.<Node>} nodesArray
  */
  positionInitially(nodesArray) {
  if (this.options.hierarchical.enabled !== true) {
- this.randomSeed = this.initialRandomSeed;
+ this._resetRNG(this.initialRandomSeed);
  let radius = nodesArray.length + 50;
  for (let i = 0; i < nodesArray.length; i++) {
  let node = nodesArray[i];
- let angle = 2 * Math.PI * this.seededRandom();
+ let angle = 2 * Math.PI * this._rng();
  if (node.x === undefined) {
  node.x = radius * Math.cos(angle);
  }
@@ -645,8 +652,8 @@ class LayoutEngine {
  // Only perturb the nodes that aren't fixed
  let node = this.body.nodes[indices[i]];
  if (node.predefinedPosition === false) {
- node.x += (0.5 - this.seededRandom())*offset;
- node.y += (0.5 - this.seededRandom())*offset;
+ node.x += (0.5 - this._rng())*offset;
+ node.y += (0.5 - this._rng())*offset;
  }
  }
 

lib/network/modules/components/physics/BarnesHutSolver.js

@@ -1,3 +1,5 @@
+import { Alea } from "vis-util";
+
 /**
  * Barnes Hut Solver
  */
@@ -12,7 +14,7 @@ class BarnesHutSolver {
  this.physicsBody = physicsBody;
  this.barnesHutTree;
  this.setOptions(options);
- this.randomSeed = 5;
+ this._rng = Alea("BARNES HUT SOLVER");
 
  // debug: show grid
  // this.body.emitter.on("afterDrawing", (ctx) => {this._debug(ctx,'#ff0000')})
@@ -30,16 +32,6 @@ class BarnesHutSolver {
  this.overlapAvoidanceFactor = 1 - Math.max(0, Math.min(1, this.options.avoidOverlap));
  }
 
- /**
- *
- * @returns {number} random integer
- */
- seededRandom() {
- var x = Math.sin(this.randomSeed++) * 10000;
- return x - Math.floor(x);
- }
-
-
  /**
  * This function calculates the forces the nodes apply on each other based on a gravitational model.
  * The Barnes Hut method is used to speed up this N-body simulation.
@@ -323,8 +315,8 @@ class BarnesHutSolver {
  // if there are two nodes exactly overlapping (on init, on opening of cluster etc.)
  // we move one node a little bit and we do not put it in the tree.
  if (children.children.data.x === node.x && children.children.data.y === node.y) {
- node.x += this.seededRandom();
- node.y += this.seededRandom();
+ node.x += this._rng();
+ node.y += this._rng();
  }
  else {
  this._splitBranch(children);

lib/network/modules/components/physics/FA2BasedRepulsionSolver.js

@@ -1,4 +1,5 @@
 import BarnesHutSolver from "./BarnesHutSolver"
+import { Alea } from "vis-util";
 
 /**
  * @extends BarnesHutSolver
@@ -11,6 +12,8 @@ class ForceAtlas2BasedRepulsionSolver extends BarnesHutSolver {
  */
  constructor(body, physicsBody, options) {
  super(body, physicsBody, options);
+
+ this._rng = Alea("FORCE ATLAS 2 BASED REPULSION SOLVER");
  }
 
  /**
@@ -25,7 +28,7 @@ class ForceAtlas2BasedRepulsionSolver extends BarnesHutSolver {
  */
  _calculateForces(distance, dx, dy, node, parentBranch) {
  if (distance === 0) {
- distance = 0.1 * Math.random();
+ distance = 0.1 * this._rng();
  dx = distance;
  }