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 (j = 0; j < i; j++) {
-      if (i !== j) {
-        links.push({
-          source: nodes[i],
-          target: nodes[j],
-        });
-      }
+  for (i = nodes.length-1; i >= 1; i--) {
+    for (j = i-1; j >= 0; j--) {
+      links.push({
+        source: nodes[i],
+        target: nodes[j],
+      });
     }
   }
 
-  // Add the links to the simulation.
-  simulation.force(forceName, d3.forceLink().links(links));
-
-  simulation
-    .alphaDecay(1 - Math.pow(0.001, 1 / ITERATIONS))
+  /* Add force
+   * Please add the distance function before feeding the force
+   *   it to the simulation or adding links.
+   *
+   * 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)
-    // The distance function that will be used to calculate distances
-    //  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();
+   .alpha(1)
+   .restart();
 }