Merged trunk into relaxed witness branch

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/relaxed-witness@1579 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: a9ca2e7a968ebf4bb80cfa795965ae78511e8dd4
author: skachano <skachano@636b058d-ea47-450e-bf9e-a15bfbe3eedb> 2016-09-28 12:33:22 +0000
committer: skachano <skachano@636b058d-ea47-450e-bf9e-a15bfbe3eedb> 2016-09-28 12:33:22 +0000
commit: d16822ea1d3cedea66dcddd390becdd4cbb557bb (patch)
tree: b1c592e415f43c1be425608db861e5348e61dcf3 /src
parent: 1c09c91ddf4d38196a91bbff5ae432fb13be6762 (diff)
parent: a138c9ed4fb9770a3612ff4ee0f914942bbe9724 (diff)
158 files changed, 14056 insertions, 3004 deletions
diff --git a/src/Alpha_complex/doc/Intro_alpha_complex.h b/src/Alpha_complex/doc/Intro_alpha_complex.h
new file mode 100644
index 00000000..f3126169
--- /dev/null
+++ b/src/Alpha_complex/doc/Intro_alpha_complex.h
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+/*    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 DOC_ALPHA_COMPLEX_INTRO_ALPHA_COMPLEX_H_
+#define DOC_ALPHA_COMPLEX_INTRO_ALPHA_COMPLEX_H_
+
+// needs namespace for Doxygen to link on classes
+namespace Gudhi {
+// needs namespace for Doxygen to link on classes
+namespace alpha_complex {
+
+/**  \defgroup alpha_complex Alpha complex
+ * 
+ * \author    Vincent Rouvreau
+ * 
+ * @{
+ * 
+ * \section definition Definition
+ * 
+ * Alpha_complex is a <a target="_blank" href="https://en.wikipedia.org/wiki/Simplicial_complex">simplicial complex</a>
+ * constructed from the finite cells of a Delaunay Triangulation.
+ * 
+ * The filtration value of each simplex is computed as the square of the circumradius of the simplex if the circumsphere is empty (the simplex is then said to be Gabriel), and as the minimum of the filtration
+ * values of the codimension 1 cofaces that make it not Gabriel otherwise.
+ * 
+ * All simplices that have a filtration value strictly greater than a given alpha squared value are not inserted into
+ * the complex.
+ * 
+ * \image html "alpha_complex_representation.png" "Alpha-complex representation"
+ * 
+ * Alpha_complex is constructing a `Simplex_tree` using <a target="_blank"
+ * href="http://doc.cgal.org/latest/Triangulation/index.html#Chapter_Triangulations">Delaunay Triangulation</a>
+ * \cite cgal:hdj-t-15b from <a target="_blank" href="http://www.cgal.org/">CGAL</a> (the Computational Geometry
+ * Algorithms Library \cite cgal:eb-15b).
+ * 
+ * The complex is a template class requiring an Epick_d <a target="_blank"
+ * href="http://doc.cgal.org/latest/Kernel_d/index.html#Chapter_dD_Geometry_Kernel">dD Geometry Kernel</a>
+ * \cite cgal:s-gkd-15b from CGAL as template parameter.
+ * 
+ * \remark When Alpha_complex is constructed with an infinite value of alpha, the complex is a Delaunay complex.
+ * 
+ * \section pointsexample Example from points
+ * 
+ * This example builds the Delaunay triangulation from the given points in a 2D static kernel, and initializes the
+ * alpha complex with it.
+ * 
+ * Then, it is asked to display information about the alpha complex.
+ * 
+ * \include Alpha_complex/Alpha_complex_from_points.cpp
+ * 
+ * When launching:
+ * 
+ * \code $> ./alphapoints
+ * \endcode
+ *
+ * the program output is:
+ * 
+ * \include Alpha_complex/alphaoffreader_for_doc_60.txt
+ * 
+ * \section algorithm Algorithm
+ * 
+ * \subsection datastructure Data structure
+ * 
+ * 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"
+ *
+ * \subsection filtrationcomputation Filtration value computation algorithm
+ * 
+ * \f{algorithm}{ 
+ * \caption{Filtration value computation algorithm}\label{alpha}
+ * \begin{algorithmic}
+ * \For{i : dimension $\rightarrow$ 0}
+ *   \ForAll{$\sigma$ of dimension i}
+ *     \If {filtration($\sigma$) is NaN}
+ *       \State filtration($\sigma$) = $\alpha^2(\sigma)$
+ *     \EndIf
+ *     \ForAll{$\tau$ face of $\sigma$} \Comment{propagate alpha filtration value}
+ *       \If {filtration($\tau$) is not NaN} 
+ *         \State filtration($\tau$) = min (filtration($\tau$), filtration($\sigma$))
+ *       \Else
+ *         \If {$\tau$ is not Gabriel for $\sigma$} 
+ *           \State filtration($\tau$) = filtration($\sigma$)
+ *         \EndIf
+ *       \EndIf
+ *     \EndFor
+ *   \EndFor
+ * \EndFor
+ * \State make\_filtration\_non\_decreasing()
+ * \State prune\_above\_filtration()
+ * \end{algorithmic}
+ * \f}
+ * 
+ * \subsubsection dimension2 Dimension 2
+ * 
+ * From the example above, it means the algorithm looks into each triangle ([0,1,2], [0,2,4], [1,2,3], ...),
+ * computes the filtration value of the triangle, and then propagates the filtration value as described
+ * here :
+ * \image html "alpha_complex_doc_420.png" "Filtration value propagation example"
+ * 
+ * \subsubsection dimension1 Dimension 1
+ * 
+ * Then, the algorithm looks into each edge ([0,1], [0,2], [1,2], ...),
+ * computes the filtration value of the edge (in this case, propagation will have no effect).
+ * 
+ * \subsubsection dimension0 Dimension 0
+ * 
+ * Finally, the algorithm looks into each vertex ([0], [1], [2], [3], [4], [5] and [6]) and
+ * sets the filtration value (0 in case of a vertex - propagation will have no effect).
+ * 
+ * \subsubsection nondecreasing Non decreasing filtration values
+ * 
+ * As the squared radii computed by CGAL are an approximation, it might happen that these alpha squared values do not quite define a proper filtration (i.e. non-decreasing with respect to inclusion).
+ * We fix that up by calling `Simplex_tree::make_filtration_non_decreasing()`.
+ * 
+ * \subsubsection pruneabove Prune above given filtration value
+ * 
+ * The simplex tree is pruned from the given maximum alpha squared value (cf. `Simplex_tree::prune_above_filtration()`).
+ * In the following example, the value is given by the user as argument of the program.
+ * 
+ * 
+ * \section offexample Example from OFF file
+ * 
+ * This example builds the Delaunay triangulation in a dynamic kernel, and initializes the alpha complex with it.
+ * 
+ * 
+ * Then, it is asked to display information about the alpha complex.
+ * 
+ * \include Alpha_complex/Alpha_complex_from_off.cpp
+ * 
+ * When launching:
+ * 
+ * \code $> ./alphaoffreader ../../data/points/alphacomplexdoc.off 32.0
+ * \endcode
+ *
+ * the program output is:
+ * 
+ * \include Alpha_complex/alphaoffreader_for_doc_32.txt
+ * 
+ * \copyright GNU General Public License v3.                         
+ * \verbatim  Contact: gudhi-users@lists.gforge.inria.fr \endverbatim
+ */
+/** @} */  // end defgroup alpha_complex
+
+}  // namespace alpha_complex
+
+namespace alphacomplex = alpha_complex;
+
+}  // namespace Gudhi
+
+#endif  // DOC_ALPHA_COMPLEX_INTRO_ALPHA_COMPLEX_H_
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+<path matrix="1 0 0 1 -40 -8" stroke="black" pen="heavier">
+150.038 609.9 m
+179.929 549.727 l
+</path>
+<use matrix="1 0 0 1 -210.178 22.1775" name="mark/fdisk(sfx)" pos="320 580" size="normal" stroke="black" fill="white"/>
+<use matrix="1 0 0 1 -210.178 22.1775" name="mark/fdisk(sfx)" pos="350 520" size="normal" stroke="black" fill="white"/>
+</page>
+</ipe>
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..7b81cd69
--- /dev/null
+++ b/src/Alpha_complex/doc/alpha_complex_representation.png
diff --git a/src/Alpha_complex/example/Alpha_complex_from_off.cpp b/src/Alpha_complex/example/Alpha_complex_from_off.cpp
new file mode 100644
index 00000000..7836d59a
--- /dev/null
+++ b/src/Alpha_complex/example/Alpha_complex_from_off.cpp
@@ -0,0 +1,56 @@
+#include <gudhi/Alpha_complex.h>
+#include <CGAL/Epick_d.h>
+
+#include <iostream>
+#include <string>
+
+void usage(int nbArgs, char * const progName) {
+  std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n";
+  std::cerr << "Usage: " << progName << " filename.off alpha_square_max_value [ouput_file.txt]\n";
+  std::cerr << "       i.e.: " << progName << " ../../data/points/alphacomplexdoc.off 60.0\n";
+  exit(-1);  // ----- >>
+}
+
+int main(int argc, char **argv) {
+  if ((argc != 3) && (argc != 4)) usage(argc, (argv[0] - 1));
+
+  std::string off_file_name(argv[1]);
+  double alpha_square_max_value = atof(argv[2]);
+
+  // ----------------------------------------------------------------------------
+  // Init of an alpha complex from an OFF file
+  // ----------------------------------------------------------------------------
+  typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kernel;
+  Gudhi::alpha_complex::Alpha_complex<Kernel> alpha_complex_from_file(off_file_name, alpha_square_max_value);
+
+  std::streambuf* streambufffer;
+  std::ofstream ouput_file_stream;
+
+  if (argc == 4) {
+    ouput_file_stream.open(std::string(argv[3]));
+    streambufffer = ouput_file_stream.rdbuf();
+  } else {
+    streambufffer = std::cout.rdbuf();
+  }
+
+  std::ostream output_stream(streambufffer);
+
+  // ----------------------------------------------------------------------------
+  // Display information about the alpha complex
+  // ----------------------------------------------------------------------------
+  output_stream << "Alpha complex is of dimension " << alpha_complex_from_file.dimension() <<
+      " - " << alpha_complex_from_file.num_simplices() << " simplices - " <<
+      alpha_complex_from_file.num_vertices() << " vertices." << std::endl;
+
+  output_stream << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" << std::endl;
+  for (auto f_simplex : alpha_complex_from_file.filtration_simplex_range()) {
+    output_stream << "   ( ";
+    for (auto vertex : alpha_complex_from_file.simplex_vertex_range(f_simplex)) {
+      output_stream << vertex << " ";
+    }
+    output_stream << ") -> " << "[" << alpha_complex_from_file.filtration(f_simplex) << "] ";
+    output_stream << std::endl;
+  }
+  ouput_file_stream.close();
+  return 0;
+}
diff --git a/src/Alpha_complex/example/Alpha_complex_from_points.cpp b/src/Alpha_complex/example/Alpha_complex_from_points.cpp
new file mode 100644
index 00000000..49f77276
--- /dev/null
+++ b/src/Alpha_complex/example/Alpha_complex_from_points.cpp
@@ -0,0 +1,62 @@
+#include <CGAL/Epick_d.h>
+#include <gudhi/Alpha_complex.h>
+
+#include <iostream>
+#include <string>
+#include <vector>
+#include <limits>  // for numeric limits
+
+typedef CGAL::Epick_d< CGAL::Dimension_tag<2> > Kernel;
+typedef Kernel::Point_d Point;
+typedef std::vector<Point> Vector_of_points;
+
+void usage(int nbArgs, char * const progName) {
+  std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n";
+  std::cerr << "Usage: " << progName << " [alpha_square_max_value]\n";
+  std::cerr << "       i.e.: " << progName << " 60.0\n";
+  exit(-1);  // ----- >>
+}
+
+int main(int argc, char **argv) {
+  if ((argc != 1) && (argc != 2)) usage(argc, (argv[0] - 1));
+
+  // Delaunay complex if alpha_square_max_value is not given by the user.
+  double alpha_square_max_value = std::numeric_limits<double>::infinity();
+  if (argc == 2)
+    alpha_square_max_value = atof(argv[1]);
+
+  // ----------------------------------------------------------------------------
+  // Init of a list of points
+  // ----------------------------------------------------------------------------
+  Vector_of_points points;
+  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
+  // ----------------------------------------------------------------------------
+  Gudhi::alpha_complex::Alpha_complex<Kernel> alpha_complex_from_points(points, alpha_square_max_value);
+
+  // ----------------------------------------------------------------------------
+  // Display information about the alpha complex
+  // ----------------------------------------------------------------------------
+  std::cout << "Alpha complex is of dimension " << alpha_complex_from_points.dimension() <<
+      " - " << alpha_complex_from_points.num_simplices() << " simplices - " <<
+      alpha_complex_from_points.num_vertices() << " vertices." << std::endl;
+
+  std::cout << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" << std::endl;
+  for (auto f_simplex : alpha_complex_from_points.filtration_simplex_range()) {
+    std::cout << "   ( ";
+    for (auto vertex : alpha_complex_from_points.simplex_vertex_range(f_simplex)) {
+      std::cout << vertex << " ";
+    }
+    std::cout << ") -> " << "[" << alpha_complex_from_points.filtration(f_simplex) << "] ";
+    std::cout << std::endl;
+  }
+  return 0;
+}
diff --git a/src/Alpha_complex/example/CMakeLists.txt b/src/Alpha_complex/example/CMakeLists.txt
new file mode 100644
index 00000000..71a95d61
--- /dev/null
+++ b/src/Alpha_complex/example/CMakeLists.txt
@@ -0,0 +1,33 @@
+cmake_minimum_required(VERSION 2.6)
+project(Alpha_complex_examples)
+
+# need CGAL 4.7
+# cmake -DCGAL_DIR=~/workspace/CGAL-4.7-Ic-41 ../../..
+if(CGAL_FOUND)
+  if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
+    if (EIGEN3_FOUND)
+      add_executable ( alphapoints Alpha_complex_from_points.cpp )
+      target_link_libraries(alphapoints  ${Boost_SYSTEM_LIBRARY} ${Boost_THREAD_LIBRARY} ${CGAL_LIBRARY})
+      add_executable ( alphaoffreader Alpha_complex_from_off.cpp )
+      target_link_libraries(alphaoffreader  ${Boost_SYSTEM_LIBRARY} ${Boost_THREAD_LIBRARY} ${CGAL_LIBRARY})
+      if (TBB_FOUND)
+        target_link_libraries(alphapoints ${TBB_LIBRARIES})
+        target_link_libraries(alphaoffreader ${TBB_LIBRARIES})
+      endif()
+
+      add_test(alphapoints ${CMAKE_CURRENT_BINARY_DIR}/alphapoints)
+      # Do not forget to copy test files in current binary dir
+      file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+      add_test(alphaoffreader_doc_60 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader alphacomplexdoc.off 60.0 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_60.txt)
+      add_test(alphaoffreader_doc_32 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader alphacomplexdoc.off 32.0 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_32.txt)
+      if (DIFF_PATH)
+        # Do not forget to copy test results files in current binary dir
+        file(COPY "alphaoffreader_for_doc_32.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+        file(COPY "alphaoffreader_for_doc_60.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+
+        add_test(alphaoffreader_doc_60_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_60.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_60.txt)
+        add_test(alphaoffreader_doc_32_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_32.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_32.txt)
+      endif()
+    endif(EIGEN3_FOUND)
+  endif(NOT CGAL_VERSION VERSION_LESS 4.7.0)
+endif(CGAL_FOUND)
diff --git a/src/Alpha_complex/example/alphaoffreader_for_doc_32.txt b/src/Alpha_complex/example/alphaoffreader_for_doc_32.txt
new file mode 100644
index 00000000..13183e86
--- /dev/null
+++ b/src/Alpha_complex/example/alphaoffreader_for_doc_32.txt
@@ -0,0 +1,22 @@
+Alpha complex is of dimension 2 - 20 simplices - 7 vertices.
+Iterator on alpha complex simplices in the filtration order, with [filtration value]:
+   ( 0 ) -> [0] 
+   ( 1 ) -> [0] 
+   ( 2 ) -> [0] 
+   ( 3 ) -> [0] 
+   ( 4 ) -> [0] 
+   ( 5 ) -> [0] 
+   ( 6 ) -> [0] 
+   ( 3 2 ) -> [6.25] 
+   ( 5 4 ) -> [7.25] 
+   ( 2 0 ) -> [8.5] 
+   ( 1 0 ) -> [9.25] 
+   ( 3 1 ) -> [10] 
+   ( 2 1 ) -> [11.25] 
+   ( 3 2 1 ) -> [12.5] 
+   ( 2 1 0 ) -> [12.9959] 
+   ( 6 5 ) -> [13.25] 
+   ( 4 2 ) -> [20] 
+   ( 6 4 ) -> [22.7367] 
+   ( 6 5 4 ) -> [22.7367] 
+   ( 6 3 ) -> [30.25] 
diff --git a/src/Alpha_complex/example/alphaoffreader_for_doc_60.txt b/src/Alpha_complex/example/alphaoffreader_for_doc_60.txt
new file mode 100644
index 00000000..71f29a00
--- /dev/null
+++ b/src/Alpha_complex/example/alphaoffreader_for_doc_60.txt
@@ -0,0 +1,27 @@
+Alpha complex is of dimension 2 - 25 simplices - 7 vertices.
+Iterator on alpha complex simplices in the filtration order, with [filtration value]:
+   ( 0 ) -> [0] 
+   ( 1 ) -> [0] 
+   ( 2 ) -> [0] 
+   ( 3 ) -> [0] 
+   ( 4 ) -> [0] 
+   ( 5 ) -> [0] 
+   ( 6 ) -> [0] 
+   ( 3 2 ) -> [6.25] 
+   ( 5 4 ) -> [7.25] 
+   ( 2 0 ) -> [8.5] 
+   ( 1 0 ) -> [9.25] 
+   ( 3 1 ) -> [10] 
+   ( 2 1 ) -> [11.25] 
+   ( 3 2 1 ) -> [12.5] 
+   ( 2 1 0 ) -> [12.9959] 
+   ( 6 5 ) -> [13.25] 
+   ( 4 2 ) -> [20] 
+   ( 6 4 ) -> [22.7367] 
+   ( 6 5 4 ) -> [22.7367] 
+   ( 6 3 ) -> [30.25] 
+   ( 6 2 ) -> [36.5] 
+   ( 6 3 2 ) -> [36.5] 
+   ( 6 4 2 ) -> [37.2449] 
+   ( 4 0 ) -> [59.7107] 
+   ( 4 2 0 ) -> [59.7107] 
diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h
new file mode 100644
index 00000000..2c95ceb4
--- /dev/null
+++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h
@@ -0,0 +1,419 @@
+/*    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 ALPHA_COMPLEX_H_
+#define ALPHA_COMPLEX_H_
+
+// to construct a simplex_tree from Delaunay_triangulation
+#include <gudhi/graph_simplicial_complex.h>
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Debug_utils.h>
+// to construct Alpha_complex from a OFF file of points
+#include <gudhi/Points_off_io.h>
+
+#include <stdlib.h>
+#include <math.h>  // isnan, fmax
+
+#include <CGAL/Delaunay_triangulation.h>
+#include <CGAL/Epick_d.h>
+#include <CGAL/Spatial_sort_traits_adapter_d.h>
+
+#include <iostream>
+#include <vector>
+#include <string>
+#include <limits>  // NaN
+#include <map>
+#include <utility>  // std::pair
+#include <stdexcept>
+#include <numeric>  // for std::iota
+
+namespace Gudhi {
+
+namespace alpha_complex {
+
+/**
+ * \class Alpha_complex Alpha_complex.h gudhi/Alpha_complex.h
+ * \brief Alpha complex data structure.
+ * 
+ * \ingroup alpha_complex
+ * 
+ * \details
+ * The data structure can be constructed from a CGAL Delaunay triangulation (for more informations on CGAL Delaunay 
+ * triangulation, please refer to the corresponding chapter in page http://doc.cgal.org/latest/Triangulation/) or from
+ * an OFF file (cf. Points_off_reader).
+ * 
+ * Please refer to \ref alpha_complex for examples.
+ *
+ * The complex is a template class requiring an Epick_d <a target="_blank"
+ * href="http://doc.cgal.org/latest/Kernel_d/index.html#Chapter_dD_Geometry_Kernel">dD Geometry Kernel</a>
+ * \cite cgal:s-gkd-15b from CGAL as template, default value is <a target="_blank"
+ * href="http://doc.cgal.org/latest/Kernel_d/classCGAL_1_1Epick__d.html">CGAL::Epick_d</a>
+ * < <a target="_blank" href="http://doc.cgal.org/latest/Kernel_23/classCGAL_1_1Dynamic__dimension__tag.html">
+ * CGAL::Dynamic_dimension_tag </a> >
+ * 
+ * \remark When Alpha_complex is constructed with an infinite value of alpha, the complex is a Delaunay complex.
+ * 
+ */
+template<class Kernel = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>>
+class Alpha_complex : public Simplex_tree<> {
+ public:
+  // Add an int in TDS to save point index in the structure
+  typedef CGAL::Triangulation_data_structure<typename Kernel::Dimension,
+                              CGAL::Triangulation_vertex<Kernel, std::ptrdiff_t>,
+                              CGAL::Triangulation_full_cell<Kernel> > TDS;
+  /** \brief A Delaunay triangulation of a set of points in \f$ \mathbb{R}^D\f$.*/
+  typedef CGAL::Delaunay_triangulation<Kernel, TDS> Delaunay_triangulation;
+
+  /** \brief A point in Euclidean space.*/
+  typedef typename Kernel::Point_d Point_d;
+  /** \brief Geometric traits class that provides the geometric types and predicates needed by Delaunay
+   * triangulations.*/
+  typedef Kernel Geom_traits;
+
+ private:
+  // From Simplex_tree
+  // Type required to insert into a simplex_tree (with or without subfaces).
+  typedef std::vector<Vertex_handle> Vector_vertex;
+
+  // Simplex_result is the type returned from simplex_tree insert function.
+  typedef typename std::pair<Simplex_handle, bool> Simplex_result;
+
+  typedef typename Kernel::Compute_squared_radius_d Squared_Radius;
+  typedef typename Kernel::Side_of_bounded_sphere_d Is_Gabriel;
+  typedef typename Kernel::Point_dimension_d        Point_Dimension;
+
+  // Type required to compute squared radius, or side of bounded sphere on a vector of points.
+  typedef typename std::vector<Point_d> Vector_of_CGAL_points;
+
+  // Vertex_iterator type from CGAL.
+  typedef typename Delaunay_triangulation::Vertex_iterator CGAL_vertex_iterator;
+
+  // size_type type from CGAL.
+  typedef typename Delaunay_triangulation::size_type size_type;
+
+  // Map type to switch from simplex tree vertex handle to CGAL vertex iterator.
+  typedef typename std::map< Vertex_handle, CGAL_vertex_iterator > Vector_vertex_iterator;
+
+ private:
+  /** \brief Vertex iterator vector to switch from simplex tree vertex handle to CGAL vertex iterator.
+   * Vertex handles are inserted sequentially, starting at 0.*/
+  Vector_vertex_iterator vertex_handle_to_iterator_;
+  /** \brief Pointer on the CGAL Delaunay triangulation.*/
+  Delaunay_triangulation* triangulation_;
+  /** \brief Kernel for triangulation_ functions access.*/
+  Kernel kernel_;
+
+ public:
+  /** \brief Alpha_complex constructor from an OFF file name.
+   * Uses the Delaunay_triangulation_off_reader to construct the Delaunay triangulation required to initialize 
+   * the Alpha_complex.
+   * 
+   * Duplicate points are inserted once in the Alpha_complex. This is the reason why the vertices may be not contiguous.
+   *
+   * @param[in] off_file_name OFF file [path and] name.
+   * @param[in] max_alpha_square maximum for alpha square value. Default value is +\f$\infty\f$.
+   */
+  Alpha_complex(const std::string& off_file_name,
+                Filtration_value max_alpha_square = std::numeric_limits<Filtration_value>::infinity())
+      : triangulation_(nullptr) {
+    Gudhi::Points_off_reader<Point_d> off_reader(off_file_name);
+    if (!off_reader.is_valid()) {
+      std::cerr << "Alpha_complex - Unable to read file " << off_file_name << "\n";
+      exit(-1);  // ----- >>
+    }
+
+    init_from_range(off_reader.get_point_cloud(), max_alpha_square);
+  }
+
+  /** \brief Alpha_complex constructor from a list of points.
+   *
+   * Duplicate points are inserted once in the Alpha_complex. This is the reason why the vertices may be not contiguous.
+   * 
+   * @param[in] points Range of points to triangulate. Points must be in Kernel::Point_d
+   * @param[in] max_alpha_square maximum for alpha square value. Default value is +\f$\infty\f$.
+   * 
+   * The type InputPointRange must be a range for which std::begin and
+   * std::end return input iterators on a Kernel::Point_d.
+   * 
+   * @post Compare num_simplices with InputPointRange points number (not the same in case of duplicate points). 
+   */
+  template<typename InputPointRange >
+  Alpha_complex(const InputPointRange& points,
+                Filtration_value max_alpha_square = std::numeric_limits<Filtration_value>::infinity())
+      : triangulation_(nullptr) {
+    init_from_range(points, max_alpha_square);
+  }
+
+  /** \brief Alpha_complex destructor.
+   *
+   * @warning Deletes the Delaunay triangulation.
+   */
+  ~Alpha_complex() {
+    delete triangulation_;
+  }
+
+  // Forbid copy/move constructor/assignment operator
+  Alpha_complex(const Alpha_complex& other) = delete;
+  Alpha_complex& operator= (const Alpha_complex& other) = delete;
+  Alpha_complex (Alpha_complex&& other) = delete;
+  Alpha_complex& operator= (Alpha_complex&& other) = delete;
+
+  /** \brief get_point returns the point corresponding to the vertex given as parameter.
+   *
+   * @param[in] vertex Vertex handle of the point to retrieve.
+   * @return The point found.
+   * @exception std::out_of_range In case vertex is not found (cf. std::vector::at).
+   */
+  Point_d get_point(Vertex_handle vertex) const {
+    return vertex_handle_to_iterator_.at(vertex)->point();
+  }
+
+ private:
+  template<typename InputPointRange >
+  void init_from_range(const InputPointRange& points, Filtration_value max_alpha_square) {
+    auto first = std::begin(points);
+    auto last = std::end(points);
+    if (first != last) {
+      // point_dimension function initialization
+      Point_Dimension point_dimension = kernel_.point_dimension_d_object();
+
+      // Delaunay triangulation is point dimension.
+      triangulation_ = new Delaunay_triangulation(point_dimension(*first));
+
+      std::vector<Point_d> points(first, last);
+
+      // Creates a vector {0, 1, ..., N-1}
+      std::vector<std::ptrdiff_t> indices(boost::counting_iterator<std::ptrdiff_t>(0),
+                                          boost::counting_iterator<std::ptrdiff_t>(points.size()));
+
+      // Sort indices considering CGAL spatial sort
+      typedef CGAL::Spatial_sort_traits_adapter_d<Kernel, Point_d*> Search_traits_d;
+      spatial_sort(indices.begin(), indices.end(), Search_traits_d(&(points[0])));
+
+      typename Delaunay_triangulation::Full_cell_handle hint;
+      for (auto index : indices) {
+        typename Delaunay_triangulation::Vertex_handle pos = triangulation_->insert(points[index], hint);
+        // Save index value as data to retrieve it after insertion
+        pos->data() = index;
+        hint = pos->full_cell();
+      }
+      init(max_alpha_square);
+    }
+  }
+
+  /** \brief Initialize the Alpha_complex from the Delaunay triangulation.
+   *
+   * @param[in] max_alpha_square maximum for alpha square value.
+   * 
+   * @warning Delaunay triangulation must be already constructed with at least one vertex and dimension must be more 
+   * than 0.
+   * 
+   * Initialization can be launched once.
+   */
+  void init(Filtration_value max_alpha_square) {
+    if (triangulation_ == nullptr) {
+      std::cerr << "Alpha_complex init - Cannot init from a NULL triangulation\n";
+      return;  // ----- >>
+    }
+    if (triangulation_->number_of_vertices() < 1) {
+      std::cerr << "Alpha_complex init - Cannot init from a triangulation without vertices\n";
+      return;  // ----- >>
+    }
+    if (triangulation_->maximal_dimension() < 1) {
+      std::cerr << "Alpha_complex init - Cannot init from a zero-dimension triangulation\n";
+      return;  // ----- >>
+    }
+    if (num_vertices() > 0) {
+      std::cerr << "Alpha_complex init - Cannot init twice\n";
+      return;  // ----- >>
+    }
+
+    set_dimension(triangulation_->maximal_dimension());
+
+    // --------------------------------------------------------------------------------------------
+    // double map to retrieve simplex tree vertex handles from CGAL vertex iterator and vice versa
+    // Loop on triangulation vertices list
+    for (CGAL_vertex_iterator vit = triangulation_->vertices_begin(); vit != triangulation_->vertices_end(); ++vit) {
+      if (!triangulation_->is_infinite(*vit)) {
+#ifdef DEBUG_TRACES
+        std::cout << "Vertex insertion - " << vit->data() << " -> " << vit->point() << std::endl;
+#endif  // DEBUG_TRACES
+        vertex_handle_to_iterator_.emplace(vit->data(), vit);
+      }
+    }
+    // --------------------------------------------------------------------------------------------
+
+    // --------------------------------------------------------------------------------------------
+    // 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) {
+      Vector_vertex vertexVector;
+#ifdef DEBUG_TRACES
+      std::cout << "Simplex_tree insertion ";
+#endif  // DEBUG_TRACES
+      for (auto vit = cit->vertices_begin(); vit != cit->vertices_end(); ++vit) {
+        if (*vit != nullptr) {
+#ifdef DEBUG_TRACES
+          std::cout << " " << (*vit)->data();
+#endif  // DEBUG_TRACES
+          // Vector of vertex construction for simplex_tree structure
+          vertexVector.push_back((*vit)->data());
+        }
+      }
+#ifdef DEBUG_TRACES
+      std::cout << std::endl;
+#endif  // DEBUG_TRACES
+      // Insert each simplex and its subfaces in the simplex tree - filtration is NaN
+      insert_simplex_and_subfaces(vertexVector, std::numeric_limits<double>::quiet_NaN());
+    }
+    // --------------------------------------------------------------------------------------------
+
+    // --------------------------------------------------------------------------------------------
+    // Will be re-used many times
+    Vector_of_CGAL_points pointVector;
+    // ### For i : d -> 0
+    for (int decr_dim = dimension(); decr_dim >= 0; decr_dim--) {
+      // ### Foreach Sigma of dim i
+      for (auto f_simplex : skeleton_simplex_range(decr_dim)) {
+        int f_simplex_dim = dimension(f_simplex);
+        if (decr_dim == f_simplex_dim) {
+          pointVector.clear();
+#ifdef DEBUG_TRACES
+          std::cout << "Sigma of dim " << decr_dim << " is";
+#endif  // DEBUG_TRACES
+          for (auto vertex : simplex_vertex_range(f_simplex)) {
+            pointVector.push_back(get_point(vertex));
+#ifdef DEBUG_TRACES
+            std::cout << " " << vertex;
+#endif  // DEBUG_TRACES
+          }
+#ifdef DEBUG_TRACES
+          std::cout << std::endl;
+#endif  // DEBUG_TRACES
+          // ### If filt(Sigma) is NaN : filt(Sigma) = alpha(Sigma)
+          if (std::isnan(filtration(f_simplex))) {
+            Filtration_value alpha_complex_filtration = 0.0;
+            // No need to compute squared_radius on a single point - alpha is 0.0
+            if (f_simplex_dim > 0) {
+              // squared_radius function initialization
+              Squared_Radius squared_radius = kernel_.compute_squared_radius_d_object();
+
+              alpha_complex_filtration = squared_radius(pointVector.begin(), pointVector.end());
+            }
+            assign_filtration(f_simplex, alpha_complex_filtration);
+#ifdef DEBUG_TRACES
+            std::cout << "filt(Sigma) is NaN : filt(Sigma) =" << filtration(f_simplex) << std::endl;
+#endif  // DEBUG_TRACES
+          }
+          propagate_alpha_filtration(f_simplex, decr_dim);
+        }
+      }
+    }
+    // --------------------------------------------------------------------------------------------
+
+    // --------------------------------------------------------------------------------------------
+    // As Alpha value is an approximation, we have to make filtration non decreasing while increasing the dimension
+    bool modified_filt = make_filtration_non_decreasing();
+    // Remove all simplices that have a filtration value greater than max_alpha_square
+    // Remark: prune_above_filtration does not require initialize_filtration to be done before.
+    modified_filt |= prune_above_filtration(max_alpha_square);
+    if (modified_filt) {
+      initialize_filtration();
+    }
+    // --------------------------------------------------------------------------------------------
+  }
+
+  template<typename Simplex_handle>
+  void propagate_alpha_filtration(Simplex_handle f_simplex, int decr_dim) {
+    // ### Foreach Tau face of Sigma
+    for (auto f_boundary : boundary_simplex_range(f_simplex)) {
+#ifdef DEBUG_TRACES
+      std::cout << " | --------------------------------------------------\n";
+      std::cout << " | Tau ";
+      for (auto vertex : simplex_vertex_range(f_boundary)) {
+        std::cout << vertex << " ";
+      }
+      std::cout << "is a face of Sigma\n";
+      std::cout << " | isnan(filtration(Tau)=" << std::isnan(filtration(f_boundary)) << std::endl;
+#endif  // DEBUG_TRACES
+      // ### If filt(Tau) is not NaN
+      if (!std::isnan(filtration(f_boundary))) {
+        // ### filt(Tau) = fmin(filt(Tau), filt(Sigma))
+        Filtration_value alpha_complex_filtration = fmin(filtration(f_boundary), filtration(f_simplex));
+        assign_filtration(f_boundary, alpha_complex_filtration);
+#ifdef DEBUG_TRACES
+        std::cout << " | filt(Tau) = fmin(filt(Tau), filt(Sigma)) = " << filtration(f_boundary) << std::endl;
+#endif  // DEBUG_TRACES
+        // ### Else
+      } else {
+        // No need to compute is_gabriel for dimension <= 2
+        // i.e. : Sigma = (3,1) => Tau = 1
+        if (decr_dim > 1) {
+          // insert the Tau points in a vector for is_gabriel function
+          Vector_of_CGAL_points pointVector;
+#ifdef DEBUG_TRACES
+          Vertex_handle vertexForGabriel = Vertex_handle();
+#endif  // DEBUG_TRACES
+          for (auto vertex : simplex_vertex_range(f_boundary)) {
+            pointVector.push_back(get_point(vertex));
+          }
+          // Retrieve the Sigma point that is not part of Tau - parameter for is_gabriel function
+          Point_d point_for_gabriel;
+          for (auto vertex : simplex_vertex_range(f_simplex)) {
+            point_for_gabriel = get_point(vertex);
+            if (std::find(pointVector.begin(), pointVector.end(), point_for_gabriel) == pointVector.end()) {
+#ifdef DEBUG_TRACES
+              // vertex is not found in Tau
+              vertexForGabriel = vertex;
+#endif  // DEBUG_TRACES
+              // No need to continue loop
+              break;
+            }
+          }
+          // is_gabriel function initialization
+          Is_Gabriel is_gabriel = kernel_.side_of_bounded_sphere_d_object();
+          bool is_gab = is_gabriel(pointVector.begin(), pointVector.end(), point_for_gabriel)
+              != CGAL::ON_BOUNDED_SIDE;
+#ifdef DEBUG_TRACES
+          std::cout << " | Tau is_gabriel(Sigma)=" << is_gab << " - vertexForGabriel=" << vertexForGabriel << std::endl;
+#endif  // DEBUG_TRACES
+          // ### If Tau is not Gabriel of Sigma
+          if (false == is_gab) {
+            // ### filt(Tau) = filt(Sigma)
+            Filtration_value alpha_complex_filtration = filtration(f_simplex);
+            assign_filtration(f_boundary, alpha_complex_filtration);
+#ifdef DEBUG_TRACES
+            std::cout << " | filt(Tau) = filt(Sigma) = " << filtration(f_boundary) << std::endl;
+#endif  // DEBUG_TRACES
+          }
+        }
+      }
+    }
+  }
+};
+
+}  // namespace alpha_complex
+
+namespace alphacomplex = alpha_complex;
+
+}  // namespace Gudhi
+
+#endif  // ALPHA_COMPLEX_H_
diff --git a/src/Alpha_complex/test/Alpha_complex_unit_test.cpp b/src/Alpha_complex/test/Alpha_complex_unit_test.cpp
new file mode 100644
index 00000000..4d7bf622
--- /dev/null
+++ b/src/Alpha_complex/test/Alpha_complex_unit_test.cpp
@@ -0,0 +1,243 @@
+/*    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/>.
+ */
+
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE "alpha_complex"
+#include <boost/test/unit_test.hpp>
+
+#include <CGAL/Delaunay_triangulation.h>
+#include <CGAL/Epick_d.h>
+
+#include <cmath>  // float comparison
+#include <limits>
+#include <string>
+#include <vector>
+
+#include <gudhi/Alpha_complex.h>
+
+// Use dynamic_dimension_tag for the user to be able to set dimension
+typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kernel_d;
+// The triangulation uses the default instantiation of the TriangulationDataStructure template parameter
+
+BOOST_AUTO_TEST_CASE(ALPHA_DOC_OFF_file) {
+  // ----------------------------------------------------------------------------
+  //
+  // Init of an alpha-complex from a OFF file
+  //
+  // ----------------------------------------------------------------------------
+  std::string off_file_name("alphacomplexdoc.off");
+  double max_alpha_square_value = 60.0;
+  std::cout << "========== OFF FILE NAME = " << off_file_name << " - alpha²=" <<
+      max_alpha_square_value << "==========" << std::endl;
+
+  Gudhi::alpha_complex::Alpha_complex<Kernel_d> alpha_complex_from_file(off_file_name, max_alpha_square_value);
+
+  const int DIMENSION = 2;
+  std::cout << "alpha_complex_from_file.dimension()=" << alpha_complex_from_file.dimension() << std::endl;
+  BOOST_CHECK(alpha_complex_from_file.dimension() == DIMENSION);
+
+  const int NUMBER_OF_VERTICES = 7;
+  std::cout << "alpha_complex_from_file.num_vertices()=" << alpha_complex_from_file.num_vertices() << std::endl;
+  BOOST_CHECK(alpha_complex_from_file.num_vertices() == NUMBER_OF_VERTICES);
+
+  const int NUMBER_OF_SIMPLICES = 25;
+  std::cout << "alpha_complex_from_file.num_simplices()=" << alpha_complex_from_file.num_simplices() << std::endl;
+  BOOST_CHECK(alpha_complex_from_file.num_simplices() == NUMBER_OF_SIMPLICES);
+
+}
+
+BOOST_AUTO_TEST_CASE(ALPHA_DOC_OFF_file_filtered) {
+  // ----------------------------------------------------------------------------
+  //
+  // Init of an alpha-complex from a OFF file
+  //
+  // ----------------------------------------------------------------------------
+  std::string off_file_name("alphacomplexdoc.off");
+  double max_alpha_square_value = 59.0;
+  std::cout << "========== OFF FILE NAME = " << off_file_name << " - alpha²=" <<
+      max_alpha_square_value << "==========" << std::endl;
+
+  // Use of the default dynamic kernel
+  Gudhi::alpha_complex::Alpha_complex<> alpha_complex_from_file(off_file_name, max_alpha_square_value);
+
+  const int DIMENSION = 2;
+  std::cout << "alpha_complex_from_file.dimension()=" << alpha_complex_from_file.dimension() << std::endl;
+  BOOST_CHECK(alpha_complex_from_file.dimension() == DIMENSION);
+
+  const int NUMBER_OF_VERTICES = 7;
+  std::cout << "alpha_complex_from_file.num_vertices()=" << alpha_complex_from_file.num_vertices() << std::endl;
+  BOOST_CHECK(alpha_complex_from_file.num_vertices() == NUMBER_OF_VERTICES);
+
+  const int NUMBER_OF_SIMPLICES = 23;
+  std::cout << "alpha_complex_from_file.num_simplices()=" << alpha_complex_from_file.num_simplices() << std::endl;
+  BOOST_CHECK(alpha_complex_from_file.num_simplices() == NUMBER_OF_SIMPLICES);
+}
+
+bool are_almost_the_same(float a, float b) {
+  return std::fabs(a - b) < std::numeric_limits<float>::epsilon();
+}
+
+// Use dynamic_dimension_tag for the user to be able to set dimension
+typedef CGAL::Epick_d< CGAL::Dimension_tag<4> > Kernel_s;
+typedef Kernel_s::Point_d Point;
+typedef std::vector<Point> Vector_of_points;
+
+
+bool is_point_in_list(Vector_of_points points_list, Point point) {
+  for (auto& point_in_list : points_list) {
+    if (point_in_list == point) {
+      return true;  // point found
+    }
+  }
+  return false;  // point not found
+}
+
+BOOST_AUTO_TEST_CASE(Alpha_complex_from_points) {
+  // ----------------------------------------------------------------------------
+  // Init of a list of points
+  // ----------------------------------------------------------------------------
+  Vector_of_points points;
+  std::vector<double> coords = { 0.0, 0.0, 0.0, 1.0 };
+  points.push_back(Point(coords.begin(), coords.end()));
+  coords = { 0.0, 0.0, 1.0, 0.0 };
+  points.push_back(Point(coords.begin(), coords.end()));
+  coords = { 0.0, 1.0, 0.0, 0.0 };
+  points.push_back(Point(coords.begin(), coords.end()));
+  coords = { 1.0, 0.0, 0.0, 0.0 };
+  points.push_back(Point(coords.begin(), coords.end()));
+
+  // ----------------------------------------------------------------------------
+  // Init of an alpha complex from the list of points
+  // ----------------------------------------------------------------------------
+  Gudhi::alpha_complex::Alpha_complex<Kernel_s> alpha_complex_from_points(points);
+
+  std::cout << "========== Alpha_complex_from_points ==========" << std::endl;
+
+  // Another way to check num_simplices
+  std::cout << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" << std::endl;
+  int num_simplices = 0;
+  for (auto f_simplex : alpha_complex_from_points.filtration_simplex_range()) {
+    num_simplices++;
+    std::cout << "   ( ";
+    for (auto vertex : alpha_complex_from_points.simplex_vertex_range(f_simplex)) {
+      std::cout << vertex << " ";
+    }
+    std::cout << ") -> " << "[" << alpha_complex_from_points.filtration(f_simplex) << "] ";
+    std::cout << std::endl;
+  }
+  BOOST_CHECK(num_simplices == 15);
+  std::cout << "alpha_complex_from_points.num_simplices()=" << alpha_complex_from_points.num_simplices() << std::endl;
+  BOOST_CHECK(alpha_complex_from_points.num_simplices() == 15);
+
+  std::cout << "alpha_complex_from_points.dimension()=" << alpha_complex_from_points.dimension() << std::endl;
+  BOOST_CHECK(alpha_complex_from_points.dimension() == 4);
+  std::cout << "alpha_complex_from_points.num_vertices()=" << alpha_complex_from_points.num_vertices() << std::endl;
+  BOOST_CHECK(alpha_complex_from_points.num_vertices() == 4);
+
+  for (auto f_simplex : alpha_complex_from_points.filtration_simplex_range()) {
+    switch (alpha_complex_from_points.dimension(f_simplex)) {
+      case 0:
+        BOOST_CHECK(are_almost_the_same(alpha_complex_from_points.filtration(f_simplex), 0.0));
+        break;
+      case 1:
+        BOOST_CHECK(are_almost_the_same(alpha_complex_from_points.filtration(f_simplex), 1.0/2.0));
+        break;
+      case 2:
+        BOOST_CHECK(are_almost_the_same(alpha_complex_from_points.filtration(f_simplex), 2.0/3.0));
+        break;
+      case 3:
+        BOOST_CHECK(are_almost_the_same(alpha_complex_from_points.filtration(f_simplex), 3.0/4.0));
+        break;
+      default:
+        BOOST_CHECK(false);  // Shall not happen
+        break;
+    }
+  }
+
+  Point p0 = alpha_complex_from_points.get_point(0);
+  std::cout << "alpha_complex_from_points.get_point(0)=" << p0 << std::endl;
+  BOOST_CHECK(4 == p0.dimension());
+  BOOST_CHECK(is_point_in_list(points, p0));
+
+  Point p1 = alpha_complex_from_points.get_point(1);
+  std::cout << "alpha_complex_from_points.get_point(1)=" << p1 << std::endl;
+  BOOST_CHECK(4 == p1.dimension());
+  BOOST_CHECK(is_point_in_list(points, p1));
+
+  Point p2 = alpha_complex_from_points.get_point(2);
+  std::cout << "alpha_complex_from_points.get_point(2)=" << p2 << std::endl;
+  BOOST_CHECK(4 == p2.dimension());
+  BOOST_CHECK(is_point_in_list(points, p2));
+
+  Point p3 = alpha_complex_from_points.get_point(3);
+  std::cout << "alpha_complex_from_points.get_point(3)=" << p3 << std::endl;
+  BOOST_CHECK(4 == p3.dimension());
+  BOOST_CHECK(is_point_in_list(points, p3));
+
+  // Test to the limit
+  BOOST_CHECK_THROW (alpha_complex_from_points.get_point(4), std::out_of_range);
+  BOOST_CHECK_THROW (alpha_complex_from_points.get_point(-1), std::out_of_range);
+  BOOST_CHECK_THROW (alpha_complex_from_points.get_point(1234), std::out_of_range);
+  
+  // Test after prune_above_filtration
+  bool modified = alpha_complex_from_points.prune_above_filtration(0.6);
+  if (modified) {
+    alpha_complex_from_points.initialize_filtration();
+  }
+  BOOST_CHECK(modified);
+  
+  // Another way to check num_simplices
+  std::cout << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" << std::endl;
+  num_simplices = 0;
+  for (auto f_simplex : alpha_complex_from_points.filtration_simplex_range()) {
+    num_simplices++;
+    std::cout << "   ( ";
+    for (auto vertex : alpha_complex_from_points.simplex_vertex_range(f_simplex)) {
+      std::cout << vertex << " ";
+    }
+    std::cout << ") -> " << "[" << alpha_complex_from_points.filtration(f_simplex) << "] ";
+    std::cout << std::endl;
+  }
+  BOOST_CHECK(num_simplices == 10);
+  std::cout << "alpha_complex_from_points.num_simplices()=" << alpha_complex_from_points.num_simplices() << std::endl;
+  BOOST_CHECK(alpha_complex_from_points.num_simplices() == 10);
+
+  std::cout << "alpha_complex_from_points.dimension()=" << alpha_complex_from_points.dimension() << std::endl;
+  BOOST_CHECK(alpha_complex_from_points.dimension() == 4);
+  std::cout << "alpha_complex_from_points.num_vertices()=" << alpha_complex_from_points.num_vertices() << std::endl;
+  BOOST_CHECK(alpha_complex_from_points.num_vertices() == 4);
+
+  for (auto f_simplex : alpha_complex_from_points.filtration_simplex_range()) {
+    switch (alpha_complex_from_points.dimension(f_simplex)) {
+      case 0:
+        BOOST_CHECK(are_almost_the_same(alpha_complex_from_points.filtration(f_simplex), 0.0));
+        break;
+      case 1:
+        BOOST_CHECK(are_almost_the_same(alpha_complex_from_points.filtration(f_simplex), 1.0/2.0));
+        break;
+      default:
+        BOOST_CHECK(false);  // Shall not happen
+        break;
+    }
+  }
+
+}
diff --git a/src/Alpha_complex/test/CMakeLists.txt b/src/Alpha_complex/test/CMakeLists.txt
new file mode 100644
index 00000000..b0723a41
--- /dev/null
+++ b/src/Alpha_complex/test/CMakeLists.txt
@@ -0,0 +1,38 @@
+cmake_minimum_required(VERSION 2.6)
+project(Alpha_complex_tests)
+
+if (GCOVR_PATH)
+  # for gcovr to make coverage reports - Corbera Jenkins plugin
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
+endif()
+if (GPROF_PATH)
+  # for gprof to make coverage reports - Jenkins
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
+endif()
+
+# need CGAL 4.7
+# cmake -DCGAL_DIR=~/workspace/CGAL-4.7-Ic-41 ../../..
+if(CGAL_FOUND)
+  if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
+    if (EIGEN3_FOUND)
+      add_executable ( AlphaComplexUT Alpha_complex_unit_test.cpp )
+      target_link_libraries(AlphaComplexUT  ${Boost_SYSTEM_LIBRARY} ${Boost_THREAD_LIBRARY} ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+      if (TBB_FOUND)
+        target_link_libraries(AlphaComplexUT ${TBB_LIBRARIES})
+      endif()
+
+      # Do not forget to copy test files in current binary dir
+      file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+
+      add_test(AlphaComplexUT ${CMAKE_CURRENT_BINARY_DIR}/AlphaComplexUT
+      # XML format for Jenkins xUnit plugin 
+      --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/AlphaComplexUT.xml --log_level=test_suite --report_level=no)
+
+    else()
+      message(WARNING "Eigen3 not found. Version 3.1.0 is required for Alpha complex unitary tests.")
+    endif()
+  else()
+    message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile Alpha complex unitary tests. Version 4.7.0 is required.")
+  endif ()
+endif()
+
diff --git a/src/Alpha_complex/test/README b/src/Alpha_complex/test/README
new file mode 100644
index 00000000..45b87d91
--- /dev/null
+++ b/src/Alpha_complex/test/README
@@ -0,0 +1,12 @@
+To compile:
+***********
+
+cmake .
+make
+
+To launch with details:
+***********************
+
+./AlphaComplexUnitTest --report_level=detailed --log_level=all 
+
+   ==> echo $? returns 0 in case of success (non-zero otherwise)
diff --git a/src/Bitmap_cubical_complex/doc/Cubical_complex_representation.ipe b/src/Bitmap_cubical_complex/doc/Cubical_complex_representation.ipe
new file mode 100644
index 00000000..bec245e7
--- /dev/null
+++ b/src/Bitmap_cubical_complex/doc/Cubical_complex_representation.ipe
@@ -0,0 +1,732 @@
+<?xml version="1.0"?>
+<!DOCTYPE ipe SYSTEM "ipe.dtd">
+<ipe version="70107" creator="Ipe 7.1.10">
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index 00000000..afb2a75e
--- /dev/null
+++ b/src/Bitmap_cubical_complex/doc/Cubical_complex_representation.png
diff --git a/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h b/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h
new file mode 100644
index 00000000..5963caa3
--- /dev/null
+++ b/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h
@@ -0,0 +1,159 @@
+/*    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):       Pawel Dlotko
+ *
+ *    Copyright (C) 2015  INRIA Sophia-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 DOC_GUDHI_CUBICAL_COMPLEX_COMPLEX_H_
+#define DOC_GUDHI_CUBICAL_COMPLEX_COMPLEX_H_
+
+namespace Gudhi {
+
+namespace cubical_complex {
+
+/**  \defgroup cubical_complex Cubical complex
+ *
+ * \author   Pawel Dlotko
+ *
+ * @{
+ *
+
+ * Bitmap_cubical_complex is an example of a structured complex useful in computational mathematics (specially rigorous
+ * numerics) and image analysis. The presented implementation of cubical complexes is based on the following
+ * definition.
+ *
+ * An <em>elementary interval</em> is an interval of a form \f$ [n,n+1] \f$, or \f$[n,n]\f$, for \f$ n \in \mathcal{Z}
+ * \f$. The first one is called <em>non-degenerate</em>, while the second one is \a degenerate interval. A
+ * <em>boundary of a elementary interval</em> is a chain  \f$\partial [n,n+1] = [n+1,n+1]-[n,n] \f$ in case of
+ * non-degenerated elementary interval and \f$\partial [n,n] = 0 \f$ in case of degenerate elementary interval. An
+ * <em>elementary cube</em> \f$ C \f$ is a product of elementary intervals, \f$C=I_1 \times \ldots \times I_n\f$.
+ * <em>Embedding dimension</em> of a cube is n, the number of elementary intervals (degenerate or not) in the product.
+ * A <em>dimension of a cube</em> \f$C=I_1 \times ... \times I_n\f$ is the number of non degenerate elementary
+ * intervals in the product. A <em>boundary of a cube</em> \f$C=I_1 \times \ldots \times I_n\f$ is a chain obtained
+ * in the following way:
+ * \f[\partial C = (\partial I_1 \times \ldots \times I_n) + (I_1 \times \partial I_2 \times \ldots \times I_n) +
+ * \ldots + (I_1 \times I_2 \times \ldots \times \partial I_n).\f]
+ * A <em>cubical complex</em> \f$\mathcal{K}\f$ is a collection of cubes closed under operation of taking boundary
+ * (i.e. boundary of every cube from the collection is in the collection). A cube \f$C\f$ in cubical complex
+ * \f$\mathcal{K}\f$ is <em>maximal</em> if it is not in a boundary of any other cube in \f$\mathcal{K}\f$. A \a
+ * support of a cube \f$C\f$ is the set in \f$\mathbb{R}^n\f$ occupied by \f$C\f$ (\f$n\f$ is the embedding dimension
+ * of \f$C\f$).
+ *
+ * Cubes may be equipped with a filtration values in which case we have filtered cubical complex. All the cubical
+ * complexes considered in this implementation are filtered cubical complexes (although, the range of a filtration may
+ * be a set of two elements).
+ *
+ * For further details and theory of cubical complexes, please consult \cite kaczynski2004computational as well as the
+ * following paper \cite peikert2012topological .
+ *
+ * \section cubicalcomplexdatastructure Data structure.
+ *
+ * The implementation of Cubical complex provides a representation of complexes that occupy a rectangular region in
+ * \f$\mathbb{R}^n\f$. This extra assumption allows for a memory efficient way of storing cubical complexes in a form
+ * of so called bitmaps. Let \f$R = [b_1,e_1] \times \ldots \times [b_n,e_n]\f$, for \f$b_1,...b_n,e_1,...,e_n \in
+ * \mathbb{Z}\f$, \f$b_i \leq d_i\f$ be the considered rectangular region and let \f$\mathcal{K}\f$ be a filtered
+ * cubical complex having the rectangle \f$R\f$ as its support. Note that the structure of the coordinate system gives
+ * a way a lexicographical ordering of cells of \f$\mathcal{K}\f$. This ordering is a base of the presented
+ * bitmap-based implementation. In this implementation, the whole cubical complex is stored as a vector of the values
+ * of filtration. This, together with dimension of \f$\mathcal{K}\f$ and the sizes of \f$\mathcal{K}\f$ in all
+ * directions, allows to determine, dimension, neighborhood, boundary and coboundary of every cube \f$C \in
+ * \mathcal{K}\f$.
+ *
+ * \image html "Cubical_complex_representation.png" Cubical complex.
+ *
+ * Note that the cubical complex in the figure above is, in a natural way, a product of one dimensional cubical
+ * complexes in \f$\mathbb{R}\f$. The number of all cubes in each direction is equal \f$2n+1\f$, where \f$n\f$ is the
+ * number of maximal cubes in the considered direction. Let us consider a cube at the position \f$k\f$ in the bitmap.
+ * Knowing the sizes of the bitmap, by a series of modulo operation, we can determine which elementary intervals are
+ * present in the product that gives the cube \f$C\f$. In a similar way, we can compute boundary and the coboundary of
+ * each cube. Further details can be found in the literature.
+ *
+ * \section inputformat Input Format.
+ *
+ * In the current implantation, filtration is given at the maximal cubes, and it is then extended by the lower star
+ * filtration to all cubes. There are a number of constructors that can be used to construct cubical complex by users
+ * who want to use the code directly. They can be found in the \a Bitmap_cubical_complex class.
+ * Currently one input from a text file is used. It uses a format used already in Perseus software
+ * (http://www.sas.upenn.edu/~vnanda/perseus/) by Vidit Nanda.
+ * Below we are providing a description of the format. The first line contains a number d begin the dimension of the
+ * bitmap (2 in the example below). Next d lines are the numbers of top dimensional cubes in each dimensions (3 and 3
+ * in the example below). Next, in lexicographical order, the filtration of top dimensional cubes is given (1 4 6 8
+ * 20 4 7 6 5 in the example below).
+ *
+ *
+ * \image html "exampleBitmap.png" "Example of a input data."
+ *
+ * The input file for the following complex is:
+ * \verbatim
+2
+3
+3
+1
+4
+6
+8
+20
+4
+7
+6
+5
+\endverbatim
+
+ * \section PeriodicBoundaryConditions Periodic boundary conditions
+ * Often one would like to impose periodic boundary conditions to the cubical complex. Let \f$ I_1\times ... \times
+ * I_n \f$ be a box that is decomposed with a cubical complex \f$ \mathcal{K} \f$. Imposing periodic boundary
+ * conditions in the direction i, means that the left and the right side of a complex \f$ \mathcal{K} \f$ are
+ * considered the same. In particular, if for a bitmap \f$ \mathcal{K} \f$ periodic boundary conditions are imposed
+ * in all directions, then complex \f$ \mathcal{K} \f$ became n-dimensional torus. One can use various constructors
+ * from the file Bitmap_cubical_complex_periodic_boundary_conditions_base.h to construct cubical complex with periodic
+ * boundary conditions. One can also use Perseus style input files. To indicate periodic boundary conditions in a
+ * given direction, then number of top dimensional cells in this direction have to be multiplied by -1. For instance:
+
+ *\verbatim
+2
+-3
+3
+1
+4
+6
+8
+20
+4
+7
+6
+5
+\endverbatim
+
+ * Indicate that we have imposed periodic boundary conditions in the direction x, but not in the direction y.
+
+ * \section BitmapExamples Examples
+ * End user programs are available in example/Bitmap_cubical_complex folder.
+ * 
+ * \copyright GNU General Public License v3.
+ */
+/** @} */  // end defgroup cubical_complex
+
+}  // namespace cubical_complex
+
+namespace Cubical_complex = cubical_complex;
+
+}  // namespace Gudhi
+
+#endif  // DOC_GUDHI_CUBICAL_COMPLEX_COMPLEX_H_
diff --git a/src/Bitmap_cubical_complex/doc/bitmapAllCubes.png b/src/Bitmap_cubical_complex/doc/bitmapAllCubes.png
new file mode 100644
index 00000000..77167b13
--- /dev/null
+++ b/src/Bitmap_cubical_complex/doc/bitmapAllCubes.png
diff --git a/src/Bitmap_cubical_complex/doc/exampleBitmap.png b/src/Bitmap_cubical_complex/doc/exampleBitmap.png
new file mode 100644
index 00000000..069c6eb2
--- /dev/null
+++ b/src/Bitmap_cubical_complex/doc/exampleBitmap.png
diff --git a/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex.cpp b/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex.cpp
new file mode 100644
index 00000000..e6bc6648
--- /dev/null
+++ b/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex.cpp
@@ -0,0 +1,72 @@
+/*    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):       Pawel Dlotko
+ *
+ *    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/>.
+ */
+
+
+#include <gudhi/reader_utils.h>
+#include <gudhi/Bitmap_cubical_complex.h>
+#include <gudhi/Persistent_cohomology.h>
+
+// standard stuff
+#include <iostream>
+#include <sstream>
+#include <vector>
+
+int main(int argc, char** argv) {
+  std::cout << "This program computes persistent homology, by using bitmap_cubical_complex class, of cubical " <<
+      "complexes provided in text files in Perseus style (the only numbered in the first line is a dimension D of a" <<
+      "bitmap. In the lines I between 2 and D+1 there are numbers of top dimensional cells in the direction I. Let " <<
+      "N denote product of the numbers in the lines between 2 and D. In the lines D+2 to D+2+N there are " <<
+      "filtrations of top dimensional cells. We assume that the cells are in the lexicographical order. See " <<
+      "CubicalOneSphere.txt or CubicalTwoSphere.txt for example.\n" << std::endl;
+
+  int p = 2;
+  double min_persistence = 0;
+
+  if (argc != 2) {
+    std::cerr << "Wrong number of parameters. Please provide the name of a file with a Perseus style bitmap at " <<
+        "the input. The program will now terminate.\n";
+    return 1;
+  }
+
+  typedef Gudhi::cubical_complex::Bitmap_cubical_complex_base<double> Bitmap_cubical_complex_base;
+  typedef Gudhi::cubical_complex::Bitmap_cubical_complex<Bitmap_cubical_complex_base> Bitmap_cubical_complex;
+  typedef Gudhi::persistent_cohomology::Field_Zp Field_Zp;
+  typedef Gudhi::persistent_cohomology::Persistent_cohomology<Bitmap_cubical_complex, Field_Zp> Persistent_cohomology;
+
+  Bitmap_cubical_complex b(argv[1]);
+
+  // Compute the persistence diagram of the complex
+  Persistent_cohomology pcoh(b);
+  pcoh.init_coefficients(p);  // initializes the coefficient field for homology
+  pcoh.compute_persistent_cohomology(min_persistence);
+
+  std::stringstream ss;
+  ss << argv[1] << "_persistence";
+  std::ofstream out(ss.str().c_str());
+  pcoh.output_diagram(out);
+  out.close();
+
+  std::cout << "Result in file: " << ss.str().c_str() << "\n";
+
+  return 0;
+}
+
diff --git a/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex_periodic_boundary_conditions.cpp b/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex_periodic_boundary_conditions.cpp
new file mode 100644
index 00000000..839a4c89
--- /dev/null
+++ b/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex_periodic_boundary_conditions.cpp
@@ -0,0 +1,74 @@
+/*    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):       Pawel Dlotko
+ *
+ *    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/>.
+ */
+
+
+#include <gudhi/reader_utils.h>
+#include <gudhi/Bitmap_cubical_complex.h>
+#include <gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h>
+#include <gudhi/Persistent_cohomology.h>
+
+// standard stuff
+#include <iostream>
+#include <sstream>
+#include <vector>
+
+int main(int argc, char** argv) {
+  std::cout << "This program computes persistent homology, by using " <<
+      "Bitmap_cubical_complex_periodic_boundary_conditions class, of cubical complexes provided in text files in " <<
+      "Perseus style (the only numbered in the first line is a dimension D of a bitmap. In the lines I between 2 " <<
+      "and D+1 there are numbers of top dimensional cells in the direction I. Let N denote product of the numbers " <<
+      "in the lines between 2 and D. In the lines D+2 to D+2+N there are filtrations of top dimensional cells. We " <<
+      "assume that the cells are in the lexicographical order. See CubicalOneSphere.txt or CubicalTwoSphere.txt for" <<
+      " example.\n" << std::endl;
+
+  int p = 2;
+  double min_persistence = 0;
+
+  if (argc != 2) {
+    std::cerr << "Wrong number of parameters. Please provide the name of a file with a Perseus style bitmap at " <<
+        "the input. The program will now terminate.\n";
+    return 1;
+  }
+
+  typedef Gudhi::cubical_complex::Bitmap_cubical_complex_periodic_boundary_conditions_base<double> Bitmap_base;
+  typedef Gudhi::cubical_complex::Bitmap_cubical_complex< Bitmap_base > Bitmap_cubical_complex;
+
+  Bitmap_cubical_complex b(argv[1]);
+
+  typedef Gudhi::persistent_cohomology::Field_Zp Field_Zp;
+  typedef Gudhi::persistent_cohomology::Persistent_cohomology<Bitmap_cubical_complex, Field_Zp> Persistent_cohomology;
+  // Compute the persistence diagram of the complex
+  Persistent_cohomology pcoh(b, true);
+  pcoh.init_coefficients(p);  // initializes the coefficient field for homology
+  pcoh.compute_persistent_cohomology(min_persistence);
+
+  std::stringstream ss;
+  ss << argv[1] << "_persistence";
+  std::ofstream out(ss.str().c_str());
+  pcoh.output_diagram(out);
+  out.close();
+
+  std::cout << "Result in file: " << ss.str().c_str() << "\n";
+
+  return 0;
+}
+
diff --git a/src/Bitmap_cubical_complex/example/CMakeLists.txt b/src/Bitmap_cubical_complex/example/CMakeLists.txt
new file mode 100644
index 00000000..2fddc514
--- /dev/null
+++ b/src/Bitmap_cubical_complex/example/CMakeLists.txt
@@ -0,0 +1,26 @@
+cmake_minimum_required(VERSION 2.6)
+project(Bitmap_cubical_complex_examples)
+
+add_executable ( Bitmap_cubical_complex Bitmap_cubical_complex.cpp )
+target_link_libraries(Bitmap_cubical_complex ${Boost_SYSTEM_LIBRARY})
+if (TBB_FOUND)
+  target_link_libraries(Bitmap_cubical_complex ${TBB_LIBRARIES})
+endif()
+add_test(Bitmap_cubical_complex_one_sphere ${CMAKE_CURRENT_BINARY_DIR}/Bitmap_cubical_complex ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalOneSphere.txt)
+add_test(Bitmap_cubical_complex_two_sphere ${CMAKE_CURRENT_BINARY_DIR}/Bitmap_cubical_complex ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt)
+
+add_executable ( Random_bitmap_cubical_complex Random_bitmap_cubical_complex.cpp )
+target_link_libraries(Random_bitmap_cubical_complex ${Boost_SYSTEM_LIBRARY})
+if (TBB_FOUND)
+  target_link_libraries(Random_bitmap_cubical_complex ${TBB_LIBRARIES})
+endif()
+add_test(Random_bitmap_cubical_complex ${CMAKE_CURRENT_BINARY_DIR}/Random_bitmap_cubical_complex 2 100 100)
+
+add_executable ( Bitmap_cubical_complex_periodic_boundary_conditions Bitmap_cubical_complex_periodic_boundary_conditions.cpp )
+target_link_libraries(Bitmap_cubical_complex_periodic_boundary_conditions ${Boost_SYSTEM_LIBRARY})
+if (TBB_FOUND)
+  target_link_libraries(Bitmap_cubical_complex_periodic_boundary_conditions ${TBB_LIBRARIES})
+endif()
+add_test(Bitmap_cubical_complex_periodic_2d_torus ${CMAKE_CURRENT_BINARY_DIR}/Bitmap_cubical_complex_periodic_boundary_conditions ${CMAKE_SOURCE_DIR}/data/bitmap/2d_torus.txt)
+add_test(Bitmap_cubical_complex_periodic_3d_torus ${CMAKE_CURRENT_BINARY_DIR}/Bitmap_cubical_complex_periodic_boundary_conditions ${CMAKE_SOURCE_DIR}/data/bitmap/3d_torus.txt)
+
diff --git a/src/Bitmap_cubical_complex/example/Random_bitmap_cubical_complex.cpp b/src/Bitmap_cubical_complex/example/Random_bitmap_cubical_complex.cpp
new file mode 100644
index 00000000..16ad65a0
--- /dev/null
+++ b/src/Bitmap_cubical_complex/example/Random_bitmap_cubical_complex.cpp
@@ -0,0 +1,83 @@
+/*    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):       Pawel Dlotko
+ *
+ *    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/>.
+ */
+
+
+// for persistence algorithm
+#include <gudhi/reader_utils.h>
+#include <gudhi/Bitmap_cubical_complex.h>
+#include <gudhi/Persistent_cohomology.h>
+
+// standard stuff
+#include <iostream>
+#include <sstream>
+#include <vector>
+
+int main(int argc, char** argv) {
+  srand(time(0));
+
+  std::cout << "This program computes persistent homology, by using bitmap_cubical_complex class, of cubical " <<
+      "complexes. The first parameter of the program is the dimension D of the bitmap. The next D parameters are " <<
+      "number of top dimensional cubes in each dimension of the bitmap. The program will create random cubical " <<
+      "complex of that sizes and compute persistent homology of it." << std::endl;
+
+  int p = 2;
+  double min_persistence = 0;
+
+  if (argc < 3) {
+    std::cerr << "Wrong number of parameters, the program will now terminate\n";
+    return 1;
+  }
+
+  size_t dimensionOfBitmap = (size_t) atoi(argv[1]);
+  std::vector< unsigned > sizes;
+  size_t multipliers = 1;
+  for (size_t dim = 0; dim != dimensionOfBitmap; ++dim) {
+    unsigned sizeInThisDimension = (unsigned) atoi(argv[2 + dim]);
+    sizes.push_back(sizeInThisDimension);
+    multipliers *= sizeInThisDimension;
+  }
+
+  std::vector< double > data;
+  for (size_t i = 0; i != multipliers; ++i) {
+    data.push_back(rand() / static_cast<double>(RAND_MAX));
+  }
+
+  typedef Gudhi::cubical_complex::Bitmap_cubical_complex_base<double> Bitmap_cubical_complex_base;
+  typedef Gudhi::cubical_complex::Bitmap_cubical_complex<Bitmap_cubical_complex_base> Bitmap_cubical_complex;
+  Bitmap_cubical_complex b(sizes, data);
+
+  // Compute the persistence diagram of the complex
+  typedef Gudhi::persistent_cohomology::Field_Zp Field_Zp;
+  typedef Gudhi::persistent_cohomology::Persistent_cohomology<Bitmap_cubical_complex, Field_Zp> Persistent_cohomology;
+  Persistent_cohomology pcoh(b);
+  pcoh.init_coefficients(p);  // initializes the coefficient field for homology
+  pcoh.compute_persistent_cohomology(min_persistence);
+
+  std::stringstream ss;
+  ss << "randomComplex_persistence";
+  std::ofstream out(ss.str().c_str());
+  pcoh.output_diagram(out);
+  out.close();
+
+  return 0;
+}
+
diff --git a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h
new file mode 100644
index 00000000..5a87b9b8
--- /dev/null
+++ b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h
@@ -0,0 +1,595 @@
+/*    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):       Pawel Dlotko
+ *
+ *    Copyright (C) 2015  INRIA Sophia-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 BITMAP_CUBICAL_COMPLEX_H_
+#define BITMAP_CUBICAL_COMPLEX_H_
+
+#include <gudhi/Bitmap_cubical_complex_base.h>
+#include <gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h>
+
+#ifdef GUDHI_USE_TBB
+#include <tbb/parallel_sort.h>
+#endif
+
+#include <limits>
+#include <utility>  // for pair<>
+#include <algorithm>  // for sort
+#include <vector>
+#include <numeric>  // for iota
+
+namespace Gudhi {
+
+namespace cubical_complex {
+
+// global variable, was used just for debugging.
+const bool globalDbg = false;
+
+template <typename T> class is_before_in_filtration;
+
+/**
+ * @brief Cubical complex represented as a bitmap.
+ * @ingroup cubical_complex
+ * @details This is a Bitmap_cubical_complex class. It joints a functionalities of Bitmap_cubical_complex_base and
+ * Bitmap_cubical_complex_periodic_boundary_conditions_base classes into
+ * Gudhi persistent homology engine. It is a template class that inherit from its template parameter. The template
+ * parameter is supposed to be either Bitmap_cubical_complex_base or
+ * Bitmap_cubical_complex_periodic_boundary_conditions_base class.
+ **/
+template <typename T>
+class Bitmap_cubical_complex : public T {
+ public:
+  //*********************************************//
+  // Typedefs and typenames
+  //*********************************************//
+  typedef size_t Simplex_key;
+  typedef typename T::filtration_type Filtration_value;
+  typedef Simplex_key Simplex_handle;
+
+
+  //*********************************************//
+  // Constructors
+  //*********************************************//
+  // Over here we need to define various input types. I am proposing the following ones:
+  // Perseus style
+  // TODO(PD) H5 files?
+  // TODO(PD) binary files with little endiangs / big endians ?
+  // TODO(PD) constructor from a vector of elements of a type T. ?
+
+  /**
+   * Constructor form a Perseus-style file.
+   **/
+  Bitmap_cubical_complex(const char* perseus_style_file) :
+      T(perseus_style_file), key_associated_to_simplex(this->total_number_of_cells + 1) {
+    if (globalDbg) {
+      std::cerr << "Bitmap_cubical_complex( const char* perseus_style_file )\n";
+    }
+    for (size_t i = 0; i != this->total_number_of_cells; ++i) {
+      this->key_associated_to_simplex[i] = i;
+    }
+    // we initialize this only once, in each constructor, when the bitmap is constructed.
+    // If the user decide to change some elements of the bitmap, then this procedure need
+    // to be called again.
+    this->initialize_simplex_associated_to_key();
+  }
+
+  /**
+   * Constructor that requires vector of elements of type unsigned, which gives number of top dimensional cells
+   * in the following directions and vector of element of a type T
+   * with filtration on top dimensional cells.
+   **/
+  Bitmap_cubical_complex(const std::vector<unsigned>& dimensions,
+                         const std::vector<typename T::filtration_type>& top_dimensional_cells) :
+      T(dimensions, top_dimensional_cells),
+      key_associated_to_simplex(this->total_number_of_cells + 1) {
+    for (size_t i = 0; i != this->total_number_of_cells; ++i) {
+      this->key_associated_to_simplex[i] = i;
+    }
+    // we initialize this only once, in each constructor, when the bitmap is constructed.
+    // If the user decide to change some elements of the bitmap, then this procedure need
+    // to be called again.
+    this->initialize_simplex_associated_to_key();
+  }
+
+  /**
+   * Constructor that requires vector of elements of type unsigned, which gives number of top dimensional cells
+   * in the following directions and vector of element of a type T::filtration_type
+   * with filtration on top dimensional cells. The last parameter of the constructor is a vector of boolean of a length
+   * equal to the dimension of cubical complex.
+   * If the position i on this vector is true, then we impose periodic boundary conditions in this direction.
+   **/
+  Bitmap_cubical_complex(const std::vector<unsigned>& dimensions,
+                         const std::vector<typename T::filtration_type>& top_dimensional_cells,
+                         std::vector< bool > directions_in_which_periodic_b_cond_are_to_be_imposed) :
+      T(dimensions, top_dimensional_cells, directions_in_which_periodic_b_cond_are_to_be_imposed),
+      key_associated_to_simplex(this->total_number_of_cells + 1) {
+    for (size_t i = 0; i != this->total_number_of_cells; ++i) {
+      this->key_associated_to_simplex[i] = i;
+    }
+    // we initialize this only once, in each constructor, when the bitmap is constructed.
+    // If the user decide to change some elements of the bitmap, then this procedure need
+    // to be called again.
+    this->initialize_simplex_associated_to_key();
+  }
+
+  /**
+   * Destructor of the Bitmap_cubical_complex class.
+   **/
+  virtual ~Bitmap_cubical_complex() {}
+
+  //*********************************************//
+  // Other 'easy' functions
+  //*********************************************//
+
+  /**
+   * Returns number of all cubes in the complex.
+   **/
+  size_t num_simplices()const {
+    return this->total_number_of_cells;
+  }
+
+  /**
+   * Returns a Simplex_handle to a cube that do not exist in this complex.
+   **/
+  static Simplex_handle null_simplex() {
+    if (globalDbg) {
+      std::cerr << "Simplex_handle null_simplex()\n";
+    }
+    return std::numeric_limits<Simplex_handle>::max();
+  }
+
+  /**
+   * Returns dimension of the complex.
+   **/
+  inline size_t dimension()const {
+    return this->sizes.size();
+  }
+
+  /**
+   * Return dimension of a cell pointed by the Simplex_handle.
+   **/
+  inline unsigned dimension(Simplex_handle sh)const {
+    if (globalDbg) {
+      std::cerr << "unsigned dimension(const Simplex_handle& sh)\n";
+    }
+    if (sh != std::numeric_limits<Simplex_handle>::max()) return this->get_dimension_of_a_cell(sh);
+    return -1;
+  }
+
+  /**
+   * Return the filtration of a cell pointed by the Simplex_handle.
+   **/
+  typename T::filtration_type filtration(Simplex_handle sh) {
+    if (globalDbg) {
+      std::cerr << "T::filtration_type filtration(const Simplex_handle& sh)\n";
+    }
+    // Returns the filtration value of a simplex.
+    if (sh != std::numeric_limits<Simplex_handle>::max()) return this->data[sh];
+    return std::numeric_limits<Simplex_handle>::max();
+  }
+
+  /**
+   * Return a key which is not a key of any cube in the considered data structure.
+   **/
+  static Simplex_key null_key() {
+    if (globalDbg) {
+      std::cerr << "Simplex_key null_key()\n";
+    }
+    return std::numeric_limits<Simplex_handle>::max();
+  }
+
+  /**
+   * Return the key of a cube pointed by the Simplex_handle.
+   **/
+  Simplex_key key(Simplex_handle sh)const {
+    if (globalDbg) {
+      std::cerr << "Simplex_key key(const Simplex_handle& sh)\n";
+    }
+    if (sh != std::numeric_limits<Simplex_handle>::max()) {
+      return this->key_associated_to_simplex[sh];
+    }
+    return this->null_key();
+  }
+
+  /**
+   * Return the Simplex_handle given the key of the cube.
+   **/
+  Simplex_handle simplex(Simplex_key key) {
+    if (globalDbg) {
+      std::cerr << "Simplex_handle simplex(Simplex_key key)\n";
+    }
+    if (key != std::numeric_limits<Simplex_handle>::max()) {
+      return this->simplex_associated_to_key[ key ];
+    }
+    return null_simplex();
+  }
+
+  /**
+   * Assign key to a cube pointed by the Simplex_handle
+   **/
+  void assign_key(Simplex_handle sh, Simplex_key key) {
+    if (globalDbg) {
+      std::cerr << "void assign_key(Simplex_handle& sh, Simplex_key key)\n";
+    }
+    if (key == std::numeric_limits<Simplex_handle>::max()) return;
+    this->key_associated_to_simplex[sh] = key;
+    this->simplex_associated_to_key[key] = sh;
+  }
+
+  /**
+   * Function called from a constructor. It is needed for Filtration_simplex_iterator to work.
+   **/
+  void initialize_simplex_associated_to_key();
+
+  //*********************************************//
+  // Iterators
+  //*********************************************//
+
+  /**
+   * Boundary_simplex_range class provides ranges for boundary iterators.
+   **/
+  typedef typename std::vector< Simplex_handle >::iterator Boundary_simplex_iterator;
+  typedef typename std::vector< Simplex_handle > Boundary_simplex_range;
+
+  /**
+   * Filtration_simplex_iterator class provides an iterator though the whole structure in the order of filtration.
+   * Secondary criteria for filtration are:
+   * (1) Dimension of a cube (lower dimensional comes first).
+   * (2) Position in the data structure (the ones that are earlies in the data structure comes first).
+   **/
+  class Filtration_simplex_range;
+
+  class Filtration_simplex_iterator : std::iterator< std::input_iterator_tag, Simplex_handle > {
+    // Iterator over all simplices of the complex in the order of the indexing scheme.
+    // 'value_type' must be 'Simplex_handle'.
+   public:
+    Filtration_simplex_iterator(Bitmap_cubical_complex* b) : b(b), position(0) { }
+
+    Filtration_simplex_iterator() : b(NULL), position(0) { }
+
+    Filtration_simplex_iterator operator++() {
+      if (globalDbg) {
+        std::cerr << "Filtration_simplex_iterator operator++\n";
+      }
+      ++this->position;
+      return (*this);
+    }
+
+    Filtration_simplex_iterator operator++(int) {
+      Filtration_simplex_iterator result = *this;
+      ++(*this);
+      return result;
+    }
+
+    Filtration_simplex_iterator& operator=(const Filtration_simplex_iterator& rhs) {
+      if (globalDbg) {
+        std::cerr << "Filtration_simplex_iterator operator =\n";
+      }
+      this->b = rhs.b;
+      this->position = rhs.position;
+      return (*this);
+    }
+
+    bool operator==(const Filtration_simplex_iterator& rhs)const {
+      if (globalDbg) {
+        std::cerr << "bool operator == ( const Filtration_simplex_iterator& rhs )\n";
+      }
+      return ( this->position == rhs.position);
+    }
+
+    bool operator!=(const Filtration_simplex_iterator& rhs)const {
+      if (globalDbg) {
+        std::cerr << "bool operator != ( const Filtration_simplex_iterator& rhs )\n";
+      }
+      return !(*this == rhs);
+    }
+
+    Simplex_handle operator*() {
+      if (globalDbg) {
+        std::cerr << "Simplex_handle operator*()\n";
+      }
+      return this->b->simplex_associated_to_key[ this->position ];
+    }
+
+    friend class Filtration_simplex_range;
+
+   private:
+    Bitmap_cubical_complex<T>* b;
+    size_t position;
+  };
+
+  /**
+   * @brief Filtration_simplex_range provides the ranges for Filtration_simplex_iterator.
+   **/
+  class Filtration_simplex_range {
+    // Range over the simplices of the complex in the order of the filtration.
+    // .begin() and .end() return type Filtration_simplex_iterator.
+   public:
+    typedef Filtration_simplex_iterator const_iterator;
+    typedef Filtration_simplex_iterator iterator;
+
+    Filtration_simplex_range(Bitmap_cubical_complex<T>* b) : b(b) { }
+
+    Filtration_simplex_iterator begin() {
+      if (globalDbg) {
+        std::cerr << "Filtration_simplex_iterator begin() \n";
+      }
+      return Filtration_simplex_iterator(this->b);
+    }
+
+    Filtration_simplex_iterator end() {
+      if (globalDbg) {
+        std::cerr << "Filtration_simplex_iterator end()\n";
+      }
+      Filtration_simplex_iterator it(this->b);
+      it.position = this->b->simplex_associated_to_key.size();
+      return it;
+    }
+
+   private:
+    Bitmap_cubical_complex<T>* b;
+  };
+
+
+
+  //*********************************************//
+  // Methods to access iterators from the container:
+
+  /**
+   * boundary_simplex_range creates an object of a Boundary_simplex_range class
+   * that provides ranges for the Boundary_simplex_iterator.
+   **/
+  Boundary_simplex_range boundary_simplex_range(Simplex_handle sh) {
+    return this->get_boundary_of_a_cell(sh);
+  }
+
+  /**
+   * filtration_simplex_range creates an object of a Filtration_simplex_range class
+   * that provides ranges for the Filtration_simplex_iterator.
+   **/
+  Filtration_simplex_range filtration_simplex_range() {
+    if (globalDbg) {
+      std::cerr << "Filtration_simplex_range filtration_simplex_range()\n";
+    }
+    // Returns a range over the simplices of the complex in the order of the filtration
+    return Filtration_simplex_range(this);
+  }
+  //*********************************************//
+
+
+
+  //*********************************************//
+  // Elements which are in Gudhi now, but I (and in all the cases I asked also Marc) do not understand why they are
+  // there.
+  // TODO(PD) the file IndexingTag.h in the Gudhi library contains an empty structure, so
+  // I understand that this is something that was planned (for simplicial maps?)
+  // but was never finished. The only idea I have here is to use the same empty structure from
+  // IndexingTag.h file, but only if the compiler needs it. If the compiler
+  // do not need it, then I would rather not add here elements which I do not understand.
+  // typedef Indexing_tag
+
+  /**
+   * Function needed for compatibility with Gudhi. Not useful for other purposes.
+   **/
+  std::pair<Simplex_handle, Simplex_handle> endpoints(Simplex_handle sh) {
+    std::vector< size_t > bdry = this->get_boundary_of_a_cell(sh);
+    if (globalDbg) {
+      std::cerr << "std::pair<Simplex_handle, Simplex_handle> endpoints( Simplex_handle sh )\n";
+      std::cerr << "bdry.size() : " << bdry.size() << std::endl;
+    }
+    // this method returns two first elements from the boundary of sh.
+    if (bdry.size() < 2)
+      throw("Error in endpoints in Bitmap_cubical_complex class. The cell have less than two elements in the "
+            "boundary.");
+    return std::make_pair(bdry[0], bdry[1]);
+  }
+
+
+  /**
+   * Class needed for compatibility with Gudhi. Not useful for other purposes.
+   **/
+  class Skeleton_simplex_range;
+
+  class Skeleton_simplex_iterator : std::iterator< std::input_iterator_tag, Simplex_handle > {
+    // Iterator over all simplices of the complex in the order of the indexing scheme.
+    // 'value_type' must be 'Simplex_handle'.
+   public:
+    Skeleton_simplex_iterator(Bitmap_cubical_complex* b, size_t d) : b(b), dimension(d) {
+      if (globalDbg) {
+        std::cerr << "Skeleton_simplex_iterator ( Bitmap_cubical_complex* b , size_t d )\n";
+      }
+      // find the position of the first simplex of a dimension d
+      this->position = 0;
+      while (
+             (this->position != b->data.size()) &&
+             (this->b->get_dimension_of_a_cell(this->position) != this->dimension)
+             ) {
+        ++this->position;
+      }
+    }
+
+    Skeleton_simplex_iterator() : b(NULL), position(0), dimension(0) { }
+
+    Skeleton_simplex_iterator operator++() {
+      if (globalDbg) {
+        std::cerr << "Skeleton_simplex_iterator operator++()\n";
+      }
+      // increment the position as long as you did not get to the next element of the dimension dimension.
+      ++this->position;
+      while (
+             (this->position != this->b->data.size()) &&
+             (this->b->get_dimension_of_a_cell(this->position) != this->dimension)
+             ) {
+        ++this->position;
+      }
+      return (*this);
+    }
+
+    Skeleton_simplex_iterator operator++(int) {
+      Skeleton_simplex_iterator result = *this;
+      ++(*this);
+      return result;
+    }
+
+    Skeleton_simplex_iterator& operator=(const Skeleton_simplex_iterator& rhs) {
+      if (globalDbg) {
+        std::cerr << "Skeleton_simplex_iterator operator =\n";
+      }
+      this->b = rhs.b;
+      this->position = rhs.position;
+      this->dimension = rhs.dimension;
+      return (*this);
+    }
+
+    bool operator==(const Skeleton_simplex_iterator& rhs)const {
+      if (globalDbg) {
+        std::cerr << "bool operator ==\n";
+      }
+      return ( this->position == rhs.position);
+    }
+
+    bool operator!=(const Skeleton_simplex_iterator& rhs)const {
+      if (globalDbg) {
+        std::cerr << "bool operator != ( const Skeleton_simplex_iterator& rhs )\n";
+      }
+      return !(*this == rhs);
+    }
+
+    Simplex_handle operator*() {
+      if (globalDbg) {
+        std::cerr << "Simplex_handle operator*() \n";
+      }
+      return this->position;
+    }
+
+    friend class Skeleton_simplex_range;
+   private:
+    Bitmap_cubical_complex<T>* b;
+    size_t position;
+    unsigned dimension;
+  };
+
+  /**
+   * @brief Class needed for compatibility with Gudhi. Not useful for other purposes.
+   **/
+  class Skeleton_simplex_range {
+    // Range over the simplices of the complex in the order of the filtration.
+    // .begin() and .end() return type Filtration_simplex_iterator.
+   public:
+    typedef Skeleton_simplex_iterator const_iterator;
+    typedef Skeleton_simplex_iterator iterator;
+
+    Skeleton_simplex_range(Bitmap_cubical_complex<T>* b, unsigned dimension) : b(b), dimension(dimension) { }
+
+    Skeleton_simplex_iterator begin() {
+      if (globalDbg) {
+        std::cerr << "Skeleton_simplex_iterator begin()\n";
+      }
+      return Skeleton_simplex_iterator(this->b, this->dimension);
+    }
+
+    Skeleton_simplex_iterator end() {
+      if (globalDbg) {
+        std::cerr << "Skeleton_simplex_iterator end()\n";
+      }
+      Skeleton_simplex_iterator it(this->b, this->dimension);
+      it.position = this->b->data.size();
+      return it;
+    }
+
+   private:
+    Bitmap_cubical_complex<T>* b;
+    unsigned dimension;
+  };
+
+  /**
+   * Function needed for compatibility with Gudhi. Not useful for other purposes.
+   **/
+  Skeleton_simplex_range skeleton_simplex_range(unsigned dimension) {
+    if (globalDbg) {
+      std::cerr << "Skeleton_simplex_range skeleton_simplex_range( unsigned dimension )\n";
+    }
+    return Skeleton_simplex_range(this, dimension);
+  }
+
+  friend class is_before_in_filtration<T>;
+
+ protected:
+  std::vector< size_t > key_associated_to_simplex;
+  std::vector< size_t > simplex_associated_to_key;
+};  // Bitmap_cubical_complex
+
+template <typename T>
+void Bitmap_cubical_complex<T>::initialize_simplex_associated_to_key() {
+  if (globalDbg) {
+    std::cerr << "void Bitmap_cubical_complex<T>::initialize_elements_ordered_according_to_filtration() \n";
+  }
+  this->simplex_associated_to_key = std::vector<size_t>(this->data.size());
+  std::iota(std::begin(simplex_associated_to_key), std::end(simplex_associated_to_key), 0);
+#ifdef GUDHI_USE_TBB
+  tbb::parallel_sort(simplex_associated_to_key.begin(), simplex_associated_to_key.end(),
+                     is_before_in_filtration<T>(this));
+#else
+  std::sort(simplex_associated_to_key.begin(), simplex_associated_to_key.end(), is_before_in_filtration<T>(this));
+#endif
+
+  // we still need to deal here with a key_associated_to_simplex:
+  for ( size_t i = 0  ; i != simplex_associated_to_key.size() ; ++i ) {
+    this->key_associated_to_simplex[ simplex_associated_to_key[i] ] = i;
+  }
+}
+
+template <typename T>
+class is_before_in_filtration {
+ public:
+  explicit is_before_in_filtration(Bitmap_cubical_complex<T> * CC)
+      : CC_(CC) { }
+
+  bool operator()(const typename Bitmap_cubical_complex<T>::Simplex_handle& sh1,
+                  const typename Bitmap_cubical_complex<T>::Simplex_handle& sh2) const {
+    // Not using st_->filtration(sh1) because it uselessly tests for null_simplex.
+    typename T::filtration_type fil1 = CC_->data[sh1];
+    typename T::filtration_type fil2 = CC_->data[sh2];
+    if (fil1 != fil2) {
+      return fil1 < fil2;
+    }
+    // in this case they are on the same filtration level, so the dimension decide.
+    size_t dim1 = CC_->get_dimension_of_a_cell(sh1);
+    size_t dim2 = CC_->get_dimension_of_a_cell(sh2);
+    if (dim1 != dim2) {
+      return dim1 < dim2;
+    }
+    // in this case both filtration and dimensions of the considered cubes are the same. To have stable sort, we simply
+    // compare their positions in the bitmap:
+    return sh1 < sh2;
+  }
+
+ protected:
+  Bitmap_cubical_complex<T>* CC_;
+};
+
+}  // namespace cubical_complex
+
+namespace Cubical_complex = cubical_complex;
+
+}  // namespace Gudhi
+
+#endif  // BITMAP_CUBICAL_COMPLEX_H_
diff --git a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex/counter.h b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex/counter.h
new file mode 100644
index 00000000..4b072f10
--- /dev/null
+++ b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex/counter.h
@@ -0,0 +1,144 @@
+/*    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):       Pawel Dlotko
+ *
+ *    Copyright (C) 2015  INRIA Sophia-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 BITMAP_CUBICAL_COMPLEX_COUNTER_H_
+#define BITMAP_CUBICAL_COMPLEX_COUNTER_H_
+
+#include <iostream>
+#include <vector>
+
+namespace Gudhi {
+
+namespace cubical_complex {
+
+/**
+ * @brief This is an implementation of a counter being a vector of integers. 
+ * @details The constructor of the class takes as an input two vectors W and V. 
+ * It assumes that W < V coordinatewise.
+ * If the initial counter W is not specified, it is assumed to be vector of zeros. 
+ * The class allows to iterate between W and V by using increment() function.
+ * The increment() function returns a bool value. 
+ * The current counter reach the end counter V if the value returned by the increment function is FALSE.
+ * This class is needed for the implementation of a bitmapCubicalComplex.
+ **/
+class counter {
+ public:
+  /**
+   * Constructor of a counter class. It takes only the parameter which is the end value of the counter. 
+   * The default beginning value is a vector of the same length as the endd, filled-in with zeros.
+   **/
+  counter(const std::vector<unsigned>& endd) : begin(endd.size(), 0), end(endd), current(endd.size(), 0) { }
+
+  /**
+   * Constructor of a counter class. It takes as the input beginn and end vector. 
+   * It assumes that begin vector is lexicographically below the end vector.
+   **/
+  counter(const std::vector< unsigned >& beginn, const std::vector< unsigned >& endd) : begin(beginn), end(endd), current(endd.size(), 0) {
+    if (beginn.size() != endd.size())
+      throw "In constructor of a counter, begin and end vectors do not have the same size. Program terminate";
+  }
+
+  /**
+   * Function to increment the counter. If the value returned by the function is true, 
+   * then the incrementation process was successful.
+   * If the value of the function is false, that means, that the counter have reached its end-value.
+   **/
+  bool increment() {
+    size_t i = 0;
+    while ((i != this->end.size()) && (this->current[i] == this->end[i])) {
+      ++i;
+    }
+
+    if (i == this->end.size())return false;
+    ++this->current[i];
+    for (size_t j = 0; j != i; ++j) {
+      this->current[j] = this->begin[j];
+    }
+    return true;
+  }
+
+  /**
+   * Function to check if we are at the end of counter.
+   **/
+  bool isFinal() {
+    for (size_t i = 0; i != this->current.size(); ++i) {
+      if (this->current[i] == this->end[i])return true;
+    }
+    return false;
+  }
+
+  /**
+   * Function required in the implementation of bitmapCubicalComplexWPeriodicBoundaryCondition. 
+   * Its aim is to find an counter corresponding to the element the following
+   * boundary element is identified with when periodic boundary conditions are imposed.
+   **/
+  std::vector< unsigned > find_opposite(const std::vector< bool >& directionsForPeriodicBCond) {
+    std::vector< unsigned > result;
+    for (size_t i = 0; i != this->current.size(); ++i) {
+      if ((this->current[i] == this->end[i]) && (directionsForPeriodicBCond[i] == true)) {
+        result.push_back(this->begin[i]);
+      } else {
+        result.push_back(this->current[i]);
+      }
+    }
+    return result;
+  }
+
+  /**
+   * Function checking at which positions the current value of a counter is the final value of the counter.
+   **/
+  std::vector< bool > directions_of_finals() {
+    std::vector< bool > result;
+    for (size_t i = 0; i != this->current.size(); ++i) {
+      if (this->current[i] == this->end[i]) {
+        result.push_back(true);
+      } else {
+        result.push_back(false);
+      }
+    }
+    return result;
+  }
+
+  /**
+   * Function to write counter to the stream.
+   **/
+  friend std::ostream& operator<<(std::ostream& out, const counter& c) {
+    // std::cerr << "c.current.size() : " << c.current.size() << endl;
+    for (size_t i = 0; i != c.current.size(); ++i) {
+      out << c.current[i] << " ";
+    }
+    return out;
+  }
+
+ private:
+  std::vector< unsigned > begin;
+  std::vector< unsigned > end;
+  std::vector< unsigned > current;
+};
+
+}  // namespace cubical_complex
+
+namespace Cubical_complex = cubical_complex;
+
+}  // namespace Gudhi
+
+#endif  // BITMAP_CUBICAL_COMPLEX_COUNTER_H_
diff --git a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h
new file mode 100644
index 00000000..0442ac34
--- /dev/null
+++ b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h
@@ -0,0 +1,817 @@
+/*    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):       Pawel Dlotko
+ *
+ *    Copyright (C) 2015  INRIA Sophia-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 BITMAP_CUBICAL_COMPLEX_BASE_H_
+#define BITMAP_CUBICAL_COMPLEX_BASE_H_
+
+#include <gudhi/Bitmap_cubical_complex/counter.h>
+
+#include <iostream>
+#include <vector>
+#include <string>
+#include <fstream>
+#include <algorithm>
+#include <iterator>
+#include <limits>
+#include <utility>  // for pair<>
+
+namespace Gudhi {
+
+namespace cubical_complex {
+
+/**
+ * @brief Cubical complex represented as a bitmap, class with basic implementation.
+ * @ingroup cubical_complex
+ * @details This is a class implementing a basic bitmap data structure to store cubical complexes.
+ * It implements only the most basic subroutines.
+ * The idea of the bitmap is the following. Our aim is to have a memory efficient
+ * data structure to store d-dimensional cubical complex
+ * C being a cubical decomposition
+ * of a rectangular region of a space. This is achieved by storing C as a
+ * vector of bits (this is where the name 'bitmap' came from).
+ * Each cell is represented by a single
+ * bit (in case of black and white bitmaps, or by a single element of a type T
+ * (here T is a filtration type of a bitmap, typically a double).
+ * All the informations needed for homology and
+ * persistent homology computations (like dimension of a cell, boundary and
+ * coboundary elements of a cell, are then obtained from the
+ * position of the element in C.
+ * The default filtration used in this implementation is the lower star filtration.
+ */
+template <typename T>
+class Bitmap_cubical_complex_base {
+ public:
+  typedef T filtration_type;
+
+  /**
+   *Default constructor
+   **/
+  Bitmap_cubical_complex_base() :
+      total_number_of_cells(0) { }
+  /**
+   * There are a few constructors of a Bitmap_cubical_complex_base class.
+   * First one, that takes vector<unsigned>, creates an empty bitmap of a dimension equal
+   * the number of elements in the
+   * input vector and size in the i-th dimension equal the number in the position i-of the input vector.
+   */
+  Bitmap_cubical_complex_base(const std::vector<unsigned>& sizes);
+  /**
+   * The second constructor takes as a input a Perseus style file. For more details,
+   * please consult the documentations of
+   * Perseus software as well as examples attached to this
+   * implementation.
+   **/
+  Bitmap_cubical_complex_base(const char* perseus_style_file);
+  /**
+   * The last constructor of a Bitmap_cubical_complex_base class accepts vector of dimensions (as the first one)
+   * together with vector of filtration values of top dimensional cells.
+   **/
+  Bitmap_cubical_complex_base(const std::vector<unsigned>& dimensions, const std::vector<T>& top_dimensional_cells);
+
+  /**
+   * Destructor of the Bitmap_cubical_complex_base class.
+   **/
+  virtual ~Bitmap_cubical_complex_base() { }
+
+  /**
+   * The functions get_boundary_of_a_cell, get_coboundary_of_a_cell, get_dimension_of_a_cell
+   * and get_cell_data are the basic
+   * functions that compute boundary / coboundary / dimension and the filtration
+   * value form a position of a cell in the structure of a bitmap. The input parameter of all of those function is a
+   * non-negative integer, indicating a position of a cube in the data structure.
+   * In the case of functions that compute (co)boundary, the output is a vector if non-negative integers pointing to
+   * the positions of (co)boundary element of the input cell.
+   */
+  virtual inline std::vector< size_t > get_boundary_of_a_cell(size_t cell)const;
+  /**
+   * The functions get_coboundary_of_a_cell, get_coboundary_of_a_cell,
+   * get_dimension_of_a_cell and get_cell_data are the basic
+   * functions that compute boundary / coboundary / dimension and the filtration
+   * value form a position of a cell in the structure of a bitmap.
+   * The input parameter of all of those function is a non-negative integer,
+   * indicating a position of a cube in the data structure.
+   * In the case of functions that compute (co)boundary, the output is a vector if
+   * non-negative integers pointing to the
+   * positions of (co)boundary element of the input cell.
+   **/
+  virtual inline std::vector< size_t > get_coboundary_of_a_cell(size_t cell)const;
+  /**
+   * In the case of get_dimension_of_a_cell function, the output is a non-negative integer
+   * indicating the dimension of a cell.
+   **/
+  inline unsigned get_dimension_of_a_cell(size_t cell)const;
+  /**
+   * In the case of get_cell_data, the output parameter is a reference to the value of a cube in a given position.
+   * This allows reading and changing the value of filtration. Note that if the value of a filtration is changed, the
+   * code do not check if we have a filtration or not. i.e. it do not check if the value of a filtration of a cell is
+   * not smaller than the value of a filtration of its boundary and not greater than the value of its coboundary.
+   **/
+  inline T& get_cell_data(size_t cell);
+
+
+  /**
+   * Typical input used to construct a baseBitmap class is a filtration given at the top dimensional cells.
+   * Then, there are a few ways one can pick the filtration of lower dimensional
+   * cells. The most typical one is by so called lower star filtration. This function is always called by any
+   * constructor which takes the top dimensional cells. If you use such a constructor,
+   * then there is no need to call this function. Call it only if you are putting the filtration
+   * of the cells by your own (for instance by using Top_dimensional_cells_iterator).
+   **/
+  void impose_lower_star_filtration();  // assume that top dimensional cells are already set.
+
+  /**
+   * Returns dimension of a complex.
+   **/
+  inline unsigned dimension()const {
+    return sizes.size();
+  }
+
+  /**
+   * Returns number of all cubes in the data structure.
+   **/
+  inline unsigned size()const {
+    return this->data.size();
+  }
+
+  /**
+   * Writing to stream operator. By using it we get the values T of cells in order in which they are stored in the
+   * structure. This procedure is used for debugging purposes.
+   **/
+  template <typename K>
+  friend std::ostream& operator<<(std::ostream & os, const Bitmap_cubical_complex_base<K>& b);
+
+  /**
+   * Function that put the input data to bins. By putting data to bins we mean rounding them to a sequence of values
+   * equally distributed in the range of data.
+   * Sometimes if most of the cells have different birth-death times, the performance of the algorithms to compute
+   * persistence gets worst. When dealing with this type of data, one may want to put different values on cells to
+   * some number of bins. The function put_data_to_bins( size_t number_of_bins ) is designed for that purpose.
+   * The parameter of the function is the number of bins (distinct values) we want to have in the cubical complex.
+   **/
+  void put_data_to_bins(size_t number_of_bins);
+
+  /**
+   * Function that put the input data to bins. By putting data to bins we mean rounding them to a sequence of values
+   * equally distributed in the range of data.
+   * Sometimes if most of the cells have different birth-death times, the performance of the algorithms to compute
+   * persistence gets worst. When dealing with this type of data, one may want to put different values on cells to
+   * some number of bins. The function put_data_to_bins( T diameter_of_bin ) is designed for that purpose.
+   * The parameter of it is the diameter of each bin. Note that the bottleneck distance between the persistence
+   * diagram of the cubical complex before and after using such a function will be bounded by the parameter
+   * diameter_of_bin.
+   **/
+  void put_data_to_bins(T diameter_of_bin);
+
+  /**
+   * Functions to find min and max values of filtration.
+   **/
+  std::pair< T, T > min_max_filtration();
+
+  // ITERATORS
+
+  /**
+   * @brief Iterator through all cells in the complex (in order they appear in the structure -- i.e.
+   * in lexicographical order).
+   **/
+  class All_cells_iterator : std::iterator< std::input_iterator_tag, T > {
+   public:
+    All_cells_iterator() {
+      this->counter = 0;
+    }
+
+    All_cells_iterator operator++() {
+      // first find first element of the counter that can be increased:
+      ++this->counter;
+      return *this;
+    }
+
+    All_cells_iterator operator++(int) {
+      All_cells_iterator result = *this;
+      ++(*this);
+      return result;
+    }
+
+    All_cells_iterator& operator=(const All_cells_iterator& rhs) {
+      this->counter = rhs.counter;
+      return *this;
+    }
+
+    bool operator==(const All_cells_iterator& rhs)const {
+      if (this->counter != rhs.counter)return false;
+      return true;
+    }
+
+    bool operator!=(const All_cells_iterator& rhs)const {
+      return !(*this == rhs);
+    }
+
+    /*
+     * The operator * returns position of a cube in the structure of cubical complex. This position can be then used as
+     * an argument of the following functions:
+     * get_boundary_of_a_cell, get_coboundary_of_a_cell, get_dimension_of_a_cell to get information about the cell
+     * boundary and coboundary and dimension
+     * and in function get_cell_data to get a filtration of a cell.
+     */
+    size_t operator*() {
+      return this->counter;
+    }
+    friend class Bitmap_cubical_complex_base;
+   protected:
+    size_t counter;
+  };
+
+  /**
+   * Function returning a All_cells_iterator to the first cell of the bitmap.
+   **/
+  All_cells_iterator all_cells_iterator_begin() {
+    All_cells_iterator a;
+    return a;
+  }
+
+  /**
+   * Function returning a All_cells_iterator to the last cell of the bitmap.
+   **/
+  All_cells_iterator all_cells_iterator_end() {
+    All_cells_iterator a;
+    a.counter = this->data.size();
+    return a;
+  }
+
+  /**
+   * @brief All_cells_range class provides ranges for All_cells_iterator
+   **/
+  class All_cells_range {
+   public:
+    All_cells_range(Bitmap_cubical_complex_base* b) : b(b) { }
+
+    All_cells_iterator begin() {
+      return b->all_cells_iterator_begin();
+    }
+
+    All_cells_iterator end() {
+      return b->all_cells_iterator_end();
+    }
+   private:
+    Bitmap_cubical_complex_base<T>* b;
+  };
+
+  All_cells_range all_cells_range() {
+    return All_cells_range(this);
+  }
+
+
+  /**
+   * Boundary_range class provides ranges for boundary iterators.
+   **/
+  typedef typename std::vector< size_t >::const_iterator Boundary_iterator;
+  typedef typename std::vector< size_t > Boundary_range;
+
+  /**
+   * boundary_simplex_range creates an object of a Boundary_simplex_range class
+   * that provides ranges for the Boundary_simplex_iterator.
+   **/
+  Boundary_range boundary_range(size_t sh) {
+    return this->get_boundary_of_a_cell(sh);
+  }
+
+  /**
+   * Coboundary_range class provides ranges for boundary iterators.
+   **/
+  typedef typename std::vector< size_t >::const_iterator Coboundary_iterator;
+  typedef typename std::vector< size_t > Coboundary_range;
+
+  /**
+   * boundary_simplex_range creates an object of a Boundary_simplex_range class
+   * that provides ranges for the Boundary_simplex_iterator.
+   **/
+  Coboundary_range coboundary_range(size_t sh) {
+    return this->get_coboundary_of_a_cell(sh);
+  }
+
+  /**
+   * @brief Iterator through top dimensional cells of the complex. The cells appear in order they are stored
+   * in the structure (i.e. in lexicographical order)
+   **/
+  class Top_dimensional_cells_iterator : std::iterator< std::input_iterator_tag, T > {
+   public:
+    Top_dimensional_cells_iterator(Bitmap_cubical_complex_base& b) : b(b) {
+      this->counter = std::vector<size_t>(b.dimension());
+      // std::fill( this->counter.begin() , this->counter.end() , 0 );
+    }
+
+    Top_dimensional_cells_iterator operator++() {
+      // first find first element of the counter that can be increased:
+      size_t dim = 0;
+      while ((dim != this->b.dimension()) && (this->counter[dim] == this->b.sizes[dim] - 1))++dim;
+
+      if (dim != this->b.dimension()) {
+        ++this->counter[dim];
+        for (size_t i = 0; i != dim; ++i) {
+          this->counter[i] = 0;
+        }
+      } else {
+        ++this->counter[0];
+      }
+      return *this;
+    }
+
+    Top_dimensional_cells_iterator operator++(int) {
+      Top_dimensional_cells_iterator result = *this;
+      ++(*this);
+      return result;
+    }
+
+    Top_dimensional_cells_iterator& operator=(const Top_dimensional_cells_iterator& rhs) {
+      this->counter = rhs.counter;
+      this->b = rhs.b;
+      return *this;
+    }
+
+    bool operator==(const Top_dimensional_cells_iterator& rhs)const {
+      if (&this->b != &rhs.b)return false;
+      if (this->counter.size() != rhs.counter.size())return false;
+      for (size_t i = 0; i != this->counter.size(); ++i) {
+        if (this->counter[i] != rhs.counter[i])return false;
+      }
+      return true;
+    }
+
+    bool operator!=(const Top_dimensional_cells_iterator& rhs)const {
+      return !(*this == rhs);
+    }
+
+    /*
+     * The operator * returns position of a cube in the structure of cubical complex. This position can be then used as
+     * an argument of the following functions:
+     * get_boundary_of_a_cell, get_coboundary_of_a_cell, get_dimension_of_a_cell to get information about the cell
+     * boundary and coboundary and dimension
+     * and in function get_cell_data to get a filtration of a cell.
+     */
+    size_t operator*() {
+      return this->compute_index_in_bitmap();
+    }
+
+    size_t compute_index_in_bitmap()const {
+      size_t index = 0;
+      for (size_t i = 0; i != this->counter.size(); ++i) {
+        index += (2 * this->counter[i] + 1) * this->b.multipliers[i];
+      }
+      return index;
+    }
+
+    void print_counter()const {
+      for (size_t i = 0; i != this->counter.size(); ++i) {
+        std::cout << this->counter[i] << " ";
+      }
+    }
+    friend class Bitmap_cubical_complex_base;
+   protected:
+    std::vector< size_t > counter;
+    Bitmap_cubical_complex_base& b;
+  };
+
+  /**
+   * Function returning a Top_dimensional_cells_iterator to the first top dimensional cell of the bitmap.
+   **/
+  Top_dimensional_cells_iterator top_dimensional_cells_iterator_begin() {
+    Top_dimensional_cells_iterator a(*this);
+    return a;
+  }
+
+  /**
+   * Function returning a Top_dimensional_cells_iterator to the last top dimensional cell of the bitmap.
+   **/
+  Top_dimensional_cells_iterator top_dimensional_cells_iterator_end() {
+    Top_dimensional_cells_iterator a(*this);
+    for (size_t i = 0; i != this->dimension(); ++i) {
+      a.counter[i] = this->sizes[i] - 1;
+    }
+    a.counter[0]++;
+    return a;
+  }
+
+  /**
+   * @brief Top_dimensional_cells_iterator_range class provides ranges for Top_dimensional_cells_iterator_range
+   **/
+  class Top_dimensional_cells_range {
+   public:
+    Top_dimensional_cells_range(Bitmap_cubical_complex_base* b) : b(b) { }
+
+    Top_dimensional_cells_iterator begin() {
+      return b->top_dimensional_cells_iterator_begin();
+    }
+
+    Top_dimensional_cells_iterator end() {
+      return b->top_dimensional_cells_iterator_end();
+    }
+   private:
+    Bitmap_cubical_complex_base<T>* b;
+  };
+
+  Top_dimensional_cells_range top_dimensional_cells_range() {
+    return Top_dimensional_cells_range(this);
+  }
+
+
+  //****************************************************************************************************************//
+  //****************************************************************************************************************//
+  //****************************************************************************************************************//
+  //****************************************************************************************************************//
+
+  inline size_t number_cells()const {
+    return this->total_number_of_cells;
+  }
+
+  //****************************************************************************************************************//
+  //****************************************************************************************************************//
+  //****************************************************************************************************************//
+  //****************************************************************************************************************//
+
+ protected:
+  std::vector<unsigned> sizes;
+  std::vector<unsigned> multipliers;
+  std::vector<T> data;
+  size_t total_number_of_cells;
+
+  void set_up_containers(const std::vector<unsigned>& sizes) {
+    unsigned multiplier = 1;
+    for (size_t i = 0; i != sizes.size(); ++i) {
+      this->sizes.push_back(sizes[i]);
+      this->multipliers.push_back(multiplier);
+      multiplier *= 2 * sizes[i] + 1;
+    }
+    this->data = std::vector<T>(multiplier, std::numeric_limits<T>::max());
+    this->total_number_of_cells = multiplier;
+  }
+
+  size_t compute_position_in_bitmap(const std::vector< unsigned >& counter) {
+    size_t position = 0;
+    for (size_t i = 0; i != this->multipliers.size(); ++i) {
+      position += this->multipliers[i] * counter[i];
+    }
+    return position;
+  }
+
+  std::vector<unsigned> compute_counter_for_given_cell(size_t cell)const {
+    std::vector<unsigned> counter;
+    counter.reserve(this->sizes.size());
+    for (size_t dim = this->sizes.size(); dim != 0; --dim) {
+      counter.push_back(cell / this->multipliers[dim - 1]);
+      cell = cell % this->multipliers[dim - 1];
+    }
+    std::reverse(counter.begin(), counter.end());
+    return counter;
+  }
+  void read_perseus_style_file(const char* perseus_style_file);
+  void setup_bitmap_based_on_top_dimensional_cells_list(const std::vector<unsigned>& sizes_in_following_directions,
+                                                        const std::vector<T>& top_dimensional_cells);
+  Bitmap_cubical_complex_base(const char* perseus_style_file, std::vector<bool> directions);
+  Bitmap_cubical_complex_base(const std::vector<unsigned>& sizes, std::vector<bool> directions);
+  Bitmap_cubical_complex_base(const std::vector<unsigned>& dimensions,
+                              const std::vector<T>& top_dimensional_cells,
+                              std::vector<bool> directions);
+};
+
+template <typename T>
+void Bitmap_cubical_complex_base<T>::put_data_to_bins(size_t number_of_bins) {
+  bool bdg = false;
+
+  std::pair< T, T > min_max = this->min_max_filtration();
+  T dx = (min_max.second - min_max.first) / (T) number_of_bins;
+
+  // now put the data into the appropriate bins:
+  for (size_t i = 0; i != this->data.size(); ++i) {
+    if (bdg) {
+      std::cerr << "Before binning : " << this->data[i] << std::endl;
+    }
+    this->data[i] = min_max.first + dx * (this->data[i] - min_max.first) / number_of_bins;
+    if (bdg) {
+      std::cerr << "After binning : " << this->data[i] << std::endl;
+      getchar();
+    }
+  }
+}
+
+template <typename T>
+void Bitmap_cubical_complex_base<T>::put_data_to_bins(T diameter_of_bin) {
+  bool bdg = false;
+  std::pair< T, T > min_max = this->min_max_filtration();
+
+  size_t number_of_bins = (min_max.second - min_max.first) / diameter_of_bin;
+  // now put the data into the appropriate bins:
+  for (size_t i = 0; i != this->data.size(); ++i) {
+    if (bdg) {
+      std::cerr << "Before binning : " << this->data[i] << std::endl;
+    }
+    this->data[i] = min_max.first + diameter_of_bin * (this->data[i] - min_max.first) / number_of_bins;
+    if (bdg) {
+      std::cerr << "After binning : " << this->data[i] << std::endl;
+      getchar();
+    }
+  }
+}
+
+template <typename T>
+std::pair< T, T > Bitmap_cubical_complex_base<T>::min_max_filtration() {
+  std::pair< T, T > min_max(std::numeric_limits<T>::max(), std::numeric_limits<T>::min());
+  for (size_t i = 0; i != this->data.size(); ++i) {
+    if (this->data[i] < min_max.first)min_max.first = this->data[i];
+    if (this->data[i] > min_max.second)min_max.second = this->data[i];
+  }
+  return min_max;
+}
+
+template <typename K>
+std::ostream& operator<<(std::ostream & out, const Bitmap_cubical_complex_base<K>& b) {
+  for (typename Bitmap_cubical_complex_base<K>::all_cells_const_iterator
+       it = b.all_cells_const_begin(); it != b.all_cells_const_end(); ++it) {
+    out << *it << " ";
+  }
+  return out;
+}
+
+template <typename T>
+Bitmap_cubical_complex_base<T>::Bitmap_cubical_complex_base
+(const std::vector<unsigned>& sizes) {
+  this->set_up_containers(sizes);
+}
+
+template <typename T>
+void Bitmap_cubical_complex_base<T>::setup_bitmap_based_on_top_dimensional_cells_list(const std::vector<unsigned>& sizes_in_following_directions,
+                                                                                      const std::vector<T>& top_dimensional_cells) {
+  this->set_up_containers(sizes_in_following_directions);
+
+  size_t number_of_top_dimensional_elements = 1;
+  for (size_t i = 0; i != sizes_in_following_directions.size(); ++i) {
+    number_of_top_dimensional_elements *= sizes_in_following_directions[i];
+  }
+  if (number_of_top_dimensional_elements != top_dimensional_cells.size()) {
+    std::cerr << "Error in constructor Bitmap_cubical_complex_base ( std::vector<size_t> sizes_in_following_directions"
+        << ", std::vector<T> top_dimensional_cells ). Number of top dimensional elements that follow from "
+        << "sizes_in_following_directions vector is different than the size of top_dimensional_cells vector."
+        << std::endl;
+    throw("Error in constructor Bitmap_cubical_complex_base( std::vector<size_t> sizes_in_following_directions,"
+           "std::vector<T> top_dimensional_cells ). Number of top dimensional elements that follow from "
+           "sizes_in_following_directions vector is different than the size of top_dimensional_cells vector.");
+  }
+
+  Bitmap_cubical_complex_base<T>::Top_dimensional_cells_iterator it(*this);
+  size_t index = 0;
+  for (it = this->top_dimensional_cells_iterator_begin(); it != this->top_dimensional_cells_iterator_end(); ++it) {
+    this->get_cell_data(*it) = top_dimensional_cells[index];
+    ++index;
+  }
+  this->impose_lower_star_filtration();
+}
+
+template <typename T>
+Bitmap_cubical_complex_base<T>::Bitmap_cubical_complex_base
+(const std::vector<unsigned>& sizes_in_following_directions, const std::vector<T>& top_dimensional_cells) {
+  this->setup_bitmap_based_on_top_dimensional_cells_list(sizes_in_following_directions, top_dimensional_cells);
+}
+
+template <typename T>
+void Bitmap_cubical_complex_base<T>::read_perseus_style_file(const char* perseus_style_file) {
+  bool dbg = false;
+  std::ifstream inFiltration;
+  inFiltration.open(perseus_style_file);
+  unsigned dimensionOfData;
+  inFiltration >> dimensionOfData;
+
+  if (dbg) {
+    std::cerr << "dimensionOfData : " << dimensionOfData << std::endl;
+    getchar();
+  }
+
+  std::vector<unsigned> sizes;
+  sizes.reserve(dimensionOfData);
+  for (size_t i = 0; i != dimensionOfData; ++i) {
+    unsigned size_in_this_dimension;
+    inFiltration >> size_in_this_dimension;
+    sizes.push_back(size_in_this_dimension);
+    if (dbg) {
+      std::cerr << "size_in_this_dimension : " << size_in_this_dimension << std::endl;
+    }
+  }
+  this->set_up_containers(sizes);
+
+  Bitmap_cubical_complex_base<T>::Top_dimensional_cells_iterator it(*this);
+  it = this->top_dimensional_cells_iterator_begin();
+
+  while (!inFiltration.eof()) {
+    T filtrationLevel;
+    inFiltration >> filtrationLevel;
+    if (dbg) {
+      std::cerr << "Cell of an index : "
+          << it.compute_index_in_bitmap()
+          << " and dimension: "
+          << this->get_dimension_of_a_cell(it.compute_index_in_bitmap())
+          << " get the value : " << filtrationLevel << std::endl;
+    }
+    this->get_cell_data(*it) = filtrationLevel;
+    ++it;
+  }
+  inFiltration.close();
+  this->impose_lower_star_filtration();
+}
+
+template <typename T>
+Bitmap_cubical_complex_base<T>::Bitmap_cubical_complex_base(const char* perseus_style_file,
+                                                            std::vector<bool> directions) {
+  // this constructor is here just for compatibility with a class that creates cubical complexes with periodic boundary
+  // conditions.
+  // It ignores the last parameter of the function.
+  this->read_perseus_style_file(perseus_style_file);
+}
+
+template <typename T>
+Bitmap_cubical_complex_base<T>::Bitmap_cubical_complex_base(const std::vector<unsigned>& sizes,
+                                                            std::vector<bool> directions) {
+  // this constructor is here just for compatibility with a class that creates cubical complexes with periodic boundary
+  // conditions.
+  // It ignores the last parameter of the function.
+  this->set_up_containers(sizes);
+}
+
+template <typename T>
+Bitmap_cubical_complex_base<T>::Bitmap_cubical_complex_base(const std::vector<unsigned>& dimensions,
+                                                            const std::vector<T>& top_dimensional_cells,
+                                                            std::vector<bool> directions) {
+  // this constructor is here just for compatibility with a class that creates cubical complexes with periodic boundary
+  // conditions.
+  // It ignores the last parameter of the function.
+  this->setup_bitmap_based_on_top_dimensional_cells_list(dimensions, top_dimensional_cells);
+}
+
+template <typename T>
+Bitmap_cubical_complex_base<T>::Bitmap_cubical_complex_base(const char* perseus_style_file) {
+  this->read_perseus_style_file(perseus_style_file);
+}
+
+template <typename T>
+std::vector< size_t > Bitmap_cubical_complex_base<T>::get_boundary_of_a_cell(size_t cell)const {
+  std::vector< size_t > boundary_elements;
+
+  // Speed traded of for memory. Check if it is better in practice.
+  boundary_elements.reserve(this->dimension()*2);
+
+  size_t cell1 = cell;
+  for (size_t i = this->multipliers.size(); i != 0; --i) {
+    unsigned position = cell1 / this->multipliers[i - 1];
+    if (position % 2 == 1) {
+      boundary_elements.push_back(cell - this->multipliers[ i - 1 ]);
+      boundary_elements.push_back(cell + this->multipliers[ i - 1 ]);
+    }
+    cell1 = cell1 % this->multipliers[i - 1];
+  }
+  return boundary_elements;
+}
+
+template <typename T>
+std::vector< size_t > Bitmap_cubical_complex_base<T>::get_coboundary_of_a_cell(size_t cell)const {
+  std::vector<unsigned> counter = this->compute_counter_for_given_cell(cell);
+  std::vector< size_t > coboundary_elements;
+  size_t cell1 = cell;
+  for (size_t i = this->multipliers.size(); i != 0; --i) {
+    unsigned position = cell1 / this->multipliers[i - 1];
+    if (position % 2 == 0) {
+      if ((cell > this->multipliers[i - 1]) && (counter[i - 1] != 0)) {
+        coboundary_elements.push_back(cell - this->multipliers[i - 1]);
+      }
+      if (
+          (cell + this->multipliers[i - 1] < this->data.size()) && (counter[i - 1] != 2 * this->sizes[i - 1])) {
+        coboundary_elements.push_back(cell + this->multipliers[i - 1]);
+      }
+    }
+    cell1 = cell1 % this->multipliers[i - 1];
+  }
+  return coboundary_elements;
+}
+
+template <typename T>
+unsigned Bitmap_cubical_complex_base<T>::get_dimension_of_a_cell(size_t cell)const {
+  bool dbg = false;
+  if (dbg) std::cerr << "\n\n\n Computing position o a cell of an index : " << cell << std::endl;
+  unsigned dimension = 0;
+  for (size_t i = this->multipliers.size(); i != 0; --i) {
+    unsigned position = cell / this->multipliers[i - 1];
+
+    if (dbg) {
+      std::cerr << "i-1 :" << i - 1 << std::endl;
+      std::cerr << "cell : " << cell << std::endl;
+      std::cerr << "position : " << position << std::endl;
+      std::cerr << "multipliers[" << i - 1 << "] = " << this->multipliers[i - 1] << std::endl;
+      getchar();
+    }
+
+    if (position % 2 == 1) {
+      if (dbg) std::cerr << "Nonzero length in this direction \n";
+      dimension++;
+    }
+    cell = cell % this->multipliers[i - 1];
+  }
+  return dimension;
+}
+
+template <typename T>
+inline T& Bitmap_cubical_complex_base<T>::get_cell_data(size_t cell) {
+  return this->data[cell];
+}
+
+template <typename T>
+void Bitmap_cubical_complex_base<T>::impose_lower_star_filtration() {
+  bool dbg = false;
+
+  // this vector will be used to check which elements have already been taken care of in imposing lower star filtration
+  std::vector<bool> is_this_cell_considered(this->data.size(), false);
+
+  size_t size_to_reserve = 1;
+  for (size_t i = 0; i != this->multipliers.size(); ++i) {
+    size_to_reserve *= (size_t) ((this->multipliers[i] - 1) / 2);
+  }
+
+  std::vector<size_t> indices_to_consider;
+  indices_to_consider.reserve(size_to_reserve);
+  // we assume here that we already have a filtration on the top dimensional cells and
+  // we have to extend it to lower ones.
+  typename Bitmap_cubical_complex_base<T>::Top_dimensional_cells_iterator it(*this);
+  for (it = this->top_dimensional_cells_iterator_begin(); it != this->top_dimensional_cells_iterator_end(); ++it) {
+    indices_to_consider.push_back(it.compute_index_in_bitmap());
+  }
+
+  while (indices_to_consider.size()) {
+    if (dbg) {
+      std::cerr << "indices_to_consider in this iteration \n";
+      for (size_t i = 0; i != indices_to_consider.size(); ++i) {
+        std::cout << indices_to_consider[i] << "  ";
+      }
+      getchar();
+    }
+    std::vector<size_t> new_indices_to_consider;
+    for (size_t i = 0; i != indices_to_consider.size(); ++i) {
+      std::vector<size_t> bd = this->get_boundary_of_a_cell(indices_to_consider[i]);
+      for (size_t boundaryIt = 0; boundaryIt != bd.size(); ++boundaryIt) {
+        if (dbg) {
+          std::cerr << "filtration of a cell : " << bd[boundaryIt] << " is : " << this->data[ bd[boundaryIt] ]
+              << " while of a cell: " << indices_to_consider[i] << " is: " << this->data[ indices_to_consider[i] ]
+              << std::endl;
+          getchar();
+        }
+        if (this->data[ bd[boundaryIt] ] > this->data[ indices_to_consider[i] ]) {
+          this->data[ bd[boundaryIt] ] = this->data[ indices_to_consider[i] ];
+          if (dbg) {
+            std::cerr << "Setting the value of a cell : " << bd[boundaryIt] << " to : "
+                << this->data[ indices_to_consider[i] ] << std::endl;
+            getchar();
+          }
+        }
+        if (is_this_cell_considered[ bd[boundaryIt] ] == false) {
+          new_indices_to_consider.push_back(bd[boundaryIt]);
+          is_this_cell_considered[ bd[boundaryIt] ] = true;
+        }
+      }
+    }
+    indices_to_consider.swap(new_indices_to_consider);
+  }
+}
+
+template <typename T>
+bool compareFirstElementsOfTuples(const std::pair< std::pair< T, size_t >, char >& first,
+                                  const std::pair< std::pair< T, size_t >, char >& second) {
+  if (first.first.first < second.first.first) {
+    return true;
+  } else {
+    if (first.first.first > second.first.first) {
+      return false;
+    }
+    // in this case first.first.first == second.first.first, so we need to compare dimensions
+    return first.second < second.second;
+  }
+}
+
+}  // namespace cubical_complex
+
+namespace Cubical_complex = cubical_complex;
+
+}  // namespace Gudhi
+
+#endif  // BITMAP_CUBICAL_COMPLEX_BASE_H_
diff --git a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h
new file mode 100644
index 00000000..c3cc93dd
--- /dev/null
+++ b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h
@@ -0,0 +1,308 @@
+/*    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):       Pawel Dlotko
+ *
+ *    Copyright (C) 2015  INRIA Sophia-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 BITMAP_CUBICAL_COMPLEX_PERIODIC_BOUNDARY_CONDITIONS_BASE_H_
+#define BITMAP_CUBICAL_COMPLEX_PERIODIC_BOUNDARY_CONDITIONS_BASE_H_
+
+#include <gudhi/Bitmap_cubical_complex_base.h>
+
+#include <cmath>
+#include <limits>  // for numeric_limits<>
+#include <vector>
+
+namespace Gudhi {
+
+namespace cubical_complex {
+
+// in this class, we are storing all the elements which are in normal bitmap (i.e. the bitmap without the periodic
+// boundary conditions). But, we set up the iterators and the procedures to compute boundary and coboundary in the way
+// that it is all right. We assume here that all the cells that are on the left / bottom and so on remains, while all
+// the cells on the right / top are not in the Bitmap_cubical_complex_periodic_boundary_conditions_base
+
+/**
+ * @brief Cubical complex with periodic boundary conditions represented as a bitmap.
+ * @ingroup cubical_complex
+ * @details This is a class implementing a bitmap data structure with periodic boundary conditions. Most of the functions are
+ * identical to the functions from Bitmap_cubical_complex_base.
+ * The ones that needed to be updated are the constructors and get_boundary_of_a_cell and get_coboundary_of_a_cell.
+ */
+template <typename T>
+class Bitmap_cubical_complex_periodic_boundary_conditions_base : public Bitmap_cubical_complex_base<T> {
+ public:
+  // constructors that take an extra parameter:
+
+  /**
+   * Default constructor of Bitmap_cubical_complex_periodic_boundary_conditions_base class.
+   */
+  Bitmap_cubical_complex_periodic_boundary_conditions_base() { }
+  /**
+   * A constructor of Bitmap_cubical_complex_periodic_boundary_conditions_base class that takes the following
+   * parameters: (1) vector with numbers of top dimensional cells in all dimensions and (2) vector of booleans. If
+   * at i-th position of this vector there is true value, that means that periodic boundary conditions are to be
+   * imposed in this direction. In case of false, the periodic boundary conditions will not be imposed in the direction
+   * i.
+   */
+  Bitmap_cubical_complex_periodic_boundary_conditions_base(const std::vector<unsigned>& sizes,
+                                                           const std::vector<bool>& directions_in_which_periodic_b_cond_are_to_be_imposed);
+  /**
+   * A constructor of Bitmap_cubical_complex_periodic_boundary_conditions_base class that takes the name of Perseus
+   * style file as an input. Please consult the documentation about the specification of the file.
+   */
+  Bitmap_cubical_complex_periodic_boundary_conditions_base(const char* perseusStyleFile);
+  /**
+   * A constructor of Bitmap_cubical_complex_periodic_boundary_conditions_base class that takes the following
+   * parameters: (1) vector with numbers of top dimensional cells in all dimensions and (2) vector of top dimensional
+   * cells (ordered lexicographically) and (3) vector of booleans. If at i-th position of this vector there is true
+   * value, that means that periodic boundary conditions are to be imposed in this direction. In case of false, the
+   * periodic boundary conditions will not be imposed in the direction i.
+   */
+  Bitmap_cubical_complex_periodic_boundary_conditions_base(const std::vector<unsigned>& dimensions,
+                                                           const std::vector<T>& topDimensionalCells,
+                                                           const std::vector< bool >& directions_in_which_periodic_b_cond_are_to_be_imposed);
+
+  /**
+   * Destructor of the Bitmap_cubical_complex_periodic_boundary_conditions_base class.
+   **/
+  virtual ~Bitmap_cubical_complex_periodic_boundary_conditions_base() {}
+
+  // overwritten methods co compute boundary and coboundary
+  /**
+   * A version of a function that return boundary of a given cell for an object of
+   * Bitmap_cubical_complex_periodic_boundary_conditions_base class.
+   */
+  virtual std::vector< size_t > get_boundary_of_a_cell(size_t cell) const;
+
+  /**
+   * A version of a function that return coboundary of a given cell for an object of
+   * Bitmap_cubical_complex_periodic_boundary_conditions_base class.
+   */
+  virtual std::vector< size_t > get_coboundary_of_a_cell(size_t cell) const;
+
+ protected:
+  std::vector< bool > directions_in_which_periodic_b_cond_are_to_be_imposed;
+
+  void set_up_containers(const std::vector<unsigned>& sizes) {
+    unsigned multiplier = 1;
+    for (size_t i = 0; i != sizes.size(); ++i) {
+      this->sizes.push_back(sizes[i]);
+      this->multipliers.push_back(multiplier);
+
+      if (directions_in_which_periodic_b_cond_are_to_be_imposed[i]) {
+        multiplier *= 2 * sizes[i];
+      } else {
+        multiplier *= 2 * sizes[i] + 1;
+      }
+    }
+    // std::reverse( this->sizes.begin() , this->sizes.end() );
+    this->data = std::vector<T>(multiplier, std::numeric_limits<T>::max());
+    this->total_number_of_cells = multiplier;
+  }
+  Bitmap_cubical_complex_periodic_boundary_conditions_base(const std::vector<unsigned>& sizes);
+  Bitmap_cubical_complex_periodic_boundary_conditions_base(const std::vector<unsigned>& dimensions,
+                                                           const std::vector<T>& topDimensionalCells);
+  void construct_complex_based_on_top_dimensional_cells(const std::vector<unsigned>& dimensions,
+                                                        const std::vector<T>& topDimensionalCells,
+                                                        const std::vector<bool>& directions_in_which_periodic_b_cond_are_to_be_imposed);
+};
+
+template <typename T>
+void Bitmap_cubical_complex_periodic_boundary_conditions_base<T>::construct_complex_based_on_top_dimensional_cells(const std::vector<unsigned>& dimensions,
+                                                                                                                   const std::vector<T>& topDimensionalCells,
+                                                                                                                   const std::vector<bool>& directions_in_which_periodic_b_cond_are_to_be_imposed) {
+  this->directions_in_which_periodic_b_cond_are_to_be_imposed = directions_in_which_periodic_b_cond_are_to_be_imposed;
+  this->set_up_containers(dimensions);
+
+  size_t i = 0;
+  for (auto it = this->top_dimensional_cells_iterator_begin(); it != this->top_dimensional_cells_iterator_end(); ++it) {
+    this->get_cell_data(*it) = topDimensionalCells[i];
+    ++i;
+  }
+  this->impose_lower_star_filtration();
+}
+
+template <typename T>
+Bitmap_cubical_complex_periodic_boundary_conditions_base<T>::Bitmap_cubical_complex_periodic_boundary_conditions_base(const std::vector<unsigned>& sizes,
+                                                                                                                      const std::vector<bool>& directions_in_which_periodic_b_cond_are_to_be_imposed) {
+  this->directions_in_which_periodic_b_cond_are_to_be_imposed(directions_in_which_periodic_b_cond_are_to_be_imposed);
+  this->set_up_containers(sizes);
+}
+
+template <typename T>
+Bitmap_cubical_complex_periodic_boundary_conditions_base<T>::Bitmap_cubical_complex_periodic_boundary_conditions_base(const char* perseus_style_file) {
+  // for Perseus style files:
+  bool dbg = false;
+
+  std::ifstream inFiltration;
+  inFiltration.open(perseus_style_file);
+  unsigned dimensionOfData;
+  inFiltration >> dimensionOfData;
+
+  this->directions_in_which_periodic_b_cond_are_to_be_imposed = std::vector<bool>(dimensionOfData, false);
+
+  std::vector<unsigned> sizes;
+  sizes.reserve(dimensionOfData);
+  for (size_t i = 0; i != dimensionOfData; ++i) {
+    int size_in_this_dimension;
+    inFiltration >> size_in_this_dimension;
+    if (size_in_this_dimension < 0) {
+      this->directions_in_which_periodic_b_cond_are_to_be_imposed[i] = true;
+    }
+    sizes.push_back(abs(size_in_this_dimension));
+  }
+  this->set_up_containers(sizes);
+
+  typename Bitmap_cubical_complex_periodic_boundary_conditions_base<T>::Top_dimensional_cells_iterator it(*this);
+  it = this->top_dimensional_cells_iterator_begin();
+
+  while (!inFiltration.eof()) {
+    double filtrationLevel;
+    inFiltration >> filtrationLevel;
+    if (inFiltration.eof())break;
+
+    if (dbg) {
+      std::cerr << "Cell of an index : "
+          << it.compute_index_in_bitmap()
+          << " and dimension: "
+          << this->get_dimension_of_a_cell(it.compute_index_in_bitmap())
+          << " get the value : " << filtrationLevel << std::endl;
+    }
+    this->get_cell_data(*it) = filtrationLevel;
+    ++it;
+  }
+  inFiltration.close();
+  this->impose_lower_star_filtration();
+}
+
+template <typename T>
+Bitmap_cubical_complex_periodic_boundary_conditions_base<T>::Bitmap_cubical_complex_periodic_boundary_conditions_base(const std::vector<unsigned>& sizes) {
+  this->directions_in_which_periodic_b_cond_are_to_be_imposed = std::vector<bool>(sizes.size(), false);
+  this->set_up_containers(sizes);
+}
+
+template <typename T>
+Bitmap_cubical_complex_periodic_boundary_conditions_base<T>::Bitmap_cubical_complex_periodic_boundary_conditions_base(const std::vector<unsigned>& dimensions,
+                                                                                                                      const std::vector<T>& topDimensionalCells) {
+  std::vector<bool> directions_in_which_periodic_b_cond_are_to_be_imposed = std::vector<bool>(dimensions.size(), false);
+  this->construct_complex_based_on_top_dimensional_cells(dimensions, topDimensionalCells,
+                                                         directions_in_which_periodic_b_cond_are_to_be_imposed);
+}
+
+template <typename T>
+Bitmap_cubical_complex_periodic_boundary_conditions_base<T>::
+Bitmap_cubical_complex_periodic_boundary_conditions_base(const std::vector<unsigned>& dimensions,
+                                                         const std::vector<T>& topDimensionalCells,
+                                                         const std::vector<bool>& directions_in_which_periodic_b_cond_are_to_be_imposed) {
+  this->construct_complex_based_on_top_dimensional_cells(dimensions, topDimensionalCells,
+                                                         directions_in_which_periodic_b_cond_are_to_be_imposed);
+}
+
+// ***********************Methods************************ //
+
+template <typename T>
+std::vector< size_t > Bitmap_cubical_complex_periodic_boundary_conditions_base<T>::get_boundary_of_a_cell(size_t cell) const {
+  bool dbg = false;
+  if (dbg) {
+    std::cerr << "Computations of boundary of a cell : " << cell << std::endl;
+  }
+
+  std::vector< size_t > boundary_elements;
+  size_t cell1 = cell;
+  for (size_t i = this->multipliers.size(); i != 0; --i) {
+    unsigned position = cell1 / this->multipliers[i - 1];
+    // this cell have a nonzero length in this direction, therefore we can compute its boundary in this direction.
+
+    if (position % 2 == 1) {
+      // if there are no periodic boundary conditions in this direction, we do not have to do anything.
+      if (!directions_in_which_periodic_b_cond_are_to_be_imposed[i - 1]) {
+        // std::cerr << "A\n";
+        boundary_elements.push_back(cell - this->multipliers[ i - 1 ]);
+        boundary_elements.push_back(cell + this->multipliers[ i - 1 ]);
+        if (dbg) {
+          std::cerr << cell - this->multipliers[ i - 1 ] << " " << cell + this->multipliers[ i - 1 ] << " ";
+        }
+      } else {
+        // in this direction we have to do boundary conditions. Therefore, we need to check if we are not at the end.
+        if (position != 2 * this->sizes[ i - 1 ] - 1) {
+          // std::cerr << "B\n";
+          boundary_elements.push_back(cell - this->multipliers[ i - 1 ]);
+          boundary_elements.push_back(cell + this->multipliers[ i - 1 ]);
+          if (dbg) {
+            std::cerr << cell - this->multipliers[ i - 1 ] << " " << cell + this->multipliers[ i - 1 ] << " ";
+          }
+        } else {
+          // std::cerr << "C\n";
+          boundary_elements.push_back(cell - this->multipliers[ i - 1 ]);
+          boundary_elements.push_back(cell - (2 * this->sizes[ i - 1 ] - 1) * this->multipliers[ i - 1 ]);
+          if (dbg) {
+            std::cerr << cell - this->multipliers[ i - 1 ] << " " <<
+                cell - (2 * this->sizes[ i - 1 ] - 1) * this->multipliers[ i - 1 ] << " ";
+          }
+        }
+      }
+    }
+    cell1 = cell1 % this->multipliers[i - 1];
+  }
+  return boundary_elements;
+}
+
+template <typename T>
+std::vector< size_t > Bitmap_cubical_complex_periodic_boundary_conditions_base<T>::get_coboundary_of_a_cell(size_t cell) const {
+  std::vector<unsigned> counter = this->compute_counter_for_given_cell(cell);
+  std::vector< size_t > coboundary_elements;
+  size_t cell1 = cell;
+  for (size_t i = this->multipliers.size(); i != 0; --i) {
+    unsigned position = cell1 / this->multipliers[i - 1];
+    // if the cell has zero length in this direction, then it will have cbd in this direction.
+    if (position % 2 == 0) {
+      if (!this->directions_in_which_periodic_b_cond_are_to_be_imposed[i - 1]) {
+        // no periodic boundary conditions in this direction
+        if ((counter[i - 1] != 0) && (cell > this->multipliers[i - 1])) {
+          coboundary_elements.push_back(cell - this->multipliers[i - 1]);
+        }
+        if ((counter[i - 1] != 2 * this->sizes[i - 1]) && (cell + this->multipliers[i - 1] < this->data.size())) {
+          coboundary_elements.push_back(cell + this->multipliers[i - 1]);
+        }
+      } else {
+        // we want to have periodic boundary conditions in this direction
+        if (counter[i - 1] != 0) {
+          coboundary_elements.push_back(cell - this->multipliers[i - 1]);
+          coboundary_elements.push_back(cell + this->multipliers[i - 1]);
+        } else {
+          // in this case counter[i-1] == 0.
+          coboundary_elements.push_back(cell + this->multipliers[i - 1]);
+          coboundary_elements.push_back(cell + (2 * this->sizes[ i - 1 ] - 1) * this->multipliers[i - 1]);
+        }
+      }
+    }
+
+    cell1 = cell1 % this->multipliers[i - 1];
+  }
+  return coboundary_elements;
+}
+
+}  // namespace cubical_complex
+
+namespace Cubical_complex = cubical_complex;
+
+}  // namespace Gudhi
+
+#endif  // BITMAP_CUBICAL_COMPLEX_PERIODIC_BOUNDARY_CONDITIONS_BASE_H_
diff --git a/src/Bitmap_cubical_complex/test/Bitmap_test.cpp b/src/Bitmap_cubical_complex/test/Bitmap_test.cpp
new file mode 100644
index 00000000..db90eb94
--- /dev/null
+++ b/src/Bitmap_cubical_complex/test/Bitmap_test.cpp
@@ -0,0 +1,1378 @@
+/*    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):       Pawel Dlotko
+ *
+ *    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/>.
+ */
+
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE "cubical_complex"
+#include <boost/test/unit_test.hpp>
+
+#include <gudhi/reader_utils.h>
+#include <gudhi/Bitmap_cubical_complex.h>
+#include <gudhi/Persistent_cohomology.h>
+
+// standard stuff
+#include <iostream>
+#include <sstream>
+#include <vector>
+
+
+typedef Gudhi::cubical_complex::Bitmap_cubical_complex_base<double> Bitmap_cubical_complex_base;
+typedef Gudhi::cubical_complex::Bitmap_cubical_complex<Bitmap_cubical_complex_base> Bitmap_cubical_complex;
+
+typedef Gudhi::cubical_complex::Bitmap_cubical_complex_periodic_boundary_conditions_base<double>
+Bitmap_cubical_complex_periodic_boundary_conditions_base;
+typedef Gudhi::cubical_complex::Bitmap_cubical_complex<Bitmap_cubical_complex_periodic_boundary_conditions_base>
+Bitmap_cubical_complex_periodic_boundary_conditions;
+
+BOOST_AUTO_TEST_CASE(check_dimension) {
+  std::vector< double > increasingFiltrationOfTopDimensionalCells({1, 2, 3, 4, 5, 6, 7, 8, 9});
+
+  std::vector<unsigned> dimensions({3, 3});
+
+  Bitmap_cubical_complex increasing(dimensions, increasingFiltrationOfTopDimensionalCells);
+  BOOST_CHECK(increasing.dimension() == 2);
+}
+
+BOOST_AUTO_TEST_CASE(topDimensionalCellsIterator_test) {
+  std::vector< double > expectedFiltrationValues1({0, 0, 0, 0, 100, 0, 0, 0, 0});
+
+  std::vector< double > expectedFiltrationValues2({1, 2, 3, 4, 5, 6, 7, 8, 9});
+
+  std::vector< double > increasingFiltrationOfTopDimensionalCells({1, 2, 3, 4, 5, 6, 7, 8, 9});
+
+  std::vector< double > oneDimensionalCycle({0, 0, 0, 0, 100, 0, 0, 0, 0});
+
+  std::vector<unsigned> dimensions({3, 3});
+
+  Bitmap_cubical_complex increasing(dimensions, increasingFiltrationOfTopDimensionalCells);
+  Bitmap_cubical_complex hole(dimensions, oneDimensionalCycle);
+
+
+  int i = 0;
+  for (Bitmap_cubical_complex::Top_dimensional_cells_iterator
+       it = increasing.top_dimensional_cells_iterator_begin(); it != increasing.top_dimensional_cells_iterator_end(); ++it) {
+    BOOST_CHECK(increasing.get_cell_data(*it) == expectedFiltrationValues2[i]);
+    ++i;
+  }
+  i = 0;
+  for (Bitmap_cubical_complex::Top_dimensional_cells_iterator
+       it = hole.top_dimensional_cells_iterator_begin(); it != hole.top_dimensional_cells_iterator_end(); ++it) {
+    BOOST_CHECK(hole.get_cell_data(*it) == expectedFiltrationValues1[i]);
+    ++i;
+  }
+}
+
+BOOST_AUTO_TEST_CASE(compute_boundary_test_1) {
+  std::vector<double> boundary0;
+  std::vector<double> boundary1;
+  boundary1.push_back(0);
+  boundary1.push_back(2);
+  std::vector<double> boundary2;
+  std::vector<double> boundary3;
+  boundary3.push_back(2);
+  boundary3.push_back(4);
+  std::vector<double> boundary4;
+  std::vector<double> boundary5;
+  boundary5.push_back(4);
+  boundary5.push_back(6);
+  std::vector<double> boundary6;
+  std::vector<double> boundary7;
+  boundary7.push_back(0);
+  boundary7.push_back(14);
+  std::vector<double> boundary8;
+  boundary8.push_back(1);
+  boundary8.push_back(15);
+  boundary8.push_back(7);
+  boundary8.push_back(9);
+  std::vector<double> boundary9;
+  boundary9.push_back(2);
+  boundary9.push_back(16);
+  std::vector<double> boundary10;
+  boundary10.push_back(3);
+  boundary10.push_back(17);
+  boundary10.push_back(9);
+  boundary10.push_back(11);
+  std::vector<double> boundary11;
+  boundary11.push_back(4);
+  boundary11.push_back(18);
+  std::vector<double> boundary12;
+  boundary12.push_back(5);
+  boundary12.push_back(19);
+  boundary12.push_back(11);
+  boundary12.push_back(13);
+  std::vector<double> boundary13;
+  boundary13.push_back(6);
+  boundary13.push_back(20);
+  std::vector<double> boundary14;
+  std::vector<double> boundary15;
+  boundary15.push_back(14);
+  boundary15.push_back(16);
+  std::vector<double> boundary16;
+  std::vector<double> boundary17;
+  boundary17.push_back(16);
+  boundary17.push_back(18);
+  std::vector<double> boundary18;
+  std::vector<double> boundary19;
+  boundary19.push_back(18);
+  boundary19.push_back(20);
+  std::vector<double> boundary20;
+  std::vector<double> boundary21;
+  boundary21.push_back(14);
+  boundary21.push_back(28);
+  std::vector<double> boundary22;
+  boundary22.push_back(15);
+  boundary22.push_back(29);
+  boundary22.push_back(21);
+  boundary22.push_back(23);
+  std::vector<double> boundary23;
+  boundary23.push_back(16);
+  boundary23.push_back(30);
+  std::vector<double> boundary24;
+  boundary24.push_back(17);
+  boundary24.push_back(31);
+  boundary24.push_back(23);
+  boundary24.push_back(25);
+  std::vector<double> boundary25;
+  boundary25.push_back(18);
+  boundary25.push_back(32);
+  std::vector<double> boundary26;
+  boundary26.push_back(19);
+  boundary26.push_back(33);
+  boundary26.push_back(25);
+  boundary26.push_back(27);
+  std::vector<double> boundary27;
+  boundary27.push_back(20);
+  boundary27.push_back(34);
+  std::vector<double> boundary28;
+  std::vector<double> boundary29;
+  boundary29.push_back(28);
+  boundary29.push_back(30);
+  std::vector<double> boundary30;
+  std::vector<double> boundary31;
+  boundary31.push_back(30);
+  boundary31.push_back(32);
+  std::vector<double> boundary32;
+  std::vector<double> boundary33;
+  boundary33.push_back(32);
+  boundary33.push_back(34);
+  std::vector<double> boundary34;
+  std::vector<double> boundary35;
+  boundary35.push_back(28);
+  boundary35.push_back(42);
+  std::vector<double> boundary36;
+  boundary36.push_back(29);
+  boundary36.push_back(43);
+  boundary36.push_back(35);
+  boundary36.push_back(37);
+  std::vector<double> boundary37;
+  boundary37.push_back(30);
+  boundary37.push_back(44);
+  std::vector<double> boundary38;
+  boundary38.push_back(31);
+  boundary38.push_back(45);
+  boundary38.push_back(37);
+  boundary38.push_back(39);
+  std::vector<double> boundary39;
+  boundary39.push_back(32);
+  boundary39.push_back(46);
+  std::vector<double> boundary40;
+  boundary40.push_back(33);
+  boundary40.push_back(47);
+  boundary40.push_back(39);
+  boundary40.push_back(41);
+  std::vector<double> boundary41;
+  boundary41.push_back(34);
+  boundary41.push_back(48);
+  std::vector<double> boundary42;
+  std::vector<double> boundary43;
+  boundary43.push_back(42);
+  boundary43.push_back(44);
+  std::vector<double> boundary44;
+  std::vector<double> boundary45;
+  boundary45.push_back(44);
+  boundary45.push_back(46);
+  std::vector<double> boundary46;
+  std::vector<double> boundary47;
+  boundary47.push_back(46);
+  boundary47.push_back(48);
+  std::vector<double> boundary48;
+  std::vector< std::vector<double> > boundaries;
+  boundaries.push_back(boundary0);
+  boundaries.push_back(boundary1);
+  boundaries.push_back(boundary2);
+  boundaries.push_back(boundary3);
+  boundaries.push_back(boundary4);
+  boundaries.push_back(boundary5);
+  boundaries.push_back(boundary6);
+  boundaries.push_back(boundary7);
+  boundaries.push_back(boundary8);
+  boundaries.push_back(boundary9);
+  boundaries.push_back(boundary10);
+  boundaries.push_back(boundary11);
+  boundaries.push_back(boundary12);
+  boundaries.push_back(boundary13);
+  boundaries.push_back(boundary14);
+  boundaries.push_back(boundary15);
+  boundaries.push_back(boundary16);
+  boundaries.push_back(boundary17);
+  boundaries.push_back(boundary18);
+  boundaries.push_back(boundary19);
+  boundaries.push_back(boundary20);
+  boundaries.push_back(boundary21);
+  boundaries.push_back(boundary22);
+  boundaries.push_back(boundary23);
+  boundaries.push_back(boundary24);
+  boundaries.push_back(boundary25);
+  boundaries.push_back(boundary26);
+  boundaries.push_back(boundary27);
+  boundaries.push_back(boundary28);
+  boundaries.push_back(boundary29);
+  boundaries.push_back(boundary30);
+  boundaries.push_back(boundary31);
+  boundaries.push_back(boundary32);
+  boundaries.push_back(boundary33);
+  boundaries.push_back(boundary34);
+  boundaries.push_back(boundary35);
+  boundaries.push_back(boundary36);
+  boundaries.push_back(boundary37);
+  boundaries.push_back(boundary38);
+  boundaries.push_back(boundary39);
+  boundaries.push_back(boundary40);
+  boundaries.push_back(boundary41);
+  boundaries.push_back(boundary42);
+  boundaries.push_back(boundary43);
+  boundaries.push_back(boundary44);
+  boundaries.push_back(boundary45);
+  boundaries.push_back(boundary46);
+  boundaries.push_back(boundary47);
+  boundaries.push_back(boundary48);
+
+
+
+  std::vector< double > increasingFiltrationOfTopDimensionalCells({1, 2, 3, 4, 5, 6, 7, 8, 9});
+
+  std::vector<unsigned> dimensions({3, 3});
+
+  Bitmap_cubical_complex increasing(dimensions, increasingFiltrationOfTopDimensionalCells);
+  for (size_t i = 0; i != increasing.size(); ++i) {
+    std::vector< size_t > bd = increasing.get_boundary_of_a_cell(i);
+    for (size_t j = 0; j != bd.size(); ++j) {
+      BOOST_CHECK(boundaries[i][j] == bd[j]);
+    }
+  }
+}
+
+BOOST_AUTO_TEST_CASE(compute_boundary_test_2) {
+  std::vector< double > increasingFiltrationOfTopDimensionalCells({1, 2, 3, 4, 5, 6, 7, 8, 9});
+
+  std::vector<unsigned> dimensions({3, 3});
+
+  Bitmap_cubical_complex increasing(dimensions, increasingFiltrationOfTopDimensionalCells);
+
+
+  std::vector<double> coboundaryElements;
+  coboundaryElements.push_back(7);
+  coboundaryElements.push_back(1);
+  coboundaryElements.push_back(8);
+  coboundaryElements.push_back(9);
+  coboundaryElements.push_back(1);
+  coboundaryElements.push_back(3);
+  coboundaryElements.push_back(10);
+  coboundaryElements.push_back(11);
+  coboundaryElements.push_back(3);
+  coboundaryElements.push_back(5);
+  coboundaryElements.push_back(12);
+  coboundaryElements.push_back(13);
+  coboundaryElements.push_back(5);
+  coboundaryElements.push_back(8);
+  coboundaryElements.push_back(8);
+  coboundaryElements.push_back(10);
+  coboundaryElements.push_back(10);
+  coboundaryElements.push_back(12);
+  coboundaryElements.push_back(12);
+  coboundaryElements.push_back(7);
+  coboundaryElements.push_back(21);
+  coboundaryElements.push_back(15);
+  coboundaryElements.push_back(8);
+  coboundaryElements.push_back(22);
+  coboundaryElements.push_back(9);
+  coboundaryElements.push_back(23);
+  coboundaryElements.push_back(15);
+  coboundaryElements.push_back(17);
+  coboundaryElements.push_back(10);
+  coboundaryElements.push_back(24);
+  coboundaryElements.push_back(11);
+  coboundaryElements.push_back(25);
+  coboundaryElements.push_back(17);
+  coboundaryElements.push_back(19);
+  coboundaryElements.push_back(12);
+  coboundaryElements.push_back(26);
+  coboundaryElements.push_back(13);
+  coboundaryElements.push_back(27);
+  coboundaryElements.push_back(19);
+  coboundaryElements.push_back(22);
+  coboundaryElements.push_back(22);
+  coboundaryElements.push_back(24);
+  coboundaryElements.push_back(24);
+  coboundaryElements.push_back(26);
+  coboundaryElements.push_back(26);
+  coboundaryElements.push_back(21);
+  coboundaryElements.push_back(35);
+  coboundaryElements.push_back(29);
+  coboundaryElements.push_back(22);
+  coboundaryElements.push_back(36);
+  coboundaryElements.push_back(23);
+  coboundaryElements.push_back(37);
+  coboundaryElements.push_back(29);
+  coboundaryElements.push_back(31);
+  coboundaryElements.push_back(24);
+  coboundaryElements.push_back(38);
+  coboundaryElements.push_back(25);
+  coboundaryElements.push_back(39);
+  coboundaryElements.push_back(31);
+  coboundaryElements.push_back(33);
+  coboundaryElements.push_back(26);
+  coboundaryElements.push_back(40);
+  coboundaryElements.push_back(27);
+  coboundaryElements.push_back(41);
+  coboundaryElements.push_back(33);
+  coboundaryElements.push_back(36);
+  coboundaryElements.push_back(36);
+  coboundaryElements.push_back(38);
+  coboundaryElements.push_back(38);
+  coboundaryElements.push_back(40);
+  coboundaryElements.push_back(40);
+  coboundaryElements.push_back(35);
+  coboundaryElements.push_back(43);
+  coboundaryElements.push_back(36);
+  coboundaryElements.push_back(37);
+  coboundaryElements.push_back(43);
+  coboundaryElements.push_back(45);
+  coboundaryElements.push_back(38);
+  coboundaryElements.push_back(39);
+  coboundaryElements.push_back(45);
+  coboundaryElements.push_back(47);
+  coboundaryElements.push_back(40);
+  coboundaryElements.push_back(41);
+  coboundaryElements.push_back(47);
+  size_t number = 0;
+  for (size_t i = 0; i != increasing.size(); ++i) {
+    std::vector< size_t > bd = increasing.get_coboundary_of_a_cell(i);
+    for (size_t j = 0; j != bd.size(); ++j) {
+      BOOST_CHECK(coboundaryElements[number] == bd[j]);
+      ++number;
+    }
+  }
+}
+
+BOOST_AUTO_TEST_CASE(compute_boundary_test_3) {
+  std::vector< double > increasingFiltrationOfTopDimensionalCells({1, 2, 3, 4, 5, 6, 7, 8, 9});
+
+  std::vector<unsigned> dimensions({3, 3});
+
+  Bitmap_cubical_complex increasing(dimensions, increasingFiltrationOfTopDimensionalCells);
+
+  std::vector<unsigned> dim;
+  dim.push_back(0);
+  dim.push_back(1);
+  dim.push_back(0);
+  dim.push_back(1);
+  dim.push_back(0);
+  dim.push_back(1);
+  dim.push_back(0);
+  dim.push_back(1);
+  dim.push_back(2);
+  dim.push_back(1);
+  dim.push_back(2);
+  dim.push_back(1);
+  dim.push_back(2);
+  dim.push_back(1);
+  dim.push_back(0);
+  dim.push_back(1);
+  dim.push_back(0);
+  dim.push_back(1);
+  dim.push_back(0);
+  dim.push_back(1);
+  dim.push_back(0);
+  dim.push_back(1);
+  dim.push_back(2);
+  dim.push_back(1);
+  dim.push_back(2);
+  dim.push_back(1);
+  dim.push_back(2);
+  dim.push_back(1);
+  dim.push_back(0);
+  dim.push_back(1);
+  dim.push_back(0);
+  dim.push_back(1);
+  dim.push_back(0);
+  dim.push_back(1);
+  dim.push_back(0);
+  dim.push_back(1);
+  dim.push_back(2);
+  dim.push_back(1);
+  dim.push_back(2);
+  dim.push_back(1);
+  dim.push_back(2);
+  dim.push_back(1);
+  dim.push_back(0);
+  dim.push_back(1);
+  dim.push_back(0);
+  dim.push_back(1);
+  dim.push_back(0);
+  dim.push_back(1);
+  dim.push_back(0);
+
+  for (size_t i = 0; i != increasing.size(); ++i) {
+    BOOST_CHECK(increasing.get_dimension_of_a_cell(i) == dim[i]);
+  }
+}
+
+BOOST_AUTO_TEST_CASE(Filtration_simplex_iterator_test) {
+  std::vector< double > increasingFiltrationOfTopDimensionalCells({1, 2, 3, 4, 5, 6, 7, 8, 9});
+
+  std::vector<unsigned> dimensions({3, 3});
+
+  Bitmap_cubical_complex increasing(dimensions, increasingFiltrationOfTopDimensionalCells);
+
+  std::vector< unsigned > dim;
+  dim.push_back(0);
+  dim.push_back(0);
+  dim.push_back(0);
+  dim.push_back(0);
+  dim.push_back(1);
+  dim.push_back(1);
+  dim.push_back(1);
+  dim.push_back(1);
+  dim.push_back(2);
+  dim.push_back(0);
+  dim.push_back(0);
+  dim.push_back(1);
+  dim.push_back(1);
+  dim.push_back(1);
+  dim.push_back(2);
+  dim.push_back(0);
+  dim.push_back(0);
+  dim.push_back(1);
+  dim.push_back(1);
+  dim.push_back(1);
+  dim.push_back(2);
+  dim.push_back(0);
+  dim.push_back(0);
+  dim.push_back(1);
+  dim.push_back(1);
+  dim.push_back(1);
+  dim.push_back(2);
+  dim.push_back(0);
+  dim.push_back(1);
+  dim.push_back(1);
+  dim.push_back(2);
+  dim.push_back(0);
+  dim.push_back(1);
+  dim.push_back(1);
+  dim.push_back(2);
+  dim.push_back(0);
+  dim.push_back(0);
+  dim.push_back(1);
+  dim.push_back(1);
+  dim.push_back(1);
+  dim.push_back(2);
+  dim.push_back(0);
+  dim.push_back(1);
+  dim.push_back(1);
+  dim.push_back(2);
+  dim.push_back(0);
+  dim.push_back(1);
+  dim.push_back(1);
+  dim.push_back(2);
+
+  std::vector<double> fil;
+  fil.push_back(1);
+  fil.push_back(1);
+  fil.push_back(1);
+  fil.push_back(1);
+  fil.push_back(1);
+  fil.push_back(1);
+  fil.push_back(1);
+  fil.push_back(1);
+  fil.push_back(1);
+  fil.push_back(2);
+  fil.push_back(2);
+  fil.push_back(2);
+  fil.push_back(2);
+  fil.push_back(2);
+  fil.push_back(2);
+  fil.push_back(3);
+  fil.push_back(3);
+  fil.push_back(3);
+  fil.push_back(3);
+  fil.push_back(3);
+  fil.push_back(3);
+  fil.push_back(4);
+  fil.push_back(4);
+  fil.push_back(4);
+  fil.push_back(4);
+  fil.push_back(4);
+  fil.push_back(4);
+  fil.push_back(5);
+  fil.push_back(5);
+  fil.push_back(5);
+  fil.push_back(5);
+  fil.push_back(6);
+  fil.push_back(6);
+  fil.push_back(6);
+  fil.push_back(6);
+  fil.push_back(7);
+  fil.push_back(7);
+  fil.push_back(7);
+  fil.push_back(7);
+  fil.push_back(7);
+  fil.push_back(7);
+  fil.push_back(8);
+  fil.push_back(8);
+  fil.push_back(8);
+  fil.push_back(8);
+  fil.push_back(9);
+  fil.push_back(9);
+  fil.push_back(9);
+  fil.push_back(9);
+
+
+  Bitmap_cubical_complex::Filtration_simplex_range range = increasing.filtration_simplex_range();
+  size_t position = 0;
+  for (Bitmap_cubical_complex::Filtration_simplex_iterator it = range.begin(); it != range.end(); ++it) {
+    BOOST_CHECK(increasing.dimension(*it) == dim[position]);
+    BOOST_CHECK(increasing.filtration(*it) == fil[position]);
+    ++position;
+  }
+}
+
+BOOST_AUTO_TEST_CASE(boudary_operator_2d_bitmap_with_periodic_bcond) {
+  std::vector< double > filtration({0, 0, 0, 0});
+
+  std::vector<unsigned> dimensions({2, 2});
+
+  std::vector<bool> periodic_directions({true, true});
+
+  Bitmap_cubical_complex_periodic_boundary_conditions cmplx(dimensions, filtration, periodic_directions);
+  BOOST_CHECK(cmplx.dimension() == 2);
+
+
+  std::vector<double> boundary0;
+  std::vector<double> boundary1;
+  boundary1.push_back(0);
+  boundary1.push_back(2);
+  std::vector<double> boundary2;
+  std::vector<double> boundary3;
+  boundary3.push_back(2);
+  boundary3.push_back(0);
+  std::vector<double> boundary4;
+  boundary4.push_back(0);
+  boundary4.push_back(8);
+  std::vector<double> boundary5;
+  boundary5.push_back(1);
+  boundary5.push_back(9);
+  boundary5.push_back(4);
+  boundary5.push_back(6);
+  std::vector<double> boundary6;
+  boundary6.push_back(2);
+  boundary6.push_back(10);
+  std::vector<double> boundary7;
+  boundary7.push_back(3);
+  boundary7.push_back(11);
+  boundary7.push_back(6);
+  boundary7.push_back(4);
+  std::vector<double> boundary8;
+  std::vector<double> boundary9;
+  boundary9.push_back(8);
+  boundary9.push_back(10);
+  std::vector<double> boundary10;
+  std::vector<double> boundary11;
+  boundary11.push_back(10);
+  boundary11.push_back(8);
+  std::vector<double> boundary12;
+  boundary12.push_back(8);
+  boundary12.push_back(0);
+  std::vector<double> boundary13;
+  boundary13.push_back(9);
+  boundary13.push_back(1);
+  boundary13.push_back(12);
+  boundary13.push_back(14);
+  std::vector<double> boundary14;
+  boundary14.push_back(10);
+  boundary14.push_back(2);
+  std::vector<double> boundary15;
+  boundary15.push_back(11);
+  boundary15.push_back(3);
+  boundary15.push_back(14);
+  boundary15.push_back(12);
+
+  std::vector< std::vector<double> > boundaries;
+  boundaries.push_back(boundary0);
+  boundaries.push_back(boundary1);
+  boundaries.push_back(boundary2);
+  boundaries.push_back(boundary3);
+  boundaries.push_back(boundary4);
+  boundaries.push_back(boundary5);
+  boundaries.push_back(boundary6);
+  boundaries.push_back(boundary7);
+  boundaries.push_back(boundary8);
+  boundaries.push_back(boundary9);
+  boundaries.push_back(boundary10);
+  boundaries.push_back(boundary11);
+  boundaries.push_back(boundary12);
+  boundaries.push_back(boundary13);
+  boundaries.push_back(boundary14);
+  boundaries.push_back(boundary15);
+
+  for (size_t i = 0; i != cmplx.size(); ++i) {
+    std::vector< size_t > bd = cmplx.get_boundary_of_a_cell(i);
+    for (size_t j = 0; j != bd.size(); ++j) {
+      BOOST_CHECK(boundaries[i][j] == bd[j]);
+    }
+  }
+}
+
+BOOST_AUTO_TEST_CASE(coboudary_operator_2d_bitmap_with_periodic_bcond) {
+  std::vector< double > filtration({0, 0, 0, 0});
+
+  std::vector<unsigned> dimensions({2, 2});
+
+  std::vector<bool> periodic_directions({true, true});
+
+  Bitmap_cubical_complex_periodic_boundary_conditions cmplx(dimensions, filtration, periodic_directions);
+  BOOST_CHECK(cmplx.dimension() == 2);
+
+
+  std::vector<double> coboundary0;
+  coboundary0.push_back(4);
+  coboundary0.push_back(12);
+  coboundary0.push_back(1);
+  coboundary0.push_back(3);
+  std::vector<double> coboundary1;
+  coboundary1.push_back(5);
+  coboundary1.push_back(13);
+  std::vector<double> coboundary2;
+  coboundary2.push_back(6);
+  coboundary2.push_back(14);
+  coboundary2.push_back(1);
+  coboundary2.push_back(3);
+  std::vector<double> coboundary3;
+  coboundary3.push_back(7);
+  coboundary3.push_back(15);
+  std::vector<double> coboundary4;
+  coboundary4.push_back(5);
+  coboundary4.push_back(7);
+  std::vector<double> coboundary5;
+  std::vector<double> coboundary6;
+  coboundary6.push_back(5);
+  coboundary6.push_back(7);
+  std::vector<double> coboundary7;
+  std::vector<double> coboundary8;
+  coboundary8.push_back(4);
+  coboundary8.push_back(12);
+  coboundary8.push_back(9);
+  coboundary8.push_back(11);
+  std::vector<double> coboundary9;
+  coboundary9.push_back(5);
+  coboundary9.push_back(13);
+  std::vector<double> coboundary10;
+  coboundary10.push_back(6);
+  coboundary10.push_back(14);
+  coboundary10.push_back(9);
+  coboundary10.push_back(11);
+  std::vector<double> coboundary11;
+  coboundary11.push_back(7);
+  coboundary11.push_back(15);
+  std::vector<double> coboundary12;
+  coboundary12.push_back(13);
+  coboundary12.push_back(15);
+  std::vector<double> coboundary13;
+  std::vector<double> coboundary14;
+  coboundary14.push_back(13);
+  coboundary14.push_back(15);
+  std::vector<double> coboundary15;
+
+  std::vector< std::vector<double> > coboundaries;
+  coboundaries.push_back(coboundary0);
+  coboundaries.push_back(coboundary1);
+  coboundaries.push_back(coboundary2);
+  coboundaries.push_back(coboundary3);
+  coboundaries.push_back(coboundary4);
+  coboundaries.push_back(coboundary5);
+  coboundaries.push_back(coboundary6);
+  coboundaries.push_back(coboundary7);
+  coboundaries.push_back(coboundary8);
+  coboundaries.push_back(coboundary9);
+  coboundaries.push_back(coboundary10);
+  coboundaries.push_back(coboundary11);
+  coboundaries.push_back(coboundary12);
+  coboundaries.push_back(coboundary13);
+  coboundaries.push_back(coboundary14);
+  coboundaries.push_back(coboundary15);
+
+  for (size_t i = 0; i != cmplx.size(); ++i) {
+    std::vector< size_t > cbd = cmplx.get_coboundary_of_a_cell(i);
+    for (size_t j = 0; j != cbd.size(); ++j) {
+      BOOST_CHECK(coboundaries[i][j] == cbd[j]);
+    }
+  }
+}
+
+BOOST_AUTO_TEST_CASE(bitmap_2d_with_periodic_bcond_filtration) {
+  std::vector< double > filtrationOrg({0, 1, 2, 3});
+
+  std::vector<unsigned> dimensions({2, 2});
+
+  std::vector<bool> periodic_directions({true, true});
+
+  Bitmap_cubical_complex_periodic_boundary_conditions cmplx(dimensions, filtrationOrg, periodic_directions);
+  BOOST_CHECK(cmplx.dimension() == 2);
+
+
+  std::vector<double> filtration;
+  filtration.push_back(0);  // 0
+  filtration.push_back(0);  // 1
+  filtration.push_back(0);  // 2
+  filtration.push_back(1);  // 3
+  filtration.push_back(0);  // 4
+  filtration.push_back(0);  // 5
+  filtration.push_back(0);  // 6
+  filtration.push_back(1);  // 7
+  filtration.push_back(0);  // 8
+  filtration.push_back(0);  // 9
+  filtration.push_back(0);  // 10
+  filtration.push_back(1);  // 11
+  filtration.push_back(2);  // 12
+  filtration.push_back(2);  // 13
+  filtration.push_back(2);  // 14
+  filtration.push_back(3);  // 15
+
+
+  for (size_t i = 0; i != cmplx.size(); ++i) {
+    BOOST_CHECK(filtration[i] == cmplx.get_cell_data(i));
+  }
+}
+BOOST_AUTO_TEST_CASE(all_cells_iterator_and_boundary_iterators_in_Bitmap_cubical_complex_base_check)
+{
+    std::vector< double > expected_filtration;
+    expected_filtration.push_back(0);
+    expected_filtration.push_back(0);
+    expected_filtration.push_back(0);
+    expected_filtration.push_back(1);
+    expected_filtration.push_back(1);
+    expected_filtration.push_back(0);
+    expected_filtration.push_back(0);
+    expected_filtration.push_back(0);
+    expected_filtration.push_back(1);
+    expected_filtration.push_back(1);
+    expected_filtration.push_back(0);
+    expected_filtration.push_back(0);
+    expected_filtration.push_back(0);
+    expected_filtration.push_back(1);
+    expected_filtration.push_back(1);
+    expected_filtration.push_back(2);
+    expected_filtration.push_back(2);
+    expected_filtration.push_back(2);
+    expected_filtration.push_back(3);
+    expected_filtration.push_back(3);
+    expected_filtration.push_back(2);
+    expected_filtration.push_back(2);
+    expected_filtration.push_back(2);
+    expected_filtration.push_back(3);
+    expected_filtration.push_back(3);
+
+    std::vector<unsigned> expected_dimension;
+    expected_dimension.push_back(0);
+    expected_dimension.push_back(1);
+    expected_dimension.push_back(0);
+    expected_dimension.push_back(1);
+    expected_dimension.push_back(0);
+    expected_dimension.push_back(1);
+    expected_dimension.push_back(2);
+    expected_dimension.push_back(1);
+    expected_dimension.push_back(2);
+    expected_dimension.push_back(1);
+    expected_dimension.push_back(0);
+    expected_dimension.push_back(1);
+    expected_dimension.push_back(0);
+    expected_dimension.push_back(1);
+    expected_dimension.push_back(0);
+    expected_dimension.push_back(1);
+    expected_dimension.push_back(2);
+    expected_dimension.push_back(1);
+    expected_dimension.push_back(2);
+    expected_dimension.push_back(1);
+    expected_dimension.push_back(0);
+    expected_dimension.push_back(1);
+    expected_dimension.push_back(0);
+    expected_dimension.push_back(1);
+    expected_dimension.push_back(0);
+
+    std::vector<size_t> expected_boundary;
+    expected_boundary.push_back(0);
+    expected_boundary.push_back(2);
+    expected_boundary.push_back(2);
+    expected_boundary.push_back(4);
+    expected_boundary.push_back(0);
+    expected_boundary.push_back(10);
+    expected_boundary.push_back(1);
+    expected_boundary.push_back(11);
+    expected_boundary.push_back(5);
+    expected_boundary.push_back(7);
+    expected_boundary.push_back(2);
+    expected_boundary.push_back(12);
+    expected_boundary.push_back(3);
+    expected_boundary.push_back(13);
+    expected_boundary.push_back(7);
+    expected_boundary.push_back(9);
+    expected_boundary.push_back(4);
+    expected_boundary.push_back(14);
+    expected_boundary.push_back(10);
+    expected_boundary.push_back(12);
+    expected_boundary.push_back(12);
+    expected_boundary.push_back(14);
+    expected_boundary.push_back(10);
+    expected_boundary.push_back(20);
+    expected_boundary.push_back(11);
+    expected_boundary.push_back(21);
+    expected_boundary.push_back(15);
+    expected_boundary.push_back(17);
+    expected_boundary.push_back(12);
+    expected_boundary.push_back(22);
+    expected_boundary.push_back(13);
+    expected_boundary.push_back(23);
+    expected_boundary.push_back(17);
+    expected_boundary.push_back(19);
+    expected_boundary.push_back(14);
+    expected_boundary.push_back(24);
+    expected_boundary.push_back(20);
+    expected_boundary.push_back(22);
+    expected_boundary.push_back(22);
+    expected_boundary.push_back(24);
+
+
+    std::vector<size_t> expected_coboundary;
+    expected_coboundary.push_back(5);
+    expected_coboundary.push_back(1);
+    expected_coboundary.push_back(6);
+    expected_coboundary.push_back(7);
+    expected_coboundary.push_back(1);
+    expected_coboundary.push_back(3);
+    expected_coboundary.push_back(8);
+    expected_coboundary.push_back(9);
+    expected_coboundary.push_back(3);
+    expected_coboundary.push_back(6);
+    expected_coboundary.push_back(6);
+    expected_coboundary.push_back(8);
+    expected_coboundary.push_back(8);
+    expected_coboundary.push_back(5);
+    expected_coboundary.push_back(15);
+    expected_coboundary.push_back(11);
+    expected_coboundary.push_back(6);
+    expected_coboundary.push_back(16);
+    expected_coboundary.push_back(7);
+    expected_coboundary.push_back(17);
+    expected_coboundary.push_back(11);
+    expected_coboundary.push_back(13);
+    expected_coboundary.push_back(8);
+    expected_coboundary.push_back(18);
+    expected_coboundary.push_back(9);
+    expected_coboundary.push_back(19);
+    expected_coboundary.push_back(13);
+    expected_coboundary.push_back(16);
+    expected_coboundary.push_back(16);
+    expected_coboundary.push_back(18);
+    expected_coboundary.push_back(18);
+    expected_coboundary.push_back(15);
+    expected_coboundary.push_back(21);
+    expected_coboundary.push_back(16);
+    expected_coboundary.push_back(17);
+    expected_coboundary.push_back(21);
+    expected_coboundary.push_back(23);
+    expected_coboundary.push_back(18);
+    expected_coboundary.push_back(19);
+    expected_coboundary.push_back(23);
+
+
+
+    std::vector< unsigned > sizes(2);
+    sizes[0] = 2;
+    sizes[1] = 2;
+
+    std::vector< double > data(4);
+    data[0] = 0;
+    data[1] = 1;
+    data[2] = 2;
+    data[3] = 3;
+
+    Bitmap_cubical_complex_base ba( sizes , data );
+    int i = 0;
+    int bd_it = 0;
+    int cbd_it = 0;
+    for ( Bitmap_cubical_complex_base::All_cells_iterator it = ba.all_cells_iterator_begin() ; it != ba.all_cells_iterator_end() ; ++it )
+    {
+        BOOST_CHECK( expected_filtration[i] == ba.get_cell_data( *it ) );
+        BOOST_CHECK( expected_dimension[i] == ba.get_dimension_of_a_cell( *it ) );
+
+        Bitmap_cubical_complex_base::Boundary_range bdrange = ba.boundary_range(*it);
+        for ( Bitmap_cubical_complex_base::Boundary_iterator bd = bdrange.begin() ; bd != bdrange.end() ; ++bd )
+        {
+            BOOST_CHECK( expected_boundary[bd_it] == *bd );
+            ++bd_it;
+        }
+
+        Bitmap_cubical_complex_base::Coboundary_range cbdrange = ba.coboundary_range(*it);
+        for ( Bitmap_cubical_complex_base::Coboundary_iterator cbd = cbdrange.begin() ; cbd != cbdrange.end() ; ++cbd )
+        {
+             BOOST_CHECK( expected_coboundary[cbd_it] == *cbd );
+            ++cbd_it;
+        }
+        ++i;
+    }
+}
+
+
+
+
+
+
+
+
+BOOST_AUTO_TEST_CASE(all_cells_iterator_and_boundary_iterators_in_Bitmap_cubical_complex_base_check_range_check_2)
+{
+    std::vector< double > expected_filtration;
+    expected_filtration.push_back(0);
+    expected_filtration.push_back(0);
+    expected_filtration.push_back(0);
+    expected_filtration.push_back(1);
+    expected_filtration.push_back(1);
+    expected_filtration.push_back(0);
+    expected_filtration.push_back(0);
+    expected_filtration.push_back(0);
+    expected_filtration.push_back(1);
+    expected_filtration.push_back(1);
+    expected_filtration.push_back(0);
+    expected_filtration.push_back(0);
+    expected_filtration.push_back(0);
+    expected_filtration.push_back(1);
+    expected_filtration.push_back(1);
+    expected_filtration.push_back(2);
+    expected_filtration.push_back(2);
+    expected_filtration.push_back(2);
+    expected_filtration.push_back(3);
+    expected_filtration.push_back(3);
+    expected_filtration.push_back(2);
+    expected_filtration.push_back(2);
+    expected_filtration.push_back(2);
+    expected_filtration.push_back(3);
+    expected_filtration.push_back(3);
+
+    std::vector<unsigned> expected_dimension;
+    expected_dimension.push_back(0);
+    expected_dimension.push_back(1);
+    expected_dimension.push_back(0);
+    expected_dimension.push_back(1);
+    expected_dimension.push_back(0);
+    expected_dimension.push_back(1);
+    expected_dimension.push_back(2);
+    expected_dimension.push_back(1);
+    expected_dimension.push_back(2);
+    expected_dimension.push_back(1);
+    expected_dimension.push_back(0);
+    expected_dimension.push_back(1);
+    expected_dimension.push_back(0);
+    expected_dimension.push_back(1);
+    expected_dimension.push_back(0);
+    expected_dimension.push_back(1);
+    expected_dimension.push_back(2);
+    expected_dimension.push_back(1);
+    expected_dimension.push_back(2);
+    expected_dimension.push_back(1);
+    expected_dimension.push_back(0);
+    expected_dimension.push_back(1);
+    expected_dimension.push_back(0);
+    expected_dimension.push_back(1);
+    expected_dimension.push_back(0);
+
+    std::vector<size_t> expected_boundary;
+    expected_boundary.push_back(0);
+    expected_boundary.push_back(2);
+    expected_boundary.push_back(2);
+    expected_boundary.push_back(4);
+    expected_boundary.push_back(0);
+    expected_boundary.push_back(10);
+    expected_boundary.push_back(1);
+    expected_boundary.push_back(11);
+    expected_boundary.push_back(5);
+    expected_boundary.push_back(7);
+    expected_boundary.push_back(2);
+    expected_boundary.push_back(12);
+    expected_boundary.push_back(3);
+    expected_boundary.push_back(13);
+    expected_boundary.push_back(7);
+    expected_boundary.push_back(9);
+    expected_boundary.push_back(4);
+    expected_boundary.push_back(14);
+    expected_boundary.push_back(10);
+    expected_boundary.push_back(12);
+    expected_boundary.push_back(12);
+    expected_boundary.push_back(14);
+    expected_boundary.push_back(10);
+    expected_boundary.push_back(20);
+    expected_boundary.push_back(11);
+    expected_boundary.push_back(21);
+    expected_boundary.push_back(15);
+    expected_boundary.push_back(17);
+    expected_boundary.push_back(12);
+    expected_boundary.push_back(22);
+    expected_boundary.push_back(13);
+    expected_boundary.push_back(23);
+    expected_boundary.push_back(17);
+    expected_boundary.push_back(19);
+    expected_boundary.push_back(14);
+    expected_boundary.push_back(24);
+    expected_boundary.push_back(20);
+    expected_boundary.push_back(22);
+    expected_boundary.push_back(22);
+    expected_boundary.push_back(24);
+
+
+    std::vector<size_t> expected_coboundary;
+    expected_coboundary.push_back(5);
+    expected_coboundary.push_back(1);
+    expected_coboundary.push_back(6);
+    expected_coboundary.push_back(7);
+    expected_coboundary.push_back(1);
+    expected_coboundary.push_back(3);
+    expected_coboundary.push_back(8);
+    expected_coboundary.push_back(9);
+    expected_coboundary.push_back(3);
+    expected_coboundary.push_back(6);
+    expected_coboundary.push_back(6);
+    expected_coboundary.push_back(8);
+    expected_coboundary.push_back(8);
+    expected_coboundary.push_back(5);
+    expected_coboundary.push_back(15);
+    expected_coboundary.push_back(11);
+    expected_coboundary.push_back(6);
+    expected_coboundary.push_back(16);
+    expected_coboundary.push_back(7);
+    expected_coboundary.push_back(17);
+    expected_coboundary.push_back(11);
+    expected_coboundary.push_back(13);
+    expected_coboundary.push_back(8);
+    expected_coboundary.push_back(18);
+    expected_coboundary.push_back(9);
+    expected_coboundary.push_back(19);
+    expected_coboundary.push_back(13);
+    expected_coboundary.push_back(16);
+    expected_coboundary.push_back(16);
+    expected_coboundary.push_back(18);
+    expected_coboundary.push_back(18);
+    expected_coboundary.push_back(15);
+    expected_coboundary.push_back(21);
+    expected_coboundary.push_back(16);
+    expected_coboundary.push_back(17);
+    expected_coboundary.push_back(21);
+    expected_coboundary.push_back(23);
+    expected_coboundary.push_back(18);
+    expected_coboundary.push_back(19);
+    expected_coboundary.push_back(23);
+
+
+
+    std::vector< unsigned > sizes(2);
+    sizes[0] = 2;
+    sizes[1] = 2;
+
+    std::vector< double > data(4);
+    data[0] = 0;
+    data[1] = 1;
+    data[2] = 2;
+    data[3] = 3;
+
+    Bitmap_cubical_complex_base ba( sizes , data );
+    int i = 0;
+    int bd_it = 0;
+    int cbd_it = 0;
+
+    Bitmap_cubical_complex_base::All_cells_range range(&ba);
+    for ( Bitmap_cubical_complex_base::All_cells_iterator it = range.begin() ; it != range.end() ; ++it )
+    {
+        BOOST_CHECK( expected_filtration[i] == ba.get_cell_data( *it ) );
+        BOOST_CHECK( expected_dimension[i] == ba.get_dimension_of_a_cell( *it ) );
+
+        Bitmap_cubical_complex_base::Boundary_range bdrange = ba.boundary_range(*it);
+        for ( Bitmap_cubical_complex_base::Boundary_iterator bd = bdrange.begin() ; bd != bdrange.end() ; ++bd )
+        {
+            BOOST_CHECK( expected_boundary[bd_it] == *bd );
+            ++bd_it;
+        }
+
+        Bitmap_cubical_complex_base::Coboundary_range cbdrange = ba.coboundary_range(*it);
+        for ( Bitmap_cubical_complex_base::Coboundary_iterator cbd = cbdrange.begin() ; cbd != cbdrange.end() ; ++cbd )
+        {
+             BOOST_CHECK( expected_coboundary[cbd_it] == *cbd );
+            ++cbd_it;
+        }
+        ++i;
+    }
+}
+
+
+
+
+
+
+BOOST_AUTO_TEST_CASE(all_cells_iterator_and_boundary_iterators_in_Bitmap_cubical_complex_base_check_range_check)
+{
+    std::vector< double > expected_filtration;
+    expected_filtration.push_back(0);
+    expected_filtration.push_back(0);
+    expected_filtration.push_back(0);
+    expected_filtration.push_back(1);
+    expected_filtration.push_back(1);
+    expected_filtration.push_back(0);
+    expected_filtration.push_back(0);
+    expected_filtration.push_back(0);
+    expected_filtration.push_back(1);
+    expected_filtration.push_back(1);
+    expected_filtration.push_back(0);
+    expected_filtration.push_back(0);
+    expected_filtration.push_back(0);
+    expected_filtration.push_back(1);
+    expected_filtration.push_back(1);
+    expected_filtration.push_back(2);
+    expected_filtration.push_back(2);
+    expected_filtration.push_back(2);
+    expected_filtration.push_back(3);
+    expected_filtration.push_back(3);
+    expected_filtration.push_back(2);
+    expected_filtration.push_back(2);
+    expected_filtration.push_back(2);
+    expected_filtration.push_back(3);
+    expected_filtration.push_back(3);
+
+    std::vector<unsigned> expected_dimension;
+    expected_dimension.push_back(0);
+    expected_dimension.push_back(1);
+    expected_dimension.push_back(0);
+    expected_dimension.push_back(1);
+    expected_dimension.push_back(0);
+    expected_dimension.push_back(1);
+    expected_dimension.push_back(2);
+    expected_dimension.push_back(1);
+    expected_dimension.push_back(2);
+    expected_dimension.push_back(1);
+    expected_dimension.push_back(0);
+    expected_dimension.push_back(1);
+    expected_dimension.push_back(0);
+    expected_dimension.push_back(1);
+    expected_dimension.push_back(0);
+    expected_dimension.push_back(1);
+    expected_dimension.push_back(2);
+    expected_dimension.push_back(1);
+    expected_dimension.push_back(2);
+    expected_dimension.push_back(1);
+    expected_dimension.push_back(0);
+    expected_dimension.push_back(1);
+    expected_dimension.push_back(0);
+    expected_dimension.push_back(1);
+    expected_dimension.push_back(0);
+
+    std::vector<size_t> expected_boundary;
+    expected_boundary.push_back(0);
+    expected_boundary.push_back(2);
+    expected_boundary.push_back(2);
+    expected_boundary.push_back(4);
+    expected_boundary.push_back(0);
+    expected_boundary.push_back(10);
+    expected_boundary.push_back(1);
+    expected_boundary.push_back(11);
+    expected_boundary.push_back(5);
+    expected_boundary.push_back(7);
+    expected_boundary.push_back(2);
+    expected_boundary.push_back(12);
+    expected_boundary.push_back(3);
+    expected_boundary.push_back(13);
+    expected_boundary.push_back(7);
+    expected_boundary.push_back(9);
+    expected_boundary.push_back(4);
+    expected_boundary.push_back(14);
+    expected_boundary.push_back(10);
+    expected_boundary.push_back(12);
+    expected_boundary.push_back(12);
+    expected_boundary.push_back(14);
+    expected_boundary.push_back(10);
+    expected_boundary.push_back(20);
+    expected_boundary.push_back(11);
+    expected_boundary.push_back(21);
+    expected_boundary.push_back(15);
+    expected_boundary.push_back(17);
+    expected_boundary.push_back(12);
+    expected_boundary.push_back(22);
+    expected_boundary.push_back(13);
+    expected_boundary.push_back(23);
+    expected_boundary.push_back(17);
+    expected_boundary.push_back(19);
+    expected_boundary.push_back(14);
+    expected_boundary.push_back(24);
+    expected_boundary.push_back(20);
+    expected_boundary.push_back(22);
+    expected_boundary.push_back(22);
+    expected_boundary.push_back(24);
+
+
+    std::vector<size_t> expected_coboundary;
+    expected_coboundary.push_back(5);
+    expected_coboundary.push_back(1);
+    expected_coboundary.push_back(6);
+    expected_coboundary.push_back(7);
+    expected_coboundary.push_back(1);
+    expected_coboundary.push_back(3);
+    expected_coboundary.push_back(8);
+    expected_coboundary.push_back(9);
+    expected_coboundary.push_back(3);
+    expected_coboundary.push_back(6);
+    expected_coboundary.push_back(6);
+    expected_coboundary.push_back(8);
+    expected_coboundary.push_back(8);
+    expected_coboundary.push_back(5);
+    expected_coboundary.push_back(15);
+    expected_coboundary.push_back(11);
+    expected_coboundary.push_back(6);
+    expected_coboundary.push_back(16);
+    expected_coboundary.push_back(7);
+    expected_coboundary.push_back(17);
+    expected_coboundary.push_back(11);
+    expected_coboundary.push_back(13);
+    expected_coboundary.push_back(8);
+    expected_coboundary.push_back(18);
+    expected_coboundary.push_back(9);
+    expected_coboundary.push_back(19);
+    expected_coboundary.push_back(13);
+    expected_coboundary.push_back(16);
+    expected_coboundary.push_back(16);
+    expected_coboundary.push_back(18);
+    expected_coboundary.push_back(18);
+    expected_coboundary.push_back(15);
+    expected_coboundary.push_back(21);
+    expected_coboundary.push_back(16);
+    expected_coboundary.push_back(17);
+    expected_coboundary.push_back(21);
+    expected_coboundary.push_back(23);
+    expected_coboundary.push_back(18);
+    expected_coboundary.push_back(19);
+    expected_coboundary.push_back(23);
+
+
+
+    std::vector< unsigned > sizes(2);
+    sizes[0] = 2;
+    sizes[1] = 2;
+
+    std::vector< double > data(4);
+    data[0] = 0;
+    data[1] = 1;
+    data[2] = 2;
+    data[3] = 3;
+
+    Bitmap_cubical_complex_base ba( sizes , data );
+    int i = 0;
+    int bd_it = 0;
+    int cbd_it = 0;
+
+    Bitmap_cubical_complex_base::All_cells_range range = ba.all_cells_range();
+    for ( Bitmap_cubical_complex_base::All_cells_iterator it = range.begin() ; it != range.end() ; ++it )
+    {
+        BOOST_CHECK( expected_filtration[i] == ba.get_cell_data( *it ) );
+        BOOST_CHECK( expected_dimension[i] == ba.get_dimension_of_a_cell( *it ) );
+
+        Bitmap_cubical_complex_base::Boundary_range bdrange = ba.boundary_range(*it);
+        for ( Bitmap_cubical_complex_base::Boundary_iterator bd = bdrange.begin() ; bd != bdrange.end() ; ++bd )
+        {
+            BOOST_CHECK( expected_boundary[bd_it] == *bd );
+            ++bd_it;
+        }
+
+        Bitmap_cubical_complex_base::Coboundary_range cbdrange = ba.coboundary_range(*it);
+        for ( Bitmap_cubical_complex_base::Coboundary_iterator cbd = cbdrange.begin() ; cbd != cbdrange.end() ; ++cbd )
+        {
+             BOOST_CHECK( expected_coboundary[cbd_it] == *cbd );
+            ++cbd_it;
+        }
+        ++i;
+    }
+}
+
+BOOST_AUTO_TEST_CASE(Top_dimensional_cells_iterator_range_check)
+{
+    std::vector< double > expected_filtration;
+    expected_filtration.push_back(0);
+    expected_filtration.push_back(0);
+    expected_filtration.push_back(0);
+    expected_filtration.push_back(1);
+    expected_filtration.push_back(1);
+    expected_filtration.push_back(0);
+    expected_filtration.push_back(0);
+    expected_filtration.push_back(0);
+    expected_filtration.push_back(1);
+    expected_filtration.push_back(1);
+    expected_filtration.push_back(0);
+    expected_filtration.push_back(0);
+    expected_filtration.push_back(0);
+    expected_filtration.push_back(1);
+    expected_filtration.push_back(1);
+    expected_filtration.push_back(2);
+    expected_filtration.push_back(2);
+    expected_filtration.push_back(2);
+    expected_filtration.push_back(3);
+    expected_filtration.push_back(3);
+    expected_filtration.push_back(2);
+    expected_filtration.push_back(2);
+    expected_filtration.push_back(2);
+    expected_filtration.push_back(3);
+    expected_filtration.push_back(3);
+
+
+    std::vector< unsigned > sizes(2);
+    sizes[0] = 2;
+    sizes[1] = 2;
+
+    std::vector< double > data(4);
+    data[0] = 0;
+    data[1] = 1;
+    data[2] = 2;
+    data[3] = 3;
+
+    Bitmap_cubical_complex_base ba( sizes , data );
+    int i = 0;
+
+    Bitmap_cubical_complex_base::Top_dimensional_cells_range range = ba.top_dimensional_cells_range();
+    for ( Bitmap_cubical_complex_base::Top_dimensional_cells_iterator it = range.begin() ; it != range.end() ; ++it )
+    {
+        BOOST_CHECK( data[i] == ba.get_cell_data( *it ) );
+        BOOST_CHECK( ba.get_dimension_of_a_cell( *it ) == 2 );
+        ++i;
+    }
+}
+
diff --git a/src/Bitmap_cubical_complex/test/CMakeLists.txt b/src/Bitmap_cubical_complex/test/CMakeLists.txt
new file mode 100644
index 00000000..daf0e14f
--- /dev/null
+++ b/src/Bitmap_cubical_complex/test/CMakeLists.txt
@@ -0,0 +1,24 @@
+cmake_minimum_required(VERSION 2.6)
+project(Bitmap_cubical_complex_tests)
+
+if (GCOVR_PATH)
+  # for gcovr to make coverage reports - Corbera Jenkins plugin
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
+endif()
+if (GPROF_PATH)
+  # for gprof to make coverage reports - Jenkins
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
+endif()
+
+add_executable ( BitmapCCUT Bitmap_test.cpp )
+target_link_libraries(BitmapCCUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+if (TBB_FOUND)
+  target_link_libraries(BitmapCCUT ${TBB_LIBRARIES})
+endif()
+
+# Unitary tests
+add_test(NAME BitmapCCUT
+  COMMAND ${CMAKE_CURRENT_BINARY_DIR}/BitmapCCUT 
+    # XML format for Jenkins xUnit plugin 
+    --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/BitmapCCUT.xml --log_level=test_suite --report_level=no)
+
diff --git a/src/Bottleneck/example/CMakeLists.txt b/src/Bottleneck/example/CMakeLists.txt
index 2ff009c4..77797202 100644
--- a/src/Bottleneck/example/CMakeLists.txt
+++ b/src/Bottleneck/example/CMakeLists.txt
@@ -1,5 +1,5 @@
 cmake_minimum_required(VERSION 2.6)
-project(GUDHIBottleneckExample)
+project(Bottleneck_examples)
 
 add_executable ( RandomDiagrams random_diagrams.cpp )
 add_test(RandomDiagrams ${CMAKE_CURRENT_BINARY_DIR}/RandomDiagrams)
diff --git a/src/Bottleneck/test/CMakeLists.txt b/src/Bottleneck/test/CMakeLists.txt
index 3dfd80cd..9d88ab25 100644
--- a/src/Bottleneck/test/CMakeLists.txt
+++ b/src/Bottleneck/test/CMakeLists.txt
@@ -1,17 +1,13 @@
 cmake_minimum_required(VERSION 2.6)
-project(GUDHIBottleneckUT)
+project(Bottleneck_tests)
 
 if (GCOVR_PATH)
   # for gcovr to make coverage reports - Corbera Jenkins plugin
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
-  set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fprofile-arcs -ftest-coverage")
-  set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fprofile-arcs -ftest-coverage")
 endif()
 if (GPROF_PATH)
   # for gprof to make coverage reports - Jenkins
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
-  set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -pg")
-  set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -pg")
 endif()
 
 add_executable ( BottleneckUT bottleneck_unit_test.cpp )
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 81e6f864..c7744c49 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -2,40 +2,86 @@ cmake_minimum_required(VERSION 2.6)
 project(GUDHI)
 
 include("CMakeGUDHIVersion.txt")
+# Generate GUDHI official version file
+configure_file(GUDHIVersion.cmake.in "${CMAKE_SOURCE_DIR}/GUDHIVersion.cmake" @ONLY)
 
 enable_testing()
 
 list(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake/modules/")
 
-find_package(Boost REQUIRED COMPONENTS system filesystem program_options chrono timer REQUIRED)
-
-if (NOT CMAKE_BUILD_TYPE)
- set(CMAKE_BUILD_TYPE "Release")
-endif()
-if(MSVC)
-  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} -std=c++11")
-endif()
-
-set(Boost_USE_STATIC_LIBS        ON)
-set(Boost_USE_MULTITHREADED      ON)
-set(Boost_USE_STATIC_RUNTIME    OFF)
-
-find_package(GMP)
-if(GMP_FOUND)
-  find_package(GMPXX)
-endif()
-
-find_package(CGAL)
-
-# Find TBB package for parallel sort - not mandatory, just optional.
-set(TBB_FIND_QUIETLY ON)
-find_package(TBB)
+find_package(Boost REQUIRED COMPONENTS system filesystem program_options chrono timer date_time REQUIRED)
 
 if(NOT Boost_FOUND)
   message(FATAL_ERROR "NOTICE: This demo requires Boost and will not be compiled.")
 else()
+
+  # For "make doxygen"
+  set(GUDHI_USER_VERSION_DIR ${CMAKE_SOURCE_DIR})
+  include(${CMAKE_MODULE_PATH}/GUDHI_doxygen_target.txt)
+
+  find_package(GMP)
+  if(GMP_FOUND)
+    message(STATUS "GMP_LIBRARIES = ${GMP_LIBRARIES}")
+    INCLUDE_DIRECTORIES(${GMP_INCLUDE_DIR})
+    find_package(GMPXX)
+    if(GMPXX_FOUND)
+      message(STATUS "GMPXX_LIBRARIES = ${GMPXX_LIBRARIES}")
+      INCLUDE_DIRECTORIES(${GMPXX_INCLUDE_DIR})
+    endif()
+  endif()
+
+  # In CMakeLists.txt, when include(${CGAL_USE_FILE}), CMAKE_CXX_FLAGS are overwritten.
+  # cf. http://doc.cgal.org/latest/Manual/installation.html#title40
+  # A workaround is to include(${CGAL_USE_FILE}) before adding "-std=c++11".
+  # A fix would be to use https://cmake.org/cmake/help/v3.1/prop_gbl/CMAKE_CXX_KNOWN_FEATURES.html 
+  # or even better https://cmake.org/cmake/help/v3.1/variable/CMAKE_CXX_STANDARD.html
+  # but it implies to use cmake version 3.1 at least.
+
+  # find CGAL in QUIET mode for cmake to be less verbose when CGAL is not found.
+  find_package(CGAL QUIET)
+  # Only CGAL versions > 4.4 supports what Gudhi uses from CGAL
+  if (CGAL_VERSION VERSION_LESS 4.4.0 AND CGAL_FOUND)
+    message("CGAL version ${CGAL_VERSION} is considered too old to be used by Gudhi.")
+    unset(CGAL_FOUND)
+  endif(CGAL_VERSION VERSION_LESS 4.4.0 AND CGAL_FOUND)
+  if(CGAL_FOUND)
+    message(STATUS "CGAL version: ${CGAL_VERSION}.")
+    include( ${CGAL_USE_FILE} )
+  endif()
+  
+  if(MSVC)
+    # Turn off some VC++ warnings
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4267 /wd4668 /wd4311 /wd4800 /wd4820 /wd4503 /wd4244 /wd4345 /wd4996 /wd4396 /wd4018")
+  else()
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -Wall -pedantic")
+  endif()
+
+  if(CMAKE_BUILD_TYPE MATCHES Debug)
+    message("++ Debug compilation flags are: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_DEBUG}")
+  else()
+    message("++ Release compilation flags are: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_RELEASE}")
+  endif()
+
+  set(Boost_USE_STATIC_LIBS        ON)
+  set(Boost_USE_MULTITHREADED      ON)
+  set(Boost_USE_STATIC_RUNTIME    OFF)
+
+  # Find TBB package for parallel sort - not mandatory, just optional.
+  set(TBB_FIND_QUIETLY ON)
+  find_package(TBB)
+  if (TBB_FOUND)
+    include(${TBB_USE_FILE})
+    message("TBB found in ${TBB_LIBRARY_DIRS}")
+    add_definitions(-DGUDHI_USE_TBB)
+  endif()
+
+  find_package(Eigen3 3.1.0)
+  if (EIGEN3_FOUND)
+    message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.")
+    include( ${EIGEN3_USE_FILE} )
+    #include_directories (BEFORE "../../include")
+  endif (EIGEN3_FOUND)
+
   # BOOST ISSUE result_of vs C++11
   add_definitions(-DBOOST_RESULT_OF_USE_DECLTYPE)
   # BOOST ISSUE with Libraries name resolution under Windows
@@ -44,15 +90,24 @@ else()
   INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS})
   LINK_DIRECTORIES(${Boost_LIBRARY_DIRS})
 
+  if (DEBUG_TRACES)
+    message(STATUS "DEBUG_TRACES are activated")
+    # For programs to be more verbose
+    add_definitions(-DDEBUG_TRACES)
+  endif()
+
   #---------------------------------------------------------------------------------------
   # Gudhi compilation part
   include_directories(include)
 
+  add_subdirectory(example/common)
   add_subdirectory(example/Simplex_tree)                   
   add_subdirectory(example/Persistent_cohomology)                   
   add_subdirectory(example/Skeleton_blocker)                   
   add_subdirectory(example/Contraction)                   
+  add_subdirectory(example/Bitmap_cubical_complex)
   add_subdirectory(example/Witness_complex)
+  add_subdirectory(example/Alpha_complex)
 
   # data points generator
   add_subdirectory(data/points/generator)
@@ -68,8 +123,9 @@ else()
   # (this registers the build-tree with a global CMake-registry)
   export(PACKAGE GUDHI)
 
+  message("++ make install will install ${PROJECT_NAME} in the following directory : ${CMAKE_INSTALL_PREFIX}")
   # Create the GUDHIConfig.cmake and GUDHIConfigVersion files
-  set(CONF_INCLUDE_DIRS "${PROJECT_SOURCE_DIR}/include")
+  set(CONF_INCLUDE_DIRS "${CMAKE_INSTALL_PREFIX}/include")
   configure_file(GUDHIConfig.cmake.in "${PROJECT_BINARY_DIR}/GUDHIConfig.cmake" @ONLY)
   configure_file(GUDHIConfigVersion.cmake.in "${PROJECT_BINARY_DIR}/GUDHIConfigVersion.cmake" @ONLY)
 
diff --git a/src/Contraction/doc/sphere_contraction_representation.png b/src/Contraction/doc/sphere_contraction_representation.png
new file mode 100644
index 00000000..edf37bf3
--- /dev/null
+++ b/src/Contraction/doc/sphere_contraction_representation.png
diff --git a/src/Contraction/example/CMakeLists.txt b/src/Contraction/example/CMakeLists.txt
index 4889b82f..4c09a0a7 100644
--- a/src/Contraction/example/CMakeLists.txt
+++ b/src/Contraction/example/CMakeLists.txt
@@ -1,5 +1,5 @@
 cmake_minimum_required(VERSION 2.6)
-project(GUDHIskbl)
+project(Contraction_examples)
 
 
 add_executable(RipsContraction Rips_contraction.cpp)
@@ -9,5 +9,7 @@ target_link_libraries(RipsContraction ${Boost_TIMER_LIBRARY} ${Boost_SYSTEM_LIBR
 target_link_libraries(GarlandHeckbert ${Boost_TIMER_LIBRARY} ${Boost_SYSTEM_LIBRARY})	
 
 
-add_test(RipsContraction.sphere.0.2 ${CMAKE_CURRENT_BINARY_DIR}/RipsContraction ${CMAKE_SOURCE_DIR}/data/points/sphere3D_2646.off 0.2)
-add_test(RipsContraction.S0310000 ${CMAKE_CURRENT_BINARY_DIR}/RipsContraction ${CMAKE_SOURCE_DIR}/data/points/SO3_10000.off 0.3)
+add_test(RipsContraction.tore3D.0.2 ${CMAKE_CURRENT_BINARY_DIR}/RipsContraction ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off 0.2)
+# TODO(DS) : These tests are too long under Windows
+#add_test(RipsContraction.sphere.0.2 ${CMAKE_CURRENT_BINARY_DIR}/RipsContraction ${CMAKE_SOURCE_DIR}/data/points/sphere3D_2646.off 0.2)
+#add_test(RipsContraction.S0310000 ${CMAKE_CURRENT_BINARY_DIR}/RipsContraction ${CMAKE_SOURCE_DIR}/data/points/SO3_10000.off 0.3)
diff --git a/src/Contraction/example/Garland_heckbert.cpp b/src/Contraction/example/Garland_heckbert.cpp
index b545a066..5347830c 100644
--- a/src/Contraction/example/Garland_heckbert.cpp
+++ b/src/Contraction/example/Garland_heckbert.cpp
@@ -35,9 +35,8 @@
 
 #include "Garland_heckbert/Error_quadric.h"
 
-using namespace std;
 using namespace Gudhi;
-using namespace skbl;
+using namespace skeleton_blocker;
 using namespace contraction;
 
 struct Geometry_trait {
diff --git a/src/Contraction/example/Garland_heckbert/Error_quadric.h b/src/Contraction/example/Garland_heckbert/Error_quadric.h
index a033aa00..076f1be0 100644
--- a/src/Contraction/example/Garland_heckbert/Error_quadric.h
+++ b/src/Contraction/example/Garland_heckbert/Error_quadric.h
@@ -1,182 +1,182 @@
-/* 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):       David Salinas
- *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-M�diterran�e (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 ERROR_QUADRIC_H_
-#define ERROR_QUADRIC_H_
-
-#include <boost/optional/optional.hpp>
-
-#include <vector>
-#include <utility>
-
-template <typename Point> class Error_quadric {
- private:
-  double coeff[10];
-
- public:
-  Error_quadric() {
-    clear();
-  }
-
-  /**
-   * Quadric corresponding to the L2 distance to the plane.
-   *
-   * According to the notation of Garland Heckbert, they
-   * denote a quadric symetric matrix as :
-   * Q = [ q11 q12 q13 q14]
-   *     [ q12 q22 q23 q24]
-   *     [ q13 q23 q33 q34]
-   *     [ q14 q24 q34 q44]
-   *
-   * which is represented by a vector with 10 elts that
-   * are denoted ci for clarity with :
-   * Q = [ c0  c1  c2  c3 ]
-   *     [ c1  c4  c5  c6 ]
-   *     [ c2  c5  c7  c8 ]
-   *     [ c3  c6  c8  c9 ]
-   *
-   * The constructor return the quadrics that represents
-   * the squared distance to the plane defined by triangle p0,p1,p2
-   * times the area of triangle p0,p1,p2.
-   */
-  Error_quadric(const Point & p0, const Point & p1, const Point & p2) {
-    Point normal(unit_normal(p0, p1, p2));
-    double a = normal[0];
-    double b = normal[1];
-    double c = normal[2];
-    double d = -a * p0[0] - b * p0[1] - c * p0[2];
-    coeff[0] = a*a;
-    coeff[1] = a*b;
-    coeff[2] = a*c;
-    coeff[3] = a*d;
-    coeff[4] = b*b;
-    coeff[5] = b*c;
-    coeff[6] = b*d;
-    coeff[7] = c*c;
-    coeff[8] = c*d;
-    coeff[9] = d*d;
-
-    double area_p0p1p2 = std::sqrt(squared_area(p0, p1, p2));
-    for (auto& x : coeff)
-      x *= area_p0p1p2;
-  }
-
-  inline double squared_area(const Point& p0, const Point& p1, const Point& p2) {
-    // if (x1,x2,x3) = p1-p0 and (y1,y2,y3) = p2-p0
-    // then the squared area is = (u^2+v^2+w^2)/4
-    // with: u = x2 * y3 - x3 * y2;
-    //       v = x3 * y1 - x1 * y3;
-    //       w = x1 * y2 - x2 * y1;
-    Point p0p1(p1 - p0);
-    Point p0p2(p2 - p0);
-    double A = p0p1[1] * p0p2[2] - p0p1[2] * p0p2[1];
-    double B = p0p1[2] * p0p2[0] - p0p1[0] * p0p2[2];
-    double C = p0p1[0] * p0p2[1] - p0p1[1] * p0p2[0];
-    return 1. / 4. * (A * A + B * B + C * C);
-  }
-
-  void clear() {
-    for (auto& x : coeff)
-      x = 0;
-  }
-
-  Error_quadric& operator+=(const Error_quadric& other) {
-    if (this != &other) {
-      for (int i = 0; i < 10; ++i)
-        coeff[i] += other.coeff[i];
-    }
-    return *this;
-  }
-
-  /**
-   * @return The quadric quost defined by the scalar product v^T Q v where Q is the quadratic form of Garland/Heckbert
-   */
-  inline double cost(const Point& point) const {
-    double cost =
-        coeff[0] * point.x() * point.x() + coeff[4] * point.y() * point.y() + coeff[7] * point.z() * point.z()
-        + 2 * (coeff[1] * point.x() * point.y() + coeff[5] * point.y() * point.z() + coeff[2] * point.z() * point.x())
-        + 2 * (coeff[3] * point.x() + coeff[6] * point.y() + coeff[8] * point.z())
-        + coeff[9];
-    if (cost < 0) {
-      return 0;
-    } else {
-      return cost;
-    }
-  }
-
-  inline double grad_determinant() const {
-    return
-    coeff[0] * coeff[4] * coeff[7]
-        - coeff[0] * coeff[5] * coeff[5]
-        - coeff[1] * coeff[1] * coeff[7]
-        + 2 * coeff[1] * coeff[5] * coeff[2]
-        - coeff[4] * coeff[2] * coeff[2];
-  }
-
-  /**
-   * Return the point such that it minimizes the gradient of the quadric.
-   * Det must be passed with the determinant value of the gradient (should be non zero).
-   */
-  inline Point solve_linear_gradient(double det) const {
-    return Point({
-                 (-coeff[1] * coeff[5] * coeff[8] + coeff[1] * coeff[7] * coeff[6] + coeff[2] * coeff[8] * coeff[4] -
-                     coeff[2] * coeff[5] * coeff[6] - coeff[3] * coeff[4] * coeff[7] + coeff[3] * coeff[5] * coeff[5])
-                     / det,
-                 (coeff[0] * coeff[5] * coeff[8] - coeff[0] * coeff[7] * coeff[6] - coeff[5] * coeff[2] * coeff[3] -
-                     coeff[1] * coeff[2] * coeff[8] + coeff[6] * coeff[2] * coeff[2] + coeff[1] * coeff[3] * coeff[7])
-                     / det,
-                 (-coeff[8] * coeff[0] * coeff[4] + coeff[8] * coeff[1] * coeff[1] + coeff[2] * coeff[3] * coeff[4] +
-                     coeff[5] * coeff[0] * coeff[6] - coeff[5] * coeff[1] * coeff[3] - coeff[1] * coeff[2] * coeff[6])
-                     / det
-    });
-  }
-
-  /**
-   * returns the point that minimizes the quadric.
-   * It inverses the quadric if its determinant is higher that a given threshold .
-   * If the determinant is lower than this value the returned value is uninitialized.
-   */
-  boost::optional<Point> min_cost(double scale = 1) const {
-    // const double min_determinant = 1e-4 * scale*scale;
-    const double min_determinant = 1e-5;
-    boost::optional<Point> pt_res;
-    double det = grad_determinant();
-    if (std::abs(det) > min_determinant)
-      pt_res = solve_linear_gradient(det);
-    return pt_res;
-  }
-
-  friend std::ostream& operator<<(std::ostream& stream, const Error_quadric& quadric) {
-    stream << "\n[ " << quadric.coeff[0] << "," << quadric.coeff[1] << "," << quadric.coeff[2] << "," <<
-        quadric.coeff[3] << ";\n";
-    stream << " " << quadric.coeff[1] << "," << quadric.coeff[4] << "," << quadric.coeff[5] << "," <<
-        quadric.coeff[6] << ";\n";
-    stream << " " << quadric.coeff[2] << "," << quadric.coeff[5] << "," << quadric.coeff[7] << "," <<
-        quadric.coeff[8] << ";\n";
-    stream << " " << quadric.coeff[3] << "," << quadric.coeff[6] << "," << quadric.coeff[8] << "," <<
-        quadric.coeff[9] << "]";
-    return stream;
-  }
-};
-
-#endif  // ERROR_QUADRIC_H_
+/* 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):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-M�diterran�e (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 ERROR_QUADRIC_H_
+#define ERROR_QUADRIC_H_
+
+#include <boost/optional/optional.hpp>
+
+#include <vector>
+#include <utility>
+
+template <typename Point> class Error_quadric {
+ private:
+  double coeff[10];
+
+ public:
+  Error_quadric() {
+    clear();
+  }
+
+  /**
+   * Quadric corresponding to the L2 distance to the plane.
+   *
+   * According to the notation of Garland Heckbert, they
+   * denote a quadric symetric matrix as :
+   * Q = [ q11 q12 q13 q14]
+   *     [ q12 q22 q23 q24]
+   *     [ q13 q23 q33 q34]
+   *     [ q14 q24 q34 q44]
+   *
+   * which is represented by a vector with 10 elts that
+   * are denoted ci for clarity with :
+   * Q = [ c0  c1  c2  c3 ]
+   *     [ c1  c4  c5  c6 ]
+   *     [ c2  c5  c7  c8 ]
+   *     [ c3  c6  c8  c9 ]
+   *
+   * The constructor return the quadrics that represents
+   * the squared distance to the plane defined by triangle p0,p1,p2
+   * times the area of triangle p0,p1,p2.
+   */
+  Error_quadric(const Point & p0, const Point & p1, const Point & p2) {
+    Point normal(unit_normal(p0, p1, p2));
+    double a = normal[0];
+    double b = normal[1];
+    double c = normal[2];
+    double d = -a * p0[0] - b * p0[1] - c * p0[2];
+    coeff[0] = a*a;
+    coeff[1] = a*b;
+    coeff[2] = a*c;
+    coeff[3] = a*d;
+    coeff[4] = b*b;
+    coeff[5] = b*c;
+    coeff[6] = b*d;
+    coeff[7] = c*c;
+    coeff[8] = c*d;
+    coeff[9] = d*d;
+
+    double area_p0p1p2 = std::sqrt(squared_area(p0, p1, p2));
+    for (auto& x : coeff)
+      x *= area_p0p1p2;
+  }
+
+  inline double squared_area(const Point& p0, const Point& p1, const Point& p2) {
+    // if (x1,x2,x3) = p1-p0 and (y1,y2,y3) = p2-p0
+    // then the squared area is = (u^2+v^2+w^2)/4
+    // with: u = x2 * y3 - x3 * y2;
+    //       v = x3 * y1 - x1 * y3;
+    //       w = x1 * y2 - x2 * y1;
+    Point p0p1(p1 - p0);
+    Point p0p2(p2 - p0);
+    double A = p0p1[1] * p0p2[2] - p0p1[2] * p0p2[1];
+    double B = p0p1[2] * p0p2[0] - p0p1[0] * p0p2[2];
+    double C = p0p1[0] * p0p2[1] - p0p1[1] * p0p2[0];
+    return 1. / 4. * (A * A + B * B + C * C);
+  }
+
+  void clear() {
+    for (auto& x : coeff)
+      x = 0;
+  }
+
+  Error_quadric& operator+=(const Error_quadric& other) {
+    if (this != &other) {
+      for (int i = 0; i < 10; ++i)
+        coeff[i] += other.coeff[i];
+    }
+    return *this;
+  }
+
+  /**
+   * @return The quadric quost defined by the scalar product v^T Q v where Q is the quadratic form of Garland/Heckbert
+   */
+  inline double cost(const Point& point) const {
+    double cost =
+        coeff[0] * point.x() * point.x() + coeff[4] * point.y() * point.y() + coeff[7] * point.z() * point.z()
+        + 2 * (coeff[1] * point.x() * point.y() + coeff[5] * point.y() * point.z() + coeff[2] * point.z() * point.x())
+        + 2 * (coeff[3] * point.x() + coeff[6] * point.y() + coeff[8] * point.z())
+        + coeff[9];
+    if (cost < 0) {
+      return 0;
+    } else {
+      return cost;
+    }
+  }
+
+  inline double grad_determinant() const {
+    return
+    coeff[0] * coeff[4] * coeff[7]
+        - coeff[0] * coeff[5] * coeff[5]
+        - coeff[1] * coeff[1] * coeff[7]
+        + 2 * coeff[1] * coeff[5] * coeff[2]
+        - coeff[4] * coeff[2] * coeff[2];
+  }
+
+  /**
+   * Return the point such that it minimizes the gradient of the quadric.
+   * Det must be passed with the determinant value of the gradient (should be non zero).
+   */
+  inline Point solve_linear_gradient(double det) const {
+    return Point({
+                 (-coeff[1] * coeff[5] * coeff[8] + coeff[1] * coeff[7] * coeff[6] + coeff[2] * coeff[8] * coeff[4] -
+                     coeff[2] * coeff[5] * coeff[6] - coeff[3] * coeff[4] * coeff[7] + coeff[3] * coeff[5] * coeff[5])
+                     / det,
+                 (coeff[0] * coeff[5] * coeff[8] - coeff[0] * coeff[7] * coeff[6] - coeff[5] * coeff[2] * coeff[3] -
+                     coeff[1] * coeff[2] * coeff[8] + coeff[6] * coeff[2] * coeff[2] + coeff[1] * coeff[3] * coeff[7])
+                     / det,
+                 (-coeff[8] * coeff[0] * coeff[4] + coeff[8] * coeff[1] * coeff[1] + coeff[2] * coeff[3] * coeff[4] +
+                     coeff[5] * coeff[0] * coeff[6] - coeff[5] * coeff[1] * coeff[3] - coeff[1] * coeff[2] * coeff[6])
+                     / det
+    });
+  }
+
+  /**
+   * returns the point that minimizes the quadric.
+   * It inverses the quadric if its determinant is higher that a given threshold .
+   * If the determinant is lower than this value the returned value is uninitialized.
+   */
+  boost::optional<Point> min_cost(double scale = 1) const {
+    // const double min_determinant = 1e-4 * scale*scale;
+    const double min_determinant = 1e-5;
+    boost::optional<Point> pt_res;
+    double det = grad_determinant();
+    if (std::abs(det) > min_determinant)
+      pt_res = solve_linear_gradient(det);
+    return pt_res;
+  }
+
+  friend std::ostream& operator<<(std::ostream& stream, const Error_quadric& quadric) {
+    stream << "\n[ " << quadric.coeff[0] << "," << quadric.coeff[1] << "," << quadric.coeff[2] << "," <<
+        quadric.coeff[3] << ";\n";
+    stream << " " << quadric.coeff[1] << "," << quadric.coeff[4] << "," << quadric.coeff[5] << "," <<
+        quadric.coeff[6] << ";\n";
+    stream << " " << quadric.coeff[2] << "," << quadric.coeff[5] << "," << quadric.coeff[7] << "," <<
+        quadric.coeff[8] << ";\n";
+    stream << " " << quadric.coeff[3] << "," << quadric.coeff[6] << "," << quadric.coeff[8] << "," <<
+        quadric.coeff[9] << "]";
+    return stream;
+  }
+};
+
+#endif  // ERROR_QUADRIC_H_
diff --git a/src/Contraction/example/Rips_contraction.cpp b/src/Contraction/example/Rips_contraction.cpp
index f80cc2dc..7f19e239 100644
--- a/src/Contraction/example/Rips_contraction.cpp
+++ b/src/Contraction/example/Rips_contraction.cpp
@@ -27,9 +27,8 @@
 #include <boost/timer/timer.hpp>
 #include <iostream>
 
-using namespace std;
 using namespace Gudhi;
-using namespace skbl;
+using namespace skeleton_blocker;
 using namespace contraction;
 
 struct Geometry_trait {
diff --git a/src/Contraction/include/gudhi/Contraction/policies/Link_condition_valid_contraction.h b/src/Contraction/include/gudhi/Contraction/policies/Link_condition_valid_contraction.h
index 919df243..250bba27 100644
--- a/src/Contraction/include/gudhi/Contraction/policies/Link_condition_valid_contraction.h
+++ b/src/Contraction/include/gudhi/Contraction/policies/Link_condition_valid_contraction.h
@@ -23,8 +23,8 @@
 #ifndef CONTRACTION_POLICIES_LINK_CONDITION_VALID_CONTRACTION_H_
 #define CONTRACTION_POLICIES_LINK_CONDITION_VALID_CONTRACTION_H_
 
-#include <gudhi/Utils.h>
 #include <gudhi/Contraction/policies/Valid_contraction_policy.h>
+#include <gudhi/Debug_utils.h>
 
 
 namespace Gudhi {
diff --git a/src/Contraction/include/gudhi/Edge_contraction.h b/src/Contraction/include/gudhi/Edge_contraction.h
index ee3e3de1..61f2d945 100644
--- a/src/Contraction/include/gudhi/Edge_contraction.h
+++ b/src/Contraction/include/gudhi/Edge_contraction.h
@@ -30,7 +30,7 @@
 #include <gudhi/Contraction/policies/Valid_contraction_policy.h>
 #include <gudhi/Contraction/policies/Dummy_valid_contraction.h>
 #include <gudhi/Contraction/policies/Link_condition_valid_contraction.h>
-#include <gudhi/Utils.h>
+#include <gudhi/Debug_utils.h>
 
 namespace Gudhi {
 
@@ -41,12 +41,12 @@ namespace contraction {
 
 \author David Salinas
 
-\section Introduction
+\section edgecontractionintroduction Introduction
 
 The purpose of this package is to offer a user-friendly interface for edge contraction simplification of huge simplicial complexes.
 It uses the \ref skbl data-structure whose size remains small  during simplification  
 of  most used geometrical complexes of topological data analysis such as the Rips or the Delaunay complexes. In practice, the 
-size of this data-structure is even uch lower than the total number of simplices.
+size of this data-structure is even much lower than the total number of simplices.
 
 The edge contraction operation consists in identifying two vertices of a simplicial complex. 
 A lot of algorithms have been developed in computer graphics that allows to reduce efficiently the size of 2-dimensional simplicial complexes
@@ -127,7 +127,7 @@ while ensuring its homotopy type is preserved during the contraction (edge are c
 
 using namespace std;
 using namespace Gudhi;
-using namespace skbl;
+using namespace skeleton_blocker;
 using namespace contraction;
 
 struct Geometry_trait{
@@ -226,7 +226,6 @@ Time to simplify and enumerate simplices:
 
 
 \copyright GNU General Public License v3.                         
-\verbatim  Contact: gudhi-users@lists.gforge.inria.fr \endverbatim
 */
 /** @} */  // end defgroup
 }  // namespace contraction
diff --git a/src/Contraction/include/gudhi/Skeleton_blocker_contractor.h b/src/Contraction/include/gudhi/Skeleton_blocker_contractor.h
index d6350a2c..df884c93 100644
--- a/src/Contraction/include/gudhi/Skeleton_blocker_contractor.h
+++ b/src/Contraction/include/gudhi/Skeleton_blocker_contractor.h
@@ -37,7 +37,7 @@
 #include <gudhi/Contraction/policies/Contraction_visitor.h>
 
 #include <gudhi/Skeleton_blocker/Skeleton_blocker_complex_visitor.h>
-#include <gudhi/Utils.h>
+#include <gudhi/Debug_utils.h>
 
 
 #include <boost/scoped_array.hpp>
@@ -100,7 +100,7 @@ Contraction_visitor<Profile>* make_remove_popable_blockers_visitor() {
  *
  */
 template<class GeometricSimplifiableComplex, class EdgeProfile = Edge_profile<GeometricSimplifiableComplex>>
-class Skeleton_blocker_contractor : private skbl::Dummy_complex_visitor<
+class Skeleton_blocker_contractor : private skeleton_blocker::Dummy_complex_visitor<
 typename GeometricSimplifiableComplex::Vertex_handle> {
   GeometricSimplifiableComplex& complex_;
 
diff --git a/src/Doxyfile b/src/Doxyfile
index 6585e50c..dd9a33fb 100644
--- a/src/Doxyfile
+++ b/src/Doxyfile
@@ -32,19 +32,19 @@ DOXYFILE_ENCODING      = UTF-8
 # title of most generated pages and in a few other places.
 # The default value is: My Project.
 
-PROJECT_NAME           = "Gudhi"
+PROJECT_NAME           = "GUDHI"
 
 # The PROJECT_NUMBER tag can be used to enter a project or revision number. This
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = "1.2.0"
+PROJECT_NUMBER         = "1.3.1"
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a
 # quick idea about the purpose of the project. Keep the description short.
 
-PROJECT_BRIEF          =
+PROJECT_BRIEF          = "C++ library for Topological Data Analysis (TDA) and Higher Dimensional Geometry Understanding."
 
 # With the PROJECT_LOGO tag one can specify an logo or icon that is included in
 # the documentation. The maximum height of the logo should not exceed 55 pixels
@@ -153,7 +153,7 @@ STRIP_FROM_PATH        =
 # specify the list of include paths that are normally passed to the compiler
 # using the -I flag.
 
-STRIP_FROM_INC_PATH    =
+STRIP_FROM_INC_PATH    = include concept
 
 # If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter (but
 # less readable) file names. This can be useful is your file systems doesn't
@@ -580,27 +580,27 @@ STRICT_PROTO_MATCHING  = NO
 # documentation.
 # The default value is: YES.
 
-GENERATE_TODOLIST      = YES
+GENERATE_TODOLIST      = NO
 
 # The GENERATE_TESTLIST tag can be used to enable ( YES) or disable ( NO) the
 # test list. This list is created by putting \test commands in the
 # documentation.
 # The default value is: YES.
 
-GENERATE_TESTLIST      = YES
+GENERATE_TESTLIST      = NO
 
 # The GENERATE_BUGLIST tag can be used to enable ( YES) or disable ( NO) the bug
 # list. This list is created by putting \bug commands in the documentation.
 # The default value is: YES.
 
-GENERATE_BUGLIST       = YES
+GENERATE_BUGLIST       = NO
 
 # The GENERATE_DEPRECATEDLIST tag can be used to enable ( YES) or disable ( NO)
 # the deprecated list. This list is created by putting \deprecated commands in
 # the documentation.
 # The default value is: YES.
 
-GENERATE_DEPRECATEDLIST= YES
+GENERATE_DEPRECATEDLIST= NO
 
 # The ENABLED_SECTIONS tag can be used to enable conditional documentation
 # sections, marked by \if <section_label> ... \endif and \cond <section_label>
@@ -673,6 +673,7 @@ LAYOUT_FILE            =
 # also \cite for info how to create references.
 
 CITE_BIB_FILES         = biblio/bibliography.bib \
+                        biblio/how_to_cite_cgal.bib \
                         biblio/how_to_cite_gudhi.bib
 
 #---------------------------------------------------------------------------
@@ -779,7 +780,11 @@ RECURSIVE              = YES
 # Note that relative paths are relative to the directory from which doxygen is
 # run.
 
-EXCLUDE                = 
+EXCLUDE                = data/ \
+	                     example/ \
+	                     GudhUI/  \
+                             cmake/   \
+                             debian/
 
 # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
 # directories that are symbolic links (a Unix file system feature) are excluded
@@ -812,14 +817,15 @@ EXCLUDE_SYMBOLS        =
 # that contain example code fragments that are included (see the \include
 # command).
 
-EXAMPLE_PATH           = biblio/
+EXAMPLE_PATH           = biblio/ \
+	example/
 
 # If the value of the EXAMPLE_PATH tag contains directories, you can use the
 # EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and
 # *.h) to filter out the source-files in the directories. If left blank all
 # files are included.
 
-EXAMPLE_PATTERNS       =
+EXAMPLE_PATTERNS       = 
 
 # If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
 # searched for input files to be used with the \include or \dontinclude commands
@@ -833,9 +839,13 @@ EXAMPLE_RECURSIVE      = NO
 # \image command).
 
 IMAGE_PATH             = doc/Skeleton_blocker/ \
+	doc/Alpha_complex/ \
 	doc/common/ \
 	doc/Contraction/ \
-	doc/Witness_complex/
+	doc/Simplex_tree/ \
+	doc/Persistent_cohomology/ \
+	doc/Witness_complex/ \
+	doc/Bitmap_cubical_complex/
 
 # The INPUT_FILTER tag can be used to specify a program that doxygen should
 # invoke to filter for each input file. Doxygen will invoke the filter program
@@ -1039,7 +1049,7 @@ HTML_FILE_EXTENSION    = .html
 # of the possible markers and block names see the documentation.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_HEADER            =
+HTML_HEADER            = doc/common/header.html
 
 # The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each
 # generated HTML page. If the tag is left blank doxygen will generate a standard
@@ -1049,7 +1059,7 @@ HTML_HEADER            =
 # that doxygen normally uses.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_FOOTER            =
+HTML_FOOTER            = doc/common/footer.html
 
 # The HTML_STYLESHEET tag can be used to specify a user-defined cascading style
 # sheet that is used by each HTML page. It can be used to fine-tune the look of
@@ -1061,7 +1071,7 @@ HTML_FOOTER            =
 # obsolete.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_STYLESHEET        =
+HTML_STYLESHEET        = doc/common/stylesheet.css
 
 # The HTML_EXTRA_STYLESHEET tag can be used to specify an additional user-
 # defined cascading style sheet that is included after the standard style sheets
@@ -1544,7 +1554,7 @@ EXTRA_SEARCH_MAPPINGS  =
 # If the GENERATE_LATEX tag is set to YES doxygen will generate LaTeX output.
 # The default value is: YES.
 
-GENERATE_LATEX         = YES
+GENERATE_LATEX         = NO
 
 # The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. If a
 # relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
@@ -1596,7 +1606,7 @@ PAPER_TYPE             = a4
 # If left blank no extra packages will be included.
 # This tag requires that the tag GENERATE_LATEX is set to YES.
 
-EXTRA_PACKAGES         = amsfonts amsmath amssymb
+EXTRA_PACKAGES         = amsfonts amsmath amssymb algorithm algpseudocode
 
 # The LATEX_HEADER tag can be used to specify a personal LaTeX header for the
 # generated LaTeX document. The header should contain everything until the first
@@ -1793,18 +1803,6 @@ GENERATE_XML           = NO
 
 XML_OUTPUT             = xml
 
-# The XML_SCHEMA tag can be used to specify a XML schema, which can be used by a
-# validating XML parser to check the syntax of the XML files.
-# This tag requires that the tag GENERATE_XML is set to YES.
-
-XML_SCHEMA             =
-
-# The XML_DTD tag can be used to specify a XML DTD, which can be used by a
-# validating XML parser to check the syntax of the XML files.
-# This tag requires that the tag GENERATE_XML is set to YES.
-
-XML_DTD                =
-
 # If the XML_PROGRAMLISTING tag is set to YES doxygen will dump the program
 # listings (including syntax highlighting and cross-referencing information) to
 # the XML output. Note that enabling this will significantly increase the size
diff --git a/src/GudhUI/CMakeLists.txt b/src/GudhUI/CMakeLists.txt
index 71f4fd1a..a43294ea 100644
--- a/src/GudhUI/CMakeLists.txt
+++ b/src/GudhUI/CMakeLists.txt
@@ -1,7 +1,6 @@
 cmake_minimum_required(VERSION 2.8)
 project(GudhUI)
 
-find_package(CGAL  COMPONENTS Qt4)
 find_package(Qt4)
 find_package(QGLViewer)
 find_package(OpenGL)
@@ -14,27 +13,8 @@ if ( CGAL_FOUND AND QT4_FOUND AND OPENGL_FOUND AND QGLVIEWER_FOUND )
   SET(Boost_USE_STATIC_LIBS ON)
   SET(Boost_USE_MULTITHREAD OFF)
 
-  INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS})
-  LINK_DIRECTORIES(${Boost_LIBRARY_DIRS})
-  
   include(${QT_USE_FILE})
 
-  include(${CGAL_USE_FILE})
-  # In CMakeLists.txt, when include(${CGAL_USE_FILE}), CXX_FLAGS are overwritten.
-  # cf. http://doc.cgal.org/latest/Manual/installation.html#title40
-  # A workaround is to add "-std=c++11" again.
-  # A fix would be to use https://cmake.org/cmake/help/v3.1/prop_gbl/CMAKE_CXX_KNOWN_FEATURES.html 
-  # or even better https://cmake.org/cmake/help/v3.1/variable/CMAKE_CXX_STANDARD.html
-  # but it implies to use cmake version 3.1 at least.
-  if(NOT MSVC)
-    include(CheckCXXCompilerFlag)
-    CHECK_CXX_COMPILER_FLAG(-std=c++11 COMPILER_SUPPORTS_CXX11)
-    if(COMPILER_SUPPORTS_CXX11)
-      set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
-    endif()
-  endif()
-  # - End of workaround
-
   include_directories (${QGLVIEWER_INCLUDE_DIR})
   include_directories(.)	
  
@@ -77,6 +57,11 @@ if ( CGAL_FOUND AND QT4_FOUND AND OPENGL_FOUND AND QGLVIEWER_FOUND )
 	
   target_link_libraries( GudhUI ${QT_LIBRARIES} ${QGLVIEWER_LIBRARIES} )
   target_link_libraries( GudhUI ${OPENGL_gl_LIBRARY} ${OPENGL_glu_LIBRARY} )	
+if (TBB_FOUND)
+  target_link_libraries( GudhUI ${TBB_LIBRARIES})
+endif()
+
+###############################################################################
 
 else()
   message(STATUS "NOTICE: GudhUI requires CGAL, the QGLViewer, OpenGL and Qt4, and will not be compiled.")
diff --git a/src/GudhUI/gui/MenuEdgeContraction.ui b/src/GudhUI/gui/MenuEdgeContraction.ui
index da2e5c82..b1696431 100644
--- a/src/GudhUI/gui/MenuEdgeContraction.ui
+++ b/src/GudhUI/gui/MenuEdgeContraction.ui
@@ -1,118 +1,118 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<ui version="4.0">
- <class>MenuEdgeContraction</class>
- <widget class="QDialog" name="MenuEdgeContraction">
-  <property name="geometry">
-   <rect>
-    <x>0</x>
-    <y>0</y>
-    <width>362</width>
-    <height>209</height>
-   </rect>
-  </property>
-  <property name="windowTitle">
-   <string>Edge contraction</string>
-  </property>
-  <layout class="QGridLayout" name="gridLayout">
-   <item row="5" column="2">
-    <widget class="QSpinBox" name="spinBox_nb_remaining_vertices">
-     <property name="minimum">
-      <number>1</number>
-     </property>
-     <property name="maximum">
-      <number>999999999</number>
-     </property>
-     <property name="value">
-      <number>1</number>
-     </property>
-    </widget>
-   </item>
-   <item row="7" column="2">
-    <widget class="QCheckBox" name="checkBox_link_condition">
-     <property name="enabled">
-      <bool>false</bool>
-     </property>
-     <property name="text">
-      <string>Link condition</string>
-     </property>
-     <property name="checked">
-      <bool>true</bool>
-     </property>
-    </widget>
-   </item>
-   <item row="3" column="2" alignment="Qt::AlignRight">
-    <widget class="QLabel" name="txt_nb_collapses">
-     <property name="text">
-      <string>1</string>
-     </property>
-    </widget>
-   </item>
-   <item row="6" column="0">
-    <widget class="QLabel" name="label">
-     <property name="text">
-      <string>Policy</string>
-     </property>
-    </widget>
-   </item>
-   <item row="6" column="2">
-    <widget class="QComboBox" name="m_simplificationMethod">
-     <item>
-      <property name="text">
-       <string>Length_midpoint</string>
-      </property>
-     </item>
-    </widget>
-   </item>
-   <item row="2" column="2" alignment="Qt::AlignRight">
-    <widget class="QLabel" name="txt_nb_vertices">
-     <property name="text">
-      <string>0</string>
-     </property>
-    </widget>
-   </item>
-   <item row="2" column="0">
-    <widget class="QLabel" name="label_5">
-     <property name="text">
-      <string>Number of vertices</string>
-     </property>
-    </widget>
-   </item>
-   <item row="3" column="0" colspan="2">
-    <widget class="QLabel" name="label_3">
-     <property name="text">
-      <string>Number of contractions</string>
-     </property>
-    </widget>
-   </item>
-   <item row="5" column="0" colspan="2">
-    <widget class="QLabel" name="label_4">
-     <property name="text">
-      <string>Number of vertices after </string>
-     </property>
-    </widget>
-   </item>
-   <item row="1" column="0">
-    <widget class="QSlider" name="horizontalSlider">
-     <property name="minimum">
-      <number>0</number>
-     </property>
-     <property name="maximum">
-      <number>100</number>
-     </property>
-     <property name="orientation">
-      <enum>Qt::Horizontal</enum>
-     </property>
-    </widget>
-   </item>
-   <item row="1" column="2">
-    <widget class="QPushButton" name="pushButton_collapse">
-     <property name="text">
-      <string>Perform collapse</string>
-     </property>
-    </widget>
-   </item>
-  </layout>
- </widget>
- <resources/>
- <connections/>
-</ui>
+<?xml version="1.0" encoding="UTF-8"?>
+<ui version="4.0">
+ <class>MenuEdgeContraction</class>
+ <widget class="QDialog" name="MenuEdgeContraction">
+  <property name="geometry">
+   <rect>
+    <x>0</x>
+    <y>0</y>
+    <width>362</width>
+    <height>209</height>
+   </rect>
+  </property>
+  <property name="windowTitle">
+   <string>Edge contraction</string>
+  </property>
+  <layout class="QGridLayout" name="gridLayout">
+   <item row="5" column="2">
+    <widget class="QSpinBox" name="spinBox_nb_remaining_vertices">
+     <property name="minimum">
+      <number>1</number>
+     </property>
+     <property name="maximum">
+      <number>999999999</number>
+     </property>
+     <property name="value">
+      <number>1</number>
+     </property>
+    </widget>
+   </item>
+   <item row="7" column="2">
+    <widget class="QCheckBox" name="checkBox_link_condition">
+     <property name="enabled">
+      <bool>false</bool>
+     </property>
+     <property name="text">
+      <string>Link condition</string>
+     </property>
+     <property name="checked">
+      <bool>true</bool>
+     </property>
+    </widget>
+   </item>
+   <item row="3" column="2" alignment="Qt::AlignRight">
+    <widget class="QLabel" name="txt_nb_collapses">
+     <property name="text">
+      <string>1</string>
+     </property>
+    </widget>
+   </item>
+   <item row="6" column="0">
+    <widget class="QLabel" name="label">
+     <property name="text">
+      <string>Policy</string>
+     </property>
+    </widget>
+   </item>
+   <item row="6" column="2">
+    <widget class="QComboBox" name="m_simplificationMethod">
+     <item>
+      <property name="text">
+       <string>Length_midpoint</string>
+      </property>
+     </item>
+    </widget>
+   </item>
+   <item row="2" column="2" alignment="Qt::AlignRight">
+    <widget class="QLabel" name="txt_nb_vertices">
+     <property name="text">
+      <string>0</string>
+     </property>
+    </widget>
+   </item>
+   <item row="2" column="0">
+    <widget class="QLabel" name="label_5">
+     <property name="text">
+      <string>Number of vertices</string>
+     </property>
+    </widget>
+   </item>
+   <item row="3" column="0" colspan="2">
+    <widget class="QLabel" name="label_3">
+     <property name="text">
+      <string>Number of contractions</string>
+     </property>
+    </widget>
+   </item>
+   <item row="5" column="0" colspan="2">
+    <widget class="QLabel" name="label_4">
+     <property name="text">
+      <string>Number of vertices after </string>
+     </property>
+    </widget>
+   </item>
+   <item row="1" column="0">
+    <widget class="QSlider" name="horizontalSlider">
+     <property name="minimum">
+      <number>0</number>
+     </property>
+     <property name="maximum">
+      <number>100</number>
+     </property>
+     <property name="orientation">
+      <enum>Qt::Horizontal</enum>
+     </property>
+    </widget>
+   </item>
+   <item row="1" column="2">
+    <widget class="QPushButton" name="pushButton_collapse">
+     <property name="text">
+      <string>Perform collapse</string>
+     </property>
+    </widget>
+   </item>
+  </layout>
+ </widget>
+ <resources/>
+ <connections/>
+</ui>
diff --git a/src/GudhUI/gui/gudhui.cpp b/src/GudhUI/gui/gudhui.cpp
index 377cd2f2..276c4a5f 100644
--- a/src/GudhUI/gui/gudhui.cpp
+++ b/src/GudhUI/gui/gudhui.cpp
@@ -1,38 +1,38 @@
-/* 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):       David Salinas
- *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (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/>.
- * 
- */
-
-#include "MainWindow.h"
-#include <QApplication>
-#include <CGAL/Qt/resources.h>
-
-int main(int argc, char** argv) {
-  QApplication application(argc, argv);
-  application.setOrganizationDomain("inria.fr");
-  application.setOrganizationName("INRIA");
-  application.setApplicationName("GudhUI");
-
-  MainWindow mw;
-  application.setQuitOnLastWindowClosed(false);
-  mw.show();
-  return application.exec();
-}
+/* 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):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (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/>.
+ * 
+ */
+
+#include "MainWindow.h"
+#include <QApplication>
+#include <CGAL/Qt/resources.h>
+
+int main(int argc, char** argv) {
+  QApplication application(argc, argv);
+  application.setOrganizationDomain("inria.fr");
+  application.setOrganizationName("INRIA");
+  application.setApplicationName("GudhUI");
+
+  MainWindow mw;
+  application.setQuitOnLastWindowClosed(false);
+  mw.show();
+  return application.exec();
+}
diff --git a/src/GudhUI/model/Complex_typedefs.h b/src/GudhUI/model/Complex_typedefs.h
index c310d4a6..a4df2c94 100644
--- a/src/GudhUI/model/Complex_typedefs.h
+++ b/src/GudhUI/model/Complex_typedefs.h
@@ -41,7 +41,7 @@ struct Geometry_trait : public CGAL::Cartesian_d<double> {
 typedef Geometry_trait::Point Point;
 
 using namespace Gudhi;
-using namespace Gudhi::skbl;
+using namespace Gudhi::skeleton_blocker;
 
 typedef Skeleton_blocker_simple_geometric_traits<Geometry_trait> Complex_geometric_traits;
 typedef Skeleton_blocker_geometric_complex< Complex_geometric_traits > Complex;
diff --git a/src/GudhUI/model/Model.h b/src/GudhUI/model/Model.h
index 07a67a0c..77e37b6c 100644
--- a/src/GudhUI/model/Model.h
+++ b/src/GudhUI/model/Model.h
@@ -71,9 +71,9 @@ class CGAL_geometric_flag_complex_wrapper {
 
   void maximal_face(std::vector<int> vertices) {
     if (!load_only_points_) {
-      std::cout << "size:" << vertices.size() << std::endl;
-      for (int i = 0; i < vertices.size(); ++i)
-        for (int j = i + 1; j < vertices.size(); ++j)
+      // std::cout << "size:" << vertices.size() << std::endl;
+      for (std::size_t i = 0; i < vertices.size(); ++i)
+        for (std::size_t j = i + 1; j < vertices.size(); ++j)
           complex_.add_edge(Vertex_handle(vertices[i]), Vertex_handle(vertices[j]));
     }
   }
diff --git a/src/GudhUI/utils/Bar_code_persistence.h b/src/GudhUI/utils/Bar_code_persistence.h
new file mode 100644
index 00000000..b527d684
--- /dev/null
+++ b/src/GudhUI/utils/Bar_code_persistence.h
@@ -0,0 +1,90 @@
+#include <math.h>  // isfinite
+
+#include <QtGui/QApplication>
+
+#include <QGraphicsView>
+#include <QGraphicsScene>
+#include <QPointF>
+#include <QVector>
+#include <QGraphicsTextItem>
+
+#include <iostream>
+#include <vector>
+#include <limits>  // NaN, infinity
+#include <utility>  // for pair
+#include <string>
+
+#ifndef UTILS_BAR_CODE_PERSISTENCE_H_
+#define UTILS_BAR_CODE_PERSISTENCE_H_
+
+class Bar_code_persistence {
+ private:
+  typedef std::vector<std::pair<double, double>> Persistence;
+  Persistence persistence_vector;
+  double min_birth;
+  double max_death;
+
+ public:
+  Bar_code_persistence()
+      : min_birth(std::numeric_limits<double>::quiet_NaN()),
+      max_death(std::numeric_limits<double>::quiet_NaN()) { }
+
+  void insert(double birth, double death) {
+    persistence_vector.push_back(std::make_pair(birth, death));
+    if (std::isfinite(birth)) {
+      if ((birth < min_birth) || (std::isnan(min_birth)))
+        min_birth = birth;
+      if ((birth > max_death) || (std::isnan(max_death)))
+        max_death = birth;
+    }
+    if (std::isfinite(death))
+      if ((death > max_death) || (std::isnan(max_death)))
+        max_death = death;
+  }
+
+  void show(const std::string& window_title) {
+    // Create a view, put a scene in it
+    QGraphicsView * view = new QGraphicsView();
+    QGraphicsScene * scene = new QGraphicsScene();
+    view->setScene(scene);
+    double ratio = 600.0 / (max_death - min_birth);
+    // std::cout << "min_birth=" << min_birth << " - max_death=" << max_death << " - ratio=" << ratio << std::endl;
+
+    double height = 0.0, birth = 0.0, death = 0.0;
+    int pers_num = 1;
+    for (auto& persistence : persistence_vector) {
+      height = 5.0 * pers_num;
+      // std::cout << "[" << pers_num << "] birth=" << persistence.first << " - death=" << persistence.second << std::endl;
+      if (std::isfinite(persistence.first))
+        birth = ((persistence.first - min_birth) * ratio) + 50.0;
+      else
+        birth = 0.0;
+
+      if (std::isfinite(persistence.second))
+        death = ((persistence.second - min_birth) * ratio) + 50.0;
+      else
+        death = 700.0;
+
+      scene->addLine(birth, height, death, height, QPen(Qt::blue, 2));
+      pers_num++;
+    }
+    height += 10.0;
+    // scale line
+    scene->addLine(0, height, 700.0, height, QPen(Qt::black, 1));
+    int modulo = 0;
+    for (double scale = 50.0; scale < 700.0; scale += 50.0) {
+      modulo++;
+      // scale small dash
+      scene->addLine(scale, height - 3.0, scale, height + 3.0, QPen(Qt::black, 1));
+      // scale text
+      QString scale_value = QString::number(((scale - 50.0) / ratio) + min_birth);
+      QGraphicsTextItem* dimText = scene->addText(scale_value, QFont("Helvetica", 8));
+      dimText->setPos(scale - (3.0 * scale_value.size()), height + 9.0 * (modulo % 2));
+    }
+    view->setWindowTitle(window_title.c_str());
+    // Show the view
+    view->show();
+  }
+};
+
+#endif  // UTILS_BAR_CODE_PERSISTENCE_H_
diff --git a/src/GudhUI/utils/Edge_contractor.h b/src/GudhUI/utils/Edge_contractor.h
index 45079a40..8a29ff4b 100644
--- a/src/GudhUI/utils/Edge_contractor.h
+++ b/src/GudhUI/utils/Edge_contractor.h
@@ -65,7 +65,7 @@ template<typename SkBlComplex> class Edge_contractor {
 
     Placement_type operator()(const EdgeProfile& profile) const override {
       std::vector<double> mid_coords(profile.p0().dimension(), 0);
-      for (size_t i = 0; i < profile.p0().dimension(); ++i) {
+      for (int i = 0; i < profile.p0().dimension(); ++i) {
         mid_coords[i] = (profile.p0()[i] + profile.p1()[i]) / 2.;
       }
       return Point(profile.p0().dimension(), mid_coords.begin(), mid_coords.end());
diff --git a/src/GudhUI/utils/Furthest_point_epsilon_net.h b/src/GudhUI/utils/Furthest_point_epsilon_net.h
index f2a216f6..98346daa 100644
--- a/src/GudhUI/utils/Furthest_point_epsilon_net.h
+++ b/src/GudhUI/utils/Furthest_point_epsilon_net.h
@@ -73,7 +73,7 @@ template<typename SkBlComplex> class Furthest_point_epsilon_net {
       complex_(complex) {
     if (!complex.empty()) {
       init_filtration();
-      for (int k = 2; k < net_filtration_.size(); ++k) {
+      for (std::size_t k = 2; k < net_filtration_.size(); ++k) {
         update_radius_value(k);
       }
     }
diff --git a/src/GudhUI/utils/Persistence_compute.h b/src/GudhUI/utils/Persistence_compute.h
index 0b9961d3..97165490 100644
--- a/src/GudhUI/utils/Persistence_compute.h
+++ b/src/GudhUI/utils/Persistence_compute.h
@@ -46,10 +46,6 @@ struct Persistence_params {
  * Show persistence into output stream
  */
 template<typename SkBlComplex> class Persistence_compute {
- private:
-  SkBlComplex& complex_;
-  std::ostream& stream_;
-
  public:
   typedef typename SkBlComplex::Vertex_handle Vertex_handle;
   typedef typename SkBlComplex::Edge_handle Edge_handle;
@@ -61,9 +57,7 @@ template<typename SkBlComplex> class Persistence_compute {
    * double threshold
    * int p for coefficient Z_p
    */
-  Persistence_compute(SkBlComplex& complex, std::ostream& stream, const Persistence_params& params) :
-      // double threshold = 0.5,unsigned dim_max = 8):
-      complex_(complex), stream_(stream) {
+  Persistence_compute(SkBlComplex& complex, std::ostream& stream, const Persistence_params& params) {
     // for now everything is copied, todo boost adapt iterators to points of SkBlComplex instead of copying to an
     // initial vector
     typedef std::vector<double> Point_t;
@@ -87,10 +81,10 @@ template<typename SkBlComplex> class Persistence_compute {
     pcoh.init_coefficients(params.p);
     // put params.min_pers
     pcoh.compute_persistent_cohomology(params.min_pers);
-    stream_ << "persistence: \n";
-    stream_ << "p dimension birth death: \n";
+    stream << "persistence: \n";
+    stream << "p dimension birth death: \n";
 
-    pcoh.output_diagram(stream_);
+    pcoh.output_diagram(stream);
   }
 };
 
diff --git a/src/GudhUI/view/FirstCoordProjector.h b/src/GudhUI/view/FirstCoordProjector.h
index 529d2d42..1333f5d3 100644
--- a/src/GudhUI/view/FirstCoordProjector.h
+++ b/src/GudhUI/view/FirstCoordProjector.h
@@ -32,8 +32,12 @@ class FirstCoordProjector3D : public Projector3D {
   typedef Projector3D::Point_3 Point_3;
 
   Point_3 operator()(const Point& p) const {
-    assert(p.dimension() >= 3);
-    return Point_3(p.x(), p.y(), p.z());
+    if (p.dimension() >= 3)
+      return Point_3(p.x(), p.y(), p.z());
+    else if  (p.dimension() >= 2)
+      return Point_3(p.x(), p.y(), 0.0);
+    else
+      return Point_3(0.0, 0.0, 0.0);
   }
 };
 
diff --git a/src/GudhUI/view/Viewer.h b/src/GudhUI/view/Viewer.h
index 276ccd3c..319c8e04 100644
--- a/src/GudhUI/view/Viewer.h
+++ b/src/GudhUI/view/Viewer.h
@@ -1,120 +1,120 @@
-/* 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):       David Salinas
- *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (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 VIEW_VIEWER_H_
-#define VIEW_VIEWER_H_
-
-// Workaround for moc-qt4 not parsing boost headers
-#include <CGAL/config.h>
-
-#include <QGLViewer/qglviewer.h>
-
-#include <vector>
-
-#include "View_parameter.h"
-#include "model/Complex_typedefs.h"
-#include "Color.h"
-#include "Viewer_instructor.h"
-
-class Viewer_instructor;
-
-class Viewer : public QGLViewer {
-  Q_OBJECT
-
-  Viewer_instructor * instructor;
-
-  /**
-   * light angles
-   */
-  double theta, phi;
-  typedef Complex::GT Gudhi_kernel;
-  typedef Gudhi_kernel::Point_3 Point_3;
-
- public:
-  Viewer(QWidget* parent);
-
-  void set_instructor(Viewer_instructor* instructor_);
-
-  void show_entire_scene();
-
-  void draw();
-
-  void set_bounding_box(const Point_3 & lower_left, const Point_3 & upper_right);
-
-  void update_GL();
-
-  void init_scene();
-
-  void init_light();
-
-  void set_light();
-
-  void set_light_direction(double theta, double phi);
-
-  /**
-   * set the light in the direction of the observer
-   */
-  void set_light_direction();
-
- protected:
-  virtual void postSelection(const QPoint& point);
-
- public:
-  ////////////////////////
-  // draw
-  ////////////////////////
-  void set_size_point(double size_points);
-
-  void set_color(const Color& color);
-
-  void draw_point(const Point_3& p, const Color& color, double size_points);
-
-  void begin_draw_points(double size, bool light = false);
-
-  void draw_points(const Point_3 & point);
-
-  void end_draw_points();
-
-  void draw_edge(const Point_3 &a, const Point_3 &b, const Color& color, double size);
-
-  void begin_draw_edges(double size, bool light = false);
-
-  void draw_edges(const Point_3 &a, const Point_3 &b);
-
-  void end_draw_edges();
-
-  void begin_draw_triangles(double size, bool light, bool transparent = false);
-
-  void draw_triangles(const Point_3& p1, const Point_3& p2, const Point_3& p3);
-
-  // todo remove
-  void draw_triangles(const std::vector<Point_3*>& points);
-
-  void end_draw_triangles();
-
-
- signals:
-  void click(const Point_3& position);
-};
-
-#endif  // VIEW_VIEWER_H_
+/* 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):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (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 VIEW_VIEWER_H_
+#define VIEW_VIEWER_H_
+
+// Workaround for moc-qt4 not parsing boost headers
+#include <CGAL/config.h>
+
+#include <QGLViewer/qglviewer.h>
+
+#include <vector>
+
+#include "View_parameter.h"
+#include "model/Complex_typedefs.h"
+#include "Color.h"
+#include "Viewer_instructor.h"
+
+class Viewer_instructor;
+
+class Viewer : public QGLViewer {
+  Q_OBJECT
+
+  Viewer_instructor * instructor;
+
+  /**
+   * light angles
+   */
+  double theta, phi;
+  typedef Complex::GT Gudhi_kernel;
+  typedef Gudhi_kernel::Point_3 Point_3;
+
+ public:
+  Viewer(QWidget* parent);
+
+  void set_instructor(Viewer_instructor* instructor_);
+
+  void show_entire_scene();
+
+  void draw();
+
+  void set_bounding_box(const Point_3 & lower_left, const Point_3 & upper_right);
+
+  void update_GL();
+
+  void init_scene();
+
+  void init_light();
+
+  void set_light();
+
+  void set_light_direction(double theta, double phi);
+
+  /**
+   * set the light in the direction of the observer
+   */
+  void set_light_direction();
+
+ protected:
+  virtual void postSelection(const QPoint& point);
+
+ public:
+  ////////////////////////
+  // draw
+  ////////////////////////
+  void set_size_point(double size_points);
+
+  void set_color(const Color& color);
+
+  void draw_point(const Point_3& p, const Color& color, double size_points);
+
+  void begin_draw_points(double size, bool light = false);
+
+  void draw_points(const Point_3 & point);
+
+  void end_draw_points();
+
+  void draw_edge(const Point_3 &a, const Point_3 &b, const Color& color, double size);
+
+  void begin_draw_edges(double size, bool light = false);
+
+  void draw_edges(const Point_3 &a, const Point_3 &b);
+
+  void end_draw_edges();
+
+  void begin_draw_triangles(double size, bool light, bool transparent = false);
+
+  void draw_triangles(const Point_3& p1, const Point_3& p2, const Point_3& p3);
+
+  // todo remove
+  void draw_triangles(const std::vector<Point_3*>& points);
+
+  void end_draw_triangles();
+
+
+ signals:
+  void click(const Point_3& position);
+};
+
+#endif  // VIEW_VIEWER_H_
diff --git a/src/GudhUI/view/Viewer_instructor.h b/src/GudhUI/view/Viewer_instructor.h
index 82c8e346..1da28009 100644
--- a/src/GudhUI/view/Viewer_instructor.h
+++ b/src/GudhUI/view/Viewer_instructor.h
@@ -1,117 +1,117 @@
-/* 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):       David Salinas
- *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (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 VIEW_VIEWER_INSTRUCTOR_H_
-#define VIEW_VIEWER_INSTRUCTOR_H_
-
-// todo do a viewer instructor that have directely a pointer to a QGLviewer and buffer ot not triangles
-
-// Workaround for moc-qt4 not parsing boost headers
-#include <CGAL/config.h>
-
-#include <QFileDialog>
-#include <QKeyEvent>
-#include <QGLViewer/camera.h>
-
-#include <memory>
-#include <utility>  // for pair<>
-
-#include "model/Complex_typedefs.h"
-
-#include "Projector3D.h"
-#include "View_parameter.h"
-#include "Viewer.h"
-
-class Viewer;
-class Viewer_parameter;
-
-class Viewer_instructor : public QWidget {
-  Q_OBJECT
-
-  typedef Geometry_trait::Point_3 Point_3;
-  typedef Complex::Point Point;
-  typedef Complex::Vertex_handle Vertex_handle;
-  typedef Complex::Edge_handle Edge_handle;
-  typedef Complex::Simplex Simplex;
-
-  Viewer* viewer_;
-  View_parameter view_params_;
-  const Complex& mesh_;
-  std::unique_ptr<Projector3D> projector_;
-
- public:
-  Viewer_instructor(QWidget* parent, Viewer* viewer, const Complex& mesh);
-
-  void initialize_bounding_box();
-
-  std::pair<Point, Point> compute_bounding_box_corners();
-
-  void show_entire_scene();
-
-  const qglviewer::Camera* camera() const;
-
-  int width() const;
-  int height() const;
-
-  /**
-   * to change display parameters
-   */
-  View_parameter& view_params();
-
- public:
-  /**
-   * gives instructions to the viewer
-   */
-  void give_instructions();
-
-  void draw_edges();
-  void draw_triangles();
-  void draw_points();
-
-  void draw_edge(const Point&, const Point&);
-
-  void draw_point(const Point&);
-
-  /**
-   * set the right color of vertex/edge/triangle considering the view_params choice
-   */
-  void set_color_vertex(Vertex_handle vh);
-  void set_color_edge(Edge_handle eh);
-
-  void set_color_triangle(const Simplex& triangle);
-
- private:
-  /**
-   * Projection to 3D needed for the viewer.
-   */
-  Point_3 proj(const Point& p) const;
-
- public slots:
-  void sceneChanged();
-  void change_draw_vertices();
-  void change_draw_edges();
-  void change_draw_triangles();
-  void change_light();
-};
-
-#endif  // VIEW_VIEWER_INSTRUCTOR_H_
+/* 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):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (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 VIEW_VIEWER_INSTRUCTOR_H_
+#define VIEW_VIEWER_INSTRUCTOR_H_
+
+// todo do a viewer instructor that have directely a pointer to a QGLviewer and buffer ot not triangles
+
+// Workaround for moc-qt4 not parsing boost headers
+#include <CGAL/config.h>
+
+#include <QFileDialog>
+#include <QKeyEvent>
+#include <QGLViewer/camera.h>
+
+#include <memory>
+#include <utility>  // for pair<>
+
+#include "model/Complex_typedefs.h"
+
+#include "Projector3D.h"
+#include "View_parameter.h"
+#include "Viewer.h"
+
+class Viewer;
+class Viewer_parameter;
+
+class Viewer_instructor : public QWidget {
+  Q_OBJECT
+
+  typedef Geometry_trait::Point_3 Point_3;
+  typedef Complex::Point Point;
+  typedef Complex::Vertex_handle Vertex_handle;
+  typedef Complex::Edge_handle Edge_handle;
+  typedef Complex::Simplex Simplex;
+
+  Viewer* viewer_;
+  View_parameter view_params_;
+  const Complex& mesh_;
+  std::unique_ptr<Projector3D> projector_;
+
+ public:
+  Viewer_instructor(QWidget* parent, Viewer* viewer, const Complex& mesh);
+
+  void initialize_bounding_box();
+
+  std::pair<Point, Point> compute_bounding_box_corners();
+
+  void show_entire_scene();
+
+  const qglviewer::Camera* camera() const;
+
+  int width() const;
+  int height() const;
+
+  /**
+   * to change display parameters
+   */
+  View_parameter& view_params();
+
+ public:
+  /**
+   * gives instructions to the viewer
+   */
+  void give_instructions();
+
+  void draw_edges();
+  void draw_triangles();
+  void draw_points();
+
+  void draw_edge(const Point&, const Point&);
+
+  void draw_point(const Point&);
+
+  /**
+   * set the right color of vertex/edge/triangle considering the view_params choice
+   */
+  void set_color_vertex(Vertex_handle vh);
+  void set_color_edge(Edge_handle eh);
+
+  void set_color_triangle(const Simplex& triangle);
+
+ private:
+  /**
+   * Projection to 3D needed for the viewer.
+   */
+  Point_3 proj(const Point& p) const;
+
+ public slots:
+  void sceneChanged();
+  void change_draw_vertices();
+  void change_draw_edges();
+  void change_draw_triangles();
+  void change_light();
+};
+
+#endif  // VIEW_VIEWER_INSTRUCTOR_H_
diff --git a/src/Persistent_cohomology/concept/FilteredComplex.h b/src/Persistent_cohomology/concept/FilteredComplex.h
index e124d524..c19698df 100644
--- a/src/Persistent_cohomology/concept/FilteredComplex.h
+++ b/src/Persistent_cohomology/concept/FilteredComplex.h
@@ -43,7 +43,7 @@ struct FilteredComplex
   * is model of IndexingTag. */
   typedef unspecified      Indexing_tag;
 
-/** Returns a Simplex_hanlde that is different from all simplex handles 
+/** Returns a Simplex_handle that is different from all simplex handles 
   * of the simplices. */
   Simplex_handle           null_simplex();
 /** \brief Returns the number of simplices in the complex.
@@ -61,12 +61,13 @@ struct FilteredComplex
 /** \brief Returns a key that is different from the keys associated 
   * to the simplices. */
   Simplex_key              null_key ();
-/** \brief Returns the key associated to a simplex. */  
+/** \brief Returns the key associated to a simplex.
+ *
+ * This is never called on null_simplex(). */
   Simplex_key              key      ( Simplex_handle sh );
-/** \brief Returns the simplex associated to a key.
-  *
-  * If key is different from null_key(), returns the simplex that
-  * has index idx in the filtration. */
+/** \brief Returns the simplex that has index idx in the filtration.
+ *
+ * This is never called on null_key(). */
   Simplex_handle           simplex  ( Simplex_key idx );
 /** \brief Assign a key to a simplex. */
   void                     assign_key(Simplex_handle sh, Simplex_key key);
@@ -138,6 +139,6 @@ Filtration_simplex_range filtration_simplex_range();
 * @todo use an enum? Just a bool?
 */
 //int is_before_in_filtration(Simplex_handle s, Simplex_handle t);
-/*************************************************/     
+/*************************************************/
 
 };
diff --git a/src/Persistent_cohomology/doc/3DTorus_poch.png b/src/Persistent_cohomology/doc/3DTorus_poch.png
new file mode 100644
index 00000000..1c9d8328
--- /dev/null
+++ b/src/Persistent_cohomology/doc/3DTorus_poch.png
diff --git a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h
new file mode 100644
index 00000000..433cfd3e
--- /dev/null
+++ b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h
@@ -0,0 +1,206 @@
+/*    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):       Clément Maria
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (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 DOC_PERSISTENT_COHOMOLOGY_INTRO_PERSISTENT_COHOMOLOGY_H_
+#define DOC_PERSISTENT_COHOMOLOGY_INTRO_PERSISTENT_COHOMOLOGY_H_
+
+// needs namespace for Doxygen to link on classes
+namespace Gudhi {
+// needs namespace for Doxygen to link on classes
+namespace persistent_cohomology {
+
+/** \defgroup persistent_cohomology Persistent Cohomology
+
+  \author    Clément Maria
+
+  Computation of persistent cohomology using the algorithm of 
+  \cite DBLP:journals/dcg/SilvaMV11 and \cite DBLP:journals/corr/abs-1208-5018 
+  and the Compressed Annotation Matrix 
+  implementation of \cite DBLP:conf/esa/BoissonnatDM13 
+       
+  The theory of homology consists in attaching to a topological space a sequence of 
+  (homology) groups, 
+  capturing global topological features 
+  like connected components, holes, cavities, etc. Persistent homology studies the evolution 
+  -- birth, life and death -- of 
+  these features when the topological space is changing. Consequently, the theory is essentially 
+  composed of three elements: 
+  topological spaces, their homology groups and an evolution scheme.
+
+ \section persistencetopolocalspaces Topological Spaces
+ Topological spaces are represented by simplicial complexes.
+ Let \f$V = \{1, \cdots ,|V|\}\f$ be a set of <EM>vertices</EM>.
+ A <EM>simplex</EM> \f$\sigma\f$ is a subset of vertices
+ \f$\sigma \subseteq V\f$. A <EM>simplicial complex</EM> \f$\mathbf{K}\f$
+ on \f$V\f$ is a collection of simplices \f$\{\sigma\}\f$,
+ \f$\sigma \subseteq V\f$, such that \f$\tau \subseteq \sigma \in \mathbf{K}
+ \Rightarrow \tau \in \mathbf{K}\f$. The dimension \f$n=|\sigma|-1\f$ of \f$\sigma\f$
+ is its number of elements minus 1. A <EM>filtration</EM> of a simplicial complex is
+ a function \f$f:\mathbf{K} \rightarrow \mathbb{R}\f$ satisfying \f$f(\tau)\leq
+ f(\sigma)\f$ whenever \f$\tau \subseteq \sigma\f$.
+
+ We define the concept FilteredComplex which enumerates the requirements for a class
+ to represent a filtered complex from which persistent homology may be computed.
+ We use the vocabulary of simplicial complexes, but the concept
+ is valid for any type of cell complex. The main requirements
+ are the definition of:
+ \li type <CODE>Indexing_tag</CODE>, which is a model of the concept
+ <CODE>IndexingTag</CODE>,
+ describing the nature of the indexing scheme,
+ \li type Simplex_handle to manipulate simplices,
+ \li method <CODE>int dimension(Simplex_handle)</CODE> returning
+ the dimension of a simplex,
+ \li type and method <CODE>Boundary_simplex_range
+ boundary_simplex_range(Simplex_handle)</CODE> that returns
+ a range giving access to the codimension 1 subsimplices of the
+ input simplex, as-well-as the coefficients \f$(-1)^i\f$ in the
+ definition of the operator \f$\partial\f$. The iterators have
+ value type <CODE>Simplex_handle</CODE>,
+ \li type and method
+ <CODE>Filtration_simplex_range filtration_simplex_range ()</CODE>
+ that returns a range giving
+ access to all the simplices of the complex read in the order
+ assigned by the indexing scheme,
+ \li type and method
+ <CODE>Filtration_value filtration (Simplex_handle)</CODE> that returns the value of
+ the filtration on the simplex represented by the handle.
+
+ \section persistencehomology Homology
+ For a ring \f$\mathcal{R}\f$, the group of <EM>n-chains</EM>,
+ denoted \f$\mathbf{C}_n(\mathbf{K},\mathcal{R})\f$, of \f$\mathbf{K}\f$ is the
+ group of formal sums of
+ n-simplices with \f$\mathcal{R}\f$ coefficients. The <EM>boundary operator</EM> is a
+ linear operator
+ \f$\partial_n: \mathbf{C}_n(\mathbf{K},\mathcal{R}) \rightarrow \mathbf{C}_{n-1}(\mathbf{K},\mathcal{R})\f$
+ such that \f$\partial_n \sigma = \partial_n [v_0, \cdots , v_n] =
+ \sum_{i=0}^n (-1)^{i}[v_0,\cdots ,\widehat{v_i}, \cdots,v_n]\f$,
+ where \f$\widehat{v_i}\f$ means \f$v_i\f$ is omitted from the list. The chain
+ groups form a sequence:
+
+ \f[\cdots \ \ \mathbf{C}_n(\mathbf{K},\mathcal{R}) \xrightarrow{\ \partial_n\ } \mathbf{C}_{n-1}(\mathbf{K},\mathcal{R})
+ \xrightarrow{\partial_{n-1}} \cdots \xrightarrow{\ \partial_2 \ }
+ \mathbf{C}_1(\mathbf{K},\mathcal{R}) \xrightarrow{\ \partial_1 \ }  \mathbf{C}_0(\mathbf{K},\mathcal{R}) \f]
+
+ of finitely many groups \f$\mathbf{C}_n(\mathbf{K},\mathcal{R})\f$ and homomorphisms
+ \f$\partial_n\f$, indexed by the dimension \f$n \geq 0\f$.
+ The boundary operators satisfy the property \f$\partial_n \circ \partial_{n+1}=0\f$
+ for every \f$n > 0\f$
+ and we define the homology groups:
+
+ \f[\mathbf{H}_n(\mathbf{K},\mathcal{R}) = \ker \partial_n / \mathrm{im} \  \partial_{n+1}\f]
+
+ We refer to \cite Munkres-elementsalgtop1984 for an introduction to homology
+ theory and to \cite DBLP:books/daglib/0025666 for an introduction to persistent homology.
+
+ \section persistenceindexingscheme Indexing Scheme
+ "Changing" a simplicial complex consists in applying a simplicial map.
+ An <EM>indexing scheme</EM> is a directed graph together with a traversal
+ order, such that two
+ consecutive nodes in the graph are connected by an arrow (either forward or backward).
+ The nodes represent simplicial complexes and the directed edges simplicial maps.
+
+ From the computational point of view, there are two types of indexing schemes of
+ interest
+ in persistent homology: <EM>linear</EM> ones
+ \f$\bullet \longrightarrow \bullet \longrightarrow \cdots \longrightarrow \bullet
+ \longrightarrow \bullet\f$
+ in persistent homology \cite DBLP:journals/dcg/ZomorodianC05 ,
+ and <EM>zigzag</EM> ones
+ \f$\bullet \longrightarrow \bullet \longleftarrow \cdots
+ \longrightarrow \bullet
+ \longleftarrow \bullet \f$ in zigzag persistent
+ homology \cite DBLP:journals/focm/CarlssonS10.
+ These indexing schemes have a natural left-to-right traversal order, and we
+ describe them with ranges and iterators.
+ In the current release of the Gudhi library, only the linear case is implemented.
+
+ In the following, we consider the case where the indexing scheme is induced
+ by a filtration.
+ Ordering the simplices
+ by increasing filtration values (breaking ties so as a simplex appears after
+ its subsimplices of same filtration value) provides an indexing scheme.
+
+\section pcohexamples Examples
+
+We provide several example files: run these examples with -h for details on their use, and read the README file.
+
+\li <a href="_persistent_cohomology_2rips_persistence_8cpp-example.html">
+Persistent_cohomology/rips_persistence.cpp</a> computes the Rips complex of a point cloud and its persistence diagram.
+
+\li <a href="_persistent_cohomology_2rips_multifield_persistence_8cpp-example.html">
+Persistent_cohomology/rips_multifield_persistence.cpp</a> computes the Rips complex of a point cloud and its
+persistence diagram with a family of field coefficients.
+
+\li <a href="_persistent_cohomology_2performance_rips_persistence_8cpp-example.html">
+Persistent_cohomology/performance_rips_persistence.cpp</a> provides timings for the construction of the Rips complex
+on a set of points sampling a Klein bottle in \f$\mathbb{R}^5\f$ with a simplex tree, its conversion to a 
+Hasse diagram and the computation of persistent homology and multi-field persistent homology for the 
+different representations.
+
+\li <a href="_persistent_cohomology_2alpha_complex_3d_persistence_8cpp-example.html">
+Persistent_cohomology/alpha_complex_3d_persistence.cpp</a> computes the persistent homology with
+\f$\mathbb{Z}/2\mathbb{Z}\f$ coefficients of the alpha complex on points sampling from an OFF file.
+\code $> ./alpha_complex_3d_persistence ../../data/points/tore3D_300.off 2 0.45 \endcode
+\code Simplex_tree dim: 3
+2  0 0 inf 
+2  1 0.0682162 1.0001 
+2  1 0.0934117 1.00003 
+2  2 0.56444 1.03938 \endcode
+
+\li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html">
+Persistent_cohomology/alpha_complex_persistence.cpp</a> computes the persistent homology with
+\f$\mathbb{Z}/p\mathbb{Z}\f$ coefficients of the alpha complex on points sampling from an OFF file.
+\code $> ./alpha_complex_persistence -r 32 -p 2 -m 0.45 ../../data/points/tore3D_300.off \endcode
+\code Alpha complex is of dimension 3 - 9273 simplices - 300 vertices.
+Simplex_tree dim: 3
+2  0 0 inf 
+2  1 0.0682162 1.0001 
+2  1 0.0934117 1.00003 
+2  2 0.56444 1.03938 \endcode
+
+\li <a href="_persistent_cohomology_2periodic_alpha_complex_3d_persistence_8cpp-example.html">
+Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp</a> computes the persistent homology with
+\f$\mathbb{Z}/2\mathbb{Z}\f$ coefficients of the periodic alpha complex on points sampling from an OFF file.
+\code $> ./periodic_alpha_complex_3d_persistence ../../data/points/grid_10_10_10_in_0_1.off 3 1.0 \endcode
+\code Periodic Delaunay computed.
+Simplex_tree dim: 3
+3  0 0 inf 
+3  1 0.0025 inf 
+3  1 0.0025 inf 
+3  1 0.0025 inf 
+3  2 0.005 inf 
+3  2 0.005 inf 
+3  2 0.005 inf 
+3  3 0.0075 inf \endcode
+
+\li <a href="_persistent_cohomology_2plain_homology_8cpp-example.html">
+Persistent_cohomology/plain_homology.cpp</a> computes the plain homology of a simple simplicial complex without
+filtration values.
+
+ \copyright GNU General Public License v3.
+ */
+
+}  // namespace persistent_cohomology
+
+}  // namespace Gudhi
+
+#endif  // DOC_PERSISTENT_COHOMOLOGY_INTRO_PERSISTENT_COHOMOLOGY_H_
diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt
index 772193c4..96d3e73a 100644
--- a/src/Persistent_cohomology/example/CMakeLists.txt
+++ b/src/Persistent_cohomology/example/CMakeLists.txt
@@ -1,5 +1,5 @@
 cmake_minimum_required(VERSION 2.6)
-project(GUDHIExPersCohom)
+project(Persistent_cohomology_examples)
 
 # problem with Visual Studio link on Boost program_options
 add_definitions( -DBOOST_ALL_NO_LIB )
@@ -7,63 +7,79 @@ add_definitions( -DBOOST_ALL_DYN_LINK )
 
 add_executable(plain_homology plain_homology.cpp)
 target_link_libraries(plain_homology ${Boost_SYSTEM_LIBRARY})
-add_test(plain_homology ${CMAKE_CURRENT_BINARY_DIR}/plain_homology)
 
 add_executable(persistence_from_simple_simplex_tree persistence_from_simple_simplex_tree.cpp)
 target_link_libraries(persistence_from_simple_simplex_tree ${Boost_SYSTEM_LIBRARY})
-add_test(persistence_from_simple_simplex_tree ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_simple_simplex_tree 1 0)
 
 add_executable(rips_persistence rips_persistence.cpp)
 target_link_libraries(rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
-   
-add_test(rips_persistence_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.2 -d 3 -p 3 -m 100)
-   
-add_executable(parallel_rips_persistence parallel_rips_persistence.cpp)
-target_link_libraries(parallel_rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
-   
-add_test(parallel_rips_persistence_3 ${CMAKE_CURRENT_BINARY_DIR}/parallel_rips_persistence ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.txt -r 0.3 -d 3 -p 3 -m 100)
-   
+
+add_executable(rips_persistence_via_boundary_matrix rips_persistence_via_boundary_matrix.cpp)
+target_link_libraries(rips_persistence_via_boundary_matrix ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
+
 add_executable(persistence_from_file persistence_from_file.cpp)
 target_link_libraries(persistence_from_file ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
+
+if (TBB_FOUND)
+  target_link_libraries(plain_homology ${TBB_LIBRARIES})
+  target_link_libraries(persistence_from_simple_simplex_tree ${TBB_LIBRARIES})
+  target_link_libraries(rips_persistence ${TBB_LIBRARIES})
+  target_link_libraries(rips_persistence_via_boundary_matrix ${TBB_LIBRARIES})
+  target_link_libraries(persistence_from_file ${TBB_LIBRARIES})
+endif()
+
+add_test(plain_homology ${CMAKE_CURRENT_BINARY_DIR}/plain_homology)
+add_test(persistence_from_simple_simplex_tree ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_simple_simplex_tree 1 0)
+add_test(rips_persistence_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.2 -d 3 -p 3 -m 100)
+add_test(rips_persistence_via_boundary_matrix_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence_via_boundary_matrix ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.txt -r 0.3 -d 3 -p 3 -m 100)
 add_test(persistence_from_file_3_2_0 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.st -p 2 -m 0)
 add_test(persistence_from_file_3_3_100 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.st -p 3 -m 100)
    
-if(GMPXX_FOUND AND GMP_FOUND)
-   message("GMPXX_LIBRARIES = ${GMPXX_LIBRARIES}")
-   message("GMP_LIBRARIES = ${GMP_LIBRARIES}")
+if(GMP_FOUND)
+   if(GMPXX_FOUND)
+      add_executable(rips_multifield_persistence rips_multifield_persistence.cpp )
+      target_link_libraries(rips_multifield_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
+      add_executable ( performance_rips_persistence performance_rips_persistence.cpp )
+      target_link_libraries(performance_rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
+      if (TBB_FOUND)
+        target_link_libraries(rips_multifield_persistence ${TBB_LIBRARIES})
+        target_link_libraries(performance_rips_persistence ${TBB_LIBRARIES})
+      endif(TBB_FOUND)
    message("CGAL_LIBRARY = ${CGAL_LIBRARY}")
 
-   add_executable(rips_multifield_persistence rips_multifield_persistence.cpp )
-   target_link_libraries(rips_multifield_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
    add_test(rips_multifield_persistence_2_71 ${CMAKE_CURRENT_BINARY_DIR}/rips_multifield_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.2 -d 3 -p 2 -q 71 -m 100)
+   endif(GMPXX_FOUND)
+endif(GMP_FOUND)
 
-   add_executable ( performance_rips_persistence performance_rips_persistence.cpp )
-   target_link_libraries(performance_rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
-
-   if(CGAL_FOUND)
-    include( ${CGAL_USE_FILE} )
-     # In CMakeLists.txt, when include(${CGAL_USE_FILE}), CXX_FLAGS are overwritten.
-     # cf. http://doc.cgal.org/latest/Manual/installation.html#title40
-     # A workaround is to add "-std=c++11" again.
-     # A fix would be to use https://cmake.org/cmake/help/v3.1/prop_gbl/CMAKE_CXX_KNOWN_FEATURES.html
-     # or even better https://cmake.org/cmake/help/v3.1/variable/CMAKE_CXX_STANDARD.html
-     # but it implies to use cmake version 3.1 at least.
-     if(NOT MSVC)
-       include(CheckCXXCompilerFlag)
-       CHECK_CXX_COMPILER_FLAG(-std=c++11 COMPILER_SUPPORTS_CXX11)
-       if(COMPILER_SUPPORTS_CXX11)
-        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
-      endif()
-     endif()
-     # - End of workaround
-     if (CMAKE_BUILD_TYPE MATCHES Debug)
-       # For programs to be more verbose
-       add_definitions(-DDEBUG_TRACES)
-     endif()
-     add_executable(alpha_shapes_persistence alpha_shapes_persistence.cpp)
-     target_link_libraries(alpha_shapes_persistence ${Boost_SYSTEM_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES} ${CGAL_LIBRARY})
-     add_test(alpha_shapes_persistence_2_0_5 ${CMAKE_CURRENT_BINARY_DIR}/alpha_shapes_persistence ${CMAKE_SOURCE_DIR}/data/points/bunny_5000 2 0.5)
-     #add_test(alpha_shapes_persistence_3_3_100 ${CMAKE_CURRENT_BINARY_DIR}/alpha_shapes_persistence ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.st -p 3 -m 100)
-   endif()
-   
-endif()
+if(CGAL_FOUND)
+  add_executable(alpha_complex_3d_persistence alpha_complex_3d_persistence.cpp)
+  target_link_libraries(alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+
+  if (TBB_FOUND)
+    target_link_libraries(alpha_complex_3d_persistence ${TBB_LIBRARIES})
+  endif(TBB_FOUND)
+  add_test(alpha_complex_3d_persistence_2_0_5 ${CMAKE_CURRENT_BINARY_DIR}/alpha_complex_3d_persistence ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off 2 0.45)
+
+
+  if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
+    if (EIGEN3_FOUND)
+      add_executable (alpha_complex_persistence alpha_complex_persistence.cpp)
+      target_link_libraries(alpha_complex_persistence  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
+
+      add_executable(periodic_alpha_complex_3d_persistence periodic_alpha_complex_3d_persistence.cpp)
+      target_link_libraries(periodic_alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+
+      add_executable(custom_persistence_sort custom_persistence_sort.cpp)
+      target_link_libraries(custom_persistence_sort ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+
+      if (TBB_FOUND)
+        target_link_libraries(alpha_complex_persistence ${TBB_LIBRARIES})
+        target_link_libraries(periodic_alpha_complex_3d_persistence ${TBB_LIBRARIES})
+        target_link_libraries(custom_persistence_sort ${TBB_LIBRARIES})
+      endif(TBB_FOUND)
+      add_test(alpha_complex_persistence_2_0_45 ${CMAKE_CURRENT_BINARY_DIR}/alpha_complex_persistence ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -m 0.45 -p 2)
+      add_test(periodic_alpha_complex_3d_persistence_2_0 ${CMAKE_CURRENT_BINARY_DIR}/periodic_alpha_complex_3d_persistence ${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off ${CMAKE_SOURCE_DIR}/data/points/iso_cuboid_3_in_0_1.txt 2 0)
+      add_test(custom_persistence_sort ${CMAKE_CURRENT_BINARY_DIR}/custom_persistence_sort)
+    endif(EIGEN3_FOUND)
+  endif (NOT CGAL_VERSION VERSION_LESS 4.7.0)
+endif(CGAL_FOUND)
diff --git a/src/Persistent_cohomology/example/README b/src/Persistent_cohomology/example/README
index 8c71ccf5..7803e5ab 100644
--- a/src/Persistent_cohomology/example/README
+++ b/src/Persistent_cohomology/example/README
@@ -4,13 +4,13 @@ cd /path-to-example/
 cmake .
 make
 
-
-Example of use :
+***********************************************************************************************************************
+Example of use of RIPS:
 
 Computation of the persistent homology with Z/2Z coefficients of the Rips complex on points 
 sampling a Klein bottle:
 
-./rips_persistence ../../../data/points/Kl.txt -r 0.25 -d 3 -p 2 -m 100
+./rips_persistence ../../data/points/Kl.txt -r 0.25 -d 3 -p 2 -m 100
 
 output:
 210  0 0 inf
@@ -29,7 +29,7 @@ where
 
 with Z/3Z coefficients:
 
-./rips_persistence ../../../data/points/Kl.txt -r 0.25 -d 3 -p 3 -m 100
+./rips_persistence ../../data/points/Kl.txt -r 0.25 -d 3 -p 3 -m 100
 
 output:
 3  0 0 inf
@@ -37,7 +37,7 @@ output:
 
 and the computation with Z/2Z and Z/3Z coefficients simultaneously:
 
-./rips_multifield_persistence ../../../data/points/Kl.txt -r 0.25 -d 3 -p 2 -q 3 -m 100
+./rips_multifield_persistence ../../data/points/Kl.txt -r 0.25 -d 3 -p 2 -q 3 -m 100
 
 output:
 6  0 0 inf
@@ -47,10 +47,106 @@ output:
 
 and finally the computation with all Z/pZ for 2 <= p <= 71 (20 first prime numbers):
 
- ./rips_multifield_persistence ../../../data/points/Kl.txt -r 0.25 -d 3 -p 2 -q 71 -m 100
+ ./rips_multifield_persistence ../../data/points/Kl.txt -r 0.25 -d 3 -p 2 -q 71 -m 100
 
 output:
 557940830126698960967415390  0 0 inf
 557940830126698960967415390  1 0.0702103 inf
 2  1 0.0702103 inf
 2  2 0.159992 inf
+
+***********************************************************************************************************************
+Example of use of ALPHA:
+
+For a more verbose mode, please run cmake with option "DEBUG_TRACES=TRUE" and recompile the programs.
+
+1) 3D special case
+------------------
+Computation of the persistent homology with Z/2Z coefficients of the alpha complex on points 
+sampling a torus 3D:
+
+./alpha_complex_3d_persistence ../../data/points/tore3D_300.off 2 0.45
+
+output:
+Simplex_tree dim: 3
+2  0 0 inf 
+2  1 0.0682162 1.0001 
+2  1 0.0934117 1.00003 
+2  2 0.56444 1.03938 
+
+Here we retrieve expected Betti numbers on a tore 3D:
+Betti numbers[0] = 1
+Betti numbers[1] = 2
+Betti numbers[2] = 1
+
+N.B.: - alpha_complex_3d_persistence accepts only OFF files in 3D dimension.
+      - filtration values are alpha square values
+
+2) d-Dimension case
+-------------------
+Computation of the persistent homology with Z/2Z coefficients of the alpha complex on points 
+sampling a torus 3D:
+
+./alpha_complex_persistence -r 32 -p 2 -m 0.45 ../../data/points/tore3D_300.off
+
+output:
+Alpha complex is of dimension 3 - 9273 simplices - 300 vertices.
+Simplex_tree dim: 3
+2  0 0 inf 
+2  1 0.0682162 1.0001 
+2  1 0.0934117 1.00003 
+2  2 0.56444 1.03938 
+
+Here we retrieve expected Betti numbers on a tore 3D:
+Betti numbers[0] = 1
+Betti numbers[1] = 2
+Betti numbers[2] = 1
+
+N.B.: - alpha_complex_persistence accepts OFF files in d-Dimension.
+      - filtration values are alpha square values
+
+3) 3D periodic special case
+---------------------------
+./periodic_alpha_complex_3d_persistence ../../data/points/grid_10_10_10_in_0_1.off 3 1.0
+
+output:
+Periodic Delaunay computed.
+Simplex_tree dim: 3
+3  0 0 inf 
+3  1 0.0025 inf 
+3  1 0.0025 inf 
+3  1 0.0025 inf 
+3  2 0.005 inf 
+3  2 0.005 inf 
+3  2 0.005 inf 
+3  3 0.0075 inf 
+
+Here we retrieve expected Betti numbers on a tore 3D:
+Betti numbers[0] = 1
+Betti numbers[1] = 3
+Betti numbers[2] = 3
+Betti numbers[3] = 1
+
+N.B.: - periodic_alpha_complex_3d_persistence accepts only OFF files in 3D dimension. In this example, the periodic cube
+is hard coded to { x = [0,1]; y = [0,1]; z = [0,1] }
+      - filtration values are alpha square values
+
+***********************************************************************************************************************
+Example of use of PLAIN HOMOLOGY:
+
+This example computes the plain homology of the following simplicial complex without filtration values:
+  /* Complex to build. */
+  /*    1   3          */
+  /*    o---o          */
+  /*   /X\ /           */
+  /*  o---o   o        */
+  /*  2   0   4        */
+
+./plain_homology 
+
+output:
+2  0 0 inf 
+2  0 0 inf 
+2  1 0 inf 
+
+Here we retrieve the 2 entities {0,1,2,3} and {4} (Betti numbers[0] = 2) and the hole in {0,1,3} (Betti numbers[1] = 1)
diff --git a/src/Persistent_cohomology/example/alpha_shapes_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp
index 92c0b065..48fbb91a 100644
--- a/src/Persistent_cohomology/example/alpha_shapes_persistence.cpp
+++ b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp
@@ -20,9 +20,9 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include <gudhi/graph_simplicial_complex.h>
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/Persistent_cohomology.h>
+#include <gudhi/Points_3D_off_io.h>
 #include <boost/variant.hpp>
 
 #include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
@@ -39,9 +39,6 @@
 #include <list>
 #include <vector>
 
-using namespace Gudhi;
-using namespace Gudhi::persistent_cohomology;
-
 // Alpha_shape_3 templates type definitions
 typedef CGAL::Exact_predicates_inexact_constructions_kernel Kernel;
 typedef CGAL::Alpha_shape_vertex_base_3<Kernel> Vb;
@@ -66,11 +63,12 @@ typedef Alpha_shape_3::Edge Edge_3;
 typedef std::list<Alpha_shape_3::Vertex_handle> Vertex_list;
 
 // gudhi type definition
-typedef Simplex_tree<Simplex_tree_options_fast_persistence> ST;
+typedef Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence> ST;
 typedef ST::Vertex_handle Simplex_tree_vertex;
 typedef std::map<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex > Alpha_shape_simplex_tree_map;
 typedef std::pair<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex> Alpha_shape_simplex_tree_pair;
 typedef std::vector< Simplex_tree_vertex > Simplex_tree_vector_vertex;
+typedef Gudhi::persistent_cohomology::Persistent_cohomology< ST, Gudhi::persistent_cohomology::Field_Zp > PCOH;
 
 Vertex_list from(const Cell_handle& ch) {
   Vertex_list the_list;
@@ -125,40 +123,33 @@ void usage(char * const progName) {
 }
 
 int main(int argc, char * const argv[]) {
-  int coeff_field_characteristic = 0;
-  int returnedScanValue = sscanf(argv[2], "%d", &coeff_field_characteristic);
-  if ((returnedScanValue == EOF) || (coeff_field_characteristic <= 0)) {
-    std::cerr << "Error: " << argv[2] << " is not correct\n";
+  // program args management
+  if (argc != 4) {
+    std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n";
     usage(argv[0]);
   }
 
+  int coeff_field_characteristic = atoi(argv[2]);
+
   Filtration_value min_persistence = 0.0;
-  returnedScanValue = sscanf(argv[3], "%lf", &min_persistence);
+  int returnedScanValue = sscanf(argv[3], "%lf", &min_persistence);
   if ((returnedScanValue == EOF) || (min_persistence < -1.0)) {
     std::cerr << "Error: " << argv[3] << " is not correct\n";
     usage(argv[0]);
   }
 
-  // program args management
-  if (argc != 4) {
-    std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n";
+  // Read points from file
+  std::string offInputFile(argv[1]);
+  // Read the OFF file (input file name given as parameter) and triangulate points
+  Gudhi::Points_3D_off_reader<Point_3> off_reader(offInputFile);
+  // Check the read operation was correct
+  if (!off_reader.is_valid()) {
+    std::cerr << "Unable to read file " << offInputFile << std::endl;
     usage(argv[0]);
   }
 
-  // Read points from file
-  std::string filegraph = argv[1];
-  std::list<Point_3> lp;
-  std::ifstream is(filegraph.c_str());
-  int n;
-  is >> n;
-#ifdef DEBUG_TRACES
-  std::cout << "Reading " << n << " points " << std::endl;
-#endif  // DEBUG_TRACES
-  Point_3 p;
-  for (; n > 0; n--) {
-    is >> p;
-    lp.push_back(p);
-  }
+  // Retrieve the triangulation
+  std::vector<Point_3> lp = off_reader.get_point_cloud();
 
   // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode.
   Alpha_shape_3 as(lp.begin(), lp.end(), 0, Alpha_shape_3::GENERAL);
@@ -240,7 +231,7 @@ int main(int argc, char * const argv[]) {
       }
     }
     // Construction of the simplex_tree
-    Filtration_value filtr = std::sqrt(*the_alpha_value_iterator);
+    Filtration_value filtr = /*std::sqrt*/(*the_alpha_value_iterator);
 #ifdef DEBUG_TRACES
     std::cout << "filtration = " << filtr << std::endl;
 #endif  // DEBUG_TRACES
@@ -282,7 +273,7 @@ int main(int argc, char * const argv[]) {
 
   std::cout << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl;
   // Compute the persistence diagram of the complex
-  Persistent_cohomology< ST, Field_Zp > pcoh(simplex_tree);
+  PCOH pcoh(simplex_tree);
   // initializes the coefficient field for homology
   pcoh.init_coefficients(coeff_field_characteristic);
 
diff --git a/src/Persistent_cohomology/example/alpha_complex_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_persistence.cpp
new file mode 100644
index 00000000..cb181936
--- /dev/null
+++ b/src/Persistent_cohomology/example/alpha_complex_persistence.cpp
@@ -0,0 +1,117 @@
+#include <boost/program_options.hpp>
+
+#include <CGAL/Epick_d.h>
+
+#include <gudhi/Alpha_complex.h>
+#include <gudhi/Persistent_cohomology.h>
+
+#include <iostream>
+#include <string>
+#include <limits>  // for numeric_limits
+
+void program_options(int argc, char * argv[]
+                     , std::string & off_file_points
+                     , std::string & output_file_diag
+                     , Filtration_value & alpha_square_max_value
+                     , int & coeff_field_characteristic
+                     , Filtration_value & min_persistence);
+
+int main(int argc, char **argv) {
+  std::string off_file_points;
+  std::string output_file_diag;
+  Filtration_value alpha_square_max_value;
+  int coeff_field_characteristic;
+  Filtration_value min_persistence;
+
+  program_options(argc, argv, off_file_points, output_file_diag, alpha_square_max_value,
+                  coeff_field_characteristic, min_persistence);
+
+  // ----------------------------------------------------------------------------
+  // Init of an alpha complex from an OFF file
+  // ----------------------------------------------------------------------------
+  using Kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >;
+  Gudhi::alpha_complex::Alpha_complex<Kernel> alpha_complex_from_file(off_file_points, alpha_square_max_value);
+
+  // ----------------------------------------------------------------------------
+  // Display information about the alpha complex
+  // ----------------------------------------------------------------------------
+  std::cout << "Alpha complex is of dimension " << alpha_complex_from_file.dimension() <<
+      " - " << alpha_complex_from_file.num_simplices() << " simplices - " <<
+      alpha_complex_from_file.num_vertices() << " vertices." << std::endl;
+
+  // Sort the simplices in the order of the filtration
+  alpha_complex_from_file.initialize_filtration();
+
+  std::cout << "Simplex_tree dim: " << alpha_complex_from_file.dimension() << std::endl;
+  // Compute the persistence diagram of the complex
+  Gudhi::persistent_cohomology::Persistent_cohomology< Gudhi::alpha_complex::Alpha_complex<Kernel>,
+      Gudhi::persistent_cohomology::Field_Zp > pcoh(alpha_complex_from_file);
+  // initializes the coefficient field for homology
+  pcoh.init_coefficients(coeff_field_characteristic);
+
+  pcoh.compute_persistent_cohomology(min_persistence);
+
+  // Output the diagram in filediag
+  if (output_file_diag.empty()) {
+    pcoh.output_diagram();
+  } else {
+    std::cout << "Result in file: " << output_file_diag << std::endl;
+    std::ofstream out(output_file_diag);
+    pcoh.output_diagram(out);
+    out.close();
+  }
+
+  return 0;
+}
+
+void program_options(int argc, char * argv[]
+                     , std::string & off_file_points
+                     , std::string & output_file_diag
+                     , Filtration_value & alpha_square_max_value
+                     , int & coeff_field_characteristic
+                     , Filtration_value & min_persistence) {
+  namespace po = boost::program_options;
+  po::options_description hidden("Hidden options");
+  hidden.add_options()
+      ("input-file", po::value<std::string>(&off_file_points),
+       "Name of file containing a point set. Format is one point per line:   X1 ... Xd ");
+
+  po::options_description visible("Allowed options", 100);
+  visible.add_options()
+      ("help,h", "produce help message")
+      ("output-file,o", po::value<std::string>(&output_file_diag)->default_value(std::string()),
+       "Name of file in which the persistence diagram is written. Default print in std::cout")
+      ("max-alpha-square-value,r",
+      po::value<Filtration_value>(&alpha_square_max_value)->default_value(std::numeric_limits<Filtration_value>::infinity()),
+       "Maximal alpha square value for the Alpha complex construction.")
+      ("field-charac,p", po::value<int>(&coeff_field_characteristic)->default_value(11),
+       "Characteristic p of the coefficient field Z/pZ for computing homology.")
+      ("min-persistence,m", po::value<Filtration_value>(&min_persistence),
+       "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals");
+
+  po::positional_options_description pos;
+  pos.add("input-file", 1);
+
+  po::options_description all;
+  all.add(visible).add(hidden);
+
+  po::variables_map vm;
+  po::store(po::command_line_parser(argc, argv).
+            options(all).positional(pos).run(), vm);
+  po::notify(vm);
+
+  if (vm.count("help") || !vm.count("input-file")) {
+    std::cout << std::endl;
+    std::cout << "Compute the persistent homology with coefficient field Z/pZ \n";
+    std::cout << "of an Alpha complex defined on a set of input points.\n \n";
+    std::cout << "The output diagram contains one bar per line, written with the convention: \n";
+    std::cout << "   p   dim b d \n";
+    std::cout << "where dim is the dimension of the homological feature,\n";
+    std::cout << "b and d are respectively the birth and death of the feature and \n";
+    std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl;
+
+    std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
+    std::cout << visible << std::endl;
+    std::abort();
+  }
+}
diff --git a/src/Persistent_cohomology/example/custom_persistence_sort.cpp b/src/Persistent_cohomology/example/custom_persistence_sort.cpp
new file mode 100644
index 00000000..9af38611
--- /dev/null
+++ b/src/Persistent_cohomology/example/custom_persistence_sort.cpp
@@ -0,0 +1,116 @@
+/*    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) 2014  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/>.
+ */
+
+#include <CGAL/Epick_d.h>
+#include <CGAL/point_generators_d.h>
+#include <CGAL/algorithm.h>
+#include <CGAL/assertions.h>
+
+#include <gudhi/Alpha_complex.h>
+#include <gudhi/Persistent_cohomology.h>
+
+#include <iostream>
+#include <iterator>
+#include <vector>
+#include <fstream>  // for std::ofstream
+#include <algorithm>  // for std::sort
+
+
+using Kernel = CGAL::Epick_d< CGAL::Dimension_tag<3> >;
+using Point = Kernel::Point_d;
+using Alpha_complex = Gudhi::alpha_complex::Alpha_complex<Kernel>;
+
+std::vector<Point> random_points() {
+  // Instanciate a random point generator
+  CGAL::Random rng(0);
+
+  // Generate "points_number" random points in a vector
+  std::vector<Point> points;
+
+  // Generates 1000 random 3D points on a sphere of radius 4.0
+  CGAL::Random_points_on_sphere_d<Point> rand_outside(3, 4.0, rng);
+  CGAL::cpp11::copy_n(rand_outside, 1000, std::back_inserter(points));
+  // Generates 2000 random 3D points in a sphere of radius 3.0
+  CGAL::Random_points_in_ball_d<Point> rand_inside(3, 3.0, rng);
+  CGAL::cpp11::copy_n(rand_inside, 2000, std::back_inserter(points));
+
+  return points;
+}
+
+/*
+ * Compare two intervals by dimension, then by length.
+ */
+struct cmp_intervals_by_dim_then_length {
+  explicit cmp_intervals_by_dim_then_length(Alpha_complex * sc)
+      : sc_(sc) { }
+
+  template<typename Persistent_interval>
+  bool operator()(const Persistent_interval & p1, const Persistent_interval & p2) {
+    if (sc_->dimension(get < 0 > (p1)) == sc_->dimension(get < 0 > (p2)))
+      return (sc_->filtration(get < 1 > (p1)) - sc_->filtration(get < 0 > (p1))
+              > sc_->filtration(get < 1 > (p2)) - sc_->filtration(get < 0 > (p2)));
+    else
+      return (sc_->dimension(get < 0 > (p1)) > sc_->dimension(get < 0 > (p2)));
+  }
+  Alpha_complex* sc_;
+};
+
+int main(int argc, char **argv) {
+  std::vector<Point> points = random_points();
+
+  // Alpha complex persistence computation from generated points
+  Alpha_complex alpha_complex_from_points(points, 0.6);
+
+  using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology< Alpha_complex,
+      Gudhi::persistent_cohomology::Field_Zp >;
+  Persistent_cohomology pcoh(alpha_complex_from_points);
+
+  // initializes the coefficient field for homology - Z/3Z
+  pcoh.init_coefficients(3);
+  pcoh.compute_persistent_cohomology(0.2);
+
+  // Custom sort and output persistence
+  cmp_intervals_by_dim_then_length cmp(&alpha_complex_from_points);
+  auto persistent_pairs = pcoh.get_persistent_pairs();
+  std::sort(std::begin(persistent_pairs), std::end(persistent_pairs), cmp);
+  for (auto pair : persistent_pairs) {
+    std::cout << alpha_complex_from_points.dimension(get<0>(pair)) << " "
+          << alpha_complex_from_points.filtration(get<0>(pair)) << " "
+          << alpha_complex_from_points.filtration(get<1>(pair)) << std::endl;
+  }
+
+  // Persistent Betti numbers
+  std::cout << "The persistent Betti numbers in interval [0.40, 0.41] are : ";
+  for (int dim = 0; dim < alpha_complex_from_points.dimension(); dim++)
+    std::cout << "b" << dim << " = " << pcoh.persistent_betti_number(dim, 0.40, 0.41) << " ; ";
+  std::cout << std::endl;
+
+  // Betti numbers
+  std::vector<int> betti_numbers = pcoh.betti_numbers();
+  std::cout << "The Betti numbers are : ";
+  for (std::size_t i = 0; i < betti_numbers.size(); i++)
+    std::cout << "b" << i << " = " << betti_numbers[i] << " ; ";
+  std::cout << std::endl;
+
+  return 0;
+}
+
diff --git a/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp
new file mode 100644
index 00000000..a199fea1
--- /dev/null
+++ b/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp
@@ -0,0 +1,313 @@
+/*    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) 2014  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/>.
+ */
+
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Persistent_cohomology.h>
+#include <gudhi/Points_3D_off_io.h>
+#include <boost/variant.hpp>
+
+#include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
+#include <CGAL/Periodic_3_Delaunay_triangulation_traits_3.h>
+#include <CGAL/Periodic_3_Delaunay_triangulation_3.h>
+#include <CGAL/Alpha_shape_3.h>
+#include <CGAL/iterator.h>
+
+#include <fstream>
+#include <cmath>
+#include <string>
+#include <tuple>
+#include <map>
+#include <utility>
+#include <list>
+#include <vector>
+
+// Traits
+using K = CGAL::Exact_predicates_inexact_constructions_kernel;
+using PK = CGAL::Periodic_3_Delaunay_triangulation_traits_3<K>;
+// Vertex type
+using DsVb = CGAL::Periodic_3_triangulation_ds_vertex_base_3<>;
+using Vb = CGAL::Triangulation_vertex_base_3<PK, DsVb>;
+using AsVb = CGAL::Alpha_shape_vertex_base_3<PK, Vb>;
+// Cell type
+using DsCb = CGAL::Periodic_3_triangulation_ds_cell_base_3<>;
+using Cb = CGAL::Triangulation_cell_base_3<PK, DsCb>;
+using AsCb = CGAL::Alpha_shape_cell_base_3<PK, Cb>;
+using Tds = CGAL::Triangulation_data_structure_3<AsVb, AsCb>;
+using P3DT3 = CGAL::Periodic_3_Delaunay_triangulation_3<PK, Tds>;
+using Alpha_shape_3 = CGAL::Alpha_shape_3<P3DT3>;
+using Point_3 = PK::Point_3;
+
+// filtration with alpha values needed type definition
+using Alpha_value_type = Alpha_shape_3::FT;
+using Object = CGAL::Object;
+using Dispatch = CGAL::Dispatch_output_iterator<
+    CGAL::cpp11::tuple<Object, Alpha_value_type>,
+    CGAL::cpp11::tuple<std::back_insert_iterator< std::vector<Object> >,
+    std::back_insert_iterator< std::vector<Alpha_value_type> > > >;
+using Cell_handle = Alpha_shape_3::Cell_handle;
+using Facet = Alpha_shape_3::Facet;
+using Edge_3 = Alpha_shape_3::Edge;
+using Vertex_list = std::list<Alpha_shape_3::Vertex_handle>;
+
+// gudhi type definition
+using ST = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
+using Simplex_tree_vertex = ST::Vertex_handle;
+using Alpha_shape_simplex_tree_map = std::map<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex >;
+using Alpha_shape_simplex_tree_pair = std::pair<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex>;
+using Simplex_tree_vector_vertex = std::vector< Simplex_tree_vertex >;
+using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<
+    ST, Gudhi::persistent_cohomology::Field_Zp >;
+
+Vertex_list from(const Cell_handle& ch) {
+  Vertex_list the_list;
+  for (auto i = 0; i < 4; i++) {
+#ifdef DEBUG_TRACES
+    std::cout << "from cell[" << i << "]=" << ch->vertex(i)->point() << std::endl;
+#endif  // DEBUG_TRACES
+    the_list.push_back(ch->vertex(i));
+  }
+  return the_list;
+}
+
+Vertex_list from(const Facet& fct) {
+  Vertex_list the_list;
+  for (auto i = 0; i < 4; i++) {
+    if (fct.second != i) {
+#ifdef DEBUG_TRACES
+      std::cout << "from facet=[" << i << "]" << fct.first->vertex(i)->point() << std::endl;
+#endif  // DEBUG_TRACES
+      the_list.push_back(fct.first->vertex(i));
+    }
+  }
+  return the_list;
+}
+
+Vertex_list from(const Edge_3& edg) {
+  Vertex_list the_list;
+  for (auto i = 0; i < 4; i++) {
+    if ((edg.second == i) || (edg.third == i)) {
+#ifdef DEBUG_TRACES
+      std::cout << "from edge[" << i << "]=" << edg.first->vertex(i)->point() << std::endl;
+#endif  // DEBUG_TRACES
+      the_list.push_back(edg.first->vertex(i));
+    }
+  }
+  return the_list;
+}
+
+Vertex_list from(const Alpha_shape_3::Vertex_handle& vh) {
+  Vertex_list the_list;
+#ifdef DEBUG_TRACES
+  std::cout << "from vertex=" << vh->point() << std::endl;
+#endif  // DEBUG_TRACES
+  the_list.push_back(vh);
+  return the_list;
+}
+
+void usage(char * const progName) {
+  std::cerr << "Usage: " << progName <<
+      " path_to_file_graph path_to_iso_cuboid_3_file coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n";
+  exit(-1);
+}
+
+int main(int argc, char * const argv[]) {
+  // program args management
+  if (argc != 5) {
+    std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n";
+    usage(argv[0]);
+  }
+
+  int coeff_field_characteristic = 0;
+  int returnedScanValue = sscanf(argv[3], "%d", &coeff_field_characteristic);
+  if ((returnedScanValue == EOF) || (coeff_field_characteristic <= 0)) {
+    std::cerr << "Error: " << argv[3] << " is not correct\n";
+    usage(argv[0]);
+  }
+
+  Filtration_value min_persistence = 0.0;
+  returnedScanValue = sscanf(argv[4], "%lf", &min_persistence);
+  if ((returnedScanValue == EOF) || (min_persistence < -1.0)) {
+    std::cerr << "Error: " << argv[4] << " is not correct\n";
+    usage(argv[0]);
+  }
+
+  // Read points from file
+  std::string offInputFile(argv[1]);
+  // Read the OFF file (input file name given as parameter) and triangulate points
+  Gudhi::Points_3D_off_reader<Point_3> off_reader(offInputFile);
+  // Check the read operation was correct
+  if (!off_reader.is_valid()) {
+    std::cerr << "Unable to read file " << offInputFile << std::endl;
+    usage(argv[0]);
+  }
+
+  // Read iso_cuboid_3 information from file
+  std::ifstream iso_cuboid_str(argv[2]);
+  double x_min, y_min, z_min, x_max, y_max, z_max;
+  if (iso_cuboid_str.good()) {
+    iso_cuboid_str >> x_min >> y_min >> z_min >> x_max >> y_max >> z_max;
+  } else {
+    std::cerr << "Unable to read file " << argv[2] << std::endl;
+    usage(argv[0]);
+  }
+
+  // Retrieve the triangulation
+  std::vector<Point_3> lp = off_reader.get_point_cloud();
+
+  // Define the periodic cube
+  P3DT3 pdt(PK::Iso_cuboid_3(x_min, y_min, z_min, x_max, y_max, z_max));
+  // Heuristic for inserting large point sets (if pts is reasonably large)
+  pdt.insert(lp.begin(), lp.end(), true);
+  // As pdt won't be modified anymore switch to 1-sheeted cover if possible
+  if (pdt.is_triangulation_in_1_sheet()) pdt.convert_to_1_sheeted_covering();
+  std::cout << "Periodic Delaunay computed." << std::endl;
+
+  // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode. This is the default mode
+  // Maybe need to set it to GENERAL mode
+  Alpha_shape_3 as(pdt, 0, Alpha_shape_3::GENERAL);
+
+  // filtration with alpha values from alpha shape
+  std::vector<Object> the_objects;
+  std::vector<Alpha_value_type> the_alpha_values;
+
+  Dispatch disp = CGAL::dispatch_output<Object, Alpha_value_type>(std::back_inserter(the_objects),
+                                                                  std::back_inserter(the_alpha_values));
+
+  as.filtration_with_alpha_values(disp);
+#ifdef DEBUG_TRACES
+  std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl;
+#endif  // DEBUG_TRACES
+
+  Alpha_shape_3::size_type count_vertices = 0;
+  Alpha_shape_3::size_type count_edges = 0;
+  Alpha_shape_3::size_type count_facets = 0;
+  Alpha_shape_3::size_type count_cells = 0;
+
+  // Loop on objects vector
+  Vertex_list vertex_list;
+  ST simplex_tree;
+  Alpha_shape_simplex_tree_map map_cgal_simplex_tree;
+  std::vector<Alpha_value_type>::iterator the_alpha_value_iterator = the_alpha_values.begin();
+  int dim_max = 0;
+  Filtration_value filtration_max = 0.0;
+  for (auto object_iterator : the_objects) {
+    // Retrieve Alpha shape vertex list from object
+    if (const Cell_handle * cell = CGAL::object_cast<Cell_handle>(&object_iterator)) {
+      vertex_list = from(*cell);
+      count_cells++;
+      if (dim_max < 3) {
+        // Cell is of dim 3
+        dim_max = 3;
+      }
+    } else if (const Facet * facet = CGAL::object_cast<Facet>(&object_iterator)) {
+      vertex_list = from(*facet);
+      count_facets++;
+      if (dim_max < 2) {
+        // Facet is of dim 2
+        dim_max = 2;
+      }
+    } else if (const Edge_3 * edge = CGAL::object_cast<Edge_3>(&object_iterator)) {
+      vertex_list = from(*edge);
+      count_edges++;
+      if (dim_max < 1) {
+        // Edge_3 is of dim 1
+        dim_max = 1;
+      }
+    } else if (const Alpha_shape_3::Vertex_handle * vertex =
+               CGAL::object_cast<Alpha_shape_3::Vertex_handle>(&object_iterator)) {
+      count_vertices++;
+      vertex_list = from(*vertex);
+    }
+    // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex
+    Simplex_tree_vector_vertex the_simplex_tree;
+    for (auto the_alpha_shape_vertex : vertex_list) {
+      Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex);
+      if (the_map_iterator == map_cgal_simplex_tree.end()) {
+        // alpha shape not found
+        Simplex_tree_vertex vertex = map_cgal_simplex_tree.size();
+#ifdef DEBUG_TRACES
+        std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl;
+#endif  // DEBUG_TRACES
+        the_simplex_tree.push_back(vertex);
+        map_cgal_simplex_tree.insert(Alpha_shape_simplex_tree_pair(the_alpha_shape_vertex, vertex));
+      } else {
+        // alpha shape found
+        Simplex_tree_vertex vertex = the_map_iterator->second;
+#ifdef DEBUG_TRACES
+        std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl;
+#endif  // DEBUG_TRACES
+        the_simplex_tree.push_back(vertex);
+      }
+    }
+    // Construction of the simplex_tree
+    Filtration_value filtr = /*std::sqrt*/(*the_alpha_value_iterator);
+#ifdef DEBUG_TRACES
+    std::cout << "filtration = " << filtr << std::endl;
+#endif  // DEBUG_TRACES
+    if (filtr > filtration_max) {
+      filtration_max = filtr;
+    }
+    simplex_tree.insert_simplex(the_simplex_tree, filtr);
+    if (the_alpha_value_iterator != the_alpha_values.end())
+      ++the_alpha_value_iterator;
+    else
+      std::cout << "This shall not happen" << std::endl;
+  }
+  simplex_tree.set_filtration(filtration_max);
+  simplex_tree.set_dimension(dim_max);
+
+#ifdef DEBUG_TRACES
+  std::cout << "vertices \t\t" << count_vertices << std::endl;
+  std::cout << "edges \t\t" << count_edges << std::endl;
+  std::cout << "facets \t\t" << count_facets << std::endl;
+  std::cout << "cells \t\t" << count_cells << std::endl;
+
+
+  std::cout << "Information of the Simplex Tree: " << std::endl;
+  std::cout << "  Number of vertices = " << simplex_tree.num_vertices() << " ";
+  std::cout << "  Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl;
+  std::cout << "  Dimension = " << simplex_tree.dimension() << " ";
+  std::cout << "  filtration = " << simplex_tree.filtration() << std::endl << std::endl;
+#endif  // DEBUG_TRACES
+
+#ifdef DEBUG_TRACES
+  std::cout << "Iterator on vertices: " << std::endl;
+  for (auto vertex : simplex_tree.complex_vertex_range()) {
+    std::cout << vertex << " ";
+  }
+#endif  // DEBUG_TRACES
+
+  // Sort the simplices in the order of the filtration
+  simplex_tree.initialize_filtration();
+
+  std::cout << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl;
+  // Compute the persistence diagram of the complex
+  Persistent_cohomology pcoh(simplex_tree, true);
+  // initializes the coefficient field for homology
+  pcoh.init_coefficients(coeff_field_characteristic);
+
+  pcoh.compute_persistent_cohomology(min_persistence);
+
+  pcoh.output_diagram();
+
+  return 0;
+}
diff --git a/src/Persistent_cohomology/example/plain_homology.cpp b/src/Persistent_cohomology/example/plain_homology.cpp
index 0a692717..ae82c817 100644
--- a/src/Persistent_cohomology/example/plain_homology.cpp
+++ b/src/Persistent_cohomology/example/plain_homology.cpp
@@ -24,6 +24,8 @@
 #include <gudhi/Persistent_cohomology.h>
 
 #include <iostream>
+#include <vector>
+#include <cstdint>  // for std::uint8_t
 
 using namespace Gudhi;
 
@@ -38,6 +40,8 @@ struct MyOptions : Simplex_tree_options_full_featured {
   static const bool store_key = true;
   // I have few vertices
   typedef short Vertex_handle;
+  // Maximum number of simplices to compute persistence is 2^8 - 1 = 255. One is reserved for null_key
+  typedef std::uint8_t Simplex_key;
 };
 typedef Simplex_tree<MyOptions> ST;
 
@@ -76,9 +80,16 @@ int main() {
 
   // Print the result. The format is, on each line: 2 dim 0 inf
   // where 2 represents the field, dim the dimension of the feature.
-  // 2  0 0 inf 
-  // 2  0 0 inf 
-  // 2  1 0 inf 
+  // 2  0 0 inf
+  // 2  0 0 inf
+  // 2  1 0 inf
   // means that in Z/2Z-homology, the Betti numbers are b0=2 and b1=1.
   pcoh.output_diagram();
+
+  // Print the Betti numbers are b0=2 and b1=1.
+  std::cout << std::endl;
+  std::cout << "The Betti numbers are : ";
+  for (int i = 0; i < st.dimension(); i++)
+    std::cout << "b" << i << " = " << pcoh.betti_number(i) << " ; ";
+  std::cout << std::endl;
 }
diff --git a/src/Persistent_cohomology/example/rips_persistence.cpp b/src/Persistent_cohomology/example/rips_persistence.cpp
index 2d926a0d..cab49395 100644
--- a/src/Persistent_cohomology/example/rips_persistence.cpp
+++ b/src/Persistent_cohomology/example/rips_persistence.cpp
@@ -30,6 +30,7 @@
 
 #include <string>
 #include <vector>
+#include <limits>  // infinity
 
 using namespace Gudhi;
 using namespace Gudhi::persistent_cohomology;
@@ -115,7 +116,7 @@ void program_options(int argc, char * argv[]
       ("help,h", "produce help message")
       ("output-file,o", po::value<std::string>(&filediag)->default_value(std::string()),
        "Name of file in which the persistence diagram is written. Default print in std::cout")
-      ("max-edge-length,r", po::value<Filtration_value>(&threshold)->default_value(0),
+      ("max-edge-length,r", po::value<Filtration_value>(&threshold)->default_value(std::numeric_limits<Filtration_value>::infinity()),
        "Maximal length of an edge for the Rips complex construction.")
       ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(1),
        "Maximal dimension of the Rips complex we want to compute.")
diff --git a/src/Persistent_cohomology/example/parallel_rips_persistence.cpp b/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp
index 4c6656f5..4c6656f5 100644
--- a/src/Persistent_cohomology/example/parallel_rips_persistence.cpp
+++ b/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp
diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
index 643b810c..b31df6a4 100644
--- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
+++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
@@ -41,154 +41,16 @@
 #include <tuple>
 #include <algorithm>
 #include <string>
+#include <stdexcept>  // for std::out_of_range
 
 namespace Gudhi {
 
 namespace persistent_cohomology {
 
-/** \defgroup persistent_cohomology Persistent Cohomology
-  *
-
-  Computation of persistent cohomology using the algorithm of 
-   \cite DBLP:journals/dcg/SilvaMV11 and \cite DBLP:journals/corr/abs-1208-5018 
-   and the Compressed Annotation Matrix 
-   implementation of \cite DBLP:conf/esa/BoissonnatDM13 
-       
-  The theory of homology consists in attaching to a topological space a sequence of 
-  (homology) groups, 
-  capturing global topological features 
-  like connected components, holes, cavities, etc. Persistent homology studies the evolution 
-  -- birth, life and death -- of 
-  these features when the topological space is changing. Consequently, the theory is essentially 
-  composed of three elements: 
-  topological spaces, their homology groups and an evolution scheme.
-
- The theory of homology consists in attaching to a topological space a sequence of
- (homology) groups,
- capturing global topological features
- like connected components, holes, cavities, etc. Persistent homology studies the evolution
- -- birth, life and death -- of
- these features when the topological space is changing. Consequently, the theory is essentially
- composed of three elements:
- topological spaces, their homology groups and an evolution scheme.
-
- <DT>Topological Spaces:</DT>
- Topological spaces are represented by simplicial complexes.
- Let \f$V = \{1, \cdots ,|V|\}\f$ be a set of <EM>vertices</EM>.
- A <EM>simplex</EM> \f$\sigma\f$ is a subset of vertices
- \f$\sigma \subseteq V\f$. A <EM>simplicial complex</EM> \f$\mathbf{K}\f$
- on \f$V\f$ is a collection of simplices \f$\{\sigma\}\f$,
- \f$\sigma \subseteq V\f$, such that \f$\tau \subseteq \sigma \in \mathbf{K}
- \Rightarrow \tau \in \mathbf{K}\f$. The dimension \f$n=|\sigma|-1\f$ of \f$\sigma\f$
- is its number of elements minus 1. A <EM>filtration</EM> of a simplicial complex is
- a function \f$f:\mathbf{K} \rightarrow \mathbb{R}\f$ satisfying \f$f(\tau)\leq
- f(\sigma)\f$ whenever \f$\tau \subseteq \sigma\f$.
-
- We define the concept FilteredComplex which enumerates the requirements for a class
- to represent a filtered complex from which persistent homology may be computed.
- We use the vocabulary of simplicial complexes, but the concept
- is valid for any type of cell complex. The main requirements
- are the definition of:
- \li type <CODE>Indexing_tag</CODE>, which is a model of the concept
- <CODE>IndexingTag</CODE>,
- describing the nature of the indexing scheme,
- \li type Simplex_handle to manipulate simplices,
- \li method <CODE>int dimension(Simplex_handle)</CODE> returning
- the dimension of a simplex,
- \li type and method <CODE>Boundary_simplex_range
- boundary_simplex_range(Simplex_handle)</CODE> that returns
- a range giving access to the codimension 1 subsimplices of the
- input simplex, as-well-as the coefficients \f$(-1)^i\f$ in the
- definition of the operator \f$\partial\f$. The iterators have
- value type <CODE>Simplex_handle</CODE>,
- \li type and method
- <CODE>Filtration_simplex_range filtration_simplex_range ()</CODE>
- that returns a range giving
- access to all the simplices of the complex read in the order
- assigned by the indexing scheme,
- \li type and method
- <CODE>Filtration_value filtration (Simplex_handle)</CODE> that returns the value of
- the filtration on the simplex represented by the handle.
-
- <DT>Homology:</DT>
- For a ring \f$\mathcal{R}\f$, the group of <EM>n-chains</EM>,
- denoted \f$\mathbf{C}_n(\mathbf{K},\mathcal{R})\f$, of \f$\mathbf{K}\f$ is the
- group of formal sums of
- n-simplices with \f$\mathcal{R}\f$ coefficients. The <EM>boundary operator</EM> is a
- linear operator
- \f$\partial_n: \mathbf{C}_n(\mathbf{K},\mathcal{R}) \rightarrow \mathbf{C}_{n-1}(\mathbf{K},\mathcal{R})\f$
- such that \f$\partial_n \sigma = \partial_n [v_0, \cdots , v_n] =
- \sum_{i=0}^n (-1)^{i}[v_0,\cdots ,\widehat{v_i}, \cdots,v_n]\f$,
- where \f$\widehat{v_i}\f$ means \f$v_i\f$ is omitted from the list. The chain
- groups form a sequence:
-
- \f[\cdots \ \ \mathbf{C}_n(\mathbf{K},\mathcal{R}) \xrightarrow{\ \partial_n\ } \mathbf{C}_{n-1}(\mathbf{K},\mathcal{R})
- \xrightarrow{\partial_{n-1}} \cdots \xrightarrow{\ \partial_2 \ }
- \mathbf{C}_1(\mathbf{K},\mathcal{R}) \xrightarrow{\ \partial_1 \ }  \mathbf{C}_0(\mathbf{K},\mathcal{R}) \f]
-
- of finitely many groups \f$\mathbf{C}_n(\mathbf{K},\mathcal{R})\f$ and homomorphisms
- \f$\partial_n\f$, indexed by the dimension \f$n \geq 0\f$.
- The boundary operators satisfy the property \f$\partial_n \circ \partial_{n+1}=0\f$
- for every \f$n > 0\f$
- and we define the homology groups:
-
- \f[\mathbf{H}_n(\mathbf{K},\mathcal{R}) = \ker \partial_n / \mathrm{im} \  \partial_{n+1}\f]
-
- We refer to \cite Munkres-elementsalgtop1984 for an introduction to homology
- theory and to \cite DBLP:books/daglib/0025666 for an introduction to persistent homology.
-
- <DT>Indexing Scheme:</DT>
- "Changing" a simplicial complex consists in applying a simplicial map.
- An <EM>indexing scheme</EM> is a directed graph together with a traversal
- order, such that two
- consecutive nodes in the graph are connected by an arrow (either forward or backward).
- The nodes represent simplicial complexes and the directed edges simplicial maps.
-
- From the computational point of view, there are two types of indexing schemes of
- interest
- in persistent homology: <EM>linear</EM> ones
- \f$\bullet \longrightarrow \bullet \longrightarrow \cdots \longrightarrow \bullet
- \longrightarrow \bullet\f$
- in persistent homology \cite DBLP:journals/dcg/ZomorodianC05 ,
- and <EM>zigzag</EM> ones
- \f$\bullet \longrightarrow \bullet \longleftarrow \cdots
- \longrightarrow \bullet
- \longleftarrow \bullet \f$ in zigzag persistent
- homology \cite DBLP:journals/focm/CarlssonS10.
- These indexing schemes have a natural left-to-right traversal order, and we
- describe them with ranges and iterators.
- In the current release of the Gudhi library, only the linear case is implemented.
-
- In the following, we consider the case where the indexing scheme is induced
- by a filtration.
- Ordering the simplices
- by increasing filtration values (breaking ties so as a simplex appears after
- its subsimplices of same filtration value) provides an indexing scheme.
-
-\section Examples
-    We provide several example files: run these examples with -h for details on their use, and read the README file.
-
-\li <CODE>rips_persistence.cpp</CODE> computes the Rips complex of a point cloud and its persistence diagram.
-
-\li <CODE>rips_multifield_persistence.cpp</CODE> computes the Rips complex of a point cloud and its persistence diagram 
-with a family of field coefficients.
-
-\li <CODE>performance_rips_persistence.cpp</CODE> provides timings for the construction of the Rips complex on a set of 
-points sampling a Klein bottle in \f$\mathbb{R}^5\f$ with a simplex tree, its conversion to a 
-Hasse diagram and the computation of persistent homology and multi-field persistent homology for the 
-different representations.
-
-
-
- \author    Clément Maria
- \version   1.0
- \date      2014
- \copyright GNU General Public License v3.
- @{  
- */
-
 /** \brief Computes the persistent cohomology of a filtered complex.
  *
+ * \ingroup persistent_cohomology
+ * 
  * The computation is implemented with a Compressed Annotation Matrix
  * (CAM)\cite DBLP:conf/esa/BoissonnatDM13,
  * and is adapted to the computation of Multi-Field Persistent Homology (MF)
@@ -197,8 +59,8 @@ different representations.
  * \implements PersistentHomology
  *
  */
-// Memory allocation policy: classic, use a mempool, etc.*/
-template<class FilteredComplex, class CoefficientField>  // to do mem allocation policy: classic, mempool, etc.
+// TODO(CM): Memory allocation policy: classic, use a mempool, etc.
+template<class FilteredComplex, class CoefficientField>
 class Persistent_cohomology {
  public:
   typedef FilteredComplex Complex_ds;
@@ -207,7 +69,7 @@ class Persistent_cohomology {
   typedef typename Complex_ds::Simplex_handle Simplex_handle;
   typedef typename Complex_ds::Filtration_value Filtration_value;
   typedef typename CoefficientField::Element Arith_element;
-// Compressed Annotation Matrix types:
+  // Compressed Annotation Matrix types:
   // Column type
   typedef Persistent_cohomology_column<Simplex_key, Arith_element> Column;  // contains 1 set_hook
   // Cell type
@@ -219,15 +81,16 @@ class Persistent_cohomology {
 
   typedef boost::intrusive::set<Column,
       boost::intrusive::constant_time_size<false> > Cam;
-// Sparse column type for the annotation of the boundary of an element.
+  // Sparse column type for the annotation of the boundary of an element.
   typedef std::vector<std::pair<Simplex_key, Arith_element> > A_ds_type;
-// Persistent interval type. The Arith_element field is used for the multi-field framework.
+  // Persistent interval type. The Arith_element field is used for the multi-field framework.
   typedef std::tuple<Simplex_handle, Simplex_handle, Arith_element> Persistent_interval;
 
   /** \brief Initializes the Persistent_cohomology class.
    *
    * @param[in] cpx Complex for which the persistent homology is computed.
-   cpx is a model of FilteredComplex
+   * cpx is a model of FilteredComplex
+   * @exception std::out_of_range In case the number of simplices is more than Simplex_key type numeric limit.
    */
   explicit Persistent_cohomology(Complex_ds& cpx)
       : cpx_(&cpx),
@@ -245,6 +108,10 @@ class Persistent_cohomology {
         interval_length_policy(&cpx, 0),
         column_pool_(),  // memory pools for the CAM
         cell_pool_() {
+    if (cpx_->num_simplices() > std::numeric_limits<Simplex_key>::max()) {
+      // num_simplices must be strictly lower than the limit, because a value is reserved for null_key.
+      throw std::out_of_range ("The number of simplices is more than Simplex_key type numeric limit.");
+    }
     Simplex_key idx_fil = 0;
     for (auto sh : cpx_->filtration_simplex_range()) {
       cpx_->assign_key(sh, idx_fil);
@@ -256,7 +123,7 @@ class Persistent_cohomology {
   /** \brief Initializes the Persistent_cohomology class.
    *
    * @param[in] cpx Complex for which the persistent homology is compiuted.
-   cpx is a model of FilteredComplex
+   * cpx is a model of FilteredComplex
    *
    * @param[in] persistence_dim_max if true, the persistent homology for the maximal dimension in the
    *                                complex is computed. If false, it is ignored. Default is false.
@@ -345,7 +212,7 @@ class Persistent_cohomology {
       persistent_pairs_.emplace_back(
           cpx_->simplex(zero_idx.second), cpx_->null_simplex(), coeff_field_.characteristic());
     }
-// Compute infinite interval of dimension > 0
+    // Compute infinite interval of dimension > 0
     for (auto cocycle : transverse_idx_) {
       persistent_pairs_.emplace_back(
           cpx_->simplex(cocycle.first), cpx_->null_simplex(), cocycle.second.characteristics_);
@@ -447,14 +314,14 @@ class Persistent_cohomology {
         // Find its annotation vector
         curr_col = ds_repr_[dsets_.find_set(key)];
         if (curr_col != NULL) {  // and insert it in annotations_in_boundary with multyiplicative factor "sign".
-	  annotations_in_boundary.emplace_back(curr_col, sign);
+          annotations_in_boundary.emplace_back(curr_col, sign);
         }
       }
       sign = -sign;
     }
     // Place identical annotations consecutively so we can easily sum their multiplicities.
     std::sort(annotations_in_boundary.begin(), annotations_in_boundary.end(),
-	[](annotation_t const& a, annotation_t const& b) { return a.first < b.first; });
+              [](annotation_t const& a, annotation_t const& b) { return a.first < b.first; });
 
     // Sum the annotations with multiplicity, using a map<key,coeff>
     // to represent a sparse vector.
@@ -464,7 +331,7 @@ class Persistent_cohomology {
       Column* col = ann_it->first;
       int mult = ann_it->second;
       while (++ann_it != annotations_in_boundary.end() && ann_it->first == col) {
-	mult += ann_it->second;
+        mult += ann_it->second;
       }
       // The following test is just a heuristic, it is not required, and it is fine that is misses p == 0.
       if (mult != coeff_field_.additive_identity()) {  // For all columns in the boundary,
@@ -705,7 +572,6 @@ class Persistent_cohomology {
    * feature exists in homology with Z/piZ coefficients.
    */
   void output_diagram(std::ostream& ostream = std::cout) {
-
     cmp_intervals_by_length cmp(cpx_);
     std::sort(std::begin(persistent_pairs_), std::end(persistent_pairs_), cmp);
     bool has_infinity = std::numeric_limits<Filtration_value>::has_infinity;
@@ -733,12 +599,105 @@ class Persistent_cohomology {
     }
   }
 
+  /** @brief Returns Betti numbers.
+   * @return A vector of Betti numbers.
+   */
+  std::vector<int> betti_numbers() const {
+    // Init Betti numbers vector with zeros until Simplicial complex dimension
+    std::vector<int> betti_numbers(cpx_->dimension(), 0);
+
+    for (auto pair : persistent_pairs_) {
+      // Count never ended persistence intervals
+      if (cpx_->null_simplex() == get<1>(pair)) {
+        // Increment corresponding betti number
+        betti_numbers[cpx_->dimension(get<0>(pair))] += 1;
+      }
+    }
+    return betti_numbers;
+  }
+
+  /** @brief Returns the Betti number of the dimension passed by parameter.
+   * @param[in] dimension The Betti number dimension to get.
+   * @return Betti number of the given dimension
+   *
+   */
+  int betti_number(int dimension) const {
+    int betti_number = 0;
+
+    for (auto pair : persistent_pairs_) {
+      // Count never ended persistence intervals
+      if (cpx_->null_simplex() == get<1>(pair)) {
+        if (cpx_->dimension(get<0>(pair)) == dimension) {
+          // Increment betti number found
+          ++betti_number;
+        }
+      }
+    }
+    return betti_number;
+  }
+
+  /** @brief Returns the persistent Betti numbers.
+   * @param[in] from The persistence birth limit to be added in the number \f$(persistent birth \leq from)\f$.
+   * @param[in] to The persistence death limit to be added in the number  \f$(persistent death > to)\f$.
+   * @return A vector of persistent Betti numbers.
+   */
+  std::vector<int> persistent_betti_numbers(Filtration_value from, Filtration_value to) const {
+    // Init Betti numbers vector with zeros until Simplicial complex dimension
+    std::vector<int> betti_numbers(cpx_->dimension(), 0);
+
+    for (auto pair : persistent_pairs_) {
+      // Count persistence intervals that covers the given interval
+      // null_simplex test : if the function is called with to=+infinity, we still get something useful. And it will
+      // still work if we change the complex filtration function to reject null simplices.
+      if (cpx_->filtration(get<0>(pair)) <= from &&
+          (get<1>(pair) == cpx_->null_simplex() || cpx_->filtration(get<1>(pair)) > to)) {
+        // Increment corresponding betti number
+        betti_numbers[cpx_->dimension(get<0>(pair))] += 1;
+      }
+    }
+    return betti_numbers;
+  }
+
+  /** @brief Returns the persistent Betti number of the dimension passed by parameter.
+   * @param[in] dimension The Betti number dimension to get.
+   * @param[in] from The persistence birth limit to be added in the number \f$(persistent birth \leq from)\f$.
+   * @param[in] to The persistence death limit to be added in the number  \f$(persistent death > to)\f$.
+   * @return Persistent Betti number of the given dimension
+   */
+  int persistent_betti_number(int dimension, Filtration_value from, Filtration_value to) const {
+    int betti_number = 0;
+
+    for (auto pair : persistent_pairs_) {
+      // Count persistence intervals that covers the given interval
+      // null_simplex test : if the function is called with to=+infinity, we still get something useful. And it will
+      // still work if we change the complex filtration function to reject null simplices.
+      if (cpx_->filtration(get<0>(pair)) <= from &&
+          (get<1>(pair) == cpx_->null_simplex() || cpx_->filtration(get<1>(pair)) > to)) {
+        if (cpx_->dimension(get<0>(pair)) == dimension) {
+          // Increment betti number found
+          ++betti_number;
+        }
+      }
+    }
+    return betti_number;
+  }
+
+  /** @brief Returns the persistent pairs.
+   * @return Persistent pairs
+   *
+   */
+  const std::vector<Persistent_interval>& get_persistent_pairs() const {
+    return persistent_pairs_;
+  }
+
  private:
   /*
    * Structure representing a cocycle.
    */
   struct cocycle {
-    cocycle() {
+    cocycle()
+        : row_(nullptr),
+          characteristics_() {
     }
     cocycle(Arith_element characteristics, Hcell * row)
         : row_(row),
@@ -779,8 +738,6 @@ class Persistent_cohomology {
   Simple_object_pool<Cell> cell_pool_;
 };
 
-/** @} */  // end defgroup persistent_cohomology
-
 }  // namespace persistent_cohomology
 
 }  // namespace Gudhi
diff --git a/src/Persistent_cohomology/test/CMakeLists.txt b/src/Persistent_cohomology/test/CMakeLists.txt
index ed63a6ac..a21f39c4 100644
--- a/src/Persistent_cohomology/test/CMakeLists.txt
+++ b/src/Persistent_cohomology/test/CMakeLists.txt
@@ -1,21 +1,23 @@
 cmake_minimum_required(VERSION 2.6)
-project(GUDHIPersistentCohomologyUT)
+project(Persistent_cohomology_tests)
 
 if (GCOVR_PATH)
   # for gcovr to make coverage reports - Corbera Jenkins plugin
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
-  set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fprofile-arcs -ftest-coverage")	
-  set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fprofile-arcs -ftest-coverage")
-endif()
+endif(GCOVR_PATH)
 if (GPROF_PATH)
   # for gprof to make coverage reports - Jenkins
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
-  set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -pg")
-  set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -pg")
-endif()
+endif(GPROF_PATH)
 
 add_executable ( PersistentCohomologyUT persistent_cohomology_unit_test.cpp )
 target_link_libraries(PersistentCohomologyUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+add_executable ( BettiNumbersUT betti_numbers_unit_test.cpp )
+target_link_libraries(BettiNumbersUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+if (TBB_FOUND)
+  target_link_libraries(PersistentCohomologyUT ${TBB_LIBRARIES})
+  target_link_libraries(BettiNumbersUT ${TBB_LIBRARIES})
+endif(TBB_FOUND)
 
 # Unitary tests
 add_test(NAME PersistentCohomologyUT 
@@ -24,9 +26,17 @@ add_test(NAME PersistentCohomologyUT
     # XML format for Jenkins xUnit plugin 
     --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/PersistentCohomologyUT.xml --log_level=test_suite --report_level=no)
 
+add_test(NAME BettiNumbersUT 
+  COMMAND ${CMAKE_CURRENT_BINARY_DIR}/BettiNumbersUT
+    # XML format for Jenkins xUnit plugin 
+    --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/BettiNumbersUT.xml --log_level=test_suite --report_level=no)
+
 if(GMPXX_FOUND AND GMP_FOUND)
   add_executable ( PersistentCohomologyMultiFieldUT persistent_cohomology_unit_test_multi_field.cpp )
   target_link_libraries(PersistentCohomologyMultiFieldUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
+  if (TBB_FOUND)
+    target_link_libraries(PersistentCohomologyMultiFieldUT ${TBB_LIBRARIES})
+  endif(TBB_FOUND)
 
   # Unitary tests
   add_test(NAME PersistentCohomologyMultiFieldUT
@@ -35,5 +45,5 @@ if(GMPXX_FOUND AND GMP_FOUND)
       # XML format for Jenkins xUnit plugin 
       --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/PersistentCohomologyMultiFieldUT.xml --log_level=test_suite --report_level=no)
 
-endif()
+endif(GMPXX_FOUND AND GMP_FOUND)
 
diff --git a/src/Persistent_cohomology/test/betti_numbers_unit_test.cpp b/src/Persistent_cohomology/test/betti_numbers_unit_test.cpp
new file mode 100644
index 00000000..40221005
--- /dev/null
+++ b/src/Persistent_cohomology/test/betti_numbers_unit_test.cpp
@@ -0,0 +1,234 @@
+#include <iostream>
+#include <string>
+#include <algorithm>
+#include <utility> // std::pair, std::make_pair
+#include <cmath> // float comparison
+#include <limits>
+
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE "betti_numbers"
+#include <boost/test/unit_test.hpp>
+
+#include "gudhi/Simplex_tree.h"
+#include "gudhi/Persistent_cohomology.h"
+
+struct MiniSTOptions : Gudhi::Simplex_tree_options_full_featured {
+  // Implicitly use 0 as filtration value for all simplices
+  static const bool store_filtration = false;
+  // The persistence algorithm needs this
+  static const bool store_key = true;
+  // I have few vertices
+  typedef short Vertex_handle;
+};
+
+using Mini_simplex_tree = Gudhi::Simplex_tree<MiniSTOptions>;
+using Mini_st_persistence =
+    Gudhi::persistent_cohomology::Persistent_cohomology<Mini_simplex_tree, Gudhi::persistent_cohomology::Field_Zp>;
+
+/*
+ * Compare two intervals by dimension, then by length.
+ */
+template<class Simplicial_complex>
+struct cmp_intervals_by_dim_then_length {
+  explicit cmp_intervals_by_dim_then_length(Simplicial_complex * sc)
+      : sc_(sc) { }
+
+  template<typename Persistent_interval>
+  bool operator()(const Persistent_interval & p1, const Persistent_interval & p2) {
+    if (sc_->dimension(get < 0 > (p1)) == sc_->dimension(get < 0 > (p2)))
+      return (sc_->filtration(get < 1 > (p1)) - sc_->filtration(get < 0 > (p1))
+              > sc_->filtration(get < 1 > (p2)) - sc_->filtration(get < 0 > (p2)));
+    else
+      return (sc_->dimension(get < 0 > (p1)) > sc_->dimension(get < 0 > (p2)));
+  }
+  Simplicial_complex* sc_;
+};
+
+BOOST_AUTO_TEST_CASE( plain_homology_betti_numbers )
+{
+  Mini_simplex_tree st;
+
+  /* Complex to build. */
+  /*    1   4          */
+  /*    o---o          */
+  /*   /3\ /           */
+  /*  o---o   o        */
+  /*  2   0   5        */
+  const short tetra0123[] = {0, 1, 2, 3};
+  const short edge04[] = {0, 4};
+  const short edge14[] = {1, 4};
+  const short vertex5[] = {5};
+  st.insert_simplex_and_subfaces(tetra0123);
+  st.insert_simplex_and_subfaces(edge04);
+  st.insert_simplex(edge14);
+  st.insert_simplex(vertex5);
+  // FIXME: Remove this line
+  st.set_dimension(3);
+
+  // Sort the simplices in the order of the filtration
+  st.initialize_filtration();
+
+  // Class for homology computation
+  Mini_st_persistence pcoh(st);
+
+  // Initialize the coefficient field Z/3Z for homology
+  pcoh.init_coefficients(3);
+
+  // Compute the persistence diagram of the complex
+  pcoh.compute_persistent_cohomology();
+
+  // Print the result. The format is, on each line: 2 dim 0 inf
+  // where 2 represents the field, dim the dimension of the feature.
+  // 2  0 0 inf 
+  // 2  0 0 inf 
+  // 2  1 0 inf 
+  // means that in Z/2Z-homology, the Betti numbers are b0=2 and b1=1.
+  
+  BOOST_CHECK(pcoh.betti_number(0) == 2);
+  BOOST_CHECK(pcoh.betti_number(1) == 1);
+  BOOST_CHECK(pcoh.betti_number(2) == 0);
+
+  std::vector<int> bns = pcoh.betti_numbers();
+  BOOST_CHECK(bns.size() == 3);
+  BOOST_CHECK(bns[0] == 2);
+  BOOST_CHECK(bns[1] == 1);
+  BOOST_CHECK(bns[2] == 0);
+  
+  // Custom sort and output persistence
+  cmp_intervals_by_dim_then_length<Mini_simplex_tree> cmp(&st);
+  auto persistent_pairs = pcoh.get_persistent_pairs();
+  
+  std::sort(std::begin(persistent_pairs), std::end(persistent_pairs), cmp);
+  
+  BOOST_CHECK(persistent_pairs.size() == 3);
+  // persistent_pairs[0] = 2  1 0 inf
+  BOOST_CHECK(st.dimension(get<0>(persistent_pairs[0])) == 1);
+  BOOST_CHECK(st.filtration(get<0>(persistent_pairs[0])) == 0);
+  BOOST_CHECK(get<1>(persistent_pairs[0]) == st.null_simplex());
+
+  // persistent_pairs[1] = 2  0 0 inf
+  BOOST_CHECK(st.dimension(get<0>(persistent_pairs[1])) == 0);
+  BOOST_CHECK(st.filtration(get<0>(persistent_pairs[1])) == 0);
+  BOOST_CHECK(get<1>(persistent_pairs[1]) == st.null_simplex());
+
+  // persistent_pairs[2] = 2  0 0 inf
+  BOOST_CHECK(st.dimension(get<0>(persistent_pairs[2])) == 0);
+  BOOST_CHECK(st.filtration(get<0>(persistent_pairs[2])) == 0);
+  BOOST_CHECK(get<1>(persistent_pairs[2]) == st.null_simplex());
+}
+
+using Simplex_tree = Gudhi::Simplex_tree<>;
+using St_persistence =
+    Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Gudhi::persistent_cohomology::Field_Zp>;
+
+BOOST_AUTO_TEST_CASE( betti_numbers )
+{
+  Simplex_tree st;
+
+  /* Complex to build. */
+  /*    1   4          */
+  /*    o---o          */
+  /*   /3\ /           */
+  /*  o---o   o        */
+  /*  2   0   5        */
+  const short tetra0123[] = {0, 1, 2, 3};
+  const short edge04[] = {0, 4};
+  const short edge14[] = {1, 4};
+  const short vertex5[] = {5};
+  st.insert_simplex_and_subfaces(tetra0123, 4.0);
+  st.insert_simplex_and_subfaces(edge04, 2.0);
+  st.insert_simplex(edge14, 2.0);
+  st.insert_simplex(vertex5, 1.0);
+  // FIXME: Remove this line
+  st.set_dimension(3);
+
+  // Sort the simplices in the order of the filtration
+  st.initialize_filtration();
+
+  // Class for homology computation
+  St_persistence pcoh(st);
+
+  // Initialize the coefficient field Z/3Z for homology
+  pcoh.init_coefficients(3);
+
+  // Compute the persistence diagram of the complex
+  pcoh.compute_persistent_cohomology();
+
+  // Check the Betti numbers are b0=2, b1=1 and b2=0.
+  BOOST_CHECK(pcoh.betti_number(0) == 2);
+  BOOST_CHECK(pcoh.betti_number(1) == 1);
+  BOOST_CHECK(pcoh.betti_number(2) == 0);
+
+  // Check the Betti numbers are b0=2, b1=1 and b2=0.
+  std::vector<int> bns = pcoh.betti_numbers();
+  BOOST_CHECK(bns.size() == 3);
+  BOOST_CHECK(bns[0] == 2);
+  BOOST_CHECK(bns[1] == 1);
+  BOOST_CHECK(bns[2] == 0);
+  
+  // Check the persistent Betti numbers in [4., 10.] are b0=2, b1=1 and b2=0.
+  BOOST_CHECK(pcoh.persistent_betti_number(0, 4., 10.) == 2);
+  BOOST_CHECK(pcoh.persistent_betti_number(1, 4., 10.) == 1);
+  BOOST_CHECK(pcoh.persistent_betti_number(2, 4., 10.) == 0);
+
+  // Check the persistent Betti numbers in [2., 100.] are b0=2, b1=0 and b2=0.
+  BOOST_CHECK(pcoh.persistent_betti_number(0, 2., 100.) == 2);
+  BOOST_CHECK(pcoh.persistent_betti_number(1, 2., 100.) == 0);
+  BOOST_CHECK(pcoh.persistent_betti_number(2, 2., 100.) == 0);
+
+  // Check the persistent Betti numbers in [1., 1000.] are b0=1, b1=0 and b2=0.
+  BOOST_CHECK(pcoh.persistent_betti_number(0, 1., 1000.) == 1);
+  BOOST_CHECK(pcoh.persistent_betti_number(1, 1., 1000.) == 0);
+  BOOST_CHECK(pcoh.persistent_betti_number(2, 1., 1000.) == 0);
+
+  // Check the persistent Betti numbers in [.9, 1000.] are b0=0, b1=0 and b2=0.
+  BOOST_CHECK(pcoh.persistent_betti_number(0, .9, 1000.) == 0);
+  BOOST_CHECK(pcoh.persistent_betti_number(1, .9, 1000.) == 0);
+  BOOST_CHECK(pcoh.persistent_betti_number(2, .9, 1000.) == 0);
+
+  // Check the persistent Betti numbers in [4.1, 10000.] are b0=2, b1=1 and b2=0.
+  bns = pcoh.persistent_betti_numbers(4.1, 10000.);
+  BOOST_CHECK(bns[0] == 2);
+  BOOST_CHECK(bns[1] == 1);
+  BOOST_CHECK(bns[2] == 0);
+  
+  // Check the persistent Betti numbers in [2.1, 100000.] are b0=2, b1=0 and b2=0.
+  bns = pcoh.persistent_betti_numbers(2.1, 100000.);
+  BOOST_CHECK(bns[0] == 2);
+  BOOST_CHECK(bns[1] == 0);
+  BOOST_CHECK(bns[2] == 0);
+
+  // Check the persistent Betti numbers in [1.1, 1000000.] are b0=1, b1=0 and b2=0.
+  bns = pcoh.persistent_betti_numbers(1.1, 1000000.);
+  BOOST_CHECK(bns[0] == 1);
+  BOOST_CHECK(bns[1] == 0);
+  BOOST_CHECK(bns[2] == 0);
+  
+  // Check the persistent Betti numbers in [.1, 10000000.] are b0=0, b1=0 and b2=0.
+  bns = pcoh.persistent_betti_numbers(.1, 10000000.);
+  BOOST_CHECK(bns[0] == 0);
+  BOOST_CHECK(bns[1] == 0);
+  BOOST_CHECK(bns[2] == 0);
+  
+  // Custom sort and output persistence
+  cmp_intervals_by_dim_then_length<Simplex_tree> cmp(&st);
+  auto persistent_pairs = pcoh.get_persistent_pairs();
+  
+  std::sort(std::begin(persistent_pairs), std::end(persistent_pairs), cmp);
+  
+  BOOST_CHECK(persistent_pairs.size() == 3);
+  // persistent_pairs[0] = 2  1 4 inf
+  BOOST_CHECK(st.dimension(get<0>(persistent_pairs[0])) == 1);
+  BOOST_CHECK(st.filtration(get<0>(persistent_pairs[0])) == 4);
+  BOOST_CHECK(get<1>(persistent_pairs[0]) == st.null_simplex());
+
+  // persistent_pairs[1] = 2  0 2 inf
+  BOOST_CHECK(st.dimension(get<0>(persistent_pairs[1])) == 0);
+  BOOST_CHECK(st.filtration(get<0>(persistent_pairs[1])) == 2);
+  BOOST_CHECK(get<1>(persistent_pairs[1]) == st.null_simplex());
+
+  // persistent_pairs[2] = 2  0 1 inf
+  BOOST_CHECK(st.dimension(get<0>(persistent_pairs[2])) == 0);
+  BOOST_CHECK(st.filtration(get<0>(persistent_pairs[2])) == 1);
+  BOOST_CHECK(get<1>(persistent_pairs[2]) == st.null_simplex());
+}
diff --git a/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp b/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp
index 194b3e74..6efd749e 100644
--- a/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp
+++ b/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp
@@ -4,6 +4,7 @@
 #include <utility> // std::pair, std::make_pair
 #include <cmath> // float comparison
 #include <limits>
+#include <cstdint>  // for std::uint8_t
 
 #define BOOST_TEST_DYN_LINK
 #define BOOST_TEST_MODULE "persistent_cohomology"
@@ -43,7 +44,7 @@ std::string test_rips_persistence(int coefficient, int min_persistence) {
   st.initialize_filtration();
 
   // Compute the persistence diagram of the complex
-  persistent_cohomology::Persistent_cohomology<Simplex_tree<>, Field_Zp> pcoh(st);
+  Persistent_cohomology<Simplex_tree<>, Field_Zp> pcoh(st);
 
   pcoh.init_coefficients( coefficient );  // initializes the coefficient field for homology
   // Check infinite rips
@@ -172,3 +173,45 @@ BOOST_AUTO_TEST_CASE( rips_persistent_cohomology_single_field_dim_5 )
 // std::string str_rips_persistence = test_rips_persistence(6, 0);
 // TODO(VR): division by zero
 // std::string str_rips_persistence = test_rips_persistence(0, 0);
+
+/** SimplexTree minimal options to test the limits.
+ * 
+ * Maximum number of simplices to compute persistence is <CODE>std::numeric_limits<std::uint8_t>::max()<\CODE> = 256.*/
+struct MiniSTOptions {
+  typedef linear_indexing_tag Indexing_tag;
+  typedef short Vertex_handle;
+  typedef double Filtration_value;
+  // Maximum number of simplices to compute persistence is 2^8 - 1 = 255. One is reserved for null_key
+  typedef std::uint8_t Simplex_key;
+  static const bool store_key = true;
+  static const bool store_filtration = false;
+  static const bool contiguous_vertices = false;
+};
+
+using Mini_simplex_tree = Gudhi::Simplex_tree<MiniSTOptions>;
+using Mini_st_persistence =
+    Gudhi::persistent_cohomology::Persistent_cohomology<Mini_simplex_tree, Gudhi::persistent_cohomology::Field_Zp>;
+
+BOOST_AUTO_TEST_CASE( persistence_constructor_exception )
+{
+  Mini_simplex_tree st;
+
+  // To make number of simplices = 255
+  const short simplex_0[] = {0, 1, 2, 3, 4, 5, 6, 7};
+  st.insert_simplex_and_subfaces(simplex_0);
+  // FIXME: Remove this line
+  st.set_dimension(8);
+
+  // Sort the simplices in the order of the filtration
+  st.initialize_filtration();
+
+  BOOST_CHECK(st.num_simplices() <= std::numeric_limits<MiniSTOptions::Simplex_key>::max());
+  // Class for homology computation
+  BOOST_CHECK_NO_THROW(Mini_st_persistence pcoh(st));
+
+  st.insert_simplex({8});
+  BOOST_CHECK(st.num_simplices() > std::numeric_limits<MiniSTOptions::Simplex_key>::max());
+  // Class for homology computation
+  BOOST_CHECK_THROW(Mini_st_persistence pcoh2(st), std::out_of_range);
+
+}
diff --git a/src/Simplex_tree/concept/SimplexKey.h b/src/Simplex_tree/concept/SimplexKey.h
index 7fdbdd84..9fbed401 100644
--- a/src/Simplex_tree/concept/SimplexKey.h
+++ b/src/Simplex_tree/concept/SimplexKey.h
@@ -22,7 +22,7 @@
 
  /** \brief Key type used as simplex identifier.
   *
-  * Must be a signed integer type.
+  * Must be an integer type.
   */
  struct SimplexKey {};
  
diff --git a/src/Simplex_tree/concept/SimplexTreeOptions.h b/src/Simplex_tree/concept/SimplexTreeOptions.h
index d072cf34..89acdc18 100644
--- a/src/Simplex_tree/concept/SimplexTreeOptions.h
+++ b/src/Simplex_tree/concept/SimplexTreeOptions.h
@@ -31,7 +31,7 @@ struct SimplexTreeOptions {
   typedef VertexHandle Vertex_handle;
   /// Must be comparable with operator<.
   typedef FiltrationValue Filtration_value;
-  /// Must be a signed integer type.
+  /// Must be an integer type.
   typedef SimplexKey Simplex_key;
   /// If true, each simplex has extra storage for one `Simplex_key`. Necessary for `Persistent_cohomology`.
   static const bool store_key;
diff --git a/src/Simplex_tree/doc/Intro_simplex_tree.h b/src/Simplex_tree/doc/Intro_simplex_tree.h
new file mode 100644
index 00000000..be061785
--- /dev/null
+++ b/src/Simplex_tree/doc/Intro_simplex_tree.h
@@ -0,0 +1,85 @@
+/*    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):       Clément Maria
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (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 DOC_SIMPLEX_TREE_INTRO_SIMPLEX_TREE_H_
+#define DOC_SIMPLEX_TREE_INTRO_SIMPLEX_TREE_H_
+
+// needs namespace for Doxygen to link on classes
+namespace Gudhi {
+
+
+/** \defgroup simplex_tree Filtered Complexes
+ * @{
+ * \author    Cl&eacute;ment Maria
+ *
+ * A simplicial complex \f$\mathbf{K}\f$ on a set of vertices \f$V = \{1, \cdots ,|V|\}\f$ is a collection of
+ * implices \f$\{\sigma\}\f$, \f$\sigma \subseteq V\f$ such that
+ * \f$\tau \subseteq \sigma \in \mathbf{K} \rightarrow \tau \in \mathbf{K}\f$. The dimension \f$n=|\sigma|-1\f$ of
+ * \f$\sigma\f$ is its number of elements minus \f$1\f$.
+ *
+ * A filtration of a simplicial complex is a function \f$f:\mathbf{K} \rightarrow \mathbb{R}\f$ satisfying
+ * \f$f(\tau)\leq f(\sigma)\f$ whenever \f$\tau \subseteq \sigma\f$. Ordering the simplices by increasing filtration
+ * values (breaking ties so as a simplex appears after its subsimplices of same filtration value) provides an
+ * indexing scheme.
+ *
+ * \section filteredcomplexesimplementation Implementations
+ * \subsection filteredcomplexessimplextree Simplex tree
+ * There are two implementation of complexes. The first on is the Simplex_tree data structure. The simplex tree is an
+ * efficient and flexible data structure for representing general (filtered) simplicial complexes. The data structure
+ * is described in \cite boissonnatmariasimplextreealgorithmica
+ * \image html "Simplex_tree_representation.png" "Simplex tree representation"
+ * 
+ * \subsubsection filteredcomplexessimplextreeexamples Examples
+ * 
+ * Here is a list of simplex tree examples :
+ * \li <a href="_simplex_tree_2simple_simplex_tree_8cpp-example.html">
+ * Simplex_tree/simple_simplex_tree.cpp</a> - Simple simplex tree construction and basic function use.
+ *
+ * \li <a href="_simplex_tree_2simplex_tree_from_cliques_of_graph_8cpp-example.html">
+ * Simplex_tree/simplex_tree_from_cliques_of_graph.cpp</a> - Simplex tree construction from cliques of graph read in
+ * a file.
+ * 
+ * Simplex tree construction with \f$\mathbb{Z}/3\mathbb{Z}\f$ coefficients on weighted graph Klein bottle file:
+ * \code $> ./simplex_tree_from_cliques_of_graph ../../data/points/Klein_bottle_complex.txt 3 \endcode
+ * \code Insert the 1-skeleton in the simplex tree in 0.000404 s. 
+max_dim = 3
+Expand the simplex tree in 3.8e-05 s. 
+Information of the Simplex Tree: 
+Number of vertices = 10   Number of simplices = 98 \endcode
+ * 
+ * \li <a href="_simplex_tree_2simplex_tree_from_alpha_shapes_3_8cpp-example.html">
+ * Simplex_tree/simplex_tree_from_alpha_shapes_3.cpp</a> - Simplex tree is computed and displayed from a 3D alpha
+ * complex (Requires CGAL, GMP and GMPXX to be installed)
+ * 
+ * 
+ * \subsection filteredcomplexeshassecomplex Hasse complex
+ * The second one is the Hasse_complex. The Hasse complex is a data structure representing explicitly all co-dimension
+ * 1 incidence relations in a complex. It is consequently faster when accessing the boundary of a simplex, but is less
+ * compact and harder to construct from scratch.
+ * 
+ * \copyright GNU General Public License v3.
+ * @}
+ */
+
+}  // namespace Gudhi
+
+#endif  // DOC_SIMPLEX_TREE_INTRO_SIMPLEX_TREE_H_
diff --git a/src/Simplex_tree/doc/Simplex_tree_representation.png b/src/Simplex_tree/doc/Simplex_tree_representation.png
new file mode 100644
index 00000000..9d401520
--- /dev/null
+++ b/src/Simplex_tree/doc/Simplex_tree_representation.png
diff --git a/src/Simplex_tree/example/CMakeLists.txt b/src/Simplex_tree/example/CMakeLists.txt
index c70cfe35..9314a805 100644
--- a/src/Simplex_tree/example/CMakeLists.txt
+++ b/src/Simplex_tree/example/CMakeLists.txt
@@ -1,11 +1,17 @@
 cmake_minimum_required(VERSION 2.6)
-project(GUDHISimplexTreeFromFile)
+project(Simplex_tree_examples)
 
 add_executable ( simplex_tree_from_cliques_of_graph simplex_tree_from_cliques_of_graph.cpp )
+if (TBB_FOUND)
+  target_link_libraries(simplex_tree_from_cliques_of_graph ${TBB_LIBRARIES})
+endif()
 add_test(simplex_tree_from_cliques_of_graph_2 ${CMAKE_CURRENT_BINARY_DIR}/simplex_tree_from_cliques_of_graph ${CMAKE_SOURCE_DIR}/data/points/Klein_bottle_complex.txt 2)
 add_test(simplex_tree_from_cliques_of_graph_3 ${CMAKE_CURRENT_BINARY_DIR}/simplex_tree_from_cliques_of_graph ${CMAKE_SOURCE_DIR}/data/points/Klein_bottle_complex.txt 3)
 
 add_executable ( simple_simplex_tree simple_simplex_tree.cpp )
+if (TBB_FOUND)
+  target_link_libraries(simple_simplex_tree ${TBB_LIBRARIES})
+endif()
 add_test(simple_simplex_tree ${CMAKE_CURRENT_BINARY_DIR}/simple_simplex_tree)
 
 add_executable ( mini_simplex_tree mini_simplex_tree.cpp )
@@ -14,11 +20,10 @@ add_test(mini_simplex_tree ${CMAKE_CURRENT_BINARY_DIR}/mini_simplex_tree)
 
 # An example with Simplex-tree using CGAL alpha_shapes_3
 if(GMP_FOUND AND CGAL_FOUND)
-   message("CGAL_lib = ${CGAL_LIBRARIES_DIR}")
-   message("GMP_LIBRARIES = ${GMP_LIBRARIES}")
-   INCLUDE_DIRECTORIES(${GMP_INCLUDE_DIR})
-   INCLUDE_DIRECTORIES(${CGAL_INCLUDE_DIRS})
-   add_executable ( simplex_tree_from_alpha_shapes_3 simplex_tree_from_alpha_shapes_3.cpp )
-   target_link_libraries(simplex_tree_from_alpha_shapes_3 ${GMP_LIBRARIES} ${CGAL_LIBRARY})
-   add_test(simplex_tree_from_alpha_shapes_3 ${CMAKE_CURRENT_BINARY_DIR}/simplex_tree_from_alpha_shapes_3 ${CMAKE_SOURCE_DIR}/data/points/bunny_5000)
+  add_executable ( simplex_tree_from_alpha_shapes_3 simplex_tree_from_alpha_shapes_3.cpp )
+  target_link_libraries(simplex_tree_from_alpha_shapes_3 ${GMP_LIBRARIES} ${CGAL_LIBRARY} ${Boost_SYSTEM_LIBRARY})
+  if (TBB_FOUND)
+    target_link_libraries(simplex_tree_from_alpha_shapes_3 ${TBB_LIBRARIES})
+  endif()
+  add_test(simplex_tree_from_alpha_shapes_3 ${CMAKE_CURRENT_BINARY_DIR}/simplex_tree_from_alpha_shapes_3 ${CMAKE_SOURCE_DIR}/data/points/bunny_5000)
 endif()
diff --git a/src/Simplex_tree/example/README b/src/Simplex_tree/example/README
index 03c759cb..e37af790 100644
--- a/src/Simplex_tree/example/README
+++ b/src/Simplex_tree/example/README
@@ -52,7 +52,7 @@ EXAMPLE OF SIMPLE INSERTION
 
 *** Simplex tree construction with Z/2Z coefficients on weighted graph Klein bottle file:
 
-./simplex_tree_from_file ../../../data/points/Klein_bottle_complex.txt 2
+./simplex_tree_from_cliques_of_graph ../../../data/points/Klein_bottle_complex.txt 2
 Insert the 1-skeleton in the simplex tree in 0 s. 
 Expand the simplex tree in 0 s. 
 Information of the Simplex Tree: 
@@ -60,7 +60,7 @@ Information of the Simplex Tree:
 
 with Z/3Z coefficients:
 
-./simplex_tree_from_file ../../../data/points/Klein_bottle_complex.txt 3
+./simplex_tree_from_cliques_of_graph ../../../data/points/Klein_bottle_complex.txt 3
 
 Insert the 1-skeleton in the simplex tree in 0 s.
 Expand the simplex tree in 0 s.
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h
index 708cdef9..63e3f0e5 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h
@@ -30,61 +30,32 @@
 
 #include <gudhi/reader_utils.h>
 #include <gudhi/graph_simplicial_complex.h>
+#include <gudhi/Debug_utils.h>
 
 #include <boost/container/flat_map.hpp>
 #include <boost/iterator/transform_iterator.hpp>
 #include <boost/graph/adjacency_list.hpp>
+#include <boost/range/adaptor/reversed.hpp>
 
 #ifdef GUDHI_USE_TBB
 #include <tbb/parallel_sort.h>
 #endif
 
-#include <algorithm>
 #include <utility>
 #include <vector>
 #include <functional>  // for greater<>
+#include <stdexcept>
+#include <limits>  // Inf
 #include <initializer_list>
+#include <algorithm>  // for std::max
+#include <cstdint>  // for std::uint32_t
 
 namespace Gudhi {
 
-/** \defgroup simplex_tree Filtered Complexes
- *
- * A simplicial complex \f$\mathbf{K}\f$
- * on a set of vertices \f$V = \{1, \cdots ,|V|\}\f$ is a collection of simplices
- * \f$\{\sigma\}\f$,
- * \f$\sigma \subseteq V\f$ such that \f$\tau \subseteq \sigma \in \mathbf{K} \rightarrow \tau \in
- * \mathbf{K}\f$. The
- * dimension \f$n=|\sigma|-1\f$ of \f$\sigma\f$ is its number of elements minus \f$1\f$.
- *
- * A filtration of a simplicial complex is
- * a function \f$f:\mathbf{K} \rightarrow \mathbb{R}\f$ satisfying \f$f(\tau)\leq f(\sigma)\f$ whenever
- * \f$\tau \subseteq \sigma\f$. Ordering the simplices by increasing filtration values
- * (breaking ties so as a simplex appears after its subsimplices of same filtration value)
- * provides an indexing scheme.
- *
-
- <DT>Implementations:</DT>
- There are two implementation of complexes. The first on is the Simplex_tree data structure.
- The simplex tree is an efficient and flexible
- data structure for representing general (filtered) simplicial complexes. The data structure
- is described in \cite boissonnatmariasimplextreealgorithmica
-
- The second one is the Hasse_complex. The Hasse complex is a data structure representing
- explicitly all co-dimension 1 incidence relations in a complex. It is consequently faster
- when accessing the boundary of a simplex, but is less compact and harder to construct from
- scratch.
-
-
- * \author    Clément Maria
- * \version   1.0
- * \date      2014
- * \copyright GNU General Public License v3.
- * @{
- */
-
 struct Simplex_tree_options_full_featured;
 
 /**
+ * \class Simplex_tree Simplex_tree.h gudhi/Simplex_tree.h
  * \brief Simplex Tree data structure for representing simplicial complexes.
  *
  * \details Every simplex \f$[v_0, \cdots ,v_d]\f$ admits a canonical orientation
@@ -107,7 +78,7 @@ class Simplex_tree {
   typedef typename Options::Filtration_value Filtration_value;
   /** \brief Key associated to each simplex.
    *
-   * Must be a signed integer type. */
+   * Must be an integer type. */
   typedef typename Options::Simplex_key Simplex_key;
   /** \brief Type for the vertex handle.
    *
@@ -138,7 +109,8 @@ class Simplex_tree {
     void assign_key(Simplex_key) { }
     Simplex_key key() const { assert(false); return -1; }
   };
-  typedef typename std::conditional<Options::store_key, Key_simplex_base_real, Key_simplex_base_dummy>::type Key_simplex_base;
+  typedef typename std::conditional<Options::store_key, Key_simplex_base_real, Key_simplex_base_dummy>::type
+      Key_simplex_base;
 
   struct Filtration_simplex_base_real {
     Filtration_simplex_base_real() : filt_(0) {}
@@ -304,7 +276,8 @@ class Simplex_tree {
    * of the simplex.
    *
    * @param[in] sh Simplex for which the boundary is computed. */
-  Boundary_simplex_range boundary_simplex_range(Simplex_handle sh) {
+  template<class SimplexHandle>
+  Boundary_simplex_range boundary_simplex_range(SimplexHandle sh) {
     return Boundary_simplex_range(Boundary_simplex_iterator(this, sh),
                                   Boundary_simplex_iterator(this));
   }
@@ -325,11 +298,10 @@ class Simplex_tree {
   Simplex_tree(const Simplex_tree& simplex_source)
       : null_vertex_(simplex_source.null_vertex_),
       threshold_(simplex_source.threshold_),
+      root_(nullptr, null_vertex_ , simplex_source.root_.members_),
       filtration_vect_(),
       dimension_(simplex_source.dimension_) {
     auto root_source = simplex_source.root_;
-    auto memb_source = root_source.members();
-    root_ = Siblings(nullptr, null_vertex_, memb_source);
     rec_copy(&root_, &root_source);
   }
 
@@ -341,7 +313,7 @@ class Simplex_tree {
         Siblings * newsib = new Siblings(sib, sh_source->first);
         newsib->members_.reserve(sh_source->second.children()->members().size());
         for (auto & child : sh_source->second.children()->members())
-          newsib->members_.emplace_hint(newsib->members_.end(), child.first, Node(sib, child.second.filtration()));
+          newsib->members_.emplace_hint(newsib->members_.end(), child.first, Node(newsib, child.second.filtration()));
         rec_copy(newsib, sh_source->second.children());
         sh->second.assign_children(newsib);
       }
@@ -446,6 +418,15 @@ class Simplex_tree {
     }
   }
 
+  /** \brief Sets the filtration value of a simplex.
+   * \exception std::invalid_argument In debug mode, if sh is a null_simplex.
+   */
+  void assign_filtration(Simplex_handle sh, Filtration_value fv) {
+    GUDHI_CHECK(sh != null_simplex(),
+                std::invalid_argument("Simplex_tree::assign_filtration - cannot assign filtration on null_simplex"));
+    sh->second.assign_filtration(fv);
+  }
+
   /** \brief Returns an upper bound of the filtration values of the simplices. */
   Filtration_value filtration() const {
     return threshold_;
@@ -515,9 +496,10 @@ 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 {
+  template<class SimplexHandle>
+  bool has_children(SimplexHandle sh) const {
     return (sh->second.children()->parent() == sh->first);
   }
 
@@ -577,13 +559,25 @@ class Simplex_tree {
   bool contiguous_vertices() const {
     if (root_.members_.empty()) return true;
     if (root_.members_.begin()->first != 0) return false;
-    if (std::prev(root_.members_.end())->first != root_.members_.size()-1) return false;
+    if (std::prev(root_.members_.end())->first != static_cast<Vertex_handle>(root_.members_.size() - 1)) return false;
     return true;
   }
 
  private:
   /** \brief Inserts a simplex represented by a vector of vertex.
-   \warning the vector must be sorted by increasing vertex handle order */
+   * @param[in]  simplex    vector of Vertex_handles, representing the vertices of the new simplex. The vector must be
+   * sorted by increasing vertex handle order.
+   * @param[in]  filtration the filtration value assigned to the new simplex.
+   * @return If the new simplex is inserted successfully (i.e. it was not in the
+   * simplicial complex yet) the bool is set to true and the Simplex_handle is the handle assigned
+   * to the new simplex.
+   * If the insertion fails (the simplex is already there), the bool is set to false. If the insertion
+   * fails and the simplex already in the complex has a filtration value strictly bigger than 'filtration',
+   * we assign this simplex with the new value 'filtration', and set the Simplex_handle field of the
+   * output pair to the Simplex_handle of the simplex. Otherwise, we set the Simplex_handle part to
+   * null_simplex.
+   * 
+  */
   std::pair<Simplex_handle, bool> insert_vertex_vector(const std::vector<Vertex_handle>& simplex,
                                                      Filtration_value filtration) {
     Siblings * curr_sib = &root_;
@@ -616,7 +610,7 @@ class Simplex_tree {
    *
    * @param[in]  simplex    range of Vertex_handles, representing the vertices of the new simplex
    * @param[in]  filtration the filtration value assigned to the new simplex.
-   * The return type is a pair. If the new simplex is inserted successfully (i.e. it was not in the
+   * @return If the new simplex is inserted successfully (i.e. it was not in the
    * simplicial complex yet) the bool is set to true and the Simplex_handle is the handle assigned
    * to the new simplex.
    * If the insertion fails (the simplex is already there), the bool is set to false. If the insertion
@@ -655,7 +649,7 @@ class Simplex_tree {
    *
    * @param[in]  Nsimplex   range of Vertex_handles, representing the vertices of the new N-simplex
    * @param[in]  filtration the filtration value assigned to the new N-simplex.
-   * The return type is a pair. If the new simplex is inserted successfully (i.e. it was not in the
+   * @return If the new simplex is inserted successfully (i.e. it was not in the
    * simplicial complex yet) the bool is set to true and the Simplex_handle is the handle assigned
    * to the new simplex.
    * If the insertion fails (the simplex is already there), the bool is set to false. If the insertion
@@ -664,7 +658,7 @@ class Simplex_tree {
    * output pair to the Simplex_handle of the simplex. Otherwise, we set the Simplex_handle part to
    * null_simplex.
    */
-  template<class InputVertexRange=std::initializer_list<Vertex_handle>>
+  template<class InputVertexRange = std::initializer_list<Vertex_handle>>
   std::pair<Simplex_handle, bool> insert_simplex_and_subfaces(const InputVertexRange& Nsimplex,
                                    Filtration_value filtration = 0) {
     auto first = std::begin(Nsimplex);
@@ -718,7 +712,7 @@ class Simplex_tree {
     } else if (the_simplex.size() == 1) {
       // When reaching the end of recursivity, vector of simplices shall be empty and filled on back recursive
       if ((to_be_inserted.size() != 0) || (to_be_propagated.size() != 0)) {
-        std::cerr << "Simplex_tree::rec_insert_simplex_and_subfaces - Error vector not empty" << std::endl;
+        std::cerr << "Simplex_tree::rec_insert_simplex_and_subfaces - Error vector not empty\n";
         exit(-1);
       }
       std::vector<Vertex_handle> first_simplex(1, the_simplex.back());
@@ -727,7 +721,7 @@ class Simplex_tree {
 
       insert_result = insert_vertex_vector(first_simplex, filtration);
     } else {
-        std::cerr << "Simplex_tree::rec_insert_simplex_and_subfaces - Recursivity error" << std::endl;
+        std::cerr << "Simplex_tree::rec_insert_simplex_and_subfaces - Recursivity error\n";
         exit(-1);
     }
     return insert_result;
@@ -740,7 +734,6 @@ class Simplex_tree {
     sh->second.assign_key(key);
   }
 
- public:
   /** Returns the two Simplex_handle corresponding to the endpoints of
    * and edge. sh must point to a 1-dimensional simplex. This is an
    * optimized version of the boundary computation. */
@@ -750,7 +743,8 @@ class Simplex_tree {
   }
 
   /** Returns the Siblings containing a simplex.*/
-  Siblings * self_siblings(Simplex_handle sh) {
+  template<class SimplexHandle>
+  Siblings* self_siblings(SimplexHandle sh) {
     if (sh->second.children()->parent() == sh->first)
       return sh->second.children()->oncles();
     else
@@ -799,10 +793,9 @@ class Simplex_tree {
      * possible.
      */
 #ifdef GUDHI_USE_TBB
-    tbb::parallel_sort(filtration_vect_, is_before_in_filtration(this));
+    tbb::parallel_sort(filtration_vect_.begin(), filtration_vect_.end(), is_before_in_filtration(this));
 #else
-    std::stable_sort(filtration_vect_.begin(), filtration_vect_.end(),
-                     is_before_in_filtration(this));
+    std::stable_sort(filtration_vect_.begin(), filtration_vect_.end(), is_before_in_filtration(this));
 #endif
   }
 
@@ -929,7 +922,7 @@ class Simplex_tree {
     bool operator()(const Simplex_handle sh1, const Simplex_handle sh2) const {
       // Not using st_->filtration(sh1) because it uselessly tests for null_simplex.
       if (sh1->second.filtration() != sh2->second.filtration()) {
-	return sh1->second.filtration() < sh2->second.filtration();
+        return sh1->second.filtration() < sh2->second.filtration();
       }
       // is sh1 a proper subface of sh2
       return st_->reverse_lexicographic_order(sh1, sh2);
@@ -1106,6 +1099,120 @@ class Simplex_tree {
     }
   }
 
+ public:
+  /** \brief Browse the simplex tree to ensure the filtration is not decreasing.
+   * The simplex tree is browsed starting from the root until the leaf, and the filtration values are set with their
+   * parent value (increased), in case the values are decreasing.
+   * @return The filtration modification information.
+   * \post Some simplex tree functions require the filtration to be valid. `make_filtration_non_decreasing()`
+   * function is not launching `initialize_filtration()` but returns the filtration modification information. If the
+   * complex has changed , please call `initialize_filtration()` to recompute it.
+   */
+  bool make_filtration_non_decreasing() {
+    bool modified = false;
+    // Loop must be from the end to the beginning, as higher dimension simplex are always on the left part of the tree
+    for (auto& simplex : boost::adaptors::reverse(root_.members())) {
+      if (has_children(&simplex)) {
+        modified |= rec_make_filtration_non_decreasing(simplex.second.children());
+      }
+    }
+    return modified;
+  }
+
+ private:
+  /** \brief Recursively Browse the simplex tree to ensure the filtration is not decreasing.
+   * @param[in] sib Siblings to be parsed.
+   * @return The filtration modification information in order to trigger initialize_filtration.
+   */
+  bool rec_make_filtration_non_decreasing(Siblings * sib) {
+    bool modified = false;
+
+    // Loop must be from the end to the beginning, as higher dimension simplex are always on the left part of the tree
+    for (auto& simplex : boost::adaptors::reverse(sib->members())) {
+      // Find the maximum filtration value in the border
+      Boundary_simplex_range boundary = boundary_simplex_range(&simplex);
+      Boundary_simplex_iterator max_border = std::max_element(std::begin(boundary), std::end(boundary),
+                                                              [](Simplex_handle sh1, Simplex_handle sh2) {
+                                                                return filtration(sh1) < filtration(sh2);
+                                                              });
+
+      Filtration_value max_filt_border_value = filtration(*max_border);
+      if (simplex.second.filtration() < max_filt_border_value) {
+        // Store the filtration modification information
+        modified = true;
+        simplex.second.assign_filtration(max_filt_border_value);
+      }
+      if (has_children(&simplex)) {
+        modified |= rec_make_filtration_non_decreasing(simplex.second.children());
+      }
+    }
+    // Make the modified information to be traced by upper call
+    return modified;
+  }
+
+ public:
+  /** \brief Prune above filtration value given as parameter.
+   * @param[in] filtration Maximum threshold value.
+   * @return The filtration modification information.
+   * \post Some simplex tree functions require the filtration to be valid. `prune_above_filtration()`
+   * function is not launching `initialize_filtration()` but returns the filtration modification information. If the
+   * complex has changed , please call `initialize_filtration()` to recompute it.
+   */
+  bool prune_above_filtration(Filtration_value filtration) {
+    return rec_prune_above_filtration(root(), filtration);
+  }
+
+ private:
+  bool rec_prune_above_filtration(Siblings* sib, Filtration_value filt) {
+    auto&& list = sib->members();
+    auto last = std::remove_if(list.begin(), list.end(), [=](Dit_value_t& simplex) {
+        if (simplex.second.filtration() <= filt) return false;
+        if (has_children(&simplex)) rec_delete(simplex.second.children());
+        return true;
+      });
+
+    bool modified = (last != list.end());
+    if (last == list.begin() && sib != root()) {
+      // Removing the whole siblings, parent becomes a leaf.
+      sib->oncles()->members()[sib->parent()].assign_children(sib->oncles());
+      delete sib;
+      return true;
+    } else {
+      // Keeping some elements of siblings. Remove the others, and recurse in the remaining ones.
+      list.erase(last, list.end());
+      for (auto&& simplex : list)
+        if (has_children(&simplex))
+          modified |= rec_prune_above_filtration(simplex.second.children(), filt);
+    }
+    return modified;
+  }
+
+ public:
+  /** \brief Remove a maximal simplex.
+   * @param[in] sh Simplex handle on the maximal simplex to remove.
+   * \pre Please check the simplex has no coface before removing it.
+   * \exception std::invalid_argument In debug mode, if sh has children.
+   * \post Be aware that removing is shifting data in a flat_map (initialize_filtration to be done).
+   */
+  void remove_maximal_simplex(Simplex_handle sh) {
+    // Guarantee the simplex has no children
+    GUDHI_CHECK(!has_children(sh),
+                std::invalid_argument("Simplex_tree::remove_maximal_simplex - argument has children"));
+
+    // Simplex is a leaf, it means the child is the Siblings owning the leaf
+    Siblings* child = sh->second.children();
+
+    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->erase(sh);
+    } else {
+      // Sibling is emptied : must be deleted, and its parent must point on his own Sibling
+      child->oncles()->members().at(child->parent()).assign_children(child->oncles());
+      delete child;
+    }
+  }
+
  private:
   Vertex_handle null_vertex_;
   /** \brief Upper bound on the filtration values of the simplices.*/
@@ -1120,7 +1227,6 @@ class Simplex_tree {
 };
 
 // Print a Simplex_tree in os.
-
 template<typename...T>
 std::ostream& operator<<(std::ostream & os, Simplex_tree<T...> & st) {
   for (auto sh : st.filtration_simplex_range()) {
@@ -1160,25 +1266,31 @@ std::istream& operator>>(std::istream & is, Simplex_tree<T...> & st) {
   return is;
 }
 
-/// Model of SimplexTreeOptions.
+/** Model of SimplexTreeOptions.
+ * 
+ * Maximum number of simplices to compute persistence is <CODE>std::numeric_limits<std::uint32_t>::max()</CODE>
+ * (about 4 billions of simplices). */
 struct Simplex_tree_options_full_featured {
   typedef linear_indexing_tag Indexing_tag;
   typedef int Vertex_handle;
   typedef double Filtration_value;
-  typedef int Simplex_key;
+  typedef std::uint32_t Simplex_key;
   static const bool store_key = true;
   static const bool store_filtration = true;
   static const bool contiguous_vertices = false;
 };
 
-/** Model of SimplexTreeOptions, faster than
-  `Simplex_tree_options_full_featured` but note the unsafe
-  `contiguous_vertices` option. */
+/** Model of SimplexTreeOptions, faster than `Simplex_tree_options_full_featured` but note the unsafe
+ * `contiguous_vertices` option.
+ * 
+ * Maximum number of simplices to compute persistence is <CODE>std::numeric_limits<std::uint32_t>::max()</CODE>
+ * (about 4 billions of simplices). */
+
 struct Simplex_tree_options_fast_persistence {
   typedef linear_indexing_tag Indexing_tag;
   typedef int Vertex_handle;
   typedef float Filtration_value;
-  typedef int Simplex_key;
+  typedef std::uint32_t Simplex_key;
   static const bool store_key = true;
   static const bool store_filtration = true;
   static const bool contiguous_vertices = true;
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h
index 936b7a1f..7e0a454d 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h
@@ -104,7 +104,8 @@ class Simplex_tree_boundary_simplex_iterator : public boost::iterator_facade<
         st_(st)  {
   }
 
-  Simplex_tree_boundary_simplex_iterator(SimplexTree * st, Simplex_handle sh)
+  template<class SimplexHandle>
+  Simplex_tree_boundary_simplex_iterator(SimplexTree * st, SimplexHandle sh)
       : last_(sh->first),
         sib_(nullptr),
         st_(st) {
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 072afc8d..1eca7f6f 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 Dictionary_it iterator) {
+    members_.erase(iterator);
+  }
+
   Simplex_tree_siblings * oncles_;
   Vertex_handle parent_;
   Dictionary members_;
diff --git a/src/Simplex_tree/test/CMakeLists.txt b/src/Simplex_tree/test/CMakeLists.txt
index c9eae163..e95d0782 100644
--- a/src/Simplex_tree/test/CMakeLists.txt
+++ b/src/Simplex_tree/test/CMakeLists.txt
@@ -1,21 +1,20 @@
 cmake_minimum_required(VERSION 2.6)
-project(GUDHISimplexTreeUT)
+project(Simplex_tree_tests)
 
 if (GCOVR_PATH)
   # for gcovr to make coverage reports - Corbera Jenkins plugin
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
-  set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fprofile-arcs -ftest-coverage")	
-  set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fprofile-arcs -ftest-coverage")
 endif()
 if (GPROF_PATH)
   # for gprof to make coverage reports - Jenkins
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
-  set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -pg")
-  set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -pg")
 endif()
 
 add_executable ( SimplexTreeUT simplex_tree_unit_test.cpp )
 target_link_libraries(SimplexTreeUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+if (TBB_FOUND)
+  target_link_libraries(SimplexTreeUT ${TBB_LIBRARIES})
+endif()
 
 # Do not forget to copy test files in current binary dir
 file(COPY "simplex_tree_for_unit_test.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
diff --git a/src/Simplex_tree/test/simplex_tree_unit_test.cpp b/src/Simplex_tree/test/simplex_tree_unit_test.cpp
index 874c3363..28bf202b 100644
--- a/src/Simplex_tree/test/simplex_tree_unit_test.cpp
+++ b/src/Simplex_tree/test/simplex_tree_unit_test.cpp
@@ -795,3 +795,355 @@ BOOST_AUTO_TEST_CASE(non_contiguous) {
   test_simplex_is_vertex(st, *++i, 3);
   BOOST_CHECK(++i == std::end(b));
 }
+
+BOOST_AUTO_TEST_CASE(make_filtration_non_decreasing) {
+  std::cout << "********************************************************************" << std::endl;
+  std::cout << "MAKE FILTRATION NON DECREASING" << std::endl;
+  typedef Simplex_tree<> typeST;
+  typeST st;
+
+  st.insert_simplex_and_subfaces({2, 1, 0}, 2.0);
+  st.insert_simplex_and_subfaces({3, 0}, 2.0);
+  st.insert_simplex_and_subfaces({3, 4, 5}, 2.0);
+  
+  /* Inserted simplex:     */
+  /*    1                  */
+  /*    o                  */
+  /*   /X\                 */
+  /*  o---o---o---o        */
+  /*  2   0   3\X/4        */
+  /*            o          */
+  /*            5          */
+
+  std::cout << "Check default insertion ensures the filtration values are non decreasing" << std::endl;
+  BOOST_CHECK(!st.make_filtration_non_decreasing());
+
+  // Because of non decreasing property of simplex tree, { 0 } , { 1 } and { 0, 1 } are going to be set from value 2.0
+  // 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
+  
+  std::cout << "Check default second insertion ensures the filtration values are non decreasing" << std::endl;
+  BOOST_CHECK(!st.make_filtration_non_decreasing());
+  
+  // Copy original simplex tree
+  typeST st_copy = st;
+
+  // Modify specific values for st to become like st_copy thanks to make_filtration_non_decreasing
+  st.assign_filtration(st.find({0,1,6,7}), 0.8);
+  st.assign_filtration(st.find({0,1,6}), 0.9);
+  st.assign_filtration(st.find({0,6}), 0.6);
+  st.assign_filtration(st.find({3,4,5}), 1.2);
+  st.assign_filtration(st.find({3,4}), 1.1);
+  st.assign_filtration(st.find({4,5}), 1.99);
+  
+  std::cout << "Check the simplex_tree is rolled back in case of decreasing filtration values" << std::endl;
+  BOOST_CHECK(st.make_filtration_non_decreasing());
+  BOOST_CHECK(st == st_copy);
+
+  // Other simplex tree
+  typeST st_other;
+  st_other.insert_simplex_and_subfaces({2, 1, 0}, 3.0);  // This one is different from st
+  st_other.insert_simplex_and_subfaces({3, 0}, 2.0);
+  st_other.insert_simplex_and_subfaces({3, 4, 5}, 2.0);
+  st_other.insert_simplex_and_subfaces({0, 1, 6, 7}, 1.0);
+
+  // Modify specific values for st to become like st_other thanks to make_filtration_non_decreasing
+  st.assign_filtration(st.find({2}), 3.0);
+  // By modifying just the simplex {2}
+  // {0,1,2}, {1,2} and {0,2} will be modified
+  
+  std::cout << "Check the simplex_tree is repaired in case of decreasing filtration values" << std::endl;
+  BOOST_CHECK(st.make_filtration_non_decreasing());
+  BOOST_CHECK(st == st_other);
+
+  // Modify specific values for st still to be non-decreasing
+  st.assign_filtration(st.find({0,1,2}), 10.0);
+  st.assign_filtration(st.find({0,2}), 9.0);
+  st.assign_filtration(st.find({0,1,6,7}), 50.0);
+  st.assign_filtration(st.find({0,1,6}), 49.0);
+  st.assign_filtration(st.find({0,1,7}), 48.0);
+  // Other copy simplex tree
+  typeST st_other_copy = st;
+  
+  std::cout << "Check the simplex_tree is not modified in case of non-decreasing filtration values" << std::endl;
+  BOOST_CHECK(!st.make_filtration_non_decreasing());
+  BOOST_CHECK(st == st_other_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;
+};
+
+BOOST_AUTO_TEST_CASE(remove_maximal_simplex) {
+  std::cout << "********************************************************************" << std::endl;
+  std::cout << "REMOVE MAXIMAL SIMPLEX" << std::endl;
+
+
+  typedef Simplex_tree<MyOptions> miniST;
+  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;
+  typedef Simplex_tree<> typeST;
+  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);
+
+  // 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
+
+  bool simplex_is_changed = false;
+  // Check the no action cases
+  // greater than initial filtration value
+  simplex_is_changed = st.prune_above_filtration(10.0);
+  if (simplex_is_changed)
+    st.initialize_filtration();
+  BOOST_CHECK(st == st_complete);
+  BOOST_CHECK(!simplex_is_changed);
+  // equal to initial filtration value
+  simplex_is_changed = st.prune_above_filtration(6.0);
+  if (simplex_is_changed)
+    st.initialize_filtration();
+  BOOST_CHECK(st == st_complete);
+  BOOST_CHECK(!simplex_is_changed);
+  // lower than initial filtration value, but still greater than the maximum filtration value
+  simplex_is_changed = st.prune_above_filtration(5.0);
+  if (simplex_is_changed)
+    st.initialize_filtration();
+  BOOST_CHECK(st == st_complete);
+  BOOST_CHECK(!simplex_is_changed);
+
+  // Display the Simplex_tree
+  std::cout << "The complex contains " << st.num_simplices() << " simplices";
+  std::cout << " - dimension " << st.dimension() << std::endl;
+  std::cout << "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
+  simplex_is_changed = st.prune_above_filtration(2.5);
+  if (simplex_is_changed)
+    st.initialize_filtration();
+  BOOST_CHECK(st == st_pruned);
+  BOOST_CHECK(simplex_is_changed);
+
+  // Display the Simplex_tree
+  std::cout << "The complex pruned at 2.5 contains " << st.num_simplices() << " simplices";
+  std::cout << " - dimension " << st.dimension() << std::endl;
+
+  simplex_is_changed = st.prune_above_filtration(2.0);
+  if (simplex_is_changed)
+    st.initialize_filtration();
+  
+  std::cout << "The complex pruned at 2.0 contains " << st.num_simplices() << " simplices";
+  std::cout << " - dimension " << st.dimension() << std::endl;
+
+  BOOST_CHECK(st == st_pruned);
+  BOOST_CHECK(!simplex_is_changed);
+
+  typeST st_empty;
+  // FIXME
+  st_empty.set_dimension(3);
+  simplex_is_changed = st.prune_above_filtration(0.0);
+  if (simplex_is_changed)
+    st.initialize_filtration();
+
+  // Display the Simplex_tree
+  std::cout << "The complex pruned at 0.0 contains " << st.num_simplices() << " simplices";
+  std::cout << " - dimension " << st.dimension() << std::endl;
+
+  BOOST_CHECK(st == st_empty);
+  BOOST_CHECK(simplex_is_changed);
+
+  // Test case to the limit
+  simplex_is_changed = st.prune_above_filtration(-1.0);
+  if (simplex_is_changed)
+    st.initialize_filtration();
+  BOOST_CHECK(st == st_empty);
+  BOOST_CHECK(!simplex_is_changed);
+}
+
+BOOST_AUTO_TEST_CASE(mini_prune_above_filtration) {
+  std::cout << "********************************************************************" << std::endl;
+  std::cout << "MINI PRUNE ABOVE FILTRATION" << std::endl;
+  typedef Simplex_tree<MyOptions> typeST;
+  typeST st;
+
+  // FIXME
+  st.set_dimension(3);
+
+  st.insert_simplex_and_subfaces({0, 1, 6, 7});
+  st.insert_simplex_and_subfaces({3, 4, 5});
+  st.insert_simplex_and_subfaces({3, 0});
+  st.insert_simplex_and_subfaces({2, 1, 0});
+
+  // st:
+  //    1   6
+  //    o---o
+  //   /X\7/
+  //  o---o---o---o
+  //  2   0   3\X/4
+  //            o
+  //            5
+
+  st.initialize_filtration();
+  
+  // Display the Simplex_tree
+  std::cout << "The complex contains " << st.num_simplices() << " simplices" << std::endl;
+  BOOST_CHECK(st.num_simplices() == 27);
+
+  // Test case to the limit - With these options, there is no filtration, which means filtration is 0
+  bool simplex_is_changed = st.prune_above_filtration(1.0);
+  if (simplex_is_changed)
+    st.initialize_filtration();
+  // Display the Simplex_tree
+  std::cout << "The complex pruned at 1.0 contains " << st.num_simplices() << " simplices" << std::endl;
+  BOOST_CHECK(!simplex_is_changed);
+  BOOST_CHECK(st.num_simplices() == 27);
+
+  simplex_is_changed = st.prune_above_filtration(0.0);
+  if (simplex_is_changed)
+    st.initialize_filtration();
+  // Display the Simplex_tree
+  std::cout << "The complex pruned at 0.0 contains " << st.num_simplices() << " simplices" << std::endl;
+  BOOST_CHECK(!simplex_is_changed);
+  BOOST_CHECK(st.num_simplices() == 27);
+
+  // Test case to the limit
+  simplex_is_changed = st.prune_above_filtration(-1.0);
+  if (simplex_is_changed)
+    st.initialize_filtration();
+  // Display the Simplex_tree
+  std::cout << "The complex pruned at -1.0 contains " << st.num_simplices() << " simplices" << std::endl;
+  BOOST_CHECK(simplex_is_changed);
+  BOOST_CHECK(st.num_simplices() == 0);
+
+  // Display the Simplex_tree
+  std::cout << "The complex contains " << st.num_simplices() << " simplices" << std::endl;
+
+}
+\ No newline at end of file
diff --git a/src/Skeleton_blocker/concept/SkeletonBlockerDS.h b/src/Skeleton_blocker/concept/SkeletonBlockerDS.h
index c0386590..d82425a0 100644
--- a/src/Skeleton_blocker/concept/SkeletonBlockerDS.h
+++ b/src/Skeleton_blocker/concept/SkeletonBlockerDS.h
@@ -1,20 +1,31 @@
-/*
- * SkeletonBlockerDS.h
+/*    This file is part of the Gudhi Library. The Gudhi library
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++
+ *    library for computational topology.
  *
- *  Created on: Feb 20, 2014 
- *      Author: David Salinas
- *  Copyright 2013 INRIA. All rights reserved
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA
+ *
+ *    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 GUDHI_SKELETONBLOCKERDS_H_
-#define GUDHI_SKELETONBLOCKERDS_H_
-
+#ifndef CONCEPT_SKELETON_BLOCKER_SKELETONBLOCKERDS_H_
+#define CONCEPT_SKELETON_BLOCKER_SKELETONBLOCKERDS_H_
 
 namespace Gudhi {
 
-namespace skbl {
-
-
+namespace skeleton_blocker {
 
 /** \brief Concept for the template class passed for Skeleton_blocker_complex.
  * Most importantly, it contains the nodes for vertices and edges
@@ -22,104 +33,97 @@ namespace skbl {
  * complex. The user can redefine these classes to attach
  * additional information to vertices and edges.
  */
-struct SkeletonBlockerDS
-{
-	/**
-	 * @brief index that allows to find the vertex in the boost graph
-	 */
-	typedef int boost_vertex_handle;
-
-
-	/**
-	 * @brief Root_vertex_handle and Vertex_handle are similar to global and local vertex descriptor
-	 * used in <a href="http://www.boost.org/doc/libs/1_38_0/libs/graph/doc/subgraph.html">boost subgraphs</a>
-	 * and allow to localize a vertex of a subcomplex on its parent root complex.
-	 *
-	 * In gross, vertices are stored in a vector
-	 * and the Root_vertex_handle and Vertex_handle store indices of a vertex in this vector.
-	 *
-	 * For the root simplicial complex, the Root_vertex_handle and Vertex_handle of a vertex
-	 * are the same.
-	 *
-	 *
-	 * For a subcomplex L of a simplicial complex K, the local descriptor, ie the Vertex_handle, of a
-	 * vertex v (that belongs to L)  is its position in the vector of vertices
-	 * of the subcomplex L whereas its Root_vertex_handle (global descriptor) is the position of v in the vector of the
-	 * vertices of the root simplicial complex K.
-	 */
-	struct Root_vertex_handle{
-
-		boost_vertex_handle vertex;
-
-		friend ostream& operator << (ostream& o, const Root_vertex_handle & v);
-	};
-
-	/**
-	 * A Vertex_handle must be Default Constructible, Assignable and Equality Comparable.
-	 */
-	struct Vertex_handle{
-		boost_vertex_handle vertex;
-
-		friend ostream& operator << (ostream& o, const Vertex_handle & v);
-	};
-
-
-	/**
-	 * \brief The type of vertices that are stored the boost graph.
-	 * A Vertex must be Default Constructible and Equality Comparable.
-	 *
-	 */
-	struct Graph_vertex{
-		/** \brief Used to deactivate a vertex for example when contracting an edge.
-		 * It allows in some cases to remove the vertex at low cost.
-		 */
-		void deactivate();
-
-		/** \brief Used to activate a vertex.
-		 */
-		void activate();
-
-		/** \brief Tells if the vertex is active.
-		 */
-		bool is_active() const;
-
-		void set_id(Root_vertex_handle i);
-		Root_vertex_handle get_id() const;
-		virtual string to_string() const ;
-		friend ostream& operator << (ostream& o, const Graph_vertex & v);
-	};
-
-
-	/**
-	 * \brief The type of edges that are stored the boost graph.
-	 * An Edge must be Default Constructible and Equality Comparable.
-	 */
-	struct Graph_edge{
-		/**
-		 * @brief Allows to modify vertices of the edge.
-		 */
-		void setId(Root_vertex_handle a,Root_vertex_handle b);
-
-		/**
-		 * @brief Returns the first vertex of the edge.
-		 */
-		Root_vertex_handle first() const ;
-
-		/**
-		 * @brief Returns the second vertex of the edge.
-		 */
-		Root_vertex_handle second() const ;
-
-		friend ostream& operator << (ostream& o, const Simple_edge & v);
-	};
-
-
+struct SkeletonBlockerDS {
+  /**
+   * @brief index that allows to find the vertex in the boost graph
+   */
+  typedef int boost_vertex_handle;
+
+  /**
+   * @brief Root_vertex_handle and Vertex_handle are similar to global and local vertex descriptor
+   * used in <a href="http://www.boost.org/doc/libs/1_38_0/libs/graph/doc/subgraph.html">boost subgraphs</a>
+   * and allow to localize a vertex of a subcomplex on its parent root complex.
+   *
+   * In gross, vertices are stored in a vector
+   * and the Root_vertex_handle and Vertex_handle store indices of a vertex in this vector.
+   *
+   * For the root simplicial complex, the Root_vertex_handle and Vertex_handle of a vertex
+   * are the same.
+   *
+   *
+   * For a subcomplex L of a simplicial complex K, the local descriptor, ie the Vertex_handle, of a
+   * vertex v (that belongs to L)  is its position in the vector of vertices
+   * of the subcomplex L whereas its Root_vertex_handle (global descriptor) is the position of v in the vector of the
+   * vertices of the root simplicial complex K.
+   */
+  struct Root_vertex_handle {
+    boost_vertex_handle vertex;
+
+    friend ostream& operator<<(ostream& o, const Root_vertex_handle & v);
+  };
+
+  /**
+   * A Vertex_handle must be Default Constructible, Assignable and Equality Comparable.
+   */
+  struct Vertex_handle {
+    boost_vertex_handle vertex;
+
+    friend ostream& operator<<(ostream& o, const Vertex_handle & v);
+  };
+
+  /**
+   * \brief The type of vertices that are stored the boost graph.
+   * A Vertex must be Default Constructible and Equality Comparable.
+   *
+   */
+  struct Graph_vertex {
+    /** \brief Used to deactivate a vertex for example when contracting an edge.
+     * It allows in some cases to remove the vertex at low cost.
+     */
+    void deactivate();
+
+    /** \brief Used to activate a vertex.
+     */
+    void activate();
+
+    /** \brief Tells if the vertex is active.
+     */
+    bool is_active() const;
+
+    void set_id(Root_vertex_handle i);
+    Root_vertex_handle get_id() const;
+    virtual string to_string() const;
+    friend ostream& operator<<(ostream& o, const Graph_vertex & v);
+  };
+
+  /**
+   * \brief The type of edges that are stored the boost graph.
+   * An Edge must be Default Constructible and Equality Comparable.
+   */
+  struct Graph_edge {
+    /**
+     * @brief Allows to modify vertices of the edge.
+     */
+    void setId(Root_vertex_handle a, Root_vertex_handle b);
+
+    /**
+     * @brief Returns the first vertex of the edge.
+     */
+    Root_vertex_handle first() const;
+
+    /**
+     * @brief Returns the second vertex of the edge.
+     */
+    Root_vertex_handle second() const;
+
+    friend ostream& operator<<(ostream& o, const Simple_edge & v);
+  };
 };
 
+}  // namespace skeleton_blocker
 
+namespace skbl = skeleton_blocker;
 
-}  // namespace skbl
-}  // namespace GUDHI
-
+}  // namespace Gudhi
 
-#endif /* GUDHI_SKELETONBLOCKERDS_H_ */
+#endif  // CONCEPT_SKELETON_BLOCKER_SKELETONBLOCKERDS_H_
diff --git a/src/Skeleton_blocker/concept/SkeletonBlockerGeometricDS.h b/src/Skeleton_blocker/concept/SkeletonBlockerGeometricDS.h
index 8fbf0d12..477464c4 100644
--- a/src/Skeleton_blocker/concept/SkeletonBlockerGeometricDS.h
+++ b/src/Skeleton_blocker/concept/SkeletonBlockerGeometricDS.h
@@ -1,16 +1,30 @@
-/*
- * SkeletonBlockerGeometricDS.h
+/*    This file is part of the Gudhi Library. The Gudhi library
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++
+ *    library for computational topology.
  *
- *  Created on: Feb 20, 2014 
- *      Author: David Salinas
- *  Copyright 2013 INRIA. All rights reserved
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA
+ *
+ *    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 GUDHI_SKELETONBLOCKERGEOMETRICDS_H_
-#define GUDHI_SKELETONBLOCKERGEOMETRICDS_H_
+#ifndef CONCEPT_SKELETON_BLOCKER_SKELETONBLOCKERGEOMETRICDS_H_
+#define CONCEPT_SKELETON_BLOCKER_SKELETONBLOCKERGEOMETRICDS_H_
 
 namespace Gudhi {
-namespace skbl {
+namespace skeleton_blocker {
 
 /** 
  * \brief Concept for template class of  Skeleton_blocker_geometric_complex .
@@ -20,55 +34,57 @@ namespace skbl {
  * Graph_edge must specify how to access to an index.
  * 
  */
- //todo the index is just for contraction, to remove
-template<typename GeometryTrait>
-struct SkeletonBlockerGeometricDS : public SkeletonBlockerDS
-{
+// TODO(DS): the index is just for contraction, to remove
 
-	/**
-	 * Geometry information.
-	 */
-	typedef GeometryTrait GT ;
+template<typename GeometryTrait>
+struct SkeletonBlockerGeometricDS : public SkeletonBlockerDS {
+  /**
+   * Geometry information.
+   */
+  typedef GeometryTrait GT;
 
-	/**
-	 * Type of point (should be the same as GT::Point).
-	 */
-	typedef typename GeometryTrait::Point Point;
+  /**
+   * Type of point (should be the same as GT::Point).
+   */
+  typedef typename GeometryTrait::Point Point;
 
-	/**
-	 * @brief Vertex that stores a point.
-	 */
-	class Graph_vertex : public SkeletonBlockerDS::Graph_vertex{
-	public:
-		/**
-		 * @brief Access to the point.
-		 */
-		Point& point();
-		/**
-		 * @brief Access to the point.
-		 */
-		const Point& point();
-	};
+  /**
+   * @brief Vertex that stores a point.
+   */
+  class Graph_vertex : public SkeletonBlockerDS::Graph_vertex {
+   public:
+    /**
+     * @brief Access to the point.
+     */
+    Point& point();
+    /**
+     * @brief Access to the point.
+     */
+    const Point& point();
+  };
 
-	/**
-	 * @brief Edge that allows to access to an index.
-	 * The indices of the edges are used to store heap information
-	 * in the edge contraction algorithm.
-	 */
-	class Graph_Edge : public SkeletonBlockerDS::Graph_edge{
-	public:
-		/**
-		 * @brief Access to the index.
-		 */
-		int& index();
-		/**
-		 * @brief Access to the index.
-		 */
-		int index();
-	};
+  /**
+   * @brief Edge that allows to access to an index.
+   * The indices of the edges are used to store heap information
+   * in the edge contraction algorithm.
+   */
+  class Graph_Edge : public SkeletonBlockerDS::Graph_edge {
+   public:
+    /**
+     * @brief Access to the index.
+     */
+    int& index();
+    /**
+     * @brief Access to the index.
+     */
+    int index();
+  };
 };
 
-}  // namespace skbl
-}  // namespace GUDHI
+}  // namespace skeleton_blocker
+
+namespace skbl = skeleton_blocker;
+
+}  // namespace Gudhi
 
-#endif /* GUDHI_SKELETONBLOCKERGEOMETRICDS_H_ */
+#endif  // CONCEPT_SKELETON_BLOCKER_SKELETONBLOCKERGEOMETRICDS_H_
diff --git a/src/Skeleton_blocker/example/CMakeLists.txt b/src/Skeleton_blocker/example/CMakeLists.txt
index de0c7bba..cc7f37f3 100644
--- a/src/Skeleton_blocker/example/CMakeLists.txt
+++ b/src/Skeleton_blocker/example/CMakeLists.txt
@@ -1,5 +1,5 @@
 cmake_minimum_required(VERSION 2.6)
-project(GUDHIskbl)
+project(Skeleton_blocker_examples)
 
 add_executable(SkeletonBlockerFromSimplices Skeleton_blocker_from_simplices.cpp)
 add_executable(SkeletonBlockerIteration Skeleton_blocker_iteration.cpp)
diff --git a/src/Skeleton_blocker/example/Skeleton_blocker_from_simplices.cpp b/src/Skeleton_blocker/example/Skeleton_blocker_from_simplices.cpp
index 5935a56d..076c6a53 100644
--- a/src/Skeleton_blocker/example/Skeleton_blocker_from_simplices.cpp
+++ b/src/Skeleton_blocker/example/Skeleton_blocker_from_simplices.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014  INRIA
  *
  *    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
@@ -29,11 +29,8 @@
 #include <sstream>
 #include <vector>
 
-using namespace std;
-using namespace Gudhi;
-using namespace skbl;
-
-typedef Skeleton_blocker_complex<Skeleton_blocker_simple_traits> Complex;
+typedef Gudhi::skeleton_blocker::Skeleton_blocker_simple_traits Traits;
+typedef Gudhi::skeleton_blocker::Skeleton_blocker_complex<Traits> Complex;
 typedef Complex::Vertex_handle Vertex_handle;
 typedef Complex::Simplex Simplex;
 
@@ -47,7 +44,7 @@ int main(int argc, char *argv[]) {
   simplices.push_back(Simplex(Vertex_handle(3), Vertex_handle(0), Vertex_handle(1)));
 
   // get complex from top faces
-  Complex complex(make_complex_from_top_faces<Complex>(simplices.begin(), simplices.end()));
+  Complex complex(Gudhi::skeleton_blocker::make_complex_from_top_faces<Complex>(simplices.begin(), simplices.end()));
 
 
   std::cout << "Simplices:" << std::endl;
diff --git a/src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp b/src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp
index 41b5ee00..6a1bc480 100644
--- a/src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp
+++ b/src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014  INRIA
  *
  *    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
@@ -30,12 +30,8 @@
 #include <fstream>
 #include <sstream>
 
-
-using namespace std;
-using namespace Gudhi;
-using namespace skbl;
-
-typedef Skeleton_blocker_complex<Skeleton_blocker_simple_traits> Complex;
+typedef Gudhi::skeleton_blocker::Skeleton_blocker_simple_traits Traits;
+typedef Gudhi::skeleton_blocker::Skeleton_blocker_complex<Traits> Complex;
 typedef Complex::Vertex_handle Vertex_handle;
 typedef Complex::Simplex Simplex;
 
diff --git a/src/Skeleton_blocker/example/Skeleton_blocker_link.cpp b/src/Skeleton_blocker/example/Skeleton_blocker_link.cpp
index 698a8106..58322038 100644
--- a/src/Skeleton_blocker/example/Skeleton_blocker_link.cpp
+++ b/src/Skeleton_blocker/example/Skeleton_blocker_link.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014  INRIA
  *
  *    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
@@ -28,11 +28,8 @@
 #include <fstream>
 #include <sstream>
 
-using namespace std;
-using namespace Gudhi;
-using namespace skbl;
-
-typedef Skeleton_blocker_complex<Skeleton_blocker_simple_traits> Complex;
+typedef Gudhi::skeleton_blocker::Skeleton_blocker_simple_traits Traits;
+typedef Gudhi::skeleton_blocker::Skeleton_blocker_complex<Traits> Complex;
 typedef Complex::Vertex_handle Vertex_handle;
 typedef Complex::Root_vertex_handle Root_vertex_handle;
 typedef Complex::Simplex Simplex;
@@ -47,25 +44,26 @@ int main(int argc, char *argv[]) {
   Simplex tetrahedron(Vertex_handle(0), Vertex_handle(1), Vertex_handle(2), Vertex_handle(3));
   complex.add_simplex(tetrahedron);
 
-  cout << "complex:" << complex.to_string() << endl;
+  std::cout << "complex:" << complex.to_string() << std::endl;
 
   // build the link of vertex 1, eg a triangle {0,2,3}
   auto link = complex.link(Vertex_handle(1));
-  cout << "link:" << link.to_string() << endl;
+  std::cout << "link:" << link.to_string() << std::endl;
 
   // Internally link is a subcomplex of 'complex' and its vertices are stored in a vector.
   // They can be accessed via Vertex_handle(x) where x is an index of the vector.
   // In that example, link has three vertices and thus it contains only
   // Vertex_handle(0),Vertex_handle(1) and Vertex_handle(2) are).
   for (int i = 0; i < 5; ++i)
-    cout << "link.contains_vertex(Vertex_handle(" << i << ")):" << link.contains_vertex(Vertex_handle(i)) << endl;
-  cout << endl;
+    std::cout << "link.contains_vertex(Vertex_handle(" << i << ")):" << link.contains_vertex(Vertex_handle(i)) <<
+        std::endl;
+  std::cout << std::endl;
 
   // To access to the initial vertices eg (0,1,2,3,4),  Root_vertex_handle must be used.
   // For instance, to test if the link contains the vertex that was labeled i:
   for (int i = 0; i < 5; ++i)
-    cout << "link.contains_vertex(Root_vertex_handle(" << i << ")):" <<
-        link.contains_vertex(Root_vertex_handle(i)) << endl;
+    std::cout << "link.contains_vertex(Root_vertex_handle(" << i << ")):" <<
+      link.contains_vertex(Root_vertex_handle(i)) << std::endl;
 
   return EXIT_SUCCESS;
 }
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h
index 615b3a81..32fe411c 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h
@@ -1,24 +1,24 @@
- /*    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):       David Salinas
-  *
-  *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (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/>.
-  */
+/*    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):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA
+ *
+ *    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 SKELETON_BLOCKER_H_
 #define SKELETON_BLOCKER_H_
@@ -31,17 +31,18 @@
 #include <gudhi/Skeleton_blocker/Skeleton_blocker_simple_traits.h>
 #include <gudhi/Skeleton_blocker/Skeleton_blocker_simple_geometric_traits.h>
 
-#include <gudhi/Utils.h>  // xxx
+#include <gudhi/Debug_utils.h>
 
 namespace Gudhi {
 
-namespace skbl {
+namespace skeleton_blocker {
 
-/** \defgroup skbl Skeleton-Blocker 
+/** \defgroup skbl Skeleton-Blocker
+@{
 
 \author David Salinas
 
-\section Introduction
+\section skblintroduction Introduction
 The Skeleton-Blocker data-structure proposes a light encoding for simplicial complexes by storing only an *implicit* representation of its
 simplices 
 \cite socg_blockers_2011,\cite blockers2012.
@@ -52,7 +53,7 @@ This data-structure handles all  simplicial complexes operations such as
  are operations that do not require simplex enumeration such as edge iteration, link computation or simplex contraction.
 
 
-\section Definitions
+\section skbldefinitions Definitions
 
 We recall briefly classical definitions of simplicial complexes  
  \cite Munkres-elementsalgtop1984.
@@ -63,7 +64,7 @@ when \f$ \tau \neq \sigma\f$ we say that \f$ \tau\f$ is a proper-face of \f$ \si
 An abstract simplicial complex is a set of simplices that contains all the faces of its simplices.
 The 1-skeleton of a simplicial complex (or its graph) consists of its elements of dimension lower than 2.
 
-*\image html "ds_representation.png" "Skeleton-blocker representation" width=20cm
+ *\image html "ds_representation.png" "Skeleton-blocker representation" width=20cm
 
 
 To encode, a simplicial complex, one can encodes all its simplices. 
@@ -85,7 +86,7 @@ in next figure. Storing the graph and blockers of such simplicial complexes is m
 their simplices.
 
 
-*\image html "blockers_curve.png" "Number of blockers of random triangulations of 3-spheres" width=10cm
+ *\image html "blockers_curve.png" "Number of blockers of random triangulations of 3-spheres" width=10cm
 
 
 
@@ -107,7 +108,7 @@ and point access in addition.
 
 
 
-\subsection Visitor
+\subsection skblvisitor Visitor
 
 The class Skeleton_blocker_complex has a visitor that is called when usual operations such as adding an edge or remove a vertex are called.
 You may want to use this visitor to compute statistics or to update another data-structure (for instance this visitor is heavily used in the \ref contr package).
@@ -115,7 +116,7 @@ You may want to use this visitor to compute statistics or to update another data
 
 
 
-\section Example
+\section skblexample Example
 
  
 \subsection Iterating Iterating through vertices, edges, blockers and simplices	
@@ -127,46 +128,46 @@ such as the Simplex Tree. The following example computes the Euler Characteristi
 of a simplicial complex.
 
   \code{.cpp}
-	typedef Skeleton_blocker_complex<Skeleton_blocker_simple_traits> Complex;
-	typedef Complex::Vertex_handle Vertex_handle;
-	typedef Complex::Simplex Simplex;
-
-  	const int n = 15;
-
-	// build a full complex with 10 vertices and 2^n-1 simplices
-	Complex complex;
-	for(int i=0;i<n;i++)
-		complex.add_vertex();
-	for(int i=0;i<n;i++)
-		for(int j=0;j<i;j++)
-			complex.add_edge_without_blockers(Vertex_handle(i),Vertex_handle(j));
-
-	// this is just to illustrate iterators, to count number of vertices
-	// or edges, complex.num_vertices() and complex.num_edges() are
-	// more appropriated!
-	unsigned num_vertices = 0;
-	for(auto v : complex.vertex_range()){
-		++num_vertices;
-	}
-
-	unsigned num_edges = 0;
-	for(auto e : complex.edge_range())
-		++num_edges;
-
-	unsigned euler = 0;
-	unsigned num_simplices = 0;
-	// we use a reference to a simplex instead of a copy
-	// value here because a simplex is a set of integers
-	// and copying it cost time
-	for(const Simplex & s : complex.star_simplex_range()){
-		++num_simplices;
-		if(s.dimension()%2 == 0) 
-			euler += 1;
-		else 
-			euler -= 1;
-	}
-	std::cout << "Saw "<<num_vertices<<" vertices, "<<num_edges<<" edges and "<<num_simplices<<" simplices"<<std::endl;
-	std::cout << "The Euler Characteristic is "<<euler<<std::endl;
+        typedef Skeleton_blocker_complex<Skeleton_blocker_simple_traits> Complex;
+        typedef Complex::Vertex_handle Vertex_handle;
+        typedef Complex::Simplex Simplex;
+
+        const int n = 15;
+
+        // build a full complex with 10 vertices and 2^n-1 simplices
+        Complex complex;
+        for(int i=0;i<n;i++)
+                complex.add_vertex();
+        for(int i=0;i<n;i++)
+                for(int j=0;j<i;j++)
+                        complex.add_edge_without_blockers(Vertex_handle(i),Vertex_handle(j));
+
+        // this is just to illustrate iterators, to count number of vertices
+        // or edges, complex.num_vertices() and complex.num_edges() are
+        // more appropriated!
+        unsigned num_vertices = 0;
+        for(auto v : complex.vertex_range()){
+                ++num_vertices;
+        }
+
+        unsigned num_edges = 0;
+        for(auto e : complex.edge_range())
+                ++num_edges;
+
+        unsigned euler = 0;
+        unsigned num_simplices = 0;
+        // we use a reference to a simplex instead of a copy
+        // value here because a simplex is a set of integers
+        // and copying it cost time
+        for(const Simplex & s : complex.star_simplex_range()){
+                ++num_simplices;
+                if(s.dimension()%2 == 0) 
+                        euler += 1;
+                else 
+                        euler -= 1;
+        }
+        std::cout << "Saw "<<num_vertices<<" vertices, "<<num_edges<<" edges and "<<num_simplices<<" simplices"<<std::endl;
+        std::cout << "The Euler Characteristic is "<<euler<<std::endl;
   \endcode
 
 
@@ -181,43 +182,43 @@ The Euler Characteristic is 1
 \subsection s Constructing a skeleton-blockers from a list of maximal faces or from a list of faces
 
   \code{.cpp}
-	std::vector<Simplex> simplices;
-
-	//add 4 triangles of a tetrahedron 0123
-	simplices.push_back(Simplex(Vertex_handle(0),Vertex_handle(1),Vertex_handle(2)));
-	simplices.push_back(Simplex(Vertex_handle(1),Vertex_handle(2),Vertex_handle(3)));
-	simplices.push_back(Simplex(Vertex_handle(3),Vertex_handle(0),Vertex_handle(2)));
-	simplices.push_back(Simplex(Vertex_handle(3),Vertex_handle(0),Vertex_handle(1)));
-
-	Complex complex;
-	//get complex from top faces
-	make_complex_from_top_faces(complex,simplices.begin(),simplices.end());
-
-	std::cout << "Simplices:"<<std::endl;
-	for(const Simplex & s : complex.star_simplex_range())
-		std::cout << s << " ";
-	std::cout << std::endl;
-
-	//One blocker as simplex 0123 is not in the complex but all its proper faces are.
-	std::cout << "Blockers: "<<complex.blockers_to_string()<<std::endl;
-
-	//now build a complex from its full list of simplices
-	simplices.clear();
-	simplices.push_back(Simplex(Vertex_handle(0)));
-	simplices.push_back(Simplex(Vertex_handle(1)));
-	simplices.push_back(Simplex(Vertex_handle(2)));
-	simplices.push_back(Simplex(Vertex_handle(0),Vertex_handle(1)));
-	simplices.push_back(Simplex(Vertex_handle(1),Vertex_handle(2)));
-	simplices.push_back(Simplex(Vertex_handle(2),Vertex_handle(0)));
-	complex = Complex(simplices.begin(),simplices.end());
-
-	std::cout << "Simplices:"<<std::endl;
-	for(const Simplex & s : complex.star_simplex_range())
-		std::cout << s << " ";
-	std::cout << std::endl;
-
-	//One blocker as simplex 012 is not in the complex but all its proper faces are.
-	std::cout << "Blockers: "<<complex.blockers_to_string()<<std::endl;
+        std::vector<Simplex> simplices;
+
+        //add 4 triangles of a tetrahedron 0123
+        simplices.push_back(Simplex(Vertex_handle(0),Vertex_handle(1),Vertex_handle(2)));
+        simplices.push_back(Simplex(Vertex_handle(1),Vertex_handle(2),Vertex_handle(3)));
+        simplices.push_back(Simplex(Vertex_handle(3),Vertex_handle(0),Vertex_handle(2)));
+        simplices.push_back(Simplex(Vertex_handle(3),Vertex_handle(0),Vertex_handle(1)));
+
+        Complex complex;
+        //get complex from top faces
+        make_complex_from_top_faces(complex,simplices.begin(),simplices.end());
+
+        std::cout << "Simplices:"<<std::endl;
+        for(const Simplex & s : complex.star_simplex_range())
+                std::cout << s << " ";
+        std::cout << std::endl;
+
+        //One blocker as simplex 0123 is not in the complex but all its proper faces are.
+        std::cout << "Blockers: "<<complex.blockers_to_string()<<std::endl;
+
+        //now build a complex from its full list of simplices
+        simplices.clear();
+        simplices.push_back(Simplex(Vertex_handle(0)));
+        simplices.push_back(Simplex(Vertex_handle(1)));
+        simplices.push_back(Simplex(Vertex_handle(2)));
+        simplices.push_back(Simplex(Vertex_handle(0),Vertex_handle(1)));
+        simplices.push_back(Simplex(Vertex_handle(1),Vertex_handle(2)));
+        simplices.push_back(Simplex(Vertex_handle(2),Vertex_handle(0)));
+        complex = Complex(simplices.begin(),simplices.end());
+
+        std::cout << "Simplices:"<<std::endl;
+        for(const Simplex & s : complex.star_simplex_range())
+                std::cout << s << " ";
+        std::cout << std::endl;
+
+        //One blocker as simplex 012 is not in the complex but all its proper faces are.
+        std::cout << "Blockers: "<<complex.blockers_to_string()<<std::endl;
  \endcode
 \verbatim
 ./SkeletonBlockerFromSimplices
@@ -236,15 +237,16 @@ The author wishes to thank Dominique Attali and André Lieutier for
 their collaboration to write the two initial papers 
 \cite socg_blockers_2011,\cite blockers2012
  about this data-structure
- and also Dominique for leaving him use a prototype. 
+ and also Dominique for leaving him use a prototype.
 
 
-\copyright GNU General Public License v3.                         
-\verbatim  Contact: gudhi-users@lists.gforge.inria.fr \endverbatim
-*/
-/** @} */  // end defgroup
+\copyright GNU General Public License v3.
 
-}  // namespace skbl
+@} */
+
+}  // namespace skeleton_blocker
+
+namespace skbl = skeleton_blocker;
 
 }  // namespace Gudhi
 
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_complex_visitor.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_complex_visitor.h
index 4ade68e7..ba3636bc 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_complex_visitor.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_complex_visitor.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014  INRIA
  *
  *    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
@@ -19,6 +19,7 @@
  *    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 SKELETON_BLOCKER_SKELETON_BLOCKER_COMPLEX_VISITOR_H_
 #define SKELETON_BLOCKER_SKELETON_BLOCKER_COMPLEX_VISITOR_H_
 
@@ -26,8 +27,8 @@
 
 namespace Gudhi {
 
-namespace skbl {
-// todo rajouter les const
+namespace skeleton_blocker {
+// TODO(DS): to be constified
 
 /**
  *@class Skeleton_blocker_complex_visitor
@@ -36,7 +37,7 @@ namespace skbl {
 template<typename Vertex_handle>
 class Skeleton_blocker_complex_visitor {
  public:
-  virtual ~Skeleton_blocker_complex_visitor() {}
+  virtual ~Skeleton_blocker_complex_visitor() { }
 
   virtual void on_add_vertex(Vertex_handle) = 0;
   virtual void on_remove_vertex(Vertex_handle) = 0;
@@ -61,9 +62,9 @@ class Skeleton_blocker_complex_visitor {
   virtual void on_swaped_edge(Vertex_handle a, Vertex_handle b,
                               Vertex_handle x) = 0;
   virtual void on_add_blocker(
-      const Skeleton_blocker_simplex<Vertex_handle>&) = 0;
+                              const Skeleton_blocker_simplex<Vertex_handle>&) = 0;
   virtual void on_delete_blocker(
-      const Skeleton_blocker_simplex<Vertex_handle>*) = 0;
+                                 const Skeleton_blocker_simplex<Vertex_handle>*) = 0;
 };
 
 /**
@@ -73,24 +74,23 @@ class Skeleton_blocker_complex_visitor {
  */
 template<typename Vertex_handle>
 class Dummy_complex_visitor : public Skeleton_blocker_complex_visitor<
-    Vertex_handle> {
+Vertex_handle> {
  public:
-  void on_add_vertex(Vertex_handle) {
-  }
-  void on_remove_vertex(Vertex_handle) {
-  }
-  void on_add_edge_without_blockers(Vertex_handle a, Vertex_handle b) {
-  }
-  void on_remove_edge(Vertex_handle a, Vertex_handle b) {
-  }
-  void on_changed_edge(Vertex_handle a, Vertex_handle b) {
-  }
-  void on_swaped_edge(Vertex_handle a, Vertex_handle b, Vertex_handle x) {
-  }
-  void on_add_blocker(const Skeleton_blocker_simplex<Vertex_handle>&) {
-  }
-  void on_delete_blocker(const Skeleton_blocker_simplex<Vertex_handle>*) {
-  }
+  void on_add_vertex(Vertex_handle) { }
+
+  void on_remove_vertex(Vertex_handle) { }
+
+  void on_add_edge_without_blockers(Vertex_handle a, Vertex_handle b) { }
+
+  void on_remove_edge(Vertex_handle a, Vertex_handle b) { }
+
+  void on_changed_edge(Vertex_handle a, Vertex_handle b) { }
+
+  void on_swaped_edge(Vertex_handle a, Vertex_handle b, Vertex_handle x) { }
+
+  void on_add_blocker(const Skeleton_blocker_simplex<Vertex_handle>&) { }
+
+  void on_delete_blocker(const Skeleton_blocker_simplex<Vertex_handle>*) { }
 };
 
 /**
@@ -100,35 +100,44 @@ class Dummy_complex_visitor : public Skeleton_blocker_complex_visitor<
  */
 template<typename Vertex_handle>
 class Print_complex_visitor : public Skeleton_blocker_complex_visitor<
-    Vertex_handle> {
+Vertex_handle> {
  public:
   void on_add_vertex(Vertex_handle v) {
     std::cerr << "on_add_vertex:" << v << std::endl;
   }
+
   void on_remove_vertex(Vertex_handle v) {
     std::cerr << "on_remove_vertex:" << v << std::endl;
   }
+
   void on_add_edge_without_blockers(Vertex_handle a, Vertex_handle b) {
     std::cerr << "on_add_edge_without_blockers:" << a << "," << b << std::endl;
   }
+
   void on_remove_edge(Vertex_handle a, Vertex_handle b) {
     std::cerr << "on_remove_edge:" << a << "," << b << std::endl;
   }
+
   void on_changed_edge(Vertex_handle a, Vertex_handle b) {
     std::cerr << "on_changed_edge:" << a << "," << b << std::endl;
   }
+
   void on_swaped_edge(Vertex_handle a, Vertex_handle b, Vertex_handle x) {
     std::cerr << "on_swaped_edge:" << a << "," << b << "," << x << std::endl;
   }
+
   void on_add_blocker(const Skeleton_blocker_simplex<Vertex_handle>& b) {
     std::cerr << "on_add_blocker:" << b << std::endl;
   }
+
   void on_delete_blocker(const Skeleton_blocker_simplex<Vertex_handle>* b) {
     std::cerr << "on_delete_blocker:" << b << std::endl;
   }
 };
 
-}  // namespace skbl
+}  // namespace skeleton_blocker
+
+namespace skbl = skeleton_blocker;
 
 }  // namespace Gudhi
 
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_link_superior.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_link_superior.h
index 876bdba9..d4b60613 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_link_superior.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_link_superior.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014  INRIA
  *
  *    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
@@ -19,6 +19,7 @@
  *    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 SKELETON_BLOCKER_SKELETON_BLOCKER_LINK_SUPERIOR_H_
 #define SKELETON_BLOCKER_SKELETON_BLOCKER_LINK_SUPERIOR_H_
 
@@ -26,7 +27,7 @@
 
 namespace Gudhi {
 
-namespace skbl {
+namespace skeleton_blocker {
 
 template<class ComplexType> class Skeleton_blocker_sub_complex;
 
@@ -36,7 +37,7 @@ template<class ComplexType> class Skeleton_blocker_sub_complex;
  */
 template<typename ComplexType>
 class Skeleton_blocker_link_superior : public Skeleton_blocker_link_complex<
-    ComplexType> {
+ComplexType> {
   typedef typename ComplexType::Edge_handle Edge_handle;
 
   typedef typename ComplexType::boost_vertex_handle boost_vertex_handle;
@@ -54,23 +55,22 @@ class Skeleton_blocker_link_superior : public Skeleton_blocker_link_complex<
   typedef typename ComplexType::Root_simplex_handle::Simplex_vertex_const_iterator IdSimplexConstIterator;
 
   Skeleton_blocker_link_superior()
-      : Skeleton_blocker_link_complex<ComplexType>(true) {
-  }
+      : Skeleton_blocker_link_complex<ComplexType>(true) { }
 
   Skeleton_blocker_link_superior(const ComplexType & parent_complex,
                                  Simplex& alpha_parent_adress)
       : Skeleton_blocker_link_complex<ComplexType>(parent_complex,
-                                                   alpha_parent_adress, true) {
-  }
+                                                   alpha_parent_adress, true) { }
 
   Skeleton_blocker_link_superior(const ComplexType & parent_complex,
                                  Vertex_handle a_parent_adress)
       : Skeleton_blocker_link_complex<ComplexType>(parent_complex,
-                                                   a_parent_adress, true) {
-  }
+                                                   a_parent_adress, true) { }
 };
 
-}  // namespace skbl
+}  // namespace skeleton_blocker
+
+namespace skbl = skeleton_blocker;
 
 }  // namespace Gudhi
 
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_off_io.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_off_io.h
index ad2d2f85..747e60f1 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_off_io.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_off_io.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014  INRIA
  *
  *    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
@@ -19,6 +19,7 @@
  *    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 SKELETON_BLOCKER_SKELETON_BLOCKER_OFF_IO_H_
 #define SKELETON_BLOCKER_SKELETON_BLOCKER_OFF_IO_H_
 
@@ -30,7 +31,7 @@
 
 namespace Gudhi {
 
-namespace skbl {
+namespace skeleton_blocker {
 
 /**
  *@brief Off reader visitor that can be passed to Off_reader to read a Skeleton_blocker_complex.
@@ -49,8 +50,8 @@ class Skeleton_blocker_off_flag_visitor_reader {
       load_only_points_(load_only_points) { }
 
   void init(int dim, int num_vertices, int num_faces, int num_edges) {
-    // todo do an assert to check that this number are correctly read
-    // todo reserve size for vector points
+    // TODO(DS): do an assert to check that this number are correctly read
+    // TODO(DS): reserve size for vector points
   }
 
   void point(const std::vector<double>& point) {
@@ -108,7 +109,7 @@ class Skeleton_blocker_off_visitor_reader {
 
   void done() {
     complex_ = make_complex_from_top_faces<Complex>(maximal_faces_.begin(), maximal_faces_.end(),
-                                           points_.begin(), points_.end() );
+                                                    points_.begin(), points_.end());
   }
 };
 
@@ -140,7 +141,7 @@ class Skeleton_blocker_off_reader {
   }
 
   /**
-   * return true iff reading did not meet problems.
+   * return true if reading did not meet problems.
    */
   bool is_valid() const {
     return valid_;
@@ -193,7 +194,9 @@ class Skeleton_blocker_off_writer {
   }
 };
 
-}  // namespace skbl
+}  // namespace skeleton_blocker
+
+namespace skbl = skeleton_blocker;
 
 }  // namespace Gudhi
 
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_geometric_traits.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_geometric_traits.h
index 8508d9a5..275376e6 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_geometric_traits.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_geometric_traits.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014  INRIA
  *
  *    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
@@ -19,6 +19,7 @@
  *    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 SKELETON_BLOCKER_SKELETON_BLOCKER_SIMPLE_GEOMETRIC_TRAITS_H_
 #define SKELETON_BLOCKER_SKELETON_BLOCKER_SIMPLE_GEOMETRIC_TRAITS_H_
 
@@ -29,7 +30,7 @@
 
 namespace Gudhi {
 
-namespace skbl {
+namespace skeleton_blocker {
 
 /**
  * @extends SkeletonBlockerGeometricDS
@@ -39,7 +40,7 @@ namespace skbl {
  */
 template<typename GeometryTrait>
 struct Skeleton_blocker_simple_geometric_traits :
-    public skbl::Skeleton_blocker_simple_traits {
+public Skeleton_blocker_simple_traits {
  public:
   typedef GeometryTrait GT;
   typedef typename GT::Point Point;
@@ -57,19 +58,20 @@ struct Skeleton_blocker_simple_geometric_traits :
     Point& point() {
       return point_;
     }
+
     const Point& point() const {
       return point_;
     }
   };
 
   class Simple_geometric_edge :
-      public Skeleton_blocker_simple_traits::Graph_edge {
+  public Skeleton_blocker_simple_traits::Graph_edge {
     int index_;
    public:
     Simple_geometric_edge()
         : Skeleton_blocker_simple_traits::Graph_edge(),
-          index_(-1) {
-    }
+        index_(-1) { }
+
     /**
      * @brief Allows to modify the index of the edge.
      * The indices of the edge are used to store heap information
@@ -78,6 +80,7 @@ struct Skeleton_blocker_simple_geometric_traits :
     int& index() {
       return index_;
     }
+
     int index() const {
       return index_;
     }
@@ -87,7 +90,9 @@ struct Skeleton_blocker_simple_geometric_traits :
   typedef Skeleton_blocker_simple_traits::Graph_edge Graph_edge;
 };
 
-}  // namespace skbl
+}  // namespace skeleton_blocker
+
+namespace skbl = skeleton_blocker;
 
 }  // namespace Gudhi
 
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_traits.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_traits.h
index 0d2de767..3835cf77 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_traits.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_traits.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014  INRIA
  *
  *    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
@@ -19,6 +19,7 @@
  *    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 SKELETON_BLOCKER_SKELETON_BLOCKER_SIMPLE_TRAITS_H_
 #define SKELETON_BLOCKER_SKELETON_BLOCKER_SIMPLE_TRAITS_H_
 
@@ -29,7 +30,7 @@
 
 namespace Gudhi {
 
-namespace skbl {
+namespace skeleton_blocker {
 
 /**
  * @extends SkeletonBlockerDS
@@ -48,9 +49,9 @@ struct Skeleton_blocker_simple_traits {
    */
   struct Root_vertex_handle {
     typedef int boost_vertex_handle;
+
     explicit Root_vertex_handle(boost_vertex_handle val = -1)
-        : vertex(val) {
-    }
+        : vertex(val) { }
     boost_vertex_handle vertex;
 
     bool operator!=(const Root_vertex_handle& other) const {
@@ -65,8 +66,8 @@ struct Skeleton_blocker_simple_traits {
       return this->vertex < other.vertex;
     }
 
-    friend std::ostream& operator <<(std::ostream& o,
-                                     const Root_vertex_handle & v) {
+    friend std::ostream& operator<<(std::ostream& o,
+                                    const Root_vertex_handle & v) {
       o << v.vertex;
       return o;
     }
@@ -74,11 +75,13 @@ struct Skeleton_blocker_simple_traits {
 
   struct Vertex_handle {
     typedef int boost_vertex_handle;
+
     explicit Vertex_handle(boost_vertex_handle val = -1)
-        : vertex(val) {
-    }
+        : vertex(val) { }
 
-    operator int() const { return static_cast<int>(vertex); }
+    operator int() const {
+      return static_cast<int> (vertex);
+    }
 
     boost_vertex_handle vertex;
 
@@ -94,7 +97,7 @@ struct Skeleton_blocker_simple_traits {
       return this->vertex < other.vertex;
     }
 
-    friend std::ostream& operator <<(std::ostream& o, const Vertex_handle & v) {
+    friend std::ostream& operator<<(std::ostream& o, const Vertex_handle & v) {
       o << v.vertex;
       return o;
     }
@@ -105,21 +108,24 @@ struct Skeleton_blocker_simple_traits {
     Root_vertex_handle id_;
 
    public:
-    virtual ~Graph_vertex() {
-    }
+    virtual ~Graph_vertex() { }
 
     void activate() {
       is_active_ = true;
     }
+
     void deactivate() {
       is_active_ = false;
     }
+
     bool is_active() const {
       return is_active_;
     }
+
     void set_id(Root_vertex_handle i) {
       id_ = i;
     }
+
     Root_vertex_handle get_id() const {
       return id_;
     }
@@ -130,7 +136,7 @@ struct Skeleton_blocker_simple_traits {
       return res.str();
     }
 
-    friend std::ostream& operator <<(std::ostream& o, const Graph_vertex & v) {
+    friend std::ostream& operator<<(std::ostream& o, const Graph_vertex & v) {
       o << v.to_string();
       return o;
     }
@@ -144,13 +150,13 @@ struct Skeleton_blocker_simple_traits {
    public:
     Graph_edge()
         : a_(-1),
-          b_(-1),
-          index_(-1) {
-    }
+        b_(-1),
+        index_(-1) { }
 
     int& index() {
       return index_;
     }
+
     int index() const {
       return index_;
     }
@@ -168,14 +174,16 @@ struct Skeleton_blocker_simple_traits {
       return b_;
     }
 
-    friend std::ostream& operator <<(std::ostream& o, const Graph_edge & v) {
+    friend std::ostream& operator<<(std::ostream& o, const Graph_edge & v) {
       o << "(" << v.a_ << "," << v.b_ << " - id = " << v.index();
       return o;
     }
   };
 };
 
-}  // namespace skbl
+}  // namespace skeleton_blocker
+
+namespace skbl = skeleton_blocker;
 
 }  // namespace Gudhi
 
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 714bf23c..aa6f2215 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
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014  INRIA
  *
  *    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
@@ -33,7 +33,7 @@
 
 namespace Gudhi {
 
-namespace skbl {
+namespace skeleton_blocker {
 
 /**
  *@brief Abstract simplex used in Skeleton blockers data-structure.
@@ -63,7 +63,6 @@ class Skeleton_blocker_simplex {
    */
   //@{
 
-  // Skeleton_blocker_simplex():simplex_set() {}
   void clear() {
     simplex_set.clear();
   }
@@ -89,8 +88,7 @@ class Skeleton_blocker_simplex {
     add_vertex(v);
   }
 
-  void add_vertices() {
-  }
+  void add_vertices() { }
 
   /**
    * Initialize a simplex with a string such as {0,1,2}
@@ -192,7 +190,6 @@ class Skeleton_blocker_simplex {
     return simplex_set.crend();
   }
 
-
   typename std::set<T>::iterator begin() {
     return simplex_set.begin();
   }
@@ -236,6 +233,7 @@ class Skeleton_blocker_simplex {
     assert(!empty());
     return *(simplex_set.rbegin());
   }
+
   /**
    * @return true iff the simplex contains the simplex a.
    */
@@ -351,8 +349,8 @@ class Skeleton_blocker_simplex {
 
   //@}
 
-  friend std::ostream& operator <<(std::ostream& o,
-                                   const Skeleton_blocker_simplex & sigma) {
+  friend std::ostream& operator<<(std::ostream& o,
+                                  const Skeleton_blocker_simplex & sigma) {
     bool first = true;
     o << "{";
     for (auto i : sigma) {
@@ -367,7 +365,9 @@ class Skeleton_blocker_simplex {
   }
 };
 
-}  // namespace skbl
+}  // namespace skeleton_blocker
+
+namespace skbl = skeleton_blocker;
 
 }  // namespace Gudhi
 
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_sub_complex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_sub_complex.h
index 50a83345..fadf6619 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_sub_complex.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_sub_complex.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014  INRIA
  *
  *    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
@@ -25,14 +25,14 @@
 
 #include <gudhi/Skeleton_blocker_complex.h>
 #include <gudhi/Skeleton_blocker/Skeleton_blocker_simplex.h>
-#include <gudhi/Utils.h>
+#include <gudhi/Debug_utils.h>
 
 #include <map>
 #include <vector>
 
 namespace Gudhi {
 
-namespace skbl {
+namespace skeleton_blocker {
 
 /**
  * @brief Simplicial subcomplex of a complex represented by a skeleton/blockers pair.
@@ -159,7 +159,7 @@ class Skeleton_blocker_sub_complex : public ComplexType {
       if (simplex.contains(*blocker)) {
         Root_simplex_handle blocker_root(parent_complex.get_id(*(blocker)));
         Simplex blocker_restr(
-            *(this->get_simplex_address(blocker_root)));
+                              *(this->get_simplex_address(blocker_root)));
         this->add_blocker(new Simplex(blocker_restr));
       }
     }
@@ -190,14 +190,15 @@ class Skeleton_blocker_sub_complex : public ComplexType {
   //  */
   // boost::optional<Simplex> get_address(const Root_simplex_handle & s) const;
 
-// private:
+  // private:
   /**
    *  same as get_address except that it will return a simplex in any case.
    *  The vertices that were not found are not added.
    */
   // @remark should be private but problem with VS
+
   std::vector<boost::optional<Vertex_handle> > get_addresses(
-      const Root_simplex_handle & s) const {
+                                                             const Root_simplex_handle & s) const {
     std::vector < boost::optional<Vertex_handle> > res;
     for (auto i : s) {
       res.push_back(get_address(i));
@@ -214,14 +215,14 @@ class Skeleton_blocker_sub_complex : public ComplexType {
  */
 template<typename ComplexType>
 bool proper_face_in_union(
-    Skeleton_blocker_sub_complex<ComplexType> & link,
-    std::vector<boost::optional<typename ComplexType::Vertex_handle> > & addresses_sigma_in_link,
-    int vertex_to_be_ignored) {
+                          Skeleton_blocker_sub_complex<ComplexType> & link,
+                          std::vector<boost::optional<typename ComplexType::Vertex_handle> > & addresses_sigma_in_link,
+                          std::size_t vertex_to_be_ignored) {
   // we test that all vertices of 'addresses_sigma_in_link' but 'vertex_to_be_ignored'
   // are in link1 if it is the case we construct the corresponding simplex
   bool vertices_sigma_are_in_link = true;
   typename ComplexType::Simplex sigma_in_link;
-  for (int i = 0; i < addresses_sigma_in_link.size(); ++i) {
+  for (std::size_t i = 0; i < addresses_sigma_in_link.size(); ++i) {
     if (i != vertex_to_be_ignored) {
       if (!addresses_sigma_in_link[i]) {
         vertices_sigma_are_in_link = false;
@@ -236,43 +237,24 @@ bool proper_face_in_union(
   return vertices_sigma_are_in_link && link.contains(sigma_in_link);
 }
 
-/*
- template<typename ComplexType>
- bool
- proper_faces_in_union(Skeleton_blocker_simplex<typename ComplexType::Root_vertex_handle> & sigma, Skeleton_blocker_sub_complex<ComplexType> & link1, Skeleton_blocker_sub_complex<ComplexType> & link2)
- {
- typedef typename ComplexType::Vertex_handle  Vertex_handle;
- std::vector<boost::optional<Vertex_handle> > addresses_sigma_in_link1 = link1.get_addresses(sigma);
- std::vector<boost::optional<Vertex_handle> > addresses_sigma_in_link2 = link2.get_addresses(sigma);
-
- for (int current_index = 0; current_index < addresses_sigma_in_link1.size(); ++current_index)
- {
-
- if (!proper_face_in_union(link1, addresses_sigma_in_link1, current_index)
- && !proper_face_in_union(link2, addresses_sigma_in_link2, current_index)){
- return false;
- }
- }
- return true;
- }*/
-
 // Remark: this function should be friend in order to leave get_adresses private
 // however doing so seemes currently not possible due to a visual studio bug c2668
 // "the compiler does not support partial ordering of template functions as specified in the C++ Standard"
 // http://www.serkey.com/error-c2668-ambiguous-call-to-overloaded-function-bb45ft.html
+
 template<typename ComplexType>
 bool proper_faces_in_union(
-    Skeleton_blocker_simplex<typename ComplexType::Root_vertex_handle> & sigma,
-    Skeleton_blocker_sub_complex<ComplexType> & link1,
-    Skeleton_blocker_sub_complex<ComplexType> & link2) {
+                           Skeleton_blocker_simplex<typename ComplexType::Root_vertex_handle> & sigma,
+                           Skeleton_blocker_sub_complex<ComplexType> & link1,
+                           Skeleton_blocker_sub_complex<ComplexType> & link2) {
   typedef typename ComplexType::Vertex_handle Vertex_handle;
   std::vector < boost::optional<Vertex_handle> > addresses_sigma_in_link1 =
       link1.get_addresses(sigma);
   std::vector < boost::optional<Vertex_handle> > addresses_sigma_in_link2 =
       link2.get_addresses(sigma);
 
-  for (int current_index = 0; current_index < addresses_sigma_in_link1.size();
-      ++current_index) {
+  for (std::size_t current_index = 0; current_index < addresses_sigma_in_link1.size();
+       ++current_index) {
     if (!proper_face_in_union(link1, addresses_sigma_in_link1, current_index)
         && !proper_face_in_union(link2, addresses_sigma_in_link2,
                                  current_index)) {
@@ -282,9 +264,10 @@ bool proper_faces_in_union(
   return true;
 }
 
-}  // namespace skbl
+}  // namespace skeleton_blocker
+
+namespace skbl = skeleton_blocker;
 
 }  // namespace Gudhi
 
 #endif  // SKELETON_BLOCKER_SKELETON_BLOCKER_SUB_COMPLEX_H_
-
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/internal/Top_faces.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/internal/Top_faces.h
index eb970195..2b681752 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/internal/Top_faces.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/internal/Top_faces.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014  INRIA
  *
  *    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
@@ -19,6 +19,7 @@
  *    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 SKELETON_BLOCKER_INTERNAL_TOP_FACES_H_
 #define SKELETON_BLOCKER_INTERNAL_TOP_FACES_H_
 
@@ -28,7 +29,7 @@
 
 namespace Gudhi {
 
-namespace skbl {
+namespace skeleton_blocker {
 
 template<typename SimplexHandle>
 std::list<SimplexHandle> subfaces(SimplexHandle top_face) {
@@ -63,8 +64,10 @@ void register_faces(std::vector< std::set<SimplexHandle> >& simplices_per_dimens
   }
 }
 
-}  // namespace skbl
+}  // namespace skeleton_blocker
+
+namespace skbl = skeleton_blocker;
 
 }  // namespace Gudhi
 
-#endif  // SKELETON_BLOCKER_INTERNAL_TOP_FACES_H_
+#endif   // SKELETON_BLOCKER_INTERNAL_TOP_FACES_H_
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/internal/Trie.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/internal/Trie.h
index 499980c4..2c9602fa 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/internal/Trie.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/internal/Trie.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (France)
+ *    Copyright (C) 2014  INRIA
  *
  *    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
@@ -21,7 +21,6 @@
  * 
  */
 
-
 #ifndef SKELETON_BLOCKER_INTERNAL_TRIE_H_
 #define SKELETON_BLOCKER_INTERNAL_TRIE_H_
 
@@ -32,7 +31,7 @@
 
 namespace Gudhi {
 
-namespace skbl {
+namespace skeleton_blocker {
 
 template<typename SimplexHandle>
 struct Trie {
@@ -148,7 +147,7 @@ struct Trie {
   }
 
   void remove_leaf() {
-    assert(is_leaf);
+    assert(is_leaf());
     if (!is_root())
       parent_->childs.erase(this);
   }
@@ -240,7 +239,7 @@ struct Tries {
 
   std::vector<Simplex> next_dimension_simplices() const {
     std::vector<Simplex> res;
-    while (!to_see_.empty() && to_see_.front()->simplex().dimension() == current_dimension_) {
+    while (!(to_see_.empty()) && (to_see_.front()->simplex().dimension() == current_dimension_)) {
       res.emplace_back(to_see_.front()->simplex());
       for (auto child : to_see_.front()->childs)
         to_see_.push_back(child.get());
@@ -257,11 +256,13 @@ struct Tries {
 
  private:
   mutable std::deque<STrie*> to_see_;
-  mutable unsigned current_dimension_ = 0;
+  mutable int current_dimension_ = 0;
   std::vector<STrie*> cofaces_;
 };
 
-}  // namespace skbl
+}  // namespace skeleton_blocker
+
+namespace skbl = skeleton_blocker;
 
 }  // namespace Gudhi
 
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_blockers_iterators.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_blockers_iterators.h
index 4a437ac6..d2fff960 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_blockers_iterators.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_blockers_iterators.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014  INRIA
  *
  *    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
@@ -19,6 +19,7 @@
  *    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 SKELETON_BLOCKER_ITERATORS_SKELETON_BLOCKERS_BLOCKERS_ITERATORS_H_
 #define SKELETON_BLOCKER_ITERATORS_SKELETON_BLOCKERS_BLOCKERS_ITERATORS_H_
 
@@ -26,7 +27,7 @@
 
 namespace Gudhi {
 
-namespace skbl {
+namespace skeleton_blocker {
 
 /**
  * @brief Iterator through the blockers of a vertex.
@@ -124,7 +125,9 @@ ReturnType
   }
 };
 
-}  // namespace skbl
+}  // namespace skeleton_blocker
+
+namespace skbl = skeleton_blocker;
 
 }  // namespace Gudhi
 
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_edges_iterators.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_edges_iterators.h
index ef4c7970..b90dcf34 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_edges_iterators.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_edges_iterators.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014  INRIA
  *
  *    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
@@ -19,6 +19,7 @@
  *    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 SKELETON_BLOCKER_ITERATORS_SKELETON_BLOCKERS_EDGES_ITERATORS_H_
 #define SKELETON_BLOCKER_ITERATORS_SKELETON_BLOCKERS_EDGES_ITERATORS_H_
 
@@ -29,7 +30,7 @@
 
 namespace Gudhi {
 
-namespace skbl {
+namespace skeleton_blocker {
 
 template<typename SkeletonBlockerComplex>
 class Edge_around_vertex_iterator : public boost::iterator_facade <Edge_around_vertex_iterator<SkeletonBlockerComplex>
@@ -137,7 +138,9 @@ class Edge_iterator : public boost::iterator_facade <Edge_iterator<SkeletonBlock
   }
 };
 
-}  // namespace skbl
+}  // namespace skeleton_blocker
+
+namespace skbl = skeleton_blocker;
 
 }  // namespace Gudhi
 
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_iterators.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_iterators.h
index cc3ed276..1351614f 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_iterators.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_iterators.h
@@ -4,7 +4,7 @@
   *
   *    Author(s):       David Salinas
   *
-  *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+  *    Copyright (C) 2014  INRIA
   *
   *    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
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_simplices_iterators.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_simplices_iterators.h
index ce565166..2acdb555 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_simplices_iterators.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_simplices_iterators.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014  INRIA
  *
  *    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
@@ -19,13 +19,14 @@
  *    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 SKELETON_BLOCKER_ITERATORS_SKELETON_BLOCKERS_SIMPLICES_ITERATORS_H_
 #define SKELETON_BLOCKER_ITERATORS_SKELETON_BLOCKERS_SIMPLICES_ITERATORS_H_
 
 #include <gudhi/Skeleton_blocker_link_complex.h>
 #include <gudhi/Skeleton_blocker/Skeleton_blocker_link_superior.h>
 #include <gudhi/Skeleton_blocker/internal/Trie.h>
-#include <gudhi/Utils.h>
+#include <gudhi/Debug_utils.h>
 
 #include <boost/iterator/iterator_facade.hpp>
 
@@ -35,7 +36,7 @@
 
 namespace Gudhi {
 
-namespace skbl {
+namespace skeleton_blocker {
 
 /**
  * Link may be Skeleton_blocker_link_complex<SkeletonBlockerComplex> to iterate over all
@@ -61,17 +62,18 @@ public boost::iterator_facade < Simplex_around_vertex_iterator<SkeletonBlockerCo
   // Link_vertex_handle == Complex_Vertex_handle but this renaming helps avoiding confusion
   typedef typename Link::Vertex_handle Link_vertex_handle;
 
-  typedef typename Gudhi::skbl::Trie<Simplex> Trie;
+  typedef typename Gudhi::skeleton_blocker::Trie<Simplex> Trie;
 
  private:
   const Complex* complex;
   Vertex_handle v;
   std::shared_ptr<Link> link_v;
   std::shared_ptr<Trie> trie;
-  std::list<Trie*> nodes_to_be_seen;  // todo deque
+  // TODO(DS): use a deque instead
+  std::list<Trie*> nodes_to_be_seen;
 
  public:
-  Simplex_around_vertex_iterator() : complex(0) {}
+  Simplex_around_vertex_iterator() : complex(0) { }
 
   Simplex_around_vertex_iterator(const Complex* complex_, Vertex_handle v_) :
       complex(complex_),
@@ -81,15 +83,16 @@ public boost::iterator_facade < Simplex_around_vertex_iterator<SkeletonBlockerCo
     compute_trie_and_nodes_to_be_seen();
   }
 
-  // todo avoid useless copy
-  // todo currently just work if copy begin iterator
+  // TODO(DS): avoid useless copy
+  // TODO(DS): currently just work if copy begin iterator
   Simplex_around_vertex_iterator(const Simplex_around_vertex_iterator& other) :
       complex(other.complex),
       v(other.v),
       link_v(other.link_v),
       trie(other.trie),
       nodes_to_be_seen(other.nodes_to_be_seen) {
-    if (!other.is_end()) {}
+    if (!other.is_end()) {
+    }
   }
 
   /**
@@ -159,7 +162,8 @@ public boost::iterator_facade < Simplex_around_vertex_iterator<SkeletonBlockerCo
 
     bool both_non_empty = !nodes_to_be_seen.empty() && !other.nodes_to_be_seen.empty();
 
-    if (!both_non_empty) return false;  // one is empty the other is not
+    // one is empty the other is not
+    if (!both_non_empty) return false;
 
     bool same_node = (**(nodes_to_be_seen.begin()) == **(other.nodes_to_be_seen.begin()));
     return same_node;
@@ -238,7 +242,6 @@ public boost::iterator_facade < Simplex_iterator<SkeletonBlockerComplex>
   }
 
  private:
-  // todo return to private
   Simplex_iterator(const Complex* complex, bool end) :
       complex_(complex) {
     set_end();
@@ -306,7 +309,7 @@ public boost::iterator_facade < Simplex_iterator<SkeletonBlockerComplex>
 
 /**
  * Iterator through the maximal faces of the coboundary of a simplex.
- */ 
+ */
 template<typename SkeletonBlockerComplex, typename Link>
 class Simplex_coboundary_iterator :
 public boost::iterator_facade < Simplex_coboundary_iterator<SkeletonBlockerComplex, Link>
@@ -329,12 +332,12 @@ public boost::iterator_facade < Simplex_coboundary_iterator<SkeletonBlockerCompl
   Complex_vertex_iterator link_vertex_end;
 
  public:
-  Simplex_coboundary_iterator() : complex(0) {}
+  Simplex_coboundary_iterator() : complex(0) { }
 
   Simplex_coboundary_iterator(const Complex* complex_, const Simplex& sigma_) :
       complex(complex_),
       sigma(sigma_),
-      //need only vertices of the link hence the true flag
+      // need only vertices of the link hence the true flag
       link(new Link(*complex_, sigma_, false, true)) {
     auto link_vertex_range = link->vertex_range();
     current_vertex = link_vertex_range.begin();
@@ -347,9 +350,9 @@ public boost::iterator_facade < Simplex_coboundary_iterator<SkeletonBlockerCompl
       link(other.link),
       current_vertex(other.current_vertex),
       link_vertex_end(other.link_vertex_end) { }
-  
+
   // returns an iterator to the end
-  Simplex_coboundary_iterator(const Complex* complex_,const Simplex& sigma_, bool end) :
+  Simplex_coboundary_iterator(const Complex* complex_, const Simplex& sigma_, bool end) :
       complex(complex_),
       sigma(sigma_) {
     // to represent an end iterator without having to build a useless link, we use
@@ -361,7 +364,7 @@ public boost::iterator_facade < Simplex_coboundary_iterator<SkeletonBlockerCompl
     return complex->convert_handle_from_another_complex(*link, link_vh);
   }
 
-public:
+ public:
   friend std::ostream& operator<<(std::ostream& stream, const Simplex_coboundary_iterator& sci) {
     return stream;
   }
@@ -369,8 +372,8 @@ public:
   // assume that iterator points to the same complex and comes from the same simplex
   bool equal(const Simplex_coboundary_iterator& other) const {
     assert(complex == other.complex && sigma == other.sigma);
-    if(is_end()) return other.is_end();
-    if(other.is_end()) return is_end();
+    if (is_end()) return other.is_end();
+    if (other.is_end()) return is_end();
     return *current_vertex == *(other.current_vertex);
   }
 
@@ -384,14 +387,15 @@ public:
     return res;
   }
 
-private:
+ private:
   bool is_end() const {
     return !link || current_vertex == link_vertex_end;
   }
 };
 
+}  // namespace skeleton_blocker
 
-}  // namespace skbl
+namespace skbl = skeleton_blocker;
 
 }  // namespace Gudhi
 
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_triangles_iterators.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_triangles_iterators.h
index 116023d7..736941dd 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_triangles_iterators.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_triangles_iterators.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014  INRIA
  *
  *    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
@@ -19,6 +19,7 @@
  *    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 SKELETON_BLOCKER_ITERATORS_SKELETON_BLOCKERS_TRIANGLES_ITERATORS_H_
 #define SKELETON_BLOCKER_ITERATORS_SKELETON_BLOCKERS_TRIANGLES_ITERATORS_H_
 
@@ -27,7 +28,7 @@
 
 namespace Gudhi {
 
-namespace skbl {
+namespace skeleton_blocker {
 
 /**
  * \brief Iterator over the triangles that are
@@ -135,7 +136,7 @@ typename SkeletonBlockerComplex::Simplex const
   Triangle_iterator(const SkeletonBlockerComplex* complex) :
       complex_(complex),
       current_vertex_(complex->vertex_range().begin()),
-      current_triangle_(complex, *current_vertex_),  // xxx this line is problematic is the complex is empty
+      current_triangle_(complex, *current_vertex_),  // this line is problematic is the complex is empty
       is_end_(false) {
     assert(!complex->empty());
     gotoFirstTriangle();
@@ -172,7 +173,8 @@ typename SkeletonBlockerComplex::Simplex const
     bool both_arent_finished = !is_finished() && !other.is_finished();
     // if the two iterators are not finished, they must have the same state
     return (complex_ == other.complex_) && (both_are_finished || ((both_arent_finished) &&
-        current_vertex_ == other.current_vertex_ && current_triangle_ == other.current_triangle_));
+                                                                  current_vertex_ == other.current_vertex_ &&
+                                                                  current_triangle_ == other.current_triangle_));
   }
 
   Simplex dereference() const {
@@ -183,8 +185,10 @@ typename SkeletonBlockerComplex::Simplex const
   // goto the next vertex that has a triangle pending or the
   // end vertex iterator if none exists
   void goto_next_vertex() {
-    assert(current_triangle_.finished());  // we mush have consume all triangles passing through the vertex
-    assert(!is_finished());  // we must not be done
+    // we must have consume all triangles passing through the vertex
+    assert(current_triangle_.finished());
+    // we must not be done
+    assert(!is_finished());
 
     ++current_vertex_;
 
@@ -213,7 +217,9 @@ typename SkeletonBlockerComplex::Simplex const
   }
 };
 
-}  // namespace skbl
+}  // namespace skeleton_blocker
+
+namespace skbl = skeleton_blocker;
 
 }  // namespace Gudhi
 
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_vertices_iterators.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_vertices_iterators.h
index 14ae136a..9e9ae961 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_vertices_iterators.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_vertices_iterators.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014  INRIA
  *
  *    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
@@ -19,6 +19,7 @@
  *    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 SKELETON_BLOCKER_ITERATORS_SKELETON_BLOCKERS_VERTICES_ITERATORS_H_
 #define SKELETON_BLOCKER_ITERATORS_SKELETON_BLOCKERS_VERTICES_ITERATORS_H_
 
@@ -28,7 +29,7 @@
 
 namespace Gudhi {
 
-namespace skbl {
+namespace skeleton_blocker {
 
 /**
  *@brief Iterator on the vertices of a simplicial complex
@@ -103,7 +104,7 @@ class Vertex_iterator : public boost::iterator_facade< Vertex_iterator <Skeleton
 };
 
 template<typename SkeletonBlockerComplex>
-class Neighbors_vertices_iterator: public boost::iterator_facade < Neighbors_vertices_iterator<SkeletonBlockerComplex>
+class Neighbors_vertices_iterator : public boost::iterator_facade < Neighbors_vertices_iterator<SkeletonBlockerComplex>
 , typename SkeletonBlockerComplex::Vertex_handle const
 , boost::forward_traversal_tag
 , typename SkeletonBlockerComplex::Vertex_handle const> {
@@ -122,9 +123,6 @@ class Neighbors_vertices_iterator: public boost::iterator_facade < Neighbors_ver
   boost_adjacency_iterator end_;
 
  public:
-  // boost_adjacency_iterator ai, ai_end;
-  // for (tie(ai, ai_end) = adjacent_vertices(v.vertex, skeleton); ai != ai_end; ++ai) {
-
   Neighbors_vertices_iterator() : complex(NULL) { }
 
   Neighbors_vertices_iterator(const Complex* complex_, Vertex_handle v_) :
@@ -157,16 +155,16 @@ class Neighbors_vertices_iterator: public boost::iterator_facade < Neighbors_ver
   }
 
  private:
-  // todo remove this ugly hack
+  // TODO(DS): remove this ugly hack
   void set_end() {
     current_ = end_;
   }
 };
 
-}  // namespace skbl
+}  // namespace skeleton_blocker
+
+namespace skbl = skeleton_blocker;
 
 }  // namespace Gudhi
 
 #endif  // SKELETON_BLOCKER_ITERATORS_SKELETON_BLOCKERS_VERTICES_ITERATORS_H_
-
-
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h
index 5b774f25..4f052ba5 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014  INRIA
  *
  *    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
@@ -31,7 +31,7 @@
 #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 <gudhi/Debug_utils.h>
 
 #include <boost/graph/adjacency_list.hpp>
 #include <boost/graph/connected_components.hpp>
@@ -52,7 +52,7 @@
 
 namespace Gudhi {
 
-namespace skbl {
+namespace skeleton_blocker {
 
 /**
  *@class Skeleton_blocker_complex
@@ -211,7 +211,6 @@ class Skeleton_blocker_complex {
       add_edge_without_blockers(e.first, e.second);
   }
 
-
   template<typename SimpleHandleOutputIterator>
   void add_blockers(SimpleHandleOutputIterator simplices_begin, SimpleHandleOutputIterator simplices_end) {
     Tries<Simplex> tries(num_vertices(), simplices_begin, simplices_end);
@@ -414,7 +413,8 @@ class Skeleton_blocker_complex {
   /**
    */
   bool contains_vertex(Vertex_handle u) const {
-    if (u.vertex < 0 || u.vertex >= boost::num_vertices(skeleton))
+    Vertex_handle num_vertices(boost::num_vertices(skeleton));
+    if (u.vertex < 0 || u.vertex >= num_vertices)
       return false;
     return (*this)[u].is_active();
   }
@@ -441,11 +441,11 @@ class Skeleton_blocker_complex {
    * @brief Given an Id return the address of the vertex having this Id in the complex.
    * @remark For a simplicial complex, the address is the id but it may not be the case for a SubComplex.
    */
-  virtual boost::optional<Vertex_handle> get_address(
-                                                     Root_vertex_handle id) const {
+  virtual boost::optional<Vertex_handle> get_address(Root_vertex_handle id) const {
     boost::optional<Vertex_handle> res;
-    if (id.vertex < boost::num_vertices(skeleton))
-      res = Vertex_handle(id.vertex);  // xxx
+    int num_vertices = boost::num_vertices(skeleton);
+    if (id.vertex < num_vertices)
+      res = Vertex_handle(id.vertex);
     return res;
   }
 
@@ -560,7 +560,7 @@ class Skeleton_blocker_complex {
     return res;
   }
 
-    /**
+  /**
    * @brief Adds all edges of s in the complex.
    */
   void add_edge(const Simplex& s) {
@@ -591,7 +591,6 @@ class Skeleton_blocker_complex {
     return *edge_handle;
   }
 
-
   /**
    * @brief Adds all edges of s in the complex without adding blockers.
    */
@@ -844,12 +843,13 @@ class Skeleton_blocker_complex {
     boost_adjacency_iterator ai, ai_end;
     for (tie(ai, ai_end) = adjacent_vertices(v.vertex, skeleton); ai != ai_end;
          ++ai) {
+      Vertex_handle value(*ai);
       if (keep_only_superior) {
-        if (*ai > v.vertex) {
-          n.add_vertex(Vertex_handle(*ai));
+        if (value > v.vertex) {
+          n.add_vertex(value);
         }
       } else {
-        n.add_vertex(Vertex_handle(*ai));
+        n.add_vertex(value);
       }
     }
   }
@@ -929,7 +929,7 @@ class Skeleton_blocker_complex {
   // xxx rename get_address et place un using dans sub_complex
 
   boost::optional<Simplex> get_simplex_address(
-                                                      const Root_simplex_handle& s) const {
+                                               const Root_simplex_handle& s) const {
     boost::optional<Simplex> res;
 
     Simplex s_address;
@@ -1001,10 +1001,9 @@ class Skeleton_blocker_complex {
     return std::distance(triangles.begin(), triangles.end());
   }
 
-
   /*
    * @brief returns the number of simplices of a given dimension in the complex.
-   */  
+   */
   size_t num_simplices() const {
     auto simplices = complex_simplex_range();
     return std::distance(simplices.begin(), simplices.end());
@@ -1012,8 +1011,8 @@ class Skeleton_blocker_complex {
 
   /*
    * @brief returns the number of simplices of a given dimension in the complex.
-   */  
-  size_t num_simplices(unsigned dimension) const {
+   */
+  size_t num_simplices(int dimension) const {
     // TODO(DS): iterator on k-simplices
     size_t res = 0;
     for (const auto& s : complex_simplex_range())
@@ -1595,7 +1594,9 @@ Complex make_complex_from_top_faces(SimplexHandleIterator simplices_begin, Simpl
   return Complex(simplices.begin(), simplices.end(), is_flag_complex);
 }
 
-}  // namespace skbl
+}  // namespace skeleton_blocker
+
+namespace skbl = skeleton_blocker;
 
 }  // namespace Gudhi
 
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_geometric_complex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_geometric_complex.h
index 5c898152..95331b7a 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_geometric_complex.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_geometric_complex.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014  INRIA
  *
  *    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
@@ -19,16 +19,17 @@
  *    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 SKELETON_BLOCKER_GEOMETRIC_COMPLEX_H_
 #define SKELETON_BLOCKER_GEOMETRIC_COMPLEX_H_
 
-#include <gudhi/Utils.h>
 #include <gudhi/Skeleton_blocker_complex.h>
 #include <gudhi/Skeleton_blocker/Skeleton_blocker_sub_complex.h>
+#include <gudhi/Debug_utils.h>
 
 namespace Gudhi {
 
-namespace skbl {
+namespace skeleton_blocker {
 
 /**
  * @brief Class that represents a geometric complex that can be simplified.
@@ -217,7 +218,9 @@ SkeletonBlockerGeometricComplex make_complex_from_top_faces(
   return complex;
 }
 
-}  // namespace skbl
+}  // namespace skeleton_blocker
+
+namespace skbl = skeleton_blocker;
 
 }  // namespace Gudhi
 
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_link_complex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_link_complex.h
index 85a6b0b5..4db075b0 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_link_complex.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_link_complex.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014  INRIA
  *
  *    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
@@ -19,15 +19,16 @@
  *    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 SKELETON_BLOCKER_LINK_COMPLEX_H_
 #define SKELETON_BLOCKER_LINK_COMPLEX_H_
 
-#include <gudhi/Utils.h>
 #include <gudhi/Skeleton_blocker_complex.h>
+#include <gudhi/Debug_utils.h>
 
 namespace Gudhi {
 
-namespace skbl {
+namespace skeleton_blocker {
 
 template<class ComplexType> class Skeleton_blocker_sub_complex;
 
@@ -39,7 +40,7 @@ template<class ComplexType> class Skeleton_blocker_sub_complex;
  */
 template<typename ComplexType>
 class Skeleton_blocker_link_complex : public Skeleton_blocker_sub_complex<
-    ComplexType> {
+ComplexType> {
   template<typename T> friend class Skeleton_blocker_link_superior;
   typedef typename ComplexType::Edge_handle Edge_handle;
 
@@ -60,8 +61,7 @@ class Skeleton_blocker_link_complex : public Skeleton_blocker_sub_complex<
   typedef typename ComplexType::Root_simplex_handle::Simplex_vertex_const_iterator Root_simplex_handle_iterator;
 
   explicit Skeleton_blocker_link_complex(bool only_superior_vertices = false)
-      : only_superior_vertices_(only_superior_vertices) {
-  }
+      : only_superior_vertices_(only_superior_vertices) { }
 
   /**
    * If the parameter only_superior_vertices is true,
@@ -95,10 +95,10 @@ class Skeleton_blocker_link_complex : public Skeleton_blocker_sub_complex<
    */
   Skeleton_blocker_link_complex(const ComplexType & parent_complex,
                                 Edge_handle edge, bool only_superior_vertices =
-                                    false)
+                                false)
       : only_superior_vertices_(only_superior_vertices) {
     Simplex alpha_simplex(parent_complex.first_vertex(edge),
-                                 parent_complex.second_vertex(edge));
+                          parent_complex.second_vertex(edge));
     build_link(parent_complex, alpha_simplex);
   }
 
@@ -151,7 +151,7 @@ class Skeleton_blocker_link_complex : public Skeleton_blocker_sub_complex<
                              bool only_superior_vertices) {
     // for a vertex we know exactly the number of vertices of the link (and the size of the corresponding vector
     this->skeleton.m_vertices.reserve(
-        parent_complex.degree(alpha_parent_adress));
+                                      parent_complex.degree(alpha_parent_adress));
 
     // For all vertex 'v' in this intersection, we go through all its adjacent blockers.
     // If one blocker minus 'v' is included in alpha then the vertex is not in the link complex.
@@ -169,21 +169,21 @@ class Skeleton_blocker_link_complex : public Skeleton_blocker_sub_complex<
       return;
 
     for (auto x_link = this->vertex_range().begin();
-        x_link != this->vertex_range().end(); ++x_link) {
+         x_link != this->vertex_range().end(); ++x_link) {
       for (auto y_link = x_link; ++y_link != this->vertex_range().end();) {
         Vertex_handle x_parent = *parent_complex.get_address(
-            this->get_id(*x_link));
+                                                             this->get_id(*x_link));
         Vertex_handle y_parent = *parent_complex.get_address(
-            this->get_id(*y_link));
+                                                             this->get_id(*y_link));
         if (parent_complex.contains_edge(x_parent, y_parent)) {
           // we check that there is no blocker subset of alpha passing trough x and y
           bool new_edge = true;
           for (auto blocker_parent : parent_complex.const_blocker_range(
-              x_parent)) {
+                                                                        x_parent)) {
             if (!is_alpha_blocker || *blocker_parent != alpha_parent_adress) {
               if (blocker_parent->contains(y_parent)) {
                 new_edge = !(alpha_parent_adress.contains_difference(
-                    *blocker_parent, x_parent, y_parent));
+                                                                     *blocker_parent, x_parent, y_parent));
                 if (!new_edge)
                   break;
               }
@@ -201,8 +201,8 @@ class Skeleton_blocker_link_complex : public Skeleton_blocker_sub_complex<
    * corresponding address in 'other_complex'.
    * It assumes that other_complex have a vertex 'this.get_id(address)'
    */
-  boost::optional<Vertex_handle> give_equivalent_vertex(
-      const ComplexType & other_complex, Vertex_handle address) const {
+  boost::optional<Vertex_handle> give_equivalent_vertex(const ComplexType & other_complex,
+                                                        Vertex_handle address) const {
     Root_vertex_handle id((*this)[address].get_id());
     return other_complex.get_address(id);
   }
@@ -269,7 +269,7 @@ class Skeleton_blocker_link_complex : public Skeleton_blocker_sub_complex<
                   bool only_vertices = false) {
     assert(is_alpha_blocker || parent_complex.contains(alpha_parent_adress));
     compute_link_vertices(parent_complex, alpha_parent_adress, only_superior_vertices_);
-    if(!only_vertices) {
+    if (!only_vertices) {
       compute_link_edges(parent_complex, alpha_parent_adress, is_alpha_blocker);
       compute_link_blockers(parent_complex, alpha_parent_adress, is_alpha_blocker);
     }
@@ -290,7 +290,9 @@ class Skeleton_blocker_link_complex : public Skeleton_blocker_sub_complex<
   }
 };
 
-}  // namespace skbl
+}  // namespace skeleton_blocker
+
+namespace skbl = skeleton_blocker;
 
 }  // namespace Gudhi
 
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 94a125c1..544e02e8 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_simplifiable_complex.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_simplifiable_complex.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014  INRIA
  *
  *    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
@@ -19,6 +19,7 @@
  *    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 SKELETON_BLOCKER_SIMPLIFIABLE_COMPLEX_H_
 #define SKELETON_BLOCKER_SIMPLIFIABLE_COMPLEX_H_
 
@@ -30,10 +31,10 @@
 
 namespace Gudhi {
 
-namespace skbl {
+namespace skeleton_blocker {
 
 /**
- * Returns true iff the blocker 'sigma' is popable.
+ * Returns true if the blocker 'sigma' is popable.
  * To define popable, let us call 'L' the complex that
  * consists in the current complex without the blocker 'sigma'.
  * A blocker 'sigma' is then "popable" if the link of 'sigma'
@@ -145,8 +146,7 @@ void Skeleton_blocker_complex<SkeletonBlockerDS>::remove_star(Vertex_handle v) {
  * whenever the dimension of tau is at least 2.
  */
 template<typename SkeletonBlockerDS>
-void Skeleton_blocker_complex<SkeletonBlockerDS>::update_blockers_after_remove_star_of_vertex_or_edge(
-    const Simplex& simplex_to_be_removed) {
+void Skeleton_blocker_complex<SkeletonBlockerDS>::update_blockers_after_remove_star_of_vertex_or_edge(const Simplex& simplex_to_be_removed) {
   std::list <Blocker_handle> blockers_to_update;
   if (simplex_to_be_removed.empty()) return;
 
@@ -224,8 +224,6 @@ void Skeleton_blocker_complex<SkeletonBlockerDS>::add_simplex(const Simplex& sig
   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;
@@ -385,7 +383,8 @@ Skeleton_blocker_complex<SkeletonBlockerDS>::contract_edge(Vertex_handle a, Vert
 
 template<typename SkeletonBlockerDS>
 void Skeleton_blocker_complex<SkeletonBlockerDS>::get_blockers_to_be_added_after_contraction(Vertex_handle a,
-    Vertex_handle b, std::set<Simplex>& blockers_to_add) {
+                                                                                             Vertex_handle b,
+                                                                                             std::set<Simplex>& blockers_to_add) {
   blockers_to_add.clear();
 
   typedef Skeleton_blocker_link_complex<Skeleton_blocker_complex<SkeletonBlockerDS> > LinkComplexType;
@@ -459,7 +458,9 @@ Skeleton_blocker_complex<SkeletonBlockerDS>::notify_changed_edges(Vertex_handle
 }
 
 
-}  // namespace skbl
+}  // namespace skeleton_blocker
+
+namespace skbl = skeleton_blocker;
 
 }  // namespace Gudhi
 
diff --git a/src/Skeleton_blocker/test/CMakeLists.txt b/src/Skeleton_blocker/test/CMakeLists.txt
index 8b6fb672..f98517f0 100644
--- a/src/Skeleton_blocker/test/CMakeLists.txt
+++ b/src/Skeleton_blocker/test/CMakeLists.txt
@@ -1,28 +1,35 @@
 cmake_minimum_required(VERSION 2.6)
-project(GUDHIskbl)
+project(Skeleton_blocker_tests)
 
 if (GCOVR_PATH)
   # for gcovr to make coverage reports - Corbera Jenkins plugin
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
-  set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fprofile-arcs -ftest-coverage")	
-  set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fprofile-arcs -ftest-coverage")
 endif()
 if (GPROF_PATH)
   # for gprof to make coverage reports - Jenkins
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
-  set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -pg")
-  set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -pg")
 endif()
 
-add_executable(TestSkeletonBlockerComplex TestSkeletonBlockerComplex.cpp)
-add_executable(TestSimplifiable TestSimplifiable.cpp)
-add_executable(TestGeometricComplex TestGeometricComplex.cpp)
+add_executable ( test_skeleton_blocker_complex test_skeleton_blocker_complex.cpp )
+target_link_libraries(test_skeleton_blocker_complex ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+add_executable ( test_skeleton_blocker_geometric_complex test_skeleton_blocker_geometric_complex.cpp )
+target_link_libraries(test_skeleton_blocker_geometric_complex ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+add_executable ( test_skeleton_blocker_simplifiable test_skeleton_blocker_simplifiable.cpp )
+target_link_libraries(test_skeleton_blocker_simplifiable ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
 
 # Do not forget to copy test files in current binary dir
-file(COPY "test.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
 file(COPY "test2.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
 
-add_test(TestSkeletonBlockerComplex ${CMAKE_CURRENT_BINARY_DIR}/TestSkeletonBlockerComplex)
-add_test(TestSimplifiable ${CMAKE_CURRENT_BINARY_DIR}/TestSimplifiable)
-add_test(TestGeometricComplex ${CMAKE_CURRENT_BINARY_DIR}/TestGeometricComplex)
-
+# Unitary tests
+add_test(NAME test_skeleton_blocker_complex
+  COMMAND ${CMAKE_CURRENT_BINARY_DIR}/test_skeleton_blocker_complex
+    # XML format for Jenkins xUnit plugin 
+    --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/skbl_complexUT.xml --log_level=test_suite --report_level=no)
+add_test(NAME test_skeleton_blocker_geometric_complex
+  COMMAND ${CMAKE_CURRENT_BINARY_DIR}/test_skeleton_blocker_geometric_complex
+    # XML format for Jenkins xUnit plugin 
+    --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/skbl_geometric_complexUT.xml --log_level=test_suite --report_level=no)
+add_test(NAME test_skeleton_blocker_simplifiable
+  COMMAND ${CMAKE_CURRENT_BINARY_DIR}/test_skeleton_blocker_simplifiable
+    # XML format for Jenkins xUnit plugin 
+    --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/skbl_simplifiableUT.xml --log_level=test_suite --report_level=no)
diff --git a/src/Skeleton_blocker/test/TestGeometricComplex.cpp b/src/Skeleton_blocker/test/TestGeometricComplex.cpp
deleted file mode 100644
index 084e2b6b..00000000
--- a/src/Skeleton_blocker/test/TestGeometricComplex.cpp
+++ /dev/null
@@ -1,118 +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):       David Salinas
- *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (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/>.
- */
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string>
-#include <fstream>
-#include <sstream>
-#include "gudhi/Test.h"
-#include "gudhi/Skeleton_blocker.h"
-
-
-using namespace std;
-using namespace Gudhi;
-using namespace skbl;
-
-struct Geometry_trait {
-  typedef std::vector<double> Point;
-};
-
-typedef Geometry_trait::Point Point;
-typedef Skeleton_blocker_simple_geometric_traits<Geometry_trait> Complex_geometric_traits;
-typedef Skeleton_blocker_geometric_complex< Complex_geometric_traits > Complex;
-typedef Complex::Vertex_handle Vertex_handle;
-
-bool test_constructor1() {
-  Complex complex;
-  Skeleton_blocker_off_reader<Complex> off_reader("test2.off", complex);
-  if (!off_reader.is_valid()) {
-    std::cerr << "Unable to read file" << std::endl;
-    return false;
-  }
-
-
-  std::cout << "complex has " <<
-      complex.num_vertices() << " vertices, " <<
-      complex.num_blockers() << " blockers, " <<
-      complex.num_edges() << " edges and" <<
-      complex.num_triangles() << " triangles.";
-
-  if (complex.num_vertices() != 7 || complex.num_edges() != 12 || complex.num_triangles() != 6)
-    return false;
-
-  Skeleton_blocker_off_writer<Complex> off_writer("tmp.off", complex);
-  Complex same;
-  Skeleton_blocker_off_reader<Complex> off_reader2("tmp.off", same);
-
-  std::cout << "\ncomplex:" << complex.to_string() << endl;
-  std::cout << "\nsame:" << same.to_string() << endl;
-
-  return (complex == same);
-}
-
-bool test_constructor2() {
-  Complex complex;
-  Skeleton_blocker_off_reader<Complex> off_reader("test2.off", complex);
-  if (!off_reader.is_valid()) {
-    std::cerr << "Unable to read file" << std::endl;
-    return false;
-  }
-  std::cout << "complex has " <<
-      complex.num_vertices() << " vertices, " <<
-      complex.num_blockers() << " blockers, " <<
-      complex.num_edges() << " edges and" <<
-      complex.num_triangles() << " triangles.";
-
-  if (complex.num_vertices() != 7 || complex.num_edges() != 12 || complex.num_triangles() != 6)
-    return false;
-
-  auto link_0 = complex.abstract_link(Vertex_handle(0));
-
-
-  std::cout << "\n link(0):" << link_0.to_string() << endl;
-
-  auto link_geometric_0 = complex.link(Vertex_handle(0));
-
-  auto print_point = [&](Vertex_handle v) {
-    for (auto x : link_geometric_0.point(v)) std::cout << x << " ";
-    std::cout << std::endl;
-  };
-
-  std::for_each(link_geometric_0.vertex_range().begin(), link_geometric_0.vertex_range().end(), print_point);
-
-  //	for(auto v : link_geometric_0.vertex_range())
-  //		std::cout<<"point("<<v<<"):"<<link_geometric_0.point(v)<<std::endl;
-
-  return link_0.num_vertices() == 2;
-}
-
-int main(int argc, char *argv[]) {
-  Tests tests_geometric_complex;
-  tests_geometric_complex.add("Test constructor 1", test_constructor1);
-  tests_geometric_complex.add("Test constructor 2", test_constructor2);
-
-  if (tests_geometric_complex.run())
-    return EXIT_SUCCESS;
-  else
-    return EXIT_FAILURE;
-}
diff --git a/src/Skeleton_blocker/test/TestSkeletonBlockerComplex.cpp b/src/Skeleton_blocker/test/test_skeleton_blocker_complex.cpp
index 42482e23..4f9888ba 100644
--- a/src/Skeleton_blocker/test/TestSkeletonBlockerComplex.cpp
+++ b/src/Skeleton_blocker/test/test_skeleton_blocker_complex.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014  INRIA
  *
  *    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
@@ -24,22 +24,18 @@
 #include <string>
 #include <fstream>
 #include <sstream>
-#include "gudhi/Utils.h"
-#include "gudhi/Test.h"
-#include "gudhi/Skeleton_blocker.h"
-//#include "gudhi/Skeleton_blocker_link_complex.h"
-//#include "gudhi/Skeleton_blocker/Skeleton_blocker_link_superior.h"
-//#include "gudhi/Skeleton_blocker/Skeleton_blocker_simple_traits.h"
-//#include "gudhi/Skeleton_blocker/internal/Trie.h"
 
-using namespace std;
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE "skeleton_blocker_complex"
+#include <boost/test/unit_test.hpp>
+#include <boost/mpl/list.hpp>
 
-using namespace Gudhi;
+#include <gudhi/Skeleton_blocker.h>
 
-using namespace skbl;
-
-
-typedef Skeleton_blocker_complex<Skeleton_blocker_simple_traits> Complex;
+template<typename ComplexType> class Skeleton_blocker_sub_complex;
+typedef Gudhi::skeleton_blocker::Skeleton_blocker_simple_traits Traits;
+typedef Gudhi::skeleton_blocker::Skeleton_blocker_complex<Traits> Complex;
+typedef Gudhi::skeleton_blocker::Skeleton_blocker_link_complex<Complex> Skeleton_blocker_link_complex;
 typedef Complex::Vertex_handle Vertex_handle;
 typedef Complex::Root_vertex_handle Root_vertex_handle;
 typedef Complex::Simplex Simplex;
@@ -47,8 +43,6 @@ typedef Complex::Root_simplex_handle Root_simplex_handle;
 typedef Simplex::Simplex_vertex_const_iterator Simplex_vertex_const_iterator;
 typedef Complex::Edge_handle Edge_handle;
 
-// true if v in complex
-
 bool assert_vertex(Complex &complex, Vertex_handle v) {
   //assert(complex.contains(v));
   return complex.contains(static_cast<Simplex> (v));
@@ -80,75 +74,59 @@ void build_complete(int n, Complex& complex) {
   for (int i = 0; i < n; i++)
     complex.add_vertex();
 
-  //	for(int i=n-1;i>=0;i--)
-  //		for(int j=i-1;j>=0;j--)
-  //			complex.add_edge_without_blockers(Vertex_handle(i),Vertex_handle(j));
-
   for (int i = 0; i < n; i++)
     for (int j = 0; j < i; j++)
       complex.add_edge_without_blockers(Vertex_handle(i), Vertex_handle(j));
 }
 
-bool test_simplex() {
-  //	PRINT("test simplex");
+BOOST_AUTO_TEST_CASE(test_skeleton_blocker_simplex) {
   Simplex simplex(Vertex_handle(0), Vertex_handle(1), Vertex_handle(2), Vertex_handle(3));
-  for (auto i = simplex.begin(); i != simplex.end(); ++i) {
-    PRINT(*i);
-    auto j = i;
-    for (++j;
-         j != simplex.end();
-         ++j) {
-      PRINT(*j);
-    }
-  }
-  return simplex.dimension() == 3;
+  BOOST_CHECK(simplex.dimension() == 3);
 }
 
-bool test_num_simplices() {
+BOOST_AUTO_TEST_CASE(test_skeleton_num_simplices) {
   int n = 4;
   Complex complex;
   build_complete(n, complex);
   size_t sum = 0;
   for (int i = 0; i < n; i++) {
-    PRINT(complex.num_simplices(i));
     sum += complex.num_simplices(i);
   }
-  return 
-    complex.num_vertices() == n && 
-    complex.num_edges() == 6 && 
-    sum == 15 && 
-    complex.num_simplices() == 15;
+  BOOST_CHECK(complex.num_vertices() == n);
+  BOOST_CHECK(complex.num_edges() == 6);
+  BOOST_CHECK(sum == 15);
+  BOOST_CHECK(complex.num_simplices() == 15);
 }
 
 
-bool test_iterator_vertices1() {
+BOOST_AUTO_TEST_CASE(test_skeleton_iterator_vertices1) {
   int n = 10;
   Complex complex(10);
-  cerr << "complex.num_vertices():" << complex.num_vertices() << endl;
+  std::cout << "complex.num_vertices():" << complex.num_vertices() << std::endl;
   int num_vertex_seen = 0;
   for (auto vi : complex.vertex_range()) {
-    cerr << "vertex:" << vi << endl;
+    std::cout << "vertex:" << vi << std::endl;
     ++num_vertex_seen;
   }
-  return num_vertex_seen == n;
+  BOOST_CHECK(num_vertex_seen == n);
 }
 
-bool test_iterator_vertices2() {
+BOOST_AUTO_TEST_CASE(test_skeleton_iterator_vertices2) {
   int n = 10;
   Complex complex;
   build_complete(10, complex);
-  cerr << "complex.num_vertices():" << complex.num_vertices() << endl;
-  cerr << "complex.num_edges():" << complex.num_edges() << endl;
+  std::cout << "complex.num_vertices():" << complex.num_vertices() << std::endl;
+  std::cout << "complex.num_edges():" << complex.num_edges() << std::endl;
   int num_vertex_seen = 0;
   for (auto vi : complex.vertex_range(Vertex_handle(2))) {
-    cerr << "vertex:" << vi << endl;
+    std::cout << "vertex:" << vi << std::endl;
     ++num_vertex_seen;
   }
-  std::cerr << "num_vertex_seen:" << num_vertex_seen << std::endl;
-  return num_vertex_seen == (n - 1);
+  std::cout << "num_vertex_seen:" << num_vertex_seen << std::endl;
+  BOOST_CHECK(num_vertex_seen == (n -1));
 }
 
-bool test_iterator_edge() {
+BOOST_AUTO_TEST_CASE(test_skeleton_iterator_edge) {
   const int n = 10;
   Complex complex(n);
   for (int i = 0; i < n; i++)
@@ -156,17 +134,17 @@ bool test_iterator_edge() {
       complex.add_edge_without_blockers(Vertex_handle(i), Vertex_handle(j));
   complex.remove_edge(Vertex_handle(2), Vertex_handle(3));
   complex.remove_edge(Vertex_handle(3), Vertex_handle(5));
-  cerr << "complex.num_edges():" << complex.num_edges() << endl;
+  std::cout << "complex.num_edges():" << complex.num_edges() << std::endl;
   int num_edges_seen = 0;
   for (auto edge : complex.edge_range()) {
-    cerr << "edge :" << complex[edge] << endl;
+    std::cout << "edge :" << complex[edge] << std::endl;
     ++num_edges_seen;
   }
 
-  return num_edges_seen == n * (n - 1) / 2 - 2;
+  BOOST_CHECK(num_edges_seen == n * (n - 1) / 2 - 2);
 }
 
-bool test_iterator_edge2() {
+BOOST_AUTO_TEST_CASE(test_skeleton_iterator_edge2) {
   const int n = 10;
   Complex complex(n);
   for (int i = 0; i < n; i++)
@@ -174,33 +152,16 @@ bool test_iterator_edge2() {
       complex.add_edge_without_blockers(Vertex_handle(i), Vertex_handle(j));
   complex.remove_edge(Vertex_handle(2), Vertex_handle(3));
   complex.remove_edge(Vertex_handle(3), Vertex_handle(5));
-  cerr << "complex.num_edges():" << complex.num_edges() << endl;
+  std::cout << "complex.num_edges():" << complex.num_edges() << std::endl;
   int num_neigbors_seen = 0;
   for (auto neighbor : complex.vertex_range(Vertex_handle(2))) {
-    cerr << "neighbor" << neighbor << endl;
+    std::cout << "neighbor" << neighbor << std::endl;
     ++num_neigbors_seen;
   }
-  return num_neigbors_seen == 8;
+  BOOST_CHECK(num_neigbors_seen == 8);
 }
 
-bool test_iterator_edge3() {
-  const int n = 10;
-  Complex complex(n);
-  for (int i = 0; i < n; i++)
-    for (int j = 0; j < i; j++)
-      complex.add_edge_without_blockers(Vertex_handle(i), Vertex_handle(j));
-  complex.remove_edge(Vertex_handle(2), Vertex_handle(3));
-  complex.remove_edge(Vertex_handle(3), Vertex_handle(5));
-  cerr << "complex.num_edges():" << complex.num_edges() << endl;
-  int num_neigbors_seen = 0;
-  for (auto edge : complex.edge_range(Vertex_handle(2))) {
-    std::cerr << edge << std::endl;
-    ++num_neigbors_seen;
-  }
-  return num_neigbors_seen == 8;
-}
-
-bool test_iterator_triangles() {
+BOOST_AUTO_TEST_CASE(test_skeleton_iterator_triangles) {
   const int n = 7;
   Complex complex(n);
   //create a "ring" around '0'
@@ -210,24 +171,20 @@ bool test_iterator_triangles() {
     complex.add_edge_without_blockers(Vertex_handle(i), Vertex_handle(i + 1));
   complex.add_edge_without_blockers(Vertex_handle(1), Vertex_handle(6));
 
-  PRINT(complex.to_string());
+  std::cout << complex.to_string() << std::endl;
 
   int num_triangles_seen = 0;
   //for (auto t : complex.triangle_range(5)){
-  TEST("triangles around 5 (should be 2 of them):");
   for (auto t : complex.triangle_range(Vertex_handle(5))) {
-    PRINT(t);
     ++num_triangles_seen;
   }
-  bool test = (num_triangles_seen == 2);
+  BOOST_CHECK(num_triangles_seen == 2);
 
   num_triangles_seen = 0;
-  TEST("triangles around 0 (should be 6 of them):");
   for (auto t : complex.triangle_range(Vertex_handle(0))) {
-    PRINT(t);
     ++num_triangles_seen;
   }
-  test = test && (num_triangles_seen == 6);
+  BOOST_CHECK(num_triangles_seen == 6);
 
   // we now add another triangle
   complex.add_vertex();
@@ -236,22 +193,14 @@ bool test_iterator_triangles() {
   complex.add_blocker(Simplex(Vertex_handle(0), Vertex_handle(1), Vertex_handle(6)));
   num_triangles_seen = 0;
 
-  TEST("triangles (should be 6 of them):");
   num_triangles_seen = 0;
   for (auto t : complex.triangle_range()) {
-    PRINT(t);
     ++num_triangles_seen;
   }
-  test = test && (num_triangles_seen == 6);
-  PRINT(num_triangles_seen);
-
-  return test;
+  BOOST_CHECK(num_triangles_seen == 6);
 }
 
-
-//#include "combinatorics/Skeleton_blocker/iterators/Skeleton_blockers_simplices_iterators.h"
-
-bool test_iterator_simplices() {
+BOOST_AUTO_TEST_CASE(test_skeleton_iterator_simplices) {
   Complex complex(6);
   complex.add_edge_without_blockers(Vertex_handle(0), Vertex_handle(1));
   complex.add_edge_without_blockers(Vertex_handle(1), Vertex_handle(2));
@@ -266,8 +215,6 @@ bool test_iterator_simplices() {
 
   complex.add_blocker(Simplex(Vertex_handle(2), Vertex_handle(3), Vertex_handle(4), Vertex_handle(5)));
 
-  bool correct_number_simplices = true;
-
   std::map<Vertex_handle, unsigned> expected_num_simplices;
 
   expected_num_simplices[Vertex_handle(0)] = 4;
@@ -278,120 +225,108 @@ bool test_iterator_simplices() {
   expected_num_simplices[Vertex_handle(5)] = 7;
 
   for (auto pair : expected_num_simplices) {
+    std::cout << "found list: ";
     unsigned num_simplices_around = 0;
     for (const auto& simplex : complex.star_simplex_range(pair.first)) {
       simplex.dimension();
-      DBGVALUE(simplex);
+      std::cout << simplex << " - ";
       ++num_simplices_around;
     }
 
-    correct_number_simplices = correct_number_simplices && (num_simplices_around == pair.second);
+    BOOST_CHECK(num_simplices_around == pair.second);
 
-    DBGMSG("current vertex:", pair.first);
-    DBGMSG("expected_num_simplices:", pair.second);
-    DBGMSG("found:", num_simplices_around);
+    std::cout << std::endl << "current vertex:" << pair.first << " - ";
+    std::cout << "expected_num_simplices:" << pair.second << " - ";
+    std::cout << "found:" << num_simplices_around << std::endl;
   }
-  return correct_number_simplices;
 }
 
-bool test_iterator_simplices2() {
+BOOST_AUTO_TEST_CASE(test_skeleton_iterator_simplices2) {
   Complex complex(2);
   complex.add_edge_without_blockers(Vertex_handle(0), Vertex_handle(1));
 
-  for (const auto& s : complex.triangle_range()) {
-    s.dimension();
-    return false; // there are no triangles
-  }
-
-  unsigned num_simplices = 0;
-
-
-  DBGVALUE(complex.to_string());
-
-  for (const auto& simplex : complex.star_simplex_range(Vertex_handle(0))) {
-    simplex.dimension();
-    DBGVALUE(simplex);
-  }
-
+  // Check there is no triangle
+  BOOST_CHECK(std::distance(complex.triangle_range().begin(), complex.triangle_range().end()) == 0);
 
-  for (const auto& simplex : complex.complex_simplex_range()) {
-    DBGVALUE(simplex);
-    simplex.dimension();
-    ++num_simplices;
-  }
-  bool correct_number_simplices = (num_simplices == 3);
-  return correct_number_simplices;
+  // Star(0) is [{0},{0,1}]
+  BOOST_CHECK(std::distance(complex.star_simplex_range(Vertex_handle(0)).begin(),
+                            complex.star_simplex_range(Vertex_handle(0)).end()) == 2);
+  
+  // No blocker
+  BOOST_CHECK(std::distance(complex.blocker_range(Vertex_handle(0)).begin(),
+                            complex.blocker_range(Vertex_handle(0)).end()) == 0);
+  
+  // Complex is [{0},{0,1},{1}]
+  BOOST_CHECK(std::distance(complex.complex_simplex_range().begin(),
+                            complex.complex_simplex_range().end()) == 3);
 }
 
-bool test_iterator_simplices3() {
+BOOST_AUTO_TEST_CASE(test_skeleton_iterator_simplices3) {
   Complex complex(3);
   complex.add_edge_without_blockers(Vertex_handle(0), Vertex_handle(1));
   complex.add_edge_without_blockers(Vertex_handle(1), Vertex_handle(2));
   complex.add_edge_without_blockers(Vertex_handle(2), Vertex_handle(0));
   complex.add_blocker(Simplex(Vertex_handle(0), Vertex_handle(1), Vertex_handle(2)));
 
-  unsigned num_simplices = 0;
-
-  for (const auto& simplex : complex.star_simplex_range(Vertex_handle(0))) {
-    simplex.dimension();
-    DBGVALUE(simplex);
-  }
+  // Check there is no triangle
+  BOOST_CHECK(std::distance(complex.triangle_range().begin(), complex.triangle_range().end()) == 0);
 
+  // Star(0) is [{0},{0,1},{0,2}]
+  BOOST_CHECK(std::distance(complex.star_simplex_range(Vertex_handle(0)).begin(),
+                            complex.star_simplex_range(Vertex_handle(0)).end()) == 3);
 
-  for (const auto& simplex : complex.complex_simplex_range()) {
-    DBGVALUE(simplex);
-    simplex.dimension();
-    ++num_simplices;
-  }
-  bool correct_number_simplices = (num_simplices == 6);
-  return correct_number_simplices;
+  // blocker(0) is [{0,1,2}]
+  BOOST_CHECK(std::distance(complex.blocker_range(Vertex_handle(0)).begin(),
+                            complex.blocker_range(Vertex_handle(0)).end()) == 1);
+  
+  // Complex is [{0},{0,1},{0,2},{1},{1,2},{2}]
+  BOOST_CHECK(std::distance(complex.complex_simplex_range().begin(),
+                            complex.complex_simplex_range().end()) == 6);
 }
 
-bool test_iterator_simplices4() {
+BOOST_AUTO_TEST_CASE(test_skeleton_iterator_simplices4) {
   Complex empty_complex;
   for (auto v : empty_complex.vertex_range()) {
-    (void) v;
+    std::cout << v;
+    BOOST_CHECK(false);
   }
   for (auto e : empty_complex.edge_range()) {
-    empty_complex[e];
+    std::cout << e;
+    BOOST_CHECK(false);
   }
   for (auto t : empty_complex.triangle_range()) {
-    t.dimension();
+    std::cout << t;
+    BOOST_CHECK(false);
   }
   for (auto s : empty_complex.complex_simplex_range()) {
-    s.dimension();
+    std::cout << s;
+    BOOST_CHECK(false);
   }
-  return true;
 }
 
-bool test_iterator_coboundary() {
+BOOST_AUTO_TEST_CASE(test_skeleton_iterator_coboundary) {
   Complex c;
   build_complete(4, c);
   c.remove_edge(Vertex_handle(1), Vertex_handle(3));
-  PRINT(c.to_string());
+  std::cout << c.to_string();
   Simplex s02(Vertex_handle(0), Vertex_handle(2));
   int n = 0;
   std::set<Simplex> expected;
   expected.insert(Simplex(Vertex_handle(0), Vertex_handle(1), Vertex_handle(2)));
   expected.insert(Simplex(Vertex_handle(0), Vertex_handle(2), Vertex_handle(3)));
   for (const auto & s : c.coboundary_range(s02)) {
-    PRINT(s);
-    if (expected.find(s) == expected.end())
-      return false;
+    BOOST_CHECK(expected.find(s) != expected.end());
     ++n;
   }
-  return n == 2;
+  BOOST_CHECK(n == 2);
 }
 
-
-
-
 template<typename Map>
 auto blocker_range(Map map) -> decltype(map | boost::adaptors::map_values) {
   return map | boost::adaptors::map_values;
 }
 
-bool test_iterator_blockers() {
+BOOST_AUTO_TEST_CASE(test_skeleton_iterator_blockers) {
   Complex complex;
   Simplex alpha;
   Simplex vertex_set_expected;
@@ -404,58 +339,62 @@ bool test_iterator_blockers() {
       complex.add_edge_without_blockers(Vertex_handle(i), Vertex_handle(j));
   }
 
-  complex.add_blocker(Simplex(Vertex_handle(10), Vertex_handle(11), Vertex_handle(12)));
-  complex.add_blocker(Simplex(Vertex_handle(2), Vertex_handle(1), Vertex_handle(10)));
-  complex.add_blocker(Simplex(Vertex_handle(10), Vertex_handle(9), Vertex_handle(15)));
-  complex.add_blocker(Simplex(Vertex_handle(1), Vertex_handle(9), Vertex_handle(8)));
+  std::vector<Simplex> myBlockers;
+  myBlockers.push_back(Simplex(Vertex_handle(10), Vertex_handle(11), Vertex_handle(12)));
+  myBlockers.push_back(Simplex(Vertex_handle(2), Vertex_handle(1), Vertex_handle(10)));
+  myBlockers.push_back(Simplex(Vertex_handle(10), Vertex_handle(9), Vertex_handle(15)));
+  myBlockers.push_back(Simplex(Vertex_handle(1), Vertex_handle(9), Vertex_handle(8)));
+
+  for (auto blocker : myBlockers)
+    complex.add_blocker(blocker);
 
-  // Print result
   int num_blockers = 0;
   for (auto blockers : complex.blocker_range(Vertex_handle(10))) {
-    TESTVALUE(*blockers);
+    // Only the first 3 blockers contain vertex 10
+    BOOST_CHECK(*blockers == myBlockers[num_blockers]);
     num_blockers++;
   }
-  bool test = (num_blockers == 3);
+  BOOST_CHECK(num_blockers == 3);
 
   num_blockers = 0;
   for (auto blockers : complex.blocker_range()) {
-    TESTVALUE(*blockers);
+// If not windows - _WIN32 is for windows 32 and 64 bits
+#ifndef _WIN32
+    for (auto block_ptr = myBlockers.begin(); block_ptr < myBlockers.end(); block_ptr++)
+      if (*block_ptr == *blockers)
+        myBlockers.erase(block_ptr);
+#endif
     num_blockers++;
   }
-  test = test && (num_blockers == 4);
-
-  return test;
+  BOOST_CHECK(num_blockers == 4);
+// If not windows - _WIN32 is for windows 32 and 64 bits
+#ifndef _WIN32
+  BOOST_CHECK(myBlockers.empty());
+#endif
 }
 
-bool test_link0() {
-
-  enum {
-    a, b, c, d, n
-  };
+BOOST_AUTO_TEST_CASE(test_skeleton_blocker_complex_link0) {
+  enum { a, b, c, d, n };
   Complex complex(n);
   complex.add_edge_without_blockers(Vertex_handle(b), Vertex_handle(c));
   complex.add_edge_without_blockers(Vertex_handle(c), Vertex_handle(d));
   Simplex alpha = Simplex(Vertex_handle(c));
-  Skeleton_blocker_link_complex<Complex> L(complex, alpha);
+  Skeleton_blocker_link_complex L(complex, alpha);
 
   auto L2 = complex.link(alpha);
-  if (L != L2) return false;
-
-  PRINT(L.num_vertices());
-  PRINT(L.to_string());
+  BOOST_CHECK(L == L2);
 
-  bool test1 = L.contains_vertex(*L.get_address(Root_vertex_handle(b)));
-  bool test2 = L.contains_vertex(*L.get_address(Root_vertex_handle(d)));
-  bool test3 = L.num_edges() == 0;
-  bool test4 = L.num_blockers() == 0;
-  return test1 && test2 && test3&&test4;
+  std::cout << L.to_string();
 
+  BOOST_CHECK(L.contains_vertex(*L.get_address(Root_vertex_handle(b))));
+  BOOST_CHECK(L.contains_vertex(*L.get_address(Root_vertex_handle(d))));
+  BOOST_CHECK(L.num_edges() == 0);
+  BOOST_CHECK(L.num_blockers() == 0);
 }
 
-bool test_link1() {
+BOOST_AUTO_TEST_CASE(test_skeleton_blocker_complex_link1) {
   Complex complex;
 
-
   // Build the complexes
   for (int i = 0; i < 20; i++) {
     complex.add_vertex();
@@ -465,30 +404,27 @@ bool test_link1() {
       complex.add_edge_without_blockers(Vertex_handle(i), Vertex_handle(j));
   }
   Simplex alpha(Vertex_handle(12), Vertex_handle(14));
-  Skeleton_blocker_link_complex<Complex> L(complex, alpha);
+  Skeleton_blocker_link_complex L(complex, alpha);
   // Complexes built
 
   auto L2 = complex.link(alpha);
-  if (L != L2) return false;
+  BOOST_CHECK(L == L2);
 
   // verification
-  bool test1 = L.contains_vertex(*L.get_address(Root_vertex_handle(10)));
-  bool test2 = L.contains_vertex(*L.get_address(Root_vertex_handle(11)));
-  bool test3 = L.contains_vertex(*L.get_address(Root_vertex_handle(13)));
-  bool test4 = L.num_edges() == 3;
-  bool test5 = L.num_blockers() == 0;
+  BOOST_CHECK(L.contains_vertex(*L.get_address(Root_vertex_handle(10))));
+  BOOST_CHECK(L.contains_vertex(*L.get_address(Root_vertex_handle(11))));
+  BOOST_CHECK(L.contains_vertex(*L.get_address(Root_vertex_handle(13))));
+  BOOST_CHECK(L.num_edges() == 3);
+  BOOST_CHECK(L.num_blockers() == 0);
   Root_simplex_handle simplex;
   simplex.add_vertex(Root_vertex_handle(10));
   simplex.add_vertex(Root_vertex_handle(11));
   simplex.add_vertex(Root_vertex_handle(13));
-  bool test6(L.get_simplex_address(simplex));
-  bool test7 = L.contains(*(L.get_simplex_address(simplex)));
-  cerr << "----> Ocomplex \n";
-  return test1 && test2 && test3 && test4 && test5 && test6&&test7;
-
+  BOOST_CHECK(L.get_simplex_address(simplex));
+  BOOST_CHECK(L.contains(*(L.get_simplex_address(simplex))));
 }
 
-bool test_link2() {
+BOOST_AUTO_TEST_CASE(test_skeleton_blocker_complex_link2) {
   Complex complex;
 
   Simplex alpha;
@@ -503,34 +439,32 @@ bool test_link2() {
   }
   complex.add_blocker(Simplex(Vertex_handle(10), Vertex_handle(11), Vertex_handle(13)));
   alpha = Simplex(Vertex_handle(12), Vertex_handle(14));
-  Skeleton_blocker_link_complex<Complex> L(complex, alpha);
+  Skeleton_blocker_link_complex L(complex, alpha);
   // Complexes built
 
   // Print result
-  cerr << "complex complex" << complex.to_string();
-  cerr << endl << endl;
-  cerr << "L= Link_complex(" << alpha << ") : \n" << L.to_string();
+  std::cout << "complex complex" << complex.to_string();
+  std::cout << std::endl << std::endl;
+  std::cout << "L= Link_complex(" << alpha << ") : \n" << L.to_string();
 
   auto L2 = complex.link(alpha);
-  if (L != L2) return false;
+  BOOST_CHECK(L == L2);
 
 
   // verification
-  bool test1 = L.contains_vertex(*L.get_address(Root_vertex_handle(10)));
-  bool test2 = L.contains_vertex(*L.get_address(Root_vertex_handle(11)));
-  bool test3 = L.contains_vertex(*L.get_address(Root_vertex_handle(13)));
-  bool test4 = L.num_edges() == 3;
-  bool test5 = L.num_blockers() == 1;
+  BOOST_CHECK(L.contains_vertex(*L.get_address(Root_vertex_handle(10))));
+  BOOST_CHECK(L.contains_vertex(*L.get_address(Root_vertex_handle(11))));
+  BOOST_CHECK(L.contains_vertex(*L.get_address(Root_vertex_handle(13))));
+  BOOST_CHECK(L.num_edges() == 3);
+  BOOST_CHECK(L.num_blockers() == 1);
   Root_simplex_handle simplex;
   simplex.add_vertex(Root_vertex_handle(10));
   simplex.add_vertex(Root_vertex_handle(11));
   simplex.add_vertex(Root_vertex_handle(13));
-  bool test6 = L.contains_blocker(*(L.get_simplex_address(simplex)));
-  cerr << "----> Ocomplex \n";
-  return test1 && test2 && test3 && test4 && test5&&test6;
+  BOOST_CHECK(L.contains_blocker(*(L.get_simplex_address(simplex))));
 }
 
-bool test_link3() {
+BOOST_AUTO_TEST_CASE(test_skeleton_blocker_complex_link3) {
   Complex complex;
 
   Simplex alpha;
@@ -545,30 +479,28 @@ bool test_link3() {
   }
   complex.add_blocker(Simplex(Vertex_handle(10), Vertex_handle(11), Vertex_handle(12)));
   alpha = Simplex(Vertex_handle(12), Vertex_handle(14));
-  Skeleton_blocker_link_complex<Complex> L(complex, alpha);
+  Skeleton_blocker_link_complex L(complex, alpha);
   // Complexes built
 
   // Print result
-  cerr << "complex complex" << complex.to_string();
-  cerr << endl << endl;
-  cerr << "L= Link_complex(" << alpha << ") : \n" << L.to_string();
+  std::cout << "complex complex" << complex.to_string();
+  std::cout << std::endl << std::endl;
+  std::cout << "L= Link_complex(" << alpha << ") : \n" << L.to_string();
 
   auto L2 = complex.link(alpha);
-  if (L != L2) return false;
-
+  BOOST_CHECK(L == L2);
 
   // verification
-  bool test = assert_vertex(L, *L.get_address(Root_vertex_handle(10)));
-  test = test && assert_vertex(L, *L.get_address(Root_vertex_handle(11)));
-  test = test && assert_vertex(L, *L.get_address(Root_vertex_handle(13)));
-  test = test && L.num_edges() == 2;
-  test = test && L.contains_edge(*L.get_address(Root_vertex_handle(10)), *L.get_address(Root_vertex_handle(13)));
-  test = test && L.contains_edge(*L.get_address(Root_vertex_handle(13)), *L.get_address(Root_vertex_handle(11)));
-  test = test && L.num_blockers() == 0;
-  return test;
+  BOOST_CHECK(L.contains(static_cast<Simplex> (*L.get_address(Root_vertex_handle(10)))));
+  BOOST_CHECK(L.contains(static_cast<Simplex> (*L.get_address(Root_vertex_handle(11)))));
+  BOOST_CHECK(L.contains(static_cast<Simplex> (*L.get_address(Root_vertex_handle(13)))));
+  BOOST_CHECK(L.num_edges() == 2);
+  BOOST_CHECK(L.contains_edge(*L.get_address(Root_vertex_handle(10)), *L.get_address(Root_vertex_handle(13))));
+  BOOST_CHECK(L.contains_edge(*L.get_address(Root_vertex_handle(13)), *L.get_address(Root_vertex_handle(11))));
+  BOOST_CHECK(L.num_blockers() == 0);
 }
 
-bool test_link4() {
+BOOST_AUTO_TEST_CASE(test_skeleton_blocker_complex_link4) {
   Complex complex;
 
   // Build the complexes
@@ -581,68 +513,62 @@ bool test_link4() {
   }
   complex.add_blocker(Simplex(Vertex_handle(10), Vertex_handle(11), Vertex_handle(12), Vertex_handle(13)));
   Simplex alpha(Vertex_handle(12), Vertex_handle(14));
-  Skeleton_blocker_link_complex<Complex> L(complex, alpha);
+  Skeleton_blocker_link_complex L(complex, alpha);
   // Complexes built
 
   // verification
-  bool test1 = L.contains_vertex(*L.get_address(Root_vertex_handle(10)));
-  bool test2 = L.contains_vertex(*L.get_address(Root_vertex_handle(11)));
-  bool test3 = L.contains_vertex(*L.get_address(Root_vertex_handle(13)));
-  bool test4 = L.num_edges() == 3;
-  bool test5 = L.num_blockers() == 1;
+  BOOST_CHECK(L.contains_vertex(*L.get_address(Root_vertex_handle(10))));
+  BOOST_CHECK(L.contains_vertex(*L.get_address(Root_vertex_handle(11))));
+  BOOST_CHECK(L.contains_vertex(*L.get_address(Root_vertex_handle(13))));
+  BOOST_CHECK(L.num_edges() == 3);
+  BOOST_CHECK(L.num_blockers() == 1);
   Root_simplex_handle simplex;
   simplex.add_vertex(Root_vertex_handle(10));
   simplex.add_vertex(Root_vertex_handle(11));
   simplex.add_vertex(Root_vertex_handle(13));
-  bool test6 = L.contains_blocker(*(L.get_simplex_address(simplex)));
-  cerr << "----> Ocomplex \n";
-  return test1 && test2 && test3 && test4 && test5&&test6;
-
+  BOOST_CHECK(L.contains_blocker(*(L.get_simplex_address(simplex))));
 }
 
-bool test_link5() {
-  Complex complex(0, new Print_complex_visitor<Vertex_handle>());
+BOOST_AUTO_TEST_CASE(test_skeleton_blocker_complex_link5) {
+  Complex complex(0);
   // Build the complexes
   build_complete(4, complex);
   complex.add_blocker(Simplex(Vertex_handle(0), Vertex_handle(1), Vertex_handle(2), Vertex_handle(3)));
 
   Simplex alpha(Vertex_handle(0), Vertex_handle(1), Vertex_handle(2));
-
-
-  Skeleton_blocker_link_complex<Complex> L(complex, alpha); // Complexes built
+  Skeleton_blocker_link_complex L(complex, alpha);
+  // Complexes built
 
   // Print result
-  PRINT(complex.to_string());
-  cerr << endl << endl;
-  PRINT(L.to_string());
+  std::cout << "Complex: " << complex.to_string()<< std::endl << std::endl;
+  std::cout << "Link: " << L.to_string() << std::endl;
 
   // verification
-  return L.num_vertices() == 0;
+  BOOST_CHECK(L.num_vertices() == 0);
 }
 
-bool test_link6() {
-  Complex complex(0, new Print_complex_visitor<Vertex_handle>());
+BOOST_AUTO_TEST_CASE(test_skeleton_blocker_complex_link6) {
+  Complex complex(0);
   // Build the complexes
   build_complete(4, complex);
   complex.add_blocker(Simplex(Vertex_handle(0), Vertex_handle(1), Vertex_handle(2)));
 
   Simplex alpha(Vertex_handle(0), Vertex_handle(1), Vertex_handle(2));
 
-  Skeleton_blocker_link_complex<Complex> link_blocker_alpha;
+  Skeleton_blocker_link_complex link_blocker_alpha;
 
   build_link_of_blocker(complex, alpha, link_blocker_alpha);
 
   // Print result
-  PRINT(complex.to_string());
-  cerr << endl << endl;
-  PRINT(link_blocker_alpha.to_string());
+  std::cout << "Complex: " << complex.to_string()<< std::endl << std::endl;
+  std::cout << "Link: " << link_blocker_alpha.to_string() << std::endl;
 
   // verification
-  return link_blocker_alpha.num_vertices() == 1;
+  BOOST_CHECK(link_blocker_alpha.num_vertices() == 1);
 }
 
-bool test_link7() {
-  Complex complex(0, new Print_complex_visitor<Vertex_handle>());
+BOOST_AUTO_TEST_CASE(test_skeleton_blocker_complex_link7) {
+  Complex complex(0);
   // Build the complexes
   build_complete(6, complex);
   complex.add_vertex();
@@ -657,38 +583,33 @@ bool test_link7() {
 
   Simplex alpha(Vertex_handle(3), Vertex_handle(4), Vertex_handle(5));
 
-  Skeleton_blocker_link_complex<Complex> link_blocker_alpha;
+  Skeleton_blocker_link_complex link_blocker_alpha;
 
   build_link_of_blocker(complex, alpha, link_blocker_alpha);
 
   //the result should be the edge {6,7} plus the blocker {0,1,2}
 
   // Print result
-  PRINT(complex.to_string());
-  cerr << endl << endl;
-  DBGVALUE(link_blocker_alpha.to_string());
+  std::cout << "Complex: " << complex.to_string()<< std::endl << std::endl;
+  std::cout << "Link: " << link_blocker_alpha.to_string() << std::endl;
 
-  Skeleton_blocker_link_complex<Complex> link_blocker_alpha_cpy = link_blocker_alpha;
+  Skeleton_blocker_link_complex link_blocker_alpha_cpy = link_blocker_alpha;
 
-  DBGVALUE(link_blocker_alpha_cpy.to_string());
+  std::cout << "Link copy: " << link_blocker_alpha_cpy.to_string() << std::endl;
 
-  bool equal_complexes =
-      (link_blocker_alpha.num_vertices() == link_blocker_alpha_cpy.num_vertices())
-      &&(link_blocker_alpha.num_blockers() == link_blocker_alpha_cpy.num_blockers())
-      &&(link_blocker_alpha.num_edges() == link_blocker_alpha_cpy.num_edges())
-      ;
-  DBGVALUE((link_blocker_alpha.num_blockers() == link_blocker_alpha_cpy.num_blockers()));
-  DBGVALUE((link_blocker_alpha.num_blockers()));
-  DBGVALUE((link_blocker_alpha_cpy.num_blockers()));
-
-  DBGVALUE(equal_complexes);
+  BOOST_CHECK(link_blocker_alpha.num_vertices() == link_blocker_alpha_cpy.num_vertices());
+  BOOST_CHECK(link_blocker_alpha.num_blockers() == link_blocker_alpha_cpy.num_blockers());
+  BOOST_CHECK(link_blocker_alpha.num_edges() == link_blocker_alpha_cpy.num_edges());
+  BOOST_CHECK((link_blocker_alpha.num_blockers() == link_blocker_alpha_cpy.num_blockers()));
 
   // verification
-  return link_blocker_alpha.num_vertices() == 5 && link_blocker_alpha.num_edges() == 4 && link_blocker_alpha.num_blockers() == 1 && equal_complexes;
+  BOOST_CHECK(link_blocker_alpha.num_vertices() == 5);
+  BOOST_CHECK(link_blocker_alpha.num_edges() == 4);
+  BOOST_CHECK(link_blocker_alpha.num_blockers() == 1);
 }
 
 template<typename SimplexHandle>
-void add_triangle_edges(int a, int b, int c, list<SimplexHandle>& simplices) {
+void add_triangle_edges(int a, int b, int c, std::list<SimplexHandle>& simplices) {
   typedef SimplexHandle Simplex;
   typedef typename SimplexHandle::Vertex_handle Vertex_handle;
 
@@ -698,14 +619,14 @@ void add_triangle_edges(int a, int b, int c, list<SimplexHandle>& simplices) {
 }
 
 template<typename SimplexHandle>
-void add_triangle(int a, int b, int c, list<SimplexHandle>& simplices) {
+void add_triangle(int a, int b, int c, std::list<SimplexHandle>& simplices) {
   typedef SimplexHandle Simplex;
   typedef typename SimplexHandle::Vertex_handle Vertex_handle;
   simplices.push_back(Simplex(Vertex_handle(a), Vertex_handle(b), Vertex_handle(c)));
 }
 
-bool test_constructor() {
-  list <Simplex> simplices;
+BOOST_AUTO_TEST_CASE(test_skeleton_blocker_complex_constructor) {
+  std::list <Simplex> simplices;
 
   simplices.push_back(Simplex(Vertex_handle(0)));
   simplices.push_back(Simplex(Vertex_handle(1)));
@@ -722,7 +643,6 @@ bool test_constructor() {
   add_triangle_edges(1, 3, 4, simplices);
   add_triangle_edges(1, 2, 4, simplices);
 
-
   add_triangle(0, 1, 5, simplices);
   add_triangle(1, 2, 3, simplices);
   add_triangle(1, 3, 4, simplices);
@@ -731,13 +651,15 @@ bool test_constructor() {
 
   Complex complex(simplices.begin(), simplices.end());
 
-  PRINT(complex.to_string());
+  std::cout << "Constructor 1:\n" << complex.to_string();
 
-  return ( complex.num_vertices() == 6 && complex.num_edges() == 10 && complex.num_blockers() == 2);
+  BOOST_CHECK(complex.num_vertices() == 6);
+  BOOST_CHECK(complex.num_edges() == 10);
+  BOOST_CHECK(complex.num_blockers() == 2);
 }
 
-list<Simplex> subfaces(Simplex top_face) {
-  list<Simplex> res;
+std::list<Simplex> subfaces(Simplex top_face) {
+  std::list<Simplex> res;
   if (top_face.dimension() == -1) return res;
   if (top_face.dimension() == 0) {
     res.push_back(top_face);
@@ -746,7 +668,7 @@ list<Simplex> subfaces(Simplex top_face) {
     Vertex_handle first_vertex = top_face.first_vertex();
     top_face.remove_vertex(first_vertex);
     res = subfaces(top_face);
-    list<Simplex> copy = res;
+    std::list<Simplex> copy = res;
     for (auto& simplex : copy) {
       simplex.add_vertex(first_vertex);
     }
@@ -756,47 +678,50 @@ list<Simplex> subfaces(Simplex top_face) {
   }
 }
 
-bool test_constructor2() {
+BOOST_AUTO_TEST_CASE(test_skeleton_blocker_complex_constructor2) {
   Simplex simplex;
   for (int i = 0; i < 5; ++i)
     simplex.add_vertex(static_cast<Vertex_handle> (i));
 
-  list <Simplex> simplices(subfaces(simplex));
+  std::list <Simplex> simplices(subfaces(simplex));
   simplices.remove(simplex);
 
   Complex complex(simplices.begin(), simplices.end());
 
-  PRINT(complex.to_string());
+  std::cout << "Constructor 2:\n" << complex.to_string();
 
   for (auto b : complex.const_blocker_range()) {
-    cout << "b:" << b << endl;
+    std::cout << "b:" << b << std::endl;
   }
 
-  return ( complex.num_vertices() == 5 && complex.num_edges() == 10 && complex.num_blockers() == 1);
+  BOOST_CHECK(complex.num_vertices() == 5);
+  BOOST_CHECK(complex.num_edges() == 10);
+  BOOST_CHECK(complex.num_blockers() == 1);
 }
 
-bool test_constructor3() {
+BOOST_AUTO_TEST_CASE(test_skeleton_blocker_complex_constructor3) {
   typedef Vertex_handle Vh;
   typedef Simplex Sh;
   std::vector<Simplex> simplices;
   auto subf(subfaces(Sh(Vh(0), Vh(1), Vh(2))));
   subf.pop_back(); //remove max face -> now a blocker 012
   simplices.insert(simplices.begin(), subf.begin(), subf.end());
-  DBGCONT(simplices);
+
   Complex complex(simplices.begin(), simplices.end());
 
-  DBGVALUE(complex.to_string());
+  std::cout << "Constructor 3:\n" << complex.to_string();
 
-  if (complex.num_blockers() != 1) return false;
+  BOOST_CHECK(complex.num_blockers() == 1);
   Sh expected_blocker(Vh(0), Vh(1), Vh(2));
   for (auto b : complex.const_blocker_range())
-    if (*b != expected_blocker) return false;
+    BOOST_CHECK(*b == expected_blocker);
 
 
-  return complex.num_vertices() == 3 && complex.num_blockers() == 1;
+  BOOST_CHECK(complex.num_vertices() == 3);
+  BOOST_CHECK(complex.num_blockers() == 1);
 }
 
-bool test_constructor4() {
+BOOST_AUTO_TEST_CASE(test_skeleton_blocker_complex_constructor4) {
   typedef Vertex_handle Vh;
   typedef Simplex Sh;
   std::vector<Simplex> simplices;
@@ -807,19 +732,20 @@ bool test_constructor4() {
   simplices.push_back(Sh(Vh(4), Vh(1)));
   simplices.push_back(Sh(Vh(4), Vh(0)));
 
-  DBGCONT(simplices);
   Complex complex(simplices.begin(), simplices.end());
 
-  DBGVALUE(complex.to_string());
-  if (complex.num_blockers() != 1) return false;
+  std::cout << "Constructor 4:\n" << complex.to_string();
+  BOOST_CHECK(complex.num_blockers() == 1);
   Sh expected_blocker(Vh(0), Vh(1), Vh(4));
   for (auto b : complex.const_blocker_range())
-    if (*b != expected_blocker) return false;
+    BOOST_CHECK(*b == expected_blocker);
 
-  return complex.num_vertices() == 5 && complex.num_blockers() == 1 && complex.num_edges() == 8;
+  BOOST_CHECK(complex.num_vertices() == 5);
+  BOOST_CHECK(complex.num_blockers() == 1);
+  BOOST_CHECK(complex.num_edges() == 8);
 }
 
-bool test_constructor5() {
+BOOST_AUTO_TEST_CASE(test_skeleton_blocker_complex_constructor5) {
   typedef Vertex_handle Vh;
   typedef Simplex Sh;
   std::vector<Simplex> simplices;
@@ -836,15 +762,16 @@ bool test_constructor5() {
   simplices.push_back(Sh(Vh(5), Vh(2)));
   simplices.push_back(Sh(Vh(5), Vh(0)));
 
-  DBGCONT(simplices);
   Complex complex(simplices.begin(), simplices.end());
 
-  DBGVALUE(complex.to_string());
+  std::cout << "Constructor 5:\n" << complex.to_string();
 
-  return complex.num_vertices() == 6 && complex.num_blockers() == 3 && complex.num_edges() == 9;
+  BOOST_CHECK(complex.num_vertices() == 6);
+  BOOST_CHECK(complex.num_blockers() == 3);
+  BOOST_CHECK(complex.num_edges() == 9);
 }
 
-bool test_constructor6() {
+BOOST_AUTO_TEST_CASE(test_skeleton_blocker_complex_constructor6) {
   typedef Vertex_handle Vh;
   typedef Simplex Sh;
   std::vector<Simplex> simplices;
@@ -855,19 +782,19 @@ bool test_constructor6() {
     if (s != s1 && s != s2) simplices.push_back(s);
   }
 
-  DBGCONT(simplices);
   Complex complex(simplices.begin(), simplices.end());
 
-  DBGVALUE(complex.to_string());
+  std::cout << "Constructor 6:\n" << complex.to_string();
 
-  if (complex.num_blockers() != 1) return false;
+  BOOST_CHECK(complex.num_vertices() == 4);
+  BOOST_CHECK(complex.num_blockers() == 1);
+  BOOST_CHECK(complex.num_edges() == 6);
   Sh expected_blocker(Vh(1), Vh(2), Vh(3));
   for (auto b : complex.const_blocker_range())
-    if (*b != expected_blocker) return false;
-  return complex.num_vertices() == 4 && complex.num_blockers() == 1 && complex.num_edges() == 6;
+    BOOST_CHECK(*b == expected_blocker);
 }
 
-bool test_constructor7() {
+BOOST_AUTO_TEST_CASE(test_skeleton_blocker_complex_constructor7) {
   typedef Vertex_handle Vh;
   typedef Simplex Sh;
   std::vector<Simplex> simplices;
@@ -877,18 +804,19 @@ bool test_constructor7() {
   simplices.push_back(Sh(Vh(3), Vh(0), Vh(1)));
 
   //get complex from top faces
-  Complex complex(make_complex_from_top_faces<Complex>(simplices.begin(), simplices.end()));
+  Complex complex(Gudhi::skeleton_blocker::make_complex_from_top_faces<Complex>(simplices.begin(), simplices.end()));
 
-  DBGVALUE(complex.to_string());
+  std::cout << "Constructor 7:\n" << complex.to_string();
 
-  if (complex.num_blockers() != 1) return false;
+  BOOST_CHECK(complex.num_vertices() == 4);
+  BOOST_CHECK(complex.num_blockers() == 1);
+  BOOST_CHECK(complex.num_edges() == 6);
   Sh expected_blocker(Vh(0), Vh(1), Vh(2), Vh(3));
   for (auto b : complex.const_blocker_range())
-    if (*b != expected_blocker) return false;
-  return complex.num_vertices() == 4 && complex.num_blockers() == 1 && complex.num_edges() == 6;
+    BOOST_CHECK(*b == expected_blocker);
 }
 
-bool test_constructor8() {
+BOOST_AUTO_TEST_CASE(test_skeleton_blocker_complex_constructor8) {
   typedef Vertex_handle Vh;
   typedef Simplex Sh;
   std::vector<Simplex> simplices;
@@ -899,54 +827,11 @@ bool test_constructor8() {
   simplices.push_back(Sh(Vh(2), Vh(3)));
 
   //get complex from top faces
-  Complex complex(make_complex_from_top_faces<Complex>(simplices.begin(), simplices.end()));
-
-  DBGVALUE(complex.to_string());
-
-  return complex.num_vertices() == 4 && complex.num_blockers() == 2 && complex.num_edges() == 5;
-}
-
-int main(int argc, char *argv[]) {
-  Tests tests_complex;
-  tests_complex.add("test simplex", test_simplex);
-  tests_complex.add("test_num_simplices", test_num_simplices);
-  tests_complex.add("test_link0", test_link0);
-  tests_complex.add("test_link1", test_link1);
-  tests_complex.add("test_link2", test_link2);
-  tests_complex.add("test_link3", test_link3);
-  tests_complex.add("test_link4", test_link4);
-  tests_complex.add("test_link5", test_link5);
-  tests_complex.add("test_link6", test_link6);
-  tests_complex.add("test_link7", test_link7);
-
-  tests_complex.add("test_constructor_list_simplices", test_constructor);
-  tests_complex.add("test_constructor_list_simplices2", test_constructor2);
-  tests_complex.add("test_constructor_list_simplices3", test_constructor3);
-  tests_complex.add("test_constructor_list_simplices4", test_constructor4);
-  tests_complex.add("test_constructor_list_simplices5", test_constructor5);
-  tests_complex.add("test_constructor_list_simplices6", test_constructor6);
-  tests_complex.add("test_constructor_list_simplices7", test_constructor7);
-  tests_complex.add("test_constructor_list_simplices8", test_constructor8);
-
-  tests_complex.add("test iterator vertices 1", test_iterator_vertices1);
-  tests_complex.add("test iterator vertices 2", test_iterator_vertices2);
-  tests_complex.add("test iterator edges", test_iterator_edge);
-  tests_complex.add("test iterator edges 2", test_iterator_edge2);
-  tests_complex.add("test iterator edges 3", test_iterator_edge3);
-  tests_complex.add("test iterator blockers", test_iterator_blockers);
-  tests_complex.add("test_iterator_triangles", test_iterator_triangles);
-  tests_complex.add("test iterator simplices", test_iterator_simplices);
-  tests_complex.add("test iterator simplices2", test_iterator_simplices2);
-  tests_complex.add("test iterator simplices3", test_iterator_simplices3);
-  tests_complex.add("test iterator simplices4", test_iterator_simplices4);
-  tests_complex.add("test iterator coboundary", test_iterator_coboundary);
-
-  if (tests_complex.run()) {
-    return EXIT_SUCCESS;
-  } else {
-    return EXIT_FAILURE;
-  }
+  Complex complex(Gudhi::skeleton_blocker::make_complex_from_top_faces<Complex>(simplices.begin(), simplices.end()));
 
-  //	test_iterator_simplices();
-}
+  std::cout << "Constructor 8:\n" << complex.to_string();
 
+  BOOST_CHECK(complex.num_vertices() == 4);
+  BOOST_CHECK(complex.num_blockers() == 2);
+  BOOST_CHECK(complex.num_edges() == 5);
+}
diff --git a/src/Skeleton_blocker/test/test_skeleton_blocker_geometric_complex.cpp b/src/Skeleton_blocker/test/test_skeleton_blocker_geometric_complex.cpp
new file mode 100644
index 00000000..d035b2c3
--- /dev/null
+++ b/src/Skeleton_blocker/test/test_skeleton_blocker_geometric_complex.cpp
@@ -0,0 +1,125 @@
+/*    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):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA
+ *
+ *    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/>.
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string>
+#include <fstream>
+#include <sstream>
+
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE "skeleton_blocker_geometric_complex"
+#include <boost/test/unit_test.hpp>
+#include <boost/mpl/list.hpp>
+
+#include <gudhi/Skeleton_blocker.h>
+
+struct Geometry_trait {
+  typedef std::vector<double> Point;
+};
+
+typedef Geometry_trait::Point Point;
+typedef Gudhi::skeleton_blocker::Skeleton_blocker_simple_geometric_traits<Geometry_trait> Complex_geometric_traits;
+typedef Gudhi::skeleton_blocker::Skeleton_blocker_geometric_complex< Complex_geometric_traits > Complex;
+typedef Complex::Vertex_handle Vertex_handle;
+typedef Complex_geometric_traits::Root_vertex_handle Root_vertex_handle;
+
+BOOST_AUTO_TEST_CASE(test_skeleton_blocker_off_reader_writer) {
+  Complex complex;
+  Gudhi::skeleton_blocker::Skeleton_blocker_off_reader<Complex> off_reader("test2.off", complex);
+  BOOST_CHECK(off_reader.is_valid());
+  
+  std::cout << "complex has " <<
+      complex.num_vertices() << " vertices, " <<
+      complex.num_blockers() << " blockers, " <<
+      complex.num_edges() << " edges and " <<
+      complex.num_triangles() << " triangles.";
+
+  BOOST_CHECK(complex.num_vertices() == 7);
+  BOOST_CHECK(complex.num_edges() == 12);
+  BOOST_CHECK(complex.num_triangles() == 6);
+
+  Gudhi::skeleton_blocker::Skeleton_blocker_off_writer<Complex> off_writer("tmp.off", complex);
+  Complex same;
+  Gudhi::skeleton_blocker::Skeleton_blocker_off_reader<Complex> off_reader2("tmp.off", same);
+
+  std::cout << "\ncomplex:" << complex.to_string() << std::endl;
+  std::cout << "\nsame:" << same.to_string() << std::endl;
+
+  BOOST_CHECK(complex == same);
+}
+
+BOOST_AUTO_TEST_CASE(test_skeleton_blocker_abstract_link) {
+  Complex complex;
+  Gudhi::skeleton_blocker::Skeleton_blocker_off_reader<Complex> off_reader("test2.off", complex);
+  BOOST_CHECK(off_reader.is_valid());
+
+  std::cout << "complex has " <<
+      complex.num_vertices() << " vertices, " <<
+      complex.num_blockers() << " blockers, " <<
+      complex.num_edges() << " edges and " <<
+      complex.num_triangles() << " triangles.";
+
+  BOOST_CHECK(complex.num_vertices() == 7);
+  BOOST_CHECK(complex.num_edges() == 12);
+  BOOST_CHECK(complex.num_triangles() == 6);
+
+  auto link_0 = complex.abstract_link(Vertex_handle(0));
+
+  std::cout << "\n link(0):" << link_0.to_string() << std::endl;
+
+  BOOST_CHECK(link_0.num_vertices() == 2);
+  BOOST_CHECK(link_0.num_edges() == 1);
+  BOOST_CHECK(link_0.num_blockers() == 0);
+  
+  // Check the 2 link vertices
+  auto vertex_handle = link_0.vertex_range().begin();
+  BOOST_CHECK(link_0[*vertex_handle].get_id() == Root_vertex_handle(1));
+  vertex_handle++;
+  BOOST_CHECK(link_0[*(vertex_handle)].get_id() == Root_vertex_handle(4));
+  
+  // Check the lonely link edge
+  auto edge_handle = link_0.edge_range().begin();
+  BOOST_CHECK(link_0[*edge_handle].first() == Root_vertex_handle(1));
+  BOOST_CHECK(link_0[*(edge_handle)].second() == Root_vertex_handle(4));
+
+  auto link_geometric_0 = complex.link(Vertex_handle(0));
+  std::cout << "\n link_geometric(0):" << link_geometric_0.to_string() << std::endl;
+
+  BOOST_CHECK(link_0 == link_geometric_0);
+
+  auto print_point = [&](Vertex_handle v) {
+    for (auto x : link_geometric_0.point(v)) std::cout << x << " ";
+    std::cout << std::endl;
+  };
+
+  std::for_each(link_geometric_0.vertex_range().begin(), link_geometric_0.vertex_range().end(), print_point);
+
+  // Check the 2 link vertices
+  vertex_handle = link_geometric_0.vertex_range().begin();
+  std::vector<double> point_1 = {0,2,0};
+  std::vector<double> point_4 = {-1,1,0};
+  BOOST_CHECK(link_geometric_0.point(*vertex_handle) == point_1);
+  vertex_handle++;
+  BOOST_CHECK(link_geometric_0.point(*vertex_handle) == point_4);
+
+}
diff --git a/src/Skeleton_blocker/test/TestSimplifiable.cpp b/src/Skeleton_blocker/test/test_skeleton_blocker_simplifiable.cpp
index b0855ce9..360b91db 100644
--- a/src/Skeleton_blocker/test/TestSimplifiable.cpp
+++ b/src/Skeleton_blocker/test/test_skeleton_blocker_simplifiable.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014  INRIA
  *
  *    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
@@ -20,44 +20,26 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-
 #include <stdio.h>
 #include <stdlib.h>
 #include <string>
 #include <fstream>
 #include <sstream>
-#include "gudhi/Test.h"
-//#include "Skeleton_blocker/Simplex.h"
-#include "gudhi/Skeleton_blocker.h"
-
-
-using namespace std;
 
-using namespace Gudhi;
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE "skeleton_blocker_simplifiable"
+#include <boost/test/unit_test.hpp>
+#include <boost/mpl/list.hpp>
 
-using namespace skbl;
+#include <gudhi/Skeleton_blocker.h>
 
 template<typename ComplexType> class Skeleton_blocker_sub_complex;
-typedef Skeleton_blocker_complex<Skeleton_blocker_simple_traits> Complex;
+typedef Gudhi::skeleton_blocker::Skeleton_blocker_simple_traits Traits;
+typedef Gudhi::skeleton_blocker::Skeleton_blocker_complex<Traits> Complex;
 typedef Complex::Vertex_handle Vertex_handle;
 typedef Complex::Root_vertex_handle Root_vertex_handle;
-typedef Skeleton_blocker_simplex<Vertex_handle> Simplex;
-// true iff v \in complex
-
-bool assert_vertex(Complex &complex, Vertex_handle v) {
-  Simplex simplex(v);
-  bool test = complex.contains(simplex);
-  assert(test);
-  return test;
-}
-
-// true iff the blocker (a,b,c) is in complex
-
-bool assert_blocker(Complex &complex, Root_vertex_handle a, Root_vertex_handle b, Root_vertex_handle c) {
+typedef Gudhi::skeleton_blocker::Skeleton_blocker_simplex<Vertex_handle> Simplex;
 
-  return complex.contains_blocker(Simplex(*complex.get_address(a), *complex.get_address(b), *complex.get_address(c)));
-  //return complex.contains_blocker((a),(b),(c));
-}
 
 void build_complete(int n, Complex& complex) {
   complex.clear();
@@ -68,11 +50,8 @@ void build_complete(int n, Complex& complex) {
       complex.add_edge_without_blockers(Vertex_handle(i), Vertex_handle(j));
 }
 
-bool test_contraction1() {
-
-  enum {
-    a, b, x, y, z, n
-  };
+BOOST_AUTO_TEST_CASE(test_skeleton_blocker_simplifiable_contraction1) {
+  enum { a, b, x, y, z, n };
   Complex complex(n);
   build_complete(n, complex);
   complex.remove_edge(static_cast<Vertex_handle> (b), static_cast<Vertex_handle> (z));
@@ -82,35 +61,35 @@ bool test_contraction1() {
                               static_cast<Vertex_handle> (y)));
 
   // Print result
-  cerr << "complex before complex" << complex.to_string() << endl;
+  std::cout << "complex before complex" << complex.to_string() << std::endl;
 
-  cerr << endl << endl;
+  std::cout << std::endl << std::endl;
   complex.contract_edge(static_cast<Vertex_handle> (a), static_cast<Vertex_handle> (b));
   // Print result
-  cerr << "ContractEdge(0,1)\n";
+  std::cout << "ContractEdge(0,1)\n";
   PRINT(complex.to_string());
 
   // verification
   for (int i = 0; i < 5; i++)
-    if (i != 1) assert_vertex(complex, static_cast<Vertex_handle> (i));
-  bool test1 = !complex.contains_edge(static_cast<Vertex_handle> (a), static_cast<Vertex_handle> (b));
-  bool test2 = assert_blocker(complex, Root_vertex_handle(a), Root_vertex_handle(x), Root_vertex_handle(y));
-  bool test3 = complex.num_edges() == 6;
-  bool test4 = complex.num_blockers() == 1;
+    if (i != 1) BOOST_CHECK(complex.contains(Simplex(static_cast<Vertex_handle> (i))));
+  BOOST_CHECK(!complex.contains_edge(static_cast<Vertex_handle> (a), static_cast<Vertex_handle> (b)));
+  
+  BOOST_CHECK(complex.contains_blocker(Simplex(*complex.get_address(Root_vertex_handle(a)),
+                                               *complex.get_address(Root_vertex_handle(x)),
+                                               *complex.get_address(Root_vertex_handle(y)))));
+  
+  BOOST_CHECK(complex.num_edges() == 6);
+  BOOST_CHECK(complex.num_blockers() == 1);
   Simplex sigma;
   sigma.add_vertex(static_cast<Vertex_handle> (a));
   sigma.add_vertex(static_cast<Vertex_handle> (x));
   sigma.add_vertex(static_cast<Vertex_handle> (y));
   sigma.add_vertex(static_cast<Vertex_handle> (z));
-  bool test5 = !(complex.contains(sigma));
-  return test1 && test2 && test3 && test4&&test5;
+  BOOST_CHECK(!(complex.contains(sigma)));
 }
 
-bool test_contraction2() {
-
-  enum {
-    a, b, x, y, z, n
-  };
+BOOST_AUTO_TEST_CASE(test_skeleton_blocker_simplifiable_contraction2) {
+  enum { a, b, x, y, z, n };
   Complex complex(n);
   build_complete(n, complex);
   complex.remove_edge(static_cast<Vertex_handle> (b), static_cast<Vertex_handle> (x));
@@ -122,83 +101,73 @@ bool test_contraction2() {
   complex.add_blocker(blocker);
 
   // Print result
-  cerr << "complex complex" << complex.to_string();
-  cerr << endl << endl;
+  std::cout << "complex complex" << complex.to_string();
+  std::cout << std::endl << std::endl;
   complex.contract_edge(static_cast<Vertex_handle> (a), static_cast<Vertex_handle> (b));
 
-  cerr << "complex.ContractEdge(a,b)" << complex.to_string();
+  std::cout << "complex.ContractEdge(a,b)" << complex.to_string();
 
-  cerr << endl << endl;
+  std::cout << std::endl << std::endl;
 
   // there should be one blocker (a,c,d,e) in the complex
-  bool test;
-  test = complex.contains_blocker(Simplex(static_cast<Vertex_handle> (a), static_cast<Vertex_handle> (x),
-                                          static_cast<Vertex_handle> (y), static_cast<Vertex_handle> (z)));
-  test = test && complex.num_blockers() == 1;
-  return test;
+  BOOST_CHECK(complex.contains_blocker(Simplex(static_cast<Vertex_handle> (a), static_cast<Vertex_handle> (x),
+                                               static_cast<Vertex_handle> (y), static_cast<Vertex_handle> (z))));
+  BOOST_CHECK(complex.num_blockers() == 1);
 }
 
-bool test_link_condition1() {
-
+BOOST_AUTO_TEST_CASE(test_skeleton_blocker_simplifiable_link_condition1) {
   Complex complex(0);
   // Build the complexes
   build_complete(4, complex);
   complex.add_blocker(Simplex(static_cast<Vertex_handle> (0), static_cast<Vertex_handle> (1), static_cast<Vertex_handle> (2)));
 
-
   // Print result
-  cerr << "complex complex" << complex.to_string();
-  cerr << endl << endl;
-
-  bool weak_link_condition = complex.link_condition(Vertex_handle(1), Vertex_handle(2), true);
+  std::cout << "complex complex" << complex.to_string();
+  std::cout << std::endl << std::endl;
 
-  bool strong_link_condition = complex.link_condition(Vertex_handle(1), Vertex_handle(2), false);
+  BOOST_CHECK(complex.link_condition(Vertex_handle(1), Vertex_handle(2), true));
 
-  return weak_link_condition && !strong_link_condition;
+  BOOST_CHECK(!complex.link_condition(Vertex_handle(1), Vertex_handle(2), false));
 }
 
-bool test_collapse0() {
+BOOST_AUTO_TEST_CASE(test_skeleton_blocker_simplifiable_collapse0) {
   Complex complex(5);
   build_complete(4, complex);
   complex.add_vertex();
   complex.add_edge_without_blockers(static_cast<Vertex_handle> (2), static_cast<Vertex_handle> (4));
   complex.add_edge_without_blockers(static_cast<Vertex_handle> (3), static_cast<Vertex_handle> (4));
   // Print result
-  cerr << "initial complex :\n" << complex.to_string();
-  cerr << endl << endl;
+  std::cout << "initial complex :\n" << complex.to_string();
+  std::cout << std::endl << std::endl;
 
   Simplex simplex_123(static_cast<Vertex_handle> (1), static_cast<Vertex_handle> (2), static_cast<Vertex_handle> (3));
   complex.remove_star(simplex_123);
-  cerr << "complex.remove_star(1,2,3):\n" << complex.to_string();
-  cerr << endl << endl;
+  std::cout << "complex.remove_star(1,2,3):\n" << complex.to_string();
+  std::cout << std::endl << std::endl;
 
   // verification
-  bool blocker123_here = complex.contains_blocker(simplex_123);
-  cerr << "----> Ocomplex \n";
-  return blocker123_here;
+  BOOST_CHECK(complex.contains_blocker(simplex_123));
 }
 
-bool test_collapse1() {
+BOOST_AUTO_TEST_CASE(test_skeleton_blocker_simplifiable_collapse1) {
   Complex complex(5);
   build_complete(4, complex);
   complex.add_blocker(Simplex(Vertex_handle(0), Vertex_handle(1), Vertex_handle(2), Vertex_handle(3)));
   // Print result
-  cerr << "initial complex :\n" << complex.to_string();
-  cerr << endl << endl;
+  std::cout << "initial complex :\n" << complex.to_string();
+  std::cout << std::endl << std::endl;
 
   Simplex simplex_123(Vertex_handle(1), Vertex_handle(2), Vertex_handle(3));
   complex.remove_star(simplex_123);
-  cerr << "complex.remove_star(1,2,3):\n" << complex.to_string();
-  cerr << endl << endl;
+  std::cout << "complex.remove_star(1,2,3):\n" << complex.to_string();
+  std::cout << std::endl << std::endl;
 
   // verification
-  bool res = complex.contains_blocker(simplex_123);
-  res = res && complex.num_blockers() == 1;
-  cerr << "----> Ocomplex \n";
-  return res;
+  BOOST_CHECK(complex.contains_blocker(simplex_123));
+  BOOST_CHECK(complex.num_blockers() == 1);
 }
 
-bool test_collapse2() {
+BOOST_AUTO_TEST_CASE(test_skeleton_blocker_simplifiable_collapse2) {
   Complex complex(5);
   build_complete(4, complex);
   complex.add_vertex();
@@ -207,21 +176,21 @@ bool test_collapse2() {
   complex.add_edge_without_blockers(Vertex_handle(3), Vertex_handle(4));
   complex.add_blocker(Simplex(Vertex_handle(1), Vertex_handle(2), Vertex_handle(3), Vertex_handle(4)));
   // Print result
-  cerr << "initial complex :\n" << complex.to_string();
-  cerr << endl << endl;
+  std::cout << "initial complex :\n" << complex.to_string();
+  std::cout << std::endl << std::endl;
 
   Simplex sigma(Vertex_handle(1), Vertex_handle(2), Vertex_handle(3));
   complex.remove_star(sigma);
-  cerr << "complex.remove_star(1,2,3):\n" << complex.to_string();
-  cerr << endl << endl;
+  std::cout << "complex.remove_star(1,2,3):\n" << complex.to_string();
+  std::cout << std::endl << std::endl;
 
   // verification
-  bool blocker_removed = !complex.contains_blocker(Simplex(Vertex_handle(1), Vertex_handle(2), Vertex_handle(3), Vertex_handle(4)));
-  bool blocker123_here = complex.contains_blocker(sigma);
-  return blocker_removed && blocker123_here;
+  BOOST_CHECK(!complex.contains_blocker(Simplex(Vertex_handle(1), Vertex_handle(2),
+                                                Vertex_handle(3), Vertex_handle(4))));
+  BOOST_CHECK(complex.contains_blocker(sigma));
 }
 
-bool test_collapse3() {
+BOOST_AUTO_TEST_CASE(test_skeleton_blocker_simplifiable_collapse3) {
   Complex complex(5);
   build_complete(4, complex);
   complex.add_vertex();
@@ -230,36 +199,37 @@ bool test_collapse3() {
   complex.add_edge_without_blockers(Vertex_handle(3), Vertex_handle(4));
   complex.add_blocker(Simplex(Vertex_handle(1), Vertex_handle(2), Vertex_handle(3), Vertex_handle(4)));
   // Print result
-  cerr << "initial complex:\n" << complex.to_string();
-  cerr << endl << endl;
+  std::cout << "initial complex:\n" << complex.to_string();
+  std::cout << std::endl << std::endl;
 
   complex.remove_star(static_cast<Vertex_handle> (2));
-  cerr << "complex after remove star of 2:\n" << complex.to_string();
+  std::cout << "complex after remove star of 2:\n" << complex.to_string();
 
-  bool blocker134_here = complex.contains_blocker(Simplex(Vertex_handle(1), Vertex_handle(3), Vertex_handle(4)));
-  bool blocker1234_here = complex.contains_blocker(Simplex(Vertex_handle(1), Vertex_handle(2), Vertex_handle(3), Vertex_handle(4)));
-  return blocker134_here && !blocker1234_here;
+  BOOST_CHECK(complex.contains_blocker(Simplex(Vertex_handle(1), Vertex_handle(3), Vertex_handle(4))));
+  BOOST_CHECK(!complex.contains_blocker(Simplex(Vertex_handle(1), Vertex_handle(2),
+                                                Vertex_handle(3), Vertex_handle(4))));
 }
 
-bool test_add_simplex() {
+BOOST_AUTO_TEST_CASE(test_skeleton_blocker_simplifiable_add_simplex) {
   Complex complex(4);
   build_complete(4, complex);
   complex.add_blocker(Simplex(Vertex_handle(0), Vertex_handle(1), Vertex_handle(3)));
-  cerr << "initial complex:\n" << complex.to_string();
-  cerr << endl << endl;
+  std::cout << "initial complex:\n" << complex.to_string();
+  std::cout << std::endl << std::endl;
 
   complex.add_simplex(Simplex(Vertex_handle(0), Vertex_handle(1), Vertex_handle(3)));
-  cerr << "complex after add_simplex:\n" << complex.to_string();
-  return complex.num_blockers() == 1
-      && complex.contains_blocker(Simplex(Vertex_handle(0), Vertex_handle(1), Vertex_handle(2), Vertex_handle(3)));
+  std::cout << "complex after add_simplex:\n" << complex.to_string();
+  BOOST_CHECK(complex.num_blockers() == 1);
+  BOOST_CHECK(complex.contains_blocker(Simplex(Vertex_handle(0), Vertex_handle(1),
+                                               Vertex_handle(2), Vertex_handle(3))));
 }
 
-bool test_add_simplex2() {
+BOOST_AUTO_TEST_CASE(test_skeleton_blocker_simplifiable_add_simplex2) {
   Complex complex;
   build_complete(4, complex);
   // Print result
-  cerr << "initial complex:\n" << complex.to_string();
-  cerr << endl << endl;
+  std::cout << "initial complex:\n" << complex.to_string();
+  std::cout << std::endl << std::endl;
 
   Complex copy(complex.num_vertices());
 
@@ -274,33 +244,33 @@ bool test_add_simplex2() {
       copy.add_simplex(simplex);
   }
 
+  std::cout << "complex after add_simplex:\n" << copy.to_string();
 
-  cerr << "complex after add_simplex:\n" << copy.to_string();
-
-
-  return complex.num_blockers() == copy.num_blockers() &&
-      complex.num_edges() == copy.num_edges() &&
-      complex.num_vertices() == copy.num_vertices();
+  BOOST_CHECK(complex.num_blockers() == copy.num_blockers());
+  BOOST_CHECK(complex.num_edges() == copy.num_edges());
+  BOOST_CHECK(complex.num_vertices() == copy.num_vertices());
 }
 
-bool test_add_simplex3() {
+BOOST_AUTO_TEST_CASE(test_skeleton_blocker_simplifiable_add_simplex3) {
   Complex complex(5);
   build_complete(5, complex);
   complex.remove_edge(Vertex_handle(3), Vertex_handle(4));
   Simplex sigma(Vertex_handle(0), Vertex_handle(1), Vertex_handle(2));
   complex.add_blocker(sigma);
   // Print result
-  cerr << "initial complex:\n" << complex.to_string();
-  cerr << endl << endl;
+  std::cout << "initial complex:\n" << complex.to_string();
+  std::cout << std::endl << std::endl;
   complex.add_simplex(sigma);
   //should create two blockers 0123 and 0124
-  cerr << "complex after adding simplex 012:\n" << complex.to_string();
-  return complex.num_blockers() == 2
-      && complex.contains_blocker(Simplex(Vertex_handle(0), Vertex_handle(1), Vertex_handle(2), Vertex_handle(3)))
-      && complex.contains_blocker(Simplex(Vertex_handle(0), Vertex_handle(1), Vertex_handle(2), Vertex_handle(4)));
+  std::cout << "complex after adding simplex 012:\n" << complex.to_string();
+  BOOST_CHECK(complex.num_blockers() == 2);
+  BOOST_CHECK(complex.contains_blocker(Simplex(Vertex_handle(0), Vertex_handle(1),
+                                               Vertex_handle(2), Vertex_handle(3))));
+  BOOST_CHECK(complex.contains_blocker(Simplex(Vertex_handle(0), Vertex_handle(1),
+                                               Vertex_handle(2), Vertex_handle(4))));
 }
 
-bool test_add_simplex4() {
+BOOST_AUTO_TEST_CASE(test_skeleton_blocker_simplifiable_add_simplex4) {
   int n = 6;
   Complex complex(n);
 
@@ -313,40 +283,38 @@ bool test_add_simplex4() {
     complex.add_simplex(s);
 
     //at step i there is only blocker 0..i
-    if (i < 2 && complex.num_blockers() > 0)
-      return false;
+    BOOST_CHECK(!(i < 2 && complex.num_blockers() > 0));
     if (i >= 2 && complex.num_blockers() != 1) {
       Simplex b;
       for (int k = 0; k < i; k++)
         b.add_vertex(Vertex_handle(i));
-      if (!complex.contains_blocker(b))
-        return false;
+      BOOST_CHECK(complex.contains_blocker(b));
     }
-    TESTVALUE(complex.blockers_to_string());
   }
   Simplex s;
   for (int k = 0; k < n; k++)
     s.add_vertex(Vertex_handle(k));
-  return complex.num_blockers() == 1 && complex.contains_blocker(s);
+  BOOST_CHECK(complex.num_blockers() == 1);
+  BOOST_CHECK(complex.contains_blocker(s));
 }
 
-bool test_add_edge() {
+BOOST_AUTO_TEST_CASE(test_skeleton_blocker_simplifiable_add_edge) {
   Complex complex(4);
   for (unsigned i = 0u; i < 4; i++)
     complex.add_edge(Vertex_handle(i), Vertex_handle((i + 1) % 4));
 
   // Print result
-  cerr << "initial complex:\n" << complex.to_string();
-  cerr << endl << endl;
+  std::cout << "initial complex:\n" << complex.to_string();
+  std::cout << std::endl << std::endl;
   complex.add_edge(Vertex_handle(1), Vertex_handle(3));
   //should create two blockers 013 and 012
-  cerr << "complex after adding edge 13:\n" << complex.to_string();
-  return complex.num_blockers() == 2
-      && complex.contains_blocker(Simplex(Vertex_handle(0), Vertex_handle(1), Vertex_handle(3)))
-      && complex.contains_blocker(Simplex(Vertex_handle(1), Vertex_handle(2), Vertex_handle(3)));
+  std::cout << "complex after adding edge 13:\n" << complex.to_string();
+  BOOST_CHECK(complex.num_blockers() == 2);
+  BOOST_CHECK(complex.contains_blocker(Simplex(Vertex_handle(0), Vertex_handle(1), Vertex_handle(3))));
+  BOOST_CHECK(complex.contains_blocker(Simplex(Vertex_handle(1), Vertex_handle(2), Vertex_handle(3))));
 }
 
-bool test_remove_popable_blockers() {
+BOOST_AUTO_TEST_CASE(test_skeleton_blocker_simplifiable_remove_popable_blockers) {
   Complex complex;
   build_complete(4, complex);
   complex.add_vertex();
@@ -357,15 +325,14 @@ bool test_remove_popable_blockers() {
 
   complex.add_blocker(sigma1);
   complex.add_blocker(sigma2);
-  cerr << "complex complex" << complex.to_string();
-  cerr << endl << endl;
-  cerr << "complex.RemovePopableBlockers();" << endl;
+  std::cout << "complex complex" << complex.to_string();
+  std::cout << std::endl << std::endl;
+  std::cout << "complex.RemovePopableBlockers();" << std::endl;
   complex.remove_popable_blockers();
-  cerr << "complex complex" << complex.to_string();
-  cerr << endl << endl;
-
-  bool test1 = (complex.num_blockers() == 1);
+  std::cout << "complex complex" << complex.to_string();
+  std::cout << std::endl << std::endl;
 
+  BOOST_CHECK(complex.num_blockers() == 1);
 
   // test 2
   complex.clear();
@@ -382,41 +349,12 @@ bool test_remove_popable_blockers() {
 
   complex.add_blocker(sigma1);
   complex.add_blocker(sigma2);
-  cerr << "complex complex" << complex.to_string();
-  cerr << endl << endl;
-  cerr << "complex.RemovePopableBlockers();" << endl;
+  std::cout << "complex complex" << complex.to_string();
+  std::cout << std::endl << std::endl;
+  std::cout << "complex.RemovePopableBlockers();" << std::endl;
   complex.remove_popable_blockers();
-  cerr << "complex complex" << complex.to_string();
-
-  cerr << endl << endl;
-  bool test2 = (complex.num_blockers() == 0);
-  return test1&&test2;
-}
-
-int main(int argc, char *argv[]) {
-  Tests tests_simplifiable_complex;
-  tests_simplifiable_complex.add("Test contraction 1", test_contraction1);
-  tests_simplifiable_complex.add("Test contraction 2", test_contraction2);
-  tests_simplifiable_complex.add("Test Link condition 1", test_link_condition1);
-  tests_simplifiable_complex.add("Test remove popable blockers", test_remove_popable_blockers);
-
-
-  tests_simplifiable_complex.add("Test collapse 0", test_collapse0);
-  tests_simplifiable_complex.add("Test collapse 1", test_collapse1);
-  tests_simplifiable_complex.add("Test collapse 2", test_collapse2);
-  tests_simplifiable_complex.add("Test collapse 3", test_collapse3);
-
-  tests_simplifiable_complex.add("Test add edge",test_add_edge);
-  tests_simplifiable_complex.add("Test add simplex", test_add_simplex);
-  tests_simplifiable_complex.add("Test add simplex2", test_add_simplex2);
-  tests_simplifiable_complex.add("Test add simplex3",test_add_simplex3);
-  tests_simplifiable_complex.add("Test add simplex4",test_add_simplex4);
-
-
-  tests_simplifiable_complex.run();
+  std::cout << "complex complex" << complex.to_string();
 
-  if (tests_simplifiable_complex.run())
-    return EXIT_SUCCESS;
-  else
-    return EXIT_FAILURE;
+  std::cout << std::endl << std::endl;
+  BOOST_CHECK(complex.num_blockers() == 0);
 }
diff --git a/src/Witness_complex/concept/Simplicial_complex.h b/src/Witness_complex/concept/Simplicial_complex_for_witness.h
index d7f3496d..caaf0db6 100644
--- a/src/Witness_complex/concept/Simplicial_complex.h
+++ b/src/Witness_complex/concept/Simplicial_complex_for_witness.h
@@ -20,8 +20,8 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef CONCEPT_WITNESS_COMPLEX_SIMPLICIAL_COMPLEX_H_
-#define CONCEPT_WITNESS_COMPLEX_SIMPLICIAL_COMPLEX_H_
+#ifndef CONCEPT_WITNESS_COMPLEX_SIMPLICIAL_COMPLEX_FOR_WITNESS_H_
+#define CONCEPT_WITNESS_COMPLEX_SIMPLICIAL_COMPLEX_FOR_WITNESS_H_
 
 namespace Gudhi {
 
@@ -31,7 +31,7 @@ namespace witness_complex {
  * for a type to implement a simplicial complex, 
  * used for example to build a 'Witness_complex'. 
  */
-struct Simplicial_complex {
+struct SimplicialComplexForWitness {
   /** Handle to specify a simplex. */
   typedef unspecified Simplex_handle;
   /** Handle to specify a vertex. Must be a non-negative integer. */
@@ -40,16 +40,11 @@ struct Simplicial_complex {
   /** Returns a Simplex_hanlde that is different from all simplex handles 
    * of the simplices. */
   Simplex_handle null_simplex();
-  /** \brief Returns the number of simplices in the complex.
-   *
-   * Does not count the empty simplex. */
-  size_t num_simplices();
 
   /** \brief Iterator over the simplices of the complex,
    * in an arbitrary order.
    *
    * 'value_type' must be 'Simplex_handle'.*/
-  typedef unspecified Complex_simplex_iterator;
   typedef unspecified Complex_simplex_range;
 
   /**
@@ -71,19 +66,17 @@ struct Simplicial_complex {
    */
   typedef unspecified Insertion_result_type;
 
-  /** \brief Input range of vertices.
-   * 'value_type' must be 'Vertex_handle'. */
-  typedef unspecified Input_vertex_range;
-
   /** \brief Inserts a simplex with vertices from a given range
    *  'vertex_range' in the simplicial complex.
    *  */
+  template< typedef Input_vertex_range >
   Insertion_result_type insert_simplex(Input_vertex_range const & vertex_range);
 
   /** \brief Finds a simplex with vertices given by a range
    *
    * If a simplex exists, its Simplex_handle is returned.
    * Otherwise null_simplex() is returned. */
+  template< typedef Input_vertex_range >
   Simplex_handle find(Input_vertex_range const & vertex_range);
 };
 
@@ -91,4 +84,4 @@ struct Simplicial_complex {
 
 }  // namespace Gudhi
 
-#endif  // CONCEPT_WITNESS_COMPLEX_SIMPLICIAL_COMPLEX_H_
+#endif  // CONCEPT_WITNESS_COMPLEX_SIMPLICIAL_COMPLEX_FOR_WITNESS_H_
diff --git a/src/Witness_complex/include/gudhi/Witness_complex_doc.h b/src/Witness_complex/doc/Witness_complex_doc.h
index e9f78170..60dfd27b 100644
--- a/src/Witness_complex/include/gudhi/Witness_complex_doc.h
+++ b/src/Witness_complex/doc/Witness_complex_doc.h
@@ -6,6 +6,8 @@
 
    \author Siargey Kachanovich
 
+   \image html "Witness_complex_representation.png" "Witness complex representation"
+
    \section Definitions
 
    Witness complex \f$ Wit(W,L) \f$  is a simplicial complex defined on two sets of points in \f$\mathbb{R}^D\f$:
@@ -18,7 +20,9 @@
 
    \f$ \sigma \subset L \f$ is witnessed if there exists a point \f$w \in W\f$ such that 
    w is closer to the vertices of \f$ \sigma \f$ than other points in \f$ L \f$ and all of its faces are witnessed as well. 
-      
+ 
+   The data structure is described in \cite boissonnatmariasimplextreealgorithmica .
+
    \section Implementation
 
    The principal class of this module is Gudhi::Witness_complex.
diff --git a/src/Witness_complex/doc/Witness_complex_representation.png b/src/Witness_complex/doc/Witness_complex_representation.png
new file mode 100644
index 00000000..1d31a490
--- /dev/null
+++ b/src/Witness_complex/doc/Witness_complex_representation.png
diff --git a/src/Witness_complex/example/CMakeLists.txt b/src/Witness_complex/example/CMakeLists.txt
index d6a958b7..4d67e0d0 100644
--- a/src/Witness_complex/example/CMakeLists.txt
+++ b/src/Witness_complex/example/CMakeLists.txt
@@ -1,5 +1,5 @@
 cmake_minimum_required(VERSION 2.6)
-project(GUDHIWitnessComplex)
+project(Witness_complex_examples)
 
 # A simple example
    add_executable( witness_complex_from_file witness_complex_from_file.cpp )
@@ -7,51 +7,10 @@ project(GUDHIWitnessComplex)
 
 if(CGAL_FOUND)
   if (NOT CGAL_VERSION VERSION_LESS 4.6.0)
-    message(STATUS "CGAL version: ${CGAL_VERSION}.")
-
-    include( ${CGAL_USE_FILE} )
-    # In CMakeLists.txt, when include(${CGAL_USE_FILE}), CXX_FLAGS are overwritten.
-    # cf. http://doc.cgal.org/latest/Manual/installation.html#title40
-    # A workaround is to add "-std=c++11" again.
-    # A fix would be to use https://cmake.org/cmake/help/v3.1/prop_gbl/CMAKE_CXX_KNOWN_FEATURES.html 
-    # or even better https://cmake.org/cmake/help/v3.1/variable/CMAKE_CXX_STANDARD.html
-    # but it implies to use cmake version 3.1 at least.
-    if(NOT MSVC)
-      include(CheckCXXCompilerFlag)
-      CHECK_CXX_COMPILER_FLAG(-std=c++11 COMPILER_SUPPORTS_CXX11)
-      if(COMPILER_SUPPORTS_CXX11)
-        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
-      endif()
-    endif()
-    # - End of workaround
-
-    find_package(Eigen3 3.1.0)
     if (EIGEN3_FOUND)
-      message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.")
-      include( ${EIGEN3_USE_FILE} )
-      message(STATUS "Eigen3 use file: ${EIGEN3_USE_FILE}.")
-      include_directories (BEFORE "../../include")
-
       add_executable ( witness_complex_sphere witness_complex_sphere.cpp )
       target_link_libraries(witness_complex_sphere ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
       add_test( witness_complex_sphere_10 ${CMAKE_CURRENT_BINARY_DIR}/witness_complex_sphere 10)   
-      add_executable ( relaxed_witness_persistence relaxed_witness_persistence.cpp )
-      target_link_libraries(relaxed_witness_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
-      add_test( relaxed_witness_persistence_10 ${CMAKE_CURRENT_BINARY_DIR}/relaxed_witness_persistence 10)   
-      add_executable ( a0_persistence a0_persistence.cpp )
-      target_link_libraries(a0_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
-      add_test( a0_persistence_10 ${CMAKE_CURRENT_BINARY_DIR}/a0_persistence 10)
-      add_executable ( bench_rwit bench_rwit.cpp )
-      target_link_libraries(bench_rwit ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
-                  
-      add_executable ( relaxed_delaunay relaxed_delaunay.cpp )
-      target_link_libraries(relaxed_delaunay ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
-      add_test( relaxed_delaunay_10 ${CMAKE_CURRENT_BINARY_DIR}/relaxed_delaunay 10)   
-      add_executable ( generate_torus generate_torus.cpp )
-    else()
-      message(WARNING "Eigen3 not found. Version 3.1.0 is required for witness_complex_sphere example.")      
-    endif()
-  else()
-    message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile witness_complex_sphere example. Version 4.6.0 is required.")
-  endif ()
+    endif(EIGEN3_FOUND)
+  endif (NOT CGAL_VERSION VERSION_LESS 4.6.0)
 endif()
diff --git a/src/Witness_complex/example/witness_complex_from_file.cpp b/src/Witness_complex/example/witness_complex_from_file.cpp
index 77109512..53207ad2 100644
--- a/src/Witness_complex/example/witness_complex_from_file.cpp
+++ b/src/Witness_complex/example/witness_complex_from_file.cpp
@@ -34,14 +34,9 @@
 #include <string>
 #include <vector>
 
-using namespace Gudhi;
-using namespace Gudhi::witness_complex;
-
 typedef std::vector< Vertex_handle > typeVectorVertex;
 typedef std::vector< std::vector <double> > Point_Vector;
 
-typedef Witness_complex< Simplex_tree<> > WitnessComplex;
-
 /**
  * \brief Customized version of read_points
  * which takes into account a possible nbP first line
@@ -68,17 +63,6 @@ read_points_cust(std::string file_name, std::vector< std::vector< double > > & p
   in_file.close();
 }
 
-/** Write a gnuplot readable file.
- *  Data range is a random access range of pairs (arg, value)
- */
-template < typename Data_range >
-void write_data(Data_range & data, std::string filename) {
-  std::ofstream ofs(filename, std::ofstream::out);
-  for (auto entry : data)
-    ofs << entry.first << ", " << entry.second << "\n";
-  ofs.close();
-}
-
 int main(int argc, char * const argv[]) {
   if (argc != 3) {
     std::cerr << "Usage: " << argv[0]
@@ -91,7 +75,7 @@ int main(int argc, char * const argv[]) {
   clock_t start, end;
 
   // Construct the Simplex Tree
-  Simplex_tree<> simplex_tree;
+  Gudhi::Simplex_tree<> simplex_tree;
 
   // Read the point file
   Point_Vector point_vector;
@@ -109,7 +93,7 @@ int main(int argc, char * const argv[]) {
 
   // Compute witness complex
   start = clock();
-  WitnessComplex(knn, simplex_tree, nbL, point_vector[0].size());
+  Gudhi::witness_complex::witness_complex(knn, nbL, point_vector[0].size(), simplex_tree);
   end = clock();
   std::cout << "Witness complex took "
       << static_cast<double>(end - start) / CLOCKS_PER_SEC << " s. \n";
diff --git a/src/Witness_complex/example/witness_complex_sphere.cpp b/src/Witness_complex/example/witness_complex_sphere.cpp
index 1ff35bff..b26c9f36 100644
--- a/src/Witness_complex/example/witness_complex_sphere.cpp
+++ b/src/Witness_complex/example/witness_complex_sphere.cpp
@@ -39,13 +39,6 @@
 
 #include "generators.h"
 
-using namespace Gudhi;
-using namespace Gudhi::witness_complex;
-
-typedef std::vector< Vertex_handle > typeVectorVertex;
-
-typedef Witness_complex< Simplex_tree<> > WitnessComplex;
-
 /** Write a gnuplot readable file.
  *  Data range is a random access range of pairs (arg, value)
  */
@@ -60,15 +53,15 @@ void write_data(Data_range & data, std::string filename) {
 int main(int argc, char * const argv[]) {
   if (argc != 2) {
     std::cerr << "Usage: " << argv[0]
-        << " nbL \n";
+        << " number_of_landmarks \n";
     return 0;
   }
 
-  int nbL = atoi(argv[1]);
+  int number_of_landmarks = atoi(argv[1]);
   clock_t start, end;
 
   // Construct the Simplex Tree
-  Simplex_tree<> simplex_tree;
+  Gudhi::Simplex_tree<> simplex_tree;
 
   std::vector< std::pair<int, double> > l_time;
 
@@ -82,14 +75,15 @@ int main(int argc, char * const argv[]) {
     // Choose landmarks
     start = clock();
     std::vector<std::vector< int > > knn;
-    Gudhi::witness_complex::landmark_choice_by_random_point(point_vector, nbL, knn);
+    Gudhi::witness_complex::landmark_choice_by_random_point(point_vector, number_of_landmarks, knn);
 
     // Compute witness complex
-    WitnessComplex(knn, simplex_tree, nbL, point_vector[0].size());
+    Gudhi::witness_complex::witness_complex(knn, number_of_landmarks, point_vector[0].size(), simplex_tree);
     end = clock();
     double time = static_cast<double>(end - start) / CLOCKS_PER_SEC;
-    std::cout << "Witness complex for " << nbL << " landmarks took "
+    std::cout << "Witness complex for " << number_of_landmarks << " landmarks took "
         << time << " s. \n";
+    std::cout << "Number of simplices is: " << simplex_tree.num_simplices() << "\n";
     l_time.push_back(std::make_pair(nbP, time));
   }
   write_data(l_time, "w_time.dat");
diff --git a/src/Witness_complex/include/gudhi/Landmark_choice_by_furthest_point.h b/src/Witness_complex/include/gudhi/Landmark_choice_by_furthest_point.h
index 47cd888d..df93155b 100644
--- a/src/Witness_complex/include/gudhi/Landmark_choice_by_furthest_point.h
+++ b/src/Witness_complex/include/gudhi/Landmark_choice_by_furthest_point.h
@@ -23,7 +23,10 @@
 #ifndef LANDMARK_CHOICE_BY_FURTHEST_POINT_H_
 #define LANDMARK_CHOICE_BY_FURTHEST_POINT_H_
 
+#include <boost/range/size.hpp>
+
 #include <limits>  // for numeric_limits<>
+#include <iterator>
 #include <algorithm>  // for sort
 #include <vector>
 
@@ -31,13 +34,19 @@ namespace Gudhi {
 
 namespace witness_complex {
 
- typedef std::vector<int> typeVectorVertex;
+  typedef std::vector<int> typeVectorVertex;
 
   /** 
+   *  \ingroup witness_complex
    *  \brief Landmark choice strategy by iteratively adding the furthest witness from the
    *  current landmark set as the new landmark. 
    *  \details It chooses nbL landmarks from a random access range `points` and
    *  writes {witness}*{closest landmarks} matrix in `knn`.
+   *
+   *  The type KNearestNeighbors can be seen as 
+   *  Witness_range<Closest_landmark_range<Vertex_handle>>, where
+   *  Witness_range and Closest_landmark_range are random access ranges 
+   *  
    */
 
   template <typename KNearestNeighbours,
@@ -45,7 +54,7 @@ namespace witness_complex {
   void landmark_choice_by_furthest_point(Point_random_access_range const &points,
                                          int nbL,
                                          KNearestNeighbours &knn) {
-    int nb_points = points.end() - points.begin();
+    int nb_points = boost::size(points);
     assert(nb_points >= nbL);
     // distance matrix witness x landmarks
     std::vector<std::vector<double>> wit_land_dist(nb_points, std::vector<double>());
@@ -59,6 +68,7 @@ namespace witness_complex {
     std::vector< double > dist_to_L(nb_points, infty);  // vector of current distances to L from points
 
     // TODO(SK) Consider using rand_r(...) instead of rand(...) for improved thread safety
+    // or better yet std::uniform_int_distribution
     int rand_int = rand() % nb_points;
     int curr_max_w = rand_int;  // For testing purposes a pseudo-random number is used here
 
@@ -67,7 +77,7 @@ namespace witness_complex {
       chosen_landmarks.push_back(curr_max_w);
       unsigned i = 0;
       for (auto& p : points) {
-        double curr_dist = euclidean_distance(p, *(points.begin() + chosen_landmarks[current_number_of_landmarks]));
+        double curr_dist = euclidean_distance(p, *(std::begin(points) + chosen_landmarks[current_number_of_landmarks]));
         wit_land_dist[i].push_back(curr_dist);
         knn[i].push_back(current_number_of_landmarks);
         if (curr_dist < dist_to_L[i])
@@ -81,9 +91,9 @@ namespace witness_complex {
           curr_max_w = i;
         }
     }
-    for (unsigned i = 0; i < points.size(); ++i)
-      std::sort(knn[i].begin(),
-                knn[i].end(),
+    for (int i = 0; i < nb_points; ++i)
+      std::sort(std::begin(knn[i]),
+                std::end(knn[i]),
                 [&wit_land_dist, i](int a, int b) {
                   return wit_land_dist[i][a] < wit_land_dist[i][b]; });
   }
diff --git a/src/Witness_complex/include/gudhi/Landmark_choice_by_random_point.h b/src/Witness_complex/include/gudhi/Landmark_choice_by_random_point.h
index dc364007..ebf6aad1 100644
--- a/src/Witness_complex/include/gudhi/Landmark_choice_by_random_point.h
+++ b/src/Witness_complex/include/gudhi/Landmark_choice_by_random_point.h
@@ -23,8 +23,11 @@
 #ifndef LANDMARK_CHOICE_BY_RANDOM_POINT_H_
 #define LANDMARK_CHOICE_BY_RANDOM_POINT_H_
 
+#include <boost/range/size.hpp>
+
 #include <queue>  // for priority_queue<>
 #include <utility>  // for pair<>
+#include <iterator>
 #include <vector>
 #include <set>
 
@@ -32,9 +35,17 @@ namespace Gudhi {
 
 namespace witness_complex {
 
-  /** \brief Landmark choice strategy by taking random vertices for landmarks.
+  /**
+   *  \ingroup witness_complex
+   * \brief Landmark choice strategy by taking random vertices for landmarks.
    *  \details It chooses nbL distinct landmarks from a random access range `points`
    *  and outputs a matrix {witness}*{closest landmarks} in knn.
+   *
+   *  The type KNearestNeighbors can be seen as 
+   *  Witness_range<Closest_landmark_range<Vertex_handle>>, where
+   *  Witness_range and Closest_landmark_range are random access ranges and
+   *  Vertex_handle is the label type of a vertex in a simplicial complex.
+   *  Closest_landmark_range needs to have push_back operation.
    */
 
   template <typename KNearestNeighbours,
@@ -42,7 +53,7 @@ namespace witness_complex {
   void landmark_choice_by_random_point(Point_random_access_range const &points,
                                        int nbL,
                                        KNearestNeighbours &knn) {
-    int nbP = points.end() - points.begin();
+    int nbP = boost::size(points);
     assert(nbP >= nbL);
     std::set<int> landmarks;
     int current_number_of_landmarks = 0;  // counter for landmarks
@@ -55,12 +66,12 @@ namespace witness_complex {
       landmarks.insert(chosen_landmark);
     }
 
-    int dim = points.begin()->size();
+    int dim = boost::size(*std::begin(points));
     typedef std::pair<double, int> dist_i;
     typedef bool (*comp)(dist_i, dist_i);
     knn = KNearestNeighbours(nbP);
     for (int points_i = 0; points_i < nbP; points_i++) {
-      std::priority_queue<dist_i, std::vector<dist_i>, comp> l_heap([&](dist_i j1, dist_i j2) {
+      std::priority_queue<dist_i, std::vector<dist_i>, comp> l_heap([](dist_i j1, dist_i j2) {
           return j1.first > j2.first;
         });
       std::set<int>::iterator landmarks_it;
diff --git a/src/Witness_complex/include/gudhi/Witness_complex.h b/src/Witness_complex/include/gudhi/Witness_complex.h
index 34cbc882..489cdf11 100644
--- a/src/Witness_complex/include/gudhi/Witness_complex.h
+++ b/src/Witness_complex/include/gudhi/Witness_complex.h
@@ -28,8 +28,7 @@
 #include <boost/graph/adjacency_list.hpp>
 #include <boost/graph/connected_components.hpp>
 
-#include <boost/container/flat_map.hpp>
-#include <boost/iterator/transform_iterator.hpp>
+#include <boost/range/size.hpp>
 
 #include <gudhi/distance_functions.h>
 
@@ -47,12 +46,13 @@ namespace Gudhi {
 
 namespace witness_complex {
 
-/** 
-    \class Witness_complex
-    \brief Constructs the witness complex for the given set of witnesses and landmarks.
-    \ingroup witness_complex
- */
-template< class Simplicial_complex>
+// /*
+//  *  \private
+//     \class Witness_complex
+//     \brief Constructs the witness complex for the given set of witnesses and landmarks.
+//     \ingroup witness_complex
+//  */
+template< class SimplicialComplex>
 class Witness_complex {
  private:
   struct Active_witness {
@@ -65,13 +65,12 @@ class Witness_complex {
   };
 
  private:
-  typedef typename Simplicial_complex::Simplex_handle Simplex_handle;
-  typedef typename Simplicial_complex::Vertex_handle Vertex_handle;
+  typedef typename SimplicialComplex::Simplex_handle Simplex_handle;
+  typedef typename SimplicialComplex::Vertex_handle Vertex_handle;
 
   typedef std::vector< double > Point_t;
   typedef std::vector< Point_t > Point_Vector;
 
-  // typedef typename Simplicial_complex::Filtration_value Filtration_value;
   typedef std::vector< Vertex_handle > typeVectorVertex;
   typedef std::pair< typeVectorVertex, Filtration_value> typeSimplex;
   typedef std::pair< Simplex_handle, bool > typePairSimplexBool;
@@ -81,19 +80,19 @@ class Witness_complex {
   typedef std::list< Vertex_handle > ActiveWitnessList;
 
  private:
-  int nbL;  // Number of landmarks
-  Simplicial_complex& sc;  // Simplicial complex
+  int nbL_;  // Number of landmarks
+  SimplicialComplex& sc_;  // Simplicial complex
 
  public:
   /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-  /** @name Constructor
+  /* @name Constructor
    */
 
   //@{
 
   // Witness_range<Closest_landmark_range<Vertex_handle>>
 
-  /**
+  /*
    *  \brief Iterative construction of the witness complex.
    *  \details The witness complex is written in sc_ basing on a matrix knn of
    *  nearest neighbours of the form {witnesses}x{landmarks}.
@@ -109,31 +108,29 @@ class Witness_complex {
    */
   template< typename KNearestNeighbors >
   Witness_complex(KNearestNeighbors const & knn,
-                  Simplicial_complex & sc_,
-                  int nbL_,
-                  int dim) : nbL(nbL_), sc(sc_) {
+                  int nbL,
+                  int dim,
+                  SimplicialComplex & sc) : nbL_(nbL), sc_(sc) {
     // Construction of the active witness list
-    int nbW = knn.size();
+    int nbW = boost::size(knn);
     typeVectorVertex vv;
     int counter = 0;
     /* The list of still useful witnesses
      * it will diminuish in the course of iterations
      */
     ActiveWitnessList active_w;  // = new ActiveWitnessList();
-    for (int i = 0; i != nbL; ++i) {
+    for (Vertex_handle i = 0; i != nbL_; ++i) {
       // initial fill of 0-dimensional simplices
       // by doing it we don't assume that landmarks are necessarily witnesses themselves anymore
       counter++;
       vv = {i};
-      sc.insert_simplex(vv);
+      sc_.insert_simplex(vv);
       // TODO(SK) Error if not inserted : normally no need here though
     }
     int k = 1; /* current dimension in iterative construction */
     for (int i = 0; i != nbW; ++i)
       active_w.push_back(i);
-    // std::cout << "Successfully added edges" << std::endl;
     while (!active_w.empty() && k < dim) {
-      // std::cout << "Started the step k=" << k << std::endl;
       typename ActiveWitnessList::iterator it = active_w.begin();
       while (it != active_w.end()) {
         typeVectorVertex simplex_vector;
@@ -142,9 +139,9 @@ class Witness_complex {
         if (ok) {
           for (int i = 0; i != k + 1; ++i)
             simplex_vector.push_back(knn[*it][i]);
-          sc.insert_simplex(simplex_vector, 0.0);
+          sc_.insert_simplex(simplex_vector);
           // TODO(SK) Error if not inserted : normally no need here though
-          it++;
+          ++it;
         } else {
           active_w.erase(it++);  // First increase the iterator and then erase the previous element
         }
@@ -156,15 +153,13 @@ class Witness_complex {
   //@}
 
  private:
-  /** \brief Check if the facets of the k-dimensional simplex witnessed 
+  /* \brief Check if the facets of the k-dimensional simplex witnessed 
    *  by witness witness_id are already in the complex.
    *  inserted_vertex is the handle of the (k+1)-th vertex witnessed by witness_id
    */
   template <typename KNearestNeighbors>
   bool all_faces_in(KNearestNeighbors const &knn, int witness_id, int k) {
-    // std::cout << "All face in with the landmark " << inserted_vertex << std::endl;
     std::vector< Vertex_handle > facet;
-    // Vertex_handle curr_vh = curr_sh->first;
     // CHECK ALL THE FACETS
     for (int i = 0; i != k + 1; ++i) {
       facet = {};
@@ -173,9 +168,8 @@ class Witness_complex {
           facet.push_back(knn[witness_id][j]);
         }
       }  // endfor
-      if (sc.find(facet) == sc.null_simplex())
+      if (sc_.find(facet) == sc_.null_simplex())
         return false;
-      // std::cout << "++++ finished loop safely\n";
     }  // endfor
     return true;
   }
@@ -194,27 +188,25 @@ class Witness_complex {
   }
 
  public:
-  /**
-   *  \brief Verification if every simplex in the complex is witnessed by witnesses in knn.
-   *  \param print_output =true will print the witnesses for each simplex
-   *  \remark Added for debugging purposes.
-   */
+  // /*
+  //  *  \brief Verification if every simplex in the complex is witnessed by witnesses in knn.
+  //  *  \param print_output =true will print the witnesses for each simplex
+  //  *  \remark Added for debugging purposes.
+  //  */
   template< class KNearestNeighbors >
   bool is_witness_complex(KNearestNeighbors const & knn, bool print_output) {
-    // bool final_result = true;
-    for (Simplex_handle sh : sc.complex_simplex_range()) {
+    for (Simplex_handle sh : sc_.complex_simplex_range()) {
       bool is_witnessed = false;
       typeVectorVertex simplex;
       int nbV = 0;  // number of verticed in the simplex
-      for (int v : sc.simplex_vertex_range(sh))
+      for (Vertex_handle v : sc_.simplex_vertex_range(sh))
         simplex.push_back(v);
       nbV = simplex.size();
       for (typeVectorVertex w : knn) {
         bool has_vertices = true;
-        for (int v : simplex)
+        for (Vertex_handle v : simplex)
           if (std::find(w.begin(), w.begin() + nbV, v) == w.begin() + nbV) {
             has_vertices = false;
-            // break;
           }
         if (has_vertices) {
           is_witnessed = true;
@@ -242,6 +234,30 @@ class Witness_complex {
   }
 };
 
+  /**
+   *  \ingroup witness_complex
+   *  \brief Iterative construction of the witness complex.
+   *  \details The witness complex is written in simplicial complex sc_
+   *   basing on a matrix knn of
+   *  nearest neighbours of the form {witnesses}x{landmarks}.
+   *
+   *  The type KNearestNeighbors can be seen as
+   *  Witness_range<Closest_landmark_range<Vertex_handle>>, where
+   *  Witness_range and Closest_landmark_range are random access ranges.
+   *
+   *  Procedure takes into account at most (dim+1)
+   *  first landmarks from each landmark range to construct simplices.
+   *
+   *  Landmarks are supposed to be in [0,nbL_-1]
+   */
+  template <class KNearestNeighbors, class SimplicialComplexForWitness>
+  void witness_complex(KNearestNeighbors const & knn,
+                       int nbL,
+                       int dim,
+                       SimplicialComplexForWitness & sc) {
+    Witness_complex<SimplicialComplexForWitness>(knn, nbL, dim, sc);
+  }
+
 }  // namespace witness_complex
 
 }  // namespace Gudhi
diff --git a/src/Witness_complex/test/CMakeLists.txt b/src/Witness_complex/test/CMakeLists.txt
index 9422c152..bb55b0f1 100644
--- a/src/Witness_complex/test/CMakeLists.txt
+++ b/src/Witness_complex/test/CMakeLists.txt
@@ -1,17 +1,13 @@
 cmake_minimum_required(VERSION 2.6)
-project(GUDHIWitnessComplexUT)
+project(Witness_complex_tests)
 
 if (GCOVR_PATH)
   # for gcovr to make coverage reports - Corbera Jenkins plugin
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
-  set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fprofile-arcs -ftest-coverage")	
-  set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fprofile-arcs -ftest-coverage")
 endif()
 if (GPROF_PATH)
   # for gprof to make coverage reports - Jenkins
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
-  set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -pg")
-  set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -pg")
 endif()
 
 add_executable ( simple_witness_complexUT simple_witness_complex.cpp )
diff --git a/src/Witness_complex/test/simple_witness_complex.cpp b/src/Witness_complex/test/simple_witness_complex.cpp
index 7d44b90c..03df78ee 100644
--- a/src/Witness_complex/test/simple_witness_complex.cpp
+++ b/src/Witness_complex/test/simple_witness_complex.cpp
@@ -53,7 +53,7 @@ BOOST_AUTO_TEST_CASE(simple_witness_complex) {
   knn.push_back({5, 0, 1, 3, 6, 2, 4});
   knn.push_back({5, 6, 1, 0, 2, 3, 4});
   knn.push_back({1, 6, 0, 5, 2, 3, 4});
-  WitnessComplex witnessComplex(knn, complex, 7, 7);
+  WitnessComplex witnessComplex(knn, 7, 7, complex);
 
   BOOST_CHECK(witnessComplex.is_witness_complex(knn, false));
 }
diff --git a/src/Witness_complex/test/witness_complex_points.cpp b/src/Witness_complex/test/witness_complex_points.cpp
index cb1639e1..bd3df604 100644
--- a/src/Witness_complex/test/witness_complex_points.cpp
+++ b/src/Witness_complex/test/witness_complex_points.cpp
@@ -52,13 +52,13 @@ BOOST_AUTO_TEST_CASE(witness_complex_points) {
   Simplex_tree complex1;
   Gudhi::witness_complex::landmark_choice_by_random_point(points, 100, knn);
   assert(!knn.empty());
-  WitnessComplex witnessComplex1(knn, complex1, 100, 3);
+  WitnessComplex witnessComplex1(knn, 100, 3, complex1);
   BOOST_CHECK(witnessComplex1.is_witness_complex(knn, b_print_output));
 
   // Second test: furthest choice
   knn.clear();
   Simplex_tree complex2;
   Gudhi::witness_complex::landmark_choice_by_furthest_point(points, 100, knn);
-  WitnessComplex witnessComplex2(knn, complex2, 100, 3);
+  WitnessComplex witnessComplex2(knn, 100, 3, complex2);
   BOOST_CHECK(witnessComplex2.is_witness_complex(knn, b_print_output));
 }
diff --git a/src/cmake/modules/FindTBB.cmake b/src/cmake/modules/FindTBB.cmake
index 414a929b..13f4d929 100644
--- a/src/cmake/modules/FindTBB.cmake
+++ b/src/cmake/modules/FindTBB.cmake
@@ -1,433 +1,425 @@
-# Locate Intel Threading Building Blocks include paths and libraries
-# FindTBB.cmake can be found at https://code.google.com/p/findtbb/
-# Written by Hannes Hofmann <hannes.hofmann _at_ informatik.uni-erlangen.de>
-# Improvements by Gino van den Bergen <gino _at_ dtecta.com>,
-#   Florian Uhlig <F.Uhlig _at_ gsi.de>,
-#   Jiri Marsik <jiri.marsik89 _at_ gmail.com>
-
-# The MIT License
-#
-# Copyright (c) 2011 Hannes Hofmann
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-# THE SOFTWARE.
-
-# GvdB: This module uses the environment variable TBB_ARCH_PLATFORM which defines architecture and compiler.
-#   e.g. "ia32/vc8" or "em64t/cc4.1.0_libc2.4_kernel2.6.16.21"
-#   TBB_ARCH_PLATFORM is set by the build script tbbvars[.bat|.sh|.csh], which can be found
-#   in the TBB installation directory (TBB_INSTALL_DIR).
-#
-# GvdB: Mac OS X distribution places libraries directly in lib directory.
-#
-# For backwards compatibility, you may explicitely set the CMake variables TBB_ARCHITECTURE and TBB_COMPILER.
-# TBB_ARCHITECTURE [ ia32 | em64t | itanium ]
-#   which architecture to use
-# TBB_COMPILER e.g. vc9 or cc3.2.3_libc2.3.2_kernel2.4.21 or cc4.0.1_os10.4.9
-#   which compiler to use (detected automatically on Windows)
-
-# This module respects
-# TBB_INSTALL_DIR or $ENV{TBB21_INSTALL_DIR} or $ENV{TBB_INSTALL_DIR}
-
-# This module defines
-# TBB_INCLUDE_DIRS, where to find task_scheduler_init.h, etc.
-# TBB_LIBRARY_DIRS, where to find TBB libraries
-# TBB_INSTALL_DIR, the base TBB install directory.
-# TBB_LIBRARIES, all the following TBB libraries (both release and debug versions, using "optimized" and "debug" CMake keywords). Note that if the debug versions are not found, the release versions will be used instead for the debug mode.
-#   TBB_RELEASE_LIBRARY, the TBB release library
-#   TBB_MALLOC_RELEASE_LIBRARY, the TBB release malloc library
-#   TBB_DEBUG_LIBRARY, the TBB debug library
-#   TBB_MALLOC_DEBUG_LIBRARY, the TBB debug malloc library
-# TBB_FOUND, If false, don't try to use TBB.
-# TBB_INTERFACE_VERSION, as defined in tbb/tbb_stddef.h
-# TBB_MALLOCPROXY_DEBUG_LIBRARY, the TBB debug malloc_proxy library (not included in TBB_LIBRARIES since it's optionnal)
-# TBB_MALLOCPROXY_RELEASE_LIBRARY, the TBB release malloc_proxy library (not included in TBB_LIBRARIES since it's optionnal)
-
-include(CheckCXXSourceCompiles)
-
-# Usage:
-#   try_TBB_with_pthread(<result_var_name> [additional linker args...])
-function(try_TBB_with_pthread result_var)
-    set(TBB_try_ts_source "
-          #include <tbb/enumerable_thread_specific.h>
-          int main() {
-            tbb::enumerable_thread_specific<
-              bool*,
-              tbb::cache_aligned_allocator<bool*>,
-              tbb::ets_key_per_instance> grid;
-          }
-          ")
-    set(CMAKE_REQUIRED_LIBRARIES ${ALL_TBB_LIBRARIES} ${ARGN})
-    set(CMAKE_REQUIRED_INCLUDES ${TBB_INCLUDE_DIR})
-    check_cxx_source_compiles("${TBB_try_ts_source}" ${result_var})
-    set(${result_var} ${${result_var}} PARENT_SCOPE)
-endfunction(try_TBB_with_pthread)
-
-if (WIN32)
-    # has em64t/vc8 em64t/vc9
-    # has ia32/vc7.1 ia32/vc8 ia32/vc9
-    set(_TBB_DEFAULT_INSTALL_DIR "C:/Program Files/Intel/TBB" "C:/Program Files (x86)/Intel/TBB")
-    set(_TBB_LIB_RELEASE_NAME "tbb")
-    set(_TBB_LIB_MALLOC_RELEASE_NAME "${_TBB_LIB_RELEASE_NAME}malloc")
-    set(_TBB_LIB_MALLOCPROXY_RELEASE_NAME "${_TBB_LIB_RELEASE_NAME}malloc_proxy")
-    set(_TBB_LIB_DEBUG_NAME "${_TBB_LIB_RELEASE_NAME}_debug")
-    set(_TBB_LIB_MALLOC_DEBUG_NAME "${_TBB_LIB_MALLOC_RELEASE_NAME}_debug")
-    set(_TBB_LIB_MALLOCPROXY_DEBUG_NAME "${_TBB_LIB_MALLOCPROXY_RELEASE_NAME}_debug")
-    if (MSVC71)
-        set (_TBB_COMPILER "vc7.1")
-    endif(MSVC71)
-    if (MSVC80)
-        set(_TBB_COMPILER "vc8")
-    endif(MSVC80)
-    if (MSVC90)
-        set(_TBB_COMPILER "vc9")
-    endif(MSVC90)
-    if(MSVC10)
-        set(_TBB_COMPILER "vc10")
-    endif(MSVC10)
-    if(MSVC11)
-        set(_TBB_COMPILER "vc11")
-    endif(MSVC11)
-    if(MSVC12)
-	set(_TBB_COMPILER "vc12")
-    endif(MSVC12)
-    #note there was no MSVC13
-    if(MSVC14)
-	if(RUNNING_CGAL_AUTO_TEST)
-	    set (TBB_FOUND "NO")
-	    return()#binaries for TBB not publicly available when CGAL-4.7 is published
-	endif(RUNNING_CGAL_AUTO_TEST)
-	message(STATUS "[Warning] FindTBB.cmake: TBB 4.4 (latest available when CGAL-4.7 is published) does not provide support for MSVC 2015.")
-    endif(MSVC14)
-    # Todo: add other Windows compilers such as ICL.
-    set(_TBB_ARCHITECTURE ${TBB_ARCHITECTURE})
-endif (WIN32)
-
-if (UNIX)
-    if (APPLE)
-        # MAC
-        set(_TBB_DEFAULT_INSTALL_DIR "/Library/Frameworks/Intel_TBB.framework/Versions")
-        # libs: libtbb.dylib, libtbbmalloc.dylib, *_debug
-        set(_TBB_LIB_RELEASE_NAME "tbb")
-        set(_TBB_LIB_MALLOC_RELEASE_NAME "${_TBB_LIB_RELEASE_NAME}malloc")
-        #set(_TBB_LIB_MALLOCPROXY_RELEASE_NAME "${_TBB_LIB_RELEASE_NAME}malloc_proxy")
-        set(_TBB_LIB_DEBUG_NAME "${_TBB_LIB_RELEASE_NAME}_debug")
-        set(_TBB_LIB_MALLOC_DEBUG_NAME "${_TBB_LIB_MALLOC_RELEASE_NAME}_debug")
-        #set(_TBB_LIB_MALLOCPROXY_DEBUG_NAME "${_TBB_LIB_MALLOCPROXY_RELEASE_NAME}_debug")
-        # default flavor on apple: ia32/cc4.0.1_os10.4.9
-        # Jiri: There is no reason to presume there is only one flavor and
-        #       that user's setting of variables should be ignored.
-        if(NOT TBB_COMPILER)
-            set(_TBB_COMPILER "cc4.0.1_os10.4.9")
-        elseif (NOT TBB_COMPILER)
-            set(_TBB_COMPILER ${TBB_COMPILER})
-        endif(NOT TBB_COMPILER)
-        if(NOT TBB_ARCHITECTURE)
-            set(_TBB_ARCHITECTURE "ia32")
-        elseif(NOT TBB_ARCHITECTURE)
-            set(_TBB_ARCHITECTURE ${TBB_ARCHITECTURE})
-        endif(NOT TBB_ARCHITECTURE)
-    else (APPLE)
-        # LINUX
-        set(_TBB_DEFAULT_INSTALL_DIR "/opt/intel/tbb" "/usr/local/include" "/usr/include")
-        set(_TBB_LIB_RELEASE_NAME "tbb")
-        set(_TBB_LIB_MALLOC_RELEASE_NAME "${_TBB_LIB_RELEASE_NAME}malloc")
-        set(_TBB_LIB_MALLOCPROXY_RELEASE_NAME "${_TBB_LIB_RELEASE_NAME}malloc_proxy")
-        set(_TBB_LIB_DEBUG_NAME "${_TBB_LIB_RELEASE_NAME}_debug")
-        set(_TBB_LIB_MALLOC_DEBUG_NAME "${_TBB_LIB_MALLOC_RELEASE_NAME}_debug")
-        set(_TBB_LIB_MALLOCPROXY_DEBUG_NAME "${_TBB_LIB_MALLOCPROXY_RELEASE_NAME}_debug")
-        # has em64t/cc3.2.3_libc2.3.2_kernel2.4.21 em64t/cc3.3.3_libc2.3.3_kernel2.6.5 em64t/cc3.4.3_libc2.3.4_kernel2.6.9 em64t/cc4.1.0_libc2.4_kernel2.6.16.21
-        # has ia32/*
-        # has itanium/*
-        set(_TBB_COMPILER ${TBB_COMPILER})
-        set(_TBB_ARCHITECTURE ${TBB_ARCHITECTURE})
-    endif (APPLE)
-endif (UNIX)
-
-if (CMAKE_SYSTEM MATCHES "SunOS.*")
-# SUN
-# not yet supported
-# has em64t/cc3.4.3_kernel5.10
-# has ia32/*
-endif (CMAKE_SYSTEM MATCHES "SunOS.*")
-
-
-#-- Clear the public variables
-set (TBB_FOUND "NO")
-
-
-#-- Find TBB install dir and set ${_TBB_INSTALL_DIR} and cached ${TBB_INSTALL_DIR}
-# first: use CMake variable TBB_INSTALL_DIR
-if (TBB_INSTALL_DIR)
-    set (_TBB_INSTALL_DIR ${TBB_INSTALL_DIR})
-endif (TBB_INSTALL_DIR)
-# second: use environment variable
-if (NOT _TBB_INSTALL_DIR)
-    if (NOT "$ENV{TBBROOT}" STREQUAL "")
-        set (_TBB_INSTALL_DIR $ENV{TBBROOT})
-    endif (NOT "$ENV{TBBROOT}" STREQUAL "")
-    if (NOT "$ENV{TBB_INSTALL_DIR}" STREQUAL "")
-        set (_TBB_INSTALL_DIR $ENV{TBB_INSTALL_DIR})
-    endif (NOT "$ENV{TBB_INSTALL_DIR}" STREQUAL "")
-    # Intel recommends setting TBB21_INSTALL_DIR
-    if (NOT "$ENV{TBB21_INSTALL_DIR}" STREQUAL "")
-        set (_TBB_INSTALL_DIR $ENV{TBB21_INSTALL_DIR})
-    endif (NOT "$ENV{TBB21_INSTALL_DIR}" STREQUAL "")
-    if (NOT "$ENV{TBB22_INSTALL_DIR}" STREQUAL "")
-        set (_TBB_INSTALL_DIR $ENV{TBB22_INSTALL_DIR})
-    endif (NOT "$ENV{TBB22_INSTALL_DIR}" STREQUAL "")
-    if (NOT "$ENV{TBB30_INSTALL_DIR}" STREQUAL "")
-        set (_TBB_INSTALL_DIR $ENV{TBB30_INSTALL_DIR})
-    endif (NOT "$ENV{TBB30_INSTALL_DIR}" STREQUAL "")
-endif (NOT _TBB_INSTALL_DIR)
-# third: try to find path automatically
-if (NOT _TBB_INSTALL_DIR)
-    if (_TBB_DEFAULT_INSTALL_DIR)
-        set (_TBB_INSTALL_DIR ${_TBB_DEFAULT_INSTALL_DIR})
-    endif (_TBB_DEFAULT_INSTALL_DIR)
-endif (NOT _TBB_INSTALL_DIR)
-# sanity check
-if (NOT _TBB_INSTALL_DIR)
-    message ("ERROR: Unable to find Intel TBB install directory. ${_TBB_INSTALL_DIR}")
-else (NOT _TBB_INSTALL_DIR)
-# finally: set the cached CMake variable TBB_INSTALL_DIR
-if (NOT TBB_INSTALL_DIR)
-    set (TBB_INSTALL_DIR ${_TBB_INSTALL_DIR} CACHE PATH "Intel TBB install directory")
-    mark_as_advanced(TBB_INSTALL_DIR)
-endif (NOT TBB_INSTALL_DIR)
-
-
-#-- A macro to rewrite the paths of the library. This is necessary, because
-#   find_library() always found the em64t/vc9 version of the TBB libs
-macro(TBB_CORRECT_LIB_DIR var_name)
-#    if (NOT "${_TBB_ARCHITECTURE}" STREQUAL "em64t")
-        string(REPLACE em64t "${_TBB_ARCHITECTURE}" ${var_name} ${${var_name}})
-#    endif (NOT "${_TBB_ARCHITECTURE}" STREQUAL "em64t")
-    string(REPLACE ia32 "${_TBB_ARCHITECTURE}" ${var_name} ${${var_name}})
-    string(REPLACE vc7.1 "${_TBB_COMPILER}" ${var_name} ${${var_name}})
-    string(REPLACE vc8 "${_TBB_COMPILER}" ${var_name} ${${var_name}})
-    string(REPLACE vc9 "${_TBB_COMPILER}" ${var_name} ${${var_name}})
-    string(REPLACE vc10 "${_TBB_COMPILER}" ${var_name} ${${var_name}})
-    string(REPLACE vc11 "${_TBB_COMPILER}" ${var_name} ${${var_name}})
-endmacro(TBB_CORRECT_LIB_DIR var_content)
-
-
-#-- Look for include directory and set ${TBB_INCLUDE_DIR}
-set (TBB_INC_SEARCH_DIR ${_TBB_INSTALL_DIR}/include)
-# Jiri: tbbvars now sets the CPATH environment variable to the directory
-#       containing the headers.
-#  LR: search first with NO_DEFAULT_PATH...
-find_path(TBB_INCLUDE_DIR
-    tbb/task_scheduler_init.h
-    PATHS ${TBB_INC_SEARCH_DIR} ENV CPATH
-    NO_DEFAULT_PATH
-)
-if(NOT TBB_INCLUDE_DIR)
-#  LR: ... and then search again with NO_DEFAULT_PATH if nothing was found in
-#  hinted paths
-  find_path(TBB_INCLUDE_DIR
-      tbb/task_scheduler_init.h
-      PATHS ${TBB_INC_SEARCH_DIR} ENV CPATH
-  )
-endif()
-mark_as_advanced(TBB_INCLUDE_DIR)
-
-
-#-- Look for libraries
-# GvdB: $ENV{TBB_ARCH_PLATFORM} is set by the build script tbbvars[.bat|.sh|.csh]
-if (NOT $ENV{TBB_ARCH_PLATFORM} STREQUAL "")
-    set (_TBB_LIBRARY_DIR
-         ${_TBB_INSTALL_DIR}/lib/$ENV{TBB_ARCH_PLATFORM}
-         ${_TBB_INSTALL_DIR}/$ENV{TBB_ARCH_PLATFORM}/lib
-        )
-endif (NOT $ENV{TBB_ARCH_PLATFORM} STREQUAL "")
-# Jiri: This block isn't mutually exclusive with the previous one
-#       (hence no else), instead I test if the user really specified
-#       the variables in question.
-if ((NOT ${TBB_ARCHITECTURE} STREQUAL "") AND (NOT ${TBB_COMPILER} STREQUAL ""))
-    # HH: deprecated
-    message(STATUS "[Warning] FindTBB.cmake: The use of TBB_ARCHITECTURE and TBB_COMPILER is deprecated and may not be supported in future versions. Please set \$ENV{TBB_ARCH_PLATFORM} (using tbbvars.[bat|csh|sh]).")
-    # Jiri: It doesn't hurt to look in more places, so I store the hints from
-    #       ENV{TBB_ARCH_PLATFORM} and the TBB_ARCHITECTURE and TBB_COMPILER
-    #       variables and search them both.
-    set (_TBB_LIBRARY_DIR "${_TBB_INSTALL_DIR}/${_TBB_ARCHITECTURE}/${_TBB_COMPILER}/lib" ${_TBB_LIBRARY_DIR})
-endif ((NOT ${TBB_ARCHITECTURE} STREQUAL "") AND (NOT ${TBB_COMPILER} STREQUAL ""))
-
-# GvdB: Mac OS X distribution places libraries directly in lib directory.
-list(APPEND _TBB_LIBRARY_DIR ${_TBB_INSTALL_DIR}/lib)
-
-# Jiri: No reason not to check the default paths. From recent versions,
-#       tbbvars has started exporting the LIBRARY_PATH and LD_LIBRARY_PATH
-#       variables, which now point to the directories of the lib files.
-#       It all makes more sense to use the ${_TBB_LIBRARY_DIR} as a HINTS
-#       argument instead of the implicit PATHS as it isn't hard-coded
-#       but computed by system introspection. Searching the LIBRARY_PATH
-#       and LD_LIBRARY_PATH environment variables is now even more important
-#       that tbbvars doesn't export TBB_ARCH_PLATFORM and it facilitates
-#       the use of TBB built from sources.
-#  LR: search first with NO_DEFAULT_PATH...
-find_library(TBB_RELEASE_LIBRARY ${_TBB_LIB_RELEASE_NAME} HINTS ${_TBB_LIBRARY_DIR}
-        PATHS ENV LIBRARY_PATH ENV LD_LIBRARY_PATH NO_DEFAULT_PATH)
-find_library(TBB_MALLOC_RELEASE_LIBRARY ${_TBB_LIB_MALLOC_RELEASE_NAME} HINTS ${_TBB_LIBRARY_DIR}
-        PATHS ENV LIBRARY_PATH ENV LD_LIBRARY_PATH NO_DEFAULT_PATH)
-find_library(TBB_MALLOCPROXY_RELEASE_LIBRARY ${_TBB_LIB_MALLOCPROXY_RELEASE_NAME} HINTS ${_TBB_LIBRARY_DIR}
-        PATHS ENV LIBRARY_PATH ENV LD_LIBRARY_PATH NO_DEFAULT_PATH)
-if(NOT TBB_RELEASE_LIBRARY OR NOT TBB_MALLOC_RELEASE_LIBRARY OR NOT TBB_MALLOCPROXY_RELEASE_LIBRARY)
-# LR: ... and then search again with NO_DEFAULT_PATH if nothing was found
-#  in hinted paths
-    find_library(TBB_RELEASE_LIBRARY ${_TBB_LIB_RELEASE_NAME} HINTS ${_TBB_LIBRARY_DIR}
-            PATHS ENV LIBRARY_PATH ENV LD_LIBRARY_PATH)
-    find_library(TBB_MALLOC_RELEASE_LIBRARY ${_TBB_LIB_MALLOC_RELEASE_NAME} HINTS ${_TBB_LIBRARY_DIR}
-            PATHS ENV LIBRARY_PATH ENV LD_LIBRARY_PATH)
-    find_library(TBB_MALLOCPROXY_RELEASE_LIBRARY ${_TBB_LIB_MALLOCPROXY_RELEASE_NAME} HINTS ${_TBB_LIBRARY_DIR}
-            PATHS ENV LIBRARY_PATH ENV LD_LIBRARY_PATH)
-endif()
-
-#Extract path from TBB_RELEASE_LIBRARY name
-get_filename_component(TBB_RELEASE_LIBRARY_DIR ${TBB_RELEASE_LIBRARY} PATH)
-
-#TBB_CORRECT_LIB_DIR(TBB_RELEASE_LIBRARY)
-#TBB_CORRECT_LIB_DIR(TBB_MALLOC_RELEASE_LIBRARY)
-#TBB_CORRECT_LIB_DIR(TBB_MALLOCPROXY_RELEASE_LIBRARY)
-mark_as_advanced(TBB_RELEASE_LIBRARY TBB_MALLOC_RELEASE_LIBRARY TBB_MALLOCPROXY_RELEASE_LIBRARY)
-
-#-- Look for debug libraries
-# Jiri: Changed the same way as for the release libraries.
-find_library(TBB_DEBUG_LIBRARY ${_TBB_LIB_DEBUG_NAME} HINTS ${_TBB_LIBRARY_DIR}
-        PATHS ENV LIBRARY_PATH ENV LD_LIBRARY_PATH NO_DEFAULT_PATH)
-find_library(TBB_MALLOC_DEBUG_LIBRARY ${_TBB_LIB_MALLOC_DEBUG_NAME} HINTS ${_TBB_LIBRARY_DIR}
-        PATHS ENV LIBRARY_PATH ENV LD_LIBRARY_PATH NO_DEFAULT_PATH)
-find_library(TBB_MALLOCPROXY_DEBUG_LIBRARY ${_TBB_LIB_MALLOCPROXY_DEBUG_NAME} HINTS ${_TBB_LIBRARY_DIR}
-        PATHS ENV LIBRARY_PATH ENV LD_LIBRARY_PATH NO_DEFAULT_PATH)
-if(NOT TBB_DEBUG_LIBRARY OR NOT TBB_MALLOC_DEBUG_LIBRARY OR NOT TBB_MALLOCPROXY_DEBUG_LIBRARY)
-    find_library(TBB_DEBUG_LIBRARY ${_TBB_LIB_DEBUG_NAME} HINTS ${_TBB_LIBRARY_DIR}
-            PATHS ENV LIBRARY_PATH ENV LD_LIBRARY_PATH)
-    find_library(TBB_MALLOC_DEBUG_LIBRARY ${_TBB_LIB_MALLOC_DEBUG_NAME} HINTS ${_TBB_LIBRARY_DIR}
-            PATHS ENV LIBRARY_PATH ENV LD_LIBRARY_PATH)
-    find_library(TBB_MALLOCPROXY_DEBUG_LIBRARY ${_TBB_LIB_MALLOCPROXY_DEBUG_NAME} HINTS ${_TBB_LIBRARY_DIR}
-            PATHS ENV LIBRARY_PATH ENV LD_LIBRARY_PATH)
-endif()
-
-# Jiri: Self-built TBB stores the debug libraries in a separate directory.
-#       Extract path from TBB_DEBUG_LIBRARY name
-get_filename_component(TBB_DEBUG_LIBRARY_DIR ${TBB_DEBUG_LIBRARY} PATH)
-
-#TBB_CORRECT_LIB_DIR(TBB_DEBUG_LIBRARY)
-#TBB_CORRECT_LIB_DIR(TBB_MALLOC_DEBUG_LIBRARY)
-#TBB_CORRECT_LIB_DIR(TBB_MALLOCPROXY_DEBUG_LIBRARY)
-mark_as_advanced(TBB_DEBUG_LIBRARY TBB_MALLOC_DEBUG_LIBRARY TBB_MALLOCPROXY_DEBUG_LIBRARY)
-
-if (TBB_INCLUDE_DIR)
-    if (TBB_RELEASE_LIBRARY)
-        set (TBB_FOUND "YES")
-
-        # NOTE: Removed because we don't want to link with the malloc_proxy by default
-        #if (NOT "${TBB_MALLOCPROXY_RELEASE_LIBRARY}" STREQUAL "TBB_MALLOCPROXY_RELEASE_LIBRARY-NOTFOUND")
-        #    mark_as_advanced(TBB_MALLOCPROXY_RELEASE_LIBRARY)
-        #    set (_TBB_MALLOCPROXY optimized ${TBB_MALLOCPROXY_RELEASE_LIBRARY})
-        #endif (NOT "${TBB_MALLOCPROXY_RELEASE_LIBRARY}" STREQUAL "TBB_MALLOCPROXY_RELEASE_LIBRARY-NOTFOUND")
-        #if (NOT "${TBB_MALLOCPROXY_DEBUG_LIBRARY}" STREQUAL "TBB_MALLOCPROXY_DEBUG_LIBRARY-NOTFOUND")
-        #    mark_as_advanced(TBB_MALLOCPROXY_DEBUG_LIBRARY)
-        #    set (_TBB_MALLOCPROXY ${_TBB_MALLOCPROXY} debug ${TBB_MALLOCPROXY_DEBUG_LIBRARY})
-        #endif (NOT "${TBB_MALLOCPROXY_DEBUG_LIBRARY}" STREQUAL "TBB_MALLOCPROXY_DEBUG_LIBRARY-NOTFOUND")
-
-        # TBB release library
-        set (ALL_TBB_LIBRARIES optimized ${TBB_RELEASE_LIBRARY})
-
-        # TBB debug library found?
-        if (TBB_DEBUG_LIBRARY)
-            list(APPEND ALL_TBB_LIBRARIES debug ${TBB_DEBUG_LIBRARY})
-        else (TBB_DEBUG_LIBRARY)
-            # Otherwise, link with the release library even in debug mode
-            list(APPEND ALL_TBB_LIBRARIES debug ${TBB_RELEASE_LIBRARY})
-        endif (TBB_DEBUG_LIBRARY)
-
-        # TBB malloc - release
-        if (TBB_MALLOC_RELEASE_LIBRARY)
-            list(APPEND ALL_TBB_LIBRARIES optimized ${TBB_MALLOC_RELEASE_LIBRARY})
-
-            # TBB malloc - debug
-            if (TBB_MALLOC_DEBUG_LIBRARY)
-                list(APPEND ALL_TBB_LIBRARIES debug ${TBB_MALLOC_DEBUG_LIBRARY})
-            else (TBB_MALLOC_DEBUG_LIBRARY)
-                list(APPEND ALL_TBB_LIBRARIES debug ${TBB_MALLOC_RELEASE_LIBRARY})
-            endif (TBB_MALLOC_DEBUG_LIBRARY)
-        endif (TBB_MALLOC_RELEASE_LIBRARY)
-
-        if(UNIX AND NOT APPLE)
-            # On Fedora, code using TBB might need -pthread
-
-            # First check without pthread
-            try_TBB_with_pthread(TBB_without_pthread)
-
-            if(NOT TBB_without_pthread)
-                # Then check with -pthread
-                try_TBB_with_pthread(TBB_with_pthread -pthread)
-                if(TBB_with_pthread)
-                    list(APPEND ALL_TBB_LIBRARIES general -pthread)
-                endif(TBB_with_pthread)
-                endif(NOT TBB_without_pthread)
-        endif(UNIX AND NOT APPLE)
-
-        set (TBB_LIBRARIES ${ALL_TBB_LIBRARIES}
-             CACHE PATH "TBB libraries" FORCE)
-
-        # Include dirs
-        set (TBB_INCLUDE_DIRS ${TBB_INCLUDE_DIR} CACHE PATH "TBB include directory" FORCE)
-
-        # Library dirs
-        if( "${TBB_DEBUG_LIBRARY_DIR}" STREQUAL "" OR "${TBB_RELEASE_LIBRARY_DIR}" STREQUAL "${TBB_DEBUG_LIBRARY_DIR}" )
-            set (TBB_LIBRARY_DIRS
-                ${TBB_RELEASE_LIBRARY_DIR}
-                CACHE PATH "TBB library directories" FORCE)
-        else( "${TBB_DEBUG_LIBRARY_DIR}" STREQUAL "" OR "${TBB_RELEASE_LIBRARY_DIR}" STREQUAL "${TBB_DEBUG_LIBRARY_DIR}" )
-            set (TBB_LIBRARY_DIRS
-                ${TBB_RELEASE_LIBRARY_DIR} ${TBB_DEBUG_LIBRARY_DIR}
-                CACHE PATH "TBB library directories" FORCE)
-        endif( "${TBB_DEBUG_LIBRARY_DIR}" STREQUAL "" OR "${TBB_RELEASE_LIBRARY_DIR}" STREQUAL "${TBB_DEBUG_LIBRARY_DIR}" )
-
-        message(STATUS "Found Intel TBB")
-    endif (TBB_RELEASE_LIBRARY)
-endif (TBB_INCLUDE_DIR)
-
-if (NOT TBB_FOUND)
-    if(NOT TBB_FIND_QUIETLY)
-        message("ERROR: Intel TBB NOT found! Please define the TBBROOT (or TBB_INSTALL_DIR) and/or TBB_ARCH_PLATFORM environment variables.")
-        message(STATUS "Looked for Threading Building Blocks in ${_TBB_INSTALL_DIR}")
-    endif(NOT TBB_FIND_QUIETLY)
-    SET(TBB_INSTALL_DIR "TBB_INSTALL_DIR_NOT_FOUND" CACHE STRING "Intel TBB install directory")
-    # do only throw fatal, if this pkg is REQUIRED
-    if (TBB_FIND_REQUIRED)
-        message(FATAL_ERROR "Could NOT find TBB library.")
-    endif (TBB_FIND_REQUIRED)
-endif (NOT TBB_FOUND)
-
-endif (NOT _TBB_INSTALL_DIR)
-
-if (TBB_FOUND)
-    set(TBB_INTERFACE_VERSION 0)
-    FILE(READ "${TBB_INCLUDE_DIRS}/tbb/tbb_stddef.h" _TBB_VERSION_CONTENTS)
-    STRING(REGEX REPLACE ".*#define TBB_INTERFACE_VERSION ([0-9]+).*" "\\1" TBB_INTERFACE_VERSION "${_TBB_VERSION_CONTENTS}")
-    set(TBB_INTERFACE_VERSION "${TBB_INTERFACE_VERSION}")
-endif (TBB_FOUND)
-
-set(TBB_USE_FILE "UseTBB")
-
-### ** Emacs settings **
-### Local Variables:
-### cmake-tab-width: 4
-### End:
+# Locate Intel Threading Building Blocks include paths and libraries
+# FindTBB.cmake can be found at https://code.google.com/p/findtbb/
+# Written by Hannes Hofmann <hannes.hofmann _at_ informatik.uni-erlangen.de>
+# Improvements by Gino van den Bergen <gino _at_ dtecta.com>,
+#   Florian Uhlig <F.Uhlig _at_ gsi.de>,
+#   Jiri Marsik <jiri.marsik89 _at_ gmail.com>
+
+# The MIT License
+#
+# Copyright (c) 2011 Hannes Hofmann
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+
+# GvdB: This module uses the environment variable TBB_ARCH_PLATFORM which defines architecture and compiler.
+#   e.g. "ia32/vc8" or "em64t/cc4.1.0_libc2.4_kernel2.6.16.21"
+#   TBB_ARCH_PLATFORM is set by the build script tbbvars[.bat|.sh|.csh], which can be found
+#   in the TBB installation directory (TBB_INSTALL_DIR).
+#
+# GvdB: Mac OS X distribution places libraries directly in lib directory.
+#
+# For backwards compatibility, you may explicitely set the CMake variables TBB_ARCHITECTURE and TBB_COMPILER.
+# TBB_ARCHITECTURE [ ia32 | em64t | itanium ]
+#   which architecture to use
+# TBB_COMPILER e.g. vc9 or cc3.2.3_libc2.3.2_kernel2.4.21 or cc4.0.1_os10.4.9
+#   which compiler to use (detected automatically on Windows)
+
+# This module respects
+# TBB_INSTALL_DIR or $ENV{TBB21_INSTALL_DIR} or $ENV{TBB_INSTALL_DIR}
+
+# This module defines
+# TBB_INCLUDE_DIRS, where to find task_scheduler_init.h, etc.
+# TBB_LIBRARY_DIRS, where to find TBB libraries
+# TBB_INSTALL_DIR, the base TBB install directory.
+# TBB_LIBRARIES, all the following TBB libraries (both release and debug versions, using "optimized" and "debug" CMake keywords). Note that if the debug versions are not found, the release versions will be used instead for the debug mode.
+#   TBB_RELEASE_LIBRARY, the TBB release library
+#   TBB_MALLOC_RELEASE_LIBRARY, the TBB release malloc library
+#   TBB_DEBUG_LIBRARY, the TBB debug library
+#   TBB_MALLOC_DEBUG_LIBRARY, the TBB debug malloc library
+# TBB_FOUND, If false, don't try to use TBB.
+# TBB_INTERFACE_VERSION, as defined in tbb/tbb_stddef.h
+# TBB_MALLOCPROXY_DEBUG_LIBRARY, the TBB debug malloc_proxy library (not included in TBB_LIBRARIES since it's optionnal)
+# TBB_MALLOCPROXY_RELEASE_LIBRARY, the TBB release malloc_proxy library (not included in TBB_LIBRARIES since it's optionnal)
+
+include(CheckCXXSourceCompiles)
+
+# Usage:
+#   try_TBB_with_pthread(<result_var_name> [additional linker args...])
+function(try_TBB_with_pthread result_var)
+    set(TBB_try_ts_source "
+          #include <tbb/enumerable_thread_specific.h>
+          int main() {
+            tbb::enumerable_thread_specific<
+              bool*,
+              tbb::cache_aligned_allocator<bool*>,
+              tbb::ets_key_per_instance> grid;
+          }
+          ")
+    set(CMAKE_REQUIRED_LIBRARIES ${ALL_TBB_LIBRARIES} ${ARGN})
+    set(CMAKE_REQUIRED_INCLUDES ${TBB_INCLUDE_DIR})
+    check_cxx_source_compiles("${TBB_try_ts_source}" ${result_var})
+    set(${result_var} ${${result_var}} PARENT_SCOPE)
+endfunction(try_TBB_with_pthread)
+
+if (WIN32)
+    # has em64t/vc8 em64t/vc9
+    # has ia32/vc7.1 ia32/vc8 ia32/vc9
+    set(_TBB_DEFAULT_INSTALL_DIR "C:/Program Files/Intel/TBB" "C:/Program Files (x86)/Intel/TBB")
+    set(_TBB_LIB_RELEASE_NAME "tbb")
+    set(_TBB_LIB_MALLOC_RELEASE_NAME "${_TBB_LIB_RELEASE_NAME}malloc")
+    set(_TBB_LIB_MALLOCPROXY_RELEASE_NAME "${_TBB_LIB_RELEASE_NAME}malloc_proxy")
+    set(_TBB_LIB_DEBUG_NAME "${_TBB_LIB_RELEASE_NAME}_debug")
+    set(_TBB_LIB_MALLOC_DEBUG_NAME "${_TBB_LIB_MALLOC_RELEASE_NAME}_debug")
+    set(_TBB_LIB_MALLOCPROXY_DEBUG_NAME "${_TBB_LIB_MALLOCPROXY_RELEASE_NAME}_debug")
+    if (MSVC71)
+        set (_TBB_COMPILER "vc7.1")
+    endif(MSVC71)
+    if (MSVC80)
+        set(_TBB_COMPILER "vc8")
+    endif(MSVC80)
+    if (MSVC90)
+        set(_TBB_COMPILER "vc9")
+    endif(MSVC90)
+    if(MSVC10)
+        set(_TBB_COMPILER "vc10")
+    endif(MSVC10)
+    if(MSVC11)
+        set(_TBB_COMPILER "vc11")
+    endif(MSVC11)
+    if(MSVC12)
+	set(_TBB_COMPILER "vc12")
+    endif(MSVC12)
+    #note there was no MSVC13
+    if(MSVC14)
+	set(_TBB_COMPILER "vc14")
+    endif(MSVC14)
+    # Todo: add other Windows compilers such as ICL.
+    set(_TBB_ARCHITECTURE ${TBB_ARCHITECTURE})
+endif (WIN32)
+
+if (UNIX)
+    if (APPLE)
+        # MAC
+        set(_TBB_DEFAULT_INSTALL_DIR "/Library/Frameworks/Intel_TBB.framework/Versions")
+        # libs: libtbb.dylib, libtbbmalloc.dylib, *_debug
+        set(_TBB_LIB_RELEASE_NAME "tbb")
+        set(_TBB_LIB_MALLOC_RELEASE_NAME "${_TBB_LIB_RELEASE_NAME}malloc")
+        #set(_TBB_LIB_MALLOCPROXY_RELEASE_NAME "${_TBB_LIB_RELEASE_NAME}malloc_proxy")
+        set(_TBB_LIB_DEBUG_NAME "${_TBB_LIB_RELEASE_NAME}_debug")
+        set(_TBB_LIB_MALLOC_DEBUG_NAME "${_TBB_LIB_MALLOC_RELEASE_NAME}_debug")
+        #set(_TBB_LIB_MALLOCPROXY_DEBUG_NAME "${_TBB_LIB_MALLOCPROXY_RELEASE_NAME}_debug")
+        # default flavor on apple: ia32/cc4.0.1_os10.4.9
+        # Jiri: There is no reason to presume there is only one flavor and
+        #       that user's setting of variables should be ignored.
+        if(NOT TBB_COMPILER)
+            set(_TBB_COMPILER "cc4.0.1_os10.4.9")
+        elseif (NOT TBB_COMPILER)
+            set(_TBB_COMPILER ${TBB_COMPILER})
+        endif(NOT TBB_COMPILER)
+        if(NOT TBB_ARCHITECTURE)
+            set(_TBB_ARCHITECTURE "ia32")
+        elseif(NOT TBB_ARCHITECTURE)
+            set(_TBB_ARCHITECTURE ${TBB_ARCHITECTURE})
+        endif(NOT TBB_ARCHITECTURE)
+    else (APPLE)
+        # LINUX
+        set(_TBB_DEFAULT_INSTALL_DIR "/opt/intel/tbb" "/usr/local/include" "/usr/include")
+        set(_TBB_LIB_RELEASE_NAME "tbb")
+        set(_TBB_LIB_MALLOC_RELEASE_NAME "${_TBB_LIB_RELEASE_NAME}malloc")
+        set(_TBB_LIB_MALLOCPROXY_RELEASE_NAME "${_TBB_LIB_RELEASE_NAME}malloc_proxy")
+        set(_TBB_LIB_DEBUG_NAME "${_TBB_LIB_RELEASE_NAME}_debug")
+        set(_TBB_LIB_MALLOC_DEBUG_NAME "${_TBB_LIB_MALLOC_RELEASE_NAME}_debug")
+        set(_TBB_LIB_MALLOCPROXY_DEBUG_NAME "${_TBB_LIB_MALLOCPROXY_RELEASE_NAME}_debug")
+        # has em64t/cc3.2.3_libc2.3.2_kernel2.4.21 em64t/cc3.3.3_libc2.3.3_kernel2.6.5 em64t/cc3.4.3_libc2.3.4_kernel2.6.9 em64t/cc4.1.0_libc2.4_kernel2.6.16.21
+        # has ia32/*
+        # has itanium/*
+        set(_TBB_COMPILER ${TBB_COMPILER})
+        set(_TBB_ARCHITECTURE ${TBB_ARCHITECTURE})
+    endif (APPLE)
+endif (UNIX)
+
+if (CMAKE_SYSTEM MATCHES "SunOS.*")
+# SUN
+# not yet supported
+# has em64t/cc3.4.3_kernel5.10
+# has ia32/*
+endif (CMAKE_SYSTEM MATCHES "SunOS.*")
+
+
+#-- Clear the public variables
+set (TBB_FOUND "NO")
+
+
+#-- Find TBB install dir and set ${_TBB_INSTALL_DIR} and cached ${TBB_INSTALL_DIR}
+# first: use CMake variable TBB_INSTALL_DIR
+if (TBB_INSTALL_DIR)
+    set (_TBB_INSTALL_DIR ${TBB_INSTALL_DIR})
+endif (TBB_INSTALL_DIR)
+# second: use environment variable
+if (NOT _TBB_INSTALL_DIR)
+    if (NOT "$ENV{TBBROOT}" STREQUAL "")
+        set (_TBB_INSTALL_DIR $ENV{TBBROOT})
+    endif (NOT "$ENV{TBBROOT}" STREQUAL "")
+    if (NOT "$ENV{TBB_INSTALL_DIR}" STREQUAL "")
+        set (_TBB_INSTALL_DIR $ENV{TBB_INSTALL_DIR})
+    endif (NOT "$ENV{TBB_INSTALL_DIR}" STREQUAL "")
+    # Intel recommends setting TBB21_INSTALL_DIR
+    if (NOT "$ENV{TBB21_INSTALL_DIR}" STREQUAL "")
+        set (_TBB_INSTALL_DIR $ENV{TBB21_INSTALL_DIR})
+    endif (NOT "$ENV{TBB21_INSTALL_DIR}" STREQUAL "")
+    if (NOT "$ENV{TBB22_INSTALL_DIR}" STREQUAL "")
+        set (_TBB_INSTALL_DIR $ENV{TBB22_INSTALL_DIR})
+    endif (NOT "$ENV{TBB22_INSTALL_DIR}" STREQUAL "")
+    if (NOT "$ENV{TBB30_INSTALL_DIR}" STREQUAL "")
+        set (_TBB_INSTALL_DIR $ENV{TBB30_INSTALL_DIR})
+    endif (NOT "$ENV{TBB30_INSTALL_DIR}" STREQUAL "")
+endif (NOT _TBB_INSTALL_DIR)
+# third: try to find path automatically
+if (NOT _TBB_INSTALL_DIR)
+    if (_TBB_DEFAULT_INSTALL_DIR)
+        set (_TBB_INSTALL_DIR ${_TBB_DEFAULT_INSTALL_DIR})
+    endif (_TBB_DEFAULT_INSTALL_DIR)
+endif (NOT _TBB_INSTALL_DIR)
+# sanity check
+if (NOT _TBB_INSTALL_DIR)
+    message ("ERROR: Unable to find Intel TBB install directory. ${_TBB_INSTALL_DIR}")
+else (NOT _TBB_INSTALL_DIR)
+# finally: set the cached CMake variable TBB_INSTALL_DIR
+if (NOT TBB_INSTALL_DIR)
+    set (TBB_INSTALL_DIR ${_TBB_INSTALL_DIR} CACHE PATH "Intel TBB install directory")
+    mark_as_advanced(TBB_INSTALL_DIR)
+endif (NOT TBB_INSTALL_DIR)
+
+
+#-- A macro to rewrite the paths of the library. This is necessary, because
+#   find_library() always found the em64t/vc9 version of the TBB libs
+macro(TBB_CORRECT_LIB_DIR var_name)
+#    if (NOT "${_TBB_ARCHITECTURE}" STREQUAL "em64t")
+        string(REPLACE em64t "${_TBB_ARCHITECTURE}" ${var_name} ${${var_name}})
+#    endif (NOT "${_TBB_ARCHITECTURE}" STREQUAL "em64t")
+    string(REPLACE ia32 "${_TBB_ARCHITECTURE}" ${var_name} ${${var_name}})
+    string(REGEX REPLACE "vc[0-9]+(\.[0-9]+)?" "${_TBB_COMPILER}" ${var_name} ${${var_name}})
+endmacro(TBB_CORRECT_LIB_DIR var_content)
+
+
+#-- Look for include directory and set ${TBB_INCLUDE_DIR}
+set (TBB_INC_SEARCH_DIR ${_TBB_INSTALL_DIR}/include)
+# Jiri: tbbvars now sets the CPATH environment variable to the directory
+#       containing the headers.
+#  LR: search first with NO_DEFAULT_PATH...
+find_path(TBB_INCLUDE_DIR
+    tbb/task_scheduler_init.h
+    PATHS ${TBB_INC_SEARCH_DIR} ENV CPATH
+    NO_DEFAULT_PATH
+)
+if(NOT TBB_INCLUDE_DIR)
+#  LR: ... and then search again with NO_DEFAULT_PATH if nothing was found in
+#  hinted paths
+  find_path(TBB_INCLUDE_DIR
+      tbb/task_scheduler_init.h
+      PATHS ${TBB_INC_SEARCH_DIR} ENV CPATH
+  )
+endif()
+mark_as_advanced(TBB_INCLUDE_DIR)
+
+
+#-- Look for libraries
+# GvdB: $ENV{TBB_ARCH_PLATFORM} is set by the build script tbbvars[.bat|.sh|.csh]
+if (NOT $ENV{TBB_ARCH_PLATFORM} STREQUAL "")
+    set (_TBB_LIBRARY_DIR
+         ${_TBB_INSTALL_DIR}/lib/$ENV{TBB_ARCH_PLATFORM}
+         ${_TBB_INSTALL_DIR}/$ENV{TBB_ARCH_PLATFORM}/lib
+        )
+endif (NOT $ENV{TBB_ARCH_PLATFORM} STREQUAL "")
+# Jiri: This block isn't mutually exclusive with the previous one
+#       (hence no else), instead I test if the user really specified
+#       the variables in question.
+if ((NOT ${TBB_ARCHITECTURE} STREQUAL "") AND (NOT ${TBB_COMPILER} STREQUAL ""))
+    # HH: deprecated
+    message(STATUS "[Warning] FindTBB.cmake: The use of TBB_ARCHITECTURE and TBB_COMPILER is deprecated and may not be supported in future versions. Please set \$ENV{TBB_ARCH_PLATFORM} (using tbbvars.[bat|csh|sh]).")
+    # Jiri: It doesn't hurt to look in more places, so I store the hints from
+    #       ENV{TBB_ARCH_PLATFORM} and the TBB_ARCHITECTURE and TBB_COMPILER
+    #       variables and search them both.
+    set (_TBB_LIBRARY_DIR "${_TBB_INSTALL_DIR}/${_TBB_ARCHITECTURE}/${_TBB_COMPILER}/lib" ${_TBB_LIBRARY_DIR})
+endif ((NOT ${TBB_ARCHITECTURE} STREQUAL "") AND (NOT ${TBB_COMPILER} STREQUAL ""))
+
+# GvdB: Mac OS X distribution places libraries directly in lib directory.
+list(APPEND _TBB_LIBRARY_DIR ${_TBB_INSTALL_DIR}/lib)
+
+# Jiri: No reason not to check the default paths. From recent versions,
+#       tbbvars has started exporting the LIBRARY_PATH and LD_LIBRARY_PATH
+#       variables, which now point to the directories of the lib files.
+#       It all makes more sense to use the ${_TBB_LIBRARY_DIR} as a HINTS
+#       argument instead of the implicit PATHS as it isn't hard-coded
+#       but computed by system introspection. Searching the LIBRARY_PATH
+#       and LD_LIBRARY_PATH environment variables is now even more important
+#       that tbbvars doesn't export TBB_ARCH_PLATFORM and it facilitates
+#       the use of TBB built from sources.
+#  LR: search first with NO_DEFAULT_PATH...
+find_library(TBB_RELEASE_LIBRARY ${_TBB_LIB_RELEASE_NAME} HINTS ${_TBB_LIBRARY_DIR}
+        PATHS ENV LIBRARY_PATH ENV LD_LIBRARY_PATH NO_DEFAULT_PATH)
+find_library(TBB_MALLOC_RELEASE_LIBRARY ${_TBB_LIB_MALLOC_RELEASE_NAME} HINTS ${_TBB_LIBRARY_DIR}
+        PATHS ENV LIBRARY_PATH ENV LD_LIBRARY_PATH NO_DEFAULT_PATH)
+find_library(TBB_MALLOCPROXY_RELEASE_LIBRARY ${_TBB_LIB_MALLOCPROXY_RELEASE_NAME} HINTS ${_TBB_LIBRARY_DIR}
+        PATHS ENV LIBRARY_PATH ENV LD_LIBRARY_PATH NO_DEFAULT_PATH)
+if(NOT TBB_RELEASE_LIBRARY OR NOT TBB_MALLOC_RELEASE_LIBRARY OR NOT TBB_MALLOCPROXY_RELEASE_LIBRARY)
+# LR: ... and then search again with NO_DEFAULT_PATH if nothing was found
+#  in hinted paths
+    find_library(TBB_RELEASE_LIBRARY ${_TBB_LIB_RELEASE_NAME} HINTS ${_TBB_LIBRARY_DIR}
+            PATHS ENV LIBRARY_PATH ENV LD_LIBRARY_PATH)
+    find_library(TBB_MALLOC_RELEASE_LIBRARY ${_TBB_LIB_MALLOC_RELEASE_NAME} HINTS ${_TBB_LIBRARY_DIR}
+            PATHS ENV LIBRARY_PATH ENV LD_LIBRARY_PATH)
+    find_library(TBB_MALLOCPROXY_RELEASE_LIBRARY ${_TBB_LIB_MALLOCPROXY_RELEASE_NAME} HINTS ${_TBB_LIBRARY_DIR}
+            PATHS ENV LIBRARY_PATH ENV LD_LIBRARY_PATH)
+endif()
+
+#Extract path from TBB_RELEASE_LIBRARY name
+get_filename_component(TBB_RELEASE_LIBRARY_DIR ${TBB_RELEASE_LIBRARY} PATH)
+
+#TBB_CORRECT_LIB_DIR(TBB_RELEASE_LIBRARY)
+#TBB_CORRECT_LIB_DIR(TBB_MALLOC_RELEASE_LIBRARY)
+#TBB_CORRECT_LIB_DIR(TBB_MALLOCPROXY_RELEASE_LIBRARY)
+mark_as_advanced(TBB_RELEASE_LIBRARY TBB_MALLOC_RELEASE_LIBRARY TBB_MALLOCPROXY_RELEASE_LIBRARY)
+
+#-- Look for debug libraries
+# Jiri: Changed the same way as for the release libraries.
+find_library(TBB_DEBUG_LIBRARY ${_TBB_LIB_DEBUG_NAME} HINTS ${_TBB_LIBRARY_DIR}
+        PATHS ENV LIBRARY_PATH ENV LD_LIBRARY_PATH NO_DEFAULT_PATH)
+find_library(TBB_MALLOC_DEBUG_LIBRARY ${_TBB_LIB_MALLOC_DEBUG_NAME} HINTS ${_TBB_LIBRARY_DIR}
+        PATHS ENV LIBRARY_PATH ENV LD_LIBRARY_PATH NO_DEFAULT_PATH)
+find_library(TBB_MALLOCPROXY_DEBUG_LIBRARY ${_TBB_LIB_MALLOCPROXY_DEBUG_NAME} HINTS ${_TBB_LIBRARY_DIR}
+        PATHS ENV LIBRARY_PATH ENV LD_LIBRARY_PATH NO_DEFAULT_PATH)
+if(NOT TBB_DEBUG_LIBRARY OR NOT TBB_MALLOC_DEBUG_LIBRARY OR NOT TBB_MALLOCPROXY_DEBUG_LIBRARY)
+    find_library(TBB_DEBUG_LIBRARY ${_TBB_LIB_DEBUG_NAME} HINTS ${_TBB_LIBRARY_DIR}
+            PATHS ENV LIBRARY_PATH ENV LD_LIBRARY_PATH)
+    find_library(TBB_MALLOC_DEBUG_LIBRARY ${_TBB_LIB_MALLOC_DEBUG_NAME} HINTS ${_TBB_LIBRARY_DIR}
+            PATHS ENV LIBRARY_PATH ENV LD_LIBRARY_PATH)
+    find_library(TBB_MALLOCPROXY_DEBUG_LIBRARY ${_TBB_LIB_MALLOCPROXY_DEBUG_NAME} HINTS ${_TBB_LIBRARY_DIR}
+            PATHS ENV LIBRARY_PATH ENV LD_LIBRARY_PATH)
+endif()
+
+# Jiri: Self-built TBB stores the debug libraries in a separate directory.
+#       Extract path from TBB_DEBUG_LIBRARY name
+get_filename_component(TBB_DEBUG_LIBRARY_DIR ${TBB_DEBUG_LIBRARY} PATH)
+
+#TBB_CORRECT_LIB_DIR(TBB_DEBUG_LIBRARY)
+#TBB_CORRECT_LIB_DIR(TBB_MALLOC_DEBUG_LIBRARY)
+#TBB_CORRECT_LIB_DIR(TBB_MALLOCPROXY_DEBUG_LIBRARY)
+mark_as_advanced(TBB_DEBUG_LIBRARY TBB_MALLOC_DEBUG_LIBRARY TBB_MALLOCPROXY_DEBUG_LIBRARY)
+
+if (TBB_INCLUDE_DIR)
+    if (TBB_RELEASE_LIBRARY)
+        set (TBB_FOUND "YES")
+
+        # NOTE: Removed because we don't want to link with the malloc_proxy by default
+        #if (NOT "${TBB_MALLOCPROXY_RELEASE_LIBRARY}" STREQUAL "TBB_MALLOCPROXY_RELEASE_LIBRARY-NOTFOUND")
+        #    mark_as_advanced(TBB_MALLOCPROXY_RELEASE_LIBRARY)
+        #    set (_TBB_MALLOCPROXY optimized ${TBB_MALLOCPROXY_RELEASE_LIBRARY})
+        #endif (NOT "${TBB_MALLOCPROXY_RELEASE_LIBRARY}" STREQUAL "TBB_MALLOCPROXY_RELEASE_LIBRARY-NOTFOUND")
+        #if (NOT "${TBB_MALLOCPROXY_DEBUG_LIBRARY}" STREQUAL "TBB_MALLOCPROXY_DEBUG_LIBRARY-NOTFOUND")
+        #    mark_as_advanced(TBB_MALLOCPROXY_DEBUG_LIBRARY)
+        #    set (_TBB_MALLOCPROXY ${_TBB_MALLOCPROXY} debug ${TBB_MALLOCPROXY_DEBUG_LIBRARY})
+        #endif (NOT "${TBB_MALLOCPROXY_DEBUG_LIBRARY}" STREQUAL "TBB_MALLOCPROXY_DEBUG_LIBRARY-NOTFOUND")
+
+        # TBB release library
+        set (ALL_TBB_LIBRARIES optimized ${TBB_RELEASE_LIBRARY})
+
+        # TBB debug library found?
+        if (TBB_DEBUG_LIBRARY)
+            list(APPEND ALL_TBB_LIBRARIES debug ${TBB_DEBUG_LIBRARY})
+        else (TBB_DEBUG_LIBRARY)
+            # Otherwise, link with the release library even in debug mode
+            list(APPEND ALL_TBB_LIBRARIES debug ${TBB_RELEASE_LIBRARY})
+        endif (TBB_DEBUG_LIBRARY)
+
+        # TBB malloc - release
+        if (TBB_MALLOC_RELEASE_LIBRARY)
+            list(APPEND ALL_TBB_LIBRARIES optimized ${TBB_MALLOC_RELEASE_LIBRARY})
+
+            # TBB malloc - debug
+            if (TBB_MALLOC_DEBUG_LIBRARY)
+                list(APPEND ALL_TBB_LIBRARIES debug ${TBB_MALLOC_DEBUG_LIBRARY})
+            else (TBB_MALLOC_DEBUG_LIBRARY)
+                list(APPEND ALL_TBB_LIBRARIES debug ${TBB_MALLOC_RELEASE_LIBRARY})
+            endif (TBB_MALLOC_DEBUG_LIBRARY)
+        endif (TBB_MALLOC_RELEASE_LIBRARY)
+
+        if(UNIX AND NOT APPLE)
+            # On Fedora, code using TBB might need -pthread
+
+            # First check without pthread
+            try_TBB_with_pthread(TBB_without_pthread)
+
+            if(NOT TBB_without_pthread)
+                # Then check with -pthread
+                try_TBB_with_pthread(TBB_with_pthread -pthread)
+                if(TBB_with_pthread)
+                    list(APPEND ALL_TBB_LIBRARIES general -pthread)
+                endif(TBB_with_pthread)
+                endif(NOT TBB_without_pthread)
+        endif(UNIX AND NOT APPLE)
+
+        set (TBB_LIBRARIES ${ALL_TBB_LIBRARIES}
+             CACHE PATH "TBB libraries" FORCE)
+
+        # Include dirs
+        set (TBB_INCLUDE_DIRS ${TBB_INCLUDE_DIR} CACHE PATH "TBB include directory" FORCE)
+
+        # Library dirs
+        if( "${TBB_DEBUG_LIBRARY_DIR}" STREQUAL "" OR "${TBB_RELEASE_LIBRARY_DIR}" STREQUAL "${TBB_DEBUG_LIBRARY_DIR}" )
+            set (TBB_LIBRARY_DIRS
+                ${TBB_RELEASE_LIBRARY_DIR}
+                CACHE PATH "TBB library directories" FORCE)
+        else( "${TBB_DEBUG_LIBRARY_DIR}" STREQUAL "" OR "${TBB_RELEASE_LIBRARY_DIR}" STREQUAL "${TBB_DEBUG_LIBRARY_DIR}" )
+            set (TBB_LIBRARY_DIRS
+                ${TBB_RELEASE_LIBRARY_DIR} ${TBB_DEBUG_LIBRARY_DIR}
+                CACHE PATH "TBB library directories" FORCE)
+        endif( "${TBB_DEBUG_LIBRARY_DIR}" STREQUAL "" OR "${TBB_RELEASE_LIBRARY_DIR}" STREQUAL "${TBB_DEBUG_LIBRARY_DIR}" )
+
+        message(STATUS "Found Intel TBB")
+    endif (TBB_RELEASE_LIBRARY)
+endif (TBB_INCLUDE_DIR)
+
+if (NOT TBB_FOUND)
+    if(NOT TBB_FIND_QUIETLY)
+        message("ERROR: Intel TBB NOT found! Please define the TBBROOT (or TBB_INSTALL_DIR) and/or TBB_ARCH_PLATFORM environment variables.")
+        message(STATUS "Looked for Threading Building Blocks in ${_TBB_INSTALL_DIR}")
+    endif(NOT TBB_FIND_QUIETLY)
+    SET(TBB_INSTALL_DIR "TBB_INSTALL_DIR_NOT_FOUND" CACHE STRING "Intel TBB install directory")
+    # do only throw fatal, if this pkg is REQUIRED
+    if (TBB_FIND_REQUIRED)
+        message(FATAL_ERROR "Could NOT find TBB library.")
+    endif (TBB_FIND_REQUIRED)
+endif (NOT TBB_FOUND)
+
+endif (NOT _TBB_INSTALL_DIR)
+
+if (TBB_FOUND)
+    set(TBB_INTERFACE_VERSION 0)
+    FILE(READ "${TBB_INCLUDE_DIRS}/tbb/tbb_stddef.h" _TBB_VERSION_CONTENTS)
+    STRING(REGEX REPLACE ".*#define TBB_INTERFACE_VERSION ([0-9]+).*" "\\1" TBB_INTERFACE_VERSION "${_TBB_VERSION_CONTENTS}")
+    set(TBB_INTERFACE_VERSION "${TBB_INTERFACE_VERSION}")
+endif (TBB_FOUND)
+
+set(TBB_USE_FILE "UseTBB")
+
+### ** Emacs settings **
+### Local Variables:
+### cmake-tab-width: 4
+### End:
diff --git a/src/cmake/modules/GUDHI_doxygen_target.txt b/src/cmake/modules/GUDHI_doxygen_target.txt
new file mode 100644
index 00000000..d2cb952d
--- /dev/null
+++ b/src/cmake/modules/GUDHI_doxygen_target.txt
@@ -0,0 +1,11 @@
+# add a target to generate API documentation with Doxygen
+find_package(Doxygen)
+if(DOXYGEN_FOUND)
+  # configure_file(${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile @ONLY)
+
+  add_custom_target(doxygen ${DOXYGEN_EXECUTABLE} ${GUDHI_USER_VERSION_DIR}/Doxyfile
+                    WORKING_DIRECTORY ${GUDHI_USER_VERSION_DIR}
+                    DEPENDS ${GUDHI_USER_VERSION_DIR}/Doxyfile ${GUDHI_DOXYGEN_DEPENDENCY}
+                    COMMENT "Generating API documentation with Doxygen in ${GUDHI_USER_VERSION_DIR}/doc/html/" VERBATIM)
+
+endif(DOXYGEN_FOUND)
diff --git a/src/cmake/modules/GUDHI_user_version_target.txt b/src/cmake/modules/GUDHI_user_version_target.txt
new file mode 100644
index 00000000..805f0a83
--- /dev/null
+++ b/src/cmake/modules/GUDHI_user_version_target.txt
@@ -0,0 +1,115 @@
+# Some functionnalities requires CMake 2.8.11 minimum
+if (NOT CMAKE_VERSION VERSION_LESS 2.8.11)
+
+  string(TIMESTAMP DATE_AND_TIME "%Y-%m-%d-%H-%M-%S")
+  
+  # Definition of the custom target user_version
+  add_custom_target(user_version)
+  
+  if(DEFINED USER_VERSION_DIR)
+    # set the GUDHI_USER_VERSION_DIR with USER_VERSION_DIR defined by the user
+    set(GUDHI_USER_VERSION_DIR ${CMAKE_CURRENT_BINARY_DIR}/${USER_VERSION_DIR})
+  else()
+    # set the GUDHI_USER_VERSION_DIR with timestamp and Gudhi version number
+    set(GUDHI_USER_VERSION_DIR ${CMAKE_CURRENT_BINARY_DIR}/${DATE_AND_TIME}_GUDHI_${GUDHI_VERSION})
+  endif()
+
+  set(GUDHI_DOXYGEN_DEPENDENCY user_version)
+
+  add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+                     make_directory ${GUDHI_USER_VERSION_DIR}
+                     COMMENT "user_version creation in ${GUDHI_USER_VERSION_DIR}")
+  
+  add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+                     copy ${CMAKE_SOURCE_DIR}/README ${GUDHI_USER_VERSION_DIR}/README)
+  add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+                     copy ${CMAKE_SOURCE_DIR}/COPYING ${GUDHI_USER_VERSION_DIR}/COPYING)
+  add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+                     copy ${CMAKE_SOURCE_DIR}/src/CMakeLists.txt ${GUDHI_USER_VERSION_DIR}/CMakeLists.txt)
+  add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+                     copy ${CMAKE_SOURCE_DIR}/src/Doxyfile ${GUDHI_USER_VERSION_DIR}/Doxyfile)
+  add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+                     copy ${CMAKE_SOURCE_DIR}/src/GUDHIConfigVersion.cmake.in ${GUDHI_USER_VERSION_DIR}/GUDHIConfigVersion.cmake.in)
+  add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+                     copy ${CMAKE_SOURCE_DIR}/src/GUDHIConfig.cmake.in ${GUDHI_USER_VERSION_DIR}/GUDHIConfig.cmake.in)
+  add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+                     copy ${CMAKE_SOURCE_DIR}/CMakeGUDHIVersion.txt ${GUDHI_USER_VERSION_DIR}/CMakeGUDHIVersion.txt)
+  add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+                     copy ${CMAKE_SOURCE_DIR}/GUDHIVersion.cmake.in ${GUDHI_USER_VERSION_DIR}/GUDHIVersion.cmake.in)
+  
+  add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+                     copy_directory ${CMAKE_SOURCE_DIR}/biblio ${GUDHI_USER_VERSION_DIR}/biblio)
+  add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+                     copy_directory ${CMAKE_SOURCE_DIR}/data ${GUDHI_USER_VERSION_DIR}/data)
+  add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+                     copy_directory ${CMAKE_SOURCE_DIR}/src/cmake ${GUDHI_USER_VERSION_DIR}/cmake)
+  add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+                     copy_directory ${CMAKE_SOURCE_DIR}/src/debian ${GUDHI_USER_VERSION_DIR}/debian)
+  add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+                     copy_directory ${CMAKE_SOURCE_DIR}/src/GudhUI ${GUDHI_USER_VERSION_DIR}/GudhUI)
+  
+  set(GUDHI_MODULES "common;Alpha_complex;Bitmap_cubical_complex;Contraction;Hasse_complex;Persistent_cohomology;Simplex_tree;Skeleton_blocker;Witness_complex")
+  
+  foreach(GUDHI_MODULE ${GUDHI_MODULES})
+    # doc files
+    file(GLOB GUDHI_DOC_FILES ${CMAKE_SOURCE_DIR}/src/${GUDHI_MODULE}/doc/*)
+  
+    foreach(GUDHI_DOC_FILE ${GUDHI_DOC_FILES})
+      get_filename_component(GUDHI_DOC_FILE_NAME ${GUDHI_DOC_FILE} NAME)
+      # GUDHI_DOC_FILE can be a file or a directory
+      if(IS_DIRECTORY ${GUDHI_DOC_FILE})
+        add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+                           copy_directory ${GUDHI_DOC_FILE} ${GUDHI_USER_VERSION_DIR}/doc/${GUDHI_MODULE}/${GUDHI_DOC_FILE_NAME})
+      else()
+        add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+                           copy ${GUDHI_DOC_FILE} ${GUDHI_USER_VERSION_DIR}/doc/${GUDHI_MODULE}/${GUDHI_DOC_FILE_NAME})
+      endif()
+    endforeach()
+  
+    # example files
+    file(GLOB GUDHI_EXAMPLE_FILES ${CMAKE_SOURCE_DIR}/src/${GUDHI_MODULE}/example/*)
+  
+    foreach(GUDHI_EXAMPLE_FILE ${GUDHI_EXAMPLE_FILES})
+      get_filename_component(GUDHI_EXAMPLE_FILE_NAME ${GUDHI_EXAMPLE_FILE} NAME)
+      # GUDHI_EXAMPLE_FILE can be a file or a directory
+      if(IS_DIRECTORY ${GUDHI_EXAMPLE_FILE})
+        add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+                           copy_directory ${GUDHI_EXAMPLE_FILE} ${GUDHI_USER_VERSION_DIR}/example/${GUDHI_MODULE}/${GUDHI_EXAMPLE_FILE_NAME})
+      else()
+        add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+                           copy ${GUDHI_EXAMPLE_FILE} ${GUDHI_USER_VERSION_DIR}/example/${GUDHI_MODULE}/${GUDHI_EXAMPLE_FILE_NAME})
+      endif()
+    endforeach()
+  
+    # include files
+    file(GLOB GUDHI_INCLUDE_FILES ${CMAKE_SOURCE_DIR}/src/${GUDHI_MODULE}/include/gudhi/*)
+  
+    foreach(GUDHI_INCLUDE_FILE ${GUDHI_INCLUDE_FILES})
+      get_filename_component(GUDHI_INCLUDE_FILE_NAME ${GUDHI_INCLUDE_FILE} NAME)
+      # GUDHI_INCLUDE_FILE can be a file or a directory
+      if(IS_DIRECTORY ${GUDHI_INCLUDE_FILE})
+        add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+                           copy_directory ${GUDHI_INCLUDE_FILE} ${GUDHI_USER_VERSION_DIR}/include/gudhi/${GUDHI_INCLUDE_FILE_NAME})
+      else()
+        add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+                           copy ${GUDHI_INCLUDE_FILE} ${GUDHI_USER_VERSION_DIR}/include/gudhi/${GUDHI_INCLUDE_FILE_NAME})
+      endif()
+    endforeach()
+  
+    # concept files
+    file(GLOB GUDHI_CONCEPT_FILES ${CMAKE_SOURCE_DIR}/src/${GUDHI_MODULE}/concept/*.h)
+  
+    foreach(GUDHI_CONCEPT_FILE ${GUDHI_CONCEPT_FILES})
+      get_filename_component(GUDHI_CONCEPT_FILE_NAME ${GUDHI_CONCEPT_FILE} NAME)
+      # GUDHI_CONCEPT_FILE can be a file or a directory
+      if(IS_DIRECTORY ${GUDHI_CONCEPT_FILE})
+        add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+                           copy_directory ${GUDHI_CONCEPT_FILE} ${GUDHI_USER_VERSION_DIR}/concept/${GUDHI_MODULE}/${GUDHI_CONCEPT_FILE_NAME})
+      else()
+        add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+                           copy ${GUDHI_CONCEPT_FILE} ${GUDHI_USER_VERSION_DIR}/concept/${GUDHI_MODULE}/${GUDHI_CONCEPT_FILE_NAME})
+      endif()
+    endforeach()
+  endforeach()
+
+endif()
diff --git a/src/common/doc/Gudhi_banner.jpg b/src/common/doc/Gudhi_banner.jpg
deleted file mode 100644
index ebd3d8af..00000000
--- a/src/common/doc/Gudhi_banner.jpg
+++ /dev/null
diff --git a/src/common/doc/Gudhi_banner.png b/src/common/doc/Gudhi_banner.png
new file mode 100644
index 00000000..18e8a672
--- /dev/null
+++ b/src/common/doc/Gudhi_banner.png
diff --git a/src/common/doc/footer.html b/src/common/doc/footer.html
new file mode 100644
index 00000000..7b4cdc5c
--- /dev/null
+++ b/src/common/doc/footer.html
@@ -0,0 +1,29 @@
+<!-- HTML footer for doxygen 1.8.6-->
+<!-- start footer part -->
+<table style="width:100%">
+  <tr class="no-bullet shadow-black">
+      <td class="network-entypo">
+<!--BEGIN PROJECT_NAME--> $projectname
+<!--BEGIN PROJECT_NUMBER-->&#160;Version $projectnumber<!--END PROJECT_NUMBER-->
+<!--BEGIN PROJECT_BRIEF-->&#160;-&#160;$projectbrief<!--END PROJECT_BRIEF-->
+<!--END PROJECT_NAME-->
+      </td>
+      <td class="network-entypo">
+<!--BEGIN GENERATE_TREEVIEW-->
+        $generatedby
+        <a href="http://www.doxygen.org/index.html">
+        <img class="footer" src="$relpath^doxygen.png" alt="doxygen"/></a> $doxygenversion
+<!--END GENERATE_TREEVIEW-->
+      </td>
+  </tr>
+</table>
+
+<!--BEGIN !GENERATE_TREEVIEW-->
+<hr class="footer"/><address class="footer"><small> tralala
+$generatedby &#160;<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="$relpath^doxygen.png" alt="doxygen"/>
+</a> $doxygenversion
+</small></address>
+<!--END !GENERATE_TREEVIEW-->
+</body>
+</html>
diff --git a/src/common/doc/header.html b/src/common/doc/header.html
new file mode 100644
index 00000000..a6f3ed9c
--- /dev/null
+++ b/src/common/doc/header.html
@@ -0,0 +1,83 @@
+<!-- HTML header for doxygen 1.8.6-->
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!-- GUDHI website : class="no-js" lang="en" is necessary -->
+<html xmlns="http://www.w3.org/1999/xhtml" class="no-js" lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen $doxygenversion"/>
+<!--BEGIN PROJECT_NAME--><title>$projectname: $title</title><!--END PROJECT_NAME-->
+<!--BEGIN !PROJECT_NAME--><title>$title</title><!--END !PROJECT_NAME-->
+<!-- GUDHI website css for header BEGIN -->
+<link rel="stylesheet" type="text/css" href="http://gudhi.gforge.inria.fr/assets/css/styles_feeling_responsive.css" />
+<!-- GUDHI website css for header END -->
+<link href="$relpath^tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="$relpath^jquery.js"></script>
+<script type="text/javascript" src="$relpath^dynsections.js"></script>
+$treeview
+$search
+$mathjax
+<link href="$relpath^$stylesheet" rel="stylesheet" type="text/css" />
+$extrastylesheet
+</head>
+<body>
+
+<!-- GUDHI website header BEGIN -->
+<div id="navigation" class="sticky">
+  <nav class="top-bar" role="navigation" data-topbar>
+    <section class="top-bar-section">
+      <ul class="right">
+              <li class="divider"></li>
+              <li><a href="http://gudhi.gforge.inria.fr/contact/">Contact</a></li>
+      </ul>
+      <ul class="left">
+              <li><a href="http://gudhi.gforge.inria.fr/"> <img src="http://gudhi.gforge.inria.fr/assets/img/home.png" alt="&nbsp;&nbsp;GUDHI">&nbsp;&nbsp;GUDHI </a></li>
+              <li class="divider"></li>
+              <li class="has-dropdown">
+                <a href="#">Project</a>
+                  <ul class="dropdown">
+                      <li><a href="http://gudhi.gforge.inria.fr/people/">People</a></li>
+                      <li><a href="http://gudhi.gforge.inria.fr/getinvolved/">Get involved</a></li>
+                      <li><a href="http://gudhi.gforge.inria.fr/partners/">Partners and Funding</a></li>
+                      <li><a href="http://gudhi.gforge.inria.fr/relatedprojects/">Related projects</a></li>
+                      <li><a href="http://gudhi.gforge.inria.fr/theyaretalkingaboutus/">They are talking about us</a></li>
+                  </ul>
+              </li>
+              <li class="divider"></li>
+              <li class="has-dropdown">
+                <a href="#">Download</a>
+                  <ul class="dropdown">
+                      <li><a href="http://gudhi.gforge.inria.fr/licensing/">Licensing</a></li>
+                      <li><a href="https://gforge.inria.fr/frs/?group_id=3865" target="_blank">Get the sources</a></li>
+                      <li><a href="http://gudhi.gforge.inria.fr/doc/latest/installation.html">Installation manual</a></li>
+                  </ul>
+              </li>
+              <li class="divider"></li>
+              <li><a href="http://gudhi.gforge.inria.fr/doc/latest/">Documentation</a></li>
+              <li class="divider"></li>
+              <li><a href="http://gudhi.gforge.inria.fr/interfaces/">Interfaces</a></li>
+              <li class="divider"></li>
+      </ul>
+    </section>
+  </nav>
+</div><!-- /#navigation -->
+<!-- GUDHI website header BEGIN -->
+    
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+
+<!--BEGIN TITLEAREA-->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 30px;">
+  <!--BEGIN DISABLE_INDEX-->
+   <!--BEGIN SEARCHENGINE-->
+   <td>$searchbox</td>
+   <!--END SEARCHENGINE-->
+  <!--END DISABLE_INDEX-->
+ </tr>
+ </tbody>
+</table>
+</div>
+<!--END TITLEAREA-->
+<!-- end header part -->
diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h
index 41b8ba1e..21cf6925 100644
--- a/src/common/doc/main_page.h
+++ b/src/common/doc/main_page.h
@@ -1,87 +1,293 @@
 /*! \mainpage
- * \image html "Gudhi_banner.jpg" "" width=20cm
+ *  \tableofcontents
+ * \image html "Gudhi_banner.png" "" width=20cm
  * 
  * \section Introduction Introduction
- * The Gudhi library (Geometric Understanding in Higher Dimensions) is a generic open source C++ library for
+ * The Gudhi library (Geometry Understanding in Higher Dimensions) is a generic open source C++ library for
  * Computational Topology and Topological Data Analysis
  * (<a class="el" target="_blank" href="https://en.wikipedia.org/wiki/Topological_data_analysis">TDA</a>).
- * The GUDHI library is developed as part of the
- * <a class="el" target="_blank" href="https://project.inria.fr/gudhi/">GUDHI project</a> supported by the European
- * Research Council. The GUDHI library intends  to help the development of new algorithmic solutions in TDA and their
- * transfer to applications. It provides robust, efficient, flexible and easy to use implementations of
- * state-of-the-art algorithms and data structures.
+ * The GUDHI library intends  to help the development of new algorithmic solutions in TDA and their transfer to
+ * applications. It provides robust, efficient, flexible and easy to use implementations of state-of-the-art
+ * algorithms and data structures.
  * 
  * The current release of the GUDHI library includes:
  * 
  * \li Data structures to represent, construct and manipulate simplicial complexes.
- * \li Algorithms to compute persistent homology and multi-field persistent homology.
- * \li Simplication of simplicial complexes by edge contraction.
+ * \li Simplification of simplicial complexes by edge contraction.
+ * \li Algorithms to compute persistent homology persistent homology.
  * 
  * All data-structures are generic and several of their aspects can be parameterized via template classes.
  * We refer to \cite gudhilibrary_ICMS14 for a detailed description of the design of the library.
  *
- * The library is available <a class="el" target="_blank" href="https://gforge.inria.fr/frs/?group_id=3865">here</a>
- * and the documentation is available at this <a class="el" href="http://gudhi.gforge.inria.fr/doc/latest/">
- * webpage</a>.
- * 
- * The library comes with data sets, \ref demos and \ref testsuites.
- * 
- * Gudhi is also accessible though the
- * <a class="el" target="_blank" href="https://cran.r-project.org/web/packages/TDA/index.html">R package TDA</a>
- * (Statistical Tools for Topological Data Analysis).
- * 
- * The development of the GUDHI library is steered by an Editorial Board composed of:
- * 
- * \li <a class="el" target="_blank" href="http://www-sop.inria.fr/members/Jean-Daniel.Boissonnat/">
- * Jean-Daniel Boissonnat</a> | INRIA Sophia Antipolis - Méditerranée
- * \li <a class="el" target="_blank" href="http://geometrica.saclay.inria.fr/team/Marc.Glisse/">Marc Glisse</a> | INRIA Saclay - Ile de France
- * \li Clément Jamin | INRIA Sophia Antipolis - Méditerranée
- * \li Vincent Rouvreau | INRIA Saclay - Ile de France
- * 
+ \section DataStructures Data structures
+ \subsection AlphaComplexDataStructure Alpha complex
+ \image html "alpha_complex_representation.png" "Alpha complex representation"
+<table border="0">
+  <tr>
+    <td width="25%">
+      <b>Author:</b> Vincent Rouvreau<br>
+      <b>Introduced in:</b> GUDHI 1.3.0<br>
+      <b>Copyright:</b> GPL v3<br>
+    </td>
+    <td width="75%">
+    Alpha_complex is a simplicial complex constructed from the finite cells of a Delaunay Triangulation.<br>
+    The filtration value of each simplex is computed as the square of the circumradius of the simplex if the
+    circumsphere is empty (the simplex is then said to be Gabriel), and as the minimum of the filtration
+    values of the codimension 1 cofaces that make it not Gabriel otherwise.
+    All simplices that have a filtration value strictly greater than a given alpha squared value are not inserted into
+    the complex.<br>
+    <b>User manual:</b> \ref alpha_complex - <b>Reference manual:</b> Gudhi::alpha_complex::Alpha_complex
+    </td>
+ </tr>
+</table>
+ \subsection CubicalComplexDataStructure Cubical complex
+ \image html "Cubical_complex_representation.png" "Cubical complex representation"
+<table border="0">
+  <tr>
+    <td width="25%">
+      <b>Author:</b> Pawel Dlotko<br>
+      <b>Introduced in:</b> GUDHI 1.3.0<br>
+      <b>Copyright:</b> GPL v3<br>
+    </td>
+    <td width="75%">
+    The cubical complex is an example of a structured complex useful in computational mathematics (specially
+    rigorous numerics) and image analysis.<br>
+    <b>User manual:</b> \ref cubical_complex - <b>Reference manual:</b> Gudhi::cubical_complex::Bitmap_cubical_complex
+    </td>
+ </tr>
+</table>
+ \subsection SimplexTreeDataStructure Simplex tree
+ \image html "Simplex_tree_representation.png" "Simplex tree representation"
+<table border="0">
+  <tr>
+    <td width="25%">
+      <b>Author:</b> Cl&eacute;ment Maria<br>
+      <b>Introduced in:</b> GUDHI 1.0.0<br>
+      <b>Copyright:</b> GPL v3<br>
+    </td>
+    <td width="75%">
+    The simplex tree is an efficient and flexible
+ data structure for representing general (filtered) simplicial complexes. The data structure
+ is described in \cite boissonnatmariasimplextreealgorithmica .<br>
+    <b>User manual:</b> \ref simplex_tree - <b>Reference manual:</b> Gudhi::Simplex_tree
+    </td>
+ </tr>
+</table>
+ \subsection SkeletonBlockerDataStructure Skeleton blocker
+ \image html "ds_representation.png" "Skeleton blocker representation"
+<table border="0">
+  <tr>
+    <td width="25%">
+      <b>Author:</b> David Salinas<br>
+      <b>Introduced in:</b> GUDHI 1.1.0<br>
+      <b>Copyright:</b> GPL v3<br>
+    </td>
+    <td width="75%">
+    The Skeleton-Blocker data-structure proposes a light encoding for simplicial complexes by storing only an *implicit*
+    representation of its simplices \cite socg_blockers_2011,\cite blockers2012. Intuitively, it just stores the
+    1-skeleton of a simplicial complex with a graph and the set of its "missing faces" that is very small in practice.
+    This data-structure handles all simplicial complexes operations such as simplex enumeration or simplex removal but
+    operations that are particularly efficient are operations that do not require simplex enumeration such as edge
+    iteration, link computation or simplex contraction.<br>
+    <b>User manual:</b> \ref skbl - <b>Reference manual:</b> Gudhi::skeleton_blocker::Skeleton_blocker_complex
+    </td>
+ </tr>
+</table>
+ \subsection WitnessComplexDataStructure Witness complex
+ \image html "Witness_complex_representation.png" "Witness complex representation"
+<table border="0">
+  <tr>
+    <td width="25%">
+      <b>Author:</b> Siargey Kachanovich<br>
+      <b>Introduced in:</b> GUDHI 1.3.0<br>
+      <b>Copyright:</b> GPL v3<br>
+    </td>
+    <td width="75%">
+    Witness complex \f$ Wit(W,L) \f$  is a simplicial complex defined on two sets of points in \f$\mathbb{R}^D\f$.
+    The data structure is described in \cite boissonnatmariasimplextreealgorithmica .<br>
+    <b>User manual:</b> \ref witness_complex - <b>Reference manual:</b> Gudhi::witness_complex::SimplicialComplexForWitness
+    </td>
+ </tr>
+</table>
+ 
+ \section Toolbox Toolbox
+ \subsection ContractionToolbox Contraction
+ \image html "sphere_contraction_representation.png" "Sphere contraction example"
+<table border="0">
+  <tr>
+    <td width="25%">
+      <b>Author:</b> David Salinas<br>
+      <b>Introduced in:</b> GUDHI 1.1.0<br>
+      <b>Copyright:</b> GPL v3<br>
+    </td>
+    <td width="75%">
+    The purpose of this package is to offer a user-friendly interface for edge contraction simplification of huge
+    simplicial complexes. It uses the \ref skbl data-structure whose size remains small  during simplification of most
+    used geometrical complexes of topological data analysis such as the Rips or the Delaunay complexes. In practice,
+    the size of this data-structure is even much lower than the total number of simplices.<br>
+    <b>User manual:</b> \ref contr
+    </td>
+ </tr>
+</table>
+ \subsection PersistentCohomologyToolbox Persistent Cohomology
+ \image html "3DTorus_poch.png" "Rips Persistent Cohomology on a 3D Torus"
+<table border="0">
+  <tr>
+    <td width="25%">
+      <b>Author:</b> Cl&eacute;ment Maria<br>
+      <b>Introduced in:</b> GUDHI 1.0.0<br>
+      <b>Copyright:</b> GPL v3<br>
+    </td>
+    <td width="75%">
+    The theory of homology consists in attaching to a topological space a sequence of (homology) groups, capturing
+    global topological features like connected components, holes, cavities, etc. Persistent homology studies the
+    evolution -- birth, life and death -- of these features when the topological space is changing. Consequently, the
+    theory is essentially composed of three elements: topological spaces, their homology groups and an evolution
+    scheme.
+    Computation of persistent cohomology using the algorithm of \cite DBLP:journals/dcg/SilvaMV11 and
+    \cite DBLP:journals/corr/abs-1208-5018 and the Compressed Annotation Matrix implementation of
+    \cite DBLP:conf/esa/BoissonnatDM13 .<br>
+    <b>User manual:</b> \ref persistent_cohomology - <b>Reference manual:</b> Gudhi::persistent_cohomology::Persistent_cohomology
+    </td>
+ </tr>
+</table>
 */
 
 /*! \page installation Gudhi installation
+ *  \tableofcontents
  * As Gudhi is a header only library, there is no need to install the library.
  * 
  * Examples of Gudhi headers inclusion can be found in \ref demos.
  * 
  * \section compiling Compiling
  * The library uses c++11 and requires <a target="_blank" href="http://www.boost.org/">Boost</a> with version 1.48.0 or
- * more recent. It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2013.
+ * more recent. It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2015.
  * 
+ * \subsection demos Demos and examples
+ * To build the demos and examples, run the following commands in a terminal:
+\verbatim  cd /path-to-gudhi/
+mkdir build
+cd build/
+cmake ..
+make \endverbatim
+ * A list of examples is available <a href="examples.html">here</a>.
+ * 
+ * \subsection testsuites Test suites
+ * To test your build, run the following command in a terminal:
+ * \verbatim  make test \endverbatim
+ * 
+ * \section optionallibrary Optional third-party library
  * \subsection gmp GMP:
  * The multi-field persistent homology algorithm requires GMP which is a free library for arbitrary-precision
  * arithmetic, operating on signed integers, rational numbers, and floating point numbers.
  * 
  * The following example requires the <a target="_blank" href="http://gmplib.org/">GNU Multiple Precision Arithmetic
  * Library</a> (GMP) and will not be built if GMP is not installed:
- * \li Persistent_cohomology/rips_multifield_persistence
+ * \li <a href="_persistent_cohomology_2performance_rips_persistence_8cpp-example.html">
+ * Persistent_cohomology/performance_rips_persistence.cpp</a>
+ * \li <a href="_persistent_cohomology_2rips_multifield_persistence_8cpp-example.html">
+ * Persistent_cohomology/rips_multifield_persistence.cpp</a>
  *
  * Having GMP version 4.2 or higher installed is recommended.
  * 
  * \subsection cgal CGAL:
- * CGAL is a C++ library which provides easy access to efficient and reliable geometric algorithms.
- * 
- * The following examples require the <a target="_blank" href="http://www.cgal.org/">Computational Geometry Algorithms
- * Library</a> (CGAL) and will not be built if CGAL is not installed:
- * \li GudhUI
- * \li Persistent_cohomology/alpha_shapes_persistence
- * \li Simplex_tree/simplex_tree_from_alpha_shapes_3
+ * The \ref alpha_complex data structure and few examples requires CGAL, which is a C++ library which provides easy
+ * access to efficient and reliable geometric algorithms.
  * 
  * Having CGAL version 4.4 or higher installed is recommended. The procedure to install this library according to
  * your operating system is detailed here http://doc.cgal.org/latest/Manual/installation.html
  * 
- * \subsection demos Demos and examples
- * To build the demos and libraries, run the following commands in a terminal:
-\verbatim  cd /path-to-gudhi/
-mkdir build
-cd build/
-cmake ..
-make \endverbatim
+ * The following examples require the <a target="_blank" href="http://www.cgal.org/">Computational Geometry Algorithms
+ * Library</a> (CGAL \cite cgal:eb-15b) and will not be built if CGAL is not installed:
+ * \li <a href="_persistent_cohomology_2alpha_complex_3d_persistence_8cpp-example.html">
+ * Persistent_cohomology/alpha_complex_3d_persistence.cpp</a>
+ * \li <a href="_simplex_tree_2simplex_tree_from_alpha_shapes_3_8cpp-example.html">
+ * Simplex_tree/simplex_tree_from_alpha_shapes_3.cpp</a>
  * 
- * \subsection testsuites Test suites
- * To test your build, run the following command in a terminal:
- * \verbatim  make test \endverbatim
+ * The following example requires CGAL version &ge; 4.6:
+ * \li <a href="_witness_complex_2witness_complex_sphere_8cpp-example.html">
+ * Witness_complex/witness_complex_sphere.cpp</a>
+ * 
+ * The following example requires CGAL version &ge; 4.7:
+ * \li <a href="_alpha_complex_2_alpha_complex_from_off_8cpp-example.html">
+ * Alpha_complex/Alpha_complex_from_off.cpp</a>
+ * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html">
+ * Alpha_complex/Alpha_complex_from_points.cpp</a>
+ * \li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html">
+ * Persistent_cohomology/alpha_complex_persistence.cpp</a>
+ * \li <a href="_persistent_cohomology_2periodic_alpha_complex_3d_persistence_8cpp-example.html">
+ * Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp</a>
+ * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html">
+ * Persistent_cohomology/custom_persistence_sort.cpp</a>
+ * 
+ * \subsection eigen3 Eigen3:
+ * The \ref alpha_complex data structure and few examples requires
+ * <a target="_blank" href="http://eigen.tuxfamily.org/">Eigen3</a> is a C++ template library for linear algebra:
+ * matrices, vectors, numerical solvers, and related algorithms.
+ * 
+ * The following example requires the <a target="_blank" href="http://eigen.tuxfamily.org/">Eigen3</a> and will not be
+ * built if Eigen3 is not installed:
+ * \li <a href="_alpha_complex_2_alpha_complex_from_off_8cpp-example.html">
+ * Alpha_complex/Alpha_complex_from_off.cpp</a> (requires also Eigen3)
+ * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html">
+ * Alpha_complex/Alpha_complex_from_points.cpp</a> (requires also Eigen3)
+ * \li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html">
+ * Persistent_cohomology/alpha_complex_persistence.cpp</a>
+ * \li <a href="_persistent_cohomology_2periodic_alpha_complex_3d_persistence_8cpp-example.html">
+ * Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp</a>
+ * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html">
+ * Persistent_cohomology/custom_persistence_sort.cpp</a>
+ * 
+ * \subsection tbb Threading Building Blocks:
+ * <a target="_blank" href="https://www.threadingbuildingblocks.org/">Intel&reg; TBB</a> lets you easily write parallel
+ * C++ programs that take full advantage of multicore performance, that are portable and composable, and that have
+ * future-proof scalability.
+ * 
+ * Having Intel&reg; TBB installed is recommended to parallelize and accelerate some GUDHI computations.
+ * 
+ * The following examples are using Intel&reg; TBB if installed:
+ * \li <a href="_alpha_complex_2_alpha_complex_from_off_8cpp-example.html">
+ * Alpha_complex/Alpha_complex_from_off.cpp</a>
+ * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html">
+ * Alpha_complex/Alpha_complex_from_points.cpp</a>
+ * \li <a href="_bitmap_cubical_complex_2_bitmap_cubical_complex_8cpp-example.html">
+ * Bitmap_cubical_complex/Bitmap_cubical_complex.cpp</a>
+ * \li <a href="_bitmap_cubical_complex_2_bitmap_cubical_complex_periodic_boundary_conditions_8cpp-example.html">
+ * Bitmap_cubical_complex/Bitmap_cubical_complex_periodic_boundary_conditions.cpp</a>
+ * \li <a href="_bitmap_cubical_complex_2_random_bitmap_cubical_complex_8cpp-example.html">
+ * Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp</a>
+ * \li <a href="_persistent_cohomology_2alpha_complex_3d_persistence_8cpp-example.html">
+ * Persistent_cohomology/alpha_complex_3d_persistence.cpp</a>
+ * \li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html">
+ * Persistent_cohomology/alpha_complex_persistence.cpp</a>
+ * \li <a href="_simplex_tree_2simple_simplex_tree_8cpp-example.html">
+ * Simplex_tree/simple_simplex_tree.cpp</a>
+ * \li <a href="_simplex_tree_2simplex_tree_from_alpha_shapes_3_8cpp-example.html">
+ * Simplex_tree/simplex_tree_from_alpha_shapes_3.cpp</a>
+ * \li <a href="_simplex_tree_2simplex_tree_from_cliques_of_graph_8cpp-example.html">
+ * Simplex_tree/simplex_tree_from_cliques_of_graph.cpp</a>
+ * \li <a href="_persistent_cohomology_2alpha_complex_3d_persistence_8cpp-example.html">
+ * Persistent_cohomology/alpha_complex_3d_persistence.cpp</a>
+ * \li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html">
+ * Persistent_cohomology/alpha_complex_persistence.cpp</a>
+ * \li <a href="_persistent_cohomology_2rips_persistence_via_boundary_matrix_8cpp-example.html">
+ * Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp</a>
+ * \li <a href="_persistent_cohomology_2performance_rips_persistence_8cpp-example.html">
+ * Persistent_cohomology/performance_rips_persistence.cpp</a>
+ * \li <a href="_persistent_cohomology_2persistence_from_file_8cpp-example.html">
+ * Persistent_cohomology/persistence_from_file.cpp</a>
+ * \li <a href="_persistent_cohomology_2persistence_from_simple_simplex_tree_8cpp-example.html">
+ * Persistent_cohomology/persistence_from_simple_simplex_tree.cpp</a>
+ * \li <a href="_persistent_cohomology_2plain_homology_8cpp-example.html">
+ * Persistent_cohomology/plain_homology.cpp</a>
+ * \li <a href="_persistent_cohomology_2rips_multifield_persistence_8cpp-example.html">
+ * Persistent_cohomology/rips_multifield_persistence.cpp</a>
+ * \li <a href="_persistent_cohomology_2rips_persistence_8cpp-example.html">
+ * Persistent_cohomology/rips_persistence.cpp</a>
+ * \li <a href="_persistent_cohomology_2periodic_alpha_complex_3d_persistence_8cpp-example.html">
+ * Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp</a>
+ * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html">
+ * Persistent_cohomology/custom_persistence_sort.cpp</a>
  * 
  * \section Contributions Bug reports and contributions
  * Please help us improving the quality of the GUDHI library. You may report bugs or suggestions to:
@@ -91,17 +297,6 @@ make \endverbatim
  * 
 */
 
-/*! \page Upcoming Upcoming
- *
- * The library is under active development. New packages to be released next include:
- * \li Alpha complex.
- * \li Bottleneck distance.
- * \li Zig zag persistence.
- * \li Witness complex.
- * \li Tangential complex.
- * \li Clustering.
-*/
-
 /*! \page Citation Acknowledging the GUDHI library
  * We kindly ask users to cite the GUDHI library as appropriately as possible in their papers, and to mention the use
  * of the GUDHI library on the web pages of their projects using GUDHI and provide us with links to these web pages.
@@ -113,3 +308,36 @@ make \endverbatim
  * \verbinclude  biblio/how_to_cite_gudhi.bib
 */
 
+// List of Gudhi examples - Doxygen needs at least a file tag to analyse comments
+/*! @file Examples
+ * @example Alpha_complex/Alpha_complex_from_off.cpp
+ * @example Alpha_complex/Alpha_complex_from_points.cpp
+ * @example Bitmap_cubical_complex/Bitmap_cubical_complex.cpp
+ * @example Bitmap_cubical_complex/Bitmap_cubical_complex_periodic_boundary_conditions.cpp
+ * @example Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp
+ * @example common/example_CGAL_3D_points_off_reader.cpp
+ * @example common/example_CGAL_points_off_reader.cpp
+ * @example Contraction/Garland_heckbert.cpp
+ * @example Contraction/Rips_contraction.cpp
+ * @example Persistent_cohomology/alpha_complex_3d_persistence.cpp
+ * @example Persistent_cohomology/alpha_complex_persistence.cpp
+ * @example Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp
+ * @example Persistent_cohomology/performance_rips_persistence.cpp
+ * @example Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp
+ * @example Persistent_cohomology/persistence_from_file.cpp
+ * @example Persistent_cohomology/persistence_from_simple_simplex_tree.cpp
+ * @example Persistent_cohomology/plain_homology.cpp
+ * @example Persistent_cohomology/rips_multifield_persistence.cpp
+ * @example Persistent_cohomology/rips_persistence.cpp
+ * @example Persistent_cohomology/custom_persistence_sort.cpp
+ * @example Simplex_tree/mini_simplex_tree.cpp
+ * @example Simplex_tree/simple_simplex_tree.cpp
+ * @example Simplex_tree/simplex_tree_from_alpha_shapes_3.cpp
+ * @example Simplex_tree/simplex_tree_from_cliques_of_graph.cpp
+ * @example Skeleton_blocker/Skeleton_blocker_from_simplices.cpp
+ * @example Skeleton_blocker/Skeleton_blocker_iteration.cpp
+ * @example Skeleton_blocker/Skeleton_blocker_link.cpp
+ * @example Witness_complex/witness_complex_from_file.cpp
+ * @example Witness_complex/witness_complex_sphere.cpp
+ */
+
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+	color: #ffffff;
+	margin-bottom: 3px;
+	margin-top: 3px;
+	padding: 0.2em;
+	border: solid thin #333;
+	border-radius: 0.5em;
+	-webkit-border-radius: .5em;
+	-moz-border-radius: .5em;
+	box-shadow: 2px 2px 3px #999;
+	-webkit-box-shadow: 2px 2px 3px #999;
+	-moz-box-shadow: rgba(0, 0, 0, 0.15) 2px 2px 2px;
+	background-image: -webkit-gradient(linear, left top, left bottom, from(#eee), to(#000),color-stop(0.3, #444));
+	background-image: -moz-linear-gradient(center top, #eee 0%, #444 40%, #000);
+}
+
+div.groupHeader {
+	margin-left: 16px;
+	margin-top: 12px;
+	font-weight: bold;
+}
+
+div.groupText {
+	margin-left: 16px;
+	font-style: italic;
+}
+
+body {
+	background-color: white;
+	color: black;
+        margin: 0;
+}
+
+div.contents {
+	margin-top: 10px;
+	margin-left: 12px;
+	margin-right: 8px;
+}
+
+td.indexkey {
+	background-color: #EBEFF6;
+	font-weight: bold;
+	border: 1px solid #C4CFE5;
+	margin: 2px 0px 2px 0;
+	padding: 2px 10px;
+        white-space: nowrap;
+        vertical-align: top;
+}
+
+td.indexvalue {
+	background-color: #EBEFF6;
+	border: 1px solid #C4CFE5;
+	padding: 2px 10px;
+	margin: 2px 0px;
+}
+
+tr.memlist {
+	background-color: #EEF1F7;
+}
+
+p.formulaDsp {
+	text-align: center;
+}
+
+img.formulaDsp {
+	
+}
+
+img.formulaInl {
+	vertical-align: middle;
+}
+
+div.center {
+	text-align: center;
+        margin-top: 0px;
+        margin-bottom: 0px;
+        padding: 0px;
+}
+
+div.center img {
+	border: 0px;
+}
+
+address.footer {
+	text-align: right;
+	padding-right: 12px;
+}
+
+img.footer {
+	border: 0px;
+	vertical-align: middle;
+}
+
+/* @group Code Colorization */
+
+span.keyword {
+	color: #008000
+}
+
+span.keywordtype {
+	color: #604020
+}
+
+span.keywordflow {
+	color: #e08000
+}
+
+span.comment {
+	color: #800000
+}
+
+span.preprocessor {
+	color: #806020
+}
+
+span.stringliteral {
+	color: #002080
+}
+
+span.charliteral {
+	color: #008080
+}
+
+span.vhdldigit { 
+	color: #ff00ff 
+}
+
+span.vhdlchar { 
+	color: #000000 
+}
+
+span.vhdlkeyword { 
+	color: #700070 
+}
+
+span.vhdllogic { 
+	color: #ff0000 
+}
+
+blockquote {
+        background-color: #F7F8FB;
+        border-left: 2px solid #9CAFD4;
+        margin: 0 24px 0 4px;
+        padding: 0 12px 0 16px;
+}
+
+/* @end */
+
+/*
+.search {
+	color: #003399;
+	font-weight: bold;
+}
+
+form.search {
+	margin-bottom: 0px;
+	margin-top: 0px;
+}
+
+input.search {
+	font-size: 75%;
+	color: #000080;
+	font-weight: normal;
+	background-color: #e8eef2;
+}
+*/
+
+td.tiny {
+	font-size: 75%;
+}
+
+.dirtab {
+	padding: 4px;
+	border-collapse: collapse;
+	border: 1px solid #A3B4D7;
+}
+
+th.dirtab {
+	background: #EBEFF6;
+	font-weight: bold;
+}
+
+hr {
+	height: 0px;
+	border: none;
+	border-top: 1px solid #4A6AAA;
+}
+
+hr.footer {
+	height: 1px;
+}
+
+/* @group Member Descriptions */
+
+table.memberdecls {
+	border-spacing: 0px;
+	padding: 0px;
+}
+
+.memberdecls td, .fieldtable tr {
+	-webkit-transition-property: background-color, box-shadow;
+	-webkit-transition-duration: 0.5s;
+	-moz-transition-property: background-color, box-shadow;
+	-moz-transition-duration: 0.5s;
+	-ms-transition-property: background-color, box-shadow;
+	-ms-transition-duration: 0.5s;
+	-o-transition-property: background-color, box-shadow;
+	-o-transition-duration: 0.5s;
+	transition-property: background-color, box-shadow;
+	transition-duration: 0.5s;
+}
+
+.memberdecls td.glow, .fieldtable tr.glow {
+	background-color: cyan;
+	box-shadow: 0 0 15px cyan;
+}
+
+.mdescLeft, .mdescRight,
+.memItemLeft, .memItemRight,
+.memTemplItemLeft, .memTemplItemRight, .memTemplParams {
+	background-color: #F9FAFC;
+	border: none;
+	margin: 4px;
+	padding: 1px 0 0 8px;
+}
+
+.mdescLeft, .mdescRight {
+	padding: 0px 8px 4px 8px;
+	color: #555;
+}
+
+.memSeparator {
+        border-bottom: 1px solid #DEE4F0;
+        line-height: 1px;
+        margin: 0px;
+        padding: 0px;
+}
+
+.memItemLeft, .memTemplItemLeft {
+        white-space: nowrap;
+}
+
+.memItemRight {
+	width: 100%;
+}
+
+.memTemplParams {
+	color: #4665A2;
+        white-space: nowrap;
+	font-size: 80%;
+}
+
+/* @end */
+
+/* @group Member Details */
+
+/* Styles for detailed member documentation */
+
+.memtemplate {
+	font-size: 80%;
+	color: #4665A2;
+	font-weight: normal;
+	margin-left: 9px;
+}
+
+.memnav {
+	background-color: #EBEFF6;
+	border: 1px solid #A3B4D7;
+	text-align: center;
+	margin: 2px;
+	margin-right: 15px;
+	padding: 2px;
+}
+
+.mempage {
+	width: 100%;
+}
+
+.memitem {
+	padding: 0;
+	margin-bottom: 10px;
+	margin-right: 5px;
+        -webkit-transition: box-shadow 0.5s linear;
+        -moz-transition: box-shadow 0.5s linear;
+        -ms-transition: box-shadow 0.5s linear;
+        -o-transition: box-shadow 0.5s linear;
+        transition: box-shadow 0.5s linear;
+        display: table !important;
+        width: 100%;
+}
+
+.memitem.glow {
+         box-shadow: 0 0 15px cyan;
+}
+
+.memname {
+        font-weight: bold;
+        margin-left: 6px;
+}
+
+.memname td {
+	vertical-align: bottom;
+}
+
+.memproto, dl.reflist dt {
+        border-top: 1px solid #A8B8D9;
+        border-left: 1px solid #A8B8D9;
+        border-right: 1px solid #A8B8D9;
+        padding: 6px 0px 6px 0px;
+        color: #253555;
+        font-weight: bold;
+        text-shadow: 0px 1px 1px rgba(255, 255, 255, 0.9);
+        background-image:url('nav_f.png');
+        background-repeat:repeat-x;
+        background-color: #E2E8F2;
+        /* opera specific markup */
+        box-shadow: 5px 5px 5px rgba(0, 0, 0, 0.15);
+        border-top-right-radius: 4px;
+        border-top-left-radius: 4px;
+        /* firefox specific markup */
+        -moz-box-shadow: rgba(0, 0, 0, 0.15) 5px 5px 5px;
+        -moz-border-radius-topright: 4px;
+        -moz-border-radius-topleft: 4px;
+        /* webkit specific markup */
+        -webkit-box-shadow: 5px 5px 5px rgba(0, 0, 0, 0.15);
+        -webkit-border-top-right-radius: 4px;
+        -webkit-border-top-left-radius: 4px;
+
+}
+
+.memdoc, dl.reflist dd {
+        border-bottom: 1px solid #A8B8D9;      
+        border-left: 1px solid #A8B8D9;      
+        border-right: 1px solid #A8B8D9; 
+        padding: 6px 10px 2px 10px;
+        background-color: #FBFCFD;
+        border-top-width: 0;
+        background-image:url('nav_g.png');
+        background-repeat:repeat-x;
+        background-color: #FFFFFF;
+        /* opera specific markup */
+        border-bottom-left-radius: 4px;
+        border-bottom-right-radius: 4px;
+        box-shadow: 5px 5px 5px rgba(0, 0, 0, 0.15);
+        /* firefox specific markup */
+        -moz-border-radius-bottomleft: 4px;
+        -moz-border-radius-bottomright: 4px;
+        -moz-box-shadow: rgba(0, 0, 0, 0.15) 5px 5px 5px;
+        /* webkit specific markup */
+        -webkit-border-bottom-left-radius: 4px;
+        -webkit-border-bottom-right-radius: 4px;
+        -webkit-box-shadow: 5px 5px 5px rgba(0, 0, 0, 0.15);
+}
+
+dl.reflist dt {
+        padding: 5px;
+}
+
+dl.reflist dd {
+        margin: 0px 0px 10px 0px;
+        padding: 5px;
+}
+
+.paramkey {
+	text-align: right;
+}
+
+.paramtype {
+	white-space: nowrap;
+}
+
+.paramname {
+	color: #602020;
+	white-space: nowrap;
+}
+.paramname em {
+	font-style: normal;
+}
+.paramname code {
+        line-height: 14px;
+}
+
+.params, .retval, .exception, .tparams {
+        margin-left: 0px;
+        padding-left: 0px;
+}       
+
+.params .paramname, .retval .paramname {
+        font-weight: bold;
+        vertical-align: top;
+}
+        
+.params .paramtype {
+        font-style: italic;
+        vertical-align: top;
+}       
+        
+.params .paramdir {
+        font-family: "courier new",courier,monospace;
+        vertical-align: top;
+}
+
+table.mlabels {
+	border-spacing: 0px;
+}
+
+td.mlabels-left {
+	width: 100%;
+	padding: 0px;
+}
+
+td.mlabels-right {
+	vertical-align: bottom;
+	padding: 0px;
+	white-space: nowrap;
+}
+
+span.mlabels {
+        margin-left: 8px;
+}
+
+span.mlabel {
+        background-color: #728DC1;
+        border-top:1px solid #5373B4;
+        border-left:1px solid #5373B4;
+        border-right:1px solid #C4CFE5;
+        border-bottom:1px solid #C4CFE5;
+	text-shadow: none;
+	color: white;
+	margin-right: 4px;
+	padding: 2px 3px;
+	border-radius: 3px;
+	font-size: 7pt;
+	white-space: nowrap;
+	vertical-align: middle;
+}
+
+
+
+/* @end */
+
+/* these are for tree view when not used as main index */
+
+div.directory {
+        margin: 10px 0px;
+        border-top: 1px solid #A8B8D9;
+        border-bottom: 1px solid #A8B8D9;
+        width: 100%;
+}
+
+.directory table {
+        border-collapse:collapse;
+}
+
+.directory td {
+        margin: 0px;
+        padding: 0px;
+	vertical-align: top;
+}
+
+.directory td.entry {
+        white-space: nowrap;
+        padding-right: 6px;
+	padding-top: 3px;
+}
+
+.directory td.entry a {
+        outline:none;
+}
+
+.directory td.entry a img {
+        border: none;
+}
+
+.directory td.desc {
+        width: 100%;
+        padding-left: 6px;
+	padding-right: 6px;
+	padding-top: 3px;
+	border-left: 1px solid rgba(0,0,0,0.05);
+}
+
+.directory tr.even {
+	padding-left: 6px;
+	background-color: #F7F8FB;
+}
+
+.directory img {
+	vertical-align: -30%;
+}
+
+.directory .levels {
+        white-space: nowrap;
+        width: 100%;
+        text-align: right;
+        font-size: 9pt;
+}
+
+.directory .levels span {
+        cursor: pointer;
+        padding-left: 2px;
+        padding-right: 2px;
+	color: #3D578C;
+}
+
+div.dynheader {
+        margin-top: 8px;
+	-webkit-touch-callout: none;
+	-webkit-user-select: none;
+	-khtml-user-select: none;
+	-moz-user-select: none;
+	-ms-user-select: none;
+	user-select: none;
+}
+
+address {
+	font-style: normal;
+	color: #2A3D61;
+}
+
+table.doxtable {
+	border-collapse:collapse;
+        margin-top: 4px;
+        margin-bottom: 4px;
+}
+
+table.doxtable td, table.doxtable th {
+	border: 1px solid #2D4068;
+	padding: 3px 7px 2px;
+}
+
+table.doxtable th {
+	background-color: #374F7F;
+	color: #FFFFFF;
+	font-size: 110%;
+	padding-bottom: 4px;
+	padding-top: 5px;
+}
+
+table.fieldtable {
+        /*width: 100%;*/
+        margin-bottom: 10px;
+        border: 1px solid #A8B8D9;
+        border-spacing: 0px;
+        -moz-border-radius: 4px;
+        -webkit-border-radius: 4px;
+        border-radius: 4px;
+        -moz-box-shadow: rgba(0, 0, 0, 0.15) 2px 2px 2px;
+        -webkit-box-shadow: 2px 2px 2px rgba(0, 0, 0, 0.15);
+        box-shadow: 2px 2px 2px rgba(0, 0, 0, 0.15);
+}
+
+.fieldtable td, .fieldtable th {
+        padding: 3px 7px 2px;
+}
+
+.fieldtable td.fieldtype, .fieldtable td.fieldname {
+        white-space: nowrap;
+        border-right: 1px solid #A8B8D9;
+        border-bottom: 1px solid #A8B8D9;
+        vertical-align: top;
+}
+
+.fieldtable td.fieldname {
+        padding-top: 3px;
+}
+
+.fieldtable td.fielddoc {
+        border-bottom: 1px solid #A8B8D9;
+        /*width: 100%;*/
+}
+
+.fieldtable td.fielddoc p:first-child {
+        margin-top: 0px;
+}       
+        
+.fieldtable td.fielddoc p:last-child {
+        margin-bottom: 2px;
+}
+
+.fieldtable tr:last-child td {
+        border-bottom: none;
+}
+
+.fieldtable th {
+        background-image:url('nav_f.png');
+        background-repeat:repeat-x;
+        background-color: #E2E8F2;
+        font-size: 90%;
+        color: #253555;
+        padding-bottom: 4px;
+        padding-top: 5px;
+        text-align:left;
+        -moz-border-radius-topleft: 4px;
+        -moz-border-radius-topright: 4px;
+        -webkit-border-top-left-radius: 4px;
+        -webkit-border-top-right-radius: 4px;
+        border-top-left-radius: 4px;
+        border-top-right-radius: 4px;
+        border-bottom: 1px solid #A8B8D9;
+}
+
+
+.tabsearch {
+	top: 0px;
+	left: 10px;
+	height: 36px;
+	background-image: url('tab_b.png');
+	z-index: 101;
+	overflow: hidden;
+	font-size: 13px;
+}
+
+.navpath ul
+{
+	font-size: 11px;
+	background-image:url('tab_b.png');
+	background-repeat:repeat-x;
+	background-position: 0 -5px;
+	height:30px;
+	line-height:30px;
+	color:#8AA0CC;
+	border:solid 1px #C2CDE4;
+	overflow:hidden;
+	margin:0px;
+	padding:0px;
+}
+
+.navpath li
+{
+	list-style-type:none;
+	float:left;
+	padding-left:10px;
+	padding-right:15px;
+	background-image:url('bc_s.png');
+	background-repeat:no-repeat;
+	background-position:right;
+	color:#364D7C;
+}
+
+.navpath li.navelem a
+{
+	height:32px;
+	display:block;
+	text-decoration: none;
+	outline: none;
+	color: #283A5D;
+	font-family: 'Lucida Grande',Geneva,Helvetica,Arial,sans-serif;
+	text-shadow: 0px 1px 1px rgba(255, 255, 255, 0.9);
+	text-decoration: none;        
+}
+
+.navpath li.navelem a:hover
+{
+	color:#6884BD;
+}
+
+.navpath li.footer
+{
+        list-style-type:none;
+        float:right;
+        padding-left:10px;
+        padding-right:15px;
+        background-image:none;
+        background-repeat:no-repeat;
+        background-position:right;
+        color:#364D7C;
+        font-size: 8pt;
+}
+
+
+div.summary
+{
+	float: right;
+	font-size: 8pt;
+	padding-right: 5px;
+	width: 50%;
+	text-align: right;
+}       
+
+div.summary a
+{
+	white-space: nowrap;
+}
+
+div.ingroups
+{
+	font-size: 8pt;
+	width: 50%;
+	text-align: left;
+}
+
+div.ingroups a
+{
+	white-space: nowrap;
+}
+
+div.header
+{
+        background-image:url('nav_h.png');
+        background-repeat:repeat-x;
+	background-color: #F9FAFC;
+	margin:  0px;
+	border-bottom: 1px solid #C4CFE5;
+}
+
+div.headertitle
+{
+	padding: 5px 5px 5px 10px;
+}
+
+dl
+{
+        padding: 0 0 0 10px;
+}
+
+/* dl.note, dl.warning, dl.attention, dl.pre, dl.post, dl.invariant, dl.deprecated, dl.todo, dl.test, dl.bug */
+dl.section
+{
+	margin-left: 0px;
+	padding-left: 0px;
+}
+
+dl.note
+{
+        margin-left:-7px;
+        padding-left: 3px;
+        border-left:4px solid;
+        border-color: #D0C000;
+}
+
+dl.warning, dl.attention
+{
+        margin-left:-7px;
+        padding-left: 3px;
+        border-left:4px solid;
+        border-color: #FF0000;
+}
+
+dl.pre, dl.post, dl.invariant
+{
+        margin-left:-7px;
+        padding-left: 3px;
+        border-left:4px solid;
+        border-color: #00D000;
+}
+
+dl.deprecated
+{
+        margin-left:-7px;
+        padding-left: 3px;
+        border-left:4px solid;
+        border-color: #505050;
+}
+
+dl.todo
+{
+        margin-left:-7px;
+        padding-left: 3px;
+        border-left:4px solid;
+        border-color: #00C0E0;
+}
+
+dl.test
+{
+        margin-left:-7px;
+        padding-left: 3px;
+        border-left:4px solid;
+        border-color: #3030E0;
+}
+
+dl.bug
+{
+        margin-left:-7px;
+        padding-left: 3px;
+        border-left:4px solid;
+        border-color: #C08050;
+}
+
+dl.section dd {
+	margin-bottom: 6px;
+}
+
+
+#projectlogo
+{
+	text-align: center;
+	vertical-align: bottom;
+	border-collapse: separate;
+}
+ 
+#projectlogo img
+{ 
+	border: 0px none;
+}
+ 
+#projectname
+{
+	border: 0px none;
+	font: 300% Tahoma, Arial,sans-serif;
+	margin: 0px;
+	padding: 2px 0px;
+}
+    
+#projectbrief
+{
+	font: 60% Tahoma, Arial,sans-serif;
+	margin: 0px;
+	padding: 0px;
+}
+
+#projectnumber
+{
+	font: 80% Tahoma, Arial,sans-serif;
+	margin: 0px;
+	padding: 0px;
+}
+
+#titlearea
+{
+	padding: 0px;
+	margin: 0px;
+	width: 100%;
+	border-bottom: 1px solid #5373B4;
+}
+
+.image
+{
+        text-align: center;
+}
+
+.dotgraph
+{
+        text-align: center;
+}
+
+.mscgraph
+{
+        text-align: center;
+}
+
+.diagraph
+{
+        text-align: center;
+}
+
+.caption
+{
+	font-weight: bold;
+}
+
+div.zoom
+{
+	border: 1px solid #90A5CE;
+}
+
+dl.citelist {
+        margin-bottom:50px;
+}
+
+dl.citelist dt {
+        color:#334975;
+        float:left;
+        font-weight:bold;
+        margin-right:10px;
+        padding:5px;
+}
+
+dl.citelist dd {
+        margin:2px 0;
+        padding:5px 0;
+}
+
+div.toc {
+        padding: 14px 25px;
+        background-color: #F4F6FA;
+        border: 1px solid #D8DFEE;
+        border-radius: 7px 7px 7px 7px;
+        float: right;
+        height: auto;
+        margin: 0 20px 10px 10px;
+        width: 200px;
+}
+
+div.toc li {
+        background: url("bdwn.png") no-repeat scroll 0 5px transparent;
+        font: 10px/1.2 Verdana,DejaVu Sans,Geneva,sans-serif;
+        margin-top: 5px;
+        padding-left: 10px;
+        padding-top: 2px;
+}
+
+div.toc h3 {
+        font: bold 12px/1.2 Arial,FreeSans,sans-serif;
+	color: #4665A2;
+        border-bottom: 0 none;
+        margin: 0;
+}
+
+div.toc ul {
+        list-style: none outside none;
+        border: medium none;
+        padding: 0px;
+}       
+
+div.toc li.level1 {
+        margin-left: 0px;
+}
+
+div.toc li.level2 {
+        margin-left: 15px;
+}
+
+div.toc li.level3 {
+        margin-left: 30px;
+}
+
+div.toc li.level4 {
+        margin-left: 45px;
+}
+
+.inherit_header {
+        font-weight: bold;
+        color: gray;
+        cursor: pointer;
+	-webkit-touch-callout: none;
+	-webkit-user-select: none;
+	-khtml-user-select: none;
+	-moz-user-select: none;
+	-ms-user-select: none;
+	user-select: none;
+}
+
+.inherit_header td {
+        padding: 6px 0px 2px 5px;
+}
+
+.inherit {
+        display: none;
+}
+
+tr.heading h2 {
+        margin-top: 12px;
+        margin-bottom: 4px;
+}
+
+/* tooltip related style info */
+
+.ttc {
+        position: absolute;
+        display: none;
+}
+
+#powerTip {
+	cursor: default;
+	white-space: nowrap;
+	background-color: white;
+	border: 1px solid gray;
+	border-radius: 4px 4px 4px 4px;
+	box-shadow: 1px 1px 7px gray;
+	display: none;
+	font-size: smaller;
+	max-width: 80%;
+	opacity: 0.9;
+	padding: 1ex 1em 1em;
+	position: absolute;
+	z-index: 2147483647;
+}
+
+#powerTip div.ttdoc {
+        color: grey;
+	font-style: italic;
+}
+
+#powerTip div.ttname a {
+        font-weight: bold;
+}
+
+#powerTip div.ttname {
+        font-weight: bold;
+}
+
+#powerTip div.ttdeci {
+        color: #006318;
+}
+
+#powerTip div {
+        margin: 0px;
+        padding: 0px;
+        font: 12px/16px Roboto,sans-serif;
+}
+
+#powerTip:before, #powerTip:after {
+	content: "";
+	position: absolute;
+	margin: 0px;
+}
+
+#powerTip.n:after,  #powerTip.n:before,
+#powerTip.s:after,  #powerTip.s:before,
+#powerTip.w:after,  #powerTip.w:before,
+#powerTip.e:after,  #powerTip.e:before,
+#powerTip.ne:after, #powerTip.ne:before,
+#powerTip.se:after, #powerTip.se:before,
+#powerTip.nw:after, #powerTip.nw:before,
+#powerTip.sw:after, #powerTip.sw:before {
+	border: solid transparent;
+	content: " ";
+	height: 0;
+	width: 0;
+	position: absolute;
+}
+
+#powerTip.n:after,  #powerTip.s:after,
+#powerTip.w:after,  #powerTip.e:after,
+#powerTip.nw:after, #powerTip.ne:after,
+#powerTip.sw:after, #powerTip.se:after {
+	border-color: rgba(255, 255, 255, 0);
+}
+
+#powerTip.n:before,  #powerTip.s:before,
+#powerTip.w:before,  #powerTip.e:before,
+#powerTip.nw:before, #powerTip.ne:before,
+#powerTip.sw:before, #powerTip.se:before {
+	border-color: rgba(128, 128, 128, 0);
+}
+
+#powerTip.n:after,  #powerTip.n:before,
+#powerTip.ne:after, #powerTip.ne:before,
+#powerTip.nw:after, #powerTip.nw:before {
+	top: 100%;
+}
+
+#powerTip.n:after, #powerTip.ne:after, #powerTip.nw:after {
+	border-top-color: #ffffff;
+	border-width: 10px;
+	margin: 0px -10px;
+}
+#powerTip.n:before {
+	border-top-color: #808080;
+	border-width: 11px;
+	margin: 0px -11px;
+}
+#powerTip.n:after, #powerTip.n:before {
+	left: 50%;
+}
+
+#powerTip.nw:after, #powerTip.nw:before {
+	right: 14px;
+}
+
+#powerTip.ne:after, #powerTip.ne:before {
+	left: 14px;
+}
+
+#powerTip.s:after,  #powerTip.s:before,
+#powerTip.se:after, #powerTip.se:before,
+#powerTip.sw:after, #powerTip.sw:before {
+	bottom: 100%;
+}
+
+#powerTip.s:after, #powerTip.se:after, #powerTip.sw:after {
+	border-bottom-color: #ffffff;
+	border-width: 10px;
+	margin: 0px -10px;
+}
+
+#powerTip.s:before, #powerTip.se:before, #powerTip.sw:before {
+	border-bottom-color: #808080;
+	border-width: 11px;
+	margin: 0px -11px;
+}
+
+#powerTip.s:after, #powerTip.s:before {
+	left: 50%;
+}
+
+#powerTip.sw:after, #powerTip.sw:before {
+	right: 14px;
+}
+
+#powerTip.se:after, #powerTip.se:before {
+	left: 14px;
+}
+
+#powerTip.e:after, #powerTip.e:before {
+	left: 100%;
+}
+#powerTip.e:after {
+	border-left-color: #ffffff;
+	border-width: 10px;
+	top: 50%;
+	margin-top: -10px;
+}
+#powerTip.e:before {
+	border-left-color: #808080;
+	border-width: 11px;
+	top: 50%;
+	margin-top: -11px;
+}
+
+#powerTip.w:after, #powerTip.w:before {
+	right: 100%;
+}
+#powerTip.w:after {
+	border-right-color: #ffffff;
+	border-width: 10px;
+	top: 50%;
+	margin-top: -10px;
+}
+#powerTip.w:before {
+	border-right-color: #808080;
+	border-width: 11px;
+	top: 50%;
+	margin-top: -11px;
+}
+
+@media print
+{
+  #top { display: none; }
+  #side-nav { display: none; }
+  #nav-path { display: none; }
+  body { overflow:visible; }
+  h1, h2, h3, h4, h5, h6 { page-break-after: avoid; }
+  .summary { display: none; }
+  .memitem { page-break-inside: avoid; }
+  #doc-content
+  {
+    margin-left:0 !important;
+    height:auto !important;
+    width:auto !important;
+    overflow:inherit;
+    display:inline;
+  }
+}
+
diff --git a/src/common/example/CMakeLists.txt b/src/common/example/CMakeLists.txt
new file mode 100644
index 00000000..b0c6d69a
--- /dev/null
+++ b/src/common/example/CMakeLists.txt
@@ -0,0 +1,21 @@
+cmake_minimum_required(VERSION 2.6)
+project(Common_examples)
+
+add_executable ( vector_double_off_reader example_vector_double_points_off_reader.cpp )
+target_link_libraries(vector_double_off_reader  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+add_test(vector_double_off_reader ${CMAKE_CURRENT_BINARY_DIR}/vector_double_off_reader ${CMAKE_SOURCE_DIR}/data/points/SO3_10000.off)
+
+if(CGAL_FOUND)
+  add_executable ( cgal_3D_off_reader example_CGAL_3D_points_off_reader.cpp )
+  target_link_libraries(cgal_3D_off_reader  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+  add_test(cgal_3D_off_reader ${CMAKE_CURRENT_BINARY_DIR}/cgal_3D_off_reader ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
+
+  # need CGAL 4.7
+  if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
+    if (EIGEN3_FOUND)
+      add_executable ( cgal_off_reader example_CGAL_points_off_reader.cpp )
+      target_link_libraries(cgal_off_reader  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+      add_test(cgal_off_reader ${CMAKE_CURRENT_BINARY_DIR}/cgal_off_reader ${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off)
+    endif(EIGEN3_FOUND)
+  endif (NOT CGAL_VERSION VERSION_LESS 4.7.0)
+endif()
diff --git a/src/common/example/cgal3Doffreader_result.txt b/src/common/example/cgal3Doffreader_result.txt
new file mode 100644
index 00000000..f992c8e3
--- /dev/null
+++ b/src/common/example/cgal3Doffreader_result.txt
@@ -0,0 +1,8 @@
+Point[1] = (0.959535, -0.418347, 0.302237)
+Point[2] = (2.16795, 1.85348, -0.52312)
+Point[3] = (-2.38753, -1.50911, -0.565889)
+Point[4] = (-2.70428, -1.25688, 0.188394)
+Point[5] = (-1.22932, -1.64337, -0.998632)
+...
+Point[300] = (-0.56244, 2.6018, -0.749591)
+
diff --git a/src/common/example/cgaloffreader_result.txt b/src/common/example/cgaloffreader_result.txt
new file mode 100644
index 00000000..1deb8dbd
--- /dev/null
+++ b/src/common/example/cgaloffreader_result.txt
@@ -0,0 +1,7 @@
+Point[0] = 1 1 
+Point[1] = 7 0 
+Point[2] = 4 6 
+Point[3] = 9 6 
+Point[4] = 0 14 
+Point[5] = 2 19 
+Point[6] = 9 17 
diff --git a/src/common/example/example_CGAL_3D_points_off_reader.cpp b/src/common/example/example_CGAL_3D_points_off_reader.cpp
new file mode 100644
index 00000000..d48bb17d
--- /dev/null
+++ b/src/common/example/example_CGAL_3D_points_off_reader.cpp
@@ -0,0 +1,41 @@
+#include <gudhi/Points_3D_off_io.h>
+
+#include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
+
+#include <iostream>
+#include <string>
+#include <vector>
+
+using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel;
+using Point_3 = Kernel::Point_3;
+
+void usage(char * const progName) {
+  std::cerr << "Usage: " << progName << " inputFile.off" << std::endl;
+  exit(-1);
+}
+
+int main(int argc, char **argv) {
+  if (argc != 2) {
+    std::cerr << "Error: Number of arguments (" << argc << ") is not correct" << std::endl;
+    usage(argv[0]);
+  }
+
+  std::string offInputFile(argv[1]);
+  // Read the OFF file (input file name given as parameter) and triangulate points
+  Gudhi::Points_3D_off_reader<Point_3> off_reader(offInputFile);
+  // Check the read operation was correct
+  if (!off_reader.is_valid()) {
+    std::cerr << "Unable to read file " << offInputFile << std::endl;
+    usage(argv[0]);
+  }
+
+  // Retrieve the triangulation
+  std::vector<Point_3> point_cloud = off_reader.get_point_cloud();
+
+  int n {0};
+  for (auto point : point_cloud) {
+    ++n;
+    std::cout << "Point[" << n << "] = (" << point[0] << ", " << point[1] << ", " << point[2] << ")\n";
+  }
+  return 0;
+}
diff --git a/src/common/example/example_CGAL_points_off_reader.cpp b/src/common/example/example_CGAL_points_off_reader.cpp
new file mode 100644
index 00000000..4522174a
--- /dev/null
+++ b/src/common/example/example_CGAL_points_off_reader.cpp
@@ -0,0 +1,46 @@
+#include <gudhi/Points_off_io.h>
+
+// For CGAL points type in dimension d
+// cf. http://doc.cgal.org/latest/Kernel_d/classCGAL_1_1Point__d.html
+#include <CGAL/Epick_d.h>
+
+#include <iostream>
+#include <string>
+#include <vector>
+
+using Kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >;
+using Point_d = Kernel::Point_d;
+
+void usage(char * const progName) {
+  std::cerr << "Usage: " << progName << " inputFile.off" << std::endl;
+  exit(-1);
+}
+
+int main(int argc, char **argv) {
+  if (argc != 2) {
+    std::cerr << "Error: Number of arguments (" << argc << ") is not correct" << std::endl;
+    usage(argv[0]);
+  }
+
+  std::string offInputFile(argv[1]);
+  // Read the OFF file (input file name given as parameter) and triangulate points
+  Gudhi::Points_off_reader<Point_d> off_reader(offInputFile);
+  // Check the read operation was correct
+  if (!off_reader.is_valid()) {
+    std::cerr << "Unable to read file " << offInputFile << std::endl;
+    usage(argv[0]);
+  }
+
+  // Retrieve the triangulation
+  std::vector<Point_d> point_cloud = off_reader.get_point_cloud();
+
+  int n {0};
+  for (auto point : point_cloud) {
+    std::cout << "Point[" << n << "] = ";
+    for (std::size_t i {0}; i < point.size(); i++)
+      std::cout << point[i] << " ";
+    std::cout << "\n";
+    ++n;
+  }
+  return 0;
+}
diff --git a/src/common/example/example_vector_double_points_off_reader.cpp b/src/common/example/example_vector_double_points_off_reader.cpp
new file mode 100644
index 00000000..8aecb26e
--- /dev/null
+++ b/src/common/example/example_vector_double_points_off_reader.cpp
@@ -0,0 +1,41 @@
+#include <gudhi/Points_off_io.h>
+
+#include <iostream>
+#include <string>
+#include <vector>
+
+using Point_d = std::vector<double>;
+
+void usage(char * const progName) {
+  std::cerr << "Usage: " << progName << " inputFile.off" << std::endl;
+  exit(-1);
+}
+
+int main(int argc, char **argv) {
+  if (argc != 2) {
+    std::cerr << "Error: Number of arguments (" << argc << ") is not correct" << std::endl;
+    usage(argv[0]);
+  }
+
+  std::string offInputFile(argv[1]);
+  // Read the OFF file (input file name given as parameter) and triangulate points
+  Gudhi::Points_off_reader<Point_d> off_reader(offInputFile);
+  // Check the read operation was correct
+  if (!off_reader.is_valid()) {
+    std::cerr << "Unable to read file " << offInputFile << std::endl;
+    usage(argv[0]);
+  }
+
+  // Retrieve the triangulation
+  std::vector<Point_d> point_cloud = off_reader.get_point_cloud();
+
+  int n {0};
+  for (auto point : point_cloud) {
+    std::cout << "Point[" << n << "] = ";
+    for (std::size_t i {0}; i < point.size(); i++)
+      std::cout << point[i] << " ";
+    std::cout << "\n";
+    ++n;
+  }
+  return 0;
+}
diff --git a/src/common/include/gudhi/Utils.h b/src/common/include/gudhi/Debug_utils.h
index 43916f11..7573a9db 100644
--- a/src/common/include/gudhi/Utils.h
+++ b/src/common/include/gudhi/Debug_utils.h
@@ -19,28 +19,37 @@
  *    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 UTILS_H_
-#define UTILS_H_
+#ifndef DEBUG_UTILS_H_
+#define DEBUG_UTILS_H_
 
+#include <iostream>
+
+#ifndef NDEBUG
+  // GUDHI_DEBUG is the Gudhi official flag for debug mode.
+  #define GUDHI_DEBUG
+#endif
+
+// GUDHI_CHECK throw an exception if expression is false in debug mode, but does nothing in release mode
+// Could assert in release mode, but cmake sets NDEBUG (for "NO DEBUG") in this mode, means assert does nothing.
+#ifdef GUDHI_DEBUG
+  #define GUDHI_CHECK(expression, excpt) if ((expression) == 0) throw excpt
+#else
+  #define GUDHI_CHECK(expression, excpt) (void) 0
+#endif
 
 #define PRINT(a) std::cerr << #a << ": " << (a) << " (DISP)" << std::endl
 
 // #define DBG_VERBOSE
 #ifdef DBG_VERBOSE
-#define DBG(a) std::cerr << "DBG: " << (a) << std::endl
-#define DBGMSG(a, b) std::cerr << "DBG: " << a << b << std::endl
-#define DBGVALUE(a) std::cerr << "DBG: " <<  #a << ": " << a << std::endl
-#define DBGCONT(a) std::cerr << "DBG: container " << #a << " -> "; for (auto x : a) std::cerr << x << ","; std::cerr <<
-std::endl
+  #define DBG(a) std::cout << "DBG: " << (a) << std::endl
+  #define DBGMSG(a, b) std::cout << "DBG: " << a << b << std::endl
+  #define DBGVALUE(a) std::cout << "DBG: " <<  #a << ": " << a << std::endl
+  #define DBGCONT(a) std::cout << "DBG: container " << #a << " -> "; for (auto x : a) std::cout << x << ","; std::cout << std::endl
 #else
-// #define DBG(a) a
-// #define DBGMSG(a,b) b
-// #define DBGVALUE(a) a
-// #define DBGCONT(a) a
-#define DBG(a)
-#define DBGMSG(a, b)
-#define DBGVALUE(a)
-#define DBGCONT(a)
+  #define DBG(a) (void) 0
+  #define DBGMSG(a, b) (void) 0
+  #define DBGVALUE(a) (void) 0
+  #define DBGCONT(a) (void) 0
 #endif
 
-#endif  // UTILS_H_
+#endif  // DEBUG_UTILS_H_
diff --git a/src/common/include/gudhi/Off_reader.h b/src/common/include/gudhi/Off_reader.h
index 81b9e634..4fcd2af2 100644
--- a/src/common/include/gudhi/Off_reader.h
+++ b/src/common/include/gudhi/Off_reader.h
@@ -31,40 +31,35 @@
 #include <iterator>
 #include <string>
 #include <vector>
+#include <fstream>
 
 namespace Gudhi {
 
-/**
- * Read an off file and calls a visitor methods while reading it.
- * An off file must have its first/snd line in this format :
- * OFF
- * num_vert num_faces num_edges
- *
- * A noff file must have its first/snd line in this format :
- * nOFF
- * dim num_vert num_faces num_edges
- *
- * The number of edges num_edges is optional and can be left to zero.
+/** \brief OFF file reader top class visitor. 
+ * 
+ * OFF file must be conform to format described here : 
+ * http://www.geomview.org/docs/html/OFF.html
  */
 class Off_reader {
  public:
   Off_reader(std::ifstream& stream) : stream_(stream) { }
-  // Off_reader(const std::string& name):stream_(name){
-  //   if(!stream_.is_open())
-  //   std::cerr <<"could not open file \n";
-  // }
 
   ~Off_reader() {
     stream_.close();
   }
 
-  /**
-   * read an off file and calls the following methods :
-   * void init(int dim,int num_vertices,int num_faces,int num_edges); //num_edges may not be set
-   * void point(const std::vector<double>& point);
-   * void maximal_face(const std::list<int>& face);
-   * void done();
-   * of the visitor when reading a point or a maximal face.
+  /** \brief
+   * Read an OFF file and calls the following methods :
+   * 
+   * <CODE>void init(int dim,int num_vertices,int num_faces,int num_edges);  // from file header - num_edges may not be set
+   * 
+   * void point(const std::vector<double>& point);  // for each point read
+   * 
+   * void maximal_face(const std::list<int>& face);  // for each face read
+   * 
+   * void done();  // upon file read is finished</CODE>
+   * 
+   * of the visitor when reading a point or a maximal face. Edges are not taken into account.
    */
   template<typename OffVisitor>
   bool read(OffVisitor& off_visitor) {
@@ -118,7 +113,7 @@ class Off_reader {
 
     if (!goto_next_uncomment_line(line)) return false;
     std::istringstream iss(line);
-    if (is_off_file) {
+    if ((is_off_file) && (!is_noff_file)) {
       off_info_.dim = 3;
       if (!(iss >> off_info_.num_vertices >> off_info_.num_faces >> off_info_.num_edges)) {
         std::cerr << "incorrect number of vertices/faces/edges\n";
@@ -126,8 +121,8 @@ class Off_reader {
       }
     } else {
       if (!(iss >> off_info_.dim >> off_info_.num_vertices >> off_info_.num_faces >> off_info_.num_edges)) {
-        std::cerr << "incorrect number of vertices/faces/edges\n";
-        return false;
+      std::cerr << "incorrect number of vertices/faces/edges\n";
+      return false;
       }
     }
     off_visitor.init(off_info_.dim, off_info_.num_vertices, off_info_.num_faces, off_info_.num_edges);
@@ -138,7 +133,7 @@ class Off_reader {
   bool goto_next_uncomment_line(std::string& uncomment_line) {
     uncomment_line.clear();
     do
-      std::getline(stream_, uncomment_line); while (uncomment_line[0] == '%');  // || uncomment_line.empty());
+      std::getline(stream_, uncomment_line); while (uncomment_line[0] == '%');
     return (uncomment_line.size() > 0 && uncomment_line[0] != '%');
   }
 
@@ -166,7 +161,7 @@ class Off_reader {
       iss >> num_face_vertices;
       std::vector<int> face;
       face.assign(std::istream_iterator<int>(iss), std::istream_iterator<int>());
-      if (face.size() != off_info_.dim) return false;
+      // if (face.size() != (off_info_.dim + 1)) return false;
       visitor.maximal_face(face);
     }
     return true;
diff --git a/src/common/include/gudhi/Points_3D_off_io.h b/src/common/include/gudhi/Points_3D_off_io.h
new file mode 100644
index 00000000..b0d24998
--- /dev/null
+++ b/src/common/include/gudhi/Points_3D_off_io.h
@@ -0,0 +1,202 @@
+/*    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 POINTS_3D_OFF_IO_H_
+#define POINTS_3D_OFF_IO_H_
+
+#include <gudhi/Off_reader.h>
+
+#include <string>
+#include <vector>
+#include <fstream>
+#include <map>
+
+namespace Gudhi {
+
+/** 
+ * @brief OFF file visitor implementation according to Off_reader in order to read points from an OFF file.
+ */
+template<typename Point_3>
+class Points_3D_off_visitor_reader {
+ private:
+  std::vector<Point_3> point_cloud_;
+  bool valid_;
+
+ public:
+  /** @brief Off_reader visitor init implementation. 
+   * 
+   * The init parameters are set from OFF file header.
+   * Dimension value is required and the value must be 3.
+   *
+   * @param[in] dim space dimension of vertices.
+   * @param[in] num_vertices number of vertices in the OFF file (not used).
+   * @param[in] num_faces number of faces in the OFF file (not used).
+   * @param[in] num_edges number of edges in the OFF file (not used).
+   */
+  void init(int dim, int num_vertices, int num_faces, int num_edges) {
+#ifdef DEBUG_TRACES
+    std::cout << "Points_3D_off_visitor_reader::init - dim=" << dim << " - num_vertices=" <<
+        num_vertices << " - num_faces=" << num_faces << " - num_edges=" << num_edges << std::endl;
+#endif  // DEBUG_TRACES
+    if (dim == 3) {
+      valid_ = true;
+    } else {
+      valid_ = false;
+      std::cerr << "Points_3D_off_reader::Points_3D_off_reader cannot read OFF files in dimension " << dim << "\n";
+    }
+
+    if (num_faces > 0) {
+      std::cerr << "Points_3D_off_visitor_reader::init faces are not taken into account from OFF file for Points.\n";
+    }
+    if (num_edges > 0) {
+      std::cerr << "Points_3D_off_visitor_reader::init edges are not taken into account from OFF file for Points.\n";
+    }
+  }
+
+  /** @brief Off_reader visitor point implementation. 
+   * 
+   * The point function is called on each vertex line from OFF file.
+   * This function inserts the vertex in the vector of points.
+   *
+   * @param[in] point vector of vertex coordinates.
+   * 
+   * @details
+   * Point_3 must have a constructor with the following form:
+   * 
+   * @code template<class InputIterator > Point_3::Point_3(double x, double y, double z) @endcode
+   */
+  void point(const std::vector<double>& point) {
+    if (valid_) {
+#ifdef DEBUG_TRACES
+      std::cout << "Points_3D_off_visitor_reader::point ";
+      for (auto coordinate : point) {
+        std::cout << coordinate << " | ";
+      }
+      std::cout << std::endl;
+#endif  // DEBUG_TRACES
+      // Fill the point cloud
+      point_cloud_.push_back(Point_3(point[0], point[1], point[2]));
+    }
+  }
+
+  // Off_reader visitor maximal_face implementation - Only points are read
+
+  void maximal_face(const std::vector<int>& face) { }
+
+  // Off_reader visitor done implementation - Only points are read
+
+  void done() { }
+
+  /** @brief Point cloud getter.
+   *
+   * @return The point cloud.
+   */
+  const std::vector<Point_3>& get_point_cloud() const {
+    return point_cloud_;
+  }
+
+  /** @brief Returns if the OFF file read operation was successful or not.
+   *
+   * @return OFF file read status.
+   */
+  bool is_valid() const {
+    return valid_;
+  }
+};
+
+/** 
+ * \@brief OFF file reader implementation in order to read dimension 3 points from an OFF file.
+ * 
+ * @details
+ * This class is using the Points_3D_off_visitor_reader to visit the OFF file according to Off_reader.
+ * 
+ * Point_3 must have a constructor with the following form:
+ * 
+ * @code template<class InputIterator > Point_3::Point_3(double x, double y, double z) @endcode
+ * 
+ * @section point3doffioexample Example
+ *
+ * This example loads points from an OFF file and builds a vector of CGAL points in dimension 3.
+ * Then, it is asked to display the points.
+ * 
+ * @include common/example_CGAL_3D_points_off_reader.cpp
+ * 
+ * When launching:
+ * 
+ * @code $> ./cgal3Doffreader ../../data/points/tore3D_300.off
+ * @endcode
+ *
+ * the program output is:
+ * 
+ * @include common/cgal3Doffreader_result.txt
+ */
+template<typename Point_3>
+class Points_3D_off_reader {
+ public:
+  /** @brief Reads the OFF file and constructs a vector of points from the points
+   * that are in the OFF file.
+   *
+   * @param[in] name_file OFF file to read.
+   * 
+   * @post Check with is_valid() function to see if read operation was successful.
+   */
+  Points_3D_off_reader(const std::string& name_file)
+      : valid_(false) {
+    std::ifstream stream(name_file);
+    if (stream.is_open()) {
+      Off_reader off_reader(stream);
+      Points_3D_off_visitor_reader<Point_3> off_visitor;
+      valid_ = off_reader.read(off_visitor);
+      valid_ = valid_ && off_visitor.is_valid();
+      if (valid_) {
+        point_cloud = off_visitor.get_point_cloud();
+      }
+    } else {
+      std::cerr << "Points_3D_off_reader::Points_3D_off_reader could not open file " << name_file << "\n";
+    }
+  }
+
+  /** @brief Returns if the OFF file read operation was successful or not.
+   *
+   * @return OFF file read status.
+   */
+  bool is_valid() const {
+    return valid_;
+  }
+
+  /** @brief Point cloud getter.
+   *
+   * @return point_cloud.
+   */
+  const std::vector<Point_3>& get_point_cloud() const {
+    return point_cloud;
+  }
+
+ private:
+  /** @brief point_cloud.*/
+  std::vector<Point_3> point_cloud;
+  /** @brief OFF file read status.*/
+  bool valid_;
+};
+
+}  // namespace Gudhi
+
+#endif  // POINTS_3D_OFF_IO_H_
diff --git a/src/common/include/gudhi/Points_off_io.h b/src/common/include/gudhi/Points_off_io.h
new file mode 100644
index 00000000..29af8a8a
--- /dev/null
+++ b/src/common/include/gudhi/Points_off_io.h
@@ -0,0 +1,183 @@
+/*    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 POINTS_OFF_IO_H_
+#define POINTS_OFF_IO_H_
+
+#include <gudhi/Off_reader.h>
+
+#include <string>
+#include <vector>
+#include <fstream>
+#include <map>
+
+namespace Gudhi {
+
+/** 
+ * \brief OFF file visitor implementation according to Off_reader in order to read points from an OFF file.
+ */
+template<typename Point_d>
+class Points_off_visitor_reader {
+ private:
+  std::vector<Point_d> point_cloud;
+
+ public:
+  /** \brief Off_reader visitor init implementation. 
+   * 
+   * The init parameters are set from OFF file header.
+   * Dimension value is required in order to construct a vector of points.
+   *
+   * @param[in] dim space dimension of vertices.
+   * @param[in] num_vertices number of vertices in the OFF file (not used).
+   * @param[in] num_faces number of faces in the OFF file (not used).
+   * @param[in] num_edges number of edges in the OFF file (not used).
+   */
+  void init(int dim, int num_vertices, int num_faces, int num_edges) {
+#ifdef DEBUG_TRACES
+    std::cout << "Points_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 << "Points_off_visitor_reader::init faces are not taken into account from OFF file for Points.\n";
+    }
+    if (num_edges > 0) {
+      std::cerr << "Points_off_visitor_reader::init edges are not taken into account from OFF file for Points.\n";
+    }
+  }
+
+  /** @brief Off_reader visitor point implementation. 
+   * 
+   * The point function is called on each vertex line from OFF file.
+   * This function inserts the vertex in the vector of points.
+   *
+   * @param[in] point vector of vertex coordinates.
+   * 
+   * @details
+   * Point_d must have a constructor with the following form:
+   * 
+   * @code template<class InputIterator > Point_d::Point_d(InputIterator first, InputIterator last) @endcode
+   * 
+   */
+  void point(const std::vector<double>& point) {
+#ifdef DEBUG_TRACES
+    std::cout << "Points_off_visitor_reader::point ";
+    for (auto coordinate : point) {
+      std::cout << coordinate << " | ";
+    }
+    std::cout << std::endl;
+#endif  // DEBUG_TRACES
+    // Fill the point cloud
+    point_cloud.push_back(Point_d(point.begin(), point.end()));
+  }
+
+  // Off_reader visitor maximal_face implementation - Only points are read
+  void maximal_face(const std::vector<int>& face) { }
+
+  // Off_reader visitor done implementation - Only points are read
+  void done() { }
+
+  /** \brief Point cloud getter.
+   *
+   * @return point_cloud.
+   */
+  const std::vector<Point_d>& get_point_cloud() const {
+    return point_cloud;
+  }
+};
+
+/** 
+ * \brief OFF file reader implementation in order to read points from an OFF file.
+ * 
+ * This class is using the Points_off_visitor_reader to visit the OFF file according to Off_reader.
+ * 
+ * Point_d must have a constructor with the following form:
+ * 
+ * \code template<class InputIterator > Point_d::Point_d(int d, InputIterator first, InputIterator last) \endcode
+ * 
+ * where d is the point dimension. 		
+ * 
+ * \section pointoffioexample Example
+ *
+ * This example loads points from an OFF file and builds a vector of points (vector of double).
+ * Then, it is asked to display the points.
+ * 
+ * \include common/example_vector_double_points_off_reader.cpp
+ * 
+ * When launching:
+ * 
+ * \code $> ./vector_double_off_reader ../../data/points/alphacomplexdoc.off
+ * \endcode
+ *
+ * the program output is:
+ * 
+ * \include common/cgaloffreader_result.txt
+ */
+template<typename Point_d>
+class Points_off_reader {
+ public:
+  /** \brief Reads the OFF file and constructs a vector of points from the points
+   * that are in the OFF file.
+   *
+   * @param[in] name_file OFF file to read.
+   * 
+   * \post Check with is_valid() function to see if read operation was successful.
+   */
+  Points_off_reader(const std::string& name_file)
+  : valid_(false) {
+    std::ifstream stream(name_file);
+    if (stream.is_open()) {
+      Off_reader off_reader(stream);
+      Points_off_visitor_reader<Point_d> off_visitor;
+      valid_ = off_reader.read(off_visitor);
+      if (valid_) {
+        point_cloud = off_visitor.get_point_cloud();
+      }
+    } else {
+      std::cerr << "Points_off_reader::Points_off_reader could not open file " << name_file << "\n";
+    }
+  }
+
+  /** \brief Returns if the OFF file read operation was successful or not.
+   *
+   * @return OFF file read status.
+   */
+  bool is_valid() const {
+    return valid_;
+  }
+
+   /** \brief Point cloud getter.
+   *
+   * @return point_cloud.
+   */
+  const std::vector<Point_d>& get_point_cloud() const {
+    return point_cloud;
+  }
+
+ private:
+  /** \brief point_cloud.*/
+  std::vector<Point_d> point_cloud;
+  /** \brief OFF file read status.*/
+  bool valid_;
+};
+
+}  // namespace Gudhi
+
+#endif  // POINTS_OFF_IO_H_
diff --git a/src/common/include/gudhi/Test.h b/src/common/include/gudhi/Test.h
deleted file mode 100644
index 6024c822..00000000
--- a/src/common/include/gudhi/Test.h
+++ /dev/null
@@ -1,105 +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):       David Salinas
- *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (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 TEST_H_
-#define TEST_H_
-
-#include <list>
-#include <string>
-#include <vector>
-#include <sstream>
-#include <iostream>
-
-
-#define TEST(a) std::cout << "TEST: " << (a) << std::endl
-#define TESTMSG(a, b) std::cout << "TEST: " << a << b << std::endl
-#define TESTVALUE(a) std::cout << "TEST: " <<  #a << ": " << a << std::endl
-
-/**
- * Class to perform test
- */
-
-class Test {
- private:
-  std::string name;
-  bool (*test)();
-
-  std::string separation() const {
-    return "+++++++++++++++++++++++++++++++++++++++++++++++++\n";
-  }
-
-  std::string print_between_plus(std::string& s) const {
-    std::stringstream res;
-    res << "+++++++++++++++++" << s << "+++++++++++++++++\n";
-    return res.str();
-  }
-
- public:
-  Test(std::string name_, bool (*test_)()) {
-    name = name_;
-    test = test_;
-  }
-
-  bool run() {
-    std::cout << print_between_plus(name);
-    return test();
-  }
-
-  std::string getName() {
-    return name;
-  }
-};
-
-class Tests {
- private:
-  std::list<Test> tests;
-
- public:
-  void add(std::string name_, bool (*test_)()) {
-    Test test(name_, test_);
-    tests.push_back(test);
-  }
-
-  bool run() {
-    bool tests_succesful(true);
-    std::vector<bool> res;
-    for (Test test : tests) {
-      res.push_back(test.run());
-    }
-    std::cout << "\n\n results of tests : " << std::endl;
-    int i = 0;
-    for (Test t : tests) {
-      std::cout << "Test " << i << " \"" << t.getName() << "\"  -->  ";
-      if (res[i++]) {
-        std::cout << "OK" << std::endl;
-      } else {
-        std::cout << "Fail" << std::endl;
-        tests_succesful = false;
-        break;
-      }
-    }
-    return tests_succesful;
-  }
-};
-
-#endif  // TEST_H_
diff --git a/src/common/include/gudhi/distance_functions.h b/src/common/include/gudhi/distance_functions.h
index e5c79ded..cd518581 100644
--- a/src/common/include/gudhi/distance_functions.h
+++ b/src/common/include/gudhi/distance_functions.h
@@ -23,6 +23,8 @@
 #ifndef DISTANCE_FUNCTIONS_H_
 #define DISTANCE_FUNCTIONS_H_
 
+#include <cmath>  // for std::sqrt
+
 /* Compute the Euclidean distance between two Points given
  * by a range of coordinates. The points are assumed to have 
  * the same dimension. */
@@ -35,7 +37,7 @@ double euclidean_distance(Point &p1, Point &p2) {
     double tmp = *it1 - *it2;
     dist += tmp*tmp;
   }
-  return sqrt(dist);
+  return std::sqrt(dist);
 }
 
 #endif  // DISTANCE_FUNCTIONS_H_
diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h
index e05714c7..899f9df6 100644
--- a/src/common/include/gudhi/reader_utils.h
+++ b/src/common/include/gudhi/reader_utils.h
@@ -58,7 +58,9 @@ inline void read_points(std::string file_name, std::vector< std::vector< double
     while (iss >> x) {
       point.push_back(x);
     }
-    points.push_back(point);
+    // Check for empty lines
+    if (!point.empty())
+      points.push_back(point);
   }
   in_file.close();
 }
@@ -159,7 +161,7 @@ bool read_simplex(std::istream & in_, std::vector< Vertex_handle > & simplex, Fi
     simplex.push_back(v);
   }
   in_ >> fil;
-  in_.ignore((std::numeric_limits<std::streamsize>::max)(), '\n'); // ignore until the carriage return
+  in_.ignore((std::numeric_limits<std::streamsize>::max)(), '\n');  // ignore until the carriage return
   return true;
 }
 
diff --git a/src/common/test/CMakeLists.txt b/src/common/test/CMakeLists.txt
new file mode 100644
index 00000000..7ccdb752
--- /dev/null
+++ b/src/common/test/CMakeLists.txt
@@ -0,0 +1,24 @@
+cmake_minimum_required(VERSION 2.6)
+project(Common_tests)
+
+if (GCOVR_PATH)
+  # for gcovr to make coverage reports - Corbera Jenkins plugin
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
+endif()
+if (GPROF_PATH)
+  # for gprof to make coverage reports - Jenkins
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
+endif()
+
+add_executable ( poffreader_UT test_points_off_reader.cpp )
+target_link_libraries(poffreader_UT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+
+# Do not forget to copy test files in current binary dir
+file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+
+# Unitary tests
+add_test(poffreader_UT ${CMAKE_CURRENT_BINARY_DIR}/poffreader_UT
+         # XML format for Jenkins xUnit plugin 
+         --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/poffreader_UT.xml --log_level=test_suite --report_level=no)
+
+
diff --git a/src/common/test/README b/src/common/test/README
new file mode 100644
index 00000000..f2a7eb5a
--- /dev/null
+++ b/src/common/test/README
@@ -0,0 +1,14 @@
+To compile:
+***********
+
+cmake .
+make
+
+To launch with details:
+***********************
+
+./dtoffrw_UT --report_level=detailed --log_level=all 
+
+   ==> echo $? returns 0 in case of success (non-zero otherwise)
+
+
diff --git a/src/common/test/dtoffrw_alphashapedoc_result.off b/src/common/test/dtoffrw_alphashapedoc_result.off
new file mode 100644
index 00000000..1deb8dbd
--- /dev/null
+++ b/src/common/test/dtoffrw_alphashapedoc_result.off
@@ -0,0 +1,7 @@
+Point[0] = 1 1 
+Point[1] = 7 0 
+Point[2] = 4 6 
+Point[3] = 9 6 
+Point[4] = 0 14 
+Point[5] = 2 19 
+Point[6] = 9 17 
diff --git a/src/common/test/test_points_off_reader.cpp b/src/common/test/test_points_off_reader.cpp
new file mode 100644
index 00000000..b4f71182
--- /dev/null
+++ b/src/common/test/test_points_off_reader.cpp
@@ -0,0 +1,73 @@
+/*    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/>.
+ */
+
+#include <gudhi/Points_off_io.h>
+
+#include <iostream>
+#include <string>
+#include <vector>
+
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE "points_off_read_write"
+#include <boost/test/unit_test.hpp>
+
+using Point_d = std::vector<double>;
+
+BOOST_AUTO_TEST_CASE( points_doc_test )
+{
+  // Read the OFF file (input file name given as parameter) and triangulates points
+  Gudhi::Points_off_reader<Point_d> off_reader("alphacomplexdoc.off");
+  // Check the read operation was correct
+  BOOST_CHECK(off_reader.is_valid());
+  
+  // Retrieve the triangulation
+  std::vector<Point_d> point_cloud = off_reader.get_point_cloud();
+  BOOST_CHECK(point_cloud.size() == 7);
+
+  std::vector<Point_d> expected_points;
+  std::vector<double> point = {1.0, 1.0};
+  expected_points.push_back(Point_d(point.begin(), point.end()));
+  point = {7.0, 0.0};
+  expected_points.push_back(Point_d(point.begin(), point.end()));
+  point = {4.0, 6.0};
+  expected_points.push_back(Point_d(point.begin(), point.end()));
+  point = {9.0, 6.0};
+  expected_points.push_back(Point_d(point.begin(), point.end()));
+  point = {0.0, 14.0};
+  expected_points.push_back(Point_d(point.begin(), point.end()));
+  point = {2.0, 19.0};
+  expected_points.push_back(Point_d(point.begin(), point.end()));
+  point = {9.0, 17.0};
+  expected_points.push_back(Point_d(point.begin(), point.end()));
+
+  BOOST_CHECK(point_cloud == expected_points);
+}
+
+BOOST_AUTO_TEST_CASE( Delaunay_triangulation_unexisting_file_read_test )
+{
+  Gudhi::Points_off_reader<Point_d> off_reader("some_impossible_weird_file_name.off");
+  // Check the read operation was correct
+  BOOST_CHECK(!off_reader.is_valid());
+  
+  std::vector<Point_d> point_cloud = off_reader.get_point_cloud();
+  BOOST_CHECK(point_cloud.size() == 0);
+}
diff --git a/src/debian/changelog b/src/debian/changelog
new file mode 100644
index 00000000..32b3f6f9
--- /dev/null
+++ b/src/debian/changelog
@@ -0,0 +1,5 @@
+gudhi (1.3.0-1) unstable; urgency=low
+
+  * Initial release.
+
+ -- Marc Glisse <marc.glisse@inria.fr>  Sat, 26 Mar 2016 10:51:01 +0100
diff --git a/src/debian/compat b/src/debian/compat
new file mode 100644
index 00000000..ec635144
--- /dev/null
+++ b/src/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/src/debian/control b/src/debian/control
new file mode 100644
index 00000000..838234a9
--- /dev/null
+++ b/src/debian/control
@@ -0,0 +1,26 @@
+Source: gudhi
+Priority: optional
+Maintainer: Marc Glisse <marc.glisse@normalesup.org>
+Build-Depends: debhelper (>= 9), cmake, libboost-dev
+Standards-Version: 3.9.6
+Section: libs
+Homepage: http://gudhi.gforge.inria.fr/
+#Vcs-Git: git://anonscm.debian.org/collab-maint/gudhi.git
+#Vcs-Browser: https://anonscm.debian.org/gitweb/?p=collab-maint/gudhi.git;a=summary
+
+Package: libgudhi-dev
+Section: libdevel
+Architecture: all
+Depends: libboost-dev, ${misc:Depends}
+Recommends: libcgal-dev
+Description: Gudhi library for topological data analysis
+ The Gudhi library (Geometric Understanding in Higher Dimensions) is a generic
+ open source C++ library for Computational Topology and Topological Data
+ Analysis (TDA).
+ .
+ The current release of the GUDHI library includes:
+ * Data structures to represent, construct and manipulate simplicial and
+ cubical complexes, including alpha-complex, witness complex, Rips complex.
+ * Algorithms to compute persistent homology and multi-field persistent
+ homology.
+ * Simplication of simplicial complexes by edge contraction.
diff --git a/src/debian/copyright b/src/debian/copyright
new file mode 100644
index 00000000..2e1f88cd
--- /dev/null
+++ b/src/debian/copyright
@@ -0,0 +1,28 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: gudhi
+Upstream-Contact: gudhi-users@lists.gforge.inria.fr
+Source: <url://http://gudhi.gforge.inria.fr/>
+
+Files: *
+Copyright: 2014-2016 Inria Sophia Antipolis-Méditerranée
+           2014-2016 Inria Saclay - Ile de France
+           2014-2016 Université Nice Sophia Antipolis
+License: GPL-3.0+
+
+License: GPL-3.0+
+ 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 package 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 <https://www.gnu.org/licenses/>.
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
+
diff --git a/src/debian/docs b/src/debian/docs
new file mode 100644
index 00000000..878a2ba1
--- /dev/null
+++ b/src/debian/docs
@@ -0,0 +1,2 @@
+Conventions.txt
+README
diff --git a/src/debian/rules b/src/debian/rules
new file mode 100755
index 00000000..c9b049af
--- /dev/null
+++ b/src/debian/rules
@@ -0,0 +1,28 @@
+#!/usr/bin/make -f
+# See debhelper(7) (uncomment to enable)
+# output every command that modifies files on the build system.
+#export DH_VERBOSE = 1
+
+# see EXAMPLES in dpkg-buildflags(1) and read /usr/share/dpkg/*
+DPKG_EXPORT_BUILDFLAGS = 1
+include /usr/share/dpkg/default.mk
+
+# see FEATURE AREAS in dpkg-buildflags(1)
+#export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+
+# see ENVIRONMENT in dpkg-buildflags(1)
+# package maintainers to append CFLAGS
+#export DEB_CFLAGS_MAINT_APPEND  = -Wall -pedantic
+# package maintainers to append LDFLAGS
+#export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed
+
+
+# main packaging script based on dh7 syntax
+%:
+	dh $@ 
+
+# dh_make generated override targets
+# This is example for Cmake (See https://bugs.debian.org/641051 )
+#override_dh_auto_configure:
+#	dh_auto_configure -- \
+#	-DCMAKE_LIBRARY_PATH=$(DEB_HOST_MULTIARCH)
diff --git a/src/debian/source/format b/src/debian/source/format
new file mode 100644
index 00000000..163aaf8d
--- /dev/null
+++ b/src/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
author	skachano <skachano@636b058d-ea47-450e-bf9e-a15bfbe3eedb>	2016-09-28 12:33:22 +0000
committer	skachano <skachano@636b058d-ea47-450e-bf9e-a15bfbe3eedb>	2016-09-28 12:33:22 +0000
commit	d16822ea1d3cedea66dcddd390becdd4cbb557bb (patch)
tree	b1c592e415f43c1be425608db861e5348e61dcf3 /src
parent	1c09c91ddf4d38196a91bbff5ae432fb13be6762 (diff)
parent	a138c9ed4fb9770a3612ff4ee0f914942bbe9724 (diff)