1 files changed, 0 insertions, 355 deletions
diff --git a/GudhUI/model/Model.h b/GudhUI/model/Model.h
deleted file mode 100644
index 1d5cc087..00000000
--- a/GudhUI/model/Model.h
+++ /dev/null
@@ -1,355 +0,0 @@
-/* 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
- *
- *    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 (std::size_t i = 0; i < vertices.size(); ++i)
-        for (std::size_t j = i + 1; j < vertices.size(); ++j)
-          complex_.add_edge_without_blockers(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) {
-    Gudhi::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;
-    Gudhi::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
-    Gudhi::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_