Corrected errors in witness_complex_cube

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/witness@680 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: e0a33544c992889344cdaaed947479a5bc458ce3

4 files changed, 44 insertions, 48 deletions

diff --git a/src/Witness_complex/example/witness_complex_cube.cpp b/src/Witness_complex/example/witness_complex_cube.cpp
index 7545f156..b6051a5f 100644
--- a/src/Witness_complex/example/witness_complex_cube.cpp
+++ b/src/Witness_complex/example/witness_complex_cube.cpp
@@ -291,8 +291,8 @@ bool triangulation_is_protected(Delaunay_triangulation& t, FT delta)
 
 void fill_landmarks(Point_Vector& W, Point_Vector& landmarks, std::vector<int>& landmarks_ind)
 {
-  for (int j = 0; j < landmarks_ind.size(); ++j)
-    landmarks.push_back(W[landmarks_ind[j]][l]);
+  for (unsigned j = 0; j < landmarks_ind.size(); ++j)
+    landmarks.push_back(W[landmarks_ind[j]]);
 }
 
 void landmark_choice_by_delaunay(Point_Vector& W, int nbP, int nbL, Point_Vector& landmarks, std::vector<int>& landmarks_ind, FT delta)
@@ -356,7 +356,7 @@ void landmark_choice_protected_delaunay(Point_Vector& W, int nbP, Point_Vector&
         }
     else
       list_it++;
-  fill_landmark_copies(W, landmarks, landmarks_ind);
+  fill_landmarks(W, landmarks, landmarks_ind);
 }
 
 
@@ -427,6 +427,7 @@ int landmark_perturbation(Point_Vector &W, int nbL, Point_Vector& landmarks, std
   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;
@@ -453,8 +454,9 @@ int landmark_perturbation(Point_Vector &W, int nbL, Point_Vector& landmarks, std
     if (count_bad[i] != 0)
       std::cout << "count_bad[" << i << "] = " << count_bad[i] << std::endl;
   std::cout << "\nBad links total: " << count_badlinks << " Points to perturb: " << perturbL.size() << std::endl;
-  
+  */
   //*********************** Perturb bad link landmarks  
+  /*
   for (auto u: perturbL)
     {
       Random_point_iterator rp(D,sqrt(lambda)/8);
@@ -486,56 +488,41 @@ int landmark_perturbation(Point_Vector &W, int nbL, Point_Vector& landmarks, std
     }
   write_edges("landmarks/edges", witnessComplex, landmarks);
   return count_badlinks;
+  */
+  return 0;
 }
 
 
 int main (int argc, char * const argv[])
 {
-  if (argc != 5)
+  if (argc != 3)
     {
       std::cerr << "Usage: " << argv[0]
-                << " nbP nbL dim delta\n";
+                << " nbP dim\n";
       return 0;
     }
   int nbP       = atoi(argv[1]);
-  int nbL       = atoi(argv[2]);
-  int dim       = atoi(argv[3]);
-  FT delta      = atof(argv[4]);
+  int dim       = atoi(argv[2]);
   
   std::cout << "Let the carnage begin!\n";
   Point_Vector point_vector;
   generate_points_random_box(point_vector, nbP, dim);
   Point_Vector L;
   std::vector<int> chosen_landmarks;
-  bool ok=false;
-  while (!ok)
-    {
-      ok = true;
-      L = {};
-      chosen_landmarks = {};
-      //landmark_choice_by_delaunay(point_vector, nbP, nbL, L, chosen_landmarks, delta);
-      landmark_choice_protected_delaunay(point_vector, nbP, L, chosen_landmarks, delta);
-      nbL = chosen_landmarks.size();
-      std::cout << "Number of landmarks is " << nbL << std::endl;
-      //int width = (int)pow(nbL, 1.0/dim); landmark_choice_bcc(point_vector, nbP, width, L, chosen_landmarks);
-      for (auto i: chosen_landmarks)
-        {
-          ok = ok && (std::count(chosen_landmarks.begin(),chosen_landmarks.end(),i) == 1);
-          if (!ok) break;
-        }
-      
-    }
-  int bl = nbL, curr_min = bl;
-  write_points("landmarks/initial_pointset",point_vector);
+  //write_points("landmarks/initial_pointset",point_vector);
   //write_points("landmarks/initial_landmarks",L);
-  //for (int i = 0; i < 1; i++)
-  for (int i = 0; bl > 0; i++)
+  for (int i = 0; i < 11; i++)
+  //for (int i = 0; bl > 0; i++)
     {
-      std::cout << "========== Start iteration " << i << "== curr_min(" << curr_min << ")========\n";
-      bl=landmark_perturbation(point_vector, nbL, L, chosen_landmarks);
-      if (bl < curr_min)
-        curr_min=bl;
-      write_points("landmarks/landmarks0",L);
+      //std::cout << "========== Start iteration " << i << "== curr_min(" << curr_min << ")========\n";
+      double delta = pow(10, -(1.0*i)/2);
+      std::cout << "delta = " << delta << std::endl;
+      L = {}; chosen_landmarks = {};
+      landmark_choice_protected_delaunay(point_vector, nbP, L, chosen_landmarks, delta);
+      int nbL = chosen_landmarks.size();
+      std::cout << "Number of landmarks = " << nbL << std::endl;
+      landmark_perturbation(point_vector, nbL, L, chosen_landmarks);
+      //write_points("landmarks/landmarks0",L);
     }
   
 }
diff --git a/src/Witness_complex/example/witness_complex_flat_torus.cpp b/src/Witness_complex/example/witness_complex_flat_torus.cpp
index 06bf5a9f..69ef5fbf 100644
--- a/src/Witness_complex/example/witness_complex_flat_torus.cpp
+++ b/src/Witness_complex/example/witness_complex_flat_torus.cpp
@@ -335,7 +335,7 @@ void generate_points_grid(Point_Vector& W, int width, int D)
       int cell_i = i;
       for (int l = 0; l < D; ++l)
         {
-          point.push_back(0.01*(cell_i%width));
+          point.push_back((2.0/width)*(cell_i%width));
           cell_i /= width;
         }
       W.push_back(point);
@@ -516,7 +516,7 @@ void landmark_choice(Point_Vector &W, int nbP, int nbL, Point_Vector& landmarks,
       //      while (!res.second)
       //  {
       do chosen_landmark = rand.get_int(0,nbP);
-      while (std::count(landmarks_ind.begin(),landmarks_ind.end(),chosen_landmark)!=0);
+      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];
@@ -672,7 +672,7 @@ int landmark_perturbation(Point_Vector &W, Point_Vector& landmarks, std::vector<
         count_badlinks++;
         //std::cout << u << " ";
         Point_d& l = landmarks[u];
-        Fuzzy_sphere fs(l, sqrt(lambda)*3, 0, traits);
+        Fuzzy_sphere fs(l, sqrt(lambda), 0, traits);
         std::vector<int> curr_perturb;
         L.search(std::insert_iterator<std::vector<int>>(curr_perturb,curr_perturb.begin()),fs);
         for (int i: curr_perturb)
diff --git a/src/Witness_complex/example/witness_complex_perturbations.cpp b/src/Witness_complex/example/witness_complex_perturbations.cpp
index b3b84b1f..f78bcdab 100644
--- a/src/Witness_complex/example/witness_complex_perturbations.cpp
+++ b/src/Witness_complex/example/witness_complex_perturbations.cpp
@@ -267,6 +267,8 @@ int landmark_perturbation(Point_Vector &W, Point_Vector& landmarks, std::vector<
   std::cout << "Enter (D+1) nearest landmarks\n";
   //std::cout << "Size of the tree is " << L.size() << std::endl;
   int D = W[0].size();
+  clock_t start, end;
+  start = clock();  
   for (int i = 0; i < nbP; i++)
     {
       //std::cout << "Entered witness number " << i << std::endl;
@@ -294,18 +296,23 @@ int landmark_perturbation(Point_Vector &W, Point_Vector& landmarks, std::vector<
             lambda = dist;
         }
       //std::cout << "\nBad links total: " << count_badlinks << " Points to perturb: " << perturbL.size() << std::endl;
-
-    }
+      }
   //std::cout << "\n";
+  end = clock();
+  std::cout << "WL matrix construction on " << nbL << " landmarks took " << (double)(end-start)/CLOCKS_PER_SEC << "s.\n";
   
+
   std::string out_file = "wl_result";
-  write_wl(out_file,WL);
+  //write_wl(out_file,WL);
   
   //******************** Constructng a witness complex
   std::cout << "Entered witness complex construction\n";
   Witness_complex<> witnessComplex;
   witnessComplex.setNbL(nbL);
+  start = clock();
   witnessComplex.witness_complex(WL);
+  end = clock();
+  std::cout << "Witness complex construction on " << nbL << " landmarks took " << (double)(end-start)/CLOCKS_PER_SEC << "s.\n";
   //******************** Making a set of bad link landmarks
   std::cout << "Entered bad links\n";
   std::set< int > perturbL;
@@ -355,7 +362,7 @@ int landmark_perturbation(Point_Vector &W, Point_Vector& landmarks, std::vector<
   std::cout << "lambda=" << lambda << std::endl;
   // Write the WL matrix in a file
  
-  
+  /*
   char buffer[100];
   int i = sprintf(buffer,"stree_result.txt");
   
@@ -366,8 +373,9 @@ int landmark_perturbation(Point_Vector &W, Point_Vector& landmarks, std::vector<
       witnessComplex.st_to_file(ofs);
       ofs.close();
     }
+  */
   //witnessComplex.write_badlinks("badlinks");
-  write_edges_gnuplot("landmarks/edges", witnessComplex, landmarks);
+  //write_edges_gnuplot("landmarks/edges", witnessComplex, landmarks);
   return count_badlinks;
 }
 
@@ -417,7 +425,7 @@ int main (int argc, char * const argv[])
       file_name.erase(0, last_slash_idx + 1);
     }
   write_points("landmarks/initial_pointset",point_vector);
-  write_points("landmarks/initial_landmarks",L);
+  //write_points("landmarks/initial_landmarks",L);
   //for (int i = 0; bl != 0; i++)
   for (int i = 0; i < 1; i++)
     {
diff --git a/src/Witness_complex/example/witness_complex_sphere.cpp b/src/Witness_complex/example/witness_complex_sphere.cpp
index 74aae875..550c9392 100644
--- a/src/Witness_complex/example/witness_complex_sphere.cpp
+++ b/src/Witness_complex/example/witness_complex_sphere.cpp
@@ -431,6 +431,7 @@ int landmark_perturbation(Point_Vector &W, Point_Vector& landmarks, std::vector<
   else
     std::cout << "??NO. IT IS NOT A WITNESS COMPLEX??\n";   
   */ 
+  */
   //******************** Making a set of bad link landmarks
   std::cout << "Entered bad links\n";
   std::set< int > perturbL;
@@ -446,7 +447,7 @@ int landmark_perturbation(Point_Vector &W, Point_Vector& landmarks, std::vector<
         count_badlinks++;
         //std::cout << u << " ";
         Point_d& l = landmarks[u];
-        Fuzzy_sphere fs(l, sqrt(lambda)*3, 0, traits);
+        Fuzzy_sphere fs(l, sqrt(lambda), 0, traits);
         std::vector<int> curr_perturb;
         L.search(std::insert_iterator<std::vector<int>>(curr_perturb,curr_perturb.begin()),fs);
         for (int i: curr_perturb)
@@ -577,8 +578,8 @@ int main (int argc, char * const argv[])
   write_points("landmarks/initial_pointset",point_vector);
   write_points("landmarks/initial_landmarks",L);
   
-  //for (int i = 0; bl > 0; i++)
-  for (int i = 0; i < 1; i++)
+  for (int i = 0; bl > 0; i++)
+    //for (int i = 0; i < 1; i++)
     {
       std::cout << "========== Start iteration " << i << "== curr_min(" << curr_min << ")========\n";
       bl=landmark_perturbation(point_vector, L, chosen_landmarks);