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

4 files changed, 0 insertions, 280 deletions

diff --git a/example/Bottleneck_distance/CMakeLists.txt b/example/Bottleneck_distance/CMakeLists.txt
deleted file mode 100644
index c6f10127..00000000
--- a/example/Bottleneck_distance/CMakeLists.txt
+++ /dev/null
@@ -1,21 +0,0 @@
-project(Bottleneck_distance_examples)
-
-if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
-  add_executable (bottleneck_basic_example bottleneck_basic_example.cpp)
-  add_executable (alpha_rips_persistence_bottleneck_distance alpha_rips_persistence_bottleneck_distance.cpp)
-  target_link_libraries(alpha_rips_persistence_bottleneck_distance ${Boost_PROGRAM_OPTIONS_LIBRARY})
-
-  if (TBB_FOUND)
-    target_link_libraries(alpha_rips_persistence_bottleneck_distance ${TBB_LIBRARIES})
-    target_link_libraries(bottleneck_basic_example ${TBB_LIBRARIES})
-  endif(TBB_FOUND)
-  
-  add_test(NAME Bottleneck_distance_example_basic COMMAND $<TARGET_FILE:bottleneck_basic_example>)
-  add_test(NAME Bottleneck_distance_example_alpha_rips_persistence_bottleneck
-      COMMAND $<TARGET_FILE:alpha_rips_persistence_bottleneck_distance>
-      "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.15" "-m" "0.12" "-d" "3" "-p" "3")
-
-  install(TARGETS bottleneck_basic_example DESTINATION bin)
-  install(TARGETS alpha_rips_persistence_bottleneck_distance DESTINATION bin)
-  
-endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
diff --git a/example/Bottleneck_distance/README b/example/Bottleneck_distance/README
deleted file mode 100644
index 01bcd74a..00000000
--- a/example/Bottleneck_distance/README
+++ /dev/null
@@ -1,19 +0,0 @@
-# Bottleneck_distance #

-

-## `alpha_rips_persistence_bottleneck_distance` ##

-This program computes the persistent homology with coefficient field Z/pZ of a Rips complex defined on a set of input points. The output diagram contains one bar per line, written with the convention:

-

-`p dim birth death`

-

-where `dim` is the dimension of the homological feature, `birth` and `death` are respectively the birth and death of the feature, and `p` is the characteristic of the field *Z/pZ* used for homology coefficients.

-

-Usage:

-`alpha_rips_persistence_bottleneck_distance [options] <OFF input file>`

-

-Allowed options:

-

-* `-h [ --help ]` Produce help message

-* `-r [ --max-edge-length ]` (default = inf) Maximal length of an edge for the Rips complex construction.`

-* `-d [ --cpx-dimension ]` (default = 1) Maximal dimension of the Rips complex we want to compute.`

-* `-p [ --field-charac ]` (default = 11)     Characteristic p of the coefficient field Z/pZ for computing homology.

-* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals.

diff --git a/example/Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp b/example/Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp
deleted file mode 100644
index 2db1ef80..00000000
--- a/example/Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp
+++ /dev/null
@@ -1,190 +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):       Vincent Rouvreau
- *
- *    Copyright (C) 2017 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/>.
- */
-
-#include <gudhi/Alpha_complex.h>
-#include <gudhi/Rips_complex.h>
-#include <gudhi/distance_functions.h>
-#include <gudhi/Simplex_tree.h>
-#include <gudhi/Persistent_cohomology.h>
-#include <gudhi/Points_off_io.h>
-#include <gudhi/Bottleneck.h>
-
-#include <CGAL/Epick_d.h>
-
-#include <boost/program_options.hpp>
-
-#include <string>
-#include <vector>
-#include <limits>  // infinity
-#include <utility>  // for pair
-#include <algorithm>  // for transform
-
-
-// Types definition
-using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
-using Filtration_value = Simplex_tree::Filtration_value;
-using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>;
-using Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
-using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp >;
-using Kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >;
-using Point_d = Kernel::Point_d;
-using Points_off_reader = Gudhi::Points_off_reader<Point_d>;
-
-void program_options(int argc, char * argv[]
-                     , std::string & off_file_points
-                     , Filtration_value & threshold
-                     , int & dim_max
-                     , int & p
-                     , Filtration_value & min_persistence);
-
-static inline std::pair<double, double> compute_root_square(std::pair<double, double> input) {
-  return std::make_pair(std::sqrt(input.first), std::sqrt(input.second));
-}
-
-int main(int argc, char * argv[]) {
-  std::string off_file_points;
-  Filtration_value threshold;
-  int dim_max;
-  int p;
-  Filtration_value min_persistence;
-
-  program_options(argc, argv, off_file_points, threshold, dim_max, p, min_persistence);
-
-  Points_off_reader off_reader(off_file_points);
-
-  // --------------------------------------------
-  // Rips persistence
-  // --------------------------------------------
-  Rips_complex rips_complex(off_reader.get_point_cloud(), threshold, Gudhi::Euclidean_distance());
-
-  // Construct the Rips complex in a Simplex Tree
-  Simplex_tree rips_stree;
-
-  rips_complex.create_complex(rips_stree, dim_max);
-  std::cout << "The Rips complex contains " << rips_stree.num_simplices() << " simplices and has dimension "
-            << rips_stree.dimension() << " \n";
-
-  // Sort the simplices in the order of the filtration
-  rips_stree.initialize_filtration();
-
-  // Compute the persistence diagram of the complex
-  Persistent_cohomology rips_pcoh(rips_stree);
-  // initializes the coefficient field for homology
-  rips_pcoh.init_coefficients(p);
-  rips_pcoh.compute_persistent_cohomology(min_persistence);
-
-  // rips_pcoh.output_diagram();
-
-  // --------------------------------------------
-  // Alpha persistence
-  // --------------------------------------------
-  Gudhi::alpha_complex::Alpha_complex<Kernel> alpha_complex(off_reader.get_point_cloud());
-
-  Simplex_tree alpha_stree;
-  alpha_complex.create_complex(alpha_stree, threshold * threshold);
-  std::cout << "The Alpha complex contains " << alpha_stree.num_simplices() << " simplices and has dimension "
-            << alpha_stree.dimension() << " \n";
-
-  // Sort the simplices in the order of the filtration
-  alpha_stree.initialize_filtration();
-
-  // Compute the persistence diagram of the complex
-  Persistent_cohomology alpha_pcoh(alpha_stree);
-  // initializes the coefficient field for homology
-  alpha_pcoh.init_coefficients(p);
-  alpha_pcoh.compute_persistent_cohomology(min_persistence * min_persistence);
-
-  // alpha_pcoh.output_diagram();
-
-  // --------------------------------------------
-  // Bottleneck distance between both persistence
-  // --------------------------------------------
-  double max_b_distance {};
-  for (int dim = 0; dim < dim_max; dim ++) {
-    std::vector< std::pair< Filtration_value , Filtration_value > > rips_intervals;
-    std::vector< std::pair< Filtration_value , Filtration_value > > alpha_intervals;
-    rips_intervals = rips_pcoh.intervals_in_dimension(dim);
-    alpha_intervals = alpha_pcoh.intervals_in_dimension(dim);
-    std::transform(alpha_intervals.begin(), alpha_intervals.end(), alpha_intervals.begin(), compute_root_square);
-
-    double bottleneck_distance = Gudhi::persistence_diagram::bottleneck_distance(rips_intervals, alpha_intervals);
-    std::cout << "In dimension " << dim << ", bottleneck distance = " << bottleneck_distance << std::endl;
-    if (bottleneck_distance > max_b_distance)
-      max_b_distance = bottleneck_distance;
-  }
-  std::cout << "================================================================================" << std::endl;
-  std::cout << "Bottleneck distance is " << max_b_distance << std::endl;
-
-  return 0;
-}
-
-void program_options(int argc, char * argv[]
-                     , std::string & off_file_points
-                     , Filtration_value & threshold
-                     , int & dim_max
-                     , int & p
-                     , Filtration_value & min_persistence) {
-  namespace po = boost::program_options;
-  po::options_description hidden("Hidden options");
-  hidden.add_options()
-      ("input-file", po::value<std::string>(&off_file_points),
-       "Name of an OFF file containing a point set.\n");
-
-  po::options_description visible("Allowed options", 100);
-  visible.add_options()
-      ("help,h", "produce help message")
-      ("max-edge-length,r",
-       po::value<Filtration_value>(&threshold)->default_value(std::numeric_limits<Filtration_value>::infinity()),
-       "Maximal length of an edge for the Rips complex construction.")
-      ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(1),
-       "Maximal dimension of the Rips complex we want to compute.")
-      ("field-charac,p", po::value<int>(&p)->default_value(11),
-       "Characteristic p of the coefficient field Z/pZ for computing homology.")
-      ("min-persistence,m", po::value<Filtration_value>(&min_persistence),
-       "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals");
-
-  po::positional_options_description pos;
-  pos.add("input-file", 1);
-
-  po::options_description all;
-  all.add(visible).add(hidden);
-
-  po::variables_map vm;
-  po::store(po::command_line_parser(argc, argv).
-            options(all).positional(pos).run(), vm);
-  po::notify(vm);
-
-  if (vm.count("help") || !vm.count("input-file")) {
-    std::cout << std::endl;
-    std::cout << "Compute the persistent homology with coefficient field Z/pZ \n";
-    std::cout << "of a Rips complex defined on a set of input points.\n \n";
-    std::cout << "The output diagram contains one bar per line, written with the convention: \n";
-    std::cout << "   p   dim b d \n";
-    std::cout << "where dim is the dimension of the homological feature,\n";
-    std::cout << "b and d are respectively the birth and death of the feature and \n";
-    std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl;
-
-    std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
-    std::cout << visible << std::endl;
-    exit(-1);
-  }
-}
diff --git a/example/Bottleneck_distance/bottleneck_basic_example.cpp b/example/Bottleneck_distance/bottleneck_basic_example.cpp
deleted file mode 100644
index 3df7d12d..00000000
--- a/example/Bottleneck_distance/bottleneck_basic_example.cpp
+++ /dev/null
@@ -1,50 +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.
- *
- *    Authors:       Francois Godi, small modifications by Pawel Dlotko
- *
- *    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/>.
- */
-
-#include <gudhi/Bottleneck.h>
-
-#include <iostream>
-#include <vector>
-#include <utility>  // for pair
-#include <limits>  // for numeric_limits
-
-int main() {
-  std::vector< std::pair<double, double> > v1, v2;
-
-  v1.emplace_back(2.7, 3.7);
-  v1.emplace_back(9.6, 14.);
-  v1.emplace_back(34.2, 34.974);
-  v1.emplace_back(3., std::numeric_limits<double>::infinity());
-
-  v2.emplace_back(2.8, 4.45);
-  v2.emplace_back(9.5, 14.1);
-  v2.emplace_back(3.2, std::numeric_limits<double>::infinity());
-
-
-  double b = Gudhi::persistence_diagram::bottleneck_distance(v1, v2);
-
-  std::cout << "Bottleneck distance = " << b << std::endl;
-
-  b = Gudhi::persistence_diagram::bottleneck_distance(v1, v2, 0.1);
-
-  std::cout << "Approx bottleneck distance = " << b << std::endl;
-}