Added the forgotten strong witness complex

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/relaxed-witness@1640 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 19e4a60b7b6a71db6148bb99f11dbf10ff8cc248

1 files changed, 198 insertions, 0 deletions

diff --git a/src/Witness_complex/include/gudhi/Strong_witness_complex.h b/src/Witness_complex/include/gudhi/Strong_witness_complex.h
new file mode 100644
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+++ b/src/Witness_complex/include/gudhi/Strong_witness_complex.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):       Siargey Kachanovich
+ *
+ *    Copyright (C) 2015  INRIA Sophia Antipolis-Méditerranée (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 STRONG_WITNESS_COMPLEX_H_
+#define STRONG_WITNESS_COMPLEX_H_
+
+#include <boost/container/flat_map.hpp>
+#include <boost/iterator/transform_iterator.hpp>
+#include <algorithm>
+#include <utility>
+#include "gudhi/reader_utils.h"
+#include "gudhi/distance_functions.h"
+#include "gudhi/Simplex_tree.h"
+#include <vector>
+#include <list>
+#include <set>
+#include <queue>
+#include <limits>
+#include <math.h>
+#include <ctime>
+#include <iostream>
+
+// Needed for nearest neighbours
+#include <CGAL/Cartesian_d.h>
+#include <CGAL/Search_traits.h>
+#include <CGAL/Search_traits_adapter.h>
+#include <CGAL/property_map.h>
+#include <CGAL/Epick_d.h>
+#include <CGAL/Orthogonal_k_neighbor_search.h>
+
+#include <boost/tuple/tuple.hpp>
+#include <boost/iterator/zip_iterator.hpp>
+#include <boost/iterator/counting_iterator.hpp>
+#include <boost/range/iterator_range.hpp>
+
+// Needed for the adjacency graph in bad link search
+#include <boost/graph/graph_traits.hpp>
+#include <boost/graph/adjacency_list.hpp>
+#include <boost/graph/connected_components.hpp>
+
+namespace gss = Gudhi::spatial_searching;
+
+namespace Gudhi {
+  
+namespace witness_complex {
+
+// /*
+//  *  \private
+//     \class Witness_complex
+//     \brief Constructs the witness complex for the given set of witnesses and landmarks.
+//     \ingroup witness_complex
+//  */
+template< class Kernel_ >
+class Strong_witness_complex {
+private:
+  typedef Kernel_                                                 K;
+  typedef typename K::Point_d                                     Point_d;
+  typedef typename K::FT                                          FT;
+  typedef std::vector<Point_d>                                    Point_range;
+  typedef gss::Kd_tree_search<Kernel_, Point_range>               Kd_tree;
+  typedef typename Kd_tree::INS_range                             Nearest_landmark_range;
+  typedef typename std::vector<Nearest_landmark_range>            Nearest_landmark_table;
+  typedef typename Nearest_landmark_range::iterator               Nearest_landmark_row_iterator;
+  //typedef std::vector<std::pair<unsigned,FT>>                     Nearest_landmarks;
+  
+  // struct Active_witness {
+  //   int witness_id;
+  //   int landmark_id;
+
+  //   Active_witness(int witness_id_, int landmark_id_)
+  //       : witness_id(witness_id_),
+  //       landmark_id(landmark_id_) { }
+  // };
+  
+  typedef std::vector< double > Point_t;
+  typedef std::vector< Point_t > Point_Vector;
+
+  typedef FT Filtration_value;
+
+  
+  typedef std::ptrdiff_t Witness_id;
+  typedef std::ptrdiff_t Landmark_id;
+  typedef std::pair<Landmark_id, FT> Id_distance_pair;
+  typedef Active_witness<Id_distance_pair, Nearest_landmark_range> ActiveWitness;
+  typedef std::list< ActiveWitness > ActiveWitnessList;
+  typedef std::vector< Landmark_id > typeVectorVertex;
+  typedef std::pair< typeVectorVertex, Filtration_value> typeSimplex;
+
+ private:
+  Point_range                         witnesses_, landmarks_;
+  Kd_tree                             landmark_tree_;
+  
+ public:
+  /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
+  /* @name Constructor
+   */
+
+  //@{
+
+  // Witness_range<Closest_landmark_range<Vertex_handle>>
+
+  /*
+   *  \brief Iterative construction of the (weak) witness complex.
+   *  \details The witness complex is written in sc_ basing on a matrix knn of
+   *  nearest neighbours of the form {witnesses}x{landmarks}.
+   *
+   *  The type KNearestNeighbors can be seen as 
+   *  Witness_range<Closest_landmark_range<Vertex_handle>>, where
+   *  Witness_range and Closest_landmark_range are random access ranges.
+   *
+   *  Constructor takes into account at most (dim+1) 
+   *  first landmarks from each landmark range to construct simplices.
+   *
+   *  Landmarks are supposed to be in [0,nbL_-1]
+   */
+  template< typename InputIteratorLandmarks,
+            typename InputIteratorWitnesses >
+  Strong_witness_complex(InputIteratorLandmarks landmarks_first,
+                  InputIteratorLandmarks landmarks_last,
+                  InputIteratorWitnesses witnesses_first,
+                  InputIteratorWitnesses witnesses_last)
+    : witnesses_(witnesses_first, witnesses_last), landmarks_(landmarks_first, landmarks_last), landmark_tree_(landmarks_)
+  {    
+  }
+
+  /** \brief Returns the point corresponding to the given vertex.
+   */
+  Point_d get_point( std::size_t vertex ) const
+  {
+    return landmarks_[vertex];
+  }
+  
+  /** \brief Outputs the (weak) witness complex with 
+   *         squared relaxation parameter 'max_alpha_square'
+   *         to simplicial complex 'complex'.
+   */
+  template < typename SimplicialComplexForWitness >
+  bool create_complex(SimplicialComplexForWitness& complex,
+                      FT  max_alpha_square)       
+  {
+    unsigned nbL = landmarks_.size();
+    if (complex.num_vertices() > 0) {
+      std::cerr << "Witness complex cannot create complex - complex is not empty.\n";
+      return false;
+    }
+    if (max_alpha_square < 0) {
+      std::cerr << "Witness complex cannot create complex - squared relaxation parameter must be non-negative.\n";
+      return false;
+    }
+    typeVectorVertex vv;
+    //ActiveWitnessList active_witnesses;// = new ActiveWitnessList();
+    for (unsigned i = 0; i != nbL; ++i) {
+      // initial fill of 0-dimensional simplices
+      vv = {i};
+      complex.insert_simplex(vv, Filtration_value(0.0));
+      /* TODO Error if not inserted : normally no need here though*/
+    }
+    for (auto w: witnesses_) {
+      ActiveWitness aw(landmark_tree_.query_incremental_nearest_neighbors(w));
+      typeVectorVertex simplex;
+      typename ActiveWitness::iterator aw_it = aw.begin();
+      float lim_d2 = aw.begin()->second + max_alpha_square;
+      while (aw_it != aw.end() && aw_it->second < lim_d2) {
+        simplex.push_back(aw_it->first);
+        complex.insert_simplex_and_subfaces(simplex, aw_it->second - aw.begin()->second);
+        aw_it++;
+      }
+    }
+    return true;
+  }
+
+  //@}
+};
+
+}  // namespace witness_complex
+
+}  // namespace Gudhi
+
+#endif