Merge last trunk modifications

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/add_utils_in_gudhi_v2@2922 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 9ea024337f05cfc4f9a1d645c6e6ee9aac9700ba

7 files changed, 34 insertions, 14 deletions

diff --git a/src/Witness_complex/doc/Witness_complex_doc.h b/src/Witness_complex/doc/Witness_complex_doc.h
index 20834be0..5d5c0735 100644
--- a/src/Witness_complex/doc/Witness_complex_doc.h
+++ b/src/Witness_complex/doc/Witness_complex_doc.h
@@ -90,8 +90,9 @@ int main(int argc, char * const argv[]) {
   Gudhi::Points_off_reader<Point_d> off_reader(file_name);
   point_vector = Point_vector(off_reader.get_point_cloud());
 
-  // Choose landmarks
-  Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks));
+  // Choose landmarks (one can choose either of the two methods below)
+  // Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks));
+  Gudhi::subsampling::choose_n_farthest_points(K(), point_vector, nbL, Gudhi::subsampling::random_starting_point, std::back_inserter(landmarks));
 
   // Compute witness complex
   Witness_complex witness_complex(landmarks,
@@ -109,6 +110,13 @@ int main(int argc, char * const argv[]) {
 
    \include Witness_complex/strong_witness_persistence.cpp
 
+   \section witnessexample3 Example3: Computing relaxed witness complex persistence from a distance matrix 
+
+   In this example we compute the relaxed witness complex persistence from a given matrix of closest landmarks to each witness.
+   Each landmark is given as the couple (index, distance).
+
+   \include Witness_complex/example_nearest_landmark_table.cpp
+
    \copyright GNU General Public License v3.
 
 
diff --git a/src/Witness_complex/example/example_strong_witness_complex_off.cpp b/src/Witness_complex/example/example_strong_witness_complex_off.cpp
index 0ee9ee90..bc069654 100644
--- a/src/Witness_complex/example/example_strong_witness_complex_off.cpp
+++ b/src/Witness_complex/example/example_strong_witness_complex_off.cpp
@@ -23,6 +23,7 @@
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/Euclidean_strong_witness_complex.h>
 #include <gudhi/pick_n_random_points.h>
+#include <gudhi/choose_n_farthest_points.h>
 #include <gudhi/Points_off_io.h>
 
 #include <CGAL/Epick_d.h>
@@ -63,9 +64,10 @@ int main(int argc, char * const argv[]) {
   std::cout << "Successfully read " << point_vector.size() << " points.\n";
   std::cout << "Ambient dimension is " << point_vector[0].dimension() << ".\n";
 
-  // Choose landmarks
-  Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks));
-
+  // Choose landmarks (decomment one of the following two lines)
+  // Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks));
+  Gudhi::subsampling::choose_n_farthest_points(K(), point_vector, nbL, Gudhi::subsampling::random_starting_point, std::back_inserter(landmarks));
+  
   // Compute witness complex
   start = clock();
   Witness_complex witness_complex(landmarks,
diff --git a/src/Witness_complex/example/example_witness_complex_off.cpp b/src/Witness_complex/example/example_witness_complex_off.cpp
index b36dac0d..be11c955 100644
--- a/src/Witness_complex/example/example_witness_complex_off.cpp
+++ b/src/Witness_complex/example/example_witness_complex_off.cpp
@@ -4,6 +4,7 @@
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/Euclidean_witness_complex.h>
 #include <gudhi/pick_n_random_points.h>
+#include <gudhi/choose_n_farthest_points.h>
 #include <gudhi/Points_off_io.h>
 
 #include <CGAL/Epick_d.h>
@@ -44,8 +45,9 @@ int main(int argc, char * const argv[]) {
   std::cout << "Successfully read " << point_vector.size() << " points.\n";
   std::cout << "Ambient dimension is " << point_vector[0].dimension() << ".\n";
 
-  // Choose landmarks
-  Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks));
+  // Choose landmarks (decomment one of the following two lines)
+  // Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks));
+  Gudhi::subsampling::choose_n_farthest_points(K(), point_vector, nbL, Gudhi::subsampling::random_starting_point, std::back_inserter(landmarks));
 
   // Compute witness complex
   start = clock();
diff --git a/src/Witness_complex/example/example_witness_complex_sphere.cpp b/src/Witness_complex/example/example_witness_complex_sphere.cpp
index 124fd99b..a66da3f9 100644
--- a/src/Witness_complex/example/example_witness_complex_sphere.cpp
+++ b/src/Witness_complex/example/example_witness_complex_sphere.cpp
@@ -25,6 +25,7 @@
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/Euclidean_witness_complex.h>
 #include <gudhi/pick_n_random_points.h>
+#include <gudhi/choose_n_farthest_points.h>
 #include <gudhi/reader_utils.h>
 
 #include <CGAL/Epick_d.h>
@@ -75,7 +76,8 @@ int main(int argc, char * const argv[]) {
 
     // Choose landmarks
     start = clock();
-    Gudhi::subsampling::pick_n_random_points(point_vector, number_of_landmarks, std::back_inserter(landmarks));
+    // Gudhi::subsampling::pick_n_random_points(point_vector, number_of_landmarks, std::back_inserter(landmarks));
+    Gudhi::subsampling::choose_n_farthest_points(K(), point_vector, number_of_landmarks, Gudhi::subsampling::random_starting_point, std::back_inserter(landmarks));
 
     // Compute witness complex
     Witness_complex witness_complex(landmarks,
diff --git a/src/Witness_complex/include/gudhi/Strong_witness_complex.h b/src/Witness_complex/include/gudhi/Strong_witness_complex.h
index c18335d3..b3d00b11 100644
--- a/src/Witness_complex/include/gudhi/Strong_witness_complex.h
+++ b/src/Witness_complex/include/gudhi/Strong_witness_complex.h
@@ -34,7 +34,8 @@ namespace Gudhi {
 
 namespace witness_complex {
 
-/* \private
+  /**
+   * \private
  * \class Strong_witness_complex
  * \brief Constructs strong witness complex for a given table of nearest landmarks with respect to witnesses.
  * \ingroup witness_complex
@@ -130,6 +131,8 @@ class Strong_witness_complex {
     return true;
   }
 
+  //@}
+
  private:
     /* \brief Adds recursively all the faces of a certain dimension dim-1 witnessed by the same witness.
      * Iterator is needed to know until how far we can take landmarks to form simplexes.
@@ -170,7 +173,6 @@ class Strong_witness_complex {
       simplex.pop_back();
     }
   }
-  //@}
 };
 
 }  // namespace witness_complex
diff --git a/src/Witness_complex/utilities/strong_witness_persistence.cpp b/src/Witness_complex/utilities/strong_witness_persistence.cpp
index f786fe7b..e3e0c1ee 100644
--- a/src/Witness_complex/utilities/strong_witness_persistence.cpp
+++ b/src/Witness_complex/utilities/strong_witness_persistence.cpp
@@ -25,6 +25,7 @@
 #include <gudhi/Persistent_cohomology.h>
 #include <gudhi/Points_off_io.h>
 #include <gudhi/pick_n_random_points.h>
+#include <gudhi/choose_n_farthest_points.h>
 
 #include <boost/program_options.hpp>
 
@@ -76,8 +77,9 @@ int main(int argc, char * argv[]) {
   std::cout << "Successfully read " << witnesses.size() << " points.\n";
   std::cout << "Ambient dimension is " << witnesses[0].dimension() << ".\n";
 
-  // Choose landmarks from witnesses
-  Gudhi::subsampling::pick_n_random_points(witnesses, nbL, std::back_inserter(landmarks));
+  // Choose landmarks (decomment one of the following two lines)
+  // Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks));
+  Gudhi::subsampling::choose_n_farthest_points(K(), witnesses, nbL, Gudhi::subsampling::random_starting_point, std::back_inserter(landmarks));
 
   // Compute witness complex
   Strong_witness_complex strong_witness_complex(landmarks,
diff --git a/src/Witness_complex/utilities/weak_witness_persistence.cpp b/src/Witness_complex/utilities/weak_witness_persistence.cpp
index a1146922..a63b0837 100644
--- a/src/Witness_complex/utilities/weak_witness_persistence.cpp
+++ b/src/Witness_complex/utilities/weak_witness_persistence.cpp
@@ -25,6 +25,7 @@
 #include <gudhi/Persistent_cohomology.h>
 #include <gudhi/Points_off_io.h>
 #include <gudhi/pick_n_random_points.h>
+#include <gudhi/choose_n_farthest_points.h>
 
 #include <boost/program_options.hpp>
 
@@ -76,8 +77,9 @@ int main(int argc, char * argv[]) {
   std::cout << "Successfully read " << witnesses.size() << " points.\n";
   std::cout << "Ambient dimension is " << witnesses[0].dimension() << ".\n";
 
-  // Choose landmarks from witnesses
-  Gudhi::subsampling::pick_n_random_points(witnesses, nbL, std::back_inserter(landmarks));
+  // Choose landmarks (decomment one of the following two lines)
+  // Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks));
+  Gudhi::subsampling::choose_n_farthest_points(K(), witnesses, nbL, Gudhi::subsampling::random_starting_point, std::back_inserter(landmarks));
 
   // Compute witness complex
   Witness_complex witness_complex(landmarks,