Moved alphashapedoc.off in data/points

Moved Delaunay triangulation OFF files read and write in src/common
Delaunay triangulation OFF files read and write documentation, examples and tests


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alphashapes@623 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: e03902736a79436e97dbf77a88504f3faa8bd9c6

2 files changed, 40 insertions, 240 deletions

diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h
index ca84d6d9..d25c05cb 100644
--- a/src/Alpha_complex/include/gudhi/Alpha_complex.h
+++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h
@@ -23,9 +23,6 @@
 #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>
@@ -46,8 +43,7 @@
 #include <iterator>
 #include <vector>
 #include <string>
-#include <limits>
-#include <map>
+#include <limits> // NaN
 
 namespace Gudhi {
 
@@ -82,59 +78,59 @@ class Alpha_complex {
  private:
   // From Simplex_tree
   /** \brief Type required to insert into a simplex_tree (with or without subfaces).*/
-  typedef std::vector<Vertex_handle> typeVectorVertex;
+  typedef std::vector<Vertex_handle> Vector_vertex;
 
+  /** \brief Simplex_handle type from simplex_tree.*/
   typedef typename Gudhi::Simplex_tree<>::Simplex_handle Simplex_handle;
+  /** \brief Simplex_result is the type returned from simplex_tree insert function.*/
   typedef typename std::pair<Simplex_handle, bool> Simplex_result;
 
+  /** \brief Filtration_simplex_range type from simplex_tree.*/
+  typedef typename Gudhi::Simplex_tree<>::Filtration_simplex_range Filtration_simplex_range;
+
+  /** \brief Simplex_vertex_range type from simplex_tree.*/
+  typedef typename Gudhi::Simplex_tree<>::Simplex_vertex_range Simplex_vertex_range;
+  
   // From CGAL
-  /** \brief Kernel for the Delaunay_triangulation->
-   * Dimension can be set dynamically.
-   */
+  /** \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-complex.
-   */
+  /** \brief Delaunay_triangulation type required to create an alpha-complex.*/
   typedef CGAL::Delaunay_triangulation<Kernel> Delaunay_triangulation;
 
   typedef typename Kernel::Compute_squared_radius_d Squared_Radius;
   typedef typename Kernel::Side_of_bounded_sphere_d Is_Gabriel;
 
-  /** \brief Type required to insert into a simplex_tree (with or without subfaces).*/
+  /** \brief Type required to compute squared radius, or side of bounded sphere on a vector of points.*/
   typedef std::vector<Kernel::Point_d> Vector_of_CGAL_points;
 
+  /** \brief Vertex_iterator type from CGAL.*/
   typedef Delaunay_triangulation::Vertex_iterator CGAL_vertex_iterator;
 
+  /** \brief Boost bimap type to switch from CGAL vertex iterator to simplex tree vertex handle and vice versa.*/
   typedef boost::bimap< CGAL_vertex_iterator, Vertex_handle > Bimap_vertex;
   
  private:
-  /** \brief Upper bound on the simplex tree of the simplicial complex.*/
+  /** \brief Alpha complex is represented internally by a simplex tree.*/
   Gudhi::Simplex_tree<> st_;
+  /** \brief Boost bimap to switch from CGAL vertex iterator to simplex tree vertex handle and vice versa.*/
   Bimap_vertex cgal_simplextree;
+  /** \brief Pointer on the CGAL Delaunay triangulation.*/
   Delaunay_triangulation* triangulation;
 
  public:
-
   Alpha_complex(std::string& off_file_name)
   : triangulation(nullptr) {
-#ifdef DEBUG_TRACES
-    char buffer[256]={0};
-    sprintf(buffer,"%p", triangulation);
-    std::cout << "pointer=" << buffer << std::endl;
-#endif  // DEBUG_TRACES
-    Gudhi::alphacomplex::Delaunay_triangulation_off_reader<Delaunay_triangulation> off_reader(off_file_name);
+    Gudhi::Delaunay_triangulation_off_reader<Delaunay_triangulation> off_reader(off_file_name);
     if (!off_reader.is_valid()) {
       std::cerr << "Unable to read file " << off_file_name << std::endl;
       exit(-1); // ----- >>
     }
     triangulation = off_reader.get_complex();
-#ifdef DEBUG_TRACES
-    //char buffer[256]={0};
-    sprintf(buffer,"%p", triangulation);
-    std::cout << "pointer=" << buffer << std::endl;
-    std::cout << "number of vertices=" << triangulation->number_of_vertices() << std::endl;
-    std::cout << "number of full cells=" << triangulation->number_of_full_cells() << std::endl;
-    std::cout << "number of finite full cells=" << triangulation->number_of_finite_full_cells() << std::endl;
-#endif  // DEBUG_TRACES
+    init();
+  }
+
+  Alpha_complex(Delaunay_triangulation* triangulation_ptr)
+  : triangulation(triangulation_ptr) {
     init();
   }
 
@@ -142,6 +138,21 @@ class Alpha_complex {
     delete triangulation;
   }
 
+  Filtration_simplex_range filtration_simplex_range() {
+    return st_.filtration_simplex_range();
+  }
+  
+  Simplex_vertex_range simplex_vertex_range(Simplex_handle sh) {
+    return st_.simplex_vertex_range(sh);
+  }
+  
+  /** \brief Returns the filtration value of a simplex.
+   *
+   * Called on the null_simplex, returns INFINITY. */
+  Gudhi::Simplex_tree<>::Filtration_value filtration(Simplex_handle sh) {
+    return st_.filtration(sh);
+  }
+
  private:
 
   void init() {
@@ -161,7 +172,7 @@ class Alpha_complex {
     // --------------------------------------------------------------------------------------------
     // Simplex_tree construction from loop on triangulation finite full cells list
     for (auto cit = triangulation->finite_full_cells_begin(); cit != triangulation->finite_full_cells_end(); ++cit) {
-      typeVectorVertex vertexVector;
+      Vector_vertex vertexVector;
 #ifdef DEBUG_TRACES
       std::cout << "Simplex_tree insertion ";
 #endif  // DEBUG_TRACES
@@ -325,7 +336,6 @@ class Alpha_complex {
   }
 
   friend std::ostream& operator<<(std::ostream& os, const Alpha_complex & alpha_complex) {
-    // TODO: Program terminated with signal SIGABRT, Aborted - Maybe because of copy constructor
     Gudhi::Simplex_tree<> st = alpha_complex.st_;
     os << st << std::endl;
     return os;
diff --git a/src/Alpha_complex/include/gudhi/Alpha_shapes/Delaunay_triangulation_off_io.h b/src/Alpha_complex/include/gudhi/Alpha_shapes/Delaunay_triangulation_off_io.h
deleted file mode 100644
index 8bda23b7..00000000
--- a/src/Alpha_complex/include/gudhi/Alpha_shapes/Delaunay_triangulation_off_io.h
+++ /dev/null
@@ -1,210 +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 <map>
-
-#include "gudhi/Off_reader.h"
-
-namespace Gudhi {
-
-namespace alphacomplex {
-
-/**
- *@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_visitor_reader {
- private:
-  Complex* _complex;
-  typedef typename Complex::Point Point;
-
- public:
-
-  // Pass a Complex as a parameter is required, even if not used. Otherwise, compilation is KO.
-  Delaunay_triangulation_off_visitor_reader(Complex* _complex_ptr)
-      : _complex(nullptr) { }
-
-  void init(int dim, int num_vertices, int num_faces, int num_edges) {
-#ifdef DEBUG_TRACES
-    std::cout << "Delaunay_triangulation_off_visitor_reader::init - dim=" << dim << " - num_vertices=" <<
-        num_vertices << " - num_faces=" << num_faces << " - num_edges=" << num_edges << std::endl;
-#endif  // DEBUG_TRACES
-    if (num_faces > 0) {
-      std::cerr << "Delaunay_triangulation_off_visitor_reader::init faces are not taken into account from OFF " <<
-          "file for Delaunay triangulation - faces are computed." << std::endl;
-    }
-    if (num_edges > 0) {
-      std::cerr << "Delaunay_triangulation_off_visitor_reader::init edges are not taken into account from OFF " <<
-          "file for Delaunay triangulation - edges are computed." << std::endl;
-    }
-    // Complex construction with dimension from file
-    _complex = new Complex(dim);
-  }
-
-  void point(const std::vector<double>& point) {
-#ifdef DEBUG_TRACES
-    std::cout << "Delaunay_triangulation_off_visitor_reader::point ";
-    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 Delaunay Triangulation, only points are read
-#ifdef DEBUG_TRACES
-    std::cout << "Delaunay_triangulation_off_visitor_reader::face ";
-    for (auto vertex : face) {
-      std::cout << vertex << " | ";
-    }
-    std::cout << std::endl;
-#endif  // DEBUG_TRACES
-  }
-
-  void done() {
-#ifdef DEBUG_TRACES
-    std::cout << "Delaunay_triangulation_off_visitor_reader::done" << std::endl;
-#endif  // DEBUG_TRACES
-  }
-
-  Complex* get_complex() {
-    return _complex;
-  }
-};
-
-/**
- *@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) : valid_(false) {
-    std::ifstream stream(name_file);
-    if (stream.is_open()) {
-      Delaunay_triangulation_off_visitor_reader<Complex> off_visitor(_complex);
-      Off_reader off_reader(stream);
-      valid_ = off_reader.read(off_visitor);
-      if (valid_) {
-        _complex = off_visitor.get_complex();
-      }
-    } else {
-      std::cerr << "Delaunay_triangulation_off_reader::Delaunay_triangulation_off_reader could not open file " <<
-          name_file << std::endl;
-    }
-
-  }
-
-  /**
-   * return true if reading did not meet problems.
-   */
-  bool is_valid() const {
-    return valid_;
-  }
-
-  Complex* get_complex() {
-    if (valid_)
-      return _complex;
-    return nullptr;
-
-  }
-
- private:
-  bool valid_;
-  Complex* _complex;
-};
-
-template<typename Complex>
-class Delaunay_triangulation_off_writer {
- public:
-  typedef typename Complex::Point Point;
-
-  /**
-   * 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, Complex* complex_ptr) {
-    std::ofstream stream(name_file);
-    if (stream.is_open()) {
-      if (complex_ptr->current_dimension() == 3) {
-        // OFF header
-        stream << "OFF" << std::endl;
-        // no endl on next line - don't know why...
-        stream << complex_ptr->number_of_vertices() << " " << complex_ptr->number_of_finite_full_cells() << " 0";
-      } else {
-        // nOFF header
-        stream << "nOFF" << std::endl;
-        // no endl on next line - don't know why...
-        stream << complex_ptr->current_dimension() << " " << complex_ptr->number_of_vertices() << " " <<
-            complex_ptr->number_of_finite_full_cells() << " 0";
-
-      }
-
-      // bimap to retrieve vertex handles from points and vice versa
-      std::map< Point, int > points_to_vh;
-      // Start to insert at default handle value
-      int vertex_handle = int();
-
-      // Points list
-      for (auto vit = complex_ptr->vertices_begin(); vit != complex_ptr->vertices_end(); ++vit) {
-        for (auto Coord = vit->point().cartesian_begin(); Coord != vit->point().cartesian_end(); ++Coord) {
-          stream << *Coord << " ";
-        }
-        stream << std::endl;
-        points_to_vh[vit->point()] = vertex_handle;
-        vertex_handle++;
-      }
-
-      for (auto cit = complex_ptr->finite_full_cells_begin(); cit != complex_ptr->finite_full_cells_end(); ++cit) {
-        std::vector<int> vertexVector;
-        stream << std::distance(cit->vertices_begin(), cit->vertices_end()) << " ";
-        for (auto vit = cit->vertices_begin(); vit != cit->vertices_end(); ++vit) {
-          stream << points_to_vh[(*vit)->point()] << " ";
-        }
-        stream << std::endl;
-      }
-      stream.close();
-    } else {
-      std::cerr << "Delaunay_triangulation_off_writer::Delaunay_triangulation_off_writer could not open file " <<
-          name_file << std::endl;
-    }
-  }
-};
-
-} // namespace alphacomplex
-
-} // namespace Gudhi
-
-#endif  // SRC_ALPHA_SHAPES_INCLUDE_GUDHI_ALPHA_SHAPES_DELAUNAY_TRIANGULATION_OFF_IO_H_