Backmerge of trunk

Add alpha complex in bibtex


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alphashapes@929 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: c8975be439b3e9e91d1fd6ad988db12c75d0395b

4 files changed, 19 insertions, 17 deletions

diff --git a/src/Contraction/example/Garland_heckbert.cpp b/src/Contraction/example/Garland_heckbert.cpp
index 70f29b6a..b545a066 100644
--- a/src/Contraction/example/Garland_heckbert.cpp
+++ b/src/Contraction/example/Garland_heckbert.cpp
@@ -145,12 +145,13 @@ class GH_visitor : public Gudhi::contraction::Contraction_visitor<EdgeProfile> {
 
 int main(int argc, char *argv[]) {
   if (argc != 4) {
-    std::cerr << "Usage " << argv[0] << " input.off output.off N to load the file input.off, contract N edges and save "
-        << "the result to output.off.\n";
+    std::cerr << "Usage " << argv[0] <<
+        " input.off output.off N to load the file input.off, contract N edges and save the result to output.off.\n";
     return EXIT_FAILURE;
   }
 
   Complex complex;
+  typedef Complex::Vertex_handle Vertex_handle;
 
   // load the points
   Skeleton_blocker_off_reader<Complex> off_reader(argv[1], complex);
@@ -159,8 +160,12 @@ int main(int argc, char *argv[]) {
     return EXIT_FAILURE;
   }
 
-  std::cout << "Load complex with " << complex.num_vertices() << " vertices" << std::endl;
+  if (!complex.empty() && !(complex.point(Vertex_handle(0)).dimension() == 3)) {
+    std::cerr << "Only points of dimension 3 are supported." << std::endl;
+    return EXIT_FAILURE;
+  }
 
+  std::cout << "Load complex with " << complex.num_vertices() << " vertices" << std::endl;
 
   int num_contractions = atoi(argv[3]);
 
@@ -178,7 +183,7 @@ int main(int argc, char *argv[]) {
 
   std::cout << "Final complex has " <<
       complex.num_vertices() << " vertices, " <<
-      complex.num_edges() << " edges and" <<
+      complex.num_edges() << " edges and " <<
       complex.num_triangles() << " triangles." << std::endl;
 
   // write simplified complex
@@ -187,6 +192,8 @@ int main(int argc, char *argv[]) {
   return EXIT_SUCCESS;
 }
 
+#endif  // GARLAND_HECKBERT_H_
+
+
 
 
-#endif  // GARLAND_HECKBERT_H_
diff --git a/src/Contraction/example/Rips_contraction.cpp b/src/Contraction/example/Rips_contraction.cpp
index d21246ed..f80cc2dc 100644
--- a/src/Contraction/example/Rips_contraction.cpp
+++ b/src/Contraction/example/Rips_contraction.cpp
@@ -49,7 +49,7 @@ void build_rips(ComplexType& complex, double offset) {
   for (auto p = vertices.begin(); p != vertices.end(); ++p)
     for (auto q = p; ++q != vertices.end(); /**/) {
       if (squared_dist(complex.point(*p), complex.point(*q)) < 4 * offset * offset)
-        complex.add_edge(*p, *q);
+        complex.add_edge_without_blockers(*p, *q);
     }
 }
 
@@ -87,7 +87,7 @@ int main(int argc, char *argv[]) {
   contractor.contract_edges();
 
   std::cout << "Counting final number of simplices \n";
-  unsigned num_simplices = std::distance(complex.simplex_range().begin(), complex.simplex_range().end());
+  unsigned num_simplices = std::distance(complex.complex_simplex_range().begin(), complex.complex_simplex_range().end());
 
   std::cout << "Final complex has " <<
       complex.num_vertices() << " vertices, " <<
diff --git a/src/Contraction/include/gudhi/Edge_contraction.h b/src/Contraction/include/gudhi/Edge_contraction.h
index 011ca9bd..a4c786be 100644
--- a/src/Contraction/include/gudhi/Edge_contraction.h
+++ b/src/Contraction/include/gudhi/Edge_contraction.h
@@ -158,7 +158,7 @@ void build_rips(ComplexType& complex, double offset){
 	for (auto p = vertices.begin(); p != vertices.end(); ++p)
 		for (auto q = p; ++q != vertices.end(); )
 			if (eucl_distance(complex.point(*p), complex.point(*q)) < 2 * offset)
-				complex.add_edge(*p,*q);
+				complex.add_edge_without_blockers(*p,*q);
 }
 
 int main (int argc, char *argv[])
@@ -194,7 +194,7 @@ int main (int argc, char *argv[])
 	contractor.contract_edges();
 
 	std::cout << "Counting final number of simplices \n";
-	unsigned num_simplices = std::distance(complex.simplex_range().begin(),complex.simplex_range().end());
+	unsigned num_simplices = std::distance(complex.star_simplex_range().begin(),complex.star_simplex_range().end());
 
 	std::cout << "Final complex has "<<
 			complex.num_vertices()<<" vertices, "<<
diff --git a/src/Contraction/include/gudhi/Skeleton_blocker_contractor.h b/src/Contraction/include/gudhi/Skeleton_blocker_contractor.h
index 47d798c0..f650473a 100644
--- a/src/Contraction/include/gudhi/Skeleton_blocker_contractor.h
+++ b/src/Contraction/include/gudhi/Skeleton_blocker_contractor.h
@@ -107,13 +107,8 @@ typename GeometricSimplifiableComplex::Vertex_handle> {
  public:
   typedef typename GeometricSimplifiableComplex::Graph_vertex Graph_vertex;
   typedef typename GeometricSimplifiableComplex::Vertex_handle Vertex_handle;
-  typedef typename GeometricSimplifiableComplex::Simplex_handle Simplex_handle;
-  typedef typename GeometricSimplifiableComplex::Simplex_handle_iterator Simplex_handle_iterator;
-
-
-
+  typedef typename GeometricSimplifiableComplex::Simplex Simplex;
   typedef typename GeometricSimplifiableComplex::Root_vertex_handle Root_vertex_handle;
-
   typedef typename GeometricSimplifiableComplex::Graph_edge Graph_edge;
   typedef typename GeometricSimplifiableComplex::Edge_handle Edge_handle;
   typedef typename GeometricSimplifiableComplex::Point Point;
@@ -535,14 +530,14 @@ typename GeometricSimplifiableComplex::Vertex_handle> {
    * All the edges that passes through the blocker may be edge-contractible
    * again and are thus reinserted in the heap.
    */
-  void on_delete_blocker(const Simplex_handle * blocker) override {
+  void on_delete_blocker(const Simplex * blocker) override {
     // we go for all pairs xy that belongs to the blocker
     // note that such pairs xy are necessarily edges of the complex
     // by definition of a blocker
 
     // todo uniqument utile pour la link condition
     // laisser a l'utilisateur ? booleen update_heap_on_removed_blocker?
-    Simplex_handle blocker_copy(*blocker);
+    Simplex blocker_copy(*blocker);
     for (auto x = blocker_copy.begin(); x != blocker_copy.end(); ++x) {
       for (auto y = x; ++y != blocker_copy.end();) {
         auto edge_descr(complex_[std::make_pair(*x, *y)]);