Commit code and doc review

Still issue and lot of logs in simplex_tree::prune_above_filtration



git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alphashapes@945 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: cd4f60ddcacb0444e0eb3b9323d8042eb49b132e

18 files changed, 436 insertions, 121 deletions

diff --git a/CMakeLists.txt b/CMakeLists.txt
index d42f7af7..d0770dd7 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -22,8 +22,8 @@ if(MSVC)
   # Turn off some VC++ warnings
   SET (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4267 /wd4668 /wd4311 /wd4800 /wd4820 /wd4503 /wd4244 /wd4345 /wd4996 /wd4396 /wd4018")
 else()
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O2 -std=c++11 -Wall -Wpedantic -Wsign-compare")
-  set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -ggdb -O0")	
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O2 -std=c++11 -fsanitize=memory -fno-omit-frame-pointer -Wall -Wpedantic -Wsign-compare")
+  set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -ggdb -O1")	
   set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE}")
 endif()
 
diff --git a/biblio/bibliography.bib b/biblio/bibliography.bib
index 859696b4..3fd1c10a 100644
--- a/biblio/bibliography.bib
+++ b/biblio/bibliography.bib
@@ -897,22 +897,6 @@ language={English}
   bibsource = {DBLP, http://dblp.uni-trier.de}
 }
 
-@ARTICLE{AlphaShapesDefinition,
-    author = {N. Akkiraju, H. Edelsbrunner, M. Facello, P. Fu, E. P. Mucke, and C. Varela},
-    title = {\href{http://pub.ist.ac.at/~edels/Papers/1995-P-06-AlphaShapesSoftware.pdf}{Alpha shapes: definition and software}},
-    journal = {Proc. Internat. Comput. Geom. Software Workshop 1995},
-    year = {1995},
-    bibsource = {http://pub.ist.ac.at}
-}
-
-@ARTICLE{AlphaShapesIntroduction,
-    author = {Kaspar Fischer},
-    title = {\href{http://www.cs.uu.nl/docs/vakken/ddm/texts/Delaunay/alphashapes.pdf}{Introduction to Alpha Shapes}},
-    journal = {Unknown},
-    year = {Unknown},
-    bibsource = {http://www.cs.uu.nl}
-}
-
 misc{buddha_stanford_scan,
  author = "",
    title = "The Stanford 3D Scanning Repository",
diff --git a/src/Alpha_complex/doc/Intro_alpha_complex.h b/src/Alpha_complex/doc/Intro_alpha_complex.h
index 685a4c2f..12d62ac0 100644
--- a/src/Alpha_complex/doc/Intro_alpha_complex.h
+++ b/src/Alpha_complex/doc/Intro_alpha_complex.h
@@ -37,10 +37,10 @@ namespace alphacomplex {
  * \section definition Definition
  * 
  * Alpha_complex is a <a target="_blank" href="https://en.wikipedia.org/wiki/Simplicial_complex">simplicial complex</a>
- * constructed from each finite cell of a Delaunay Triangulation.
+ * constructed from the finite cells of a Delaunay Triangulation.
  * 
- * The filtration value of each simplex is computed from the alpha square value of the simplex if it is Gabriel or
- * from the alpha value of the simplex coface that makes the simplex not Gabriel.
+ * The filtration value of each simplex is computed from the circumradius of the simplex if it is Gabriel or
+ * from the alpha value of the simplex cofaces that make it not Gabriel.
  * 
  * All simplices that have a filtration value strictly greater than a given alpha square value are not inserted into
  * the simplex.
@@ -78,7 +78,7 @@ namespace alphacomplex {
  * 
  * \subsection datastructure Data structure
  * 
- * In order to build the alpha complex, first, a Simplex tree is build from the cells of a Delaunay Triangulation.
+ * In order to build the alpha complex, first, a Simplex tree is built from the cells of a Delaunay Triangulation.
  * (The filtration value is set to NaN, which stands for unknown value):
  * \image html "alpha_complex_doc.png" "Simplex tree structure construction example"
  *
diff --git a/src/Alpha_complex/doc/alpha_complex_doc.ipe b/src/Alpha_complex/doc/alpha_complex_doc.ipe
index b5601143..e74f9bc4 100644
--- a/src/Alpha_complex/doc/alpha_complex_doc.ipe
+++ b/src/Alpha_complex/doc/alpha_complex_doc.ipe
@@ -1,7 +1,7 @@
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@@ -202,13 +202,13 @@ h
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diff --git a/src/Alpha_complex/doc/alpha_complex_doc.png b/src/Alpha_complex/doc/alpha_complex_doc.png
index 601ac051..c9eab275 100644
--- a/src/Alpha_complex/doc/alpha_complex_doc.png
+++ b/src/Alpha_complex/doc/alpha_complex_doc.png
diff --git a/src/Alpha_complex/doc/alpha_complex_doc_135.ipe b/src/Alpha_complex/doc/alpha_complex_doc_135.ipe
index 28b893b8..5d1d29d4 100644
--- a/src/Alpha_complex/doc/alpha_complex_doc_135.ipe
+++ b/src/Alpha_complex/doc/alpha_complex_doc_135.ipe
@@ -1,7 +1,7 @@
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@@ -202,13 +202,13 @@ h
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+<textsize name="tiny" value="\tiny"/>
 <textsize name="Large" value="\Large"/>
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 243.428 591.569 m
 186.061 643.28 l
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 <text matrix="1 0 0 1 0 80" transformations="translations" pos="212.724 627.389" stroke="darkcyan" type="label" width="18.785" height="4.294" depth="1.49" valign="baseline">$\alpha_{420}$</text>
-<use matrix="1 0 0 1 -264 -162" name="mark/fdisk(sfx)" pos="280 660" size="normal" stroke="black" fill="white"/>
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@@ -325,7 +310,6 @@ h
 modified (NaN)
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@@ -391,10 +367,7 @@ modified (NaN)
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 <text matrix="1 0 0 1 -199.21 -189.117" transformations="translations" pos="380 530" stroke="darkred" type="label" width="168.308" height="8.965" depth="2.99" valign="baseline" size="large">[0,4] is not Gabriel $\rightarrow$ $\alpha_{40} = \alpha_{420}$</text>
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@@ -420,16 +393,6 @@ modified (NaN)
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@@ -505,10 +467,48 @@ modified (NaN)
 <text matrix="1 0 0 1 39.645 -2.36686" transformations="translations" pos="199.703 569.464" stroke="darkblue" type="label" width="93.206" height="7.473" depth="2.49" valign="baseline">For all faces of [4,2,0]</text>
 <text matrix="1 0 0 1 -93.391 2.68003" transformations="translations" pos="104.437 300.174" stroke="black" type="label" width="208.621" height="6.926" depth="1.93" valign="baseline">N.B. : is Gabriel on a single point has no sense.</text>
 <text matrix="1 0 0 1 -36.9231 10" transformations="translations" pos="48 784" stroke="black" type="label" width="118.324" height="7.473" depth="2.49" valign="baseline">Dimension =2 - $\sigma$ = [4,2,0]</text>
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+<use matrix="1 0 0 1 -38 -164" name="mark/fdisk(sfx)" pos="280 660" size="normal" stroke="black" fill="white"/>
 </page>
 </ipe>
diff --git a/src/Alpha_complex/doc/alpha_complex_doc_135.png b/src/Alpha_complex/doc/alpha_complex_doc_135.png
index 5dce5edd..ef7187f7 100644
--- a/src/Alpha_complex/doc/alpha_complex_doc_135.png
+++ b/src/Alpha_complex/doc/alpha_complex_doc_135.png
diff --git a/src/Alpha_complex/doc/alpha_complex_representation.png b/src/Alpha_complex/doc/alpha_complex_representation.png
new file mode 100644
index 00000000..06e54c06
--- /dev/null
+++ b/src/Alpha_complex/doc/alpha_complex_representation.png
diff --git a/src/Alpha_complex/example/Alpha_complex_from_points.cpp b/src/Alpha_complex/example/Alpha_complex_from_points.cpp
index 62f594d1..00e988a6 100644
--- a/src/Alpha_complex/example/Alpha_complex_from_points.cpp
+++ b/src/Alpha_complex/example/Alpha_complex_from_points.cpp
@@ -30,21 +30,13 @@ int main(int argc, char **argv) {
   // Init of a list of points
   // ----------------------------------------------------------------------------
   Vector_of_points points;
-
-  std::vector<double> coords = { 1.0, 1.0 };
-  points.push_back(Point(coords.begin(), coords.end()));
-  coords = { 7.0, 0.0 };
-  points.push_back(Point(coords.begin(), coords.end()));
-  coords = { 4.0, 6.0 };
-  points.push_back(Point(coords.begin(), coords.end()));
-  coords = { 9.0, 6.0 };
-  points.push_back(Point(coords.begin(), coords.end()));
-  coords = { 0.0, 14.0 };
-  points.push_back(Point(coords.begin(), coords.end()));
-  coords = { 2.0, 19.0 };
-  points.push_back(Point(coords.begin(), coords.end()));
-  coords = { 9.0, 17.0 };
-  points.push_back(Point(coords.begin(), coords.end()));
+  points.push_back(Point(1.0, 1.0));
+  points.push_back(Point(7.0, 0.0));
+  points.push_back(Point(4.0, 6.0));
+  points.push_back(Point(9.0, 6.0));
+  points.push_back(Point(0.0, 14.0));
+  points.push_back(Point(2.0, 19.0));
+  points.push_back(Point(9.0, 17.0));
 
   // ----------------------------------------------------------------------------
   // Init of an alpha complex from the list of points
diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h
index 2dae4028..9f931066 100644
--- a/src/Alpha_complex/include/gudhi/Alpha_complex.h
+++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h
@@ -125,7 +125,9 @@ class Alpha_complex : public Simplex_tree<> {
 
   /** \brief Alpha_complex constructor from a Delaunay triangulation.
    *
-   * @param[in] triangulation_ptr Pointer on a Delaunay triangulation.
+   * @param[in] triangulation_ptr Pointer on a <a target="_blank"
+   * href="http://doc.cgal.org/latest/Triangulation/index.html#Chapter_Triangulations">
+   * CGAL::Delaunay_triangulation<Kernel></a> \cite cgal:hdj-t-15b.
    * @param[in] max_alpha_square maximum for alpha square value. Default value is +\f$\infty\f$.
    */
   Alpha_complex(Delaunay_triangulation* triangulation_ptr,
@@ -170,7 +172,7 @@ class Alpha_complex : public Simplex_tree<> {
     }
   }
 
-  /** \brief Alpha_complex destructor from a Delaunay triangulation.
+  /** \brief Alpha_complex destructor.
    *
    * @warning Deletes the Delaunay triangulation.
    */
diff --git a/src/Alpha_complex/test/CMakeLists.txt b/src/Alpha_complex/test/CMakeLists.txt
index fa24e1b1..d7c13da0 100644
--- a/src/Alpha_complex/test/CMakeLists.txt
+++ b/src/Alpha_complex/test/CMakeLists.txt
@@ -18,6 +18,8 @@ if(CGAL_FOUND)
       add_executable ( AlphaComplexUT Alpha_complex_unit_test.cpp )
       target_link_libraries(AlphaComplexUT  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
 
+      add_executable ( cerr cerr.cpp )
+
       # Do not forget to copy test files in current binary dir
       file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
 
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h
index 3adf06d3..4b04e75a 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h
@@ -530,7 +530,7 @@ class Simplex_tree {
     return dimension_;
   }
 
-  /** \brief Returns true iff the node in the simplex tree pointed by
+  /** \brief Returns true if the node in the simplex tree pointed by
    * sh has children.*/
   bool has_children(Simplex_handle sh) const {
     return (sh->second.children()->parent() == sh->first);
@@ -1134,7 +1134,6 @@ class Simplex_tree {
       if (sh->second.filtration() < upper_filtration) {
         // Store the filtration modification information
         modified = true;
-        std::cout << "modified" << std::endl;
         sh->second.assign_filtration(upper_filtration);
       }
       if (has_children(sh)) {
@@ -1154,21 +1153,51 @@ class Simplex_tree {
    * call `initialize_filtration()` to recompute it.
    */
   void prune_above_filtration(Filtration_value filtration) {
-    if (filtration < threshold_) {
-      threshold_ = filtration;
-      // Initialize filtration_vect_ if required
-      if (filtration_vect_.empty()) {
-        initialize_filtration();
-      }
+std::cout << "prune_above_filtration - filtration=" << filtration << std::endl;
+    // No action if filtration is not stored
+    if (Options::store_filtration) {
+      if (filtration < threshold_) {
+        threshold_ = filtration;
+        // Initialize filtration_vect_ if required
+        if (filtration_vect_.empty()) {
+std::cout << "prune_above_filtration - initialize_filtration" << std::endl;
+          initialize_filtration();
+        }
+
+std::cout << "prune_above_filtration - after initialize_filtration ";
+for(auto sh : filtration_vect_) {
+for (auto vertex : simplex_vertex_range(sh)) {
+std::cout << (int) vertex << ", ";
+}
+std::cout <<  " - filtration=" << sh->second.filtration() <<  " - " << &(sh->second) << std::endl;
+}
     
-      // Loop in reverse mode until threshold is reached
-      auto f_simplex = filtration_vect_.rbegin();
-      for (; f_simplex != filtration_vect_.rend() && ((*f_simplex)->second.filtration() > threshold_); f_simplex++) {
-        remove_maximal_simplex(*f_simplex);
+        
+        // Loop in reverse mode until threshold is reached
+        auto f_simplex = filtration_vect_.rbegin();
+        for (; (f_simplex != filtration_vect_.rend()) && ((*f_simplex)->second.filtration() > threshold_); f_simplex++) {
+          
+std::cout << "prune_above_filtration - remove ";
+for (auto vertex : simplex_vertex_range(*f_simplex)) {
+std::cout << (int) vertex << ", ";
+}
+std::cout <<  " - " << &((*f_simplex)->second) << std::endl;
+
+          remove_maximal_simplex(*f_simplex);
+        }
+std::cout << "prune_above_filtration - remove STOPPED ON ";
+for (auto vertex : simplex_vertex_range(*f_simplex)) {
+std::cout << (int) vertex << ", ";
+}
+std::cout <<  " - filtration=" << (*f_simplex)->second.filtration() <<  " - " << &(*f_simplex->second) << std::endl;
+        if (f_simplex != filtration_vect_.rbegin()) {
+          // Do not forget to update filtration_vect_ - resize is enough
+          std::size_t new_size = filtration_vect_.size() - (f_simplex - filtration_vect_.rbegin());
+std::cout << "prune_above_filtration - resize" << new_size << std::endl;
+          filtration_vect_.resize(new_size);
+        }
+
       }
-      // Do not forget to update filtration_vect_ - resize is enough
-      std::size_t new_size = filtration_vect_.size() - (f_simplex - filtration_vect_.rbegin());
-      filtration_vect_.resize(new_size);
     }
   }
 
@@ -1187,14 +1216,46 @@ class Simplex_tree {
     if ((child->size() > 1) || (child == root())) {
       // Not alone, just remove it from members
       // Special case when child is the root of the simplex tree, just remove it from members
-      child->members().erase(sh->first);
+std::cout << "remove_maximal_simplex - members removal" << std::endl;
+      child->erase(sh->first);
     } else {
       // Sibling is emptied : must be deleted, and its parent must point on his own Sibling
+std::cout << "remove_maximal_simplex - members is empty" << std::endl;
       child->oncles()->members().at(child->parent()).assign_children(child->oncles());
       delete child;
     }
   }
-  
+/***************************************************************************************************************/  
+   public:
+  /** \brief Prints the simplex_tree hierarchically. 
+   * Since it prints the vertices recursively, one can watch its tree shape.
+   */
+  void print_tree() {
+    for (auto sh = root_.members().begin(); sh != root_.members().end(); ++sh) {
+      std::cout << sh->first << " ";
+      if (has_children(sh)) {
+        std::cout << "(";
+        rec_print(sh->second.children());
+        std::cout << ")";
+      }
+      std::cout << std::endl;
+    }
+  }
+
+
+  /** \brief Recursively prints the simplex_tree, using depth first search. */
+ private:
+  void rec_print(Siblings * sib) {
+    for (auto sh = sib->members().begin(); sh != sib->members().end(); ++sh) {
+      std::cout << " " << sh->first << " ";
+      if (has_children(sh)) {
+        std::cout << "(";
+        rec_print(sh->second.children());
+        std::cout << ")";
+      }
+    }
+  }
+/*****************************************************************************************************************/
  private:
   Vertex_handle null_vertex_;
   /** \brief Upper bound on the filtration values of the simplices.*/
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_siblings.h b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_siblings.h
index 158ee1f7..c1ff8bf2 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_siblings.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_siblings.h
@@ -116,6 +116,10 @@ class Simplex_tree_siblings {
     return members_.size();
   }
 
+  void erase(const Vertex_handle vh) {
+    members_.erase(vh);
+  }
+
   Simplex_tree_siblings * oncles_;
   Vertex_handle parent_;
   Dictionary members_;
diff --git a/src/Simplex_tree/test/simplex_tree_unit_test.cpp b/src/Simplex_tree/test/simplex_tree_unit_test.cpp
index 00cf69bc..f6bd5411 100644
--- a/src/Simplex_tree/test/simplex_tree_unit_test.cpp
+++ b/src/Simplex_tree/test/simplex_tree_unit_test.cpp
@@ -362,7 +362,9 @@ BOOST_AUTO_TEST_CASE(simplex_tree_insertion) {
 
 }
 
-bool sort_in_decr_order (Vertex_handle i,Vertex_handle j) { return (i>j); }
+bool sort_in_decr_order(Vertex_handle i, Vertex_handle j) {
+  return (i > j);
+}
 
 BOOST_AUTO_TEST_CASE(NSimplexAndSubfaces_tree_insertion) {
   std::cout << "********************************************************************" << std::endl;
@@ -476,7 +478,7 @@ BOOST_AUTO_TEST_CASE(NSimplexAndSubfaces_tree_insertion) {
     BOOST_CHECK(vertex == SimplexVector6[position]);
     position++;
   }
-  
+
   /* Inserted simplex:        */
   /*    1   6                 */
   /*    o---o                 */
@@ -720,14 +722,268 @@ BOOST_AUTO_TEST_CASE(copy_move_on_simplex_tree) {
   // Check there is a new simplex tree reference
   BOOST_CHECK(&st_move != &st_copy);
   BOOST_CHECK(&st_move != &st);
-  
+
   typeST st_empty;
   // Check st has been emptied by the move
   BOOST_CHECK(st == st_empty);
   BOOST_CHECK(st.filtration() == 0);
   BOOST_CHECK(st.dimension() == -1);
   BOOST_CHECK(st.num_simplices() == 0);
-  BOOST_CHECK(st.num_vertices() == (size_t)0);
-  
+  BOOST_CHECK(st.num_vertices() == (size_t) 0);
+
   std::cout << "Printing st once again- address = " << &st << std::endl;
 }
+
+BOOST_AUTO_TEST_CASE(make_filtration_non_decreasing) {
+  std::cout << "********************************************************************" << std::endl;
+  std::cout << "MAKE FILTRATION NON DECREASING" << std::endl;
+  typeST st;
+
+  st.insert_simplex_and_subfaces({2, 1, 0}, 4.0);
+  st.insert_simplex_and_subfaces({3, 0}, 3.0);
+  st.insert_simplex_and_subfaces({3, 4, 5}, 2.0);
+  // Because of non decreasing property of simplex tree, { 0 } , { 1 } and { 0, 1 } are going to be set from value 4.0
+  // to 1.0
+  st.insert_simplex_and_subfaces({0, 1, 6, 7}, 1.0);
+
+  /* Inserted simplex:        */
+  /*    1   6                 */
+  /*    o---o                 */
+  /*   /X\7/                  */
+  /*  o---o---o---o           */
+  /*  2   0   3\X/4           */
+  /*            o             */
+  /*            5             */
+
+  // FIXME
+  st.set_dimension(3);
+
+  // Copy constructor  
+  typeST st_copy = st;
+
+  // Check default insertion ensures the filtration values are non decreasing
+  BOOST_CHECK(!st.make_filtration_non_decreasing());
+  // Check the simplex tree is not modified by the function
+  BOOST_CHECK(st == st_copy);
+
+  // Make { 0, 1 } decreasing
+  st.assign_filtration(st.find({0, 1}), 0.5);
+  // Make { 1, 6, 7 } decreasing
+  st.assign_filtration(st.find({1, 6, 7}), 0.4);
+  // Make { 3, 4 } decreasing
+  st.assign_filtration(st.find({3, 4}), 0.3);
+  // Make { 4, 5 } decreasing
+  st.assign_filtration(st.find({4, 5}), 0.1);
+
+  // Check the filtration values were decreasing
+  BOOST_CHECK(st.make_filtration_non_decreasing());
+  // Check the simplex tree has been modified by the function to retrieve the initial simplex tree
+  BOOST_CHECK(st == st_copy);
+
+  // Change { 0, 3 }, but still non decreasing
+  st.assign_filtration(st.find({0, 3}), 1.01);
+  // Change { 0, 1, 6, 7 }, but still non decreasing
+  st.assign_filtration(st.find({0, 1, 6, 7}), 1.201);
+  // Change { 1, 2 }, but still non decreasing
+  st.assign_filtration(st.find({1, 2}), 1.05);
+  // Change { 4 }, but still non decreasing
+  st.assign_filtration(st.find({4}), 1.123);
+
+  // Check the filtration values are non decreasing
+  BOOST_CHECK(!st.make_filtration_non_decreasing());
+  // Check the simplex tree has been modified from the original
+  BOOST_CHECK(st != st_copy);
+
+}
+
+struct MyOptions : Simplex_tree_options_full_featured {
+  // Not doing persistence, so we don't need those
+  static const bool store_key = false;
+  static const bool store_filtration = false;
+  // I have few vertices
+  typedef short Vertex_handle;
+};
+typedef Simplex_tree<MyOptions> miniST;
+
+/*BOOST_AUTO_TEST_CASE(remove_maximal_simplex) {
+  std::cout << "********************************************************************" << std::endl;
+  std::cout << "REMOVE MAXIMAL SIMPLEX" << std::endl;
+
+  miniST st;
+
+  // FIXME
+  st.set_dimension(3);
+
+  st.insert_simplex_and_subfaces({0, 1, 6, 7});
+  st.insert_simplex_and_subfaces({3, 4, 5});
+
+  // Constructs a copy at this state for further test purpose
+  miniST st_pruned = st;
+
+  st.insert_simplex_and_subfaces({3, 0});
+  st.insert_simplex_and_subfaces({2, 1, 0});
+
+  // Constructs a copy at this state for further test purpose
+  miniST st_complete = st;
+  // st_complete and st:
+  //    1   6
+  //    o---o
+  //   /X\7/
+  //  o---o---o---o
+  //  2   0   3\X/4
+  //            o
+  //            5
+  // st_pruned:
+  //    1   6
+  //    o---o
+  //     \7/
+  //      o   o---o
+  //      0   3\X/4
+  //            o
+  //            5
+
+#ifdef GUDHI_DEBUG
+  std::cout << "Check exception throw in debug mode" << std::endl;
+  // throw excpt because sh has children
+  BOOST_CHECK_THROW (st.remove_maximal_simplex(st.find({0, 1, 6})), std::invalid_argument);
+  BOOST_CHECK_THROW (st.remove_maximal_simplex(st.find({3})), std::invalid_argument);
+  BOOST_CHECK(st == st_complete);
+#endif
+  
+  st.remove_maximal_simplex(st.find({0, 2}));
+  st.remove_maximal_simplex(st.find({0, 1, 2}));
+  st.remove_maximal_simplex(st.find({1, 2}));
+  st.remove_maximal_simplex(st.find({2}));
+  st.remove_maximal_simplex(st.find({0, 3}));
+  
+  BOOST_CHECK(st == st_pruned);
+  // Remove all, but as the simplex tree is not storing filtration, there is no modification
+  st.prune_above_filtration(0.0);
+  BOOST_CHECK(st == st_pruned);
+  
+  miniST st_wo_seven;
+  // FIXME
+  st_wo_seven.set_dimension(3);
+
+  st_wo_seven.insert_simplex_and_subfaces({0, 1, 6});
+  st_wo_seven.insert_simplex_and_subfaces({3, 4, 5});
+  // st_wo_seven:
+  //    1   6
+  //    o---o
+  //     \X/
+  //      o   o---o
+  //      0   3\X/4
+  //            o
+  //            5
+
+  // Remove all 7 to test the both remove_maximal_simplex cases (when _members is empty or not)
+  st.remove_maximal_simplex(st.find({0, 1, 6, 7}));
+  st.remove_maximal_simplex(st.find({0, 1, 7}));
+  st.remove_maximal_simplex(st.find({0, 6, 7}));
+  st.remove_maximal_simplex(st.find({0, 7}));
+  st.remove_maximal_simplex(st.find({1, 6, 7}));
+  st.remove_maximal_simplex(st.find({1, 7}));
+  st.remove_maximal_simplex(st.find({6, 7}));
+  st.remove_maximal_simplex(st.find({7}));
+  
+  BOOST_CHECK(st == st_wo_seven);
+}*/
+
+BOOST_AUTO_TEST_CASE(prune_above_filtration) {
+  std::cout << "********************************************************************" << std::endl;
+  std::cout << "PRUNE ABOVE FILTRATION" << std::endl;
+  typeST st;
+
+  // FIXME
+  st.set_dimension(3);
+
+  st.insert_simplex_and_subfaces({0, 1, 6, 7}, 1.0);
+  st.insert_simplex_and_subfaces({3, 4, 5}, 2.0);
+  st.set_filtration(6.0);
+
+  // Constructs a copy at this state for further test purpose
+  typeST st_pruned = st;
+  st_pruned.initialize_filtration(); // reset
+
+  st.insert_simplex_and_subfaces({3, 0}, 3.0);
+  st.insert_simplex_and_subfaces({2, 1, 0}, 4.0);
+
+  // Constructs a copy at this state for further test purpose
+  typeST st_complete = st;
+  // st_complete and st:
+  //    1   6
+  //    o---o
+  //   /X\7/
+  //  o---o---o---o
+  //  2   0   3\X/4
+  //            o
+  //            5
+  // st_pruned:
+  //    1   6
+  //    o---o
+  //     \7/
+  //      o   o---o
+  //      0   3\X/4
+  //            o
+  //            5
+
+  // Check the no action cases
+  // greater than initial filtration value
+  st.prune_above_filtration(10.0);
+  BOOST_CHECK(st == st_complete);
+  // equal to initial filtration value
+  st.prune_above_filtration(6.0);
+  BOOST_CHECK(st == st_complete);
+  // lower than initial filtration value, but still greater than the maximum filtration value
+  st_complete.set_filtration(5.0);
+  st.prune_above_filtration(5.0);
+  BOOST_CHECK(st == st_complete);
+
+  // Display the Simplex_tree - Can not be done in the middle of 2 inserts
+  std::cout << "The complex contains " << st.num_simplices() << " simplices" << std::endl;
+  std::cout << "   - dimension " << st.dimension() << "   - filtration " << st.filtration() << std::endl;
+  std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl;
+  for (auto f_simplex : st.filtration_simplex_range()) {
+    std::cout << "   " << "[" << st.filtration(f_simplex) << "] ";
+    for (auto vertex : st.simplex_vertex_range(f_simplex)) {
+      std::cout << (int) vertex << " ";
+    }
+    std::cout << std::endl;
+  }
+
+  // Check the pruned cases
+  // Set the st_pruned filtration for operator==
+  st_pruned.set_filtration(2.5);
+  st.prune_above_filtration(2.5);
+  /*BOOST_CHECK(st == st_pruned);
+
+  st_pruned.set_filtration(2.0);
+  st.prune_above_filtration(2.0);
+  BOOST_CHECK(st == st_pruned);
+*/
+/*  std::cout << "The complex contains " << st.num_simplices() << " simplices --------------------------" << std::endl;
+  std::cout << "   - dimension " << st.dimension() << "   - filtration " << st.filtration() << std::endl;
+  st.print_tree();
+
+  std::cout << "The pruned complex contains " << st_pruned.num_simplices() << " simplices --------------------------" << std::endl;
+  std::cout << "   - dimension " << st_pruned.dimension() << "   - filtration " << st_pruned.filtration() << std::endl;
+  st_pruned.print_tree();
+  
+  typeST st_empty;
+  // FIXME
+  st_empty.set_dimension(3);
+  st.prune_above_filtration(0.0);
+ */
+  /*BOOST_CHECK(st == st_empty);
+
+  // Test case to the limit
+  st.prune_above_filtration(-1.0);
+  st_empty.set_filtration(-1.0);
+  BOOST_CHECK(st == st_empty);
+*/
+}
+
+/*BOOST_AUTO_TEST_CASE(sanitizer) {
+  int a[2] = {1, 0};
+  int b=a[2];
+}*/
diff --git a/src/common/example/dtoffrw_alphashapedoc_result.off b/src/common/example/dtoffrw_alphashapedoc_result.off
new file mode 100644
index 00000000..03b7ca75
--- /dev/null
+++ b/src/common/example/dtoffrw_alphashapedoc_result.off
@@ -0,0 +1,15 @@
+nOFF
+2 7 6 0
+1 1 
+7 0 
+4 6 
+9 6 
+0 14 
+2 19 
+9 17 
+3 0 1 2 
+3 3 2 1 
+3 4 0 2 
+3 4 2 6 
+3 6 2 3 
+3 5 4 6 
diff --git a/src/common/example/dtoffrw_alphashapedoc_result.txt b/src/common/example/dtoffrw_alphashapedoc_result.txt
index 57761d14..8e659740 100644
--- a/src/common/example/dtoffrw_alphashapedoc_result.txt
+++ b/src/common/example/dtoffrw_alphashapedoc_result.txt
@@ -1,3 +1,2 @@
 Number of vertices= 7
 Number of finite full cells= 6
-
diff --git a/src/common/include/gudhi/Delaunay_triangulation_off_io.h b/src/common/include/gudhi/Delaunay_triangulation_off_io.h
index 6335d243..b3f4a299 100644
--- a/src/common/include/gudhi/Delaunay_triangulation_off_io.h
+++ b/src/common/include/gudhi/Delaunay_triangulation_off_io.h
@@ -135,7 +135,7 @@ class Delaunay_triangulation_off_visitor_reader {
  * 
  * When launching:
  * 
- * \code $> ./dtoffrw ../../data/points/alphashapedoc.off triangulated.off
+ * \code $> ./dtoffrw ../../data/points/alphacomplexdoc triangulated.off
  * \endcode
  *
  * the program output is:
diff --git a/src/common/test/dtoffrw_unit_test.cpp b/src/common/test/dtoffrw_unit_test.cpp
index 20094229..f682df1a 100644
--- a/src/common/test/dtoffrw_unit_test.cpp
+++ b/src/common/test/dtoffrw_unit_test.cpp
@@ -64,7 +64,7 @@ BOOST_AUTO_TEST_CASE( Delaunay_triangulation_doc_test )
 
 BOOST_AUTO_TEST_CASE( Delaunay_triangulation_unexisting_file_read_test )
 {
-  Gudhi::Delaunay_triangulation_off_reader<T> off_reader("pouetpouet_tralala.off");
+  Gudhi::Delaunay_triangulation_off_reader<T> off_reader("some_impossible_weird_file_name.off");
   // Check the read operation was correct
   BOOST_CHECK(!off_reader.is_valid());
   T* triangulation = off_reader.get_complex();
@@ -80,7 +80,7 @@ BOOST_AUTO_TEST_CASE( Delaunay_triangulation_unexisting_file_write_test )
   T* triangulation = off_reader.get_complex();
 
   // Write the OFF file (output file name given as parameter) with the points and triangulated cells as faces
-  Gudhi::Delaunay_triangulation_off_writer<T> off_writer("/pouetpouet_tralala/pouetpouet_tralala/pouetpouet_tralala.off", triangulation);
+  Gudhi::Delaunay_triangulation_off_writer<T> off_writer("/some_impossible_weird_directory_name/another_weird_directory_name/some_impossible_weird_file_name.off", triangulation);
 
   // Check the write operation was correct
   BOOST_CHECK(!off_writer.is_valid());