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

13 files changed, 218 insertions, 103 deletions

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_points_for_doc.txt b/src/Rips_complex/example/full_skeleton_rips_for_doc.txt
index 319931e0..319931e0 100644
--- a/src/Rips_complex/example/full_skeleton_rips_points_for_doc.txt
+++ b/src/Rips_complex/example/full_skeleton_rips_for_doc.txt
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_points_for_doc.txt b/src/Rips_complex/example/one_skeleton_rips_for_doc.txt
index b0e25cc5..b0e25cc5 100644
--- a/src/Rips_complex/example/one_skeleton_rips_points_for_doc.txt
+++ b/src/Rips_complex/example/one_skeleton_rips_for_doc.txt
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);