Checkin for rollback purpose. Compiles but do not work.

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alphashapes@607 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: e163ca16ebc76a13cec21bf881fe3b03e0617711

5 files changed, 80 insertions, 35 deletions

diff --git a/src/Alpha_shapes/example/Delaunay_triangulation_off_rw.cpp b/src/Alpha_shapes/example/Delaunay_triangulation_off_rw.cpp
index a31c44ab..6c9fcdab 100644
--- a/src/Alpha_shapes/example/Delaunay_triangulation_off_rw.cpp
+++ b/src/Alpha_shapes/example/Delaunay_triangulation_off_rw.cpp
@@ -82,7 +82,7 @@ int main(int argc, char **argv) {
   }
   std::cout << std::endl;*/
  
-  int i = 0, j = 0;
+  /*int i = 0, j = 0;
   typedef T::Full_cell_iterator Full_cell_iterator;
   typedef T::Facet Facet;
 
@@ -96,7 +96,7 @@ int main(int argc, char **argv) {
   }
   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);
diff --git a/src/Alpha_shapes/example/Simplex_tree_from_delaunay_triangulation.cpp b/src/Alpha_shapes/example/Simplex_tree_from_delaunay_triangulation.cpp
index 11079a03..0a24fb56 100644
--- a/src/Alpha_shapes/example/Simplex_tree_from_delaunay_triangulation.cpp
+++ b/src/Alpha_shapes/example/Simplex_tree_from_delaunay_triangulation.cpp
@@ -66,12 +66,12 @@ int main(int argc, char **argv) {
   //
   // ----------------------------------------------------------------------------
   Gudhi::alphashapes::Alpha_shapes alpha_shapes_from_file(off_file_name);
-  //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;
+  //std::cout << alpha_shapes_from_file << std::endl;
 
   return 0;
 }
\ No newline at end of file
diff --git a/src/Alpha_shapes/example/alphashapedoc.off b/src/Alpha_shapes/example/alphashapedoc.off
new file mode 100755
index 00000000..bb790193
--- /dev/null
+++ b/src/Alpha_shapes/example/alphashapedoc.off
@@ -0,0 +1,10 @@
+nOFF
+2 7 0 0
+1.0 1.0
+7.0 0.0
+4.0 6.0
+9.0 6.0
+0.0 14.0
+2.0 19.0
+9.0 17.0
+
diff --git a/src/Alpha_shapes/include/gudhi/Alpha_shapes.h b/src/Alpha_shapes/include/gudhi/Alpha_shapes.h
index 6f290938..6de675f6 100644
--- a/src/Alpha_shapes/include/gudhi/Alpha_shapes.h
+++ b/src/Alpha_shapes/include/gudhi/Alpha_shapes.h
@@ -96,13 +96,13 @@ class Alpha_shapes {
 
  private:
   /** \brief Upper bound on the simplex tree of the simplicial complex.*/
-  Gudhi::Simplex_tree<> _st;
+  Gudhi::Simplex_tree<> st_;
 
  public:
 
-  Alpha_shapes(std::string off_file_name) {
+  Alpha_shapes(std::string& off_file_name) {
     // Construct a default Delaunay_triangulation (dim=0) - dim will be set in visitor reader init function
-    Delaunay_triangulation dt(3);
+    Delaunay_triangulation dt(2);
     Gudhi::alphashapes::Delaunay_triangulation_off_reader<Delaunay_triangulation> off_reader(off_file_name, dt);
     if (!off_reader.is_valid()) {
       std::cerr << "Unable to read file " << off_file_name << std::endl;
@@ -117,7 +117,7 @@ class Alpha_shapes {
   }
 
   template<typename T>
-  Alpha_shapes(T triangulation) {
+  Alpha_shapes(T& triangulation) {
     init<T>(triangulation);
   }
 
@@ -126,8 +126,8 @@ class Alpha_shapes {
  private:
 
   template<typename T>
-  void init(T triangulation) {
-    _st.set_dimension(triangulation.maximal_dimension());
+  void init(T& triangulation) {
+    st_.set_dimension(triangulation.maximal_dimension());
     Filtration_value filtration_max = 0.0;
 
     Kernel k;
@@ -148,11 +148,11 @@ class Alpha_shapes {
           // Vector of points for alpha_shapes filtration value computation
           pointVector.push_back((*vit)->point());
 #ifdef DEBUG_TRACES
-          std::cout << "Point ";
+          /*std::cout << "Point ";
           for (auto Coord = (*vit)->point().cartesian_begin(); Coord != (*vit)->point().cartesian_end(); ++Coord) {
             std::cout << *Coord << " | ";
           }
-          std::cout << std::endl;
+          std::cout << std::endl;*/
 #endif  // DEBUG_TRACES
         }
       }
@@ -161,66 +161,71 @@ class Alpha_shapes {
       if (!triangulation.is_infinite(cit)) {
         alpha_shapes_filtration = squared_radius(pointVector.begin(), pointVector.end());
 #ifdef DEBUG_TRACES
-        std::cout << "Alpha_shape filtration value = " << alpha_shapes_filtration << std::endl;
+        //std::cout << "Alpha_shape filtration value = " << alpha_shapes_filtration << std::endl;
 #endif  // DEBUG_TRACES
       } else {
         Filtration_value tmp_filtration = 0.0;
         bool is_gab = true;
-        for (auto vit = triangulation.finite_vertices_begin(); vit != triangulation.finite_vertices_end(); ++vit) {
+        /*for (auto vit = triangulation.finite_vertices_begin(); vit != triangulation.finite_vertices_end(); ++vit) {
           if (CGAL::ON_UNBOUNDED_SIDE != is_gabriel(pointVector.begin(), pointVector.end(), vit->point())) {
             is_gab = false;
             // TODO(VR) : Compute minimum 
             
           }
-        }
+        }*/
         if (true == is_gab) {
           alpha_shapes_filtration = squared_radius(pointVector.begin(), pointVector.end());
 #ifdef DEBUG_TRACES
-          std::cout << "Alpha_shape filtration value = " << alpha_shapes_filtration << std::endl;
+          //std::cout << "Alpha_shape filtration value = " << alpha_shapes_filtration << std::endl;
 #endif  // DEBUG_TRACES
         }
       }
       // Insert each point in the simplex tree
-      _st.insert_simplex_and_subfaces(vertexVector, alpha_shapes_filtration);
+      st_.insert_simplex_and_subfaces(vertexVector, alpha_shapes_filtration);
 
 #ifdef DEBUG_TRACES
       std::cout << "C" << std::distance(triangulation.full_cells_begin(), cit) << ":";
       for (auto value : vertexVector) {
         std::cout << value << ' ';
       }
-      std::cout << std::endl;
+      std::cout << " | alpha=" << alpha_shapes_filtration << std::endl;
 #endif  // DEBUG_TRACES
     }
-    _st.set_filtration(filtration_max);
+    st_.set_filtration(filtration_max);
+  }
+
+  template<typename T>
+  void recursive_init(T& triangulation, typeVectorVertex vertexVector) {
+    
   }
 
  public:
 
   /** \brief Returns the number of vertices in the complex. */
   size_t num_vertices() {
-    return _st.num_vertices();
+    return st_.num_vertices();
   }
 
   /** \brief Returns the number of simplices in the complex.
    *
    * Does not count the empty simplex. */
   const unsigned int& num_simplices() const {
-    return _st.num_simplices();
+    return st_.num_simplices();
   }
 
   /** \brief Returns an upper bound on the dimension of the simplicial complex. */
   int dimension() {
-    return _st.dimension();
+    return st_.dimension();
   }
 
   /** \brief Returns an upper bound of the filtration values of the simplices. */
   Filtration_value filtration() {
-    return _st.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;
+    Gudhi::Simplex_tree<> st = alpha_shape.st_;
     os << st << std::endl;
     return os;
   }
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
index 3215c8f6..1413ad89 100644
--- 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
@@ -25,6 +25,7 @@
 #include <string>
 #include <vector>
 #include <fstream>
+#include <iterator>     // std::distance
 
 #include "gudhi/Off_reader.h"
 
@@ -47,7 +48,7 @@ class Delaunay_triangulation_off_visitor_reader {
 
   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=" << 
+    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) {
@@ -121,7 +122,7 @@ class Delaunay_triangulation_off_reader {
   bool is_valid() const {
     return valid_;
   }
-  
+
  private:
   bool valid_;
 };
@@ -138,10 +139,19 @@ class Delaunay_triangulation_off_writer {
   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";
+      if (save_complex.current_dimension() == 3) {
+        // 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";
+      } else {
+        // nOFF header
+        stream << "nOFF" << std::endl;
+        // no endl on next line - don't know why...
+        stream << save_complex.current_dimension() << " " << 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) {
@@ -151,16 +161,36 @@ class Delaunay_triangulation_off_writer {
         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 cit = save_complex.full_cells_begin(); cit != save_complex.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) {
-          auto vertexHdl = *vit;
-          // auto vertexHdl = std::distance(save_complex.vertices_begin(), *vit) - 1;
-          // stream << std::distance(save_complex.vertices_begin(), *(vit)) - 1 << " ";
+          // Vector of vertex construction for simplex_tree structure
+          // Vertex handle is distance - 1
+          //int vertexHdl = std::distance(save_complex.vertices_begin(), *vit);
+          // infinite cell is -1 for infinite
+          //vertexVector.push_back(vertexHdl);
+          // Vector of points for alpha_shapes filtration value computation
         }
         stream << std::endl;
       }
+
+
+
+
+
+      /*
+              // Finite cells list
+              for (auto cit = save_complex.full_cells_begin(); cit != save_complex.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 << "Delaunay_triangulation_off_writer::Delaunay_triangulation_off_writer could not open file " <<