Fix some cpplint

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_representation_integration@2502 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 0a6422b0fa27105b9aaba743371da3328d9039be

38 files changed, 108 insertions, 134 deletions

diff --git a/src/Persistence_representations/example/CMakeLists.txt b/src/Persistence_representations/example/CMakeLists.txt
index 3c783d36..3357017a 100644
--- a/src/Persistence_representations/example/CMakeLists.txt
+++ b/src/Persistence_representations/example/CMakeLists.txt
@@ -1,27 +1,24 @@
 cmake_minimum_required(VERSION 2.6)
-project(GUDHI_STAT)
+project(Persistence_representations_example)
 
 file(COPY "simple_diagram.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+
 add_executable ( persistence_landscape_on_grid persistence_landscape_on_grid.cpp )
 target_link_libraries(persistence_landscape_on_grid ${Boost_SYSTEM_LIBRARY})
 add_test ( persistence_landscape_on_grid ${CMAKE_CURRENT_BINARY_DIR}/persistence_landscape_on_grid )
 
-file(COPY "simple_diagram.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
 add_executable ( persistence_landscape persistence_landscape.cpp )
 target_link_libraries(persistence_landscape ${Boost_SYSTEM_LIBRARY})
 add_test ( persistence_landscape ${CMAKE_CURRENT_BINARY_DIR}/persistence_landscape )
 
-file(COPY "simple_diagram.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
 add_executable ( persistence_intervals persistence_intervals.cpp )
 target_link_libraries(persistence_intervals ${Boost_SYSTEM_LIBRARY})
 add_test ( persistence_intervals ${CMAKE_CURRENT_BINARY_DIR}/persistence_intervals simple_diagram.txt )
 
-file(COPY "simple_diagram.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
 add_executable ( persistence_vectors persistence_vectors.cpp )
 target_link_libraries(persistence_vectors ${Boost_SYSTEM_LIBRARY})
 add_test ( persistence_vectors ${CMAKE_CURRENT_BINARY_DIR}/persistence_vectors )
 
-file(COPY "simple_diagram.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
 add_executable ( persistence_heat_maps persistence_heat_maps.cpp )
 target_link_libraries(persistence_heat_maps ${Boost_SYSTEM_LIBRARY})
 add_test ( persistence_heat_maps ${CMAKE_CURRENT_BINARY_DIR}/persistence_heat_maps )
diff --git a/src/Persistence_representations/example/persistence_heat_maps.cpp b/src/Persistence_representations/example/persistence_heat_maps.cpp
index a9ac5df5..2a472ac6 100644
--- a/src/Persistence_representations/example/persistence_heat_maps.cpp
+++ b/src/Persistence_representations/example/persistence_heat_maps.cpp
@@ -20,17 +20,14 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include <gudhi/reader_utils.h>
 #include <gudhi/Persistence_heat_maps.h>
 
 #include <iostream>
 #include <vector>
 #include <utility>
 
-using namespace Gudhi;
-using namespace Gudhi::Persistence_representations;
-
-double epsilon = 0.0000005;
+using constant_scaling_function = Gudhi::Persistence_representations::constant_scaling_function;
+using Persistence_heat_maps = Gudhi::Persistence_representations::Persistence_heat_maps<constant_scaling_function>;
 
 int main(int argc, char** argv) {
   // create two simple vectors with birth--death pairs:
@@ -50,30 +47,30 @@ int main(int argc, char** argv) {
 
   // over here we define a function we sill put on a top on every birth--death pair in the persistence interval. It can
   // be anything. Over here we will use standard Gaussian
-  std::vector<std::vector<double> > filter = create_Gaussian_filter(5, 1);
+  std::vector<std::vector<double> > filter = Gudhi::Persistence_representations::create_Gaussian_filter(5, 1);
 
   // creating two heat maps.
-  Persistence_heat_maps<constant_scaling_function> hm1(persistence1, filter, false, 20, 0, 11);
-  Persistence_heat_maps<constant_scaling_function> hm2(persistence2, filter, false, 20, 0, 11);
+  Persistence_heat_maps hm1(persistence1, filter, false, 20, 0, 11);
+  Persistence_heat_maps hm2(persistence2, filter, false, 20, 0, 11);
 
-  std::vector<Persistence_heat_maps<constant_scaling_function>*> vector_of_maps;
+  std::vector<Persistence_heat_maps*> vector_of_maps;
   vector_of_maps.push_back(&hm1);
   vector_of_maps.push_back(&hm2);
 
   // compute median/mean of a vector of heat maps:
-  Persistence_heat_maps<constant_scaling_function> mean;
+  Persistence_heat_maps mean;
   mean.compute_mean(vector_of_maps);
-  Persistence_heat_maps<constant_scaling_function> median;
+  Persistence_heat_maps median;
   median.compute_median(vector_of_maps);
 
   // to compute L^1 distance between hm1 and hm2:
   std::cout << "The L^1 distance is : " << hm1.distance(hm2, 1) << std::endl;
 
   // to average of hm1 and hm2:
-  std::vector<Persistence_heat_maps<constant_scaling_function>*> to_average;
+  std::vector<Persistence_heat_maps*> to_average;
   to_average.push_back(&hm1);
   to_average.push_back(&hm2);
-  Persistence_heat_maps<constant_scaling_function> av;
+  Persistence_heat_maps av;
   av.compute_average(to_average);
 
   // to compute scalar product of hm1 and hm2:
diff --git a/src/Persistence_representations/example/persistence_intervals.cpp b/src/Persistence_representations/example/persistence_intervals.cpp
index 29cd66f3..c1ceb458 100644
--- a/src/Persistence_representations/example/persistence_intervals.cpp
+++ b/src/Persistence_representations/example/persistence_intervals.cpp
@@ -20,15 +20,13 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include <gudhi/reader_utils.h>
 #include <gudhi/Persistence_intervals.h>
 
 #include <iostream>
 #include <utility>
 #include <vector>
 
-using namespace Gudhi;
-using namespace Gudhi::Persistence_representations;
+using Persistence_intervals = Gudhi::Persistence_representations::Persistence_intervals;
 
 int main(int argc, char** argv) {
   if (argc != 2) {
diff --git a/src/Persistence_representations/example/persistence_landscape.cpp b/src/Persistence_representations/example/persistence_landscape.cpp
index 1bcc524a..400a9ae1 100644
--- a/src/Persistence_representations/example/persistence_landscape.cpp
+++ b/src/Persistence_representations/example/persistence_landscape.cpp
@@ -26,8 +26,7 @@
 #include <vector>
 #include <utility>
 
-using namespace Gudhi;
-using namespace Gudhi::Persistence_representations;
+using Persistence_landscape = Gudhi::Persistence_representations::Persistence_landscape;
 
 int main(int argc, char** argv) {
   // create two simple vectors with birth--death pairs:
diff --git a/src/Persistence_representations/example/persistence_landscape_on_grid.cpp b/src/Persistence_representations/example/persistence_landscape_on_grid.cpp
index 0cede07e..b201b397 100644
--- a/src/Persistence_representations/example/persistence_landscape_on_grid.cpp
+++ b/src/Persistence_representations/example/persistence_landscape_on_grid.cpp
@@ -26,8 +26,7 @@
 #include <utility>
 #include <vector>
 
-using namespace Gudhi;
-using namespace Gudhi::Persistence_representations;
+using Persistence_landscape_on_grid = Gudhi::Persistence_representations::Persistence_landscape_on_grid;
 
 int main(int argc, char** argv) {
   // create two simple vectors with birth--death pairs:
diff --git a/src/Persistence_representations/example/persistence_vectors.cpp b/src/Persistence_representations/example/persistence_vectors.cpp
index c6581039..59eca152 100644
--- a/src/Persistence_representations/example/persistence_vectors.cpp
+++ b/src/Persistence_representations/example/persistence_vectors.cpp
@@ -21,7 +21,6 @@
  */
 
 #include <gudhi/Persistence_vectors.h>
-#include <gudhi/reader_utils.h>
 
 #include <iostream>
 #include <vector>
@@ -30,8 +29,8 @@
 #include <limits>
 #include <utility>
 
-using namespace Gudhi;
-using namespace Gudhi::Persistence_representations;
+using Vector_distances_in_diagram =
+  Gudhi::Persistence_representations::Vector_distances_in_diagram<Gudhi::Euclidean_distance>;
 
 int main(int argc, char** argv) {
   // create two simple vectors with birth--death pairs:
@@ -50,17 +49,15 @@ int main(int argc, char** argv) {
   persistence2.push_back(std::make_pair(6, 10));
 
   // create two persistence vectors based on persistence1 and persistence2:
-  Vector_distances_in_diagram<Euclidean_distance> v1 =
-      Vector_distances_in_diagram<Euclidean_distance>(persistence1, std::numeric_limits<size_t>::max());
-  Vector_distances_in_diagram<Euclidean_distance> v2 =
-      Vector_distances_in_diagram<Euclidean_distance>(persistence2, std::numeric_limits<size_t>::max());
+  Vector_distances_in_diagram v1(persistence1, std::numeric_limits<size_t>::max());
+  Vector_distances_in_diagram v2(persistence2, std::numeric_limits<size_t>::max());
 
   // writing to a stream:
   std::cout << "v1 : " << v1 << std::endl;
   std::cout << "v2 : " << v2 << std::endl;
 
   // averages:
-  Vector_distances_in_diagram<Euclidean_distance> average;
+  Vector_distances_in_diagram average;
   average.compute_average({&v1, &v2});
   std::cout << "Average : " << average << std::endl;
 
diff --git a/src/Persistence_representations/test/persistence_heat_maps_test.cpp b/src/Persistence_representations/test/persistence_heat_maps_test.cpp
index fef397a3..1f1502f5 100644
--- a/src/Persistence_representations/test/persistence_heat_maps_test.cpp
+++ b/src/Persistence_representations/test/persistence_heat_maps_test.cpp
@@ -21,7 +21,7 @@
  */
 
 #define BOOST_TEST_DYN_LINK
-#define BOOST_TEST_MODULE "Persistence_representations"
+#define BOOST_TEST_MODULE "Persistence_heat_maps_test"
 #include <boost/test/unit_test.hpp>
 #include <gudhi/reader_utils.h>
 #include <gudhi/Persistence_heat_maps.h>
diff --git a/src/Persistence_representations/test/persistence_intervals_test.cpp b/src/Persistence_representations/test/persistence_intervals_test.cpp
index 7a3a058f..51d8a0f9 100644
--- a/src/Persistence_representations/test/persistence_intervals_test.cpp
+++ b/src/Persistence_representations/test/persistence_intervals_test.cpp
@@ -21,7 +21,7 @@
  */
 
 #define BOOST_TEST_DYN_LINK
-#define BOOST_TEST_MODULE "Persistence_representations"
+#define BOOST_TEST_MODULE "Persistence_intervals_test"
 #include <boost/test/unit_test.hpp>
 #include <gudhi/reader_utils.h>
 #include "gudhi/Persistence_intervals.h"
diff --git a/src/Persistence_representations/test/persistence_intervals_with_distances_test.cpp b/src/Persistence_representations/test/persistence_intervals_with_distances_test.cpp
index c6d4796c..7b70eee3 100644
--- a/src/Persistence_representations/test/persistence_intervals_with_distances_test.cpp
+++ b/src/Persistence_representations/test/persistence_intervals_with_distances_test.cpp
@@ -21,7 +21,7 @@
  */
 
 #define BOOST_TEST_DYN_LINK
-#define BOOST_TEST_MODULE "Persistence_representations"
+#define BOOST_TEST_MODULE "Persistence_intervals_with_distances_test"
 #include <boost/test/unit_test.hpp>
 #include <gudhi/reader_utils.h>
 #include "gudhi/Persistence_intervals_with_distances.h"
diff --git a/src/Persistence_representations/test/persistence_lanscapes_on_grid_test.cpp b/src/Persistence_representations/test/persistence_lanscapes_on_grid_test.cpp
index 098e08b2..8ab7449e 100644
--- a/src/Persistence_representations/test/persistence_lanscapes_on_grid_test.cpp
+++ b/src/Persistence_representations/test/persistence_lanscapes_on_grid_test.cpp
@@ -21,7 +21,7 @@
  */
 
 #define BOOST_TEST_DYN_LINK
-#define BOOST_TEST_MODULE "Persistence_representations"
+#define BOOST_TEST_MODULE "Persistence_landscapes_on_grid_test"
 #include <boost/test/unit_test.hpp>
 #include <gudhi/reader_utils.h>
 #include <gudhi/Persistence_landscape_on_grid.h>
diff --git a/src/Persistence_representations/test/persistence_lanscapes_test.cpp b/src/Persistence_representations/test/persistence_lanscapes_test.cpp
index 6749fbd8..1141edfb 100644
--- a/src/Persistence_representations/test/persistence_lanscapes_test.cpp
+++ b/src/Persistence_representations/test/persistence_lanscapes_test.cpp
@@ -21,7 +21,7 @@
  */
 
 #define BOOST_TEST_DYN_LINK
-#define BOOST_TEST_MODULE "Persistence_representations"
+#define BOOST_TEST_MODULE "Persistence_landscapes_test"
 #include <boost/test/unit_test.hpp>
 #include <gudhi/reader_utils.h>
 #include <gudhi/Persistence_landscape.h>
diff --git a/src/Persistence_representations/utilities/CMakeLists.txt b/src/Persistence_representations/utilities/CMakeLists.txt
new file mode 100644
index 00000000..66524666
--- /dev/null
+++ b/src/Persistence_representations/utilities/CMakeLists.txt
@@ -0,0 +1,6 @@
+add_subdirectory(persistence_heat_maps)
+add_subdirectory(persistence_intervals)
+add_subdirectory(persistence_landscapes)
+add_subdirectory(persistence_landscapes_on_grid)
+add_subdirectory(persistence_vectors)
+
diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_heat_maps/CMakeLists.txt
index c90c637d..4ad924cb 100644
--- a/src/Persistence_representations/utilities/persistence_heat_maps/CMakeLists.txt
+++ b/src/Persistence_representations/utilities/persistence_heat_maps/CMakeLists.txt
@@ -1,11 +1,10 @@
 cmake_minimum_required(VERSION 2.6)
-project(GUDHI_STAT)
+project(Persistence_representations_heat_maps_utilities)
 
 #persitence heat maps
 
 add_executable ( create_persistence_heat_maps create_persistence_heat_maps.cpp )
 target_link_libraries(create_persistence_heat_maps ${Boost_SYSTEM_LIBRARY})
-#add_test ( create_persistence_heat_maps ${CMAKE_CURRENT_BINARY_DIR}/create_persistence_heat_maps   10 -1 -1 4 -1  simple_diagram.txt )
 add_test ( create_persistence_heat_maps ${CMAKE_CURRENT_BINARY_DIR}/create_persistence_heat_maps   10 -1 -1 4 -1   "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt" )
 
 add_executable ( create_pssk create_pssk.cpp )
diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/average_persistence_heat_maps.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/average_persistence_heat_maps.cpp
index b4e2be89..4e81375a 100644
--- a/src/Persistence_representations/utilities/persistence_heat_maps/average_persistence_heat_maps.cpp
+++ b/src/Persistence_representations/utilities/persistence_heat_maps/average_persistence_heat_maps.cpp
@@ -22,12 +22,12 @@
 
 #include <gudhi/Persistence_heat_maps.h>
 
-using namespace Gudhi;
-using namespace Gudhi::Persistence_representations;
-
 #include <iostream>
 #include <vector>
 
+using constant_scaling_function = Gudhi::Persistence_representations::constant_scaling_function;
+using Persistence_heat_maps = Gudhi::Persistence_representations::Persistence_heat_maps<constant_scaling_function>;
+
 int main(int argc, char** argv) {
   std::cout << "This program computes average persistence landscape of persistence landscapes created based on "
                "persistence diagrams provided as an input. Please call this program with the names of files with "
@@ -44,14 +44,14 @@ int main(int argc, char** argv) {
   }
 
   std::cout << "Creating persistence landscapes...\n";
-  std::vector<Persistence_heat_maps<constant_scaling_function>*> maps;
+  std::vector<Persistence_heat_maps*> maps;
   for (size_t i = 0; i != filenames.size(); ++i) {
-    Persistence_heat_maps<constant_scaling_function>* l = new Persistence_heat_maps<constant_scaling_function>;
+    Persistence_heat_maps* l = new Persistence_heat_maps;
     l->load_from_file(filenames[i]);
     maps.push_back(l);
   }
 
-  Persistence_heat_maps<constant_scaling_function> av;
+  Persistence_heat_maps av;
   av.compute_average(maps);
 
   av.print_to_file("average.mps");
diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp
index 56b2d336..a9e8821f 100644
--- a/src/Persistence_representations/utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp
+++ b/src/Persistence_representations/utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp
@@ -22,14 +22,14 @@
 
 #include <gudhi/Persistence_heat_maps.h>
 
-using namespace Gudhi;
-using namespace Gudhi::Persistence_representations;
-
 #include <iostream>
 #include <sstream>
 #include <limits>
 #include <vector>
 
+using constant_scaling_function = Gudhi::Persistence_representations::constant_scaling_function;
+using Persistence_heat_maps = Gudhi::Persistence_representations::Persistence_heat_maps<constant_scaling_function>;
+
 int main(int argc, char** argv) {
   std::cout << "This program compute distance of persistence heat maps stored in a file (the file needs to be created "
                "beforehand). \n";
@@ -52,10 +52,10 @@ int main(int argc, char** argv) {
   for (int i = 2; i < argc; ++i) {
     filenames.push_back(argv[i]);
   }
-  std::vector<Persistence_heat_maps<constant_scaling_function> > maps;
+  std::vector<Persistence_heat_maps> maps;
   maps.reserve(filenames.size());
   for (size_t file_no = 0; file_no != filenames.size(); ++file_no) {
-    Persistence_heat_maps<constant_scaling_function> l;
+    Persistence_heat_maps l;
     l.load_from_file(filenames[file_no]);
     maps.push_back(l);
   }
diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp
index ec9482f0..1cee1f82 100644
--- a/src/Persistence_representations/utilities/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp
+++ b/src/Persistence_representations/utilities/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp
@@ -22,13 +22,13 @@
 
 #include <gudhi/Persistence_heat_maps.h>
 
-using namespace Gudhi;
-using namespace Gudhi::Persistence_representations;
-
 #include <iostream>
 #include <sstream>
 #include <vector>
 
+using constant_scaling_function = Gudhi::Persistence_representations::constant_scaling_function;
+using Persistence_heat_maps = Gudhi::Persistence_representations::Persistence_heat_maps<constant_scaling_function>;
+
 int main(int argc, char** argv) {
   std::cout << "This program compute scalar product of persistence landscapes stored in a file (the file needs to be "
                "created beforehand). \n";
@@ -38,10 +38,10 @@ int main(int argc, char** argv) {
   for (int i = 1; i < argc; ++i) {
     filenames.push_back(argv[i]);
   }
-  std::vector<Persistence_heat_maps<constant_scaling_function> > maps;
+  std::vector<Persistence_heat_maps> maps;
   maps.reserve(filenames.size());
   for (size_t file_no = 0; file_no != filenames.size(); ++file_no) {
-    Persistence_heat_maps<constant_scaling_function> l;
+    Persistence_heat_maps l;
     l.load_from_file(filenames[file_no]);
     maps.push_back(l);
   }
diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp
index 68c75059..2bf185a3 100644
--- a/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp
+++ b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp
@@ -22,14 +22,15 @@
 
 #include <gudhi/Persistence_heat_maps.h>
 
-using namespace Gudhi;
-using namespace Gudhi::Persistence_representations;
-
 #include <iostream>
 #include <sstream>
 #include <limits>
 #include <vector>
 
+using arc_tan_of_persistence_of_point = Gudhi::Persistence_representations::arc_tan_of_persistence_of_point;
+using Persistence_heat_maps =
+  Gudhi::Persistence_representations::Persistence_heat_maps<arc_tan_of_persistence_of_point>;
+
 int main(int argc, char** argv) {
   std::cout << "This program creates persistence heat map of diagrams provided as an input. The Gaussian kernels are "
                "weighted by the arc tangential of their persistence.\n";
@@ -68,12 +69,11 @@ int main(int argc, char** argv) {
   }
 
   std::cout << "Creating persistence heat maps...\n";
-  std::vector<std::vector<double> > filter = create_Gaussian_filter(stdiv, 1);
+  std::vector<std::vector<double> > filter = Gudhi::Persistence_representations::create_Gaussian_filter(stdiv, 1);
 
   for (size_t i = 0; i != filenames.size(); ++i) {
     std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl;
-    Persistence_heat_maps<arc_tan_of_persistence_of_point> l(filenames[i], filter, false, size_of_grid, min_, max_,
-                                                             dimension);
+    Persistence_heat_maps l(filenames[i], filter, false, size_of_grid, min_, max_, dimension);
 
     std::stringstream ss;
     ss << filenames[i] << ".mps";
diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp
index a56393a3..ec9477f1 100644
--- a/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp
+++ b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp
@@ -22,14 +22,15 @@
 
 #include <gudhi/Persistence_heat_maps.h>
 
-using namespace Gudhi;
-using namespace Gudhi::Persistence_representations;
-
 #include <iostream>
 #include <sstream>
 #include <limits>
 #include <vector>
 
+using distance_from_diagonal_scaling = Gudhi::Persistence_representations::distance_from_diagonal_scaling;
+using Persistence_heat_maps =
+  Gudhi::Persistence_representations::Persistence_heat_maps<distance_from_diagonal_scaling>;
+
 int main(int argc, char** argv) {
   std::cout << "This program creates persistence heat map of diagrams provided as an input. The Gaussian kernels are "
                "weighted by the distance of a center from the diagonal.\n";
@@ -68,12 +69,11 @@ int main(int argc, char** argv) {
   }
 
   std::cout << "Creating persistence heat maps...\n";
-  std::vector<std::vector<double> > filter = create_Gaussian_filter(stdiv, 1);
+  std::vector<std::vector<double> > filter = Gudhi::Persistence_representations::create_Gaussian_filter(stdiv, 1);
 
   for (size_t i = 0; i != filenames.size(); ++i) {
     std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl;
-    Persistence_heat_maps<distance_from_diagonal_scaling> l(filenames[i], filter, false, size_of_grid, min_, max_,
-                                                            dimension);
+    Persistence_heat_maps l(filenames[i], filter, false, size_of_grid, min_, max_, dimension);
 
     std::stringstream ss;
     ss << filenames[i] << ".mps";
diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp
index 44115329..cb7e282c 100644
--- a/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp
+++ b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp
@@ -22,14 +22,15 @@
 
 #include <gudhi/Persistence_heat_maps.h>
 
-using namespace Gudhi;
-using namespace Gudhi::Persistence_representations;
-
 #include <iostream>
 #include <sstream>
 #include <limits>
 #include <vector>
 
+using squared_distance_from_diagonal_scaling = Gudhi::Persistence_representations::squared_distance_from_diagonal_scaling;
+using Persistence_heat_maps =
+  Gudhi::Persistence_representations::Persistence_heat_maps<squared_distance_from_diagonal_scaling>;
+
 int main(int argc, char** argv) {
   std::cout << "This program creates persistence heat map of diagrams provided as an input. The Gaussian kernels are "
                "weighted by the square of distance of a center from the diagonal.\n";
@@ -68,12 +69,11 @@ int main(int argc, char** argv) {
   }
 
   std::cout << "Creating persistence heat maps...\n";
-  std::vector<std::vector<double> > filter = create_Gaussian_filter(stdiv, 1);
+  std::vector<std::vector<double> > filter = Gudhi::Persistence_representations::create_Gaussian_filter(stdiv, 1);
 
   for (size_t i = 0; i != filenames.size(); ++i) {
     std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl;
-    Persistence_heat_maps<squared_distance_from_diagonal_scaling> l(filenames[i], filter, false, size_of_grid, min_,
-                                                                    max_, dimension);
+    Persistence_heat_maps l(filenames[i], filter, false, size_of_grid, min_, max_, dimension);
 
     std::stringstream ss;
     ss << filenames[i] << ".mps";
diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp
index ebc82f82..bd5ec89a 100644
--- a/src/Persistence_representations/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp
+++ b/src/Persistence_representations/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp
@@ -22,14 +22,14 @@
 
 #include <gudhi/Persistence_heat_maps.h>
 
-using namespace Gudhi;
-using namespace Gudhi::Persistence_representations;
-
 #include <iostream>
 #include <sstream>
 #include <limits>
 #include <vector>
 
+using constant_scaling_function = Gudhi::Persistence_representations::constant_scaling_function;
+using Persistence_heat_maps = Gudhi::Persistence_representations::Persistence_heat_maps<constant_scaling_function>;
+
 int main(int argc, char** argv) {
   std::cout << "This program creates persistence heat map of diagrams provided as an input.\n";
   std::cout << "The first parameter of a program is an integer, a size of a grid.\n";
@@ -65,12 +65,11 @@ int main(int argc, char** argv) {
   }
 
   std::cout << "Creating persistence heat maps...\n";
-  std::vector<std::vector<double> > filter = create_Gaussian_filter(stdiv, 1);
+  std::vector<std::vector<double> > filter = Gudhi::Persistence_representations::create_Gaussian_filter(stdiv, 1);
 
   for (size_t i = 0; i != filenames.size(); ++i) {
     std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl;
-    Persistence_heat_maps<constant_scaling_function> l(filenames[i], filter, false, size_of_grid, min_, max_,
-                                                       dimension);
+    Persistence_heat_maps l(filenames[i], filter, false, size_of_grid, min_, max_, dimension);
 
     std::stringstream ss;
     ss << filenames[i] << ".mps";
diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/create_pssk.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/create_pssk.cpp
index 7b24bb7c..6aefbb00 100644
--- a/src/Persistence_representations/utilities/persistence_heat_maps/create_pssk.cpp
+++ b/src/Persistence_representations/utilities/persistence_heat_maps/create_pssk.cpp
@@ -22,14 +22,13 @@
 
 #include <gudhi/PSSK.h>
 
-using namespace Gudhi;
-using namespace Gudhi::Persistence_representations;
-
 #include <iostream>
 #include <sstream>
 #include <limits>
 #include <vector>
 
+using PSSK = Gudhi::Persistence_representations::PSSK;
+
 int main(int argc, char** argv) {
   std::cout << "This program creates PSSK of diagrams provided as an input.\n";
   std::cout << "The first parameter of a program is an integer, a size of a grid.\n";
@@ -67,7 +66,7 @@ int main(int argc, char** argv) {
   }
 
   std::cout << "Creating persistence heat maps...\n";
-  std::vector<std::vector<double> > filter = create_Gaussian_filter(stdiv, 1);
+  std::vector<std::vector<double> > filter = Gudhi::Persistence_representations::create_Gaussian_filter(stdiv, 1);
 
   for (size_t i = 0; i != filenames.size(); ++i) {
     std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl;
diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/plot_persistence_heat_map.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/plot_persistence_heat_map.cpp
index 0b7841d1..a7c9f2d8 100644
--- a/src/Persistence_representations/utilities/persistence_heat_maps/plot_persistence_heat_map.cpp
+++ b/src/Persistence_representations/utilities/persistence_heat_maps/plot_persistence_heat_map.cpp
@@ -22,16 +22,16 @@
 
 #include <gudhi/Persistence_heat_maps.h>
 
-using namespace Gudhi;
-using namespace Gudhi::Persistence_representations;
-
 #include <iostream>
 #include <sstream>
 
+using constant_scaling_function = Gudhi::Persistence_representations::constant_scaling_function;
+using Persistence_heat_maps = Gudhi::Persistence_representations::Persistence_heat_maps<constant_scaling_function>;
+
 int main(int argc, char** argv) {
   std::cout << "This program plot persistence landscape stored in a file (the file needs to be created beforehand). "
                "Please call the code with the name of a landscape file \n";
-  Persistence_heat_maps<constant_scaling_function> l;
+  Persistence_heat_maps l;
   l.load_from_file(argv[1]);
   l.plot(argv[1]);
   return 0;
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 72c56e92..66fa31ca 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
@@ -28,8 +28,7 @@
 #include <limits>
 #include <utility>
 
-using namespace Gudhi;
-using namespace Gudhi::Persistence_representations;
+using Persistence_intervals = Gudhi::Persistence_representations::Persistence_intervals;
 
 int main(int argc, char** argv) {
   std::cout << "This program compute the range of birth and death times of persistence pairs in diagrams provided as "
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 6a872b7a..0b1b526d 100644
--- a/src/Persistence_representations/utilities/persistence_intervals/compute_bottleneck_distance.cpp
+++ b/src/Persistence_representations/utilities/persistence_intervals/compute_bottleneck_distance.cpp
@@ -23,14 +23,13 @@
 #include <gudhi/Persistence_intervals_with_distances.h>
 #include <gudhi/read_persistence_from_file.h>
 
-using namespace Gudhi;
-using namespace Gudhi::Persistence_representations;
-
 #include <iostream>
 #include <sstream>
 #include <limits>
 #include <vector>
 
+using Persistence_intervals_with_distances = Gudhi::Persistence_representations::Persistence_intervals_with_distances;
+
 int main(int argc, char** argv) {
   std::cout << "This program compute the bottleneck distance of persistence diagrams stored in a files. \n";
   std::cout << "The first parameter of the program is the dimension of persistence to be used to construct persistence "
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 5fbbef14..1286ca57 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
@@ -28,8 +28,7 @@
 #include <vector>
 #include <utility>
 
-using namespace Gudhi;
-using namespace Gudhi::Persistence_representations;
+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 "
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 b8f96b60..d68f4584 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
@@ -28,8 +28,7 @@
 #include <limits>
 #include <utility>
 
-using namespace Gudhi;
-using namespace Gudhi::Persistence_representations;
+using Persistence_intervals = Gudhi::Persistence_representations::Persistence_intervals;
 
 int main(int argc, char** argv) {
   std::cout << "This program compute a histogram of barcode's length. A number of bins in the histogram is a parameter "
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 521621b2..da2b9319 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
@@ -28,8 +28,7 @@
 #include <limits>
 #include <utility>
 
-using namespace Gudhi;
-using namespace Gudhi::Persistence_representations;
+using Persistence_intervals = Gudhi::Persistence_representations::Persistence_intervals;
 
 int main(int argc, char** argv) {
   std::cout << "This program compute a plot of persistence Betti numbers. The input parameter is a file with "
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 e76906e9..e7d29e84 100644
--- a/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_intervals.cpp
+++ b/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_intervals.cpp
@@ -29,10 +29,7 @@
 #include <vector>
 #include <utility>
 
-using namespace Gudhi;
-using namespace Gudhi::Persistence_representations;
-
-double epsilon = 0.0000005;
+using Persistence_intervals = Gudhi::Persistence_representations::Persistence_intervals;
 
 int main(int argc, char** argv) {
   if (argc < 2) {
@@ -50,7 +47,7 @@ int main(int argc, char** argv) {
     dimension = (unsigned)dim;
   }
   std::vector<std::pair<double, double> > intervals =
-      read_persistence_intervals_in_one_dimension_from_file(argv[1], dimension);
+      Gudhi::Persistence_representations::read_persistence_intervals_in_one_dimension_from_file(argv[1], dimension);
   Persistence_intervals b(intervals);
   b.plot(argv[1]);
   return 0;
diff --git a/src/Persistence_representations/utilities/persistence_landscapes/average_landscapes.cpp b/src/Persistence_representations/utilities/persistence_landscapes/average_landscapes.cpp
index f885a7a7..526130e9 100644
--- a/src/Persistence_representations/utilities/persistence_landscapes/average_landscapes.cpp
+++ b/src/Persistence_representations/utilities/persistence_landscapes/average_landscapes.cpp
@@ -22,12 +22,11 @@
 
 #include <gudhi/Persistence_landscape.h>
 
-using namespace Gudhi;
-using namespace Gudhi::Persistence_representations;
-
 #include <iostream>
 #include <vector>
 
+using Persistence_landscape = Gudhi::Persistence_representations::Persistence_landscape;
+
 int main(int argc, char** argv) {
   std::cout << "This program computes average persistence landscape of persistence landscapes created based on "
                "persistence diagrams provided as an input (you must create them first).\n";
diff --git a/src/Persistence_representations/utilities/persistence_landscapes/compute_distance_of_landscapes.cpp b/src/Persistence_representations/utilities/persistence_landscapes/compute_distance_of_landscapes.cpp
index 7028b98b..b3881d6a 100644
--- a/src/Persistence_representations/utilities/persistence_landscapes/compute_distance_of_landscapes.cpp
+++ b/src/Persistence_representations/utilities/persistence_landscapes/compute_distance_of_landscapes.cpp
@@ -22,12 +22,12 @@
 
 #include <gudhi/Persistence_landscape.h>
 
-using namespace Gudhi;
-using namespace Gudhi::Persistence_representations;
-
 #include <iostream>
 #include <sstream>
 #include <limits>
+#include <vector>
+
+using Persistence_landscape = Gudhi::Persistence_representations::Persistence_landscape;
 
 int main(int argc, char** argv) {
   std::cout << "This program compute distance of persistence landscapes stored in a file (the file needs to be created "
diff --git a/src/Persistence_representations/utilities/persistence_landscapes/compute_scalar_product_of_landscapes.cpp b/src/Persistence_representations/utilities/persistence_landscapes/compute_scalar_product_of_landscapes.cpp
index 76a9d433..8dad7b4d 100644
--- a/src/Persistence_representations/utilities/persistence_landscapes/compute_scalar_product_of_landscapes.cpp
+++ b/src/Persistence_representations/utilities/persistence_landscapes/compute_scalar_product_of_landscapes.cpp
@@ -22,13 +22,12 @@
 
 #include <gudhi/Persistence_landscape.h>
 
-using namespace Gudhi;
-using namespace Gudhi::Persistence_representations;
-
 #include <iostream>
 #include <sstream>
 #include <vector>
 
+using Persistence_landscape = Gudhi::Persistence_representations::Persistence_landscape;
+
 int main(int argc, char** argv) {
   std::cout << "This program compute scalar product of persistence landscapes stored in a file (the file needs to be "
                "created beforehand). \n";
diff --git a/src/Persistence_representations/utilities/persistence_landscapes/create_landscapes.cpp b/src/Persistence_representations/utilities/persistence_landscapes/create_landscapes.cpp
index a6b33225..325081d1 100644
--- a/src/Persistence_representations/utilities/persistence_landscapes/create_landscapes.cpp
+++ b/src/Persistence_representations/utilities/persistence_landscapes/create_landscapes.cpp
@@ -22,14 +22,13 @@
 
 #include <gudhi/Persistence_landscape.h>
 
-using namespace Gudhi;
-using namespace Gudhi::Persistence_representations;
-
 #include <iostream>
 #include <sstream>
 #include <vector>
 #include <limits>
 
+using Persistence_landscape = Gudhi::Persistence_representations::Persistence_landscape;
+
 int main(int argc, char** argv) {
   std::cout << "This program creates persistence landscapes of diagrams provided as an input. \n";
   std::cout << "The first parameter of the program is the dimension of persistence to be used to construct persistence "
diff --git a/src/Persistence_representations/utilities/persistence_landscapes/plot_landscapes.cpp b/src/Persistence_representations/utilities/persistence_landscapes/plot_landscapes.cpp
index 35262fe2..ebdb20a1 100644
--- a/src/Persistence_representations/utilities/persistence_landscapes/plot_landscapes.cpp
+++ b/src/Persistence_representations/utilities/persistence_landscapes/plot_landscapes.cpp
@@ -22,12 +22,11 @@
 
 #include <gudhi/Persistence_landscape.h>
 
-using namespace Gudhi;
-using namespace Gudhi::Persistence_representations;
-
 #include <iostream>
 #include <sstream>
 
+using Persistence_landscape = Gudhi::Persistence_representations::Persistence_landscape;
+
 int main(int argc, char** argv) {
   std::cout << "This program plot persistence landscape stored in a file (the file needs to be created beforehand). "
                "Please call the code with the name of a landscape file \n";
diff --git a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp
index a17a8998..d50118a0 100644
--- a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp
+++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp
@@ -22,10 +22,10 @@
 
 #include <gudhi/Persistence_landscape_on_grid.h>
 
-using namespace Gudhi;
-using namespace Gudhi::Persistence_representations;
-
 #include <iostream>
+#include <vector>
+
+using Persistence_landscape_on_grid = Gudhi::Persistence_representations::Persistence_landscape_on_grid;
 
 int main(int argc, char** argv) {
   std::cout << "This program computes average persistence landscape on grid of persistence landscapes on grid created "
diff --git a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp
index 4694e897..859c6991 100644
--- a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp
+++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp
@@ -22,14 +22,13 @@
 
 #include <gudhi/Persistence_landscape_on_grid.h>
 
-using namespace Gudhi;
-using namespace Gudhi::Persistence_representations;
-
 #include <iostream>
 #include <sstream>
 #include <limits>
 #include <vector>
 
+using Persistence_landscape_on_grid = Gudhi::Persistence_representations::Persistence_landscape_on_grid;
+
 int main(int argc, char** argv) {
   std::cout << "This program compute distance of persistence landscapes on grid stored in a file (the file needs to be "
                "created beforehand). \n";
diff --git a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp
index 75c33cb1..e95bf8ad 100644
--- a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp
+++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp
@@ -22,13 +22,12 @@
 
 #include <gudhi/Persistence_landscape_on_grid.h>
 
-using namespace Gudhi;
-using namespace Gudhi::Persistence_representations;
-
 #include <iostream>
 #include <sstream>
 #include <vector>
 
+using Persistence_landscape_on_grid = Gudhi::Persistence_representations::Persistence_landscape_on_grid;
+
 int main(int argc, char** argv) {
   std::cout << "This program compute scalar product of persistence landscapes on grid stored in a file (the file needs "
                "to be created beforehand). \n";
diff --git a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp
index 490a1c25..8d747c14 100644
--- a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp
+++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp
@@ -22,14 +22,13 @@
 
 #include <gudhi/Persistence_landscape_on_grid.h>
 
-using namespace Gudhi;
-using namespace Gudhi::Persistence_representations;
-
 #include <iostream>
 #include <sstream>
 #include <limits>
 #include <vector>
 
+using Persistence_landscape_on_grid = Gudhi::Persistence_representations::Persistence_landscape_on_grid;
+
 int main(int argc, char** argv) {
   std::cout << "This program creates persistence landscape on grid of diagrams provided as an input.\n";
   std::cout << "The first parameter of a program is an integer, a size of a grid.\n";
diff --git a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp
index f5a70826..42822a01 100644
--- a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp
+++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp
@@ -22,12 +22,11 @@
 
 #include <gudhi/Persistence_landscape_on_grid.h>
 
-using namespace Gudhi;
-using namespace Gudhi::Persistence_representations;
-
 #include <iostream>
 #include <sstream>
 
+using Persistence_landscape_on_grid = Gudhi::Persistence_representations::Persistence_landscape_on_grid;
+
 int main(int argc, char** argv) {
   std::cout << "This program plot persistence landscape on grid stored in a file (the file needs to be created "
                "beforehand). Please call the code with the name of a landscape on grid file \n";