Delete all files in order to incorporate upstream's move to git.

6 files changed, 0 insertions, 436 deletions

diff --git a/example/Witness_complex/CMakeLists.txt b/example/Witness_complex/CMakeLists.txt
deleted file mode 100644
index 3d838c0d..00000000
--- a/example/Witness_complex/CMakeLists.txt
+++ /dev/null
@@ -1,34 +0,0 @@
-project(Witness_complex_examples)
-
-add_executable ( Witness_complex_example_nearest_landmark_table example_nearest_landmark_table.cpp )
-if (TBB_FOUND)
-  target_link_libraries(Witness_complex_example_nearest_landmark_table ${TBB_LIBRARIES})
-endif()
-add_test(NAME Witness_complex_example_nearest_landmark_table
-    COMMAND $<TARGET_FILE:Witness_complex_example_nearest_landmark_table>)
-
-install(TARGETS Witness_complex_example_nearest_landmark_table DESTINATION bin)
-
-# CGAL and Eigen3 are required for Euclidean version of Witness
-if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
-  add_executable( Witness_complex_example_off example_witness_complex_off.cpp )
-  add_executable ( Witness_complex_example_sphere example_witness_complex_sphere.cpp )
-  
-  add_executable( Witness_complex_example_strong_off example_strong_witness_complex_off.cpp )
-  target_link_libraries(Witness_complex_example_strong_off)
-
-  add_test(NAME Witness_complex_example_off_test_torus
-      COMMAND $<TARGET_FILE:Witness_complex_example_off>
-      "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "20" "1.0" "3")
-  add_test(NAME Witness_complex_example_test_sphere_10
-      COMMAND $<TARGET_FILE:Witness_complex_example_sphere> "10")
-  add_test(NAME Witness_complex_example_strong_off_test_torus
-      COMMAND $<TARGET_FILE:Witness_complex_example_strong_off>
-      "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "20" "1.0" "3")
-      
-  install(TARGETS Witness_complex_example_off DESTINATION bin)
-  install(TARGETS Witness_complex_example_sphere DESTINATION bin)
-  install(TARGETS Witness_complex_example_strong_off DESTINATION bin)
-
-
-endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
diff --git a/example/Witness_complex/example_nearest_landmark_table.cpp b/example/Witness_complex/example_nearest_landmark_table.cpp
deleted file mode 100644
index acaf7c54..00000000
--- a/example/Witness_complex/example_nearest_landmark_table.cpp
+++ /dev/null
@@ -1,47 +0,0 @@
-#define BOOST_PARAMETER_MAX_ARITY 12
-
-#include <gudhi/Simplex_tree.h>
-#include <gudhi/Witness_complex.h>
-#include <gudhi/Persistent_cohomology.h>
-
-#include <iostream>
-#include <fstream>
-#include <utility>
-#include <string>
-#include <vector>
-
-int main(int argc, char * const argv[]) {
-  using Nearest_landmark_range = std::vector<std::pair<std::size_t, double>>;
-  using Nearest_landmark_table = std::vector<Nearest_landmark_range>;
-  using Witness_complex = Gudhi::witness_complex::Witness_complex<Nearest_landmark_table>;
-  using Simplex_tree = Gudhi::Simplex_tree<>;
-  using Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
-  using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp>;
-
-  Simplex_tree simplex_tree;
-  Nearest_landmark_table nlt;
-
-  // Example contains 5 witnesses and 5 landmarks
-  Nearest_landmark_range w0 = {std::make_pair(0, 0), std::make_pair(1, 1), std::make_pair(2, 2),
-                               std::make_pair(3, 3), std::make_pair(4, 4)}; nlt.push_back(w0);
-  Nearest_landmark_range w1 = {std::make_pair(1, 0), std::make_pair(2, 1), std::make_pair(3, 2),
-                               std::make_pair(4, 3), std::make_pair(0, 4)}; nlt.push_back(w1);
-  Nearest_landmark_range w2 = {std::make_pair(2, 0), std::make_pair(3, 1), std::make_pair(4, 2),
-                               std::make_pair(0, 3), std::make_pair(1, 4)}; nlt.push_back(w2);
-  Nearest_landmark_range w3 = {std::make_pair(3, 0), std::make_pair(4, 1), std::make_pair(0, 2),
-                               std::make_pair(1, 3), std::make_pair(2, 4)}; nlt.push_back(w3);
-  Nearest_landmark_range w4 = {std::make_pair(4, 0), std::make_pair(0, 1), std::make_pair(1, 2),
-                               std::make_pair(2, 3), std::make_pair(3, 4)}; nlt.push_back(w4);
-
-  Witness_complex witness_complex(nlt);
-  witness_complex.create_complex(simplex_tree, 4.1);
-
-  std::cout << "Number of simplices: " << simplex_tree.num_simplices() << std::endl;
-
-  Persistent_cohomology pcoh(simplex_tree);
-  // initializes the coefficient field for homology
-  pcoh.init_coefficients(11);
-
-  pcoh.compute_persistent_cohomology(-0.1);
-  pcoh.output_diagram();
-}
diff --git a/example/Witness_complex/example_strong_witness_complex_off.cpp b/example/Witness_complex/example_strong_witness_complex_off.cpp
deleted file mode 100644
index 19f73836..00000000
--- a/example/Witness_complex/example_strong_witness_complex_off.cpp
+++ /dev/null
@@ -1,57 +0,0 @@
-#include <gudhi/Simplex_tree.h>
-#include <gudhi/Euclidean_strong_witness_complex.h>
-#include <gudhi/pick_n_random_points.h>
-#include <gudhi/choose_n_farthest_points.h>
-#include <gudhi/Points_off_io.h>
-
-#include <CGAL/Epick_d.h>
-
-#include <iostream>
-#include <fstream>
-#include <ctime>
-#include <string>
-#include <vector>
-
-using K = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>;
-using Point_d = typename K::Point_d;
-using Witness_complex = Gudhi::witness_complex::Euclidean_strong_witness_complex<K>;
-using Point_vector = std::vector<Point_d>;
-
-int main(int argc, char* const argv[]) {
-  if (argc != 5) {
-    std::cerr << "Usage: " << argv[0] << " path_to_point_file number_of_landmarks max_squared_alpha limit_dimension\n";
-    return 0;
-  }
-
-  std::string file_name = argv[1];
-  int nbL = atoi(argv[2]), lim_dim = atoi(argv[4]);
-  double alpha2 = atof(argv[3]);
-  clock_t start, end;
-  Gudhi::Simplex_tree<> simplex_tree;
-
-  // Read the point file
-  Point_vector point_vector, landmarks;
-  Gudhi::Points_off_reader<Point_d> off_reader(file_name);
-  if (!off_reader.is_valid()) {
-    std::cerr << "Strong witness complex - Unable to read file " << file_name << "\n";
-    exit(-1);  // ----- >>
-  }
-  point_vector = Point_vector(off_reader.get_point_cloud());
-
-  std::cout << "Successfully read " << point_vector.size() << " points.\n";
-  std::cout << "Ambient dimension is " << point_vector[0].dimension() << ".\n";
-
-  // Choose landmarks (decomment one of the following two lines)
-  // Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks));
-  Gudhi::subsampling::choose_n_farthest_points(K(), point_vector, nbL, Gudhi::subsampling::random_starting_point,
-                                               std::back_inserter(landmarks));
-
-  // Compute witness complex
-  start = clock();
-  Witness_complex witness_complex(landmarks, point_vector);
-
-  witness_complex.create_complex(simplex_tree, alpha2, lim_dim);
-  end = clock();
-  std::cout << "Strong witness complex took " << static_cast<double>(end - start) / CLOCKS_PER_SEC << " s. \n";
-  std::cout << "Number of simplices is: " << simplex_tree.num_simplices() << "\n";
-}
diff --git a/example/Witness_complex/example_witness_complex_off.cpp b/example/Witness_complex/example_witness_complex_off.cpp
deleted file mode 100644
index be11c955..00000000
--- a/example/Witness_complex/example_witness_complex_off.cpp
+++ /dev/null
@@ -1,62 +0,0 @@
-#include <sys/types.h>
-#include <sys/stat.h>
-
-#include <gudhi/Simplex_tree.h>
-#include <gudhi/Euclidean_witness_complex.h>
-#include <gudhi/pick_n_random_points.h>
-#include <gudhi/choose_n_farthest_points.h>
-#include <gudhi/Points_off_io.h>
-
-#include <CGAL/Epick_d.h>
-
-#include <iostream>
-#include <fstream>
-#include <ctime>
-#include <string>
-#include <vector>
-
-using K = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>;
-using Point_d = K::Point_d;
-using Witness_complex = Gudhi::witness_complex::Euclidean_witness_complex<K>;
-using Point_vector = std::vector< Point_d >;
-
-int main(int argc, char * const argv[]) {
-  if (argc != 5) {
-    std::cerr << "Usage: " << argv[0]
-        << " path_to_point_file number_of_landmarks max_squared_alpha limit_dimension\n";
-    return 0;
-  }
-
-  std::string file_name = argv[1];
-  int nbL = atoi(argv[2]), lim_dim = atoi(argv[4]);
-  double alpha2 = atof(argv[3]);
-  clock_t start, end;
-  Gudhi::Simplex_tree<> simplex_tree;
-
-  // Read the point file
-  Point_vector point_vector, landmarks;
-  Gudhi::Points_off_reader<Point_d> off_reader(file_name);
-  if (!off_reader.is_valid()) {
-      std::cerr << "Witness complex - Unable to read file " << file_name << "\n";
-      exit(-1);  // ----- >>
-    }
-  point_vector = Point_vector(off_reader.get_point_cloud());
-
-  std::cout << "Successfully read " << point_vector.size() << " points.\n";
-  std::cout << "Ambient dimension is " << point_vector[0].dimension() << ".\n";
-
-  // Choose landmarks (decomment one of the following two lines)
-  // Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks));
-  Gudhi::subsampling::choose_n_farthest_points(K(), point_vector, nbL, Gudhi::subsampling::random_starting_point, std::back_inserter(landmarks));
-
-  // Compute witness complex
-  start = clock();
-  Witness_complex witness_complex(landmarks,
-                                  point_vector);
-
-  witness_complex.create_complex(simplex_tree, alpha2, lim_dim);
-  end = clock();
-  std::cout << "Witness complex took "
-      << static_cast<double>(end - start) / CLOCKS_PER_SEC << " s. \n";
-  std::cout << "Number of simplices is: " << simplex_tree.num_simplices() << "\n";
-}
diff --git a/example/Witness_complex/example_witness_complex_sphere.cpp b/example/Witness_complex/example_witness_complex_sphere.cpp
deleted file mode 100644
index 9e3c972d..00000000
--- a/example/Witness_complex/example_witness_complex_sphere.cpp
+++ /dev/null
@@ -1,70 +0,0 @@
-#define BOOST_PARAMETER_MAX_ARITY 12
-
-#include <gudhi/Simplex_tree.h>
-#include <gudhi/Euclidean_witness_complex.h>
-#include <gudhi/pick_n_random_points.h>
-#include <gudhi/choose_n_farthest_points.h>
-#include <gudhi/reader_utils.h>
-
-#include <CGAL/Epick_d.h>
-
-#include <iostream>
-#include <fstream>
-#include <ctime>
-#include <utility>
-#include <string>
-#include <vector>
-
-#include "generators.h"
-
-/** Write a gnuplot readable file.
- *  Data range is a random access range of pairs (arg, value)
- */
-template <typename Data_range>
-void write_data(Data_range& data, std::string filename) {
-  std::ofstream ofs(filename, std::ofstream::out);
-  for (auto entry : data) ofs << entry.first << ", " << entry.second << "\n";
-  ofs.close();
-}
-
-int main(int argc, char* const argv[]) {
-  using Kernel = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>;
-  using Witness_complex = Gudhi::witness_complex::Euclidean_witness_complex<Kernel>;
-
-  if (argc != 2) {
-    std::cerr << "Usage: " << argv[0] << " number_of_landmarks \n";
-    return 0;
-  }
-
-  int number_of_landmarks = atoi(argv[1]);
-
-  std::vector<std::pair<int, double> > l_time;
-
-  // Generate points
-  for (int nbP = 500; nbP < 10000; nbP += 500) {
-    clock_t start, end;
-    // Construct the Simplex Tree
-    Gudhi::Simplex_tree<> simplex_tree;
-    Point_Vector point_vector, landmarks;
-    generate_points_sphere(point_vector, nbP, 4);
-    std::cout << "Successfully generated " << point_vector.size() << " points.\n";
-    std::cout << "Ambient dimension is " << point_vector[0].size() << ".\n";
-
-    // Choose landmarks
-    start = clock();
-    // Gudhi::subsampling::pick_n_random_points(point_vector, number_of_landmarks, std::back_inserter(landmarks));
-    Gudhi::subsampling::choose_n_farthest_points(K(), point_vector, number_of_landmarks,
-                                                 Gudhi::subsampling::random_starting_point,
-                                                 std::back_inserter(landmarks));
-
-    // Compute witness complex
-    Witness_complex witness_complex(landmarks, point_vector);
-    witness_complex.create_complex(simplex_tree, 0);
-    end = clock();
-    double time = static_cast<double>(end - start) / CLOCKS_PER_SEC;
-    std::cout << "Witness complex for " << number_of_landmarks << " landmarks took " << time << " s. \n";
-    std::cout << "Number of simplices is: " << simplex_tree.num_simplices() << "\n";
-    l_time.push_back(std::make_pair(nbP, time));
-  }
-  write_data(l_time, "w_time.dat");
-}
diff --git a/example/Witness_complex/generators.h b/example/Witness_complex/generators.h
deleted file mode 100644
index 4b755daa..00000000
--- a/example/Witness_complex/generators.h
+++ /dev/null
@@ -1,166 +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
- *
- *    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 GENERATORS_H_
-#define GENERATORS_H_
-
-#include <CGAL/Epick_d.h>
-#include <CGAL/point_generators_d.h>
-#include <CGAL/Random.h>
-
-#include <fstream>
-#include <string>
-#include <vector>
-#include <cmath>
-
-using K = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>;
-using FT = K::FT;
-using Point_d = K::Point_d;
-using Point_Vector = std::vector<Point_d>;
-using Random_cube_iterator = CGAL::Random_points_in_cube_d<Point_d>;
-using Random_point_iterator = CGAL::Random_points_in_ball_d<Point_d>;
-
-/**
- * \brief Rock age method of reading off file
- *
- */
-inline void
-off_reader_cust(std::string file_name, std::vector<Point_d> & 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;
-  // Line OFF. No need in it
-  if (!getline(in_file, line)) {
-    std::cerr << "No line OFF\n";
-    return;
-  }
-  // Line with 3 numbers. No need
-  if (!getline(in_file, line)) {
-    std::cerr << "No line with 3 numbers\n";
-    return;
-  }
-  // Reading points
-  while (getline(in_file, line)) {
-    std::vector< double > point;
-    std::istringstream iss(line);
-    while (iss >> x) {
-      point.push_back(x);
-    }
-    points.push_back(Point_d(point));
-  }
-  in_file.close();
-}
-
-/**
- * \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();
-}
-
-/** \brief Generate points on a grid in a cube of side 2
- * having {+-1}^D as vertices and insert them in W.
- * The grid has "width" points on each side. 
- * If torus is true then it is supposed that the cube represents
- * a flat torus, hence the opposite borders are associated.
- * The points on border in this case are not placed twice.
- */
-void generate_points_grid(Point_Vector& W, int width, int D, bool torus) {
-  int nb_points = 1;
-  for (int i = 0; i < D; ++i)
-    nb_points *= width;
-  for (int i = 0; i < nb_points; ++i) {
-    std::vector<double> point;
-    int cell_i = i;
-    for (int l = 0; l < D; ++l) {
-      if (torus)
-        point.push_back(-1 + (2.0 / (width - 1))*(cell_i % width));
-      else
-        point.push_back(-1 + (2.0 / width)*(cell_i % width));
-      // attention: the bottom and the right are covered too!
-      cell_i /= width;
-    }
-    W.push_back(point);
-  }
-}
-
-/** \brief Generate nbP points uniformly in a cube of side 2
- * having {+-1}^dim as its vertices and insert them in W.
- */
-void generate_points_random_box(Point_Vector& W, int nbP, int dim) {
-  Random_cube_iterator rp(dim, 1.0);
-  for (int i = 0; i < nbP; i++) {
-    W.push_back(*rp++);
-  }
-}
-
-/** \brief Generate nbP points uniformly on a (dim-1)-sphere
- *  and insert them in W.
- */
-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++);
-}
-
-/** \brief Generate nbP points on a (flat) d-torus embedded in R^{2d}
- *
- */
-void generate_points_torus(Point_Vector& W, int nbP, int dim) {
-  CGAL::Random rand;
-  const double pi = std::acos(-1);
-  for (int i = 0; i < nbP; i++) {
-    std::vector<FT> point;
-    for (int j = 0; j < dim; j++) {
-      double alpha = rand.uniform_real(static_cast<double>(0), 2*pi);
-      point.push_back(sin(alpha));
-      point.push_back(cos(alpha));
-    }
-    W.push_back(Point_d(point));
-  }
-}
-
-#endif  // GENERATORS_H_