Separate a Link Force with optimization

examples/js/src/neighbourSampling-papaparsing.js

@@ -41,7 +41,8 @@ var nodes, // as in Data points
   fileName = "",
   selectedData,
   clickedIndex = -1,
-  paused = false;
+  paused = false,
+  alreadyRanIterations;
 
 // Default parameters
 var MULTIPLIER = 50,
@@ -119,10 +120,16 @@ function processData(data, error) {
   props.pop(); //Hide Iris index / last column from distance function
 
   //Put the nodes in random starting positions
+  //TODO Change this back
+  nodes.forEach(function (d) {
+    d.x = 0;
+    d.y = 0;
+  });
+  /*
   nodes.forEach(function (d) {
     d.x = (Math.random()-0.5) * 100000;
     d.y = (Math.random()-0.5) * 100000;
-  });
+  });*/
 
   addNodesToDOM(nodes);
 
@@ -180,6 +187,8 @@ function addNodesToDOM(data) {
 }
 
 function ticked() {
+  console.log("ticked");
+  alreadyRanIterations++;
   // If rendering is selected, then draw at every iteration.
   if (rendering === true) {
     node // Each sub-circle in the SVG, update cx and cy
@@ -194,9 +203,14 @@ function ticked() {
   if (springForce) {
     intercom.emit("passedData", simulation.force(forceName).distributionData());
   }
+  if(alreadyRanIterations == ITERATIONS) {
+    simulation.stop();
+    ended();
+  }
 }
 
 function ended() {
+  console.log("ended");
   if (rendering !== true) { // Never drawn anything before? Now it's time.
     node
       .attr("cx", function (d) {

examples/js/src/neighbourSampling-papaparsing/linkForce.js

@@ -1,40 +1,45 @@
-
 /**
  * Initialize the link force algorithm and start simulation.
  */
 function startLinkSimulation() {
   console.log("startLinkSimulation")
   springForce = false;
+  alreadyRanIterations = 0;
   simulation.stop();
   p1 = performance.now();
   let links = [];
 
   // Initialize link array.
   nodes = simulation.nodes();
-  for (i = 0; i < nodes.length; i++) {
+  for (i = nodes.length-1; i >= 1; i--) {
-    for (j = 0; j < i; j++) {
+    for (j = i-1; j >= 0; j--) {
-      if (i !== j) {
+      links.push({
-        links.push({
+        source: nodes[i],
-          source: nodes[i],
+        target: nodes[j],
-          target: nodes[j],
+      });
-        });
-      }
     }
   }
 
-  // Add the links to the simulation.
+  /* Add force
-  simulation.force(forceName, d3.forceLink().links(links));
+   * Please add the distance function before feeding the force
-
+   *   it to the simulation or adding links.
-  simulation
+   *
-    .alphaDecay(1 - Math.pow(0.001, 1 / ITERATIONS))
+   * On setting the distance fn and being initialized by the simulation, the
+   *   force will pre-calculate high-dimensional distances of every link and
+   *   store that as cache.
+   * Adding distance fn before links means that the first pre-calculation will
+   *   calculate noting as there was no link.
+   * The full pre-calculation will then occur once when the force is being
+   *   initialized by the simulation.
+   */
+  simulation.force(forceName,
+    d3.forceLinkOptimized()
+      .distance(function (n) {
+         return distanceFunction(n.source, n.target, props, norm);
+       })
+    .links(links)
+  ).alphaDecay(0)
     //.velocityDecay(0.8)
-    .force(forceName)
+   .alpha(1)
-    // The distance function that will be used to calculate distances
+   .restart();
-    //  between nodes.
-    .distance(function (n) {
-      return distanceFunction(n.source, n.target, props, norm);
-    })
-    // Set the parameter for the algorithm (optional).
-  // Restart the simulation.
-  simulation.alpha(1).restart();
 }

index.js

@@ -1,28 +1,20 @@
-/*export {
+/*
-  default as forceNeighbourSampling
+export {default as forceNeighbourSampling}
-}
   from "./src/neighbourSampling";
-export {
+export {default as forceNeighbourSamplingPre}
-  default as forceNeighbourSamplingPre
+  from "./src/neighbourSamplingPre";
-}
+*/
-  from "./src/neighbourSamplingPre";*/
+export {default as forceNeighbourSamplingDistance}
-export {
-  default as forceNeighbourSamplingDistance
-}
   from "./src/neighbourSamplingDistance";
-export {
+
-  default as forceBarnesHut
+export { default as forceBarnesHut}
-}
   from "./src/barnesHut";
-export {
+
-  default as tSNE
+export { default as tSNE}
-}
   from "./src/t-sne";
-export {
+
-  default as forceLink
+export { default as forceLinkOptimized}
-}
   from "./src/link";
-export {
+
-  default as hybridSimulation
+export { default as hybridSimulation}
-}
   from "./src/hybridSimulation";

src/link.js

@@ -1,100 +1,53 @@
 import constant from "./constant";
 import jiggle from "./jiggle";
-import {map} from "d3-collection";
-import {getStress} from "./stress";
 
 /**
- * Extended link force algorithm to include the stress metric for
+ * Modified link force algorithm
- * comparisons between the different algorithms.
+ * - ignore alpha
- * Everything else is the same as in D3 force module.
+ * - removed location prediction, and bias
+ * - modified strength calculation
+ * - removed other unused functions
+ * Making it more suitable for the spring model.
  */
 
-function index(d, i) {
-  return i;
-}
-
-function find(nodeById, nodeId) {
-  var node = nodeById.get(nodeId);
-  if (!node) throw new Error("missing: " + nodeId);
-  return node;
-}
-
 export default function(links) {
-  var id = index,
+  var dataSizeFactor,
-      strength = defaultStrength,
-      strengths,
       distance = constant(30),
-      distances,
+      distances = [],
       nodes,
-      count,
-      bias,
       iterations = 1;
 
   if (links == null) links = [];
 
-  function defaultStrength(link) {
+  function force() {
-    return 1 / Math.min(count[link.source.index], count[link.target.index]);
-  }
-
-  function force(alpha) {
     for (var k = 0, n = links.length; k < iterations; ++k) { // Each iteration in a tick
-      for (var i = 0, link, source, target, x, y, l, b; i < n; ++i) { //For each link
+      for (var i = 0, link, source, target, x, y, l, b; i < n; ++i) { // For each link
         link = links[i];
+        // jiggle so it wont divide / multiply by zero after this
         source = link.source;
         target = link.target;
-        x = target.x + target.vx - source.x - source.vx || jiggle();
+        x = target.x - source.x || jiggle();
-        y = target.y + target.vy - source.y - source.vy || jiggle();
+        y = target.y - source.y || jiggle();
         l = Math.sqrt(x * x + y * y);
-        l = (l - distances[i]) / l * alpha * strengths[i];
+        l = (l - distances[i]) / l  * dataSizeFactor;
         x *= l, y *= l;
-        target.vx -= x * (b = bias[i]);
+        target.vx -= x;
-        target.vy -= y * b;
+        target.vy -= y;
-        source.vx += x * (b = 1 - b);
+        source.vx += x;
-        source.vy += y * b;
+        source.vy += y;
       }
     }
   }
 
   function initialize() {
     if (!nodes) return;
-
+    console.log("CUSTOM LINK FORCE");
-    var i,
+    dataSizeFactor = 0.5/(nodes.length-1);
-        n = nodes.length,
+    initializeDistance();
-        m = links.length,
-        nodeById = map(nodes, id),
-        link;
-
-    for (i = 0, count = new Array(n); i < n; ++i) {
-      count[i] = 0;
-    }
-
-    for (i = 0; i < m; ++i) {
-      link = links[i];
-      link.index = i;
-      //if (typeof link.source !== "object") link.source = find(nodeById, link.source);
-      //if (typeof link.target !== "object") link.target = find(nodeById, link.target);
-      ++count[link.source.index];
-      ++count[link.target.index];
-    }
-
-    for (i = 0, bias = new Array(m); i < m; ++i) {
-      link = links[i];
-      bias[i] = count[link.source.index] / (count[link.source.index] + count[link.target.index]);
-    }
-
-    strengths = new Array(m), initializeStrength();
-    distances = new Array(m), initializeDistance();
-  }
-
-  function initializeStrength() {
-    if (!nodes) return;
-
-    for (var i = 0, n = links.length; i < n; ++i) {
-      strengths[i] = +strength(links[i], i, links);
-    }
   }
 
   function initializeDistance() {
+    console.log("INIT DISTANCE", links.length);
     if (!nodes) return;
 
     for (var i = 0, n = links.length; i < n; ++i) {
@@ -119,17 +72,9 @@ export default function(links) {
     return arguments.length ? (iterations = +_, force) : iterations;
   };
 
-  force.strength = function(_) {
-    return arguments.length ? (strength = typeof _ === "function" ? _ : constant(+_), initializeStrength(), force) : strength;
-  };
-
   force.distance = function(_) {
     return arguments.length ? (distance = typeof _ === "function" ? _ : constant(+_), initializeDistance(), force) : distance;
   };
 
-  force.stress = function() {
-    return getStress(nodes, function(s,t){return distance({source: s, target: t});});
-  }
-
   return force;
 }