Merge last trunk modification

Fix doc issue
Still doc issue


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@1739 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 0a99345f06e93a3525691699a6fe1505979e8e8e

8 files changed, 233 insertions, 131 deletions

diff --git a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h
index c8081cac..433cfd3e 100644
--- a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h
+++ b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h
@@ -46,7 +46,7 @@ namespace persistent_cohomology {
   composed of three elements: 
   topological spaces, their homology groups and an evolution scheme.
 
- <DT>Topological Spaces:</DT>
+ \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
@@ -84,7 +84,7 @@ namespace persistent_cohomology {
  <CODE>Filtration_value filtration (Simplex_handle)</CODE> that returns the value of
  the filtration on the simplex represented by the handle.
 
- <DT>Homology:</DT>
+ \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
@@ -111,7 +111,7 @@ namespace persistent_cohomology {
  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>
+ \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
@@ -139,19 +139,63 @@ namespace persistent_cohomology {
  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.
+\section pcohexamples Examples
 
-\li <CODE>rips_persistence.cpp</CODE> computes the Rips complex of a point cloud and its persistence diagram.
+We provide several example files: run these examples with -h for details on their use, and read the README file.
 
-\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 <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 <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 
+\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.
  */
 
diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt
index 5fb4ba12..758bd6b1 100644
--- a/src/Persistent_cohomology/example/CMakeLists.txt
+++ b/src/Persistent_cohomology/example/CMakeLists.txt
@@ -30,17 +30,13 @@ 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)
+add_test(rips_persistence_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.16 -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/Kl.txt -r 0.16 -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/filtered_simplicial_complex/bunny_5000_complex.fsc -p 2 -m 0)
+add_test(persistence_from_file_3_3_100 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc -p 3 -m 100)
    
 if(GMP_FOUND)
-   message("GMP_LIBRARIES = ${GMP_LIBRARIES}")
-
    if(GMPXX_FOUND)
-      message("GMPXX_LIBRARIES = ${GMPXX_LIBRARIES}")
-
       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 )
@@ -52,53 +48,37 @@ if(GMP_FOUND)
 
    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)
-else()
-  # message(WARNING "GMP not found.")
 endif(GMP_FOUND)
 
-  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)
-      message(STATUS "CGAL version: ${CGAL_VERSION}.")
-
-      find_package(Eigen3 3.1.0)
-      if (EIGEN3_FOUND)
-        message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.")
-        include( ${EIGEN3_USE_FILE} )
-
-        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)
-
-      else()
-        message(WARNING "Eigen3 not found. Version 3.1.0 is required for Alpha shapes feature.")
-      endif(EIGEN3_FOUND)
-    else()
-      message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile Alpha shapes feature. Version 4.6.0 is required.")
-    endif ()
-  else()
-    # message(WARNING "CGAL not found.")
-  endif(CGAL_FOUND)
-   
+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/alpha_complex_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_persistence.cpp
index cb181936..2412569a 100644
--- a/src/Persistent_cohomology/example/alpha_complex_persistence.cpp
+++ b/src/Persistent_cohomology/example/alpha_complex_persistence.cpp
@@ -4,6 +4,8 @@
 
 #include <gudhi/Alpha_complex.h>
 #include <gudhi/Persistent_cohomology.h>
+// to construct a simplex_tree from alpha complex
+#include <gudhi/Simplex_tree.h>
 
 #include <iostream>
 #include <string>
@@ -30,35 +32,38 @@ int main(int argc, char **argv) {
   // 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();
+  Gudhi::alpha_complex::Alpha_complex<Kernel> alpha_complex_from_file(off_file_points);
+
+  Gudhi::Simplex_tree<> simplex;
+  if (alpha_complex_from_file.create_complex(simplex, alpha_square_max_value)) {
+    // ----------------------------------------------------------------------------
+    // Display information about the alpha complex
+    // ----------------------------------------------------------------------------
+    std::cout << "Simplicial complex is of dimension " << simplex.dimension() <<
+        " - " << simplex.num_simplices() << " simplices - " <<
+        simplex.num_vertices() << " vertices." << std::endl;
+
+    // Sort the simplices in the order of the filtration
+    simplex.initialize_filtration();
+
+    std::cout << "Simplex_tree dim: " << simplex.dimension() << std::endl;
+    // Compute the persistence diagram of the complex
+    Gudhi::persistent_cohomology::Persistent_cohomology< Gudhi::Simplex_tree<>,
+        Gudhi::persistent_cohomology::Field_Zp > pcoh(simplex);
+    // 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;
diff --git a/src/Persistent_cohomology/example/custom_persistence_sort.cpp b/src/Persistent_cohomology/example/custom_persistence_sort.cpp
index 9af38611..64f2a4dc 100644
--- a/src/Persistent_cohomology/example/custom_persistence_sort.cpp
+++ b/src/Persistent_cohomology/example/custom_persistence_sort.cpp
@@ -27,6 +27,8 @@
 
 #include <gudhi/Alpha_complex.h>
 #include <gudhi/Persistent_cohomology.h>
+// to construct a simplex_tree from alpha complex
+#include <gudhi/Simplex_tree.h>
 
 #include <iostream>
 #include <iterator>
@@ -38,6 +40,9 @@
 using Kernel = CGAL::Epick_d< CGAL::Dimension_tag<3> >;
 using Point = Kernel::Point_d;
 using Alpha_complex = Gudhi::alpha_complex::Alpha_complex<Kernel>;
+using Simplex_tree = Gudhi::Simplex_tree<>;
+using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology< Simplex_tree,
+      Gudhi::persistent_cohomology::Field_Zp >;
 
 std::vector<Point> random_points() {
   // Instanciate a random point generator
@@ -60,7 +65,7 @@ std::vector<Point> random_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)
+  explicit cmp_intervals_by_dim_then_length(Simplex_tree * sc)
       : sc_(sc) { }
 
   template<typename Persistent_interval>
@@ -71,46 +76,62 @@ struct cmp_intervals_by_dim_then_length {
     else
       return (sc_->dimension(get < 0 > (p1)) > sc_->dimension(get < 0 > (p2)));
   }
-  Alpha_complex* sc_;
+  Simplex_tree* sc_;
 };
 
 int main(int argc, char **argv) {
   std::vector<Point> points = random_points();
 
+  std::cout << "Points size=" << points.size() << std::endl;
   // 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;
+  Alpha_complex alpha_complex_from_points(points);
+  std::cout << "alpha_complex_from_points" << std::endl;
+
+  Simplex_tree simplex;
+  std::cout << "simplex" << std::endl;
+  if (alpha_complex_from_points.create_complex(simplex, 0.6)) {
+    std::cout << "simplex" << std::endl;
+    // ----------------------------------------------------------------------------
+    // Display information about the alpha complex
+    // ----------------------------------------------------------------------------
+    std::cout << "Simplicial complex is of dimension " << simplex.dimension() <<
+        " - " << simplex.num_simplices() << " simplices - " <<
+        simplex.num_vertices() << " vertices." << std::endl;
+
+    // Sort the simplices in the order of the filtration
+    simplex.initialize_filtration();
+
+    std::cout << "Simplex_tree dim: " << simplex.dimension() << std::endl;
+
+    Persistent_cohomology pcoh(simplex);
+
+    // 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(&simplex);
+    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 << simplex.dimension(get<0>(pair)) << " "
+            << simplex.filtration(get<0>(pair)) << " "
+            << simplex.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 < simplex.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;
   }
-
-  // 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/plain_homology.cpp b/src/Persistent_cohomology/example/plain_homology.cpp
index 2156ffd9..ae82c817 100644
--- a/src/Persistent_cohomology/example/plain_homology.cpp
+++ b/src/Persistent_cohomology/example/plain_homology.cpp
@@ -25,6 +25,7 @@
 
 #include <iostream>
 #include <vector>
+#include <cstdint>  // for std::uint8_t
 
 using namespace Gudhi;
 
@@ -39,6 +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;
 
diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
index 5b371f2b..108a53d7 100644
--- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
+++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
@@ -41,6 +41,7 @@
 #include <tuple>
 #include <algorithm>
 #include <string>
+#include <stdexcept>  // for std::out_of_range
 
 namespace Gudhi {
 
@@ -89,6 +90,7 @@ class Persistent_cohomology {
    *
    * @param[in] cpx Complex for which the persistent homology is computed.
    * 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),
@@ -106,6 +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);
diff --git a/src/Persistent_cohomology/test/betti_numbers_unit_test.cpp b/src/Persistent_cohomology/test/betti_numbers_unit_test.cpp
index a4e00b45..40221005 100644
--- a/src/Persistent_cohomology/test/betti_numbers_unit_test.cpp
+++ b/src/Persistent_cohomology/test/betti_numbers_unit_test.cpp
@@ -12,7 +12,7 @@
 #include "gudhi/Simplex_tree.h"
 #include "gudhi/Persistent_cohomology.h"
 
-struct MyOptions : Gudhi::Simplex_tree_options_full_featured {
+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
@@ -21,7 +21,7 @@ struct MyOptions : Gudhi::Simplex_tree_options_full_featured {
   typedef short Vertex_handle;
 };
 
-using Mini_simplex_tree = Gudhi::Simplex_tree<MyOptions>;
+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>;
 
diff --git a/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp b/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp
index 5c54ed5f..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"
@@ -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);
+
+}