Added perturbation witness complex construction

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/witness@590 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 5c478d127e0fefa8696be5ca72ab89efa2e2dfc6

2 files changed, 404 insertions, 2 deletions

diff --git a/src/Witness_complex/example/CMakeLists.txt b/src/Witness_complex/example/CMakeLists.txt
index 315ffc36..a3e7b3f5 100644
--- a/src/Witness_complex/example/CMakeLists.txt
+++ b/src/Witness_complex/example/CMakeLists.txt
@@ -56,12 +56,37 @@ if(CGAL_FOUND)
       add_executable ( witness_complex_knn_landmarks witness_complex_knn_landmarks.cpp )
       target_link_libraries(witness_complex_knn_landmarks ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
       add_test(witness_complex_knn_landmarks ${CMAKE_CURRENT_BINARY_DIR}/witness_complex_knn_landmarks ${CMAKE_SOURCE_DIR}/data/points/bunny_5000 100)
-
+      #add_executable ( witness_complex_perturbations witness_complex_perturbations.cpp )
+      #target_link_libraries(witness_complex_perturbations ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+      #add_test(witness_complex_perturbations ${CMAKE_CURRENT_BINARY_DIR}/witness_complex_perturbations ${CMAKE_SOURCE_DIR}/data/points/bunny_5000 100)
     else()
-      message(WARNING "Eigen3 not found. Version 3.1.0 is required for Alpha shapes feature.")
+      message(WARNING "Eigen3 not found. Version 3.1.0 is required for Alpha shapes feature.")      
     endif()
   else()
     message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile Alpha shapes feature. Version 4.6.0 is required.")
   endif ()
 endif()
+if(CGAL_FOUND)
+  if (NOT CGAL_VERSION VERSION_LESS 4.6.0)
+    message(STATUS "CGAL version: ${CGAL_VERSION}.")
 
+    include( ${CGAL_USE_FILE} )
+
+    find_package(Eigen3 3.1.0)
+    if (EIGEN3_FOUND)
+      message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.")
+      include( ${EIGEN3_USE_FILE} )
+      include_directories (BEFORE "../../include")
+      add_executable ( witness_complex_perturbations witness_complex_perturbations.cpp )
+      target_link_libraries(witness_complex_perturbations ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+      add_test(witness_complex_perturbations ${CMAKE_CURRENT_BINARY_DIR}/witness_complex_perturbations ${CMAKE_SOURCE_DIR}/data/points/bunny_5000 100)
+      add_executable ( range_queries range_queries.cpp )
+      target_link_libraries(range_queries ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+      add_test(range_queries ${CMAKE_CURRENT_BINARY_DIR}/range_queries ${CMAKE_SOURCE_DIR}/data/points/bunny_5000 100)
+    else()
+      message(WARNING "Eigen3 not found. Version 3.1.0 is required for Alpha shapes feature.")      
+    endif()
+  else()
+    message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile Alpha shapes feature. Version 4.6.0 is required.")
+  endif ()
+endif()
diff --git a/src/Witness_complex/example/witness_complex_perturbations.cpp b/src/Witness_complex/example/witness_complex_perturbations.cpp
new file mode 100644
index 00000000..afb42807
--- /dev/null
+++ b/src/Witness_complex/example/witness_complex_perturbations.cpp
@@ -0,0 +1,377 @@
+/*    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 <set>
+#include <iterator>
+
+#include <sys/types.h>
+#include <sys/stat.h>
+//#include <stdlib.h>
+
+//#include "gudhi/graph_simplicial_complex.h"
+#include "gudhi/Witness_complex.h"
+#include "gudhi/reader_utils.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_k_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/Origin.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 std::vector< Vertex_handle > typeVectorVertex;
+
+//typedef std::pair<typeVectorVertex, Filtration_value> typeSimplex;
+//typedef std::pair< Simplex_tree<>::Simplex_handle, bool > typePairSimplexBool;
+
+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::Search_traits_adapter<
+  std::ptrdiff_t, Point_d*, Traits_base> STraits;
+//typedef K TreeTraits;
+typedef CGAL::Orthogonal_k_neighbor_search<STraits> K_neighbor_search;
+typedef K_neighbor_search::Tree Tree;
+typedef K_neighbor_search::Distance Distance;
+typedef K_neighbor_search::iterator KNS_iterator;
+typedef K_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 CGAL::Euclidean_distance<Traits_base> Euclidean_distance;
+//typedef K::Equal_d Equal_d;
+typedef CGAL::Random_points_in_ball_d<Point_d> Random_point_iterator;
+/**
+ * \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 read_points_to_tree (std::string file_name, Tree& tree)
+{
+  //I assume here that tree is empty
+  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> coords;
+      std::istringstream iss( line );
+      while(iss >> x) { coords.push_back(x); }
+      if (coords.size() != 1)
+        {
+          Point_d point(coords.begin(), coords.end());
+          tree.insert(point);
+        }
+    }
+  in_file.close();
+}
+*/
+
+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();
+}
+
+
+
+/** 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;
+  srand(24660);
+  for (int i = 0; i < nbL; i++)
+    {
+      //      while (!res.second)
+      //  {
+      chosen_landmark = rand()%nbP;
+      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;
+    }
+ }
+
+
+int landmark_perturbation(Point_Vector &W, Point_Vector& landmarks, std::vector<int>& landmarks_ind)
+{
+  //******************** Constructing a WL matrix
+  int nbP = W.size();
+  int nbL = landmarks.size();
+  //Point_Vector landmarks_ = landmarks;
+  Euclidean_distance ed;
+  //Equal_d ed;
+  FT lambda = ed.transformed_distance(landmarks[0],landmarks[1]);
+    //FT lambda = 0.1;//Euclidean_distance();
+  std::vector< std::vector <int> > WL(nbP);
+  Tree L(boost::counting_iterator<std::ptrdiff_t>(0),
+         boost::counting_iterator<std::ptrdiff_t>(nbL),
+         typename Tree::Splitter(),
+         STraits(&(landmarks[0])));
+  /*Tree2 L2(boost::counting_iterator<std::ptrdiff_t>(0),
+           boost::counting_iterator<std::ptrdiff_t>(nbL),
+           typename Tree::Splitter(),
+           STraits(&(landmarks[0])));
+  */
+  std::cout << "Enter (D+1) nearest landmarks\n";
+  //std::cout << "Size of the tree is " << L.size() << std::endl;
+  int D = W[0].size();
+  for (int i = 0; i < nbP; i++)
+    {
+      //std::cout << "Entered witness number " << i << std::endl;
+      Point_d& w = W[i];
+      //std::cout << "Safely constructed a point\n";
+      ////Search D+1 nearest neighbours from the tree of landmarks L 
+      K_neighbor_search search(L, w, D+1, FT(0), true,
+                               CGAL::Distance_adapter<std::ptrdiff_t,Point_d*,CGAL::Euclidean_distance<Traits_base>>(&(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; 
+        }
+      if (i == landmarks_ind[WL[i][0]])
+        {
+          //std::cout << "'";
+          FT dist = ed.transformed_distance(W[i], landmarks[WL[i][1]]);
+          if (dist < lambda)
+            lambda = dist;
+        }
+    }
+  //std::cout << "\n";
+  /*
+  std::string out_file = "wl_result";
+  write_wl(out_file,WL);
+  */
+  //******************** Constructng a witness complex
+  std::cout << "Entered witness complex construction\n";
+  Witness_complex<> witnessComplex;
+  witnessComplex.setNbL(nbL);
+  witnessComplex.witness_complex(WL);
+  //******************** Making a set of bad link landmarks
+  std::cout << "Entered bad links\n";
+  std::set< int > perturbL;
+  int count_badlinks = 0;
+  std::cout << "Bad links around ";
+  for (auto u: witnessComplex.complex_vertex_range())
+    if (!witnessComplex.has_good_link(u))
+      {
+        //std::cout << "Landmark " << u << " start!" << std::endl;
+        //perturbL.insert(u);
+        count_badlinks++;
+        std::cout << u << " ";
+        Point_d& l = landmarks[u];
+        Fuzzy_sphere fs(l, sqrt(lambda)*2, 0, STraits(&(landmarks[0])));
+        L.search(std::insert_iterator<std::set<int>>(perturbL,perturbL.begin()),fs);
+        //L.search(std::inserter(perturbL,perturbL.begin()),fs);
+        //L.search(std::ostream_iterator<int>(std::cout,"\n"),fs);
+        //std::cout << "PerturbL size is " << perturbL.size() << std::endl;
+      }
+  std::cout << "\nBad links total: " << count_badlinks << " Points to perturb: " << perturbL.size() << std::endl;
+  //std::cout << "landmark[0][0] before" << landmarks[0][0] << std::endl;
+  //*********************** Perturb bad link landmarks
+  
+  for (auto u: perturbL)
+    {
+      Random_point_iterator rp(D,sqrt(lambda)/2);
+      //std::cout << landmarks[u] << std::endl;
+      
+      std::vector<FT> point;
+      for (int i = 0; i < D; i++)
+        {
+          point.push_back(W[landmarks_ind[u]][i] + (*rp)[i]);
+        }
+      landmarks[u] = Point_d(point);
+      //std::cout << landmarks[u] << std::endl;
+    }
+  
+  //std::cout << "landmark[0][0] after" << landmarks[0][0] << std::endl;
+  std::cout << "lambda=" << lambda << std::endl;
+  // Write the WL matrix in a file
+  /*
+  mkdir("output", S_IRWXU);
+  const size_t last_slash_idx = file_name.find_last_of("/");
+  if (std::string::npos != last_slash_idx)
+    {
+      file_name.erase(0, last_slash_idx + 1);
+    }
+  
+  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();
+    }
+  */
+  return count_badlinks;
+}
+
+
+int main (int argc, char * const argv[])
+{
+  if (argc != 3)
+    {
+      std::cerr << "Usage: " << argv[0]
+                << " path_to_point_file nbL \n";
+      return 0;
+    }
+  /*
+  boost::filesystem::path p;
+
+  for (; argc > 2; --argc, ++argv)
+    p /= argv[1];
+  */
+  std::string file_name   = argv[1];
+  int nbL       = atoi(argv[2]);
+  
+  //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);
+  //std::cout << "Successfully read the points\n";
+  //witnessComplex.setNbL(nbL);
+  //  witnessComplex.witness_complex_from_points(point_vector);
+  int nbP = point_vector.size();
+  //std::vector<std::vector< int > > WL(nbP);
+  //std::set<int> L;
+  Point_Vector L;
+  std::vector<int> chosen_landmarks;
+  //Point_etiquette_map L_i;
+  //start = clock();
+  //witnessComplex.landmark_choice_by_furthest_points(point_vector, point_vector.size(), WL);
+  landmark_choice(point_vector, nbP, nbL, L, chosen_landmarks);
+  int bl = 1;
+  for (int i = 0; bl != 0; i++)
+    {
+      std::cout << "========== Start iteration " << i << " ========\n";
+      bl = landmark_perturbation(point_vector, L, chosen_landmarks);
+    }
+  //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();
+  */
+}