Removed relaxed_witness_complex_sphere from repository

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/witness@971 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 886ea9c52839e6cb21872da5097a55037b027ca7

1 files changed, 0 insertions, 461 deletions

diff --git a/src/Witness_complex/example/relaxed_witness_complex_sphere.cpp b/src/Witness_complex/example/relaxed_witness_complex_sphere.cpp
deleted file mode 100644
index 067321ce..00000000
--- a/src/Witness_complex/example/relaxed_witness_complex_sphere.cpp
+++ /dev/null
@@ -1,461 +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):       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/>.
- */
-
-#include <iostream>
-#include <fstream>
-#include <ctime>
-#include <utility>
-#include <algorithm>
-#include <set>
-#include <queue>
-#include <iterator>
-
-#include <sys/types.h>
-#include <sys/stat.h>
-//#include <stdlib.h>
-
-//#include "gudhi/graph_simplicial_complex.h"
-#include "gudhi/Relaxed_witness_complex.h"
-#include "gudhi/reader_utils.h"
-#include "gudhi/Collapse/Collapse.h"
-//#include <boost/filesystem.hpp> 
-
-//#include <CGAL/Delaunay_triangulation.h>
-#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_incremental_neighbor_search.h>
-#include <CGAL/Kd_tree.h>
-#include <CGAL/Euclidean_distance.h>
-
-#include <CGAL/Kernel_d/Vector_d.h>
-#include <CGAL/point_generators_d.h>
-#include <CGAL/constructions_d.h>
-#include <CGAL/Fuzzy_sphere.h>
-#include <CGAL/Random.h>
-
-
-#include <boost/tuple/tuple.hpp>
-#include <boost/iterator/zip_iterator.hpp>
-#include <boost/iterator/counting_iterator.hpp>
-#include <boost/range/iterator_range.hpp>
-
-using namespace Gudhi;
-//using namespace boost::filesystem;
-
-typedef CGAL::Epick_d<CGAL::Dynamic_dimension_tag> K;
-typedef K::FT FT;
-typedef K::Point_d Point_d;
-typedef CGAL::Search_traits<
-  FT, Point_d,
-  typename K::Cartesian_const_iterator_d,
-  typename K::Construct_cartesian_const_iterator_d> Traits_base;
-typedef CGAL::Euclidean_distance<Traits_base> Euclidean_distance;
-
-typedef std::vector< Vertex_handle > typeVectorVertex;
-
-//typedef std::pair<typeVectorVertex, Filtration_value> typeSimplex;
-//typedef std::pair< Simplex_tree<>::Simplex_handle, bool > typePairSimplexBool;
-
-typedef CGAL::Search_traits_adapter<
-  std::ptrdiff_t, Point_d*, Traits_base> STraits;
-//typedef K TreeTraits;
-//typedef CGAL::Distance_adapter<std::ptrdiff_t,Point_d*,Euclidean_distance > Euclidean_adapter;
-//typedef CGAL::Kd_tree<STraits> Kd_tree;
-typedef CGAL::Orthogonal_incremental_neighbor_search<STraits, CGAL::Distance_adapter<std::ptrdiff_t,Point_d*,Euclidean_distance>> Neighbor_search;
-typedef Neighbor_search::Tree Tree;
-typedef Neighbor_search::Distance Distance;
-typedef Neighbor_search::iterator KNS_iterator;
-typedef Neighbor_search::iterator KNS_range;
-typedef boost::container::flat_map<int, int> Point_etiquette_map;
-typedef CGAL::Kd_tree<STraits> Tree2;
-
-typedef CGAL::Fuzzy_sphere<STraits> Fuzzy_sphere;
-
-typedef std::vector<Point_d> Point_Vector;
-
-//typedef K::Equal_d Equal_d;
-typedef CGAL::Random_points_in_cube_d<Point_d> Random_cube_iterator;
-typedef CGAL::Random_points_in_ball_d<Point_d> Random_point_iterator;
-
-bool toric=false;
-
-/**
- * \brief Customized version of read_points
- * which takes into account a possible nbP first line
- *
- */
-inline void
-read_points_cust ( std::string file_name , Point_Vector & points)
-{  
-  std::ifstream in_file (file_name.c_str(),std::ios::in);
-  if(!in_file.is_open())
-    {
-      std::cerr << "Unable to open file " << file_name << std::endl;
-      return;
-    }
-  std::string line;
-  double x;
-  while( getline ( in_file , line ) )
-    {
-      std::vector< double > point;
-      std::istringstream iss( line );
-      while(iss >> x) { point.push_back(x); }
-      Point_d p(point.begin(), point.end());
-      if (point.size() != 1)
-        points.push_back(p);
-    }
-  in_file.close();
-}
-
-
-void generate_points_sphere(Point_Vector& W, int nbP, int dim)
-{
-  CGAL::Random_points_on_sphere_d<Point_d> rp(dim,1);
-  for (int i = 0; i < nbP; i++)
-    W.push_back(*rp++);
-}
-
-
-void write_wl( std::string file_name, std::vector< std::vector <int> > & WL)
-{
-  std::ofstream ofs (file_name, std::ofstream::out);
-  for (auto w : WL)
-    {
-      for (auto l: w)
-        ofs << l << " ";
-      ofs << "\n";
-    }
-  ofs.close();
-}
-
-void write_rl( std::string file_name, std::vector< std::vector <std::vector<int>::iterator> > & rl)
-{
-  std::ofstream ofs (file_name, std::ofstream::out);
-  for (auto w : rl)
-    {
-      for (auto l: w)
-        ofs << *l << " ";
-      ofs << "\n";
-    }
-  ofs.close();
-}
-
-std::vector<Point_d> convert_to_torus(std::vector< Point_d>& points)
-{
-  std::vector< Point_d > points_torus;
-  for (auto p: points)
-    {
-      FT theta = M_PI*p[0];
-      FT phi = M_PI*p[1];
-      std::vector<FT> p_torus;
-      p_torus.push_back((1+0.2*cos(theta))*cos(phi));
-      p_torus.push_back((1+0.2*cos(theta))*sin(phi));
-      p_torus.push_back(0.2*sin(theta));
-      points_torus.push_back(Point_d(p_torus));
-    }
-  return points_torus;
-}
-
-
-void write_points_torus( std::string file_name, std::vector< Point_d > & points)
-{
-  std::ofstream ofs (file_name, std::ofstream::out);
-  std::vector<Point_d> points_torus = convert_to_torus(points);
-  for (auto w : points_torus)
-    {
-      for (auto it = w.cartesian_begin(); it != w.cartesian_end(); ++it)
-        ofs << *it << " ";
-      ofs << "\n";
-    }
-  ofs.close();
-}
-
-
-void write_points( std::string file_name, std::vector< Point_d > & points)
-{
-  if (toric) write_points_torus(file_name, points);
-  else
-    {
-      std::ofstream ofs (file_name, std::ofstream::out);
-      for (auto w : points)
-        {
-          for (auto it = w.cartesian_begin(); it != w.cartesian_end(); ++it)
-            ofs << *it << " ";
-          ofs << "\n";
-        }
-      ofs.close();
-    }
-}
-
-
-void write_edges_torus(std::string file_name, Witness_complex<>& witness_complex, Point_Vector& landmarks)
-{
-  std::ofstream ofs (file_name, std::ofstream::out);
-  Point_Vector l_torus = convert_to_torus(landmarks);
-  for (auto u: witness_complex.complex_vertex_range())
-    for (auto v: witness_complex.complex_vertex_range())
-      {
-        typeVectorVertex edge = {u,v};
-        if (u < v && witness_complex.find(edge) != witness_complex.null_simplex())   
-          {
-            for (auto it = l_torus[u].cartesian_begin(); it != l_torus[u].cartesian_end(); ++it)
-              ofs << *it << " ";
-            ofs << "\n";
-            for (auto it = l_torus[v].cartesian_begin(); it != l_torus[v].cartesian_end(); ++it)
-              ofs << *it << " ";
-            ofs << "\n\n\n";
-          }
-    }
-  ofs.close();
-}
-
-void write_edges(std::string file_name, Witness_complex<>& witness_complex, Point_Vector& landmarks)
-{
-  std::ofstream ofs (file_name, std::ofstream::out);
-  if (toric) write_edges_torus(file_name, witness_complex, landmarks);
-  else
-    {
-      for (auto u: witness_complex.complex_vertex_range())
-        for (auto v: witness_complex.complex_vertex_range())
-          {
-            typeVectorVertex edge = {u,v};
-            if (u < v && witness_complex.find(edge) != witness_complex.null_simplex())   
-              {
-                for (auto it = landmarks[u].cartesian_begin(); it != landmarks[u].cartesian_end(); ++it)
-                  ofs << *it << " ";
-                ofs << "\n";
-                for (auto it = landmarks[v].cartesian_begin(); it != landmarks[v].cartesian_end(); ++it)
-                  ofs << *it << " ";
-                ofs << "\n\n\n";
-              }
-          }
-      ofs.close();
-    }
-}
-
-
-/** Function that chooses landmarks from W and place it in the kd-tree L.
- *  Note: nbL hould be removed if the code moves to Witness_complex
- */
-void landmark_choice(Point_Vector &W, int nbP, int nbL, Point_Vector& landmarks, std::vector<int>& landmarks_ind)
-{
-  std::cout << "Enter landmark choice to kd tree\n";
-  //std::vector<Point_d> landmarks;
-  int chosen_landmark;
-  //std::pair<Point_etiquette_map::iterator,bool> res = std::make_pair(L_i.begin(),false);
-  Point_d* p;
-  CGAL::Random rand;
-  for (int i = 0; i < nbL; i++)
-    {
-      //      while (!res.second)
-      //  {
-      do chosen_landmark = rand.get_int(0,nbP);
-      while (std::find(landmarks_ind.begin(), landmarks_ind.end(), chosen_landmark) != landmarks_ind.end());
-      //rand++;
-      //std::cout << "Chose " << chosen_landmark << std::endl;
-      p = &W[chosen_landmark];
-      //L_i.emplace(chosen_landmark,i);
-      //  }
-      landmarks.push_back(*p);
-      landmarks_ind.push_back(chosen_landmark);
-      //std::cout << "Added landmark " << chosen_landmark << std::endl;
-    }
- }
-
-
-void landmarks_to_witness_complex(Point_Vector &W, Point_Vector& landmarks, std::vector<int>& landmarks_ind, FT alpha)
-{
-  //********************Preface: origin point
-  unsigned D = W[0].size();
-  std::vector<FT> orig_vector;
-  for (unsigned i = 0; i < D; i++)
-    orig_vector.push_back(0);
-  Point_d origin(orig_vector);
-  //Distance dist;
-  //dist.transformed_distance(0,1);
-  //******************** Constructing a WL matrix
-  int nbP = W.size();
-  int nbL = landmarks.size();
-  STraits traits(&(landmarks[0]));
-  Euclidean_distance ed;
-  std::vector< std::vector <int> > WL(nbP);
-  std::vector< std::vector< typename std::vector<int>::iterator > > ope_limits(nbP);
-  Tree L(boost::counting_iterator<std::ptrdiff_t>(0),
-         boost::counting_iterator<std::ptrdiff_t>(nbL),
-         typename Tree::Splitter(),
-         traits);
-
-  std::cout << "Enter (D+1) nearest landmarks\n";
-  //std::cout << "Size of the tree is " << L.size() << std::endl;
-  for (int i = 0; i < nbP; i++)
-    {
-      //std::cout << "Entered witness number " << i << std::endl;
-      Point_d& w = W[i];
-      std::queue< typename std::vector<int>::iterator > ope_queue; // queue of points at (1+epsilon) distance to current landmark
-      Neighbor_search search(L, w, FT(0), true, CGAL::Distance_adapter<std::ptrdiff_t,Point_d*,Euclidean_distance>(&(landmarks[0])));
-      Neighbor_search::iterator search_it = search.begin();
-      
-      //Incremental search and filling WL
-      while (WL[i].size() < D)
-        WL[i].push_back((search_it++)->first);
-      FT dtow = ed.transformed_distance(w, landmarks[WL[i][D-1]]);
-      while (search_it->second < dtow + alpha)
-        WL[i].push_back((search_it++)->first);
-
-      //Filling the (1+epsilon)-limits table
-      for (std::vector<int>::iterator wl_it = WL[i].begin(); wl_it != WL[i].end(); ++wl_it)
-        {
-          ope_queue.push(wl_it);
-          FT d_to_curr_l = ed.transformed_distance(w, landmarks[*wl_it]);
-          //std::cout << "d_to_curr_l=" << d_to_curr_l << std::endl;
-          //std::cout << "d_to_front+alpha=" << d_to_curr_l << std::endl;
-          while (d_to_curr_l > alpha + ed.transformed_distance(w, landmarks[*(ope_queue.front())]))
-            {
-              ope_limits[i].push_back(wl_it);
-              ope_queue.pop();
-            }
-        }
-      while (ope_queue.size() > 0)
-        {
-          ope_limits[i].push_back(WL[i].end());
-          ope_queue.pop();
-        }
-      //std::cout << "Safely constructed a point\n";
-      ////Search D+1 nearest neighbours from the tree of landmarks L
-      /*
-      if (w[0]>0.95)
-        std::cout << i << std::endl;
-      */
-      //K_neighbor_search search(L, w, D, FT(0), true,
-      //                         CGAL::Distance_adapter<std::ptrdiff_t,Point_d*,Euclidean_distance>(&(landmarks[0])) );
-      //std::cout << "Safely found nearest landmarks\n";
-      /* 
-      for(K_neighbor_search::iterator it = search.begin(); it != search.end(); ++it)
-        {
-          //std::cout << "Entered KNN_it with point at distance " << it->second << "\n";
-          //Point_etiquette_map::iterator itm = L_i.find(it->first);
-          //assert(itm != L_i.end());
-          //std::cout << "Entered KNN_it with point at distance " << it->second << "\n";
-          WL[i].push_back(it->first);
-          //std::cout << "ITFIRST " << it->first << std::endl;
-          //std::cout << i << " " << it->first << ": " << it->second << std::endl; 
-        }
-      */
-    }
-  //std::cout << "\n";
-  
-  //std::string out_file = "wl_result";
-  write_wl("wl_result",WL);
-  write_rl("rl_result",ope_limits);
-  
-  //******************** Constructng a witness complex
-  std::cout << "Entered witness complex construction\n";
-  Witness_complex<> witnessComplex;
-  witnessComplex.setNbL(nbL);
-  witnessComplex.relaxed_witness_complex(WL, ope_limits);
-  char buffer[100];
-  int i = sprintf(buffer,"stree_result.txt");
-  
-  if (i >= 0)
-    {
-      std::string out_file = (std::string)buffer;
-      std::ofstream ofs (out_file, std::ofstream::out);
-      witnessComplex.st_to_file(ofs);
-      ofs.close();
-    }
-  write_edges("landmarks/edges", witnessComplex, landmarks);
-  std::cout << Distance().transformed_distance(Point_d(std::vector<double>({0.1,0.1})), Point_d(std::vector<double>({1.9,1.9}))) << std::endl;
-}
-
-
-int main (int argc, char * const argv[])
-{
-  
-  if (argc != 5)
-    {
-      std::cerr << "Usage: " << argv[0]
-                << " nbP nbL dim alpha\n";
-      return 0;
-    }
-  /*
-  boost::filesystem::path p;
-  for (; argc > 2; --argc, ++argv)
-    p /= argv[1];
-  */
-  
-  int nbP       = atoi(argv[1]);
-  int nbL       = atoi(argv[2]);
-  int dim       = atoi(argv[3]);
-  double alpha  = atof(argv[4]);
-  //clock_t start, end;
-  //Construct the Simplex Tree
-  Witness_complex<> witnessComplex;
- 
-  std::cout << "Let the carnage begin!\n";
-  Point_Vector point_vector;
-  //read_points_cust(file_name, point_vector);
-  generate_points_sphere(point_vector, nbP, dim);
-  /*
-  for (auto &p: point_vector)
-    {
-      assert(std::count(point_vector.begin(),point_vector.end(),p) == 1);
-    }
-  */
-  //std::cout << "Successfully read the points\n";
-  //witnessComplex.setNbL(nbL);
-  Point_Vector L;
-  std::vector<int> chosen_landmarks;
-  landmark_choice(point_vector, nbP, nbL, L, chosen_landmarks);
-  //start = clock();
-  
-  write_points("landmarks/initial_pointset",point_vector);
-  write_points("landmarks/initial_landmarks",L);
-  
-  landmarks_to_witness_complex(point_vector, L, chosen_landmarks, alpha);
-  //end = clock();
-  
-  /*
-  std::cout << "Landmark choice took "
-            << (double)(end-start)/CLOCKS_PER_SEC << " s. \n";
-  start = clock();
-  witnessComplex.witness_complex(WL);
-  //
-  end = clock();
-  std::cout << "Howdy world! The process took "
-       << (double)(end-start)/CLOCKS_PER_SEC << " s. \n";
-  */
-  
-  /*
-  out_file = "output/"+file_name+"_"+argv[2]+".stree";
-  std::ofstream ofs (out_file, std::ofstream::out);
-  witnessComplex.st_to_file(ofs);
-  ofs.close();
-
-  out_file = "output/"+file_name+"_"+argv[2]+".badlinks";
-  std::ofstream ofs2(out_file, std::ofstream::out);
-  witnessComplex.write_bad_links(ofs2);
-  ofs2.close();
-  */
-}