Merge last trunk modificat

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/rips_complex_from_correlation_matrix@3212 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: ea6296547b67ad82f5983d4309493e9131da7dd0

6 files changed, 349 insertions, 16 deletions

diff --git a/src/Rips_complex/doc/Intro_rips_complex.h b/src/Rips_complex/doc/Intro_rips_complex.h
index 401b689b..0c1acba7 100644
--- a/src/Rips_complex/doc/Intro_rips_complex.h
+++ b/src/Rips_complex/doc/Intro_rips_complex.h
@@ -169,8 +169,6 @@ namespace rips_complex {
  * 
  * All the other constructions discussed for Rips complex for distance matrix can be also performed for Rips complexes construction from correlation matrices.
  * 
- * \copyright GNU General Public License v3.                         
- * \verbatim  Contact: gudhi-users@lists.gforge.inria.fr \endverbatim
  */
 /** @} */  // end defgroup rips_complex
 
diff --git a/src/Rips_complex/test/test_rips_complex.cpp b/src/Rips_complex/test/test_rips_complex.cpp
index fc83f5f7..89afbc25 100644
--- a/src/Rips_complex/test/test_rips_complex.cpp
+++ b/src/Rips_complex/test/test_rips_complex.cpp
@@ -36,6 +36,7 @@
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/distance_functions.h>
 #include <gudhi/reader_utils.h>
+#include <gudhi/Unitary_tests_utils.h>
 
 // Type definitions
 using Point = std::vector<double>;
@@ -44,10 +45,6 @@ using Filtration_value = Simplex_tree::Filtration_value;
 using Rips_complex = Gudhi::rips_complex::Rips_complex<Simplex_tree::Filtration_value>;
 using Distance_matrix = std::vector<std::vector<Filtration_value>>;
 
-bool are_almost_the_same(float a, float b) {
-  return std::fabs(a - b) < std::numeric_limits<float>::epsilon();
-}
-
 BOOST_AUTO_TEST_CASE(RIPS_DOC_OFF_file) {
   // ----------------------------------------------------------------------------
   //
@@ -92,7 +89,7 @@ BOOST_AUTO_TEST_CASE(RIPS_DOC_OFF_file) {
       std::cout << ") - distance =" << Gudhi::Euclidean_distance()(vp.at(0), vp.at(1)) <<
           " - filtration =" << st.filtration(f_simplex) << std::endl;
       BOOST_CHECK(vp.size() == 2);
-      BOOST_CHECK(are_almost_the_same(st.filtration(f_simplex), Gudhi::Euclidean_distance()(vp.at(0), vp.at(1))));
+      GUDHI_TEST_FLOAT_EQUALITY_CHECK(st.filtration(f_simplex), Gudhi::Euclidean_distance()(vp.at(0), vp.at(1)));
     }
   }
 
@@ -113,14 +110,14 @@ BOOST_AUTO_TEST_CASE(RIPS_DOC_OFF_file) {
   Simplex_tree::Filtration_value f12 = st2.filtration(st2.find({1, 2}));
   Simplex_tree::Filtration_value f012 = st2.filtration(st2.find({0, 1, 2}));
   std::cout << "f012= " << f012 << " | f01= " << f01 << " - f02= " << f02 << " - f12= " << f12 << std::endl;
-  BOOST_CHECK(are_almost_the_same(f012, std::max(f01, std::max(f02,f12))));
+  GUDHI_TEST_FLOAT_EQUALITY_CHECK(f012, std::max(f01, std::max(f02,f12)));
   
   Simplex_tree::Filtration_value f45 = st2.filtration(st2.find({4, 5}));
   Simplex_tree::Filtration_value f56 = st2.filtration(st2.find({5, 6}));
   Simplex_tree::Filtration_value f46 = st2.filtration(st2.find({4, 6}));
   Simplex_tree::Filtration_value f456 = st2.filtration(st2.find({4, 5, 6}));
   std::cout << "f456= " << f456 << " | f45= " << f45 << " - f56= " << f56 << " - f46= " << f46 << std::endl;
-  BOOST_CHECK(are_almost_the_same(f456, std::max(f45, std::max(f56,f46))));
+  GUDHI_TEST_FLOAT_EQUALITY_CHECK(f456, std::max(f45, std::max(f56,f46)));
 
   const int DIMENSION_3 = 3;
   Simplex_tree st3;
@@ -140,7 +137,7 @@ BOOST_AUTO_TEST_CASE(RIPS_DOC_OFF_file) {
   Simplex_tree::Filtration_value f0123 = st3.filtration(st3.find({0, 1, 2, 3}));
   std::cout << "f0123= " << f0123 << " | f012= " << f012 << " - f123= " << f123 << " - f013= " << f013 <<
       " - f023= " << f023 << std::endl;
-  BOOST_CHECK(are_almost_the_same(f0123, std::max(f012, std::max(f123, std::max(f013, f023)))));
+  GUDHI_TEST_FLOAT_EQUALITY_CHECK(f0123, std::max(f012, std::max(f123, std::max(f013, f023))));
 
 }
 
@@ -219,12 +216,12 @@ BOOST_AUTO_TEST_CASE(Rips_complex_from_points) {
     std::cout << "dimension(" << st.dimension(f_simplex) << ") - f = " << st.filtration(f_simplex) << std::endl;
     switch (st.dimension(f_simplex)) {
       case 0:
-        BOOST_CHECK(are_almost_the_same(st.filtration(f_simplex), 0.0));
+        GUDHI_TEST_FLOAT_EQUALITY_CHECK(st.filtration(f_simplex), 0.0);
         break;
       case 1:
       case 2:
       case 3:
-        BOOST_CHECK(are_almost_the_same(st.filtration(f_simplex), 2.0));
+        GUDHI_TEST_FLOAT_EQUALITY_CHECK(st.filtration(f_simplex), 2.0);
         break;
       default:
         BOOST_CHECK(false);  // Shall not happen
@@ -276,7 +273,7 @@ BOOST_AUTO_TEST_CASE(Rips_doc_csv_file) {
       }
       std::cout << ") - filtration =" << st.filtration(f_simplex) << std::endl;
       BOOST_CHECK(vvh.size() == 2);
-      BOOST_CHECK(are_almost_the_same(st.filtration(f_simplex), distances[vvh.at(0)][vvh.at(1)]));
+      GUDHI_TEST_FLOAT_EQUALITY_CHECK(st.filtration(f_simplex), distances[vvh.at(0)][vvh.at(1)]);
     }
   }
 
@@ -297,14 +294,14 @@ BOOST_AUTO_TEST_CASE(Rips_doc_csv_file) {
   Simplex_tree::Filtration_value f12 = st2.filtration(st2.find({1, 2}));
   Simplex_tree::Filtration_value f012 = st2.filtration(st2.find({0, 1, 2}));
   std::cout << "f012= " << f012 << " | f01= " << f01 << " - f02= " << f02 << " - f12= " << f12 << std::endl;
-  BOOST_CHECK(are_almost_the_same(f012, std::max(f01, std::max(f02,f12))));
+  GUDHI_TEST_FLOAT_EQUALITY_CHECK(f012, std::max(f01, std::max(f02,f12)));
   
   Simplex_tree::Filtration_value f45 = st2.filtration(st2.find({4, 5}));
   Simplex_tree::Filtration_value f56 = st2.filtration(st2.find({5, 6}));
   Simplex_tree::Filtration_value f46 = st2.filtration(st2.find({4, 6}));
   Simplex_tree::Filtration_value f456 = st2.filtration(st2.find({4, 5, 6}));
   std::cout << "f456= " << f456 << " | f45= " << f45 << " - f56= " << f56 << " - f46= " << f46 << std::endl;
-  BOOST_CHECK(are_almost_the_same(f456, std::max(f45, std::max(f56,f46))));
+  GUDHI_TEST_FLOAT_EQUALITY_CHECK(f456, std::max(f45, std::max(f56,f46)));
 
   const int DIMENSION_3 = 3;
   Simplex_tree st3;
@@ -324,7 +321,7 @@ BOOST_AUTO_TEST_CASE(Rips_doc_csv_file) {
   Simplex_tree::Filtration_value f0123 = st3.filtration(st3.find({0, 1, 2, 3}));
   std::cout << "f0123= " << f0123 << " | f012= " << f012 << " - f123= " << f123 << " - f013= " << f013 <<
       " - f023= " << f023 << std::endl;
-  BOOST_CHECK(are_almost_the_same(f0123, std::max(f012, std::max(f123, std::max(f013, f023)))));
+  GUDHI_TEST_FLOAT_EQUALITY_CHECK(f0123, std::max(f012, std::max(f123, std::max(f013, f023))));
 
 }
 
diff --git a/src/Rips_complex/utilities/CMakeLists.txt b/src/Rips_complex/utilities/CMakeLists.txt
new file mode 100644
index 00000000..baa571fa
--- /dev/null
+++ b/src/Rips_complex/utilities/CMakeLists.txt
@@ -0,0 +1,21 @@
+cmake_minimum_required(VERSION 2.6)
+project(Rips_complex_utilities)
+
+add_executable(rips_distance_matrix_persistence rips_distance_matrix_persistence.cpp)
+target_link_libraries(rips_distance_matrix_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY})
+
+add_executable(rips_persistence rips_persistence.cpp)
+target_link_libraries(rips_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY})
+
+if (TBB_FOUND)
+  target_link_libraries(rips_distance_matrix_persistence ${TBB_LIBRARIES})
+  target_link_libraries(rips_persistence ${TBB_LIBRARIES})
+endif()
+
+add_test(NAME Rips_complex_utility_from_rips_distance_matrix COMMAND $<TARGET_FILE:rips_distance_matrix_persistence>
+    "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" "-r" "1.0" "-d" "3" "-p" "3" "-m" "0")
+add_test(NAME Rips_complex_utility_from_rips_on_tore_3D COMMAND $<TARGET_FILE:rips_persistence>
+    "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3")
+
+install(TARGETS rips_distance_matrix_persistence DESTINATION bin)
+install(TARGETS rips_persistence DESTINATION bin)
diff --git a/src/Rips_complex/utilities/rips_distance_matrix_persistence.cpp b/src/Rips_complex/utilities/rips_distance_matrix_persistence.cpp
new file mode 100644
index 00000000..ca3c0327
--- /dev/null
+++ b/src/Rips_complex/utilities/rips_distance_matrix_persistence.cpp
@@ -0,0 +1,133 @@
+/*    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 = Gudhi::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;
+
+  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/Rips_complex/utilities/rips_persistence.cpp b/src/Rips_complex/utilities/rips_persistence.cpp
new file mode 100644
index 00000000..8405c014
--- /dev/null
+++ b/src/Rips_complex/utilities/rips_persistence.cpp
@@ -0,0 +1,135 @@
+/*    This file is part of the Gudhi Library. The Gudhi library
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++
+ *    library for computational topology.
+ *
+ *    Author(s):       Clément Maria
+ *
+ *    Copyright (C) 2014  INRIA
+ *
+ *    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/distance_functions.h>
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Persistent_cohomology.h>
+#include <gudhi/Points_off_io.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 Point = std::vector<double>;
+using Points_off_reader = Gudhi::Points_off_reader<Point>;
+
+void program_options(int argc, char* argv[], std::string& off_file_points, std::string& filediag,
+                     Filtration_value& threshold, int& dim_max, int& p, Filtration_value& min_persistence);
+
+int main(int argc, char* argv[]) {
+  std::string off_file_points;
+  std::string filediag;
+  Filtration_value threshold;
+  int dim_max;
+  int p;
+  Filtration_value min_persistence;
+
+  program_options(argc, argv, off_file_points, filediag, threshold, dim_max, p, min_persistence);
+
+  Points_off_reader off_reader(off_file_points);
+  Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold, Gudhi::Euclidean_distance());
+
+  // Construct the Rips complex in a Simplex Tree
+  Simplex_tree simplex_tree;
+
+  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& off_file_points, 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>(&off_file_points),
+                       "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()),
+      "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 input points.\n \n";
+    std::cout << "The output diagram contains one bar per line, written with the convention: \n";
+    std::cout << "   p   dim b d \n";
+    std::cout << "where dim is the dimension of the homological feature,\n";
+    std::cout << "b and d are respectively the birth and death of the feature and \n";
+    std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl;
+
+    std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
+    std::cout << visible << std::endl;
+    std::abort();
+  }
+}
diff --git a/src/Rips_complex/utilities/ripscomplex.md b/src/Rips_complex/utilities/ripscomplex.md
new file mode 100644
index 00000000..4291fae7
--- /dev/null
+++ b/src/Rips_complex/utilities/ripscomplex.md
@@ -0,0 +1,49 @@
+
+
+# Rips complex #
+
+## rips_persistence ##
+This program computes the persistent homology with coefficient field *Z/pZ* of a Rips complex defined on a set of input points, using Euclidean distance. The output diagram contains one bar per line, written with the convention:
+
+`p dim birth death`
+
+where `dim` is the dimension of the homological feature, `birth` and `death` are respectively the birth and death of the feature, and `p` is the characteristic of the field *Z/pZ* used for homology coefficients (`p` must be a prime number).
+
+**Usage**
+
+`rips_persistence [options] <OFF input file>`
+
+**Allowed options**
+
+* `-h [ --help ]` Produce help message
+* `-o [ --output-file ]` Name of file in which the persistence diagram is written. Default print in standard output.
+* `-r [ --max-edge-length ]` (default = inf) Maximal length of an edge for the Rips complex construction.
+* `-d [ --cpx-dimension ]` (default = 1) Maximal dimension of the Rips complex we want to compute.
+* `-p [ --field-charac ]` (default = 11)     Characteristic p of the coefficient field Z/pZ for computing homology.
+* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals.
+
+Beware: this program may use a lot of RAM and take a lot of time if `max-edge-length` is set to a large value.
+
+**Example 1 with Z/2Z coefficients**
+
+`rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 2`
+
+**Example 2 with Z/3Z coefficients**
+
+`rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 3`
+
+
+## rips_distance_matrix_persistence ##
+
+Same as `rips_persistence` but taking a distance matrix as input.
+
+**Usage**
+
+`rips_persistence [options] <CSV input file>`
+
+where
+`<CSV input file>` is the path to the file containing a distance matrix. Can be square or lower triangular matrix. Separator is ';'.
+
+**Example**
+
+`rips_distance_matrix_persistence data/distance_matrix/full_square_distance_matrix.csv -r 15 -d 3 -p 3 -m 0`