Alpha_shapes removal. Alpha_complex will be added on feature delivery

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/compil_fix@685 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 5e661587777dc5e07ae6ee42f2f5f207189c6a13

12 files changed, 0 insertions, 959 deletions

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 02e0c614..7091eef6 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -57,7 +57,6 @@ else()
   message(STATUS "boost include dirs:" ${Boost_INCLUDE_DIRS})
 
   include_directories(src/common/include/)
-  include_directories(src/Alpha_shapes/include/)
   include_directories(src/Bottleneck/include/)
   include_directories(src/Contraction/include/)
   include_directories(src/Hasse_complex/include/)
@@ -73,8 +72,6 @@ else()
   add_subdirectory(src/Skeleton_blocker/example) 
   add_subdirectory(src/Contraction/example)
   add_subdirectory(src/Hasse_complex/example)
-  add_subdirectory(src/Alpha_shapes/example)
-  add_subdirectory(src/Alpha_shapes/test)
   add_subdirectory(src/Bottleneck/example)
   add_subdirectory(src/Bottleneck/test)
 
diff --git a/src/Alpha_shapes/example/CMakeLists.txt b/src/Alpha_shapes/example/CMakeLists.txt
deleted file mode 100644
index 753238a5..00000000
--- a/src/Alpha_shapes/example/CMakeLists.txt
+++ /dev/null
@@ -1,32 +0,0 @@
-cmake_minimum_required(VERSION 2.6)
-project(GUDHIAlphaShapesExample)
-
-# need CGAL 4.6
-# cmake -DCGAL_DIR=~/workspace/CGAL-4.6-beta1 ../../..
-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 ( dtoffrw Delaunay_triangulation_off_rw.cpp )
-      target_link_libraries(dtoffrw  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
-      add_test(dtoffrw_tore3D ${CMAKE_CURRENT_BINARY_DIR}/dtoffrw ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off 3)
-
-      # uncomment to display debug traces
-      # add_definitions(-DDEBUG_TRACES)
-      add_executable ( stfromdt Simplex_tree_from_delaunay_triangulation.cpp )
-      target_link_libraries(stfromdt  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
-    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/Alpha_shapes/example/Delaunay_triangulation_off_rw.cpp b/src/Alpha_shapes/example/Delaunay_triangulation_off_rw.cpp
deleted file mode 100644
index 03f6440d..00000000
--- a/src/Alpha_shapes/example/Delaunay_triangulation_off_rw.cpp
+++ /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):       Vincent Rouvreau
- *
- *    Copyright (C) 2014  INRIA Saclay (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/>.
- */
-
-// to construct a Delaunay_triangulation from a OFF file
-#include "gudhi/Alpha_shapes/Delaunay_triangulation_off_io.h"
-
-#include <CGAL/Delaunay_triangulation.h>
-#include <CGAL/Epick_d.h>
-#include <CGAL/point_generators_d.h>
-#include <CGAL/algorithm.h>
-#include <CGAL/assertions.h>
-
-#include <iostream>
-#include <iterator>
-#include <vector>
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string>
-
-// Use dynamic_dimension_tag for the user to be able to set dimension
-typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > K;
-typedef CGAL::Delaunay_triangulation<K> T;
-// The triangulation uses the default instanciation of the 
-// TriangulationDataStructure template parameter
-
-void usage(char * const progName) {
-  std::cerr << "Usage: " << progName << " filename.off dimension" << std::endl;
-  exit(-1); // ----- >>
-}
-
-int main(int argc, char **argv) {
-  if (argc != 3) {
-    std::cerr << "Error: Number of arguments (" << argc << ") is not correct" << std::endl;
-    usage(argv[0]);
-  }
-
-  int dimension = 0;
-  int returnedScanValue = sscanf(argv[2], "%d", &dimension);
-  if ((returnedScanValue == EOF) || (dimension <= 0)) {
-    std::cerr << "Error: " << argv[2] << " is not correct" << std::endl;
-    usage(argv[0]);
-  }
-
-  T dt(dimension);
-  std::string offFileName(argv[1]);
-  Gudhi::alphashapes::Delaunay_triangulation_off_reader<T> off_reader(offFileName, dt, true, true);
-  if (!off_reader.is_valid()) {
-    std::cerr << "Unable to read file " << offFileName << std::endl;
-    exit(-1); // ----- >>
-  }
-
-  std::cout << "number of vertices=" << dt.number_of_vertices() << std::endl;
-  std::cout << "number of full cells=" << dt.number_of_full_cells() << std::endl;
-  std::cout << "number of finite full cells=" << dt.number_of_finite_full_cells() << std::endl;
-
-  // Points list
-  /*for (T::Vertex_iterator vit = dt.vertices_begin(); vit != dt.vertices_end(); ++vit) {
-        for (auto Coord = vit->point().cartesian_begin(); Coord != vit->point().cartesian_end(); ++Coord) {
-          std::cout << *Coord << " ";
-        }
-        std::cout << std::endl;
-  }
-  std::cout << std::endl;*/
- 
-  int i = 0, j = 0;
-  typedef T::Full_cell_iterator Full_cell_iterator;
-  typedef T::Facet Facet;
-
-  for (Full_cell_iterator cit = dt.full_cells_begin(); cit != dt.full_cells_end(); ++cit) {
-    if (!dt.is_infinite(cit)) {
-      j++;
-      continue;
-    }
-    Facet fct(cit, cit->index(dt.infinite_vertex()));
-    i++;
-  }
-  std::cout << "There are " << i << " facets on the convex hull." << std::endl;
-  std::cout << "There are " << j << " facets not on the convex hull." << std::endl;
-
-
-  std::string offOutputFile("out.off");
-  Gudhi::alphashapes::Delaunay_triangulation_off_writer<T> off_writer(offOutputFile, dt);
-
-  return 0;
-}
\ No newline at end of file
diff --git a/src/Alpha_shapes/example/Simplex_tree_from_delaunay_triangulation.cpp b/src/Alpha_shapes/example/Simplex_tree_from_delaunay_triangulation.cpp
deleted file mode 100644
index 3a17b519..00000000
--- a/src/Alpha_shapes/example/Simplex_tree_from_delaunay_triangulation.cpp
+++ /dev/null
@@ -1,103 +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) 2014  INRIA Saclay (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/>.
- */
-
-// to construct a Delaunay_triangulation from a OFF file
-#include "gudhi/Alpha_shapes/Delaunay_triangulation_off_io.h"
-#include "gudhi/Alpha_shapes.h"
-
-// to construct a simplex_tree from Delaunay_triangulation
-#include "gudhi/graph_simplicial_complex.h"
-#include "gudhi/Simplex_tree.h"
-
-#include <CGAL/Delaunay_triangulation.h>
-#include <CGAL/Epick_d.h>
-#include <CGAL/point_generators_d.h>
-#include <CGAL/algorithm.h>
-#include <CGAL/assertions.h>
-
-#include <iostream>
-#include <iterator>
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string>
-
-// Use dynamic_dimension_tag for the user to be able to set dimension
-typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > K;
-typedef CGAL::Delaunay_triangulation<K> T;
-// The triangulation uses the default instanciation of the 
-// TriangulationDataStructure template parameter
-
-void usage(char * const progName) {
-  std::cerr << "Usage: " << progName << " filename.off dimension" << std::endl;
-  exit(-1); // ----- >>
-}
-
-int main(int argc, char **argv) {
-  if (argc != 3) {
-    std::cerr << "Error: Number of arguments (" << argc << ") is not correct" << std::endl;
-    usage(argv[0]);
-  }
-
-  int dimension = 0;
-  int returnedScanValue = sscanf(argv[2], "%d", &dimension);
-  if ((returnedScanValue == EOF) || (dimension <= 0)) {
-    std::cerr << "Error: " << argv[2] << " is not correct" << std::endl;
-    usage(argv[0]);
-  }
-
-  // ----------------------------------------------------------------------------
-  //
-  // Init of an alpha-shape from a Delaunay triangulation
-  //
-  // ----------------------------------------------------------------------------
-  T dt(dimension);
-  std::string off_file_name(argv[1]);
-
-  Gudhi::alphashapes::Delaunay_triangulation_off_reader<T> off_reader(off_file_name, dt, false, false);
-  if (!off_reader.is_valid()) {
-    std::cerr << "Unable to read file " << off_file_name << std::endl;
-    exit(-1); // ----- >>
-  }
-
-  std::cout << "number of vertices=" << dt.number_of_vertices() << std::endl;
-  std::cout << "number of full cells=" << dt.number_of_full_cells() << std::endl;
-  std::cout << "number of finite full cells=" << dt.number_of_finite_full_cells() << std::endl;
-
-  Gudhi::alphashapes::Alpha_shapes alpha_shapes_from_dt(dt);
-  //std::cout << alpha_shapes_from_dt << std::endl;
-
-  // ----------------------------------------------------------------------------
-  //
-  // Init of an alpha-shape from a OFF file
-  //
-  // ----------------------------------------------------------------------------
-  Gudhi::alphashapes::Alpha_shapes alpha_shapes_from_file(off_file_name, dimension);
-  //std::cout << alpha_shapes_from_file << std::endl;
-  
-  std::cout << "alpha_shapes_from_file.dimension()=" << alpha_shapes_from_file.dimension() << std::endl;
-  std::cout << "alpha_shapes_from_file.filtration()=" << alpha_shapes_from_file.filtration() << std::endl;
-  std::cout << "alpha_shapes_from_file.num_simplices()=" << alpha_shapes_from_file.num_simplices() << std::endl;
-  std::cout << "alpha_shapes_from_file.num_vertices()=" << alpha_shapes_from_file.num_vertices() << std::endl;
-
-  return 0;
-}
\ No newline at end of file
diff --git a/src/Alpha_shapes/include/gudhi/Alpha_shapes.h b/src/Alpha_shapes/include/gudhi/Alpha_shapes.h
deleted file mode 100644
index ae2ee80d..00000000
--- a/src/Alpha_shapes/include/gudhi/Alpha_shapes.h
+++ /dev/null
@@ -1,200 +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) 2015  INRIA Saclay (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 SRC_ALPHA_SHAPES_INCLUDE_GUDHI_ALPHA_SHAPES_H_
-#define SRC_ALPHA_SHAPES_INCLUDE_GUDHI_ALPHA_SHAPES_H_
-
-// to construct a Delaunay_triangulation from a OFF file
-#include <gudhi/Alpha_shapes/Delaunay_triangulation_off_io.h>
-
-// to construct a simplex_tree from Delaunay_triangulation
-#include <gudhi/graph_simplicial_complex.h>
-#include <gudhi/Simplex_tree.h>
-
-#include <stdio.h>
-#include <stdlib.h>
-
-#include <CGAL/Delaunay_triangulation.h>
-#include <CGAL/Epick_d.h>
-#include <CGAL/algorithm.h>
-#include <CGAL/assertions.h>
-
-#include <iostream>
-#include <iterator>
-#include <vector>
-#include <string>
-
-namespace Gudhi {
-
-namespace alphashapes {
-
-/** \defgroup alpha_shapes Alpha shapes in dimension N
- *
- <DT>Implementations:</DT>
- Alpha shapes in dimension N are a subset of Delaunay Triangulation in dimension N.
-
-
- * \author    Vincent Rouvreau
- * \version   1.0
- * \date      2015
- * \copyright GNU General Public License v3.
- * @{
- */
-
-/**
- * \brief Alpha shapes data structure.
- *
- * \details Every simplex \f$[v_0, \cdots ,v_d]\f$ admits a canonical orientation
- * induced by the order relation on vertices \f$ v_0 < \cdots < v_d \f$.
- *
- * Details may be found in \cite boissonnatmariasimplextreealgorithmica.
- *
- * \implements FilteredComplex
- *
- */
-class Alpha_shapes {
- private:
-  // From Simplex_tree
-  /** \brief Type required to insert into a simplex_tree (with or without subfaces).*/
-  typedef std::vector<Vertex_handle> typeVectorVertex;
-
-  // From CGAL
-  /** \brief Kernel for the Delaunay_triangulation.
-   * Dimension can be set dynamically.
-   */
-  typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kernel;
-  /** \brief Delaunay_triangulation type required to create an alpha-shape.
-   */
-  typedef CGAL::Delaunay_triangulation<Kernel> Delaunay_triangulation;
-
- private:
-  /** \brief Upper bound on the simplex tree of the simplicial complex.*/
-  Gudhi::Simplex_tree<> _st;
-
- public:
-
-  Alpha_shapes(std::string off_file_name, int dimension) {
-    Delaunay_triangulation dt(dimension);
-    Gudhi::alphashapes::Delaunay_triangulation_off_reader<Delaunay_triangulation>
-        off_reader(off_file_name, dt, true, true);
-    if (!off_reader.is_valid()) {
-      std::cerr << "Unable to read file " << off_file_name << std::endl;
-      exit(-1); // ----- >>
-    }
-#ifdef DEBUG_TRACES
-    std::cout << "number of vertices=" << dt.number_of_vertices() << std::endl;
-    std::cout << "number of full cells=" << dt.number_of_full_cells() << std::endl;
-    std::cout << "number of finite full cells=" << dt.number_of_finite_full_cells() << std::endl;
-#endif  // DEBUG_TRACES
-    init<Delaunay_triangulation>(dt);
-  }
-
-  template<typename T>
-  Alpha_shapes(T triangulation) {
-    init<T>(triangulation);
-  }
-
-  ~Alpha_shapes() { }
-
- private:
-
-  template<typename T>
-  void init(T triangulation) {
-    _st.set_dimension(triangulation.maximal_dimension());
-    _st.set_filtration(0.0);
-    // triangulation points list
-    for (auto vit = triangulation.finite_vertices_begin();
-         vit != triangulation.finite_vertices_end(); ++vit) {
-      typeVectorVertex vertexVector;
-      Vertex_handle vertexHdl = std::distance(triangulation.finite_vertices_begin(), vit);
-      vertexVector.push_back(vertexHdl);
-
-      // Insert each point in the simplex tree
-      _st.insert_simplex(vertexVector, 0.0);
-
-#ifdef DEBUG_TRACES
-      std::cout << "P" << vertexHdl << ":";
-      for (auto Coord = vit->point().cartesian_begin(); Coord != vit->point().cartesian_end(); ++Coord) {
-        std::cout << *Coord << " ";
-      }
-      std::cout << std::endl;
-#endif  // DEBUG_TRACES
-    }
-    // triangulation finite full cells list
-    for (auto cit = triangulation.finite_full_cells_begin();
-         cit != triangulation.finite_full_cells_end(); ++cit) {
-      typeVectorVertex vertexVector;
-      for (auto vit = cit->vertices_begin(); vit != cit->vertices_end(); ++vit) {
-        // Vertex handle is distance - 1
-        Vertex_handle vertexHdl = std::distance(triangulation.vertices_begin(), *vit) - 1;
-        vertexVector.push_back(vertexHdl);
-      }
-      // Insert each point in the simplex tree
-      _st.insert_simplex_and_subfaces(vertexVector, 0.0);
-
-#ifdef DEBUG_TRACES
-      std::cout << "C" << std::distance(triangulation.finite_full_cells_begin(), cit) << ":";
-      for (auto value : vertexVector) {
-        std::cout << value << ' ';
-      }
-      std::cout << std::endl;
-#endif  // DEBUG_TRACES
-    }
-  }
-
- public:
-
-  /** \brief Returns the number of vertices in the complex. */
-  size_t num_vertices() {
-    return _st.num_vertices();
-  }
-
-  /** \brief Returns the number of simplices in the complex.
-   *
-   * Does not count the empty simplex. */
-  unsigned num_simplices() const {
-    return _st.num_simplices();
-  }
-
-  /** \brief Returns an upper bound on the dimension of the simplicial complex. */
-  int dimension() {
-    return _st.dimension();
-  }
-
-  /** \brief Returns an upper bound of the filtration values of the simplices. */
-  Filtration_value filtration() {
-    return _st.filtration();
-  }
-
-  friend std::ostream& operator<<(std::ostream& os, const Alpha_shapes& alpha_shape) {
-    // TODO: Program terminated with signal SIGABRT, Aborted - Maybe because of copy constructor
-    Gudhi::Simplex_tree<> st = alpha_shape._st;
-    os << st << std::endl;
-    return os;
-  }
-};
-
-} // namespace alphashapes
-
-} // namespace Gudhi
-
-#endif  // SRC_ALPHA_SHAPES_INCLUDE_GUDHI_ALPHA_SHAPES_H_
diff --git a/src/Alpha_shapes/include/gudhi/Alpha_shapes/Delaunay_triangulation_off_io.h b/src/Alpha_shapes/include/gudhi/Alpha_shapes/Delaunay_triangulation_off_io.h
deleted file mode 100644
index 693b393e..00000000
--- a/src/Alpha_shapes/include/gudhi/Alpha_shapes/Delaunay_triangulation_off_io.h
+++ /dev/null
@@ -1,213 +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) 2015  INRIA Saclay (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 SRC_ALPHA_SHAPES_INCLUDE_GUDHI_ALPHA_SHAPES_DELAUNAY_TRIANGULATION_OFF_IO_H_
-#define SRC_ALPHA_SHAPES_INCLUDE_GUDHI_ALPHA_SHAPES_DELAUNAY_TRIANGULATION_OFF_IO_H_
-
-#include <string>
-#include <vector>
-#include <fstream>
-
-#include "gudhi/Off_reader.h"
-
-namespace Gudhi {
-
-namespace alphashapes {
-
-/**
- *@brief Off reader visitor with flag that can be passed to Off_reader to read a Delaunay_triangulation_complex.
- */
-template<typename Complex>
-class Delaunay_triangulation_off_flag_visitor_reader {
-  Complex& complex_;
-  typedef typename Complex::Point Point;
-
-  const bool load_only_points_;
-
- public:
-  explicit Delaunay_triangulation_off_flag_visitor_reader(Complex& complex, bool load_only_points = false) :
-      complex_(complex),
-      load_only_points_(load_only_points) { }
-
-  void init(int dim, int num_vertices, int num_faces, int num_edges) {
-#ifdef DEBUG_TRACES
-    std::cout << "init" << std::endl;
-#endif  // DEBUG_TRACES
-  }
-
-  void point(const std::vector<double>& point) {
-#ifdef DEBUG_TRACES
-    std::cout << "p ";
-    for (auto coordinate: point) {
-      std::cout << coordinate << " | ";
-    }
-    std::cout << std::endl;
-#endif  // DEBUG_TRACES
-    complex_.insert(Point(point.size(), point.begin(), point.end()));
-  }
-
-  void maximal_face(const std::vector<int>& face) {
-    // For alpha shapes, only points are read
-  }
-
-  void done() {
-#ifdef DEBUG_TRACES
-    std::cout << "done" << std::endl;
-#endif  // DEBUG_TRACES
-  }
-};
-
-/**
- *@brief Off reader visitor that can be passed to Off_reader to read a Delaunay_triangulation_complex.
- */
-template<typename Complex>
-class Delaunay_triangulation_off_visitor_reader {
-  Complex& complex_;
-  // typedef typename Complex::Vertex_handle Vertex_handle;
-  // typedef typename Complex::Simplex_handle Simplex_handle;
-  typedef typename Complex::Point Point;
-
-  const bool load_only_points_;
-  std::vector<Point> points_;
-  // std::vector<Simplex_handle> maximal_faces_;
-
- public:
-  explicit Delaunay_triangulation_off_visitor_reader(Complex& complex, bool load_only_points = false) :
-      complex_(complex),
-      load_only_points_(load_only_points) { }
-
-  void init(int dim, int num_vertices, int num_faces, int num_edges) {
-#ifdef DEBUG_TRACES
-    std::cout << "init - " << num_vertices << std::endl;
-#endif  // DEBUG_TRACES
-    // maximal_faces_.reserve(num_faces);
-    points_.reserve(num_vertices);
-  }
-
-  void point(const std::vector<double>& point) {
-#ifdef DEBUG_TRACES
-    std::cout << "p ";
-    for (auto coordinate: point) {
-      std::cout << coordinate << " | ";
-    }
-    std::cout << std::endl;
-#endif  // DEBUG_TRACES
-    points_.emplace_back(Point(point.size(), point.begin(), point.end()));
-  }
-
-  void maximal_face(const std::vector<int>& face) {
-    // For alpha shapes, only points are read
-  }
-
-  void done() {
-    complex_.insert(points_.begin(), points_.end());
-#ifdef DEBUG_TRACES
-    std::cout << "done" << std::endl;
-#endif  // DEBUG_TRACES
-  }
-};
-
-/**
- *@brief Class that allows to load a Delaunay_triangulation_complex from an off file.
- */
-template<typename Complex>
-class Delaunay_triangulation_off_reader {
- public:
-  /**
-   * name_file : file to read
-   * read_complex : complex that will receive the file content
-   * read_only_points : specify true if only the points must be read
-   */
-  Delaunay_triangulation_off_reader(const std::string & name_file, Complex& read_complex, bool read_only_points = false,
-                                    bool is_flag = false) : valid_(false) {
-    std::ifstream stream(name_file);
-    if (stream.is_open()) {
-      if (is_flag) {
-        // For alpha shapes, only points are read
-        Delaunay_triangulation_off_flag_visitor_reader<Complex> off_visitor(read_complex, true);
-        Off_reader off_reader(stream);
-        valid_ = off_reader.read(off_visitor);
-      } else {
-        // For alpha shapes, only points are read
-        Delaunay_triangulation_off_visitor_reader<Complex> off_visitor(read_complex, true);
-        Off_reader off_reader(stream);
-        valid_ = off_reader.read(off_visitor);
-      }
-    }
-  }
-
-  /**
-   * return true if reading did not meet problems.
-   */
-  bool is_valid() const {
-    return valid_;
-  }
-
- private:
-  bool valid_;
-};
-
-template<typename Complex>
-class Delaunay_triangulation_off_writer {
- public:
-  /**
-   * name_file : file where the off will be written
-   * save_complex : complex that be outputted in the file
-   * for now only save triangles.
-   */
-  Delaunay_triangulation_off_writer(const std::string & name_file, const Complex& save_complex) {
-    std::ofstream stream(name_file);
-    if (stream.is_open()) {
-      // OFF header
-      stream << "OFF" << std::endl;
-      // no endl on next line - don't know why...
-      stream << save_complex.number_of_vertices() << " " << save_complex.number_of_finite_full_cells() << " 0";
-
-      // Points list
-      for (auto vit = save_complex.vertices_begin(); vit != save_complex.vertices_end(); ++vit) {
-        for (auto Coord = vit->point().cartesian_begin(); Coord != vit->point().cartesian_end(); ++Coord) {
-          stream << *Coord << " ";
-        }
-        stream << std::endl;
-      }
-
-      // Finite cells list
-      for (auto cit = save_complex.finite_full_cells_begin(); cit != save_complex.finite_full_cells_end(); ++cit) {
-        stream << std::distance(cit->vertices_begin(), cit->vertices_end()) << " ";  // Dimension
-        for (auto vit = cit->vertices_begin(); vit != cit->vertices_end(); ++vit) {
-          auto vertexHdl = *vit;
-          // auto vertexHdl = std::distance(save_complex.vertices_begin(), *vit) - 1;
-          // stream << std::distance(save_complex.vertices_begin(), *(vit)) - 1 << " ";
-        }
-        stream << std::endl;
-      }
-      stream.close();
-    } else {
-      std::cerr << "could not open file " << name_file << std::endl;
-    }
-  }
-};
-
-}  // namespace alphashapes
-
-}  // namespace Gudhi
-
-#endif  // SRC_ALPHA_SHAPES_INCLUDE_GUDHI_ALPHA_SHAPES_DELAUNAY_TRIANGULATION_OFF_IO_H_
diff --git a/src/Alpha_shapes/test/Alpha_shapes_unit_test.cpp b/src/Alpha_shapes/test/Alpha_shapes_unit_test.cpp
deleted file mode 100644
index b4c32321..00000000
--- a/src/Alpha_shapes/test/Alpha_shapes_unit_test.cpp
+++ /dev/null
@@ -1,126 +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) 2015  INRIA Saclay (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/>.
- */
-
-#define BOOST_TEST_MODULE alpha_shapes test
-#include <boost/test/included/unit_test.hpp>
-#include <boost/system/error_code.hpp>
-#include <boost/chrono/thread_clock.hpp>
-// to construct a Delaunay_triangulation from a OFF file
-#include "gudhi/Alpha_shapes/Delaunay_triangulation_off_io.h"
-#include "gudhi/Alpha_shapes.h"
-
-// to construct a simplex_tree from Delaunay_triangulation
-#include "gudhi/graph_simplicial_complex.h"
-#include "gudhi/Simplex_tree.h"
-
-#include <CGAL/Delaunay_triangulation.h>
-#include <CGAL/Epick_d.h>
-#include <CGAL/point_generators_d.h>
-#include <CGAL/algorithm.h>
-#include <CGAL/assertions.h>
-
-#include <iostream>
-#include <iterator>
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string>
-
-// Use dynamic_dimension_tag for the user to be able to set dimension
-typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > K;
-typedef CGAL::Delaunay_triangulation<K> T;
-// The triangulation uses the default instanciation of the 
-// TriangulationDataStructure template parameter
-
-BOOST_AUTO_TEST_CASE( OFF_file ) {
-  // ----------------------------------------------------------------------------
-  //
-  // Init of an alpha-shape from a OFF file
-  //
-  // ----------------------------------------------------------------------------
-  std::string off_file_name("S4_100.off");
-  std::cout << "========== OFF FILE NAME = " << off_file_name << " ==========" << std::endl;
-  
-  Gudhi::alphashapes::Alpha_shapes alpha_shapes_from_file(off_file_name, 4);
-
-  const int DIMENSION = 4;
-  std::cout << "alpha_shapes_from_file.dimension()=" << alpha_shapes_from_file.dimension() << std::endl;
-  BOOST_CHECK(alpha_shapes_from_file.dimension() == DIMENSION);
-  
-  const double FILTRATION = 0.0;
-  std::cout << "alpha_shapes_from_file.filtration()=" << alpha_shapes_from_file.filtration() << std::endl;
-  BOOST_CHECK(alpha_shapes_from_file.filtration() == FILTRATION);
-  
-  const int NUMBER_OF_VERTICES = 100;
-  std::cout << "alpha_shapes_from_file.num_vertices()=" << alpha_shapes_from_file.num_vertices() << std::endl;
-  BOOST_CHECK(alpha_shapes_from_file.num_vertices() == NUMBER_OF_VERTICES);
-  
-  const int NUMBER_OF_SIMPLICES = 6779;
-  std::cout << "alpha_shapes_from_file.num_simplices()=" << alpha_shapes_from_file.num_simplices() << std::endl;
-  BOOST_CHECK(alpha_shapes_from_file.num_simplices() == NUMBER_OF_SIMPLICES);
-
-}
-
-BOOST_AUTO_TEST_CASE( Delaunay_triangulation ) {
-  // ----------------------------------------------------------------------------
-  //
-  // Init of an alpha-shape from a Delauny triangulation
-  //
-  // ----------------------------------------------------------------------------
-  T dt(8);
-  std::string off_file_name("S8_10.off");
-  std::cout << "========== OFF FILE NAME = " << off_file_name << " ==========" << std::endl;
-  
-  Gudhi::alphashapes::Delaunay_triangulation_off_reader<T> off_reader(off_file_name, dt, true, true);
-  std::cout << "off_reader.is_valid()=" << off_reader.is_valid() << std::endl;
-  BOOST_CHECK(off_reader.is_valid());
-
-  const int NUMBER_OF_VERTICES = 10;
-  std::cout << "dt.number_of_vertices()=" << dt.number_of_vertices() << std::endl;
-  BOOST_CHECK(dt.number_of_vertices() == NUMBER_OF_VERTICES);
-  
-  const int NUMBER_OF_FULL_CELLS = 30;
-  std::cout << "dt.number_of_full_cells()=" << dt.number_of_full_cells() << std::endl;
-  BOOST_CHECK(dt.number_of_full_cells() == NUMBER_OF_FULL_CELLS);
-  
-  const int NUMBER_OF_FINITE_FULL_CELLS = 6;
-  std::cout << "dt.number_of_finite_full_cells()=" << dt.number_of_finite_full_cells() << std::endl;
-  BOOST_CHECK(dt.number_of_finite_full_cells() == NUMBER_OF_FINITE_FULL_CELLS);
-
-  Gudhi::alphashapes::Alpha_shapes alpha_shapes_from_dt(dt);
-
-  const int DIMENSION = 8;
-  std::cout << "alpha_shapes_from_dt.dimension()=" << alpha_shapes_from_dt.dimension() << std::endl;
-  BOOST_CHECK(alpha_shapes_from_dt.dimension() == DIMENSION);
-  
-  const double FILTRATION = 0.0;
-  std::cout << "alpha_shapes_from_dt.filtration()=" << alpha_shapes_from_dt.filtration() << std::endl;
-  BOOST_CHECK(alpha_shapes_from_dt.filtration() == FILTRATION);
-  
-  std::cout << "alpha_shapes_from_dt.num_vertices()=" << alpha_shapes_from_dt.num_vertices() << std::endl;
-  BOOST_CHECK(alpha_shapes_from_dt.num_vertices() == NUMBER_OF_VERTICES);
-  
-  const int NUMBER_OF_SIMPLICES = 997;
-  std::cout << "alpha_shapes_from_dt.num_simplices()=" << alpha_shapes_from_dt.num_simplices() << std::endl;
-  BOOST_CHECK(alpha_shapes_from_dt.num_simplices() == NUMBER_OF_SIMPLICES);
-}
-
diff --git a/src/Alpha_shapes/test/CMakeLists.txt b/src/Alpha_shapes/test/CMakeLists.txt
deleted file mode 100644
index e0d33827..00000000
--- a/src/Alpha_shapes/test/CMakeLists.txt
+++ /dev/null
@@ -1,48 +0,0 @@
-cmake_minimum_required(VERSION 2.6)
-project(GUDHIAlphaShapesUT)
-
-# need CGAL 4.6
-# cmake -DCGAL_DIR=~/workspace/CGAL-4.6-beta1 ../../..
-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( ${EIGEN3_USE_FILE} )
-      include_directories (BEFORE "../../include")
-
-      if (GCOVR_PATH)
-        # for gcovr to make coverage reports - Corbera Jenkins plugin
-        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
-        set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fprofile-arcs -ftest-coverage")
-        set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fprofile-arcs -ftest-coverage")
-      endif()
-      if (GPROF_PATH)
-        # for gprof to make coverage reports - Jenkins
-        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
-        set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -pg")
-        set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -pg")
-      endif()
-
-      # uncomment to display debug traces
-      # add_definitions(-DDEBUG_TRACES)
-      add_executable ( AlphaShapesUT Alpha_shapes_unit_test.cpp )
-      target_link_libraries(AlphaShapesUT  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
-      add_test(NAME AlphaShapesUT 
-        COMMAND ${CMAKE_CURRENT_BINARY_DIR}/AlphaShapesUT
-        # XML format for Jenkins xUnit plugin 
-        --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/AlphaShapesUT.xml --log_level=test_suite --report_level=no)
-
-
-    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/Alpha_shapes/test/README b/src/Alpha_shapes/test/README
deleted file mode 100644
index cddd46ca..00000000
--- a/src/Alpha_shapes/test/README
+++ /dev/null
@@ -1,14 +0,0 @@
-To compile:
-***********
-
-cd /path-to-gudhi/
-cmake .
-cd /path-to-test/
-make
-
-To launch with details:
-***********************
-
-./AlphaShapesUT --report_level=detailed --log_level=all 
-
-   ==> echo $? returns 0 in case of success (non-zero otherwise)
diff --git a/src/Alpha_shapes/test/S4_100.off b/src/Alpha_shapes/test/S4_100.off
deleted file mode 100644
index 0a5dc58c..00000000
--- a/src/Alpha_shapes/test/S4_100.off
+++ /dev/null
@@ -1,102 +0,0 @@
-OFF
-100 0 0
-0.562921 -0.735261 -0.256472 0.277007
--0.803733 -0.0527915 -0.315125 0.501918
--0.24946 -0.354982 -0.410773 -0.801887
-0.916381 -0.0512295 0.371049 0.141223
-0.182222 0.940836 -0.171362 -0.228599
--0.787145 -0.129213 0.568102 -0.202402
-0.0187866 -0.22093 -0.832882 -0.507095
--0.4702 -0.533814 0.353776 0.607286
--0.159798 -0.504771 0.263586 0.806346
-0.295546 0.162541 0.452931 0.825279
-0.242043 -0.107437 -0.913612 -0.308521
-0.875759 -0.113035 -0.469189 -0.0114505
-0.547877 -0.762247 -0.256972 -0.229729
--0.172302 0.521057 0.412013 -0.727363
--0.724729 -0.0574074 -0.0290602 0.686023
-0.700434 -0.102636 0.687285 0.162779
--0.681386 0.0946893 0.610047 0.393178
--0.847553 -0.357132 0.383743 0.0827718
-0.72297 -0.161631 -0.608517 0.284424
-0.757394 0.141549 0.196065 -0.606528
-0.78094 0.00901997 0.434536 0.448586
-0.14166 -0.619339 0.614589 -0.467582
-0.473105 -0.537832 -0.0103746 0.697711
--0.208004 0.536218 0.818027 0.00605288
-0.743694 -0.628926 0.188072 0.126488
--0.462228 -0.278147 0.35514 -0.76345
--0.17361 0.249211 0.758567 -0.57648
-0.416958 -0.254924 -0.576373 -0.654946
--0.590751 -0.286089 -0.424896 0.623402
--0.639538 -0.739693 -0.203745 0.0482932
-0.0731787 0.132121 0.864022 0.480266
--0.149644 -0.164724 -0.249746 -0.94239
--0.348592 0.0120379 -0.928656 -0.126239
-0.395328 -0.54513 0.149976 -0.723917
--0.974164 0.14707 0.157191 0.068302
--0.166425 0.119943 -0.627304 -0.751269
-0.031947 -0.358518 -0.708301 -0.607251
-0.93781 -0.155368 -0.30951 0.0240237
-0.276094 -0.753155 -0.597088 -0.00387459
--0.642876 -0.200551 -0.263517 -0.690687
-0.178711 0.604987 -0.262989 0.729993
--0.520347 0.497922 -0.676144 0.155374
--0.703999 0.500219 -0.484381 0.139789
--0.131013 0.835735 0.506779 0.166004
--0.536116 -0.566557 0.229226 0.582279
--0.334105 0.158252 0.926091 0.0754059
--0.0362677 0.296076 0.897108 0.325915
--0.57486 0.798575 0.15324 -0.0912754
-0.498602 0.0186805 0.72824 0.469801
--0.960329 0.0473356 0.261005 -0.0860505
-0.899134 -0.381392 -0.214508 0.00921711
-0.570576 0.567224 0.393019 -0.445237
--0.761763 -0.614589 -0.0546476 -0.197513
-0.188584 0.289531 0.174031 0.922129
--0.458506 -0.583876 0.639297 -0.2004
-0.785343 -0.21571 0.0794082 -0.574804
-0.0819036 0.65961 -0.247426 0.704973
-0.573125 0.49706 0.373026 0.534145
--0.513286 -0.626226 0.208535 -0.548536
-0.460558 0.468686 0.507832 -0.55707
-0.716158 -0.488201 0.388209 -0.313164
-0.881074 0.152441 0.380128 -0.236589
-0.885793 0.0386389 0.161009 -0.433537
--0.365162 0.298384 0.292846 0.831784
-0.364934 0.632269 -0.197205 -0.654346
--0.31469 -0.429991 0.665304 -0.522923
--0.734198 0.462914 -0.135691 -0.477756
--0.422885 0.674444 -0.364143 -0.483419
-0.829218 -0.154622 -0.381147 0.378439
-0.887881 0.310479 -0.109528 0.321363
--0.354398 -0.693974 0.456019 -0.429941
--0.492045 -0.160008 0.044387 0.854587
-0.0595532 0.158421 0.412577 -0.895062
--0.211441 0.491794 -0.153521 0.83058
--0.33558 -0.504711 0.353831 -0.71236
--0.735211 -0.197714 0.525626 0.379593
-0.465818 -0.424245 0.769469 -0.104627
--0.641071 -0.286339 -0.704442 -0.103923
--0.00446569 0.0249849 -0.194417 -0.980591
--0.610081 -0.252448 0.176698 -0.729966
--0.0859217 -0.154471 0.715027 0.676382
-0.091315 0.0723382 -0.855023 -0.505337
-0.165362 0.200983 -0.428242 -0.865373
--0.587465 0.303019 -0.152442 0.734729
-0.454946 -0.319828 0.437063 -0.706902
--0.384368 0.277509 0.879225 -0.0470385
-0.523335 -0.330233 -0.208592 0.757335
-0.895086 0.0448492 0.268089 -0.353466
--0.0272491 -0.567336 -0.72254 -0.39411
--0.0745014 -0.121818 -0.882466 0.448179
-0.382304 -0.240135 0.851109 -0.267941
--0.418057 -0.852847 -0.3128 0.00606452
--0.554046 0.304237 0.272381 -0.725453
-0.155115 -0.0894732 -0.245017 -0.952838
-0.114459 -0.130722 0.953669 0.245614
-0.0913002 -0.462466 0.244433 0.847374
--0.198849 0.0785111 0.131441 -0.967997
--0.303154 -0.686484 0.639333 0.167604
-0.521455 0.256835 -0.0584503 -0.811606
--0.109787 0.870544 0.161523 0.451676
diff --git a/src/Alpha_shapes/test/S8_10.off b/src/Alpha_shapes/test/S8_10.off
deleted file mode 100644
index 1d67e10f..00000000
--- a/src/Alpha_shapes/test/S8_10.off
+++ /dev/null
@@ -1,12 +0,0 @@
-OFF
-10 0 0
-0.440036 -0.574754 -0.200485 0.216537 -0.501251 -0.0329236 -0.196529 0.313023
--0.129367 -0.184089 -0.213021 -0.415848 0.783529 -0.0438025 0.317256 0.120749
-0.132429 0.683748 -0.124536 -0.166133 -0.540695 -0.0887576 0.390234 -0.139031
-0.0137399 -0.161581 -0.609142 -0.370872 -0.320669 -0.364053 0.24127 0.41416
--0.115313 -0.36425 0.190208 0.581871 0.204605 0.112527 0.313562 0.571337
-0.168272 -0.0746917 -0.635156 -0.214488 0.629498 -0.0812499 -0.337255 -0.00823068
-0.369896 -0.514626 -0.173493 -0.1551 -0.127105 0.384377 0.303936 -0.536566
--0.49013 -0.0388242 -0.0196532 0.463953 0.515962 -0.0756047 0.506276 0.119908
--0.434258 0.060347 0.388793 0.250579 -0.653127 -0.275207 0.295714 0.0637842
-0.596172 -0.133284 -0.501793 0.234541 0.428452 0.0800735 0.110912 -0.343109
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 3be05c4f..9f6db2c7 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -44,7 +44,6 @@ else()
   add_subdirectory(example/Skeleton_blocker)                   
   add_subdirectory(example/Contraction)                   
   add_subdirectory(example/Hasse_complex)
-  add_subdirectory(example/Alpha_shapes)
   add_subdirectory(example/Bottleneck)
 
   # GudhUI