Modify examples

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/rips_complex_module@1757 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 4b6f26947ad16f440ea4d4b7cb5e145a58f28dcb

8 files changed, 7 insertions, 209 deletions

diff --git a/src/Witness_complex/example/witness_complex_from_file.cpp b/src/Witness_complex/example/witness_complex_from_file.cpp
index 59dd28e0..5dd18d0a 100644
--- a/src/Witness_complex/example/witness_complex_from_file.cpp
+++ b/src/Witness_complex/example/witness_complex_from_file.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Siargey Kachanovich
  *
- *    Copyright (C) 2015  INRIA Sophia Antipolis-Méditerranée (France)
+ *    Copyright (C) 2015  INRIA
  *
  *    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
@@ -36,9 +36,9 @@
 #include <string>
 #include <vector>
 
-typedef std::vector< int > typeVectorVertex;
-typedef std::vector< std::vector <double> > Point_Vector;
 typedef Gudhi::Simplex_tree<> Simplex_tree;
+typedef std::vector< Simplex_tree::Vertex_handle > typeVectorVertex;
+typedef std::vector< std::vector <double> > Point_Vector;
 
 int main(int argc, char * const argv[]) {
   if (argc != 3) {
diff --git a/src/Witness_complex/example/witness_complex_sphere.cpp b/src/Witness_complex/example/witness_complex_sphere.cpp
index 7ab86cc0..60e02225 100644
--- a/src/Witness_complex/example/witness_complex_sphere.cpp
+++ b/src/Witness_complex/example/witness_complex_sphere.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Siargey Kachanovich
  *
- *    Copyright (C) 2015  INRIA Sophia Antipolis-Méditerranée (France)
+ *    Copyright (C) 2015  INRIA
  *
  *    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
diff --git a/src/Witness_complex/include/gudhi/Construct_closest_landmark_table.h b/src/Witness_complex/include/gudhi/Construct_closest_landmark_table.h
index ec93ae71..1ae2e393 100644
--- a/src/Witness_complex/include/gudhi/Construct_closest_landmark_table.h
+++ b/src/Witness_complex/include/gudhi/Construct_closest_landmark_table.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Siargey Kachanovich
  *
- *    Copyright (C) 2015  INRIA Sophia Antipolis-Méditerranée (France)
+ *    Copyright (C) 2015  INRIA
  *
  *    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
diff --git a/src/Witness_complex/include/gudhi/Landmark_choice_by_furthest_point.h b/src/Witness_complex/include/gudhi/Landmark_choice_by_furthest_point.h
deleted file mode 100644
index bcb89e00..00000000
--- a/src/Witness_complex/include/gudhi/Landmark_choice_by_furthest_point.h
+++ /dev/null
@@ -1,105 +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/>.
- */
-
-#ifndef LANDMARK_CHOICE_BY_FURTHEST_POINT_H_
-#define LANDMARK_CHOICE_BY_FURTHEST_POINT_H_
-
-#include <boost/range/size.hpp>
-
-#include <limits>  // for numeric_limits<>
-#include <iterator>
-#include <algorithm>  // for sort
-#include <vector>
-
-namespace Gudhi {
-
-namespace witness_complex {
-
-  typedef std::vector<int> typeVectorVertex;
-
-  /** 
-   *  \ingroup witness_complex
-   *  \brief Landmark choice strategy by iteratively adding the furthest witness from the
-   *  current landmark set as the new landmark. 
-   *  \details It chooses nbL landmarks from a random access range `points` and
-   *  writes {witness}*{closest landmarks} matrix in `knn`.
-   *
-   *  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 
-   *  
-   */
-
-  template <typename KNearestNeighbours,
-  typename Point_random_access_range>
-  void landmark_choice_by_furthest_point(Point_random_access_range const &points,
-                                         int nbL,
-                                         KNearestNeighbours &knn) {
-    int nb_points = boost::size(points);
-    assert(nb_points >= nbL);
-    // distance matrix witness x landmarks
-    std::vector<std::vector<double>> wit_land_dist(nb_points, std::vector<double>());
-    // landmark list
-    typeVectorVertex chosen_landmarks;
-
-    knn = KNearestNeighbours(nb_points, std::vector<int>());
-    int current_number_of_landmarks = 0;  // counter for landmarks
-    double curr_max_dist = 0;  // used for defining the furhest point from L
-    const double infty = std::numeric_limits<double>::infinity();  // infinity (see next entry)
-    std::vector< double > dist_to_L(nb_points, infty);  // vector of current distances to L from points
-
-    // TODO(SK) Consider using rand_r(...) instead of rand(...) for improved thread safety
-    // or better yet std::uniform_int_distribution
-    int rand_int = rand() % nb_points;
-    int curr_max_w = rand_int;  // For testing purposes a pseudo-random number is used here
-
-    for (current_number_of_landmarks = 0; current_number_of_landmarks != nbL; current_number_of_landmarks++) {
-      // curr_max_w at this point is the next landmark
-      chosen_landmarks.push_back(curr_max_w);
-      unsigned i = 0;
-      for (auto& p : points) {
-        double curr_dist = euclidean_distance<double>(p, *(std::begin(points) + chosen_landmarks[current_number_of_landmarks]));
-        wit_land_dist[i].push_back(curr_dist);
-        knn[i].push_back(current_number_of_landmarks);
-        if (curr_dist < dist_to_L[i])
-          dist_to_L[i] = curr_dist;
-        ++i;
-      }
-      curr_max_dist = 0;
-      for (i = 0; i < dist_to_L.size(); i++)
-        if (dist_to_L[i] > curr_max_dist) {
-          curr_max_dist = dist_to_L[i];
-          curr_max_w = i;
-        }
-    }
-    for (int i = 0; i < nb_points; ++i)
-      std::sort(std::begin(knn[i]),
-                std::end(knn[i]),
-                [&wit_land_dist, i](int a, int b) {
-                  return wit_land_dist[i][a] < wit_land_dist[i][b]; });
-  }
-
-}  // namespace witness_complex
-
-}  // namespace Gudhi
-
-#endif  // LANDMARK_CHOICE_BY_FURTHEST_POINT_H_
diff --git a/src/Witness_complex/include/gudhi/Landmark_choice_by_random_point.h b/src/Witness_complex/include/gudhi/Landmark_choice_by_random_point.h
deleted file mode 100644
index b5aab9d5..00000000
--- a/src/Witness_complex/include/gudhi/Landmark_choice_by_random_point.h
+++ /dev/null
@@ -1,96 +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/>.
- */
-
-#ifndef LANDMARK_CHOICE_BY_RANDOM_POINT_H_
-#define LANDMARK_CHOICE_BY_RANDOM_POINT_H_
-
-#include <boost/range/size.hpp>
-
-#include <queue>  // for priority_queue<>
-#include <utility>  // for pair<>
-#include <iterator>
-#include <vector>
-#include <set>
-
-namespace Gudhi {
-
-namespace witness_complex {
-
-  /**
-   *  \ingroup witness_complex
-   * \brief Landmark choice strategy by taking random vertices for landmarks.
-   *  \details It chooses nbL distinct landmarks from a random access range `points`
-   *  and outputs a matrix {witness}*{closest landmarks} in knn.
-   *
-   *  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 and
-   *  Vertex_handle is the label type of a vertex in a simplicial complex.
-   *  Closest_landmark_range needs to have push_back operation.
-   */
-
-  template <typename KNearestNeighbours,
-            typename Point_random_access_range>
-  void landmark_choice_by_random_point(Point_random_access_range const &points,
-                                       int nbL,
-                                       KNearestNeighbours &knn) {
-    int nbP = boost::size(points);
-    assert(nbP >= nbL);
-    std::set<int> landmarks;
-    int current_number_of_landmarks = 0;  // counter for landmarks
-
-    // TODO(SK) Consider using rand_r(...) instead of rand(...) for improved thread safety
-    int chosen_landmark = rand() % nbP;
-    for (current_number_of_landmarks = 0; current_number_of_landmarks != nbL; current_number_of_landmarks++) {
-      while (landmarks.find(chosen_landmark) != landmarks.end())
-        chosen_landmark = rand() % nbP;
-      landmarks.insert(chosen_landmark);
-    }
-
-    int dim = boost::size(*std::begin(points));
-    typedef std::pair<double, int> dist_i;
-    typedef bool (*comp)(dist_i, dist_i);
-    knn = KNearestNeighbours(nbP);
-    for (int points_i = 0; points_i < nbP; points_i++) {
-      std::priority_queue<dist_i, std::vector<dist_i>, comp> l_heap([](dist_i j1, dist_i j2) {
-          return j1.first > j2.first;
-        });
-      std::set<int>::iterator landmarks_it;
-      int landmarks_i = 0;
-      for (landmarks_it = landmarks.begin(), landmarks_i = 0; landmarks_it != landmarks.end();
-           ++landmarks_it, landmarks_i++) {
-        dist_i dist = std::make_pair(euclidean_distance<double>(points[points_i], points[*landmarks_it]), landmarks_i);
-        l_heap.push(dist);
-      }
-      for (int i = 0; i < dim + 1; i++) {
-        dist_i dist = l_heap.top();
-        knn[points_i].push_back(dist.second);
-        l_heap.pop();
-      }
-    }
-  }
-
-}  // namespace witness_complex
-
-}  // namespace Gudhi
-
-#endif  // LANDMARK_CHOICE_BY_RANDOM_POINT_H_
diff --git a/src/Witness_complex/include/gudhi/Witness_complex.h b/src/Witness_complex/include/gudhi/Witness_complex.h
index 2cec921a..1eb126f1 100644
--- a/src/Witness_complex/include/gudhi/Witness_complex.h
+++ b/src/Witness_complex/include/gudhi/Witness_complex.h
@@ -72,7 +72,6 @@ class Witness_complex {
   typedef std::vector< Point_t > Point_Vector;
 
   typedef std::vector< Vertex_handle > typeVectorVertex;
-  //typedef std::pair< typeVectorVertex, Filtration_value> typeSimplex;
   typedef std::pair< Simplex_handle, bool > typePairSimplexBool;
 
   typedef int Witness_id;
diff --git a/src/Witness_complex/test/simple_witness_complex.cpp b/src/Witness_complex/test/simple_witness_complex.cpp
index adaadfb0..6be39f58 100644
--- a/src/Witness_complex/test/simple_witness_complex.cpp
+++ b/src/Witness_complex/test/simple_witness_complex.cpp
@@ -33,7 +33,7 @@
 #include <vector>
 
 typedef Gudhi::Simplex_tree<> Simplex_tree;
-typedef std::vector< int > typeVectorVertex;
+typedef std::vector< Simplex_tree::Vertex_handle > typeVectorVertex;
 typedef Gudhi::witness_complex::Witness_complex<Simplex_tree> WitnessComplex;
 
 BOOST_AUTO_TEST_CASE(simple_witness_complex) {
diff --git a/src/Witness_complex/test/witness_complex_points.cpp b/src/Witness_complex/test/witness_complex_points.cpp
index b7067f87..92f53417 100644
--- a/src/Witness_complex/test/witness_complex_points.cpp
+++ b/src/Witness_complex/test/witness_complex_points.cpp
@@ -34,8 +34,8 @@
 #include <vector>
 
 typedef std::vector<double> Point;
-typedef std::vector< int > typeVectorVertex;
 typedef Gudhi::Simplex_tree<> Simplex_tree;
+typedef std::vector< Simplex_tree::Vertex_handle > typeVectorVertex;
 typedef Gudhi::witness_complex::Witness_complex<Simplex_tree> WitnessComplex;
 
 BOOST_AUTO_TEST_CASE(witness_complex_points) {