Merge from trunk

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/add_utils_in_gudhi_v2@2732 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 7872aa224ee471c05e9213b81192d304254e608a

5 files changed, 21 insertions, 22 deletions

diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt
index eb31e050..98ed753d 100644
--- a/src/Persistent_cohomology/example/CMakeLists.txt
+++ b/src/Persistent_cohomology/example/CMakeLists.txt
@@ -2,19 +2,17 @@ cmake_minimum_required(VERSION 2.6)
 project(Persistent_cohomology_examples)
 
 add_executable(plain_homology plain_homology.cpp)
-target_link_libraries(plain_homology ${Boost_SYSTEM_LIBRARY})
 
 add_executable(persistence_from_simple_simplex_tree persistence_from_simple_simplex_tree.cpp)
-target_link_libraries(persistence_from_simple_simplex_tree ${Boost_SYSTEM_LIBRARY})
 
 add_executable(rips_persistence_step_by_step rips_persistence_step_by_step.cpp)
-target_link_libraries(rips_persistence_step_by_step ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
+target_link_libraries(rips_persistence_step_by_step ${Boost_PROGRAM_OPTIONS_LIBRARY})
 
 add_executable(rips_persistence_via_boundary_matrix rips_persistence_via_boundary_matrix.cpp)
-target_link_libraries(rips_persistence_via_boundary_matrix ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
+target_link_libraries(rips_persistence_via_boundary_matrix ${Boost_PROGRAM_OPTIONS_LIBRARY})
 
 add_executable(persistence_from_file persistence_from_file.cpp)
-target_link_libraries(persistence_from_file ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
+target_link_libraries(persistence_from_file ${Boost_PROGRAM_OPTIONS_LIBRARY})
 
 if (TBB_FOUND)
   target_link_libraries(plain_homology ${TBB_LIBRARIES})
@@ -46,7 +44,7 @@ if(GMP_FOUND)
    if(GMPXX_FOUND)
       add_executable(rips_multifield_persistence rips_multifield_persistence.cpp )
       target_link_libraries(rips_multifield_persistence
-          ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
+          ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
       if (TBB_FOUND)
         target_link_libraries(rips_multifield_persistence ${TBB_LIBRARIES})
       endif(TBB_FOUND)
@@ -58,9 +56,9 @@ endif(GMP_FOUND)
 
 if(CGAL_FOUND)
   add_executable(exact_alpha_complex_3d_persistence exact_alpha_complex_3d_persistence.cpp)
-  target_link_libraries(exact_alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+  target_link_libraries(exact_alpha_complex_3d_persistence ${CGAL_LIBRARY})
   add_executable(weighted_alpha_complex_3d_persistence weighted_alpha_complex_3d_persistence.cpp)
-  target_link_libraries(weighted_alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+  target_link_libraries(weighted_alpha_complex_3d_persistence ${CGAL_LIBRARY})
 
   if (TBB_FOUND)
     target_link_libraries(exact_alpha_complex_3d_persistence ${TBB_LIBRARIES})
@@ -76,7 +74,7 @@ if(CGAL_FOUND)
 
   if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
     add_executable(custom_persistence_sort custom_persistence_sort.cpp)
-    target_link_libraries(custom_persistence_sort ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+    target_link_libraries(custom_persistence_sort ${CGAL_LIBRARY})
 
     if (TBB_FOUND)
       target_link_libraries(custom_persistence_sort ${TBB_LIBRARIES})
diff --git a/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp
index fa49dcee..8ce68406 100644
--- a/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp
+++ b/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp
@@ -77,8 +77,9 @@ using Simplex_tree_vector_vertex = std::vector< Simplex_tree_vertex >;
 using PCOH = Gudhi::persistent_cohomology::Persistent_cohomology< ST, Gudhi::persistent_cohomology::Field_Zp >;
 
 void usage(char * const progName) {
-  std::cerr << "Usage: " << progName <<
-      " path_to_file_graph coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n";
+  std::cerr << "Usage:\n" << progName << " path_to_OFF_file coeff_field_characteristic[integer " <<
+               "> 0] min_persistence[float >= -1.0]\n";
+  std::cerr << "  path_to_OFF_file is the path to your points cloud in OFF format.\n";
   exit(-1);
 }
 
@@ -204,7 +205,6 @@ int main(int argc, char * const argv[]) {
     else
       std::cout << "This shall not happen" << std::endl;
   }
-  simplex_tree.set_filtration(filtration_max);
   simplex_tree.set_dimension(dim_max);
 
 #ifdef DEBUG_TRACES
@@ -218,7 +218,6 @@ int main(int argc, char * const argv[]) {
   std::cout << "  Number of vertices = " << simplex_tree.num_vertices() << " ";
   std::cout << "  Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl;
   std::cout << "  Dimension = " << simplex_tree.dimension() << " ";
-  std::cout << "  filtration = " << simplex_tree.filtration() << std::endl << std::endl;
 #endif  // DEBUG_TRACES
 
 #ifdef DEBUG_TRACES
diff --git a/src/Persistent_cohomology/example/persistence_from_file.cpp b/src/Persistent_cohomology/example/persistence_from_file.cpp
index 67235467..eafa3fd5 100644
--- a/src/Persistent_cohomology/example/persistence_from_file.cpp
+++ b/src/Persistent_cohomology/example/persistence_from_file.cpp
@@ -61,8 +61,7 @@ int main(int argc, char * argv[]) {
   simplex_tree_stream >> simplex_tree;
 
   std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices" << std::endl;
-  std::cout << "   - dimension " << simplex_tree.dimension() << "   - filtration " << simplex_tree.filtration()
-      << std::endl;
+  std::cout << "   - dimension " << simplex_tree.dimension() << std::endl;
 
   /*
   std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl;
diff --git a/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp b/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp
index 7ca9410a..8214d66a 100644
--- a/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp
+++ b/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp
@@ -143,11 +143,10 @@ int main(int argc, char * const argv[]) {
   /*   An edge [10,12,2]      */
 
   st.set_dimension(2);
-  st.set_filtration(0.4);
 
   std::cout << "The complex contains " << st.num_simplices() << " simplices - " << st.num_vertices() << " vertices "
       << std::endl;
-  std::cout << "   - dimension " << st.dimension() << "   - filtration " << st.filtration() << std::endl;
+  std::cout << "   - dimension " << st.dimension() << std::endl;
   std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:"
       << std::endl;
   std::cout << "**************************************************************" << std::endl;
diff --git a/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp
index 4a2b10f3..a4ecf9da 100644
--- a/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp
+++ b/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp
@@ -81,8 +81,13 @@ using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomolog
     ST, Gudhi::persistent_cohomology::Field_Zp >;
 
 void usage(char * const progName) {
-  std::cerr << "Usage: " << progName <<
-      " path_to_file_graph path_to_weight_file coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n";
+  std::cerr << "Usage:\n" << progName << " path_to_OFF_file path_to_weight_file coeff_field_characteristic[integer " <<
+               "> 0] min_persistence[float >= -1.0]\n";
+  std::cerr << "  path_to_OFF_file is the path to your points cloud in OFF format.\n";
+  std::cerr << "  path_to_weight_file is the path to the weights of your points cloud (one value per line.)\n";
+  std::cerr << "  Weights values are explained on CGAL documentation:\n";
+  std::cerr << "    https://doc.cgal.org/latest/Alpha_shapes_3/index.html#title0\n";
+  std::cerr << "    https://doc.cgal.org/latest/Triangulation_3/index.html#Triangulation3secclassRegulartriangulation\n";
   exit(-1);
 }
 
@@ -115,6 +120,7 @@ int main(int argc, char * const argv[]) {
   if (weights_ifstr.good()) {
     double weight = 0.0;
     std::size_t index = 0;
+    wp.reserve(lp.size());
     // Attempt read the weight in a double format, return false if it fails
     while ((weights_ifstr >> weight) && (index < lp.size())) {
       wp.push_back(Weighted_point_3(lp[index], weight));
@@ -130,7 +136,7 @@ int main(int argc, char * const argv[]) {
   }
 
   // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode.
-  Alpha_shape_3 as(lp.begin(), lp.end(), 0, Alpha_shape_3::GENERAL);
+  Alpha_shape_3 as(wp.begin(), wp.end(), 0, Alpha_shape_3::GENERAL);
 #ifdef DEBUG_TRACES
   std::cout << "Alpha shape computed in GENERAL mode" << std::endl;
 #endif  // DEBUG_TRACES
@@ -222,7 +228,6 @@ int main(int argc, char * const argv[]) {
     else
       std::cout << "This shall not happen" << std::endl;
   }
-  simplex_tree.set_filtration(filtration_max);
   simplex_tree.set_dimension(dim_max);
 
 #ifdef DEBUG_TRACES
@@ -236,7 +241,6 @@ int main(int argc, char * const argv[]) {
   std::cout << "  Number of vertices = " << simplex_tree.num_vertices() << " ";
   std::cout << "  Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl;
   std::cout << "  Dimension = " << simplex_tree.dimension() << " ";
-  std::cout << "  filtration = " << simplex_tree.filtration() << std::endl << std::endl;
 #endif  // DEBUG_TRACES
 
 #ifdef DEBUG_TRACES