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#include <gudhi/FlagComplexSpMatrix.h>
#include <gudhi/Rips_complex.h>
#include <gudhi/Simplex_tree.h>
#include <gudhi/Persistent_cohomology.h>
#include <gudhi/Rips_edge_list.h>
#include <gudhi/distance_functions.h>
#include <gudhi/reader_utils.h>
#include <gudhi/PointSetGen.h>
// Types definition
using Vector_of_points = std::vector<Point>;
using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
using Filtration_value = double;
using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>;
using Rips_edge_list = Gudhi::rips_edge_list::Rips_edge_list<Filtration_value>;
using Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp>;
using Distance_matrix = std::vector<std::vector<Filtration_value>>;
class filt_edge_to_dist_matrix
{
public:
template<class Distance_matrix, class Filtered_sorted_edge_list>
filt_edge_to_dist_matrix(Distance_matrix & distance_mat, Filtered_sorted_edge_list & edge_filt, std::size_t number_of_points)
{
double inf = std::numeric_limits<double>::max();
doubleVector distances ;
std::pair<std::size_t, std::size_t> e;
for(std::size_t indx = 0; indx < number_of_points; indx++) {
for (int j = 0; j <= indx; j++) {
if( j == indx)
distances.push_back(0);
else
distances.push_back(inf);
}
distance_mat.push_back(distances);
distances.clear();
}
for(auto edIt = edge_filt.begin(); edIt != edge_filt.end(); edIt++) {
e=std::minmax(std::get<1>(*edIt),std::get<2>(*edIt));
distance_mat.at(std::get<1>(e)).at(std::get<0>(e)) = std::get<0>(*edIt);
}
}
};
int main(int argc, char * const argv[]) {
auto the_begin = std::chrono::high_resolution_clock::now();
PointSetGen point_generator;
std::string out_file_name = "default";
std::string in_file_name = "default";
std::size_t number_of_points;
typedef size_t Vertex_handle;
typedef std::vector< std::tuple<Filtration_value, Vertex_handle, Vertex_handle > > Filtered_sorted_edge_list;
int dimension;
double end_threshold;
double steps;
char manifold;
Vector_of_points * point_vector;
int dim_max = 2;
point_generator.program_options(argc, argv, steps, end_threshold, manifold, dimension, dim_max, in_file_name, out_file_name);
std::cout << "The current input values to run the program is: "<< std::endl;
std::cout << "steps, end_threshold, manifold, dimension, max_complex_dimension, in_file_name, out_file_name" << std::endl;
std::cout << steps << ", " << end_threshold << ", " << manifold << ", " << dimension << ", " << dim_max << ", " << in_file_name << ", " << out_file_name << std::endl;
Map map_empty;
std::string filediag_aft ("./PersistenceOutput/collapsed_persistence_diags") ;
filediag_aft = filediag_aft+"_"+ out_file_name+ ".txt";
double currentCreationTime = 0.0;
Distance_matrix distances;
Distance_matrix *sparse_distances = new Distance_matrix();
if(manifold == 'f' || manifold =='f') {
Gudhi::Points_off_reader<Point> off_reader(in_file_name);
if (!off_reader.is_valid()) {
std::cerr << "Unable to read file " << in_file_name << "\n";
exit(-1); // ----- >>
}
point_vector = new Vector_of_points(off_reader.get_point_cloud().begin(), off_reader.get_point_cloud().end());
dimension = point_vector->at(0).dimension() ;
number_of_points = point_vector->size();
std::cout << "Successfully read " << number_of_points << " point_vector.\n";
std::cout << "Ambient dimension is " << dimension << ".\n";
}
else if (manifold == 'm'){
std::string csv_file_name(in_file_name);
distances = Gudhi::read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_file_name);
number_of_points = distances.size();
std::cout << "Read the distance matrix succesfully, of size: " << number_of_points << std::endl;
}
else {
std::cerr << "Wrong parameters for input manifold..." <<std::endl;
exit(-1);
}
std::cout << "Point Set Generated." <<std::endl;
Filtered_sorted_edge_list * edge_t = new Filtered_sorted_edge_list();
std::cout << "Computing the one-skeleton for threshold: " << end_threshold << std::endl;
if(manifold == 'm') { //Input is a distance 'm'atrix //Creating the edge list
Rips_edge_list Rips_edge_list_from_file(distances, end_threshold);
Rips_edge_list_from_file.create_edges(*edge_t);
std::cout<< "Sorted edge list computed" << std::endl;
}
else{ //Point cloud input //Creating the edge list
Rips_edge_list Rips_edge_list_from_points(*point_vector, end_threshold, Gudhi::Euclidean_distance());
Rips_edge_list_from_points.create_edges(*edge_t);
std::cout<< "Sorted edge list computed" << std::endl;
std::cout << "Total number of edges before collapse are: " << edge_t->size() << std::endl;
}
//Now we will perform filtered edge collapse to sparsify the edge list edge_t.
std::cout<< "Filtered edge collapse begins" << std::endl;
FlagComplexSpMatrix * mat_filt_edge_coll = new FlagComplexSpMatrix(number_of_points,*edge_t);
std::cout<< "Matrix instansiated" << std::endl;
if(edge_t->size() >0){
delete edge_t;
edge_t = new Filtered_sorted_edge_list();
*edge_t = mat_filt_edge_coll->filtered_edge_collapse();
filt_edge_to_dist_matrix(*sparse_distances, *edge_t, number_of_points);
std::cout << "Total number of vertices after collapse in the sparse matrix are: " << mat_filt_edge_coll->num_vertices() << std::endl;
}
else
{
std::cerr << "Total number of egdes are zero." <<std::endl;
exit(-1) ;
}
// Rips_complex rips_complex_before_collapse(distances, end_threshold);
Rips_complex rips_complex_after_collapse(*sparse_distances, end_threshold);
Simplex_tree simplex_tree_aft;
rips_complex_after_collapse.create_complex(simplex_tree_aft, dim_max);
std::cout << "The complex contains " << simplex_tree_aft.num_simplices() << " simplices after collapse. \n";
std::cout << " and has dimension " << simplex_tree_aft.dimension() << " \n";
// Sort the simplices in the order of the filtration
simplex_tree_aft.initialize_filtration();
// Compute the persistence diagram of the complex
Persistent_cohomology pcoh_aft(simplex_tree_aft);
// initializes the coefficient field for homology
pcoh_aft.init_coefficients(2);
// pcoh_bfr.compute_persistent_cohomology(steps);
pcoh_aft.compute_persistent_cohomology(steps);
if (filediag_aft.empty()) {
pcoh_aft.output_diagram();
}
else {
std::ofstream out(filediag_aft);
pcoh_aft.output_diagram(out);
out.close();
}
auto the_end = std::chrono::high_resolution_clock::now();
std::cout << "Total computation time : " << std::chrono::duration<double, std::milli>(the_end- the_begin).count()
<< " ms\n" << std::endl;
return 0;
}
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