Add tangential complex

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@1773 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: b47285aafaa430c883c8fe5432ac667d6cedaf37

1 files changed, 220 insertions, 0 deletions

diff --git a/src/cython/include/Tangential_complex_interface.h b/src/cython/include/Tangential_complex_interface.h
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+++ b/src/cython/include/Tangential_complex_interface.h
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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):       Vincent Rouvreau
+ *
+ *    Copyright (C) 2016 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 TANGENTIAL_COMPLEX_INTERFACE_H
+#define	TANGENTIAL_COMPLEX_INTERFACE_H
+
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Tangential_complex.h>
+#include <gudhi/Points_off_io.h>
+#include <CGAL/Epick_d.h>
+
+#include "Persistent_cohomology_interface.h"
+
+#include <vector>
+#include <utility>  // std::pair
+#include <iostream>
+
+namespace Gudhi {
+
+namespace tangential_complex {
+
+class Tangential_complex_interface {
+  using Dynamic_kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >;
+  using Point_d = Dynamic_kernel::Point_d;
+  typedef typename Simplex_tree<>::Simplex_handle Simplex_handle;
+  typedef typename std::pair<Simplex_handle, bool> Insertion_result;
+  using Simplex = std::vector<Vertex_handle>;
+  using Filtered_complex = std::pair<Simplex, Filtration_value>;
+  using Complex_tree = std::vector<Filtered_complex>;
+  using TC = Tangential_complex<Dynamic_kernel, CGAL::Dynamic_dimension_tag, CGAL::Parallel_tag>;
+
+ public:
+  Tangential_complex_interface(std::vector<std::vector<double>>&points, double max_alpha_square)
+  : pcoh_(nullptr) {
+    Dynamic_kernel k;
+    unsigned intrisic_dim = 0;
+    if (points.size() > 0)
+      intrisic_dim = points[0].size();
+    
+    tangential_complex_ = new TC(points, intrisic_dim, k);
+    tangential_complex_->create_complex(simplex_tree_, max_alpha_square);
+    simplex_tree_.initialize_filtration();
+  }
+
+  Tangential_complex_interface(std::string off_file_name, double max_alpha_square, bool from_file = true)
+  : pcoh_(nullptr) {
+    Gudhi::Points_off_reader<Point_d> off_reader(off_file_name);
+    Dynamic_kernel k;
+    unsigned intrisic_dim = 0;
+    std::vector<Point_d> points = off_reader.get_point_cloud();
+    if (points.size() > 0)
+      intrisic_dim = points[0].size();
+
+    tangential_complex_ = new TC(points, intrisic_dim, k);
+    tangential_complex_->create_complex(simplex_tree_, max_alpha_square);
+    simplex_tree_.initialize_filtration();
+  }
+
+  bool find_simplex(const Simplex& vh) {
+    return (simplex_tree_.find(vh) != simplex_tree_.null_simplex());
+  }
+
+  bool insert_simplex_and_subfaces(const Simplex& complex, Filtration_value filtration = 0) {
+    Insertion_result result = simplex_tree_.insert_simplex_and_subfaces(complex, filtration);
+    return (result.second);
+  }
+
+  Filtration_value simplex_filtration(const Simplex& complex) {
+    return simplex_tree_.filtration(simplex_tree_.find(complex));
+  }
+
+  void remove_maximal_simplex(const Simplex& complex) {
+    return simplex_tree_.remove_maximal_simplex(simplex_tree_.find(complex));
+  }
+
+  Complex_tree get_filtered_tree() {
+    Complex_tree filtered_tree;
+    for (auto f_simplex : simplex_tree_.filtration_simplex_range()) {
+      Simplex simplex;
+      for (auto vertex : simplex_tree_.simplex_vertex_range(f_simplex)) {
+        simplex.insert(simplex.begin(), vertex);
+      }
+      filtered_tree.push_back(std::make_pair(simplex, simplex_tree_.filtration(f_simplex)));
+    }
+    return filtered_tree;
+
+  }
+
+  Complex_tree get_skeleton_tree(int dimension) {
+    Complex_tree skeleton_tree;
+    for (auto f_simplex : simplex_tree_.skeleton_simplex_range(dimension)) {
+      Simplex simplex;
+      for (auto vertex : simplex_tree_.simplex_vertex_range(f_simplex)) {
+        simplex.insert(simplex.begin(), vertex);
+      }
+      skeleton_tree.push_back(std::make_pair(simplex, simplex_tree_.filtration(f_simplex)));
+    }
+    return skeleton_tree;
+  }
+
+  Complex_tree get_star_tree(const Simplex& complex) {
+    Complex_tree star_tree;
+    for (auto f_simplex : simplex_tree_.star_simplex_range(simplex_tree_.find(complex))) {
+      Simplex simplex;
+      for (auto vertex : simplex_tree_.simplex_vertex_range(f_simplex)) {
+        simplex.insert(simplex.begin(), vertex);
+      }
+      star_tree.push_back(std::make_pair(simplex, simplex_tree_.filtration(f_simplex)));
+    }
+    return star_tree;
+  }
+
+  Complex_tree get_coface_tree(const Simplex& complex, int dimension) {
+    Complex_tree coface_tree;
+    for (auto f_simplex : simplex_tree_.cofaces_simplex_range(simplex_tree_.find(complex), dimension)) {
+      Simplex simplex;
+      for (auto vertex : simplex_tree_.simplex_vertex_range(f_simplex)) {
+        simplex.insert(simplex.begin(), vertex);
+      }
+      coface_tree.push_back(std::make_pair(simplex, simplex_tree_.filtration(f_simplex)));
+    }
+    return coface_tree;
+  }
+
+  // Specific to Witness complex because no inheritance
+  Filtration_value filtration() const {
+    return simplex_tree_.filtration();
+  }
+
+  void set_filtration(Filtration_value fil) {
+    simplex_tree_.set_filtration(fil);
+  }
+
+  void initialize_filtration() {
+    simplex_tree_.initialize_filtration();
+  }
+
+  size_t num_vertices() const {
+    return simplex_tree_.num_vertices();
+  }
+
+  size_t num_simplices() {
+    return simplex_tree_.num_simplices();
+  }
+
+  int dimension() const {
+    return simplex_tree_.dimension();
+  }
+
+  void set_dimension(int dimension) {
+    simplex_tree_.set_dimension(dimension);
+  }
+
+  std::vector<double> get_point(int vh) {
+    std::vector<double> vd;
+    try {
+      Point_d ph = tangential_complex_->get_point(vh);
+      for (auto coord = ph.cartesian_begin(); coord < ph.cartesian_end(); coord++)
+        vd.push_back(*coord);
+    } catch (std::out_of_range outofrange) {
+      // std::out_of_range is thrown in case not found. Other exceptions must be re-thrown
+    }
+    return vd;
+  }
+
+  std::vector<std::pair<int, std::pair<double, double>>> get_persistence(int homology_coeff_field, double min_persistence) {
+    if (pcoh_ != nullptr) {
+      delete pcoh_;
+    }
+    pcoh_ = new Persistent_cohomology_interface<Simplex_tree<>>(&simplex_tree_);
+    return pcoh_->get_persistence(homology_coeff_field, min_persistence);
+  }
+  
+  std::vector<int> get_betti_numbers() const {
+    if (pcoh_ != nullptr) {
+      return pcoh_->betti_numbers();
+    }
+    std::vector<int> betti_numbers;
+    return betti_numbers;
+  }
+
+  std::vector<int> get_persistent_betti_numbers(Filtration_value from, Filtration_value to) const {
+    if (pcoh_ != nullptr) {
+      return pcoh_->persistent_betti_numbers(from, to);
+    }
+    std::vector<int> persistent_betti_numbers;
+    return persistent_betti_numbers;
+  }
+  
+ private:
+  Simplex_tree<> simplex_tree_;
+  Persistent_cohomology_interface<Simplex_tree<>>* pcoh_;
+  TC* tangential_complex_;
+};
+
+}  // namespace tangential_complex
+
+} // namespace Gudhi
+
+#endif  // TANGENTIAL_COMPLEX_INTERFACE_H
+