Merge last trunk modification

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_remove_useless_global_filtration@2720 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 37cec1ea1e06c9e9656962614fcddc0fa022c5d0

7 files changed, 34 insertions, 18 deletions

diff --git a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
index 1408681a..24d73c57 100644
--- a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
+++ b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
@@ -25,21 +25,21 @@
 #include <iostream>
 #include <vector>
 #include <utility>  // for pair
-#include <fstream>
-#include <sstream>
 #include <string>
+#include <limits>  // for numeric_limits
 
 int main(int argc, char** argv) {
   if (argc < 3) {
-    std::cout << "To run this program please provide as an input two files with persistence diagrams. Each file " <<
-        "should contain a birth-death pair per line. Third, optional parameter is an error bound on a bottleneck" <<
-        " distance (set by default to zero). The program will now terminate \n";
+    std::cout << "To run this program please provide as an input two files with persistence diagrams. Each file" <<
+        " should contain a birth-death pair per line. Third, optional parameter is an error bound on a bottleneck" <<
+        " distance (set by default to the smallest positive double value). If you set the error bound to 0, be" <<
+        " aware this version is exact but expensive. The program will now terminate \n";
     return -1;
   }
   std::vector<std::pair<double, double>> diag1 = Gudhi::read_persistence_intervals_in_dimension(argv[1]);
   std::vector<std::pair<double, double>> diag2 = Gudhi::read_persistence_intervals_in_dimension(argv[2]);
 
-  double tolerance = 0.;
+  double tolerance = std::numeric_limits<double>::min();
   if (argc == 4) {
     tolerance = atof(argv[3]);
   }
diff --git a/src/Doxyfile b/src/Doxyfile
index 6c01aefc..7f5975eb 100644
--- a/src/Doxyfile
+++ b/src/Doxyfile
@@ -38,7 +38,7 @@ PROJECT_NAME           = "GUDHI"
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = "2.0.1-rc1"
+PROJECT_NUMBER         = "2.0.1-rc2"
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a
diff --git a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp
index 53e50a69..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);
 }
 
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 acb34bcb..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);
 }
 
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 f731d349..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);
 }
 
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 9728f22d..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
diff --git a/src/cython/doc/bottleneck_distance_user.rst b/src/cython/doc/bottleneck_distance_user.rst
index 0066992f..7692dce2 100644
--- a/src/cython/doc/bottleneck_distance_user.rst
+++ b/src/cython/doc/bottleneck_distance_user.rst
@@ -25,7 +25,7 @@ This example computes the bottleneck distance from 2 persistence diagrams:
     message = "Bottleneck distance approximation=" + '%.2f' % gudhi.bottleneck_distance(diag1, diag2, 0.1)
     print(message)
 
-    message = "Bottleneck distance exact value=" + '%.2f' % gudhi.bottleneck_distance(diag1, diag2, 0)
+    message = "Bottleneck distance value=" + '%.2f' % gudhi.bottleneck_distance(diag1, diag2)
     print(message)
 
 The output is:
@@ -33,4 +33,4 @@ The output is:
 .. testoutput::
 
     Bottleneck distance approximation=0.81
-    Bottleneck distance exact value=0.75
+    Bottleneck distance value=0.75