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+/* This file is part of the Gudhi Library. The Gudhi library
+ * (Geometric Understanding in Higher Dimensions) is a generic C++
+ * library for computational topology.
+ *
+ * Author(s): David Salinas
+ *
+ * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+#ifndef MODEL_MODEL_H_
+#define MODEL_MODEL_H_
+
+#include <gudhi/Clock.h>
+#include <gudhi/Skeleton_blocker/Skeleton_blocker_simple_geometric_traits.h>
+#include <gudhi/Skeleton_blocker_geometric_complex.h>
+#include <gudhi/Off_reader.h>
+
+#include <CGAL/Euclidean_distance.h>
+
+#include <fstream>
+#include <limits>
+#include <string>
+#include <vector>
+
+#include "utils/UI_utils.h"
+#include "utils/Lloyd_builder.h"
+#include "utils/Rips_builder.h"
+#include "utils/K_nearest_builder.h"
+#include "utils/Vertex_collapsor.h"
+#include "utils/Edge_collapsor.h"
+#include "utils/Edge_contractor.h"
+#include "utils/Persistence_compute.h"
+#include "utils/Critical_points.h"
+#include "utils/Is_manifold.h"
+
+#include "Complex_typedefs.h"
+
+template<typename Complex>
+class CGAL_geometric_flag_complex_wrapper {
+ Complex& complex_;
+ typedef typename Complex::Vertex_handle Vertex_handle;
+ typedef typename Complex::Point Point;
+
+ const bool load_only_points_;
+
+ public:
+ CGAL_geometric_flag_complex_wrapper(Complex& complex, bool load_only_points = false) :
+ complex_(complex),
+ load_only_points_(load_only_points) { }
+
+ void init(int dim, int num_vertices, int num_max_faces, int num_edges) const { }
+
+ void point(const std::vector<double>& coords) {
+ Point p(coords.size(), coords.begin(), coords.end());
+ complex_.add_vertex(p);
+ }
+
+ void maximal_face(std::vector<int> vertices) {
+ if (!load_only_points_) {
+ // std::cout << "size:" << vertices.size() << std::endl;
+ for (int i = 0; i < vertices.size(); ++i)
+ for (int j = i + 1; j < vertices.size(); ++j)
+ complex_.add_edge(Vertex_handle(vertices[i]), Vertex_handle(vertices[j]));
+ }
+ }
+
+ void done() const { }
+};
+
+class Model {
+ public:
+ Complex complex_;
+ typedef Complex::Vertex_handle Vertex_handle;
+
+ Model() : complex_() { }
+
+ public:
+ void off_file_open(const std::string& name_file) {
+ UIDBGMSG("load off file", name_file);
+ complex_.clear();
+ CGAL_geometric_flag_complex_wrapper<Complex> read_wraper(complex_, false);
+ Gudhi::read_off(name_file, read_wraper);
+ }
+
+ void off_points_open(const std::string& name_file) {
+ UIDBGMSG("load off points", name_file);
+ complex_.clear();
+ CGAL_geometric_flag_complex_wrapper<Complex> read_wraper(complex_, true);
+ Gudhi::read_off(name_file, read_wraper);
+ }
+
+ void off_file_save(const std::string& name_file) {
+ UIDBG("save off file");
+ UIDBG("save off off_points_save");
+ std::ofstream file(name_file);
+ if (file.is_open()) {
+ file << "OFF\n";
+ file << complex_.num_vertices() << " " << complex_.num_edges() << " 0\n";
+ for (auto v : complex_.vertex_range()) {
+ const auto& pt(complex_.point(v));
+ for (auto it = pt.cartesian_begin(); it != pt.cartesian_end(); ++it)
+ file << *it << " ";
+ file << std::endl;
+ }
+ for (auto e : complex_.edge_range())
+ file << "2 " << complex_.first_vertex(e) << " " << complex_.second_vertex(e) << "\n";
+ file.close();
+ } else {
+ std::cerr << "Could not open file " << name_file << std::endl;
+ }
+ }
+
+ void off_points_save(const std::string& name_file) {
+ UIDBG("save off off_points_save");
+ std::ofstream file(name_file);
+ if (file.is_open()) {
+ file << "OFF\n";
+ file << complex_.num_vertices() << " 0 0\n";
+ for (auto v : complex_.vertex_range()) {
+ const auto& pt(complex_.point(v));
+ for (auto it = pt.cartesian_begin(); it != pt.cartesian_end(); ++it)
+ file << *it << " ";
+ file << std::endl;
+ }
+ file.close();
+ } else {
+ std::cerr << "Could not open file " << name_file << std::endl;
+ }
+ }
+
+ // point sets operations
+ void uniform_noise(double amplitude) {
+ UIDBG("unif noise");
+ for (auto v : complex_.vertex_range())
+ complex_.point(v) = add_uniform_noise(complex_.point(v), amplitude);
+ }
+
+ private:
+ Point add_uniform_noise(const Point& point, double amplitude) {
+ std::vector<double> new_point(point.dimension());
+ for (int i = 0; i < point.dimension(); ++i) {
+ new_point[i] = point[i] + (rand() % 2 - .5) * amplitude;
+ }
+ return Point(point.dimension(), new_point.begin(), new_point.end());
+ }
+
+ public:
+ void lloyd(int num_iterations, int num_closest_neighbors) {
+ UIDBG("lloyd");
+ Lloyd_builder<Complex> lloyd_builder(complex_, 1);
+ }
+
+ double squared_eucl_distance(const Point& p1, const Point& p2) const {
+ return Geometry_trait::Squared_distance_d()(p1, p2);
+ }
+
+ // complex operations from points
+
+ void build_rips(double alpha) {
+ UIDBG("build_rips");
+ Rips_builder<Complex> rips_builder(complex_, alpha);
+ }
+
+ void build_k_nearest_neighbors(unsigned k) {
+ UIDBG("build_k_nearest");
+ complex_.keep_only_vertices();
+ K_nearest_builder<Complex> k_nearest_builder(complex_, k);
+ }
+
+ void build_delaunay() {
+ UIDBG("build_delaunay");
+ complex_.keep_only_vertices();
+ }
+
+ void contract_edges(unsigned num_contractions) {
+ Clock c;
+ Edge_contractor<Complex> contractor(complex_, num_contractions);
+ std::cout << "Time to simplify: " << c.num_seconds() << "s" << std::endl;
+ }
+
+ void collapse_vertices(unsigned num_collapses) {
+ auto old_num_vertices = complex_.num_vertices();
+ Vertex_collapsor<Complex> collapsor(complex_, complex_.num_vertices());
+ UIDBGMSG("num vertices collapsed:", old_num_vertices - complex_.num_vertices());
+ }
+
+ void collapse_edges(unsigned num_collapses) {
+ Edge_collapsor<Complex> collapsor(complex_, num_collapses);
+ }
+
+ void show_graph_stats() {
+ std::cout << "++++++ Graph stats +++++++" << std::endl;
+ std::cout << "Num vertices : " << complex_.num_vertices() << std::endl;
+ std::cout << "Num edges : " << complex_.num_edges() << std::endl;
+ std::cout << "Num connected components : " << complex_.num_connected_components() << std::endl;
+ std::cout << "Min/avg/max degree : " << min_degree() << "/" << avg_degree() << "/" << max_degree() << std::endl;
+ std::cout << "Num connected components : " << complex_.num_connected_components() << std::endl;
+ std::cout << "Num connected components : " << complex_.num_connected_components() << std::endl;
+ std::cout << "+++++++++++++++++++++++++" << std::endl;
+ }
+
+ private:
+ int min_degree() const {
+ int res = (std::numeric_limits<int>::max)();
+ for (auto v : complex_.vertex_range())
+ res = (std::min)(res, complex_.degree(v));
+ return res;
+ }
+
+ int max_degree() const {
+ int res = 0;
+ for (auto v : complex_.vertex_range())
+ res = (std::max)(res, complex_.degree(v));
+ return res;
+ }
+
+ int avg_degree() const {
+ int res = 0;
+ for (auto v : complex_.vertex_range())
+ res += complex_.degree(v);
+ return res / complex_.num_vertices();
+ }
+
+ public:
+ void show_complex_stats() {
+ std::cout << "++++++ Mesh stats +++++++" << std::endl;
+ std::cout << "Num vertices : " << complex_.num_vertices() << std::endl;
+ std::cout << "Num edges : " << complex_.num_edges() << std::endl;
+ std::cout << "Num connected components : " << complex_.num_connected_components() << std::endl;
+ std::cout << "+++++++++++++++++++++++++" << std::endl;
+ }
+
+ void show_complex_dimension() {
+ unsigned num_simplices = 0;
+ int euler = 0;
+ int dimension = 0;
+ Clock clock;
+ for (const auto &s : complex_.complex_simplex_range()) {
+ num_simplices++;
+ dimension = (std::max)(s.dimension(), dimension);
+ if (s.dimension() % 2 == 0)
+ euler += 1;
+ else
+ euler -= 1;
+ }
+ clock.end();
+ std::cout << "++++++ Mesh dimension +++++++" << std::endl;
+ std::cout << "Dimension : " << dimension << std::endl;
+ std::cout << "Euler characteristic : " << euler << std::endl;
+ std::cout << "Num simplices : " << num_simplices << std::endl;
+ std::cout << "Total time: " << clock << std::endl;
+ std::cout << "Time per simplex: " << clock.num_seconds() / num_simplices << " s" << std::endl;
+ std::cout << "+++++++++++++++++++++++++" << std::endl;
+ }
+
+ void show_homology_group() {
+#ifdef _WIN32
+ std::cout << "Works only on linux x64 for the moment\n";
+#else
+ Clock clock;
+ run_chomp();
+ clock.end();
+#endif
+ }
+
+ void show_euler_characteristic() {
+ unsigned num_simplices = 0;
+ int euler = 0;
+ int dimension = 0;
+ for (const auto &s : complex_.complex_simplex_range()) {
+ num_simplices++;
+ dimension = (std::max)(s.dimension(), dimension);
+ if (s.dimension() % 2 == 0)
+ euler += 1;
+ else
+ euler -= 1;
+ }
+ std::cout << "Saw " << num_simplices << " simplices with maximum dimension " << dimension << std::endl;
+ std::cout << "The euler characteristic is : " << euler << std::endl;
+ }
+
+ void show_persistence(int p, double threshold, int max_dim, double min_pers) {
+ Persistence_compute<Complex> persistence(complex_, std::cout, Persistence_params(p, threshold, max_dim, min_pers));
+ }
+
+ void show_critical_points(double max_distance) {
+ Critical_points<Complex> critical_points(complex_, std::cout, max_distance);
+ }
+
+ void show_is_manifold() {
+ unsigned dim;
+ bool is_manifold;
+ Is_manifold<Complex> test_manifold(complex_, dim, is_manifold);
+
+ if (is_manifold) {
+ std::cout << "The complex is a " << dim << "-manifold\n";
+ } else {
+ if (dim < 4) {
+ std::cout << "The complex has dimension greater than " << dim << " and is not a manifold\n";
+ } else {
+ std::cout << "The complex has dimension>=4 and may or may not be a manifold\n";
+ }
+ }
+ }
+
+ private:
+ void run_chomp() {
+ save_complex_in_file_for_chomp();
+ std::cout << "Call CHOMP library\n";
+ int returnValue = system("utils/homsimpl chomp.sim");
+ std::cout << "CHOMP returns" << returnValue << std::endl;
+ }
+
+ void save_complex_in_file_for_chomp() {
+ std::ofstream file;
+ file.open("chomp.sim");
+ for (const auto &s : complex_.complex_simplex_range()) {
+ bool first = true;
+ file << "(";
+ for (auto x : s) {
+ if (first)
+ first = false;
+ else
+ file << ",";
+ file << x;
+ }
+ file << ")\n";
+ }
+ }
+
+ public:
+ unsigned num_vertices() const {
+ return complex_.num_vertices();
+ }
+
+ unsigned num_edges() const {
+ return complex_.num_edges();
+ }
+};
+
+#endif // MODEL_MODEL_H_
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