From a44280759ecb78d4e3395a500355d9d90e55bf12 Mon Sep 17 00:00:00 2001
From: Beusekom <n.a.c.v.beusekom@tue.nl>
Date: Mon, 29 Aug 2022 14:06:13 +0200
Subject: [PATCH 1/4] Changes to generate poster images

---
 examples/matrix.js                     | 17 ++++++++++++++++-
 examples/miserables/index.html         |  1 +
 examples/timeseries/index.html         |  2 +-
 examples/timeseries/order_functions.js |  4 ++--
 nbproject/private/private.properties   |  1 +
 nbproject/private/private.xml          | 15 +++++++++++++++
 src/nn_2opt.js                         |  5 ++++-
 7 files changed, 40 insertions(+), 5 deletions(-)
 create mode 100644 nbproject/private/private.properties
 create mode 100644 nbproject/private/private.xml

diff --git a/examples/matrix.js b/examples/matrix.js
index 00970bd..fcb12ba 100644
--- a/examples/matrix.js
+++ b/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;
diff --git a/examples/miserables/index.html b/examples/miserables/index.html
index 5d5f86a..14664a6 100644
--- a/examples/miserables/index.html
+++ b/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">
diff --git a/examples/timeseries/index.html b/examples/timeseries/index.html
index 9eadf92..b404c6a 100644
--- a/examples/timeseries/index.html
+++ b/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">
diff --git a/examples/timeseries/order_functions.js b/examples/timeseries/order_functions.js
index 9558845..6da8d74 100644
--- a/examples/timeseries/order_functions.js
+++ b/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();
diff --git a/nbproject/private/private.properties b/nbproject/private/private.properties
new file mode 100644
index 0000000..3b1a22e
--- /dev/null
+++ b/nbproject/private/private.properties
@@ -0,0 +1 @@
+browser=Chrome.INTEGRATED
diff --git a/nbproject/private/private.xml b/nbproject/private/private.xml
new file mode 100644
index 0000000..c47be72
--- /dev/null
+++ b/nbproject/private/private.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project-private xmlns="http://www.netbeans.org/ns/project-private/1">
+    <editor-bookmarks xmlns="http://www.netbeans.org/ns/editor-bookmarks/2" lastBookmarkId="0"/>
+    <open-files xmlns="http://www.netbeans.org/ns/projectui-open-files/2">
+        <group>
+            <file>file:/C:/Users/20184261/Documents/reorder.js/examples/timeseries/index.html</file>
+            <file>file:/C:/Users/20184261/Documents/reorder.js/src/nn_2opt.js</file>
+            <file>file:/C:/Users/20184261/Documents/reorder.js/examples/miserables/index.html</file>
+            <file>file:/C:/Users/20184261/Documents/reorder.js/test/nn_2opt-test.js</file>
+            <file>file:/C:/Users/20184261/Documents/reorder.js/examples/timeseries/order_functions.js</file>
+            <file>file:/C:/Users/20184261/Documents/reorder.js/examples/matrix.js</file>
+            <file>file:/C:/Users/20184261/Documents/reorder.js/src/optimal_leaf_order.js</file>
+        </group>
+    </open-files>
+</project-private>
diff --git a/src/nn_2opt.js b/src/nn_2opt.js
index 9f29575..41a24d6 100644
--- a/src/nn_2opt.js
+++ b/src/nn_2opt.js
@@ -28,7 +28,7 @@ export function nn_2opt() {
     if (distanceMatrix === null) {
       distanceMatrix = dist().distance(distance)(matrix);
     }
-    let lowest_dist = -1;
+    let lowest_dist = Number.MIN_VALUE;
     let best_order = [];
     // Try each row as the initial permutation
     for (let s = 0; s < distanceMatrix.length; s++) {
@@ -83,6 +83,7 @@ export function nn_2opt() {
         }
       }
     }
+    console.log(best_order);
     return best_order;
   }
 
@@ -103,5 +104,7 @@ export function nn_2opt() {
     return nn_2opt;
   };
 
+  nn_2opt.distanceMatrix = nn_2opt.distance_matrix; // compatability
+
   return nn_2opt;
 }

From 9f8fe3fac674e6175a1f5d1131d7dae9959bd0b7 Mon Sep 17 00:00:00 2001
From: Beusekom <n.a.c.v.beusekom@tue.nl>
Date: Wed, 31 Aug 2022 11:50:56 +0200
Subject: [PATCH 2/4] Fix NN-2OPT bugs

---
 .gitignore                   |  1 +
 nbproject/project.properties |  3 +++
 nbproject/project.xml        |  9 +++++++
 src/nn_2opt.js               | 46 ++++++++++++++++++++----------------
 4 files changed, 38 insertions(+), 21 deletions(-)
 create mode 100644 nbproject/project.properties
 create mode 100644 nbproject/project.xml

diff --git a/.gitignore b/.gitignore
index 8601a29..aa06c47 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,3 +5,4 @@ coverage
 *~
 #*
 *.swp
+/nbproject/private/
diff --git a/nbproject/project.properties b/nbproject/project.properties
new file mode 100644
index 0000000..da97eba
--- /dev/null
+++ b/nbproject/project.properties
@@ -0,0 +1,3 @@
+files.encoding=UTF-8
+site.root.folder=
+source.folder=
diff --git a/nbproject/project.xml b/nbproject/project.xml
new file mode 100644
index 0000000..fef2fdc
--- /dev/null
+++ b/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>
diff --git a/src/nn_2opt.js b/src/nn_2opt.js
index 41a24d6..97b56e1 100644
--- a/src/nn_2opt.js
+++ b/src/nn_2opt.js
@@ -28,13 +28,13 @@ export function nn_2opt() {
     if (distanceMatrix === null) {
       distanceMatrix = dist().distance(distance)(matrix);
     }
-    let lowest_dist = Number.MIN_VALUE;
-    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;
@@ -52,45 +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;
+        }
     }
-    console.log(best_order);
-    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;
   }

From e5885b6f1f7c316c64c03b0b970be604b63f76b6 Mon Sep 17 00:00:00 2001
From: Beusekom <n.a.c.v.beusekom@tue.nl>
Date: Wed, 31 Aug 2022 12:04:02 +0200
Subject: [PATCH 3/4] Remove editor files and gitignore line

---
 .gitignore                           |  1 -
 nbproject/private/private.properties |  1 -
 nbproject/private/private.xml        | 15 ---------------
 nbproject/project.properties         |  3 ---
 nbproject/project.xml                |  9 ---------
 5 files changed, 29 deletions(-)
 delete mode 100644 nbproject/private/private.properties
 delete mode 100644 nbproject/private/private.xml
 delete mode 100644 nbproject/project.properties
 delete mode 100644 nbproject/project.xml

diff --git a/.gitignore b/.gitignore
index aa06c47..8601a29 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,4 +5,3 @@ coverage
 *~
 #*
 *.swp
-/nbproject/private/
diff --git a/nbproject/private/private.properties b/nbproject/private/private.properties
deleted file mode 100644
index 3b1a22e..0000000
--- a/nbproject/private/private.properties
+++ /dev/null
@@ -1 +0,0 @@
-browser=Chrome.INTEGRATED
diff --git a/nbproject/private/private.xml b/nbproject/private/private.xml
deleted file mode 100644
index c47be72..0000000
--- a/nbproject/private/private.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project-private xmlns="http://www.netbeans.org/ns/project-private/1">
-    <editor-bookmarks xmlns="http://www.netbeans.org/ns/editor-bookmarks/2" lastBookmarkId="0"/>
-    <open-files xmlns="http://www.netbeans.org/ns/projectui-open-files/2">
-        <group>
-            <file>file:/C:/Users/20184261/Documents/reorder.js/examples/timeseries/index.html</file>
-            <file>file:/C:/Users/20184261/Documents/reorder.js/src/nn_2opt.js</file>
-            <file>file:/C:/Users/20184261/Documents/reorder.js/examples/miserables/index.html</file>
-            <file>file:/C:/Users/20184261/Documents/reorder.js/test/nn_2opt-test.js</file>
-            <file>file:/C:/Users/20184261/Documents/reorder.js/examples/timeseries/order_functions.js</file>
-            <file>file:/C:/Users/20184261/Documents/reorder.js/examples/matrix.js</file>
-            <file>file:/C:/Users/20184261/Documents/reorder.js/src/optimal_leaf_order.js</file>
-        </group>
-    </open-files>
-</project-private>
diff --git a/nbproject/project.properties b/nbproject/project.properties
deleted file mode 100644
index da97eba..0000000
--- a/nbproject/project.properties
+++ /dev/null
@@ -1,3 +0,0 @@
-files.encoding=UTF-8
-site.root.folder=
-source.folder=
diff --git a/nbproject/project.xml b/nbproject/project.xml
deleted file mode 100644
index fef2fdc..0000000
--- a/nbproject/project.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?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>

From cfa34d2adcc6351bbd4cb7d3164407bd44a37426 Mon Sep 17 00:00:00 2001
From: Beusekom <n.a.c.v.beusekom@tue.nl>
Date: Wed, 14 Sep 2022 15:12:06 +0200
Subject: [PATCH 4/4] prepare for merge

---
 .gitignore                   | 1 +
 nbproject/project.properties | 3 +++
 nbproject/project.xml        | 9 +++++++++
 3 files changed, 13 insertions(+)
 create mode 100644 nbproject/project.properties
 create mode 100644 nbproject/project.xml

diff --git a/.gitignore b/.gitignore
index 8601a29..aa06c47 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,3 +5,4 @@ coverage
 *~
 #*
 *.swp
+/nbproject/private/
diff --git a/nbproject/project.properties b/nbproject/project.properties
new file mode 100644
index 0000000..da97eba
--- /dev/null
+++ b/nbproject/project.properties
@@ -0,0 +1,3 @@
+files.encoding=UTF-8
+site.root.folder=
+source.folder=
diff --git a/nbproject/project.xml b/nbproject/project.xml
new file mode 100644
index 0000000..fef2fdc
--- /dev/null
+++ b/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>