10 files changed, 145 insertions, 39 deletions

diff --git a/src/Witness_complex/doc/Witness_complex_doc.h b/src/Witness_complex/doc/Witness_complex_doc.h
index 171a185f..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,
@@ -107,7 +108,14 @@ int main(int argc, char * const argv[]) {
 
    Here is an example of constructing a strong witness complex filtration and computing persistence on it:
 
-   \include Witness_complex/example_strong_witness_persistence.cpp
+   \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/CMakeLists.txt b/src/Witness_complex/example/CMakeLists.txt
index cbc53902..a8231392 100644
--- a/src/Witness_complex/example/CMakeLists.txt
+++ b/src/Witness_complex/example/CMakeLists.txt
@@ -13,39 +13,23 @@ install(TARGETS Witness_complex_example_nearest_landmark_table DESTINATION bin)
 # CGAL and Eigen3 are required for Euclidean version of Witness
 if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
   add_executable( Witness_complex_example_off example_witness_complex_off.cpp )
-  add_executable( Witness_complex_example_strong_off example_strong_witness_complex_off.cpp )
   add_executable ( Witness_complex_example_sphere example_witness_complex_sphere.cpp )
-
-  add_executable ( Witness_complex_example_witness_persistence example_witness_complex_persistence.cpp )
-  target_link_libraries(Witness_complex_example_witness_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY})
-
-  add_executable ( Witness_complex_example_strong_witness_persistence example_strong_witness_persistence.cpp )
-  target_link_libraries(Witness_complex_example_strong_witness_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY})
-
-  if (TBB_FOUND)
-    target_link_libraries(Witness_complex_example_witness_persistence ${TBB_LIBRARIES})
-    target_link_libraries(Witness_complex_example_strong_witness_persistence ${TBB_LIBRARIES})
-  endif()
+  
+  add_executable( Witness_complex_example_strong_off example_strong_witness_complex_off.cpp )
+  target_link_libraries(Witness_complex_example_strong_off)
 
   add_test(NAME Witness_complex_example_off_test_torus
       COMMAND $<TARGET_FILE:Witness_complex_example_off>
       "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "20" "1.0" "3")
+  add_test(NAME Witness_complex_example_test_sphere_10
+      COMMAND $<TARGET_FILE:Witness_complex_example_sphere> "10")
   add_test(NAME Witness_complex_example_strong_off_test_torus
       COMMAND $<TARGET_FILE:Witness_complex_example_strong_off>
       "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "20" "1.0" "3")
-  add_test(NAME Witness_complex_example_test_sphere_10
-      COMMAND $<TARGET_FILE:Witness_complex_example_sphere> "10")
-  add_test(NAME Witness_complex_example_test_torus_persistence
-      COMMAND $<TARGET_FILE:Witness_complex_example_witness_persistence>
-      "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-l" "20" "-a" "0.5")
-  add_test(NAME Witness_complex_example_strong_test_torus_persistence
-      COMMAND $<TARGET_FILE:Witness_complex_example_strong_witness_persistence>
-      "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-l" "20" "-a" "0.5")
-
+      
   install(TARGETS Witness_complex_example_off DESTINATION bin)
-  install(TARGETS Witness_complex_example_strong_off DESTINATION bin)
   install(TARGETS Witness_complex_example_sphere DESTINATION bin)
-  install(TARGETS Witness_complex_example_witness_persistence DESTINATION bin)
-  install(TARGETS Witness_complex_example_strong_witness_persistence DESTINATION bin)
+  install(TARGETS Witness_complex_example_strong_off DESTINATION bin)
+
 
 endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
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/CMakeLists.txt b/src/Witness_complex/utilities/CMakeLists.txt
new file mode 100644
index 00000000..125a41ff
--- /dev/null
+++ b/src/Witness_complex/utilities/CMakeLists.txt
@@ -0,0 +1,28 @@
+cmake_minimum_required(VERSION 2.6)
+project(Witness_complex_utilities)
+
+# CGAL and Eigen3 are required for Euclidean version of Witness
+if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
+  
+  add_executable ( Witness_complex_strong_witness_persistence strong_witness_persistence.cpp )
+  target_link_libraries(Witness_complex_strong_witness_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY})
+
+  add_executable ( Witness_complex_weak_witness_persistence weak_witness_persistence.cpp )
+  target_link_libraries(Witness_complex_weak_witness_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY})
+
+  if (TBB_FOUND)
+    target_link_libraries(Witness_complex_strong_witness_persistence ${TBB_LIBRARIES})
+    target_link_libraries(Witness_complex_weak_witness_persistence ${TBB_LIBRARIES})
+  endif()
+
+  add_test(NAME Witness_complex_strong_test_torus_persistence
+      COMMAND $<TARGET_FILE:Witness_complex_strong_witness_persistence>
+      "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-l" "20" "-a" "0.5")
+  add_test(NAME Witness_complex_weak_test_torus_persistence
+      COMMAND $<TARGET_FILE:Witness_complex_weak_witness_persistence>
+      "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-l" "20" "-a" "0.5")
+
+  install(TARGETS Witness_complex_strong_witness_persistence DESTINATION bin)
+  install(TARGETS Witness_complex_weak_witness_persistence DESTINATION bin)
+
+endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
diff --git a/src/Witness_complex/utilities/README b/src/Witness_complex/utilities/README
new file mode 100644
index 00000000..1141033e
--- /dev/null
+++ b/src/Witness_complex/utilities/README
@@ -0,0 +1,74 @@
+# Witness_complex #

+

+For more details about the witness complex, please read the [user manual of the package](http://gudhi.gforge.inria.fr/doc/latest/group__witness__complex.html).

+

+## `weak_witness_persistence` ##

+This program computes the persistent homology with coefficient field *Z/pZ* of a Weak witness complex defined on a set of input points. The output diagram contains one bar per line, written with the convention:

+

+`p dim birth death`

+

+where `dim` is the dimension of the homological feature, `birth` and `death` are respectively the birth and death of the feature, and `p` is the characteristic of the field *Z/pZ* used for homology coefficients.

+

+*Usage*

+`weak_witness_persistence [options] <OFF input file>`

+

+*Allowed options*

+

+* `-h [ --help ]` Produce help message

+* `-l [ --landmarks ]` Number of landmarks to choose from the point cloud.

+* `-o [ --output-file ]` Name of file in which the persistence diagram is written. By default, print in std::cout.

+* `-a [ --max-sq-alpha ]` (default = inf) Maximal squared relaxation parameter.

+* `-p [ --field-charac ]` (default = 11) Characteristic p of the coefficient field Z/pZ for computing homology.

+* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals.

+* `-d [ --cpx-dimension ]` (default = 2147483647) Maximal dimension of the weak witness complex we want to compute.

+

+*Example*

+`weak_witness_persistence data/points/tore3D_1307.off -l 20 -a 0.5 -m 0.006`

+

+outputs:

+```

+Successfully read 1307 points.

+Ambient dimension is 3.

+The complex contains 732 simplices and has dimension 8 

+11  0 0 inf 

+11  1 0 inf 

+11  2 0.0275251 0.0534586 

+11  1 0 0.0239952 

+```

+

+N.B.: output is random as the 20 landmarks are chosen randomly.

+

+## `strong_witness_persistence` ##

+This program computes the persistent homology with coefficient field *Z/pZ* of a Strong witness complex defined on a set of input points. The output diagram contains one bar per line, written with the convention:

+

+`p dim birth death`

+

+where `dim` is the dimension of the homological feature, `birth` and `death` are respectively the birth and death of the feature, and `p` is the characteristic of the field *Z/pZ* used for homology coefficients.

+

+*Usage*

+`strong_witness_persistence [options] <OFF input file>`

+

+*Allowed options*

+

+* `-h [ --help ]` Produce help message

+* `-l [ --landmarks ]` Number of landmarks to choose from the point cloud.

+* `-o [ --output-file ]` Name of file in which the persistence diagram is written. By default, print in std::cout.

+* `-a [ --max-sq-alpha ]` (default = inf) Maximal squared relaxation parameter.

+* `-p [ --field-charac ]` (default = 11) Characteristic p of the coefficient field Z/pZ for computing homology.

+* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals.

+* `-d [ --cpx-dimension ]` (default = 2147483647) Maximal dimension of the weak witness complex we want to compute.

+

+*Example*

+`strong_witness_persistence data/points/tore3D_1307.off -l 20 -a 0.5 -m 0.06`

+

+outputs:

+```

+Successfully read 1307 points.

+Ambient dimension is 3.

+The complex contains 1836 simplices and has dimension 8 

+11  0 0 inf 

+11  1 0.00674748 inf 

+11  2 0.0937751 0.235354 

+```

+

+N.B.: output is random as the 20 landmarks are chosen randomly.

diff --git a/src/Witness_complex/example/example_strong_witness_persistence.cpp b/src/Witness_complex/utilities/strong_witness_persistence.cpp
index f786fe7b..e3e0c1ee 100644
--- a/src/Witness_complex/example/example_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/example/example_witness_complex_persistence.cpp b/src/Witness_complex/utilities/weak_witness_persistence.cpp
index a1146922..a63b0837 100644
--- a/src/Witness_complex/example/example_witness_complex_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,