Remove tower assembler as not used by edge collapse

2 files changed, 0 insertions, 265 deletions

diff --git a/src/Collapse/example/rips_persistence_with_sc.cpp b/src/Collapse/example/rips_persistence_with_sc.cpp
index 5336b202..65b886f7 100644
--- a/src/Collapse/example/rips_persistence_with_sc.cpp
+++ b/src/Collapse/example/rips_persistence_with_sc.cpp
@@ -1,4 +1,3 @@
-#include <gudhi/TowerAssembler_FlagComplex.h>
 #include <gudhi/Rips_complex.h>
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/Persistent_cohomology.h>
@@ -46,83 +45,7 @@ public:
       
     }
 };
-class strong_filtered_vertex_collapse
-{
-public:
-    template<class Filtered_sorted_edge_list, class Distance_matrix>
-    strong_filtered_vertex_collapse(std::size_t number_of_points, Filtered_sorted_edge_list & edge_t, double steps, Distance_matrix & sparse_distances)
-    {
-         auto the_collapse_begin = std::chrono::high_resolution_clock::now();
-        //An additional vector <edge_filt> to perform binary search to find the index of given threshold
-        std::vector<Filtration_value> * edge_filt = new std::vector<Filtration_value>();
-        edge_filt->clear();
-        for(auto edIt = edge_t.begin(); edIt != edge_t.end(); edIt++) {
-            edge_filt->push_back(std::get<0>(*edIt));
-        }
-        double begin_thresold = edge_filt->at(0);
-        double end_threshold = edge_filt->at(edge_filt->size()-1);
-        double totAssembleTime = 0.0;
-        Filtered_sorted_edge_list * sub_skeleton  = new Filtered_sorted_edge_list();  
-        TowerAssembler_FlagComplex twr_assembler(number_of_points) ;
-
-        std::cout<< "Begin and end thresholds (filteration values) are , " << begin_thresold <<", " << end_threshold << "." <<std::endl;
-
-        // int iterations = (end_threshold - begin_thresold)/steps;
-        // std::cout << "Total number of iterations to be run are: " << iterations << std::endl;
-       
-        auto threshold =  begin_thresold;  
-
-        FlagComplexSpMatrix * mat_coll       = new FlagComplexSpMatrix(); 
-        FlagComplexSpMatrix * mat_prev_coll  = new FlagComplexSpMatrix(number_of_points); 
-
-        std::cout << "Going for vertex collapse and tower assembly" << std::endl;
-
-        int i = 1;
-        Map * redmap;
-        while(edge_filt->size() > 0) {
-           
-            if(steps > 0)
-                extract_sub_one_skeleton(threshold, *sub_skeleton, edge_t, *edge_filt);
 
-            else
-                extract_one_new_edge(*sub_skeleton, edge_t, *edge_filt);
-
-
-            mat_coll = new FlagComplexSpMatrix(number_of_points, *sub_skeleton);
-            // mat_coll->strong_vertex_edge_collapse();
-            mat_coll->strong_vertex_collapse();
-            // std::cout<< " Total number of current edges are " << sub_skeleton->size() << std::endl;
-                       
-            redmap = new Map();
-            *redmap = mat_coll->reduction_map(); 
-            
-            // std::cout << "Subcomplex #" << i << " of threshold "<< threshold << " Collapsed" << std::endl;
-            totAssembleTime += twr_assembler.build_tower_for_two_cmplxs(*mat_prev_coll, *mat_coll, *redmap, threshold, "./PersistenceOutput/CollapsedTowerRips.txt");
-            // std::cout << "Tower updated for subcomplex #" << i << std::endl; 
-            
-            delete mat_prev_coll;
-            mat_prev_coll = new FlagComplexSpMatrix();
-            mat_prev_coll = mat_coll;
-            mat_coll  = new FlagComplexSpMatrix();
-            i++;
-            delete redmap;
-            if(steps > 0) {
-                threshold = threshold+steps;
-                if(threshold > end_threshold)
-                    threshold = end_threshold; 
-            }
-            else {
-                if(edge_filt->size() > 0)
-                    threshold = edge_filt->at(0);  
-            }    
-        }
-        std::cout << "Tower updated for subcomplex #" << i << std::endl; 
-        auto the_collapse = std::chrono::high_resolution_clock::now();    
-        sparse_distances = twr_assembler.distance_matrix();
-        std::cout << "Collapse And assembly time : " <<  std::chrono::duration<double, std::milli>(the_collapse- the_collapse_begin).count() << " ms\n" << std::endl;
-    }    
-
-};
 class filt_edge_to_dist_matrix
 {
 public:
@@ -320,10 +243,6 @@ int main(int argc, char * const argv[]) {
         exit(-1) ;
     }
     
-
-    // std::cout<< "Vertex strong-collapse begins" << std::endl;
-    // strong_filtered_vertex_collapse(number_of_points, *edge_t, steps, *sparse_distances); 
-
     auto end_full_cmplx = std::chrono::high_resolution_clock::now();
     currentCreationTime = std::chrono::duration<double, std::milli>(end_full_cmplx - begin_full_cmplx).count();
     maxCreationTime = currentCreationTime;
diff --git a/src/Collapse/include/gudhi/TowerAssembler_FlagComplex.h b/src/Collapse/include/gudhi/TowerAssembler_FlagComplex.h
deleted file mode 100644
index 01d86642..00000000
--- a/src/Collapse/include/gudhi/TowerAssembler_FlagComplex.h
+++ /dev/null
@@ -1,184 +0,0 @@
-#pragma once
-#include <gudhi/FlagComplexSpMatrix.h>
-#include <gudhi/Rips_edge_list.h>
-
-#include <set>
-#include <fstream>
-#include <string>
-#include <algorithm>
-#include <limits>
-#include <cmath>
-
-
-typedef std::size_t Vertex;
-using Edge                  = std::pair<Vertex,Vertex>;
-using edge_list             = std::vector<Edge>;
-using Simplex               = std::vector<Vertex>;
-
-using vectorVertex          = std::vector<Vertex>;
-using vert_unSet            = std::unordered_set<Vertex>;
-using Map                   = std::unordered_map<Vertex,Vertex>;
-using Distance_matrix       = std::vector<std::vector<double>>;
-// using infinity              = std::numeric_limits<double>::max();
-// assumptions : (1) K1 and K2 have the same vertex set
-//               (2) The set of simplices of K1 is a subset of set of simplices of K2
-// K1  ->  K2    [Original Simplicial Complexes]
-// |       |
-// |       |
-// K1c ->  K2c   [Strongly Collapsed Flag Complexes]
-
-class TowerAssembler_FlagComplex
-{
-  private:
-	Map renamedVertices; 
-    Map representative_map;
-	std::size_t current_rename_counter;
-    Distance_matrix * distance_mat;
-    size_t total_vertices;
-
-    // Filtered_sorted_edge_list * edge_t = new Filtered_sorted_edge_list();
-    FlagComplexSpMatrix * flag_Filtration; 
-    typedef std::vector< std::tuple< double, Vertex, Vertex > > Filtered_sorted_edge_list;
-
-	
-  public:
-    
-    TowerAssembler_FlagComplex(std::size_t numVert)
-    {
-    	for (std::size_t i = 0; i <= numVert; ++i){
-    		renamedVertices[i] = i;
-        }
-    	total_vertices = 0;
-        current_rename_counter = numVert+1;
-        
-        flag_Filtration = new FlagComplexSpMatrix((numVert*log2(numVert)) +1);
-        distance_mat    = new Distance_matrix();
-        // distance_mat->push_back({0});
-    }
-    
-    ~TowerAssembler_FlagComplex(){};
-    double build_tower_for_two_cmplxs(FlagComplexSpMatrix mat_1, const FlagComplexSpMatrix & mat_2,  Map redmap_2,  double filtration_value, std::string outFile) // mat_1 and mat_2 are simplex_trees of K1c and K2c (the collapsed ones), redmap_2 is the map of K2 -> K2c
-    {
-        auto begin_print  = std::chrono::high_resolution_clock::now();
-        std::ofstream myfile (outFile, std::ios::app);
-        if (myfile.is_open())
-        {   
-            for (auto & v : mat_1.vertex_set()) {
-                auto collapsed_to = redmap_2.find(v);  // If v collapsed to something?
-                if(collapsed_to != redmap_2.end()) {  // Collapse happened, because there is a vertex in the map
-                    if(mat_1.membership(collapsed_to->second)) { // Collapsed to an existing vertex in mat_1.
-
-                    	// myfile << filtration_value  << " c " << renamedVertices.at(v) << " " << renamedVertices.at(collapsed_to->second) << std::endl; 
-                    	std::cout << filtration_value << " c " << renamedVertices.at(v) << " " << renamedVertices.at(collapsed_to->second) << std::endl;
-                        flag_Filtration->active_strong_expansion(renamedVertices.at(v), renamedVertices.at(collapsed_to->second), filtration_value);
-                        renamedVertices.at(v) = current_rename_counter;
-                        current_rename_counter++;                        
-                    }
-                    else {
-	                    // myfile << filtration_value << " i " << renamedVertices.at(collapsed_to->second) << std::endl;
-	                    // myfile  << filtration_value << " c " << renamedVertices.at(v) << " " << renamedVertices.at(collapsed_to->second) << std::endl; 
-	                    flag_Filtration->active_strong_expansion(renamedVertices.at(v), renamedVertices.at(collapsed_to->second),filtration_value);
-                        std::cout << filtration_value << " i " << renamedVertices.at(collapsed_to->second) << std::endl;
-                        std::cout  << filtration_value << " c " << renamedVertices.at(v) << " " << renamedVertices.at(collapsed_to->second) << std::endl; 
-                        renamedVertices.at(v) = current_rename_counter;
-	                    current_rename_counter++;
-                    }
-                     // If the vertex "collapsed_to->second" is not a member of mat_1, the contraction function will simply add and then collapse
-                     mat_1.contraction(v, collapsed_to->second);
-                     // std::cout << " Contraction Done " << std::endl;
-
-                }
-            }
-
-            //The core K1c (mat_1) has gone through the transformation(re-labeling)/collapse and it is now a subcomplex of K2c, the remaining simplices need to be included
-            // Writing the inclusion of all remaining simplices...
-            // std::cout << "Begining the inclusion of edges " << std::endl;
-            for( const Edge & e  : mat_2.all_edges()) {
-                auto u = std::get<0>(e);
-                auto v = std::get<1>(e);
-                // std::cout << "Going to insert the edge :" << renamedVertices.at(u) << ", " << renamedVertices.at(v) << std::endl;
-                // std::cout << "Going to insert the vertex :" << u << std::endl;
-                if(!mat_1.membership(u)) {
-                    flag_Filtration->insert_vertex(renamedVertices.at(u),filtration_value);
-                    // std::cout << "Inserted the vertex :" << renamedVertices.at(u) <<  " in the new distance matrix"<< std::endl;
-                    // myfile << filtration_value << " i";
-                    // myfile  << " " << renamedVertices.at(u);
-                    // myfile  << std::endl;
-                    mat_1.insert_vertex(u,1);
-                    // std::cout << "Inserted the vertex :" << renamedVertices.at(u) <<  " in the old skeleton matrix"<< std::endl;
-
-
-                }
-
-                // std::cout << "Going to insert the vertex :" << v << std::endl ;
-                if(!mat_1.membership(v)) {
-                    // std::cout << "Begining the insertion the vertex :" << renamedVertices.at(v) <<  " in the new distance matrix"<< std::endl;
-
-                    flag_Filtration->insert_vertex(renamedVertices.at(v),filtration_value);
-                    // std::cout << "Inserted the vertex :" << renamedVertices.at(v) <<  " in the new distance matrix"<< std::endl;
-
-                    // myfile << filtration_value << " i";
-                    // myfile  << " " << renamedVertices.at(v);
-                    // myfile  << std::endl;
-                    mat_1.insert_vertex(v,1);
-                    // std::cout << "Inserted the vertex :" << v <<  " in the old skeleton matrix"<< std::endl;
-
-                }
-                // std::cout << "Going to insert the edge :" << u << ", " << v << std::endl;
-                if(!mat_1.membership(e)){
-                    flag_Filtration->insert_new_edges(renamedVertices.at(u),renamedVertices.at(v), filtration_value);
-                    // std::cout << "Inserted the edge :" << renamedVertices.at(u) << ","<< renamedVertices.at(v) <<  " in the new distance matrix"<< std::endl;
-
-                    // myfile << filtration_value << " i";
-                    // myfile  << " " <<  renamedVertices.at(u) << ", " << renamedVertices.at(v);
-                    // myfile  << std::endl;
-                    // std::cout << "Going to insert the edge :" << u << ","<< v <<  " in the old skeleton"<< std::endl;
-                    mat_1.insert_new_edges(u,v,1);
-                    // std::cout << "Inserted the edge :" << u << ","<< v <<  " in the old skeleton"<< std::endl;
-                } 
-                 // std::cout << " Insertion Done " << std::endl;        
-            }
-
-            // myfile << "# Tower updated for the additional subcomplex.\n";
-            myfile.close();
-        }
-        else {
-            std::cerr << "Unable to open file";
-            exit(-1) ;
-        }
-        
-        auto end_print  = std::chrono::high_resolution_clock::now();
-        auto printTime = std::chrono::duration<double, std::milli>(end_print- begin_print).count();
-        // std::cout << " Time to print the tower : " << printTime << " ms\n" << std::endl;
-        return printTime;
-    } 
-    Distance_matrix distance_matrix()
-    {
-        size_t non_zero_rw = flag_Filtration->num_vertices();
-        double inf = std::numeric_limits<double>::max();
-        sparseRowMatrix mat = flag_Filtration->uncollapsed_matrix();
-        doubleVector distances ;  
-        for(size_t indx = 0; indx < non_zero_rw; indx++){ 
-            rowInnerIterator it(mat, indx);   
-            for(size_t j = 0; j <= indx; j++) {             // Iterate over the non-zero columns
-                //std::cout << "j = " << j << " - it.index = " << it.index() << " - indx = " << indx << std::endl;
-                if(it.index() == j && j != indx){
-                    distances.push_back(it.value());  // inner index, here it is equal to it.columns()
-                    ++it;
-                }
-                else if( j == indx)
-                    distances.push_back(0);
-                else
-                     distances.push_back(inf);
-
-            }
-            distance_mat->push_back(distances);
-            distances.clear();
-        }        
-        return *distance_mat;
-    }      
-   void print_sparse_matrix(){
-        flag_Filtration->print_sparse_skeleton();
-   }
-    
-};