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

7 files changed, 22 insertions, 23 deletions

diff --git a/src/Persistence_representations/utilities/persistence_intervals/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_intervals/CMakeLists.txt
index a025183e..118c1e9b 100644
--- a/src/Persistence_representations/utilities/persistence_intervals/CMakeLists.txt
+++ b/src/Persistence_representations/utilities/persistence_intervals/CMakeLists.txt
@@ -3,17 +3,16 @@ project(Persistence_representations_intervals_utilities)
 
 add_executable ( plot_histogram_of_intervals_lengths plot_histogram_of_intervals_lengths.cpp )
 
-add_test(NAME plot_histogram_of_intervals_lengths COMMAND $<TARGET_FILE:plot_histogram_of_intervals_lengths>
+add_test(NAME Persistence_representation_utilities_plot_histogram_of_intervals_lengths COMMAND $<TARGET_FILE:plot_histogram_of_intervals_lengths>
     "${CMAKE_CURRENT_BINARY_DIR}/../first.pers" "-1")
 
 install(TARGETS plot_histogram_of_intervals_lengths DESTINATION bin)
 
-add_persistence_representation_plot_utility(plot_persistence_intervals "")
-add_persistence_representation_plot_utility(plot_persistence_Betti_numbers "")
+add_persistence_representation_plot_utility(plot_histogram_of_intervals_lengths plot_persistence_intervals "")
+add_persistence_representation_plot_utility(plot_histogram_of_intervals_lengths plot_persistence_Betti_numbers "")
 
 add_persistence_representation_creation_utility(compute_birth_death_range_in_persistence_diagram "-1")
 
-
 add_executable ( compute_number_of_dominant_intervals compute_number_of_dominant_intervals.cpp )
 add_test(NAME Persistence_representation_utilities_compute_number_of_dominant_intervals
     COMMAND $<TARGET_FILE:compute_number_of_dominant_intervals>
diff --git a/src/Persistence_representations/utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp b/src/Persistence_representations/utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp
index 519cc47d..72325cad 100644
--- a/src/Persistence_representations/utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp
+++ b/src/Persistence_representations/utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp
@@ -18,7 +18,7 @@
 using Persistence_intervals = Gudhi::Persistence_representations::Persistence_intervals;
 
 int main(int argc, char** argv) {
-  std::cout << "This program computes the range of birth and death times of persistence pairs in diagrams provided as "
+  std::clog << "This program computes the range of birth and death times of persistence pairs in diagrams provided as "
             << "an input.\n"
             << "The first parameter is the dimension of persistence to be used to create persistence intervals. "
             << "If your file contains the information about dimension of persistence pairs, please provide here the "
@@ -27,7 +27,7 @@ int main(int argc, char** argv) {
             << "The remaining parameters of the program are the names of files with persistence diagrams.\n";
 
   if (argc < 3) {
-    std::cout << "Wrong parameter list, the program will now terminate \n";
+    std::clog << "Wrong parameter list, the program will now terminate \n";
     return 1;
   }
 
@@ -45,12 +45,12 @@ int main(int argc, char** argv) {
   double max_ = -std::numeric_limits<double>::max();
 
   for (size_t file_no = 0; file_no != filenames.size(); ++file_no) {
-    std::cout << "Creating diagram based on a file : " << filenames[file_no] << std::endl;
+    std::clog << "Creating diagram based on a file : " << filenames[file_no] << std::endl;
     Persistence_intervals p(filenames[file_no], dimension);
     std::pair<double, double> min_max_ = p.get_x_range();
     if (min_max_.first < min_) min_ = min_max_.first;
     if (min_max_.second > max_) max_ = min_max_.second;
   }
-  std::cout << "Birth-death range : min: " << min_ << ", max: " << max_ << std::endl;
+  std::clog << "Birth-death range : min: " << min_ << ", max: " << max_ << std::endl;
   return 0;
 }
diff --git a/src/Persistence_representations/utilities/persistence_intervals/compute_bottleneck_distance.cpp b/src/Persistence_representations/utilities/persistence_intervals/compute_bottleneck_distance.cpp
index 6155727a..465bf72e 100644
--- a/src/Persistence_representations/utilities/persistence_intervals/compute_bottleneck_distance.cpp
+++ b/src/Persistence_representations/utilities/persistence_intervals/compute_bottleneck_distance.cpp
@@ -18,7 +18,7 @@
 using Persistence_intervals_with_distances = Gudhi::Persistence_representations::Persistence_intervals_with_distances;
 
 int main(int argc, char** argv) {
-  std::cout << "This program computes the bottleneck distance of persistence pairs in diagrams provided as "
+  std::clog << "This program computes the bottleneck distance of persistence pairs in diagrams provided as "
             << "an input.\n"
             << "The first parameter is the dimension of persistence to be used to create persistence intervals. "
             << "If your file contains the information about dimension of persistence pairs, please provide here the "
@@ -27,7 +27,7 @@ int main(int argc, char** argv) {
             << "The remaining parameters of the program are the names of files with persistence diagrams.\n";
 
   if (argc < 3) {
-    std::cout << "Wrong number of parameters, the program will now terminate \n";
+    std::clog << "Wrong number of parameters, the program will now terminate \n";
     return 1;
   }
 
@@ -70,14 +70,14 @@ int main(int argc, char** argv) {
   out.open("distance.itv");
   for (size_t i = 0; i != distance.size(); ++i) {
     for (size_t j = 0; j != distance.size(); ++j) {
-      std::cout << distance[i][j] << " ";
+      std::clog << distance[i][j] << " ";
       out << distance[i][j] << " ";
     }
-    std::cout << std::endl;
+    std::clog << std::endl;
     out << std::endl;
   }
   out.close();
 
-  std::cout << "Distance can be found in 'distance.itv' file\n";
+  std::clog << "Distance can be found in 'distance.itv' file\n";
   return 0;
 }
diff --git a/src/Persistence_representations/utilities/persistence_intervals/compute_number_of_dominant_intervals.cpp b/src/Persistence_representations/utilities/persistence_intervals/compute_number_of_dominant_intervals.cpp
index dd6e1a5b..ea1fe717 100644
--- a/src/Persistence_representations/utilities/persistence_intervals/compute_number_of_dominant_intervals.cpp
+++ b/src/Persistence_representations/utilities/persistence_intervals/compute_number_of_dominant_intervals.cpp
@@ -18,10 +18,10 @@
 using Persistence_intervals = Gudhi::Persistence_representations::Persistence_intervals;
 
 int main(int argc, char** argv) {
-  std::cout << "This program compute the dominant intervals. A number of intervals to be displayed is a parameter of "
+  std::clog << "This program compute the dominant intervals. A number of intervals to be displayed is a parameter of "
                "this program. \n";
   if (argc != 4) {
-    std::cout << "To run this program, please provide the name of a file with persistence diagram, dimension of "
+    std::clog << "To run this program, please provide the name of a file with persistence diagram, dimension of "
                  "intervals that should be taken into account (if your file contains only persistence pairs in a "
                  "single dimension, set it up to -1) and number of dominant intervals you would like to get \n";
     return 1;
@@ -33,9 +33,9 @@ int main(int argc, char** argv) {
   }
   Persistence_intervals p(argv[1], dimension);
   std::vector<std::pair<double, double> > dominant_intervals = p.dominant_intervals(atoi(argv[3]));
-  std::cout << "Here are the dominant intervals : " << std::endl;
+  std::clog << "Here are the dominant intervals : " << std::endl;
   for (size_t i = 0; i != dominant_intervals.size(); ++i) {
-    std::cout << " " << dominant_intervals[i].first << "," << dominant_intervals[i].second << " " << std::endl;
+    std::clog << " " << dominant_intervals[i].first << "," << dominant_intervals[i].second << " " << std::endl;
   }
 
   return 0;
diff --git a/src/Persistence_representations/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp b/src/Persistence_representations/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp
index 13d2133f..e5eec3f5 100644
--- a/src/Persistence_representations/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp
+++ b/src/Persistence_representations/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp
@@ -18,10 +18,10 @@
 using Persistence_intervals = Gudhi::Persistence_representations::Persistence_intervals;
 
 int main(int argc, char** argv) {
-  std::cout << "This program computes a histogram of barcode's length. A number of bins in the histogram is a "
+  std::clog << "This program computes a histogram of barcode's length. A number of bins in the histogram is a "
             << "parameter of this program. \n";
   if ((argc != 3) && (argc != 4)) {
-    std::cout << "To run this program, please provide the name of a file with persistence diagram and number of "
+    std::clog << "To run this program, please provide the name of a file with persistence diagram and number of "
               << "dominant intervals you would like to get. Set a negative number dominant intervals value "
               << "If your file contains only birth-death pairs.\n"
               << "The third parameter is the dimension of the persistence that is to be used. If your "
@@ -59,7 +59,7 @@ int main(int argc, char** argv) {
   out << std::endl;
   out.close();
 
-  std::cout << "To visualize, install gnuplot and type the command: gnuplot -persist -e \"load \'"
+  std::clog << "To visualize, install gnuplot and type the command: gnuplot -persist -e \"load \'"
             << gnuplot_script.str().c_str() << "\'\"" << std::endl;
   return 0;
 }
diff --git a/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_Betti_numbers.cpp b/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_Betti_numbers.cpp
index 451be77f..27c69e07 100644
--- a/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_Betti_numbers.cpp
+++ b/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_Betti_numbers.cpp
@@ -19,7 +19,7 @@ using Persistence_intervals = Gudhi::Persistence_representations::Persistence_in
 
 int main(int argc, char** argv) {
   if ((argc != 3) && (argc != 2)) {
-    std::cout << "This program creates a gnuplot script of Betti numbers from a single persistence diagram file"
+    std::clog << "This program creates a gnuplot script of Betti numbers from a single persistence diagram file"
               << "(*.pers).\n"
               << "To run this program, please provide the name of a file with persistence diagram.\n"
               << "The second optional parameter of a program is the dimension of the persistence that is to be used. "
@@ -68,7 +68,7 @@ int main(int argc, char** argv) {
   out << std::endl;
   out.close();
 
-  std::cout << "To visualize, install gnuplot and type the command: gnuplot -persist -e \"load \'"
+  std::clog << "To visualize, install gnuplot and type the command: gnuplot -persist -e \"load \'"
             << gnuplot_script.str().c_str() << "\'\"" << std::endl;
 
   return 0;
diff --git a/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_intervals.cpp b/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_intervals.cpp
index 09a56869..199a3266 100644
--- a/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_intervals.cpp
+++ b/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_intervals.cpp
@@ -19,7 +19,7 @@ using Persistence_intervals = Gudhi::Persistence_representations::Persistence_in
 
 int main(int argc, char** argv) {
   if ((argc != 3) && (argc != 2)) {
-    std::cout << "This program creates a gnuplot script from a single persistence diagram file (*.pers).\n"
+    std::clog << "This program creates a gnuplot script from a single persistence diagram file (*.pers).\n"
               << "To run this program, please provide the name of a file with persistence diagram.\n"
               << "The second optional parameter of a program is the dimension of the persistence that is to be used. "
               << "If your file contains only birth-death pairs, you can skip this parameter.\n";