Merge last trunk modifications

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/rips_complex_from_correlation_matrix@2725 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 78f35b92214c207f00b26ea87ca88d20abeea53d

8 files changed, 29 insertions, 25 deletions

diff --git a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp
index fd227b82..f63ff0f6 100644
--- a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp
+++ b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp
@@ -76,8 +76,9 @@ 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(const std::string& 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);
 }
 
@@ -202,7 +203,6 @@ 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
@@ -216,7 +216,6 @@ 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/exact_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp
index 8a335075..09561d03 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/periodic_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp
index 8928cfc2..8140a3c5 100644
--- a/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp
+++ b/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp
@@ -84,8 +84,16 @@ 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_iso_cuboid_3_file coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n";
+  std::cerr << "Usage:\n" << progName << " path_to_OFF_file path_to_iso_cuboid_3_file coeff_field_characteristic[" <<
+               "integer > 0] min_persistence[float >= -1.0]\n" <<
+               "  path_to_OFF_file is the path to your points cloud in OFF format.\n" <<
+               "  path_to_iso_cuboid_3_file is the path to the iso cuboid file with the following format :\n" <<
+               "    x_min y_min z_min x_max y_max z_max\n" <<
+               "  In this example, the periodic cube will be " <<
+               "{ x = [x_min,x_max]; y = [y_min,y_max]; z = [z_min,z_max] }.\n" <<
+               "  For more information, please refer to\n" <<
+               "    https://doc.cgal.org/latest/Kernel_23/classCGAL_1_1Iso__cuboid__3.html\n";
+
   exit(-1);
 }
 
@@ -221,7 +229,6 @@ 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
@@ -235,7 +242,6 @@ 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 34b90933..72268511 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
diff --git a/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp b/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp
index f8174020..f53987b6 100644
--- a/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp
+++ b/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp
@@ -31,12 +31,11 @@ std::string test_rips_persistence(int coefficient, int min_persistence) {
 
   // Display the Simplex_tree
   std::cout << "The complex contains " << st.num_simplices() << " simplices" << " - dimension= " << st.dimension()
-      << " - filtration= " << st.filtration() << std::endl;
+      << std::endl;
 
   // Check
   BOOST_CHECK(st.num_simplices() == 98);
   BOOST_CHECK(st.dimension() == 3);
-  BOOST_CHECK(st.filtration() == 1.89);
 
   // Sort the simplices in the order of the filtration
   st.initialize_filtration();
diff --git a/src/Persistent_cohomology/test/persistent_cohomology_unit_test_multi_field.cpp b/src/Persistent_cohomology/test/persistent_cohomology_unit_test_multi_field.cpp
index 3537cfa4..9e767943 100644
--- a/src/Persistent_cohomology/test/persistent_cohomology_unit_test_multi_field.cpp
+++ b/src/Persistent_cohomology/test/persistent_cohomology_unit_test_multi_field.cpp
@@ -31,12 +31,11 @@ std::string test_rips_persistence(int min_coefficient, int max_coefficient, doub
 
   // Display the Simplex_tree
   std::cout << "The complex contains " << st.num_simplices() << " simplices" << " - dimension= " << st.dimension()
-      << " - filtration= " << st.filtration() << std::endl;
+      << std::endl;
 
   // Check
   BOOST_CHECK(st.num_simplices() == 58);
   BOOST_CHECK(st.dimension() == 3);
-  BOOST_CHECK(st.filtration() == 0.4);
 
   // Sort the simplices in the order of the filtration
   st.initialize_filtration();