Merge last trunk modification

Fix doc issue
Still doc issue


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@1739 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 0a99345f06e93a3525691699a6fe1505979e8e8e

3 files changed, 24 insertions, 66 deletions

diff --git a/src/Witness_complex/example/CMakeLists.txt b/src/Witness_complex/example/CMakeLists.txt
index e6a916cd..857ec819 100644
--- a/src/Witness_complex/example/CMakeLists.txt
+++ b/src/Witness_complex/example/CMakeLists.txt
@@ -3,42 +3,15 @@ project(Witness_complex_examples)
 
 # A simple example
    add_executable( witness_complex_from_file witness_complex_from_file.cpp )
-   add_test( witness_complex_from_bunny ${CMAKE_CURRENT_BINARY_DIR}/witness_complex_from_file ${CMAKE_SOURCE_DIR}/data/points/bunny_5000 100)   
+   add_test( witness_complex_from_bunny ${CMAKE_CURRENT_BINARY_DIR}/witness_complex_from_file
+             ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.off 100)   
 
 if(CGAL_FOUND)
   if (NOT CGAL_VERSION VERSION_LESS 4.6.0)
-    message(STATUS "CGAL version: ${CGAL_VERSION}.")
-
-    include( ${CGAL_USE_FILE} )
-    # In CMakeLists.txt, when include(${CGAL_USE_FILE}), CXX_FLAGS are overwritten.
-    # cf. http://doc.cgal.org/latest/Manual/installation.html#title40
-    # A workaround is to add "-std=c++11" again.
-    # A fix would be to use https://cmake.org/cmake/help/v3.1/prop_gbl/CMAKE_CXX_KNOWN_FEATURES.html 
-    # or even better https://cmake.org/cmake/help/v3.1/variable/CMAKE_CXX_STANDARD.html
-    # but it implies to use cmake version 3.1 at least.
-    if(NOT MSVC)
-      include(CheckCXXCompilerFlag)
-      CHECK_CXX_COMPILER_FLAG(-std=c++11 COMPILER_SUPPORTS_CXX11)
-      if(COMPILER_SUPPORTS_CXX11)
-        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
-      endif()
-    endif()
-    # - End of workaround
-
-    find_package(Eigen3 3.1.0)
     if (EIGEN3_FOUND)
-      message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.")
-      include( ${EIGEN3_USE_FILE} )
-      message(STATUS "Eigen3 use file: ${EIGEN3_USE_FILE}.")
-      include_directories (BEFORE "../../include")
-
       add_executable ( witness_complex_sphere witness_complex_sphere.cpp )
       target_link_libraries(witness_complex_sphere ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
       add_test( witness_complex_sphere_10 ${CMAKE_CURRENT_BINARY_DIR}/witness_complex_sphere 10)   
-    else()
-      message(WARNING "Eigen3 not found. Version 3.1.0 is required for witness_complex_sphere example.")      
-    endif()
-  else()
-    message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile witness_complex_sphere example. Version 4.6.0 is required.")
-  endif ()
+    endif(EIGEN3_FOUND)
+  endif (NOT CGAL_VERSION VERSION_LESS 4.6.0)
 endif()
diff --git a/src/Witness_complex/example/witness_complex_from_file.cpp b/src/Witness_complex/example/witness_complex_from_file.cpp
index 53207ad2..bb641b3c 100644
--- a/src/Witness_complex/example/witness_complex_from_file.cpp
+++ b/src/Witness_complex/example/witness_complex_from_file.cpp
@@ -23,9 +23,11 @@
 #include <sys/types.h>
 #include <sys/stat.h>
 
+#include <gudhi/Points_off_io.h>
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/Witness_complex.h>
-#include <gudhi/Landmark_choice_by_random_point.h>
+#include <gudhi/Construct_closest_landmark_table.h>
+#include <gudhi/pick_n_random_points.h>
 #include <gudhi/reader_utils.h>
 
 #include <iostream>
@@ -37,56 +39,37 @@
 typedef std::vector< Vertex_handle > typeVectorVertex;
 typedef std::vector< std::vector <double> > Point_Vector;
 
-/**
- * \brief Customized version of read_points
- * which takes into account a possible nbP first line
- *
- */
-inline void
-read_points_cust(std::string file_name, std::vector< std::vector< double > > & points) {
-  std::ifstream in_file(file_name.c_str(), std::ios::in);
-  if (!in_file.is_open()) {
-    std::cerr << "Unable to open file " << file_name << std::endl;
-    return;
-  }
-  std::string line;
-  double x;
-  while (getline(in_file, line)) {
-    std::vector< double > point;
-    std::istringstream iss(line);
-    while (iss >> x) {
-      point.push_back(x);
-    }
-    if (point.size() != 1)
-      points.push_back(point);
-  }
-  in_file.close();
-}
-
 int main(int argc, char * const argv[]) {
   if (argc != 3) {
     std::cerr << "Usage: " << argv[0]
-        << " path_to_point_file nbL \n";
+        << " path_to_point_file.off nbL \n";
     return 0;
   }
 
-  std::string file_name = argv[1];
+  std::string off_file_name = argv[1];
   int nbL = atoi(argv[2]);
   clock_t start, end;
 
   // Construct the Simplex Tree
   Gudhi::Simplex_tree<> simplex_tree;
 
+  // Read the OFF file (input file name given as parameter) and triangulate points
+  Gudhi::Points_off_reader<std::vector <double>> off_reader(off_file_name);
+  // Check the read operation was correct
+  if (!off_reader.is_valid()) {
+    std::cerr << "Unable to read file " << off_file_name << std::endl;
+  }
   // Read the point file
-  Point_Vector point_vector;
-  read_points_cust(file_name, point_vector);
+  Point_Vector point_vector = off_reader.get_point_cloud();
   std::cout << "Successfully read " << point_vector.size() << " points.\n";
   std::cout << "Ambient dimension is " << point_vector[0].size() << ".\n";
 
   // Choose landmarks
   start = clock();
   std::vector<std::vector< int > > knn;
-  Gudhi::witness_complex::landmark_choice_by_random_point(point_vector, nbL, knn);
+  Point_Vector landmarks;
+  Gudhi::subsampling::pick_n_random_points(point_vector, 100, std::back_inserter(landmarks));
+  Gudhi::witness_complex::construct_closest_landmark_table(point_vector, landmarks, knn);
   end = clock();
   std::cout << "Landmark choice for " << nbL << " landmarks took "
       << static_cast<double>(end - start) / CLOCKS_PER_SEC << " s. \n";
diff --git a/src/Witness_complex/example/witness_complex_sphere.cpp b/src/Witness_complex/example/witness_complex_sphere.cpp
index b26c9f36..e6f88274 100644
--- a/src/Witness_complex/example/witness_complex_sphere.cpp
+++ b/src/Witness_complex/example/witness_complex_sphere.cpp
@@ -27,7 +27,8 @@
 
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/Witness_complex.h>
-#include <gudhi/Landmark_choice_by_random_point.h>
+#include <gudhi/Construct_closest_landmark_table.h>
+#include <gudhi/pick_n_random_points.h>
 #include <gudhi/reader_utils.h>
 
 #include <iostream>
@@ -67,7 +68,7 @@ int main(int argc, char * const argv[]) {
 
   // Read the point file
   for (int nbP = 500; nbP < 10000; nbP += 500) {
-    Point_Vector point_vector;
+    Point_Vector point_vector, landmarks;
     generate_points_sphere(point_vector, nbP, 4);
     std::cout << "Successfully generated " << point_vector.size() << " points.\n";
     std::cout << "Ambient dimension is " << point_vector[0].size() << ".\n";
@@ -75,7 +76,8 @@ int main(int argc, char * const argv[]) {
     // Choose landmarks
     start = clock();
     std::vector<std::vector< int > > knn;
-    Gudhi::witness_complex::landmark_choice_by_random_point(point_vector, number_of_landmarks, knn);
+    Gudhi::subsampling::pick_n_random_points(point_vector, 100, std::back_inserter(landmarks));
+    Gudhi::witness_complex::construct_closest_landmark_table(point_vector, landmarks, knn);
 
     // Compute witness complex
     Gudhi::witness_complex::witness_complex(knn, number_of_landmarks, point_vector[0].size(), simplex_tree);