Added everything missing

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/relaxed-witness@1265 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: c148ce9136bb0786acc1c9ae49827cb3958326c6

1 files changed, 461 insertions, 0 deletions

diff --git a/src/Witness_complex/example/relaxed_witness_complex_sphere.cpp b/src/Witness_complex/example/relaxed_witness_complex_sphere.cpp
new file mode 100644
index 00000000..067321ce
--- /dev/null
+++ b/src/Witness_complex/example/relaxed_witness_complex_sphere.cpp
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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/>.
+ */
+
+#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();
+  */
+}