skbl: correct typo in test and small renamings

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/skb_simplex_insertion_merge@918 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 543ae94051051e1a79f95192db24fcd411dbea28

6 files changed, 48 insertions, 40 deletions

diff --git a/src/Skeleton_blocker/example/Skeleton_blocker_link.cpp b/src/Skeleton_blocker/example/Skeleton_blocker_link.cpp
index 5c717938..5e429728 100644
--- a/src/Skeleton_blocker/example/Skeleton_blocker_link.cpp
+++ b/src/Skeleton_blocker/example/Skeleton_blocker_link.cpp
@@ -39,9 +39,12 @@ typedef Complex::Simplex Simplex;
 
 int main(int argc, char *argv[]) {
   // build a full complex with 4 vertices and 2^4-1 simplices
-  // Initial vertices are (0,1,2,3,4)
-  Simplex tetrahedron(Vertex_handle(0), Vertex_handle(1), Vertex_handle(2), Vertex_handle(3));
+  
+  // Create a complex with four vertices (0,1,2,3)
   Complex complex;
+
+  // Add a tetrahedron to this complex
+  Simplex tetrahedron(Vertex_handle(0), Vertex_handle(1), Vertex_handle(2), Vertex_handle(3));
   complex.add_simplex(tetrahedron);
 
   cout << "complex:" << complex.to_string() << endl;
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simplex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simplex.h
index 0d838d50..714bf23c 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simplex.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simplex.h
@@ -218,7 +218,7 @@ class Skeleton_blocker_simplex {
   }
 
   /**
-   * Returns the first vertex of the (oriented) simplex.
+   * Returns the first and smallest vertex of the simplex.
    *
    * Be careful : assumes the simplex is non-empty.
    */
@@ -228,7 +228,7 @@ class Skeleton_blocker_simplex {
   }
 
   /**
-   * Returns the last vertex of the (oriented) simplex.
+   * Returns the last and greatest vertex of the simplex.
    *
    * Be careful : assumes the simplex is non-empty.
    */
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h
index b1995783..cf156a58 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h
@@ -23,16 +23,26 @@
 #ifndef SKELETON_BLOCKER_COMPLEX_H_
 #define SKELETON_BLOCKER_COMPLEX_H_
 
+#include <iostream>
+#include <fstream>
+#include <sstream>
+#include <memory>
+#include <map>
+#include <list>
+#include <set>
+#include <vector>
+#include <string>
+#include <algorithm>
+#include <utility>
+
 #include <gudhi/Skeleton_blocker/iterators/Skeleton_blockers_iterators.h>
 #include <gudhi/Skeleton_blocker_link_complex.h>
 #include <gudhi/Skeleton_blocker/Skeleton_blocker_link_superior.h>
 #include <gudhi/Skeleton_blocker/Skeleton_blocker_sub_complex.h>
 #include <gudhi/Skeleton_blocker/Skeleton_blocker_simplex.h>
-
 #include <gudhi/Skeleton_blocker/Skeleton_blocker_complex_visitor.h>
 #include <gudhi/Skeleton_blocker/internal/Top_faces.h>
 #include <gudhi/Skeleton_blocker/internal/Trie.h>
-
 #include <gudhi/Utils.h>
 
 #include <boost/graph/adjacency_list.hpp>
@@ -40,18 +50,6 @@
 #include <boost/iterator/transform_iterator.hpp>
 #include <boost/range/adaptor/map.hpp>
 
-#include <iostream>
-#include <fstream>
-#include <sstream>
-#include <memory>
-#include <map>
-#include <list>
-#include <set>
-#include <vector>
-#include <string>
-#include <algorithm>
-#include <utility>
-
 namespace Gudhi {
 
 namespace skbl {
@@ -182,25 +180,28 @@ class Skeleton_blocker_complex {
    * @details is_flag_complex indicates if the complex is a flag complex or not (to know if blockers have to be computed or not).
    */
   template<typename SimpleHandleOutputIterator>
-  Skeleton_blocker_complex(SimpleHandleOutputIterator simplex_begin, SimpleHandleOutputIterator simplex_end,
+  Skeleton_blocker_complex(SimpleHandleOutputIterator simplices_begin, SimpleHandleOutputIterator simplices_end,
                            bool is_flag_complex = false, Visitor* visitor_ = NULL)
       : num_vertices_(0),
       num_blockers_(0),
       visitor(visitor_) {
-    add_vertex_and_edges(simplex_begin, simplex_end);
+    add_vertices_and_edges(simplices_begin, simplices_end);
 
     if (!is_flag_complex)
       // need to compute blockers
-      add_blockers(simplex_begin, simplex_end);
+      add_blockers(simplices_begin, simplices_end);
   }
 
  private:
+  /**
+   * Add vertices and edges of a simplex in one pass
+   */
   template<typename SimpleHandleOutputIterator>
-  void add_vertex_and_edges(SimpleHandleOutputIterator simplex_begin, SimpleHandleOutputIterator simplex_end) {
+  void add_vertices_and_edges(SimpleHandleOutputIterator simplices_begin, SimpleHandleOutputIterator simplices_end) {
     std::vector<std::pair<Vertex_handle, Vertex_handle>> edges;
     // first pass to add vertices and edges
     int num_vertex = -1;
-    for (auto s_it = simplex_begin; s_it != simplex_end; ++s_it) {
+    for (auto s_it = simplices_begin; s_it != simplices_end; ++s_it) {
       if (s_it->dimension() == 0) num_vertex = (std::max)(num_vertex, s_it->first_vertex().vertex);
       if (s_it->dimension() == 1) edges.emplace_back(s_it->first_vertex(), s_it->last_vertex());
     }
@@ -210,9 +211,10 @@ class Skeleton_blocker_complex {
       add_edge_without_blockers(e.first, e.second);
   }
 
+
   template<typename SimpleHandleOutputIterator>
-  void add_blockers(SimpleHandleOutputIterator simplex_begin, SimpleHandleOutputIterator simplex_end) {
-    Tries<Simplex> tries(num_vertices(), simplex_begin, simplex_end);
+  void add_blockers(SimpleHandleOutputIterator simplices_begin, SimpleHandleOutputIterator simplices_end) {
+    Tries<Simplex> tries(num_vertices(), simplices_begin, simplices_end);
     tries.init_next_dimension();
     auto simplices(tries.next_dimension_simplices());
 
@@ -378,6 +380,7 @@ class Skeleton_blocker_complex {
 
   /**
    * @brief Adds a vertex to the simplicial complex and returns its Vertex_handle.
+   * @remark Vertex representation is contiguous.
    */
   Vertex_handle add_vertex() {
     Vertex_handle address(boost::add_vertex(skeleton));
@@ -1128,13 +1131,10 @@ class Skeleton_blocker_complex {
   void remove_star(const Simplex& sigma);
 
   /**
-   * @brief add a simplex.
-   * @details the simplex must have dimension greater than one (otherwise use add_vertex or add_edge_without_blockers).
-   * and all vertices lower than the higher vertex of sigma must already be in the complex.
-   * if some edges of sigma are not in the complex, then insert_edges_of_sigma flag must be 
-   * set to true.
+   * @brief add a simplex and all its faces.
+   * @details the simplex must have dimension greater than one (otherwise use add_vertex or add_edge_without_blockers).   
    */
-  void add_simplex(const Simplex& sigma, bool insert_edges_of_sigma = false);
+  void add_simplex(const Simplex& sigma);
 
  private:
   void add_blockers_after_simplex_insertion(Simplex s);
@@ -1583,12 +1583,12 @@ class Skeleton_blocker_complex {
  * return the total number of simplices
  */
 template<typename Complex, typename SimplexHandleIterator>
-Complex make_complex_from_top_faces(SimplexHandleIterator simplex_begin, SimplexHandleIterator simplex_end,
+Complex make_complex_from_top_faces(SimplexHandleIterator simplices_begin, SimplexHandleIterator simplices_end,
                                     bool is_flag_complex = false) {
   //todo use add_simplex instead! should be more efficient and more elegant :)
   typedef typename Complex::Simplex Simplex;
   std::vector<Simplex> simplices;
-  for (auto top_face = simplex_begin; top_face != simplex_end; ++top_face) {
+  for (auto top_face = simplices_begin; top_face != simplices_end; ++top_face) {
     auto subfaces_topface = subfaces(*top_face);
     simplices.insert(simplices.end(), subfaces_topface.begin(), subfaces_topface.end());
   }
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_simplifiable_complex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_simplifiable_complex.h
index 79a7ed79..1b7d58ff 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_simplifiable_complex.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_simplifiable_complex.h
@@ -206,21 +206,26 @@ void Skeleton_blocker_complex<SkeletonBlockerDS>::remove_star(const Simplex& sig
 }
 
 template<typename SkeletonBlockerDS>
-void Skeleton_blocker_complex<SkeletonBlockerDS>::add_simplex(const Simplex& sigma, bool insert_edges_of_sigma) {
+void Skeleton_blocker_complex<SkeletonBlockerDS>::add_simplex(const Simplex& sigma) {
   // to add a simplex s, all blockers included in s are first removed
   // and then all simplex in the coboundary of s are added as blockers
   assert(!this->contains(sigma));
   assert(sigma.dimension() > 1);
+  if (!contains_vertices(sigma)) {
+    std::cerr << "add_simplex: Some vertices were not present in the complex, adding them" << std::endl;
+    size_t num_vertices_to_add = sigma.last_vertex() - this->num_vertices() + 1;
+    for (size_t i = 0; i < num_vertices_to_add; ++i)
+      this->add_vertex();
+  }
   assert(contains_vertices(sigma));
-
-  if(insert_edges_of_sigma)
+  if(!contains_edges(sigma))
     add_edge(sigma);
-  else 
-    assert(contains_edges(sigma));
   remove_blocker_include_in_simplex(sigma);
   add_blockers_after_simplex_insertion(sigma);
 }
 
+
+
 template<typename SkeletonBlockerDS>
 void Skeleton_blocker_complex<SkeletonBlockerDS>::add_blockers_after_simplex_insertion(Simplex sigma){
   if(sigma.dimension() < 1) return;
diff --git a/src/Skeleton_blocker/test/TestSimplifiable.cpp b/src/Skeleton_blocker/test/TestSimplifiable.cpp
index 76d5ba89..b0855ce9 100644
--- a/src/Skeleton_blocker/test/TestSimplifiable.cpp
+++ b/src/Skeleton_blocker/test/TestSimplifiable.cpp
@@ -310,7 +310,7 @@ bool test_add_simplex4() {
     for (int k = 0; k < n; k++)
       s.add_vertex(Vertex_handle(k));
     s.remove_vertex(Vertex_handle(i));
-    complex.add_simplex(s, true);
+    complex.add_simplex(s);
 
     //at step i there is only blocker 0..i
     if (i < 2 && complex.num_blockers() > 0)
diff --git a/src/Skeleton_blocker/test/TestSkeletonBlockerComplex.cpp b/src/Skeleton_blocker/test/TestSkeletonBlockerComplex.cpp
index 69abd279..42482e23 100644
--- a/src/Skeleton_blocker/test/TestSkeletonBlockerComplex.cpp
+++ b/src/Skeleton_blocker/test/TestSkeletonBlockerComplex.cpp
@@ -367,7 +367,7 @@ bool test_iterator_simplices4() {
 bool test_iterator_coboundary() {
   Complex c;
   build_complete(4, c);
-  c.remove_edge(Vertex_handle(0), Vertex_handle(2));
+  c.remove_edge(Vertex_handle(1), Vertex_handle(3));
   PRINT(c.to_string());
   Simplex s02(Vertex_handle(0), Vertex_handle(2));
   int n = 0;