From d03c111cbb3329018d72c7ed8bea2d7ac9a57045 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Mon, 21 Nov 2016 09:59:09 +0000
Subject: Add distance matrix reader test cases

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/distance_matrix_in_rips_module@1763 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: cae9765c56ff6e0a213a7835bab56f3618e4d942
---
 src/common/test/CMakeLists.txt                  |  9 +++
 src/common/test/test_distance_matrix_reader.cpp | 85 +++++++++++++++++++++++++
 src/common/test/test_points_off_reader.cpp      |  2 +-
 3 files changed, 95 insertions(+), 1 deletion(-)
 create mode 100644 src/common/test/test_distance_matrix_reader.cpp

(limited to 'src/common/test')

diff --git a/src/common/test/CMakeLists.txt b/src/common/test/CMakeLists.txt
index 7ccdb752..baa24539 100644
--- a/src/common/test/CMakeLists.txt
+++ b/src/common/test/CMakeLists.txt
@@ -13,12 +13,21 @@ endif()
 add_executable ( poffreader_UT test_points_off_reader.cpp )
 target_link_libraries(poffreader_UT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
 
+add_executable ( distancematrixreader_UT test_distance_matrix_reader.cpp )
+target_link_libraries(distancematrixreader_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 ${CMAKE_CURRENT_BINARY_DIR}/)
+file(COPY "${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+file(COPY "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" 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)
 
+add_test(distancematrixreader_UT ${CMAKE_CURRENT_BINARY_DIR}/distancematrixreader_UT
+         # XML format for Jenkins xUnit plugin 
+         --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/distancematrixreader_UT.xml --log_level=test_suite --report_level=no)
+
 
diff --git a/src/common/test/test_distance_matrix_reader.cpp b/src/common/test/test_distance_matrix_reader.cpp
new file mode 100644
index 00000000..7eb7e846
--- /dev/null
+++ b/src/common/test/test_distance_matrix_reader.cpp
@@ -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):       Vincent Rouvreau
+ *
+ *    Copyright (C) 2016  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 <gudhi/reader_utils.h>
+
+#include <iostream>
+#include <string>
+#include <vector>
+
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE "distance_matrix_reader"
+#include <boost/test/unit_test.hpp>
+
+using Distance_matrix = std::vector<std::vector<double>>;
+
+BOOST_AUTO_TEST_CASE( lower_triangular_distance_matrix )
+{
+  Distance_matrix from_lower_triangular;
+  // Read lower_triangular_distance_matrix.csv file where the separator is a ','
+  from_lower_triangular = read_lower_triangular_matrix_from_csv_file<double>("lower_triangular_distance_matrix.csv",
+                                                                             ',');
+  for (auto& i : from_lower_triangular) {
+    for (auto j : i) {
+      std::cout << j << " ";
+    }
+    std::cout << std::endl;
+  }
+  std::cout << "from_lower_triangular size = " << from_lower_triangular.size() << std::endl;
+  BOOST_CHECK(from_lower_triangular.size() == 5);
+
+  for (int i = 0; i < from_lower_triangular.size(); i++) {
+    std::cout << "from_lower_triangular[" << i << "] size = " << from_lower_triangular[i].size() << std::endl;
+    BOOST_CHECK(from_lower_triangular[i].size() == i);
+  }
+  std::vector<double> expected = {1};
+  BOOST_CHECK(from_lower_triangular[0] == expected);
+  
+  expected = {2,3};
+  BOOST_CHECK(from_lower_triangular[0] == expected);
+  
+  expected = {4,5,6};
+  BOOST_CHECK(from_lower_triangular[0] == expected);
+  
+  expected = {7,8,9,10};
+  BOOST_CHECK(from_lower_triangular[0] == expected);
+  
+}
+
+BOOST_AUTO_TEST_CASE( full_square_distance_matrix )
+{
+  Distance_matrix from_full_square;
+  // Read full_square_distance_matrix.csv file where the separator is the default one ';'
+  from_full_square = read_lower_triangular_matrix_from_csv_file<double>("full_square_distance_matrix.csv");
+  for (auto& i : from_full_square) {
+    for (auto j : i) {
+      std::cout << j << " ";
+    }
+    std::cout << std::endl;
+  }
+  std::cout << "from_full_square size = " << from_full_square.size() << std::endl;
+  BOOST_CHECK(from_full_square.size() == 5);
+  for (int i = 0; i < from_lower_triangular.size(); i++) {
+    std::cout << "from_lower_triangular[" << i << "] size = " << from_lower_triangular[i].size() << std::endl;
+    BOOST_CHECK(from_lower_triangular[i].size() == i);
+  }  
+}
diff --git a/src/common/test/test_points_off_reader.cpp b/src/common/test/test_points_off_reader.cpp
index b4f71182..0a78d190 100644
--- a/src/common/test/test_points_off_reader.cpp
+++ b/src/common/test/test_points_off_reader.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Vincent Rouvreau
  *
- *    Copyright (C) 2015  INRIA Saclay (France)
+ *    Copyright (C) 2015
  *
  *    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
-- 
cgit v1.2.3


From 1a728400187d89db914e865a979c85c7260b0b02 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Mon, 21 Nov 2016 16:24:15 +0000
Subject: Add distance matrix rips construction (doc, code, test)

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/distance_matrix_in_rips_module@1766 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 6b9bdecbaf0aca12facb023e66bdea71e8e8cd38
---
 biblio/how_to_cite_gudhi.bib                       |  9 +++
 src/Doxyfile                                       |  6 +-
 src/Rips_complex/doc/Intro_rips_complex.h          | 52 ++++++++++++--
 src/Rips_complex/example/CMakeLists.txt            | 23 ++++++
 ...mple_one_skeleton_rips_from_distance_matrix.cpp | 68 ++++++++++++++++++
 .../example_one_skeleton_rips_from_points.cpp      |  2 -
 ..._rips_complex_from_csv_distance_matrix_file.cpp | 72 +++++++++++++++++++
 .../full_skeleton_rips_distance_for_doc.txt        | 32 +++++++++
 .../example/one_skeleton_rips_distance_for_doc.txt | 17 +++++
 src/Rips_complex/include/gudhi/Rips_complex.h      | 13 ++++
 src/common/doc/main_page.h                         |  3 +-
 src/common/include/gudhi/distance_functions.h      | 11 +--
 .../include/gudhi/graph_simplicial_complex.h       |  2 +-
 src/common/include/gudhi/reader_utils.h            | 84 +++++++++++-----------
 src/common/test/test_distance_matrix_reader.cpp    | 16 ++---
 15 files changed, 347 insertions(+), 63 deletions(-)
 create mode 100644 src/Rips_complex/example/example_one_skeleton_rips_from_distance_matrix.cpp
 create mode 100644 src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp
 create mode 100644 src/Rips_complex/example/full_skeleton_rips_distance_for_doc.txt
 create mode 100644 src/Rips_complex/example/one_skeleton_rips_distance_for_doc.txt

(limited to 'src/common/test')

diff --git a/biblio/how_to_cite_gudhi.bib b/biblio/how_to_cite_gudhi.bib
index 03c05728..77b6e284 100644
--- a/biblio/how_to_cite_gudhi.bib
+++ b/biblio/how_to_cite_gudhi.bib
@@ -94,4 +94,13 @@
 , booktitle =   "{GUDHI} User and Reference Manual"
 , url = "http://gudhi.gforge.inria.fr/doc/latest/group__tangential__complex.html"
 , year =        2016
+}
+
+@incollection{gudhi:RipsComplex
+, author =  "Cl\'ement Maria, Pawel Dlotko, Vincent Rouvreau"
+, title =   "Rips complex"
+, publisher =  "{GUDHI Editorial Board}"
+, booktitle =   "{GUDHI} User and Reference Manual"
+, url = "http://gudhi.gforge.inria.fr/doc/latest/group__rips__complex.html"
+, year =        2016
 }
\ No newline at end of file
diff --git a/src/Doxyfile b/src/Doxyfile
index e7c1a0e1..cf79755f 100644
--- a/src/Doxyfile
+++ b/src/Doxyfile
@@ -500,7 +500,7 @@ HIDE_SCOPE_NAMES       = NO
 # the files that are included by a file in the documentation of that file.
 # The default value is: YES.
 
-SHOW_INCLUDE_FILES     = YES
+SHOW_INCLUDE_FILES     = NO
 
 # If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each
 # grouped member an include statement to the documentation, telling the reader
@@ -2151,7 +2151,7 @@ TEMPLATE_RELATIONS     = YES
 # The default value is: YES.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
-INCLUDE_GRAPH          = YES
+INCLUDE_GRAPH          = NO
 
 # If the INCLUDED_BY_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are
 # set to YES then doxygen will generate a graph for each documented file showing
@@ -2160,7 +2160,7 @@ INCLUDE_GRAPH          = YES
 # The default value is: YES.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
-INCLUDED_BY_GRAPH      = YES
+INCLUDED_BY_GRAPH      = NO
 
 # If the CALL_GRAPH tag is set to YES then doxygen will generate a call
 # dependency graph for every global function or class method.
diff --git a/src/Rips_complex/doc/Intro_rips_complex.h b/src/Rips_complex/doc/Intro_rips_complex.h
index a71946b5..d01b14bb 100644
--- a/src/Rips_complex/doc/Intro_rips_complex.h
+++ b/src/Rips_complex/doc/Intro_rips_complex.h
@@ -2,7 +2,7 @@
  *    (Geometric Understanding in Higher Dimensions) is a generic C++
  *    library for computational topology.
  *
- *    Author(s):       Clément Maria, Vincent Rouvreau
+ *    Author(s):       Clément Maria, Pawel Dlotko, Vincent Rouvreau
  *
  *    Copyright (C) 2016  INRIA
  *
@@ -29,7 +29,7 @@ namespace rips_complex {
 
 /**  \defgroup rips_complex Rips complex
  * 
- * \author    Clément Maria, Vincent Rouvreau
+ * \author    Clément Maria, Pawel Dlotko, Vincent Rouvreau
  * 
  * @{
  * 
@@ -54,7 +54,9 @@ namespace rips_complex {
  * value set with \f$max(filtration(4,5), filtration(4,6), filtration(5,6))\f$.
  * And so on for simplex (0,1,2,3).
  * 
- * \section ripspointsexample Example from points
+ * \section ripspointsdistance Point cloud and distance function
+ * 
+ * \subsection ripspointscloudexample Example from a point cloud and a distance function
  * 
  * This example builds the one skeleton graph from the given points, threshold value, and distance function.
  * Then it creates a `Simplex_tree` with it.
@@ -73,7 +75,7 @@ namespace rips_complex {
  * 
  * \include Rips_complex/one_skeleton_rips_points_for_doc.txt
  * 
- * \section ripsoffexample Example from OFF file
+ * \subsection ripsoffexample Example from OFF file
  * 
  * This example builds the one skeleton graph from the given points in an OFF file, threshold value, and distance
  * function.
@@ -93,6 +95,48 @@ namespace rips_complex {
  * 
  * \include Rips_complex/full_skeleton_rips_points_for_doc.txt
  * 
+ * 
+ * 
+ * \section ripsdistancematrix Distance matrix
+ * 
+ * \subsection ripsdistancematrixexample Example from a distance matrix
+ * 
+ * This example builds the one skeleton graph from the given distance matrix and threshold value.
+ * Then it creates a `Simplex_tree` with it.
+ * 
+ * Then, it is asked to display information about the simplicial complex.
+ * 
+ * \include Rips_complex/example_one_skeleton_rips_from_distance_matrix.cpp
+ * 
+ * When launching (rips maximal distance between 2 points is 1.0, is expanded until dimension 1 - one skeleton graph
+ * with other words):
+ * 
+ * \code $> ./oneskeletonripsdistance 1.0
+ * \endcode
+ *
+ * the program output is:
+ * 
+ * \include Rips_complex/one_skeleton_rips_distance_for_doc.txt
+ * 
+ * \subsection ripscsvdistanceexample Example from a distance matrix read in a csv file
+ * 
+ * This example builds the one skeleton graph from the given distance matrix read in a csv file and threshold value.
+ * Then it creates a `Simplex_tree` with it.
+ * 
+ * 
+ * Then, it is asked to display information about the rips complex.
+ * 
+ * \include Rips_complex/example_rips_complex_from_csv_distance_matrix_file.cpp
+ * 
+ * When launching:
+ * 
+ * \code $> ./ripscsvdistancereader ../../data/distance_matrix/full_square_distance_matrix.csv 1.0 3
+ * \endcode
+ *
+ * the program output is:
+ * 
+ * \include Rips_complex/full_skeleton_rips_distance_for_doc.txt
+ * 
  * \copyright GNU General Public License v3.                         
  * \verbatim  Contact: gudhi-users@lists.gforge.inria.fr \endverbatim
  */
diff --git a/src/Rips_complex/example/CMakeLists.txt b/src/Rips_complex/example/CMakeLists.txt
index 3962b15e..9ba9d941 100644
--- a/src/Rips_complex/example/CMakeLists.txt
+++ b/src/Rips_complex/example/CMakeLists.txt
@@ -1,27 +1,50 @@
 cmake_minimum_required(VERSION 2.6)
 project(Rips_complex_examples)
 
+# Point cloud
 add_executable ( ripsoffreader example_rips_complex_from_off_file.cpp )
 target_link_libraries(ripsoffreader  ${Boost_SYSTEM_LIBRARY})
 
 add_executable ( oneskeletonripspoints example_one_skeleton_rips_from_points.cpp )
 target_link_libraries(oneskeletonripspoints  ${Boost_SYSTEM_LIBRARY})
 
+# Distance matrix
+add_executable ( oneskeletonripsdistance example_one_skeleton_rips_from_distance_matrix.cpp )
+target_link_libraries(oneskeletonripsdistance  ${Boost_SYSTEM_LIBRARY})
+
+add_executable ( ripscsvdistancereader example_rips_complex_from_csv_distance_matrix_file.cpp )
+target_link_libraries(ripscsvdistancereader  ${Boost_SYSTEM_LIBRARY})
+
 if (TBB_FOUND)
   target_link_libraries(ripsoffreader ${TBB_LIBRARIES})
   target_link_libraries(oneskeletonripspoints ${TBB_LIBRARIES})
+  target_link_libraries(oneskeletonripsdistance ${TBB_LIBRARIES})
+  target_link_libraries(ripscsvdistancereader ${TBB_LIBRARIES})
 endif()
 
 add_test(oneskeletonripspoints ${CMAKE_CURRENT_BINARY_DIR}/oneskeletonripspoints 12.0)
+
+add_test(oneskeletonripsdistance ${CMAKE_CURRENT_BINARY_DIR}/oneskeletonripspoints 1.0)
+
 # Do not forget to copy test files in current binary dir
 file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
 add_test(ripsoffreader_doc_12_1 ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader alphacomplexdoc.off 12.0 1 ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_1.txt)
 add_test(ripsoffreader_doc_12_3 ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader alphacomplexdoc.off 12.0 3 ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_3.txt)
+
+file(COPY "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+add_test(ripscsvdistancereader_doc_1_1 ${CMAKE_CURRENT_BINARY_DIR}/ripscsvdistancereader full_square_distance_matrix.csv 1.0 1 ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_1_1.txt)
+add_test(ripscsvdistancereader_doc_1_3 ${CMAKE_CURRENT_BINARY_DIR}/ripscsvdistancereader full_square_distance_matrix.csv 1.0 3 ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_1_3.txt)
+
+
 if (DIFF_PATH)
   # Do not forget to copy test results files in current binary dir
   file(COPY "one_skeleton_rips_points_for_doc.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
   file(COPY "full_skeleton_rips_points_for_doc.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+  file(COPY "one_skeleton_rips_distance_for_doc.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+  file(COPY "full_skeleton_rips_distance_for_doc.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
 
   add_test(ripsoffreader_doc_12_1_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_1.txt ${CMAKE_CURRENT_BINARY_DIR}/one_skeleton_rips_points_for_doc.txt)
   add_test(ripsoffreader_doc_12_3_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_3.txt ${CMAKE_CURRENT_BINARY_DIR}/full_skeleton_rips_points_for_doc.txt)
+  add_test(ripscsvreader_doc_1_1_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_1_1.txt ${CMAKE_CURRENT_BINARY_DIR}/one_skeleton_rips_distance_for_doc.txt)
+  add_test(ripscsvreader_doc_1_3_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_1_3.txt ${CMAKE_CURRENT_BINARY_DIR}/full_skeleton_rips_distance_for_doc.txt)
 endif()
diff --git a/src/Rips_complex/example/example_one_skeleton_rips_from_distance_matrix.cpp b/src/Rips_complex/example/example_one_skeleton_rips_from_distance_matrix.cpp
new file mode 100644
index 00000000..54fa3aa1
--- /dev/null
+++ b/src/Rips_complex/example/example_one_skeleton_rips_from_distance_matrix.cpp
@@ -0,0 +1,68 @@
+#include <gudhi/Rips_complex.h>
+// to construct a simplex_tree from rips complex
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/distance_functions.h>
+
+#include <iostream>
+#include <string>
+#include <limits>  // for std::numeric_limits
+
+void usage(int nbArgs, char * const progName) {
+  std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n";
+  std::cerr << "Usage: " << progName << " threshold\n";
+  std::cerr << "       i.e.: " << progName << " 12.0\n";
+  exit(-1);  // ----- >>
+}
+
+int main(int argc, char **argv) {
+  if (argc != 2) usage(argc, argv[0]);
+
+  double threshold = atof(argv[1]);
+
+  // Type definitions
+  using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
+  using Filtration_value = Simplex_tree::Filtration_value;
+  using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>;
+  using Distance_matrix = std::vector<std::vector<Filtration_value>>;
+
+  // User defined distance matrix is:
+  // | 0    0.94 0.77 0.99 0.11  |
+  // | 0.94 0    0.26 0.99 0.39  |
+  // | 0.77 0.26 0    0.28 0.97  |
+  // | 0.99 0.99 0.28 0    0.30  |
+  // | 0.11 0.39 0.97 0.30 0     |
+
+  Distance_matrix distances;
+  distances.push_back({});
+  distances.push_back({0.94});
+  distances.push_back({0.77, 0.26});
+  distances.push_back({0.99, 0.99, 0.28});
+  distances.push_back({0.11, 0.39, 0.97, 0.30});
+  
+  // ----------------------------------------------------------------------------
+  // Init of a rips complex from points
+  // ----------------------------------------------------------------------------
+  Rips_complex rips_complex_from_points(distances, threshold);
+
+  Simplex_tree simplex;
+  if (rips_complex_from_points.create_complex(simplex, 1)) {
+    // ----------------------------------------------------------------------------
+    // Display information about the one skeleton rips complex
+    // ----------------------------------------------------------------------------
+    std::cout << "Rips complex is of dimension " << simplex.dimension() <<
+        " - " << simplex.num_simplices() << " simplices - " <<
+        simplex.num_vertices() << " vertices." << std::endl;
+
+    std::cout << "Iterator on rips complex simplices in the filtration order, with [filtration value]:" <<
+        std::endl;
+    for (auto f_simplex : simplex.filtration_simplex_range()) {
+      std::cout << "   ( ";
+      for (auto vertex : simplex.simplex_vertex_range(f_simplex)) {
+        std::cout << vertex << " ";
+      }
+      std::cout << ") -> " << "[" << simplex.filtration(f_simplex) << "] ";
+      std::cout << std::endl;
+    }
+  }
+  return 0;
+}
diff --git a/src/Rips_complex/example/example_one_skeleton_rips_from_points.cpp b/src/Rips_complex/example/example_one_skeleton_rips_from_points.cpp
index 2e63d9a6..26517876 100644
--- a/src/Rips_complex/example/example_one_skeleton_rips_from_points.cpp
+++ b/src/Rips_complex/example/example_one_skeleton_rips_from_points.cpp
@@ -1,6 +1,4 @@
 #include <gudhi/Rips_complex.h>
-// to construct Rips_complex from a OFF file of points
-#include <gudhi/Points_off_io.h>
 // to construct a simplex_tree from rips complex
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/distance_functions.h>
diff --git a/src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp b/src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp
new file mode 100644
index 00000000..cfada84a
--- /dev/null
+++ b/src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp
@@ -0,0 +1,72 @@
+#include <gudhi/Rips_complex.h>
+// to construct Rips_complex from a OFF file of points
+#include <gudhi/reader_utils.h>
+// to construct a simplex_tree from rips complex
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/distance_functions.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.csv threshold dim_max [ouput_file.txt]\n";
+  std::cerr << "       i.e.: " << progName << " ../../data/distance_matrix/full_square_distance_matrix.csv 1.0 3\n";
+  exit(-1);  // ----- >>
+}
+
+int main(int argc, char **argv) {
+  if ((argc != 4) && (argc != 5)) usage(argc, (argv[0] - 1));
+
+  std::string csv_file_name(argv[1]);
+  double threshold = atof(argv[2]);
+  int dim_max = atoi(argv[3]);
+
+  // Type definitions
+  using Simplex_tree = Gudhi::Simplex_tree<>;
+  using Filtration_value = Simplex_tree::Filtration_value;
+  using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>;
+  using Distance_matrix = std::vector<std::vector<Filtration_value>>;
+
+  // ----------------------------------------------------------------------------
+  // Init of a rips complex from a distance matrix in a csv file
+  // Default separator is ';'
+  // ----------------------------------------------------------------------------
+  Distance_matrix distances = read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_file_name);
+  Rips_complex rips_complex_from_file(distances, threshold);
+
+  std::streambuf* streambufffer;
+  std::ofstream ouput_file_stream;
+
+  if (argc == 5) {
+    ouput_file_stream.open(std::string(argv[4]));
+    streambufffer = ouput_file_stream.rdbuf();
+  } else {
+    streambufffer = std::cout.rdbuf();
+  }
+
+  Simplex_tree simplex;
+  if (rips_complex_from_file.create_complex(simplex, dim_max)) {
+    std::ostream output_stream(streambufffer);
+
+    // ----------------------------------------------------------------------------
+    // Display information about the rips complex
+    // ----------------------------------------------------------------------------
+    output_stream << "Rips complex is of dimension " << simplex.dimension() <<
+        " - " << simplex.num_simplices() << " simplices - " <<
+        simplex.num_vertices() << " vertices." << std::endl;
+
+    output_stream << "Iterator on rips complex simplices in the filtration order, with [filtration value]:" <<
+        std::endl;
+    for (auto f_simplex : simplex.filtration_simplex_range()) {
+      output_stream << "   ( ";
+      for (auto vertex : simplex.simplex_vertex_range(f_simplex)) {
+        output_stream << vertex << " ";
+      }
+      output_stream << ") -> " << "[" << simplex.filtration(f_simplex) << "] ";
+      output_stream << std::endl;
+    }
+  }
+  ouput_file_stream.close();
+  return 0;
+}
diff --git a/src/Rips_complex/example/full_skeleton_rips_distance_for_doc.txt b/src/Rips_complex/example/full_skeleton_rips_distance_for_doc.txt
new file mode 100644
index 00000000..6744532d
--- /dev/null
+++ b/src/Rips_complex/example/full_skeleton_rips_distance_for_doc.txt
@@ -0,0 +1,32 @@
+Rips complex is of dimension 3 - 30 simplices - 5 vertices.
+Iterator on rips complex simplices in the filtration order, with [filtration value]:
+   ( 0 ) -> [0] 
+   ( 1 ) -> [0] 
+   ( 2 ) -> [0] 
+   ( 3 ) -> [0] 
+   ( 4 ) -> [0] 
+   ( 4 0 ) -> [0.11] 
+   ( 2 1 ) -> [0.26] 
+   ( 3 2 ) -> [0.28] 
+   ( 4 3 ) -> [0.3] 
+   ( 4 1 ) -> [0.39] 
+   ( 2 0 ) -> [0.77] 
+   ( 1 0 ) -> [0.94] 
+   ( 2 1 0 ) -> [0.94] 
+   ( 4 1 0 ) -> [0.94] 
+   ( 4 2 ) -> [0.97] 
+   ( 4 2 0 ) -> [0.97] 
+   ( 4 2 1 ) -> [0.97] 
+   ( 4 2 1 0 ) -> [0.97] 
+   ( 4 3 2 ) -> [0.97] 
+   ( 3 0 ) -> [0.99] 
+   ( 3 1 ) -> [0.99] 
+   ( 3 1 0 ) -> [0.99] 
+   ( 3 2 0 ) -> [0.99] 
+   ( 3 2 1 ) -> [0.99] 
+   ( 3 2 1 0 ) -> [0.99] 
+   ( 4 3 0 ) -> [0.99] 
+   ( 4 3 1 ) -> [0.99] 
+   ( 4 3 1 0 ) -> [0.99] 
+   ( 4 3 2 0 ) -> [0.99] 
+   ( 4 3 2 1 ) -> [0.99] 
diff --git a/src/Rips_complex/example/one_skeleton_rips_distance_for_doc.txt b/src/Rips_complex/example/one_skeleton_rips_distance_for_doc.txt
new file mode 100644
index 00000000..9bb1a7ab
--- /dev/null
+++ b/src/Rips_complex/example/one_skeleton_rips_distance_for_doc.txt
@@ -0,0 +1,17 @@
+Rips complex is of dimension 1 - 15 simplices - 5 vertices.
+Iterator on rips complex simplices in the filtration order, with [filtration value]:
+   ( 0 ) -> [0] 
+   ( 1 ) -> [0] 
+   ( 2 ) -> [0] 
+   ( 3 ) -> [0] 
+   ( 4 ) -> [0] 
+   ( 4 0 ) -> [0.11] 
+   ( 2 1 ) -> [0.26] 
+   ( 3 2 ) -> [0.28] 
+   ( 4 3 ) -> [0.3] 
+   ( 4 1 ) -> [0.39] 
+   ( 2 0 ) -> [0.77] 
+   ( 1 0 ) -> [0.94] 
+   ( 4 2 ) -> [0.97] 
+   ( 3 0 ) -> [0.99] 
+   ( 3 1 ) -> [0.99] 
diff --git a/src/Rips_complex/include/gudhi/Rips_complex.h b/src/Rips_complex/include/gudhi/Rips_complex.h
index 6f947f41..63207892 100644
--- a/src/Rips_complex/include/gudhi/Rips_complex.h
+++ b/src/Rips_complex/include/gudhi/Rips_complex.h
@@ -78,6 +78,19 @@ class Rips_complex {
     compute_proximity_graph<InputPointRange, Distance >(points, threshold, distance);
   }
 
+  /** \brief Rips_complex constructor from a distance matrix.
+   *
+   * @param[in] distance_matrix Range of distances.
+   * @param[in] threshold rips value.
+   * 
+   * The type InputDistanceRange must be a range for which std::begin and std::end return input iterators on a point.
+   */
+  template<typename InputDistanceRange>
+  Rips_complex(const InputDistanceRange& distance_matrix, Filtration_value threshold) {
+    compute_proximity_graph(boost::irange((size_t)0,distance_matrix.size()), threshold,
+                            [&](size_t i, size_t j){return distance_matrix[j][i];});
+  }
+
   /** \brief Initializes the simplicial complex from the 1-skeleton graph and expands it until a given maximal
    * dimension.
    *
diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h
index 85310f66..85ae8679 100644
--- a/src/common/doc/main_page.h
+++ b/src/common/doc/main_page.h
@@ -60,7 +60,7 @@
 <table border="0">
   <tr>
     <td width="25%">
-      <b>Author:</b> Cl&eacute;ment Maria<br>
+      <b>Author:</b> Cl&eacute;ment Maria, Pawel Dlotko, Vincent Rouvreau<br>
       <b>Introduced in:</b> GUDHI 1.4.0<br>
       <b>Copyright:</b> GPL v3<br>
     </td>
@@ -68,6 +68,7 @@
     Rips_complex is a simplicial complex constructed from a one skeleton graph.<br>
     The filtration value of each edge is computed from a user-given distance function and is inserted until a
     user-given threshold value.<br>
+    This complex can be built from a point cloud and a distance function, or from a distance matrix.<br>
     <b>User manual:</b> \ref rips_complex - <b>Reference manual:</b> Gudhi::rips_complex::Rips_complex
     </td>
  </tr>
diff --git a/src/common/include/gudhi/distance_functions.h b/src/common/include/gudhi/distance_functions.h
index 006df275..ed2c1f5d 100644
--- a/src/common/include/gudhi/distance_functions.h
+++ b/src/common/include/gudhi/distance_functions.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Clément Maria
  *
- *    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
@@ -25,9 +25,12 @@
 
 #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. */
+/** @file
+ * @brief Global distance functions
+ */
+
+/** @brief Compute the Euclidean distance between two Points given by a range of coordinates. The points are assumed to
+ * have the same dimension. */
 template< typename Filtration_value, typename Point >
 Filtration_value euclidean_distance(const Point &p1,const Point &p2) {
   Filtration_value dist = 0.;
diff --git a/src/common/include/gudhi/graph_simplicial_complex.h b/src/common/include/gudhi/graph_simplicial_complex.h
index 9dbcd891..5fe7c826 100644
--- a/src/common/include/gudhi/graph_simplicial_complex.h
+++ b/src/common/include/gudhi/graph_simplicial_complex.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Clément Maria
  *
- *    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
diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h
index 40d566d8..3799e583 100644
--- a/src/common/include/gudhi/reader_utils.h
+++ b/src/common/include/gudhi/reader_utils.h
@@ -34,14 +34,20 @@
 #include <string>
 #include <vector>
 
+// Keep this file tag for Doxygen to parse the code, otherwise, functions are not documented.
+// It is required for global functions and variables.
+
+/** @file
+ * @brief This file includes common file reader for GUDHI
+ */
+
 /**
- * \brief Read a set of points to turn it
- * into a vector< vector<double> > by filling points
+ * @brief Read a set of points to turn it into a vector< vector<double> > by filling points.
  *
- * File format: 1 point per line
- * X11 X12 ... X1d 
- * X21 X22 ... X2d
- * etc
+ * File format: 1 point per line<br>
+ * X11 X12 ... X1d<br>
+ * X21 X22 ... X2d<br>
+ * etc<br>
  */
 inline void read_points(std::string file_name, std::vector< std::vector< double > > & points) {
   std::ifstream in_file(file_name.c_str(), std::ios::in);
@@ -66,12 +72,12 @@ inline void read_points(std::string file_name, std::vector< std::vector< double
 }
 
 /**
- * \brief Read a graph from a file.
+ * @brief Read a graph from a file.
  *
- * File format: 1 simplex per line
- * Dim1 X11 X12 ... X1d Fil1 
- * Dim2 X21 X22 ... X2d Fil2
- * etc
+ * File format: 1 simplex per line<br>
+ * Dim1 X11 X12 ... X1d Fil1<br>
+ * Dim2 X21 X22 ... X2d Fil2<br>
+ * etc<br>
  *
  * The vertices must be labeled from 0 to n-1.
  * Every simplex must appear exactly once.
@@ -141,12 +147,12 @@ inline Graph_t read_graph(std::string file_name) {
 }
 
 /**
- * \brief Read a face from a file.
+ * @brief Read a face from a file.
  *
- * File format: 1 simplex per line
- * Dim1 X11 X12 ... X1d Fil1 
- * Dim2 X21 X22 ... X2d Fil2
- * etc
+ * File format: 1 simplex per line<br>
+ * Dim1 X11 X12 ... X1d Fil1<br>
+ * Dim2 X21 X22 ... X2d Fil2<br>
+ * etc<br>
  *
  * The vertices must be labeled from 0 to n-1.
  * Every simplex must appear exactly once.
@@ -167,18 +173,16 @@ bool read_simplex(std::istream & in_, std::vector< Vertex_handle > & simplex, Fi
 }
 
 /**
- * \brief Read a hasse simplex from a file.
+ * @brief Read a hasse simplex from a file.
  *
- * File format: 1 simplex per line
- * Dim1 k11 k12 ... k1Dim1 Fil1 
- * Dim2 k21 k22 ... k2Dim2 Fil2
- * etc
+ * File format: 1 simplex per line<br>
+ * Dim1 k11 k12 ... k1Dim1 Fil1<br>
+ * Dim2 k21 k22 ... k2Dim2 Fil2<br>
+ * etc<br>
  *
- * The key of a simplex is its position in the filtration order
- * and also the number of its row in the file.
- * Dimi ki1 ki2 ... kiDimi Fili means that the ith simplex in the 
- * filtration has dimension Dimi, filtration value fil1 and simplices with 
- * key ki1 ... kiDimi in its boundary.*/
+ * The key of a simplex is its position in the filtration order and also the number of its row in the file.
+ * Dimi ki1 ki2 ... kiDimi Fili means that the ith simplex in the filtration has dimension Dimi, filtration value
+ * fil1 and simplices with key ki1 ... kiDimi in its boundary.*/
 template< typename Simplex_key, typename Filtration_value >
 bool read_hasse_simplex(std::istream & in_, std::vector< Simplex_key > & boundary, Filtration_value & fil) {
   int dim;
@@ -197,27 +201,27 @@ bool read_hasse_simplex(std::istream & in_, std::vector< Simplex_key > & boundar
 }
 
 /**
- * \brief Read a lower triangular distance matrix from a csv file. We assume that the .csv store the whole
+ * @brief Read a lower triangular distance matrix from a csv file. We assume that the .csv store the whole
  * (square) matrix.
  * 
- * \author Pawel Dlotko
+ * @author Pawel Dlotko
  *
- * Square matrix file format:
- * 0;D12;...;D1j
- * D21;0;...;D2j
- * ...
- * Dj1;Dj2;...;0
+ * Square matrix file format:<br>
+ * 0;D12;...;D1j<br>
+ * D21;0;...;D2j<br>
+ * ...<br>
+ * Dj1;Dj2;...;0<br>
  *
- * lower matrix file format:
- * 0
- * D21;
- * D31;D32;
- * ...
- * Dj1;Dj2;...;Dj(j-1);
+ * lower matrix file format:<br>
+ * 0<br>
+ * D21;<br>
+ * D31;D32;<br>
+ * ...<br>
+ * Dj1;Dj2;...;Dj(j-1);<br>
  *
  **/
 template< typename Filtration_value >
-std::vector< std::vector< Filtration_value > > read_lower_triangular_matrix_from_csv_file(std::string filename,
+std::vector< std::vector< Filtration_value > > read_lower_triangular_matrix_from_csv_file(const std::string& filename,
                                                                                           const char separator=';') {
   bool dbg = false;
   if (dbg) {
diff --git a/src/common/test/test_distance_matrix_reader.cpp b/src/common/test/test_distance_matrix_reader.cpp
index 7eb7e846..a4c46bb1 100644
--- a/src/common/test/test_distance_matrix_reader.cpp
+++ b/src/common/test/test_distance_matrix_reader.cpp
@@ -47,21 +47,21 @@ BOOST_AUTO_TEST_CASE( lower_triangular_distance_matrix )
   std::cout << "from_lower_triangular size = " << from_lower_triangular.size() << std::endl;
   BOOST_CHECK(from_lower_triangular.size() == 5);
 
-  for (int i = 0; i < from_lower_triangular.size(); i++) {
+  for (std::size_t i = 0; i < from_lower_triangular.size(); i++) {
     std::cout << "from_lower_triangular[" << i << "] size = " << from_lower_triangular[i].size() << std::endl;
     BOOST_CHECK(from_lower_triangular[i].size() == i);
   }
   std::vector<double> expected = {1};
-  BOOST_CHECK(from_lower_triangular[0] == expected);
+  BOOST_CHECK(from_lower_triangular[1] == expected);
   
   expected = {2,3};
-  BOOST_CHECK(from_lower_triangular[0] == expected);
+  BOOST_CHECK(from_lower_triangular[2] == expected);
   
   expected = {4,5,6};
-  BOOST_CHECK(from_lower_triangular[0] == expected);
+  BOOST_CHECK(from_lower_triangular[3] == expected);
   
   expected = {7,8,9,10};
-  BOOST_CHECK(from_lower_triangular[0] == expected);
+  BOOST_CHECK(from_lower_triangular[4] == expected);
   
 }
 
@@ -78,8 +78,8 @@ BOOST_AUTO_TEST_CASE( full_square_distance_matrix )
   }
   std::cout << "from_full_square size = " << from_full_square.size() << std::endl;
   BOOST_CHECK(from_full_square.size() == 5);
-  for (int i = 0; i < from_lower_triangular.size(); i++) {
-    std::cout << "from_lower_triangular[" << i << "] size = " << from_lower_triangular[i].size() << std::endl;
-    BOOST_CHECK(from_lower_triangular[i].size() == i);
+  for (std::size_t i = 0; i < from_full_square.size(); i++) {
+    std::cout << "from_full_square[" << i << "] size = " << from_full_square[i].size() << std::endl;
+    BOOST_CHECK(from_full_square[i].size() == i);
   }  
 }
-- 
cgit v1.2.3


From 71f9bed6df48dedc0d4e8ef620496af9c494eccc Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 22 Nov 2016 13:29:59 +0000
Subject: Fix examples and tests

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/distance_matrix_in_rips_module@1767 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 4a1c78aec05d443e0525bf24a0cc7f7b5c628629
---
 .../full_square_distance_matrix.csv                |  12 +-
 src/Persistent_cohomology/example/CMakeLists.txt   |   9 +-
 src/Persistent_cohomology/example/README           |  50 ++++---
 .../example/rips_distance_matrix_persistence.cpp   | 145 +++++++++++++++++++++
 .../example/rips_persistence.cpp                   |   5 +-
 src/Rips_complex/doc/Intro_rips_complex.h          |   8 +-
 src/Rips_complex/example/CMakeLists.txt            |  20 ++-
 .../full_skeleton_rips_distance_for_doc.txt        |  32 -----
 .../example/full_skeleton_rips_for_doc.txt         |  26 ++++
 .../example/full_skeleton_rips_points_for_doc.txt  |  26 ----
 .../example/one_skeleton_rips_distance_for_doc.txt |  17 ---
 .../example/one_skeleton_rips_for_doc.txt          |  20 +++
 .../example/one_skeleton_rips_points_for_doc.txt   |  20 ---
 src/common/include/gudhi/reader_utils.h            |  21 ++-
 src/common/test/test_distance_matrix_reader.cpp    |   2 +-
 15 files changed, 264 insertions(+), 149 deletions(-)
 create mode 100644 src/Persistent_cohomology/example/rips_distance_matrix_persistence.cpp
 delete mode 100644 src/Rips_complex/example/full_skeleton_rips_distance_for_doc.txt
 create mode 100644 src/Rips_complex/example/full_skeleton_rips_for_doc.txt
 delete mode 100644 src/Rips_complex/example/full_skeleton_rips_points_for_doc.txt
 delete mode 100644 src/Rips_complex/example/one_skeleton_rips_distance_for_doc.txt
 create mode 100644 src/Rips_complex/example/one_skeleton_rips_for_doc.txt
 delete mode 100644 src/Rips_complex/example/one_skeleton_rips_points_for_doc.txt

(limited to 'src/common/test')

diff --git a/data/distance_matrix/full_square_distance_matrix.csv b/data/distance_matrix/full_square_distance_matrix.csv
index 7225a5fd..51512b03 100644
--- a/data/distance_matrix/full_square_distance_matrix.csv
+++ b/data/distance_matrix/full_square_distance_matrix.csv
@@ -1,5 +1,7 @@
-0;0.94;0.77;0.99;0.11;
-0.94;0;0.26;0.99;0.39;
-0.77;0.26;0;0.28;0.97;
-0.99;0.99;0.28;0;0.30;
-0.11;0.39;0.97;0.30;0;
+0;6.0827625303;5.8309518948;9.4339811321;13.0384048104;18.0277563773;17.88854382;
+6.0827625303;0;6.7082039325;6.3245553203;15.6524758425;19.6468827044;17.1172427686;
+5.8309518948;6.7082039325;0;5;8.94427191;13.152946438;12.0830459736;
+9.4339811321;6.3245553203;5;0;12.0415945788;14.7648230602;11;
+13.0384048104;15.6524758425;8.94427191;12.0415945788;0;5.3851648071;9.4868329805;
+18.0277563773;19.6468827044;13.152946438;14.7648230602;5.3851648071;0;7.2801098893;
+17.88854382;17.1172427686;12.0830459736;11;9.4868329805;7.2801098893;0;
\ No newline at end of file
diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt
index e50e8ca9..b2ac9736 100644
--- a/src/Persistent_cohomology/example/CMakeLists.txt
+++ b/src/Persistent_cohomology/example/CMakeLists.txt
@@ -11,6 +11,9 @@ target_link_libraries(plain_homology ${Boost_SYSTEM_LIBRARY})
 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_executable(rips_distance_matrix_persistence rips_distance_matrix_persistence.cpp)
+target_link_libraries(rips_distance_matrix_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
+
 add_executable(rips_persistence rips_persistence.cpp)
 target_link_libraries(rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
 
@@ -23,6 +26,7 @@ target_link_libraries(persistence_from_file ${Boost_SYSTEM_LIBRARY} ${Boost_PROG
 if (TBB_FOUND)
   target_link_libraries(plain_homology ${TBB_LIBRARIES})
   target_link_libraries(persistence_from_simple_simplex_tree ${TBB_LIBRARIES})
+  target_link_libraries(rips_distance_matrix_persistence ${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})
@@ -30,7 +34,8 @@ 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 0.16 -d 3 -p 3 -m 100)
+add_test(rips_distance_matrix ${CMAKE_CURRENT_BINARY_DIR}/rips_distance_matrix_persistence ${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv -r 1.0 -d 3 -p 3 -m 0)
+add_test(rips_persistence_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 3)
 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)
@@ -42,7 +47,7 @@ if(GMP_FOUND)
       if (TBB_FOUND)
         target_link_libraries(rips_multifield_persistence ${TBB_LIBRARIES})
       endif(TBB_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)
+   add_test(rips_multifield_persistence_2_71 ${CMAKE_CURRENT_BINARY_DIR}/rips_multifield_persistence ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 2 -q 71)
    endif(GMPXX_FOUND)
 endif(GMP_FOUND)
 
diff --git a/src/Persistent_cohomology/example/README b/src/Persistent_cohomology/example/README
index 7803e5ab..1063ea41 100644
--- a/src/Persistent_cohomology/example/README
+++ b/src/Persistent_cohomology/example/README
@@ -10,13 +10,13 @@ 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/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 2
 
 output:
-210  0 0 inf
-210  1 0.0702103 inf
-2  1 0.0702103 inf
-2  2 0.159992 inf
+2  0 0 inf 
+2  1 0.0983494 inf 
+2  1 0.104347 inf 
+2  2 0.138335 inf 
 
 
 Every line is of this format: p1*...*pr   dim b d
@@ -29,31 +29,45 @@ where
 
 with Z/3Z coefficients:
 
-./rips_persistence ../../data/points/Kl.txt -r 0.25 -d 3 -p 3 -m 100
+./rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 3
 
 output:
-3  0 0 inf
-3  1 0.0702103 inf
+3  0 0 inf 
+3  1 0.0983494 inf 
+3  1 0.104347 inf 
+3  2 0.138335 inf 
 
 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/tore3D_1307.off -r 0.25 -m 0.12 -d 3 -p 2 -q 3
 
 output:
-6  0 0 inf
-6  1 0.0702103 inf
-2  1 0.0702103 inf
-2  2 0.159992 inf
+6  0 0 inf 
+6  1 0.0983494 inf 
+6  1 0.104347 inf 
+6  2 0.138335 inf 
+6  0 0 0.122545 
+6  0 0 0.121171 
+6  0 0 0.120964 
+6  0 0 0.12057 
+6  0 0 0.12047 
+6  0 0 0.120414 
 
 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 -m 0.5 -d 3 -p 2 -q 71
 
 output:
-557940830126698960967415390  0 0 inf
-557940830126698960967415390  1 0.0702103 inf
-2  1 0.0702103 inf
-2  2 0.159992 inf
+557940830126698960967415390  0 0 inf 
+557940830126698960967415390  1 0.0983494 inf 
+557940830126698960967415390  1 0.104347 inf 
+557940830126698960967415390  2 0.138335 inf 
+557940830126698960967415390  0 0 0.122545 
+557940830126698960967415390  0 0 0.121171 
+557940830126698960967415390  0 0 0.120964 
+557940830126698960967415390  0 0 0.12057 
+557940830126698960967415390  0 0 0.12047 
+557940830126698960967415390  0 0 0.120414 
 
 ***********************************************************************************************************************
 Example of use of ALPHA:
diff --git a/src/Persistent_cohomology/example/rips_distance_matrix_persistence.cpp b/src/Persistent_cohomology/example/rips_distance_matrix_persistence.cpp
new file mode 100644
index 00000000..7a9e9c8b
--- /dev/null
+++ b/src/Persistent_cohomology/example/rips_distance_matrix_persistence.cpp
@@ -0,0 +1,145 @@
+/*    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, Vincent Rouvreau
+ *
+ *    Copyright (C) 2016  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 <gudhi/Rips_complex.h>
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Persistent_cohomology.h>
+#include <gudhi/reader_utils.h>
+
+#include <boost/program_options.hpp>
+
+#include <string>
+#include <vector>
+#include <limits>  // infinity
+
+// Types definition
+using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
+using Filtration_value = Simplex_tree::Filtration_value;
+using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>;
+using Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
+using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp >;
+using Distance_matrix = std::vector<std::vector<Filtration_value>>;
+
+void program_options(int argc, char * argv[]
+                     , std::string & csv_matrix_file
+                     , std::string & filediag
+                     , Filtration_value & threshold
+                     , int & dim_max
+                     , int & p
+                     , Filtration_value & min_persistence);
+
+int main(int argc, char * argv[]) {
+  std::string csv_matrix_file;
+  std::string filediag;
+  Filtration_value threshold;
+  int dim_max;
+  int p;
+  Filtration_value min_persistence;
+
+  program_options(argc, argv, csv_matrix_file, filediag, threshold, dim_max, p, min_persistence);
+
+  Distance_matrix distances = read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_matrix_file);
+  Rips_complex rips_complex_from_file(distances, threshold);
+
+  // Construct the Rips complex in a Simplex Tree
+  Simplex_tree simplex_tree;
+
+  if (rips_complex_from_file.create_complex(simplex_tree, dim_max)) {
+    std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n";
+    std::cout << "   and has dimension " << simplex_tree.dimension() << " \n";
+  
+    // Sort the simplices in the order of the filtration
+    simplex_tree.initialize_filtration();
+  
+    // Compute the persistence diagram of the complex
+    Persistent_cohomology pcoh(simplex_tree);
+    // initializes the coefficient field for homology
+    pcoh.init_coefficients(p);
+  
+    pcoh.compute_persistent_cohomology(min_persistence);
+  
+    // Output the diagram in filediag
+    if (filediag.empty()) {
+      pcoh.output_diagram();
+    } else {
+      std::ofstream out(filediag);
+      pcoh.output_diagram(out);
+      out.close();
+    }
+  }
+  return 0;
+}
+
+void program_options(int argc, char * argv[]
+                     , std::string & csv_matrix_file
+                     , std::string & filediag
+                     , Filtration_value & threshold
+                     , int & dim_max
+                     , int & p
+                     , Filtration_value & min_persistence) {
+  namespace po = boost::program_options;
+  po::options_description hidden("Hidden options");
+  hidden.add_options()
+      ("input-file", po::value<std::string>(&csv_matrix_file),
+       "Name of file containing a distance matrix. Can be square or lower triangular matrix. Separator is ';'.");
+
+  po::options_description visible("Allowed options", 100);
+  visible.add_options()
+      ("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(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.")
+      ("field-charac,p", po::value<int>(&p)->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 a Rips complex defined on a set of distance matrix.\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/rips_persistence.cpp b/src/Persistent_cohomology/example/rips_persistence.cpp
index 709c2eab..3fa8aa30 100644
--- a/src/Persistent_cohomology/example/rips_persistence.cpp
+++ b/src/Persistent_cohomology/example/rips_persistence.cpp
@@ -104,14 +104,15 @@ void program_options(int argc, char * argv[]
   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 ");
+       "Name of an OFF file containing a point set.\n");
 
   po::options_description visible("Allowed options", 100);
   visible.add_options()
       ("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(std::numeric_limits<Filtration_value>::infinity()),
+      ("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/Rips_complex/doc/Intro_rips_complex.h b/src/Rips_complex/doc/Intro_rips_complex.h
index d01b14bb..0ae89ffc 100644
--- a/src/Rips_complex/doc/Intro_rips_complex.h
+++ b/src/Rips_complex/doc/Intro_rips_complex.h
@@ -73,7 +73,7 @@ namespace rips_complex {
  *
  * the program output is:
  * 
- * \include Rips_complex/one_skeleton_rips_points_for_doc.txt
+ * \include Rips_complex/one_skeleton_rips_for_doc.txt
  * 
  * \subsection ripsoffexample Example from OFF file
  * 
@@ -93,7 +93,7 @@ namespace rips_complex {
  *
  * the program output is:
  * 
- * \include Rips_complex/full_skeleton_rips_points_for_doc.txt
+ * \include Rips_complex/full_skeleton_rips_for_doc.txt
  * 
  * 
  * 
@@ -116,7 +116,7 @@ namespace rips_complex {
  *
  * the program output is:
  * 
- * \include Rips_complex/one_skeleton_rips_distance_for_doc.txt
+ * \include Rips_complex/one_skeleton_rips_for_doc.txt
  * 
  * \subsection ripscsvdistanceexample Example from a distance matrix read in a csv file
  * 
@@ -135,7 +135,7 @@ namespace rips_complex {
  *
  * the program output is:
  * 
- * \include Rips_complex/full_skeleton_rips_distance_for_doc.txt
+ * \include Rips_complex/full_skeleton_rips_for_doc.txt
  * 
  * \copyright GNU General Public License v3.                         
  * \verbatim  Contact: gudhi-users@lists.gforge.inria.fr \endverbatim
diff --git a/src/Rips_complex/example/CMakeLists.txt b/src/Rips_complex/example/CMakeLists.txt
index 9ba9d941..c15a13d0 100644
--- a/src/Rips_complex/example/CMakeLists.txt
+++ b/src/Rips_complex/example/CMakeLists.txt
@@ -32,19 +32,17 @@ add_test(ripsoffreader_doc_12_1 ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader alphac
 add_test(ripsoffreader_doc_12_3 ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader alphacomplexdoc.off 12.0 3 ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_3.txt)
 
 file(COPY "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
-add_test(ripscsvdistancereader_doc_1_1 ${CMAKE_CURRENT_BINARY_DIR}/ripscsvdistancereader full_square_distance_matrix.csv 1.0 1 ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_1_1.txt)
-add_test(ripscsvdistancereader_doc_1_3 ${CMAKE_CURRENT_BINARY_DIR}/ripscsvdistancereader full_square_distance_matrix.csv 1.0 3 ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_1_3.txt)
+add_test(ripscsvdistancereader_doc_12_1 ${CMAKE_CURRENT_BINARY_DIR}/ripscsvdistancereader full_square_distance_matrix.csv 12.0 1 ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_12_1.txt)
+add_test(ripscsvdistancereader_doc_12_3 ${CMAKE_CURRENT_BINARY_DIR}/ripscsvdistancereader full_square_distance_matrix.csv 12.0 3 ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_12_3.txt)
 
 
 if (DIFF_PATH)
   # Do not forget to copy test results files in current binary dir
-  file(COPY "one_skeleton_rips_points_for_doc.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
-  file(COPY "full_skeleton_rips_points_for_doc.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
-  file(COPY "one_skeleton_rips_distance_for_doc.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
-  file(COPY "full_skeleton_rips_distance_for_doc.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
-
-  add_test(ripsoffreader_doc_12_1_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_1.txt ${CMAKE_CURRENT_BINARY_DIR}/one_skeleton_rips_points_for_doc.txt)
-  add_test(ripsoffreader_doc_12_3_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_3.txt ${CMAKE_CURRENT_BINARY_DIR}/full_skeleton_rips_points_for_doc.txt)
-  add_test(ripscsvreader_doc_1_1_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_1_1.txt ${CMAKE_CURRENT_BINARY_DIR}/one_skeleton_rips_distance_for_doc.txt)
-  add_test(ripscsvreader_doc_1_3_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_1_3.txt ${CMAKE_CURRENT_BINARY_DIR}/full_skeleton_rips_distance_for_doc.txt)
+  file(COPY "one_skeleton_rips_for_doc.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+  file(COPY "full_skeleton_rips_for_doc.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+
+  add_test(ripsoffreader_doc_12_1_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_1.txt ${CMAKE_CURRENT_BINARY_DIR}/one_skeleton_rips_for_doc.txt)
+  add_test(ripsoffreader_doc_12_3_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_3.txt ${CMAKE_CURRENT_BINARY_DIR}/full_skeleton_rips_for_doc.txt)
+  add_test(ripscsvreader_doc_12_1_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_12_1.txt ${CMAKE_CURRENT_BINARY_DIR}/one_skeleton_rips_for_doc.txt)
+  add_test(ripscsvreader_doc_12_3_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_12_3.txt ${CMAKE_CURRENT_BINARY_DIR}/full_skeleton_rips_for_doc.txt)
 endif()
diff --git a/src/Rips_complex/example/full_skeleton_rips_distance_for_doc.txt b/src/Rips_complex/example/full_skeleton_rips_distance_for_doc.txt
deleted file mode 100644
index 6744532d..00000000
--- a/src/Rips_complex/example/full_skeleton_rips_distance_for_doc.txt
+++ /dev/null
@@ -1,32 +0,0 @@
-Rips complex is of dimension 3 - 30 simplices - 5 vertices.
-Iterator on rips complex simplices in the filtration order, with [filtration value]:
-   ( 0 ) -> [0] 
-   ( 1 ) -> [0] 
-   ( 2 ) -> [0] 
-   ( 3 ) -> [0] 
-   ( 4 ) -> [0] 
-   ( 4 0 ) -> [0.11] 
-   ( 2 1 ) -> [0.26] 
-   ( 3 2 ) -> [0.28] 
-   ( 4 3 ) -> [0.3] 
-   ( 4 1 ) -> [0.39] 
-   ( 2 0 ) -> [0.77] 
-   ( 1 0 ) -> [0.94] 
-   ( 2 1 0 ) -> [0.94] 
-   ( 4 1 0 ) -> [0.94] 
-   ( 4 2 ) -> [0.97] 
-   ( 4 2 0 ) -> [0.97] 
-   ( 4 2 1 ) -> [0.97] 
-   ( 4 2 1 0 ) -> [0.97] 
-   ( 4 3 2 ) -> [0.97] 
-   ( 3 0 ) -> [0.99] 
-   ( 3 1 ) -> [0.99] 
-   ( 3 1 0 ) -> [0.99] 
-   ( 3 2 0 ) -> [0.99] 
-   ( 3 2 1 ) -> [0.99] 
-   ( 3 2 1 0 ) -> [0.99] 
-   ( 4 3 0 ) -> [0.99] 
-   ( 4 3 1 ) -> [0.99] 
-   ( 4 3 1 0 ) -> [0.99] 
-   ( 4 3 2 0 ) -> [0.99] 
-   ( 4 3 2 1 ) -> [0.99] 
diff --git a/src/Rips_complex/example/full_skeleton_rips_for_doc.txt b/src/Rips_complex/example/full_skeleton_rips_for_doc.txt
new file mode 100644
index 00000000..319931e0
--- /dev/null
+++ b/src/Rips_complex/example/full_skeleton_rips_for_doc.txt
@@ -0,0 +1,26 @@
+Rips complex is of dimension 3 - 24 simplices - 7 vertices.
+Iterator on rips 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 ) -> [5] 
+   ( 5 4 ) -> [5.38516] 
+   ( 2 0 ) -> [5.83095] 
+   ( 1 0 ) -> [6.08276] 
+   ( 3 1 ) -> [6.32456] 
+   ( 2 1 ) -> [6.7082] 
+   ( 2 1 0 ) -> [6.7082] 
+   ( 3 2 1 ) -> [6.7082] 
+   ( 6 5 ) -> [7.28011] 
+   ( 4 2 ) -> [8.94427] 
+   ( 3 0 ) -> [9.43398] 
+   ( 3 1 0 ) -> [9.43398] 
+   ( 3 2 0 ) -> [9.43398] 
+   ( 3 2 1 0 ) -> [9.43398] 
+   ( 6 4 ) -> [9.48683] 
+   ( 6 5 4 ) -> [9.48683] 
+   ( 6 3 ) -> [11] 
diff --git a/src/Rips_complex/example/full_skeleton_rips_points_for_doc.txt b/src/Rips_complex/example/full_skeleton_rips_points_for_doc.txt
deleted file mode 100644
index 319931e0..00000000
--- a/src/Rips_complex/example/full_skeleton_rips_points_for_doc.txt
+++ /dev/null
@@ -1,26 +0,0 @@
-Rips complex is of dimension 3 - 24 simplices - 7 vertices.
-Iterator on rips 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 ) -> [5] 
-   ( 5 4 ) -> [5.38516] 
-   ( 2 0 ) -> [5.83095] 
-   ( 1 0 ) -> [6.08276] 
-   ( 3 1 ) -> [6.32456] 
-   ( 2 1 ) -> [6.7082] 
-   ( 2 1 0 ) -> [6.7082] 
-   ( 3 2 1 ) -> [6.7082] 
-   ( 6 5 ) -> [7.28011] 
-   ( 4 2 ) -> [8.94427] 
-   ( 3 0 ) -> [9.43398] 
-   ( 3 1 0 ) -> [9.43398] 
-   ( 3 2 0 ) -> [9.43398] 
-   ( 3 2 1 0 ) -> [9.43398] 
-   ( 6 4 ) -> [9.48683] 
-   ( 6 5 4 ) -> [9.48683] 
-   ( 6 3 ) -> [11] 
diff --git a/src/Rips_complex/example/one_skeleton_rips_distance_for_doc.txt b/src/Rips_complex/example/one_skeleton_rips_distance_for_doc.txt
deleted file mode 100644
index 9bb1a7ab..00000000
--- a/src/Rips_complex/example/one_skeleton_rips_distance_for_doc.txt
+++ /dev/null
@@ -1,17 +0,0 @@
-Rips complex is of dimension 1 - 15 simplices - 5 vertices.
-Iterator on rips complex simplices in the filtration order, with [filtration value]:
-   ( 0 ) -> [0] 
-   ( 1 ) -> [0] 
-   ( 2 ) -> [0] 
-   ( 3 ) -> [0] 
-   ( 4 ) -> [0] 
-   ( 4 0 ) -> [0.11] 
-   ( 2 1 ) -> [0.26] 
-   ( 3 2 ) -> [0.28] 
-   ( 4 3 ) -> [0.3] 
-   ( 4 1 ) -> [0.39] 
-   ( 2 0 ) -> [0.77] 
-   ( 1 0 ) -> [0.94] 
-   ( 4 2 ) -> [0.97] 
-   ( 3 0 ) -> [0.99] 
-   ( 3 1 ) -> [0.99] 
diff --git a/src/Rips_complex/example/one_skeleton_rips_for_doc.txt b/src/Rips_complex/example/one_skeleton_rips_for_doc.txt
new file mode 100644
index 00000000..b0e25cc5
--- /dev/null
+++ b/src/Rips_complex/example/one_skeleton_rips_for_doc.txt
@@ -0,0 +1,20 @@
+Rips complex is of dimension 1 - 18 simplices - 7 vertices.
+Iterator on rips 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 ) -> [5] 
+   ( 5 4 ) -> [5.38516] 
+   ( 2 0 ) -> [5.83095] 
+   ( 1 0 ) -> [6.08276] 
+   ( 3 1 ) -> [6.32456] 
+   ( 2 1 ) -> [6.7082] 
+   ( 6 5 ) -> [7.28011] 
+   ( 4 2 ) -> [8.94427] 
+   ( 3 0 ) -> [9.43398] 
+   ( 6 4 ) -> [9.48683] 
+   ( 6 3 ) -> [11] 
diff --git a/src/Rips_complex/example/one_skeleton_rips_points_for_doc.txt b/src/Rips_complex/example/one_skeleton_rips_points_for_doc.txt
deleted file mode 100644
index b0e25cc5..00000000
--- a/src/Rips_complex/example/one_skeleton_rips_points_for_doc.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-Rips complex is of dimension 1 - 18 simplices - 7 vertices.
-Iterator on rips 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 ) -> [5] 
-   ( 5 4 ) -> [5.38516] 
-   ( 2 0 ) -> [5.83095] 
-   ( 1 0 ) -> [6.08276] 
-   ( 3 1 ) -> [6.32456] 
-   ( 2 1 ) -> [6.7082] 
-   ( 6 5 ) -> [7.28011] 
-   ( 4 2 ) -> [8.94427] 
-   ( 3 0 ) -> [9.43398] 
-   ( 6 4 ) -> [9.48683] 
-   ( 6 3 ) -> [11] 
diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h
index 3799e583..ddec5ba7 100644
--- a/src/common/include/gudhi/reader_utils.h
+++ b/src/common/include/gudhi/reader_utils.h
@@ -223,10 +223,9 @@ bool read_hasse_simplex(std::istream & in_, std::vector< Simplex_key > & boundar
 template< typename Filtration_value >
 std::vector< std::vector< Filtration_value > > read_lower_triangular_matrix_from_csv_file(const std::string& filename,
                                                                                           const char separator=';') {
-  bool dbg = false;
-  if (dbg) {
-    std::cerr << "Using procedure read_lower_triangular_matrix_from_csv_file \n";
-  }
+#ifdef DEBUG_TRACES
+  std::cout << "Using procedure read_lower_triangular_matrix_from_csv_file \n";
+#endif  // DEBUG_TRACES
   std::vector< std::vector< Filtration_value > > result;
   std::ifstream in;
   in.open(filename.c_str());
@@ -278,15 +277,15 @@ std::vector< std::vector< Filtration_value > > read_lower_triangular_matrix_from
   }
   in.close();
 
-  if (dbg) {
-    std::cerr << "Here is the matrix we read : \n";
-    for (size_t i = 0; i != result.size(); ++i) {
-      for (size_t j = 0; j != result[i].size(); ++j) {
-        std::cerr << result[i][j] << " ";
-      }
-      std::cerr << std::endl;
+#ifdef DEBUG_TRACES
+  std::cerr << "Here is the matrix we read : \n";
+  for (size_t i = 0; i != result.size(); ++i) {
+    for (size_t j = 0; j != result[i].size(); ++j) {
+      std::cerr << result[i][j] << " ";
     }
+    std::cerr << std::endl;
   }
+#endif  // DEBUG_TRACES
 
   return result;
 }  // read_lower_triangular_matrix_from_csv_file
diff --git a/src/common/test/test_distance_matrix_reader.cpp b/src/common/test/test_distance_matrix_reader.cpp
index a4c46bb1..95a73bd9 100644
--- a/src/common/test/test_distance_matrix_reader.cpp
+++ b/src/common/test/test_distance_matrix_reader.cpp
@@ -77,7 +77,7 @@ BOOST_AUTO_TEST_CASE( full_square_distance_matrix )
     std::cout << std::endl;
   }
   std::cout << "from_full_square size = " << from_full_square.size() << std::endl;
-  BOOST_CHECK(from_full_square.size() == 5);
+  BOOST_CHECK(from_full_square.size() == 7);
   for (std::size_t i = 0; i < from_full_square.size(); i++) {
     std::cout << "from_full_square[" << i << "] size = " << from_full_square[i].size() << std::endl;
     BOOST_CHECK(from_full_square[i].size() == i);
-- 
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