Merge pull request #40 from nvbeusekom/simul_integration

Fixing bugs in NN_2OPT

.gitignore

@@ -5,3 +5,4 @@ coverage
 *~
 #*
 *.swp
+/nbproject/private/

examples/matrix.js

@@ -101,6 +101,15 @@ function matrix(json) {
 
 	return nodes.map(function(n) { return n.spectral; });
     }
+
+    function computeNN2OPT() {
+	var order = leafOrder(adjacency);
+
+	order.forEach(function(lo, i) {
+	    nodes[i].leafOrder = lo;
+	});
+	return nodes.map(function(n) { return n.leafOrder; });
+    }
 
   // Precompute the orders.
     var orders = {
@@ -114,7 +123,8 @@ function matrix(json) {
 	leafOrderDist: computeLeaforderDist,
 	barycenter: computeBarycenter,
 	rcm: computeRCM,
-	spectral: computeSpectral
+	spectral: computeSpectral,
+        nn2opt: computeNN2OPT
     };
 
   // The default sort order.
@@ -240,6 +250,11 @@ function matrix(json) {
 	    order("leafOrderDist");
 	    //d3.select("#order").property("selectedIndex", 4);
 	}
+        else if (currentOrder == 'nn2opt') {
+	    orders.nn2opt = computeNN2OPT;
+	    order("nn2opt");
+	    //d3.select("#order").property("selectedIndex", 4);
+	}
 
 	// leafOrder.forEach(function(lo, i) {
 	// 	    nodes[lo].leafOrder = i;

examples/miserables/index.html

@@ -47,6 +47,7 @@ <h1><i>Les Misérables</i> Co-occurrence</h1>
   <option value="barycenter">by Crossing Reduction</option>
   <option value="rcm">by Bandwidth Reduction (RCM)</option>
   <option value="spectral">Spectral</option>
+  <option value="nn2opt">NN-2OPT</option>
 </select>
 
 <p>Distance: <select id="distance">

examples/timeseries/index.html

@@ -48,7 +48,7 @@
         <div style="margin-top:4px;margin-bottom: 4px">
         <button type="button" onclick="random_permute(tables)">Random Order</button>
         <button type="button" onclick="initial_order_permute(tables)">Initial Order</button>
-        <button type="button" onclick="max_mi_gx(tables)">NN-2OPT on Graph Gx</button>
+        <button type="button" onclick="nn_2opt_gx(tables)">NN-2OPT on Graph Gx</button>
 
         </div>
         <div style="margin-top:4px;margin-bottom: 4px">

examples/timeseries/order_functions.js

@@ -51,7 +51,7 @@ function random_permute(t) {
     computeQualities(t);
 }
 
-function max_mi_gx(t) {
+function nn_2opt_gx(t) {
     let timestep = getTimestep();
     let start = new Date().getTime();
 
@@ -60,7 +60,7 @@ function max_mi_gx(t) {
     let dist_rows = dist(matrices[timestep]);
 //      let transpose = reorder.transpose(matrices[timestep]),
 //      dist_cols = reorder.dist()(transpose);
-    let order = reorder.optimal_leaf_order(),
+    let order = reorder.nn_2opt(),
     row_perm = order.distanceMatrix(dist_rows)(matrices[timestep]);
 //      let col_perm = order.distanceMatrix(dist_cols)(transpose);
     let end = new Date().getTime();

nbproject/project.properties

@@ -0,0 +1,3 @@
+files.encoding=UTF-8
+site.root.folder=
+source.folder=

nbproject/project.xml

@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://www.netbeans.org/ns/project/1">
+    <type>org.netbeans.modules.web.clientproject</type>
+    <configuration>
+        <data xmlns="http://www.netbeans.org/ns/clientside-project/1">
+            <name>reorder.js</name>
+        </data>
+    </configuration>
+</project>

src/nn_2opt.js

@@ -28,13 +28,13 @@ export function nn_2opt() {
     if (distanceMatrix === null) {
       distanceMatrix = dist().distance(distance)(matrix);
     }
-    let lowest_dist = -1;
-    let best_order = [];
-    // Try each row as the initial permutation
+    let lowest_dist_all = Number.MAX_VALUE;
+    let best_order_all = [];
+
+    // Try each row as the initial permutation for NN-2OPT
     for (let s = 0; s < distanceMatrix.length; s++) {
-      let initial = s;
       let order = [];
-      order.push(initial);
+      order.push(s);
       // NN
       while (order.length < distanceMatrix.length) {
         let nearest = -1;
@@ -52,44 +52,49 @@ export function nn_2opt() {
         }
         order.push(nearest);
       }
-      let oldm = 0;
-      let newm = getTotal(order);
+      let newdist = getTotal(order);
+      let olddist = newdist - (epsilon + 1);
       // 2-OPT
-      while (newm - oldm > epsilon) {
+      let lowest_dist_2opt = Number.MAX_VALUE;
+      let best_order_2opt = [];
+      while (newdist - olddist > epsilon) {
         for (let i = 0; i < order.length; i++) {
           for (let j = i + 2; j < order.length - 1; j++) {
             // edge 1: (i,i+1) edge2: (j,j+1)
-            let olddist = distanceMatrix[i][i + 1] + distanceMatrix[j][j + 1];
-            let newdist = distanceMatrix[i][j] + distanceMatrix[i + 1][j + 1];
-            if (newdist < olddist) {
+            let currentd = distanceMatrix[order[i]][order[i + 1]] + distanceMatrix[order[j]][order[j + 1]];
+            let candidated = distanceMatrix[order[i]][order[j]] + distanceMatrix[order[i + 1]][order[j + 1]];
+            if (candidated < currentd) {               
               let check = [];
               for (let k = 0; k < order.length; k++) {
                 check[k] = order[k];
               }
               // Reverse i+1 to j
-              for (let k = 0; k < j - (i + 1); k++) {
-                // TODO: check indices
+              for (let k = 0; k <= j - (i + 1); k++) {
                 check[i + 1 + k] = order[j - k];
               }
               order = check;
             }
           }
         }
-        oldm = newm;
-        newm = getTotal(order);
-        if (newm > lowest_dist) {
-          lowest_dist = newm;
-          best_order = order;
+        olddist = newdist;
+        newdist = getTotal(order);
+        if (newdist < lowest_dist_2opt) {
+          lowest_dist_2opt = newdist;
+          best_order_2opt = order;
         }
       }
+      if (lowest_dist_2opt < lowest_dist_all) {
+          lowest_dist_all = lowest_dist_2opt;
+          best_order_all = best_order_2opt;
+        }
     }
-    return best_order;
+    return best_order_all;
   }
 
   function getTotal(order) {
     let sum = 0;
     for (let i = 0; i < order.length - 1; i++) {
-      sum += distanceMatrix[i][i + 1];
+      sum += distanceMatrix[order[i]][order[i + 1]];
     }
     return sum;
   }
@@ -103,5 +108,7 @@ export function nn_2opt() {
     return nn_2opt;
   };
 
+  nn_2opt.distanceMatrix = nn_2opt.distance_matrix; // compatability
+
   return nn_2opt;
 }