Merge tag 'tags/gudhi-release-3.2.0' into dfsg/latest

9 files changed, 76 insertions, 76 deletions

diff --git a/src/Cech_complex/benchmark/CMakeLists.txt b/src/Cech_complex/benchmark/CMakeLists.txt
index b7697764..c04bca53 100644
--- a/src/Cech_complex/benchmark/CMakeLists.txt
+++ b/src/Cech_complex/benchmark/CMakeLists.txt
@@ -5,7 +5,7 @@ project(Cech_complex_benchmark)
 file(COPY "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
 
 add_executable(cech_complex_benchmark cech_complex_benchmark.cpp)
-target_link_libraries(cech_complex_benchmark ${Boost_SYSTEM_LIBRARY} ${Boost_FILESYSTEM_LIBRARY})
+target_link_libraries(cech_complex_benchmark Boost::filesystem)
 
 if (TBB_FOUND)
   target_link_libraries(cech_complex_benchmark ${TBB_LIBRARIES})
diff --git a/src/Cech_complex/benchmark/cech_complex_benchmark.cpp b/src/Cech_complex/benchmark/cech_complex_benchmark.cpp
index d2d71dbf..e489e8a4 100644
--- a/src/Cech_complex/benchmark/cech_complex_benchmark.cpp
+++ b/src/Cech_complex/benchmark/cech_complex_benchmark.cpp
@@ -68,24 +68,24 @@ int main(int argc, char* argv[]) {
   Proximity_graph euclidean_prox_graph = Gudhi::compute_proximity_graph<Simplex_tree>(
       off_reader.get_point_cloud(), threshold, Gudhi::Euclidean_distance());
 
-  std::cout << euclidean_clock << std::endl;
+  std::clog << euclidean_clock << std::endl;
 
   Gudhi::Clock miniball_clock("Minimal_enclosing_ball_radius");
   // Compute the proximity graph of the points
   Proximity_graph miniball_prox_graph = Gudhi::compute_proximity_graph<Simplex_tree>(
       off_reader.get_point_cloud(), threshold, Minimal_enclosing_ball_radius());
-  std::cout << miniball_clock << std::endl;
+  std::clog << miniball_clock << std::endl;
 
   Gudhi::Clock common_miniball_clock("Gudhi::Minimal_enclosing_ball_radius()");
   // Compute the proximity graph of the points
   Proximity_graph common_miniball_prox_graph = Gudhi::compute_proximity_graph<Simplex_tree>(
       off_reader.get_point_cloud(), threshold, Gudhi::Minimal_enclosing_ball_radius());
-  std::cout << common_miniball_clock << std::endl;
+  std::clog << common_miniball_clock << std::endl;
 
   boost::filesystem::path full_path(boost::filesystem::current_path());
-  std::cout << "Current path is : " << full_path << std::endl;
+  std::clog << "Current path is : " << full_path << std::endl;
 
-  std::cout << "File name;Radius;Rips time;Cech time; Ratio Rips/Cech time;Rips nb simplices;Cech nb simplices;"
+  std::clog << "File name;Radius;Rips time;Cech time; Ratio Rips/Cech time;Rips nb simplices;Cech nb simplices;"
             << std::endl;
   boost::filesystem::directory_iterator end_itr;  // default construction yields past-the-end
   for (boost::filesystem::directory_iterator itr(boost::filesystem::current_path()); itr != end_itr; ++itr) {
@@ -96,8 +96,8 @@ int main(int argc, char* argv[]) {
         Point p0 = off_reader.get_point_cloud()[0];
 
         for (Filtration_value radius = 0.1; radius < 0.4; radius += 0.1) {
-          std::cout << itr->path().stem() << ";";
-          std::cout << radius << ";";
+          std::clog << itr->path().stem() << ";";
+          std::clog << radius << ";";
           Gudhi::Clock rips_clock("Rips computation");
           Rips_complex rips_complex_from_points(off_reader.get_point_cloud(), radius,
                                                 Gudhi::Minimal_enclosing_ball_radius());
@@ -107,7 +107,7 @@ int main(int argc, char* argv[]) {
           // Display information about the Rips complex
           // ------------------------------------------
           double rips_sec = rips_clock.num_seconds();
-          std::cout << rips_sec << ";";
+          std::clog << rips_sec << ";";
 
           Gudhi::Clock cech_clock("Cech computation");
           Cech_complex cech_complex_from_points(off_reader.get_point_cloud(), radius);
@@ -117,12 +117,12 @@ int main(int argc, char* argv[]) {
           // Display information about the Cech complex
           // ------------------------------------------
           double cech_sec = cech_clock.num_seconds();
-          std::cout << cech_sec << ";";
-          std::cout << cech_sec / rips_sec << ";";
+          std::clog << cech_sec << ";";
+          std::clog << cech_sec / rips_sec << ";";
 
           assert(rips_stree.num_simplices() >= cech_stree.num_simplices());
-          std::cout << rips_stree.num_simplices() << ";";
-          std::cout << cech_stree.num_simplices() << ";" << std::endl;
+          std::clog << rips_stree.num_simplices() << ";";
+          std::clog << cech_stree.num_simplices() << ";" << std::endl;
         }
       }
     }
diff --git a/src/Cech_complex/example/CMakeLists.txt b/src/Cech_complex/example/CMakeLists.txt
index ab391215..98757988 100644
--- a/src/Cech_complex/example/CMakeLists.txt
+++ b/src/Cech_complex/example/CMakeLists.txt
@@ -2,7 +2,7 @@ cmake_minimum_required(VERSION 2.6)
 project(Cech_complex_examples)
 
 add_executable ( Cech_complex_example_step_by_step cech_complex_step_by_step.cpp )
-target_link_libraries(Cech_complex_example_step_by_step ${Boost_PROGRAM_OPTIONS_LIBRARY})
+target_link_libraries(Cech_complex_example_step_by_step Boost::program_options)
 if (TBB_FOUND)
   target_link_libraries(Cech_complex_example_step_by_step ${TBB_LIBRARIES})
 endif()
diff --git a/src/Cech_complex/example/cech_complex_example_from_points.cpp b/src/Cech_complex/example/cech_complex_example_from_points.cpp
index 3cc5a4df..1a1f708c 100644
--- a/src/Cech_complex/example/cech_complex_example_from_points.cpp
+++ b/src/Cech_complex/example/cech_complex_example_from_points.cpp
@@ -37,18 +37,18 @@ int main() {
   // ----------------------------------------------------------------------------
   // Display information about the one skeleton Cech complex
   // ----------------------------------------------------------------------------
-  std::cout << "Cech complex is of dimension " << stree.dimension() << " - " << stree.num_simplices() << " simplices - "
+  std::clog << "Cech complex is of dimension " << stree.dimension() << " - " << stree.num_simplices() << " simplices - "
             << stree.num_vertices() << " vertices." << std::endl;
 
-  std::cout << "Iterator on Cech complex simplices in the filtration order, with [filtration value]:" << std::endl;
+  std::clog << "Iterator on Cech complex simplices in the filtration order, with [filtration value]:" << std::endl;
   for (auto f_simplex : stree.filtration_simplex_range()) {
-    std::cout << "   ( ";
+    std::clog << "   ( ";
     for (auto vertex : stree.simplex_vertex_range(f_simplex)) {
-      std::cout << vertex << " ";
+      std::clog << vertex << " ";
     }
-    std::cout << ") -> "
+    std::clog << ") -> "
               << "[" << stree.filtration(f_simplex) << "] ";
-    std::cout << std::endl;
+    std::clog << std::endl;
   }
   return 0;
 }
diff --git a/src/Cech_complex/example/cech_complex_step_by_step.cpp b/src/Cech_complex/example/cech_complex_step_by_step.cpp
index b3d05697..f59f0293 100644
--- a/src/Cech_complex/example/cech_complex_step_by_step.cpp
+++ b/src/Cech_complex/example/cech_complex_step_by_step.cpp
@@ -51,12 +51,12 @@ class Cech_blocker {
     for (auto vertex : simplex_tree_.simplex_vertex_range(sh)) {
       points.push_back(point_cloud_[vertex]);
 #ifdef DEBUG_TRACES
-      std::cout << "#(" << vertex << ")#";
+      std::clog << "#(" << vertex << ")#";
 #endif  // DEBUG_TRACES
     }
     Filtration_value radius = Gudhi::Minimal_enclosing_ball_radius()(points);
 #ifdef DEBUG_TRACES
-    std::cout << "radius = " << radius << " - " << (radius > max_radius_) << std::endl;
+    std::clog << "radius = " << radius << " - " << (radius > max_radius_) << std::endl;
 #endif  // DEBUG_TRACES
     simplex_tree_.assign_filtration(sh, radius);
     return (radius > max_radius_);
@@ -96,23 +96,23 @@ int main(int argc, char* argv[]) {
   // expand the graph until dimension dim_max
   st.expansion_with_blockers(dim_max, Cech_blocker(st, max_radius, off_reader.get_point_cloud()));
 
-  std::cout << "The complex contains " << st.num_simplices() << " simplices \n";
-  std::cout << "   and has dimension " << st.dimension() << " \n";
+  std::clog << "The complex contains " << st.num_simplices() << " simplices \n";
+  std::clog << "   and has dimension " << st.dimension() << " \n";
 
   // Sort the simplices in the order of the filtration
   st.initialize_filtration();
 
 #if DEBUG_TRACES
-  std::cout << "********************************************************************\n";
-  std::cout << "* The complex contains " << st.num_simplices() << " simplices - dimension=" << st.dimension() << "\n";
-  std::cout << "* Iterator on Simplices in the filtration, with [filtration value]:\n";
+  std::clog << "********************************************************************\n";
+  std::clog << "* The complex contains " << st.num_simplices() << " simplices - dimension=" << st.dimension() << "\n";
+  std::clog << "* Iterator on Simplices in the filtration, with [filtration value]:\n";
   for (auto f_simplex : st.filtration_simplex_range()) {
-    std::cout << "   "
+    std::clog << "   "
               << "[" << st.filtration(f_simplex) << "] ";
     for (auto vertex : st.simplex_vertex_range(f_simplex)) {
-      std::cout << static_cast<int>(vertex) << " ";
+      std::clog << static_cast<int>(vertex) << " ";
     }
-    std::cout << std::endl;
+    std::clog << std::endl;
   }
 #endif  // DEBUG_TRACES
 
@@ -144,11 +144,11 @@ void program_options(int argc, char* argv[], std::string& off_file_points, Filtr
   po::notify(vm);
 
   if (vm.count("help") || !vm.count("input-file")) {
-    std::cout << std::endl;
-    std::cout << "Construct a Cech complex defined on a set of input points.\n \n";
+    std::clog << std::endl;
+    std::clog << "Construct a Cech complex defined on a set of input points.\n \n";
 
-    std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
-    std::cout << visible << std::endl;
+    std::clog << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
+    std::clog << visible << std::endl;
     exit(-1);
   }
 }
diff --git a/src/Cech_complex/include/gudhi/Cech_complex_blocker.h b/src/Cech_complex/include/gudhi/Cech_complex_blocker.h
index 068cdde3..31b9aab5 100644
--- a/src/Cech_complex/include/gudhi/Cech_complex_blocker.h
+++ b/src/Cech_complex/include/gudhi/Cech_complex_blocker.h
@@ -53,12 +53,12 @@ class Cech_blocker {
     for (auto vertex : sc_ptr_->simplex_vertex_range(sh)) {
       points.push_back(cc_ptr_->get_point(vertex));
 #ifdef DEBUG_TRACES
-      std::cout << "#(" << vertex << ")#";
+      std::clog << "#(" << vertex << ")#";
 #endif  // DEBUG_TRACES
     }
     Filtration_value radius = Gudhi::Minimal_enclosing_ball_radius()(points);
 #ifdef DEBUG_TRACES
-    if (radius > cc_ptr_->max_radius()) std::cout << "radius > max_radius => expansion is blocked\n";
+    if (radius > cc_ptr_->max_radius()) std::clog << "radius > max_radius => expansion is blocked\n";
 #endif  // DEBUG_TRACES
     sc_ptr_->assign_filtration(sh, radius);
     return (radius > cc_ptr_->max_radius());
diff --git a/src/Cech_complex/test/test_cech_complex.cpp b/src/Cech_complex/test/test_cech_complex.cpp
index c6b15d7f..6e00d7b5 100644
--- a/src/Cech_complex/test/test_cech_complex.cpp
+++ b/src/Cech_complex/test/test_cech_complex.cpp
@@ -58,7 +58,7 @@ BOOST_AUTO_TEST_CASE(Cech_complex_for_documentation) {
   points.push_back({-0.5, 2.});                // 10
 
   Filtration_value max_radius = 1.0;
-  std::cout << "========== NUMBER OF POINTS = " << points.size() << " - Cech max_radius = " << max_radius
+  std::clog << "========== NUMBER OF POINTS = " << points.size() << " - Cech max_radius = " << max_radius
             << "==========" << std::endl;
 
   Cech_complex cech_complex_for_doc(points, max_radius);
@@ -72,14 +72,14 @@ BOOST_AUTO_TEST_CASE(Cech_complex_for_documentation) {
   const int DIMENSION_1 = 1;
   Simplex_tree st;
   cech_complex_for_doc.create_complex(st, DIMENSION_1);
-  std::cout << "st.dimension()=" << st.dimension() << std::endl;
+  std::clog << "st.dimension()=" << st.dimension() << std::endl;
   BOOST_CHECK(st.dimension() == DIMENSION_1);
 
   const int NUMBER_OF_VERTICES = 11;
-  std::cout << "st.num_vertices()=" << st.num_vertices() << std::endl;
+  std::clog << "st.num_vertices()=" << st.num_vertices() << std::endl;
   BOOST_CHECK(st.num_vertices() == NUMBER_OF_VERTICES);
 
-  std::cout << "st.num_simplices()=" << st.num_simplices() << std::endl;
+  std::clog << "st.num_simplices()=" << st.num_simplices() << std::endl;
   BOOST_CHECK(st.num_simplices() == 27);
 
   // Check filtration values of vertices is 0.0
@@ -91,12 +91,12 @@ BOOST_AUTO_TEST_CASE(Cech_complex_for_documentation) {
   for (auto f_simplex : st.skeleton_simplex_range(DIMENSION_1)) {
     if (DIMENSION_1 == st.dimension(f_simplex)) {
       std::vector<Point> vp;
-      std::cout << "vertex = (";
+      std::clog << "vertex = (";
       for (auto vertex : st.simplex_vertex_range(f_simplex)) {
-        std::cout << vertex << ",";
+        std::clog << vertex << ",";
         vp.push_back(points.at(vertex));
       }
-      std::cout << ") - distance =" << Gudhi::Minimal_enclosing_ball_radius()(vp.at(0), vp.at(1))
+      std::clog << ") - distance =" << Gudhi::Minimal_enclosing_ball_radius()(vp.at(0), vp.at(1))
                 << " - filtration =" << st.filtration(f_simplex) << std::endl;
       BOOST_CHECK(vp.size() == 2);
       GUDHI_TEST_FLOAT_EQUALITY_CHECK(st.filtration(f_simplex),
@@ -112,13 +112,13 @@ BOOST_AUTO_TEST_CASE(Cech_complex_for_documentation) {
 
   Simplex_tree st2;
   cech_complex_for_doc.create_complex(st2, DIMENSION_2);
-  std::cout << "st2.dimension()=" << st2.dimension() << std::endl;
+  std::clog << "st2.dimension()=" << st2.dimension() << std::endl;
   BOOST_CHECK(st2.dimension() == DIMENSION_2);
 
-  std::cout << "st2.num_vertices()=" << st2.num_vertices() << std::endl;
+  std::clog << "st2.num_vertices()=" << st2.num_vertices() << std::endl;
   BOOST_CHECK(st2.num_vertices() == NUMBER_OF_VERTICES);
 
-  std::cout << "st2.num_simplices()=" << st2.num_simplices() << std::endl;
+  std::clog << "st2.num_simplices()=" << st2.num_simplices() << std::endl;
   BOOST_CHECK(st2.num_simplices() == 30);
 
   Point_cloud points012;
@@ -129,7 +129,7 @@ BOOST_AUTO_TEST_CASE(Cech_complex_for_documentation) {
   Min_sphere ms012(dimension, points012.begin(), points012.end());
 
   Simplex_tree::Filtration_value f012 = st2.filtration(st2.find({0, 1, 2}));
-  std::cout << "f012= " << f012 << " | ms012_radius= " << std::sqrt(ms012.squared_radius()) << std::endl;
+  std::clog << "f012= " << f012 << " | ms012_radius= " << std::sqrt(ms012.squared_radius()) << std::endl;
 
   GUDHI_TEST_FLOAT_EQUALITY_CHECK(f012, std::sqrt(ms012.squared_radius()));
 
@@ -140,7 +140,7 @@ BOOST_AUTO_TEST_CASE(Cech_complex_for_documentation) {
   Min_sphere ms1410(dimension, points1410.begin(), points1410.end());
 
   Simplex_tree::Filtration_value f1410 = st2.filtration(st2.find({1, 4, 10}));
-  std::cout << "f1410= " << f1410 << " | ms1410_radius= " << std::sqrt(ms1410.squared_radius()) << std::endl;
+  std::clog << "f1410= " << f1410 << " | ms1410_radius= " << std::sqrt(ms1410.squared_radius()) << std::endl;
 
   GUDHI_TEST_FLOAT_EQUALITY_CHECK(f1410, std::sqrt(ms1410.squared_radius()));
 
@@ -151,7 +151,7 @@ BOOST_AUTO_TEST_CASE(Cech_complex_for_documentation) {
   Min_sphere ms469(dimension, points469.begin(), points469.end());
 
   Simplex_tree::Filtration_value f469 = st2.filtration(st2.find({4, 6, 9}));
-  std::cout << "f469= " << f469 << " | ms469_radius= " << std::sqrt(ms469.squared_radius()) << std::endl;
+  std::clog << "f469= " << f469 << " | ms469_radius= " << std::sqrt(ms469.squared_radius()) << std::endl;
 
   GUDHI_TEST_FLOAT_EQUALITY_CHECK(f469, std::sqrt(ms469.squared_radius()));
 
@@ -178,35 +178,35 @@ BOOST_AUTO_TEST_CASE(Cech_complex_from_points) {
   // ----------------------------------------------------------------------------
   Cech_complex cech_complex_from_points(points, 2.0);
 
-  std::cout << "========== cech_complex_from_points ==========" << std::endl;
+  std::clog << "========== cech_complex_from_points ==========" << std::endl;
   Simplex_tree st;
   const int DIMENSION = 3;
   cech_complex_from_points.create_complex(st, DIMENSION);
 
   // Another way to check num_simplices
-  std::cout << "Iterator on Cech complex simplices in the filtration order, with [filtration value]:" << std::endl;
+  std::clog << "Iterator on Cech complex simplices in the filtration order, with [filtration value]:" << std::endl;
   int num_simplices = 0;
   for (auto f_simplex : st.filtration_simplex_range()) {
     num_simplices++;
-    std::cout << "   ( ";
+    std::clog << "   ( ";
     for (auto vertex : st.simplex_vertex_range(f_simplex)) {
-      std::cout << vertex << " ";
+      std::clog << vertex << " ";
     }
-    std::cout << ") -> "
+    std::clog << ") -> "
               << "[" << st.filtration(f_simplex) << "] ";
-    std::cout << std::endl;
+    std::clog << std::endl;
   }
   BOOST_CHECK(num_simplices == 15);
-  std::cout << "st.num_simplices()=" << st.num_simplices() << std::endl;
+  std::clog << "st.num_simplices()=" << st.num_simplices() << std::endl;
   BOOST_CHECK(st.num_simplices() == 15);
 
-  std::cout << "st.dimension()=" << st.dimension() << std::endl;
+  std::clog << "st.dimension()=" << st.dimension() << std::endl;
   BOOST_CHECK(st.dimension() == DIMENSION);
-  std::cout << "st.num_vertices()=" << st.num_vertices() << std::endl;
+  std::clog << "st.num_vertices()=" << st.num_vertices() << std::endl;
   BOOST_CHECK(st.num_vertices() == 4);
 
   for (auto f_simplex : st.filtration_simplex_range()) {
-    std::cout << "dimension(" << st.dimension(f_simplex) << ") - f = " << st.filtration(f_simplex) << std::endl;
+    std::clog << "dimension(" << st.dimension(f_simplex) << ") - f = " << st.filtration(f_simplex) << std::endl;
     switch (st.dimension(f_simplex)) {
       case 0:
         GUDHI_TEST_FLOAT_EQUALITY_CHECK(st.filtration(f_simplex), 0.0);
@@ -236,7 +236,7 @@ BOOST_AUTO_TEST_CASE(Cech_create_complex_throw) {
   // ----------------------------------------------------------------------------
   std::string off_file_name("alphacomplexdoc.off");
   double max_radius = 12.0;
-  std::cout << "========== OFF FILE NAME = " << off_file_name << " - Cech max_radius=" << max_radius
+  std::clog << "========== OFF FILE NAME = " << off_file_name << " - Cech max_radius=" << max_radius
             << "==========" << std::endl;
 
   Gudhi::Points_off_reader<Point> off_reader(off_file_name);
@@ -245,7 +245,7 @@ BOOST_AUTO_TEST_CASE(Cech_create_complex_throw) {
   Simplex_tree stree;
   std::vector<int> simplex = {0, 1, 2};
   stree.insert_simplex_and_subfaces(simplex);
-  std::cout << "Check exception throw in debug mode" << std::endl;
+  std::clog << "Check exception throw in debug mode" << std::endl;
   // throw excpt because stree is not empty
   BOOST_CHECK_THROW(cech_complex_from_file.create_complex(stree, 1), std::invalid_argument);
 }
diff --git a/src/Cech_complex/utilities/CMakeLists.txt b/src/Cech_complex/utilities/CMakeLists.txt
index 30b99729..253d7304 100644
--- a/src/Cech_complex/utilities/CMakeLists.txt
+++ b/src/Cech_complex/utilities/CMakeLists.txt
@@ -2,7 +2,7 @@ cmake_minimum_required(VERSION 2.6)
 project(Cech_complex_utilities)
 
 add_executable(cech_persistence cech_persistence.cpp)
-target_link_libraries(cech_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY})
+target_link_libraries(cech_persistence Boost::program_options)
 
 if (TBB_FOUND)
   target_link_libraries(cech_persistence ${TBB_LIBRARIES})
diff --git a/src/Cech_complex/utilities/cech_persistence.cpp b/src/Cech_complex/utilities/cech_persistence.cpp
index 8cfe018b..daea08e2 100644
--- a/src/Cech_complex/utilities/cech_persistence.cpp
+++ b/src/Cech_complex/utilities/cech_persistence.cpp
@@ -50,8 +50,8 @@ int main(int argc, char* argv[]) {
   Simplex_tree simplex_tree;
 
   cech_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";
+  std::clog << "The complex contains " << simplex_tree.num_simplices() << " simplices \n";
+  std::clog << "   and has dimension " << simplex_tree.dimension() << " \n";
 
   // Sort the simplices in the order of the filtration
   simplex_tree.initialize_filtration();
@@ -85,7 +85,7 @@ void program_options(int argc, char* argv[], std::string& off_file_points, std::
   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")(
+      "Name of file in which the persistence diagram is written. Default print in std::clog")(
       "max-radius,r",
       po::value<Filtration_value>(&max_radius)->default_value(std::numeric_limits<Filtration_value>::infinity()),
       "Maximal length of an edge for the Cech complex construction.")(
@@ -108,17 +108,17 @@ void program_options(int argc, char* argv[], std::string& off_file_points, std::
   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 Cech 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::clog << std::endl;
+    std::clog << "Compute the persistent homology with coefficient field Z/pZ \n";
+    std::clog << "of a Cech complex defined on a set of input points.\n \n";
+    std::clog << "The output diagram contains one bar per line, written with the convention: \n";
+    std::clog << "   p   dim b d \n";
+    std::clog << "where dim is the dimension of the homological feature,\n";
+    std::clog << "b and d are respectively the birth and death of the feature and \n";
+    std::clog << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl;
+
+    std::clog << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
+    std::clog << visible << std::endl;
     exit(-1);
   }
 }