Bug: fixed broken guided traversal. Discovered that guided traversal

rotates the dfs tree.

README.md

@@ -0,0 +1 @@
+This branch tests the idea of using fuzzing to choose the direction of mutation

deferred_planarity_test/include/mps.h

@@ -56,8 +56,17 @@ public:
 	node* adj(int i);
 	void set_adj_list(vector<node*> vec);
 	void DFS_visit(vector<node*> &dfsList, int &index);
-	void guided_DFS_visit(vector<node*> &dfsList, vector<node*> &node_list, int &index, vector<int> rev_post_order);
-	void mutated_DFS_visit(vector<node*> &dfsList, vector<node*> &node_list, int &index, vector<int> rev_post_order, int &mutate_point);
+    void guided_DFS_visit(vector<node *> &dfsList,
+                          vector<node *> &node_list,
+                          int &return_index,
+                          vector<int> rev_post_order,
+                          int prev_node);
+    void mutated_DFS_visit(vector<node*> &dfsList, 
+                           vector<node*> &node_list, 
+                           int &index, 
+                           int &traversal_index, 
+                           vector<int> rev_post_order, 
+                           int mutate_point);
 
 	//PARENT-CHILDREN
 	void set_parent(node* n) ;
@@ -150,13 +159,16 @@ public:
 	int compute_removed_edge_size(string input_file, vector<int> post_order);
 	vector<int> generate_post_order(string input_file);
 	vector<int> generate_mutated_post_order(string input_file, vector<int> post_order);
+	vector<int> generate_guided_post_order(string input_file, vector<int> post_order);
 	node* get_new_node(node_type t);
     void read_from_gml(string input_file);
 	int output_removed_edge_size();
-	vector<int> postOrderTraversal();
-	vector<int> mutatedPostOrderTraversal(vector<int> post_order);
+    vector<int> return_post_order();
+	void postOrderTraversal();
 	void guidedPostOrderTraversal(vector<int> post_order);
-    void set_post_order(vector<int> post_order);
+	void mutatedPostOrderTraversal(vector<int> post_order);
+    // void set_post_order(vector<int> post_order);
+    void print_post_order();
 	void sort_adj_list();
 	void determine_edges();
 	void back_edge_traversal();

deferred_planarity_test/src/main.cpp

@@ -21,44 +21,42 @@ int compute_removed_edge_size(string input_file, vector<int> post_order);
 
 vector<int> generate_post_order(string input_file);
 vector<int> generate_mutated_post_order(string input_file, vector<int> post_order);
+vector<int> generate_guided_post_order(string input_file, vector<int> post_order);
 
-double temp_decay(int k, int k_max) {
-    return 1.0 - ((k + 1.0) / (k_max));
-}
 
-vector<int> sa_solve(string input_file, int k_max) {
-
-    // create sampling function
-    std::random_device rd;
-    std::mt19937 rng(rd());
-    std::uniform_real_distribution<> distribution(0.0, 1.0);
-
-    // generate first state
+vector<int> repeated_mutation(string input_file, int k_max) {
+    // generate first post order
+    std::cout << "generate first post order" << std::endl;
     vector<int> state_old = generate_post_order(input_file);
     vector<int> state_new;
-    int e_old = compute_removed_edge_size(input_file, state_old);
-    int e_new = 0;
-    int delta = 0;
-    // initialize terms
-    double temp;
-
+    int num_removed_edges;
     for (int k = 0; k < k_max; ++k) {
-        temp = START_TEMP * temp_decay(k, k_max);
-
-        state_new = generate_mutated_post_order(input_file, state_old);
-        e_new = compute_removed_edge_size(input_file, state_new);
-        delta = e_new - e_old;
-
-        if (std::exp( -(delta) / temp) > distribution(rng)) {
-            state_old = state_new; 
-            e_old = e_new;
+        // rotate it first
+        std::cout << "cycle:" << k << std::endl;
+        std::cout << "rotate the dfs tree" << std::endl;
+        state_new = generate_guided_post_order(input_file, state_old);
+        // then the next traversal will rotate it back
+        std::cout << "mutate the dfs tree" << std::endl;
+        state_new = generate_mutated_post_order(input_file, state_new);
+        // num_removed_edges = compute_removed_edge_size(input_file, state_new);
+        // first time will rotate the tree
+        std::cout << "rotate the dfs tree" << std::endl;
+        state_new = generate_guided_post_order(input_file, state_new);
+        // second time will rotate back the rotated tree
+        std::cout << "print the mutated tree again" << std::endl;
+        state_new = generate_guided_post_order(input_file, state_new);
+        std::cout << std::endl;
     }
+    return state_new;
 }
 
-    return state_old;
-
+void test_correctness(string input_file) {
+    vector<int> state_old = generate_post_order(input_file);
+    int num_removed_edges;
+    num_removed_edges = compute_removed_edge_size(input_file, state_old);
 }
 
+
 int get_graph_size(string input_file) {
     ogdf::Graph G;
 
@@ -80,14 +78,15 @@ int main(int argc, char* argv[]) {
     int k_max = std::stoi(argv[2]);
 
     // generate order here
-    vector<int> post_order = sa_solve(input_file, k_max);
+    vector<int> post_order = repeated_mutation(input_file, k_max);
+    // test_correctness(input_file);
 
-    // std::copy(post_order.begin(), post_order.end(), std::ostream_iterator<int>(std::cout, " "));
+    // // print final order and number of edges
+    // // print post_order
+    // std::copy(post_order.begin(), post_order.end(), std::ostream_iterator<int>(std::cout, ","));
     // std::cout << std::endl;
-
-    // print order
-    int removed_edges = compute_removed_edge_size(input_file, post_order);
-    std::cout << "Number of removed edges: " << removed_edges << std::endl;
+    // int removed_edges = compute_removed_edge_size(input_file, post_order);
+    // std::cout << "Number of removed edges: " << removed_edges << std::endl;
 
 	return 0;
 }

deferred_planarity_test/src/mps.cpp

@@ -3,6 +3,9 @@
 //-----------------------------------------------------------------------------------
 
 #include "mps.h"
+#include <iterator>
+
+// #define DEBUG
 
 // constructor can be made empty
 maximal_planar_subgraph_finder::maximal_planar_subgraph_finder() {}
@@ -19,17 +22,8 @@ maximal_planar_subgraph_finder::get_new_node(node_type t) {
 	return _new_node_list[_new_node_list.size()-1];
 }
 
-//Determine the post-order-list by a DFS-traversal.
 vector<int>
-maximal_planar_subgraph_finder::postOrderTraversal() {
-	node::init_mark();
-	int postOrderID = 0;
-	for (int i = 0; i < _node_list.size(); ++i) {
-		if (!_node_list[i]->is_marked()) {
-			_node_list[i]->DFS_visit(_post_order_list, postOrderID);
-		}
-	}
-
+maximal_planar_subgraph_finder::return_post_order() {
     vector<int> post_order;
     for (int i = 0; i < _post_order_list.size(); ++i) {
         post_order.push_back(_post_order_list[i]->node_id());
@@ -37,8 +31,23 @@ maximal_planar_subgraph_finder::postOrderTraversal() {
     return post_order;
 }
 
+//Determine the post-order-list by a DFS-traversal.
+void
+maximal_planar_subgraph_finder::postOrderTraversal() {
+	node::init_mark();
+    // always start with node 0
+	int postOrderID = 0;
+	for (int i = 0; i < _node_list.size(); ++i) {
+		if (!_node_list[i]->is_marked()) {
+			_node_list[i]->DFS_visit(_post_order_list, postOrderID);
+		}
+	}
+}
+
 
 // Determine the post-order-list by a DFS-traversal.
+// take in a post-order argument then traces the graph in the same order
+// return is by reference via _post_order_list
 void 
 maximal_planar_subgraph_finder::guidedPostOrderTraversal(vector<int> post_order) {
 	node::init_mark();
@@ -52,27 +61,30 @@ maximal_planar_subgraph_finder::guidedPostOrderTraversal(vector<int> post_order)
     int end_condition = _node_list.size();
     int start = rev_post_order[0];
     int i = start;
+    
+    int prev_node = INT_MAX;
     while (true)
     {
         if (((start > 0) && (i == (start - 1))) || ((start == 0 ) && (i == end_condition - 1)))
         {
             if (!_node_list[i]->is_marked())
             {
-                _node_list[i]->guided_DFS_visit(_post_order_list, _node_list, postOrderID, rev_post_order);
+                _node_list[i]->guided_DFS_visit(_post_order_list, _node_list, postOrderID, rev_post_order, prev_node);
             }
             break;
         }
-        // std::cout << _node_list[i]->node_id() << ", " << !_node_list[i]->is_marked() << std::endl;
         if (!_node_list[i]->is_marked())
         {
-            _node_list[i]->guided_DFS_visit(_post_order_list, _node_list, postOrderID, rev_post_order);
+            _node_list[i]->guided_DFS_visit(_post_order_list, _node_list, postOrderID, rev_post_order, prev_node);
         }
         i = (i + 1) % end_condition;
     }
 }
 
 //Determine the post-order-list by a DFS-traversal.
-vector<int> 
+// take in a post-order argument then traces the graph in the same order
+// return is by reference via _post_order_list
+void
 maximal_planar_subgraph_finder::mutatedPostOrderTraversal(vector<int> post_order) {
 	node::init_mark();
 
@@ -81,6 +93,7 @@ maximal_planar_subgraph_finder::mutatedPostOrderTraversal(vector<int> post_order
         rev_post_order.push_back(post_order[i]);
     }
 	int postOrderID = 0;
+    int traversal_index = 0;
 
     // introduce random selection
     std::random_device rd;
@@ -105,45 +118,46 @@ maximal_planar_subgraph_finder::mutatedPostOrderTraversal(vector<int> post_order
 
 
     int end_condition = _node_list.size();
+    // this loop assumes start is not from 0
+    // if starting index is not 0, it just increments and loops around until it encounters the element before it
     while (true)
     {
         if (((start > 0) && (i == (start - 1))) || ((start == 0 ) && (i == end_condition - 1)))
         {
             if (!_node_list[i]->is_marked())
             {
-                _node_list[i]->mutated_DFS_visit(_post_order_list, _node_list, postOrderID, rev_post_order, mutate_point);
+                _node_list[i]->mutated_DFS_visit(_post_order_list, _node_list, postOrderID, traversal_index, rev_post_order, mutate_point);
             }
             break;
         }
-        // std::cout << _node_list[i]->node_id() << ", " << !_node_list[i]->is_marked() << std::endl;
         if (!_node_list[i]->is_marked())
         {
-            _node_list[i]->mutated_DFS_visit(_post_order_list, _node_list, postOrderID, rev_post_order, mutate_point);
+            _node_list[i]->mutated_DFS_visit(_post_order_list, _node_list, postOrderID, traversal_index, rev_post_order, mutate_point);
         }
         i = (i + 1) % end_condition;
     }
-
-    vector<int> return_order;
-    for (int i = 0; i < _post_order_list.size(); ++i) {
-        return_order.push_back(_post_order_list[i]->node_id());
 }
 
-    // we have to reverse the order as we add to list in the forward direction of recursion
-    // unlike that of previous methods where we add to list in the return direction of recursion
-    std::reverse(return_order.begin(), return_order.end());
-    return return_order;
-}
-
-
-
-//Set the post-order-list via given list
 void
-maximal_planar_subgraph_finder::set_post_order(vector<int> post_order) {
-    for (int i = 0; i < _node_list.size(); ++i) {
-        _node_list[i]->set_post_order_index(post_order[i]);
+maximal_planar_subgraph_finder::print_post_order() {
+    int current_index;
+    for (int i = 0; i < _post_order_list.size(); ++i) {
+        current_index = _post_order_list[i]->node_id();
+        std::cout << current_index << ",";
     }
+    std::cout << std::endl;
 }
 
+
+// this function is not used anywhere
+//Set the post-order-list via given list
+// void
+// maximal_planar_subgraph_finder::set_post_order(vector<int> post_order) {
+//     for (int i = 0; i < _node_list.size(); ++i) {
+//         _node_list[i]->set_post_order_index(post_order[i]);
+//     }
+// }
+
 //Sort the adj-list of every node increasingly according to post-order-index.
 void
 maximal_planar_subgraph_finder::sort_adj_list() {

deferred_planarity_test/src/mps_test.cpp

@@ -5,6 +5,8 @@
 #include "mps.h"
 #include <ogdf/fileformats/GraphIO.h>
 
+#define DEBUG
+
 //-----------------------------------------------------------------------------------
 // Finding MPS
 //-----------------------------------------------------------------------------------
@@ -31,12 +33,22 @@ vector<int> generate_mutated_post_order(string input_file, vector<int> post_orde
     return m.generate_mutated_post_order(input_file, post_order);
 }
 
+vector<int> generate_guided_post_order(string input_file, vector<int> post_order) {
+    maximal_planar_subgraph_finder m;
+    return m.generate_guided_post_order(input_file, post_order);
+}
+
 
 // ---------
 
 int maximal_planar_subgraph_finder::find_mps(string input_file) {
 	read_from_gml(input_file);
 	postOrderTraversal();
+
+    #ifdef DEBUG
+    print_post_order();
+    #endif
+
 	sort_adj_list();
 	determine_edges();
 	back_edge_traversal();
@@ -45,31 +57,52 @@ int maximal_planar_subgraph_finder::find_mps(string input_file) {
 
 vector<int> maximal_planar_subgraph_finder::generate_post_order(string input_file) {
     read_from_gml(input_file);
-    return postOrderTraversal();
+    postOrderTraversal();
+
+    #ifdef DEBUG
+    std::cout << "standard post order traversal" << std::endl;
+    print_post_order();
+    #endif
+
+    return return_post_order();
 }
 
+// result of this will be used as input to "compute_removed_edge_size"
 vector<int> maximal_planar_subgraph_finder::generate_mutated_post_order(string input_file, vector<int> post_order) {
     read_from_gml(input_file);
-    return mutatedPostOrderTraversal(post_order);
+    mutatedPostOrderTraversal(post_order);
+
+    #ifdef DEBUG
+    std::cout << "mutated post order traversal" << std::endl;
+    print_post_order();
+    #endif
+
+    return return_post_order();
 }
 
+// result of this will be used as input to "compute_removed_edge_size"
+vector<int> maximal_planar_subgraph_finder::generate_guided_post_order(string input_file, vector<int> post_order) {
+    read_from_gml(input_file);
+    guidedPostOrderTraversal(post_order);
+
+    #ifdef DEBUG
+    std::cout << "guided post order traversal" << std::endl;
+    print_post_order();
+    #endif
+
+    return return_post_order();
+}
+
+
 
 int maximal_planar_subgraph_finder::compute_removed_edge_size(string input_file, vector<int> post_order) {
 	read_from_gml(input_file);
     guidedPostOrderTraversal(post_order);
     
-    // let's reverse the order
-    std::reverse(_post_order_list.begin(), _post_order_list.end());
-    // then set post_order_index
-    for (int i = 0; i < _post_order_list.size(); ++i) {
-        _node_list[_post_order_list[i]->node_id()]->set_post_order_index(i);
-    }
-
-    // std::cout << "check order of duplicated traversal" << std::endl;
-    // for (int i = 0; i < _post_order_list.size(); ++i) {
-    //     std::cout << _post_order_list[i]->node_id() << " ";
-    // }
-    // std::cout << std::endl;
+    #ifdef DEBUG
+    std::cout << "guided post order traversal" << std::endl;
+    print_post_order();
+    #endif
 
 	sort_adj_list();
 	determine_edges();

deferred_planarity_test/src/node.cpp

@@ -4,6 +4,8 @@
 
 #include "mps.h"
 
+// #define DEBUG
+
 //-----------------------------------------------------------------------------------
 // CONSTRUCTOR
 //-----------------------------------------------------------------------------------
@@ -67,101 +69,121 @@ void node::DFS_visit(vector<node*> &dfsList, int &index) {
 }
 
 
-void node::guided_DFS_visit(vector<node*> &dfsList, vector<node*> &node_list, int &index, vector<int> rev_post_order) {
+void node::guided_DFS_visit(vector<node *> &dfsList, 
+                            vector<node *> &node_list, 
+                            int &return_index, 
+                            vector<int> rev_post_order,
+                            int prev_node)
+{
+
 	mark();
-    // you will want to sort the neighbor nodes by the order they appear in the rev_post_order
-    vector<node *> neighbor_list;
-    std::unordered_set<int> neighbor_set; 
+
+    // purpose of this block: create list of neighbors ordered in the order they appear in rev_post_order
+    // we want to select neighbors that match the rev_post_order at the specific traversal_index
 
     // create an unordered set to efficiently check for presence of an element
+    std::unordered_set<int> neighbor_set; 
     for (int i = 0; i < _adj_list.size(); ++i) {
         neighbor_set.insert(_adj_list[i]->node_id());
     }
-
     // when an element in rev_post_order is found in neighbor_set, we add that to neighbor_list
+    // this produces a neighbor_list that follows the order by which they occur in the rev_post_order
+    // it is ok if the neighbor was already visited before, 
+    // it would've been marked and will be subsequently ignored
+    vector<node *> neighbor_list;
     for (int i = 0; i < rev_post_order.size(); ++i) {
         if (neighbor_set.find(rev_post_order[i]) != neighbor_set.end()) {
+            // only add if newly encountered
+            if (!node_list[rev_post_order[i]]->is_marked()) {
                 neighbor_list.push_back(node_list[rev_post_order[i]]);
             }
         }
+    }
+
+    #ifdef DEBUG
+    std::cout << "current node:" << this->node_id() << std::endl;
+    std::cout << "prev node:" << prev_node << std::endl;
+    for (int i = 0; i < neighbor_list.size(); ++i) {
+        std::cout << neighbor_list[i]->node_id() << "(" << neighbor_list[i]->is_marked() << ")" << ",";
+    }
+    std::cout << std::endl;
+    #endif
 
-    // print the neighbors
-    // std::cout << "current index: " << this->node_id() << std::endl;
-    // for (int i = 0; i < neighbor_list.size(); ++i) {
-    //     std::cout << neighbor_list[i]->node_id() << " ";
-    // }
-    // std::cout << std::endl;
 
-	set_post_order_index(index);
-	dfsList.push_back(this);
-	++index;
 	
 	for (int i = 0; i < neighbor_list.size(); ++i) {
 		if (!neighbor_list[i]->is_marked()) {
 			neighbor_list[i]->_parent = this;
-			neighbor_list[i]->guided_DFS_visit(dfsList, node_list, index, rev_post_order);
-		}
+			neighbor_list[i]->guided_DFS_visit(dfsList, node_list, return_index, rev_post_order, this->node_id());
 		}
 	}
 
+    set_post_order_index(return_index);
+	dfsList.push_back(this);
+	++return_index;
+}
 
-void node::mutated_DFS_visit(vector<node*> &dfsList, vector<node*> &node_list, int &index, vector<int> rev_post_order, int &mutate_point) {
+
+void node::mutated_DFS_visit(vector<node*> &dfsList, 
+                             vector<node*> &node_list, 
+                             int &return_index, 
+                             int &traversal_index, 
+                             vector<int> rev_post_order, 
+                             int mutate_point)
+{
+
+    // mark current node
 	mark();
-    // you will want to sort the neighbor nodes by the order they appear in the rev_post_order
-    vector<node *> neighbor_list;
-    std::unordered_set<int> neighbor_set; 
+    
+    // purpose of this block: create list of neighbors ordered in the order they appear in rev_post_order
+    // we want to select neighbors that match the rev_post_order at the specific traversal_index
 
     // create an unordered set to efficiently check for presence of an element
+    std::unordered_set<int> neighbor_set; 
     for (int i = 0; i < _adj_list.size(); ++i) {
         neighbor_set.insert(_adj_list[i]->node_id());
     }
-
     // when an element in rev_post_order is found in neighbor_set, we add that to neighbor_list
+    // this produces a neighbor_list that follows the order by which they occur in the rev_post_order
+    // it is ok if the neighbor was already visited before, 
+    // it would've been marked and will be subsequently ignored
+    vector<node *> neighbor_list;
     for (int i = 0; i < rev_post_order.size(); ++i) {
         if (neighbor_set.find(rev_post_order[i]) != neighbor_set.end()) {
             neighbor_list.push_back(node_list[rev_post_order[i]]);
         }
     }
 
-    // print the neighbors
-    // std::cout << "current index: " << this->node_id() << std::endl;
-    // for (int i = 0; i < neighbor_list.size(); ++i) {
-    //     std::cout << neighbor_list[i]->node_id() << " ";
-    // }
-    // std::cout << std::endl;
     
-	set_post_order_index(index);
-	dfsList.push_back(this);
-	++index;
 
-    if (index - 1 == mutate_point) {
+    // since we increment the index before this line, the current index is "index - 1"
+    // if the current index matches the mutate_point, then we know this is the cycle to mutate
+    if (traversal_index == mutate_point) {
         // Create a random number generator and seed it
         // std::cout << "mutated at index: " << index - 1<< "and at mutate point: " << mutate_point << std::endl;
         std::random_device rd;
         std::mt19937 rng(rd());
         // Use std::shuffle to shuffle the elements in the vector
         std::shuffle(neighbor_list.begin(), neighbor_list.end(), rng);
-        // // print the neighbors
-        // std::cout << "order after mutation: " << std::endl;
-        // std::cout << "current index: " << this->node_id() << std::endl;
-        // for (int i = 0; i < neighbor_list.size(); ++i)
-        // {
-        //     std::cout << neighbor_list[i]->node_id() << " ";
-        // }
-        // std::cout << std::endl;
     } 
 
+    // increment traversal index after checking
+    // next node will receive incremented index
+    traversal_index++;
+    
     for (int i = 0; i < neighbor_list.size(); ++i)
     {
         if (!neighbor_list[i]->is_marked())
         {
             neighbor_list[i]->_parent = this;
-            neighbor_list[i]->mutated_DFS_visit(dfsList, node_list, index, rev_post_order, mutate_point);
-        }
+            neighbor_list[i]->mutated_DFS_visit(dfsList, node_list, return_index, traversal_index, rev_post_order, mutate_point);
         }
     }
 
-
+	set_post_order_index(return_index);
+	dfsList.push_back(this);
+	++return_index;
+}
 
 //-----------------------------------------------------------------------------------
 // PARENT-CHILDREN