Merged trunk into relaxed witness branch

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/relaxed-witness@1579 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: a9ca2e7a968ebf4bb80cfa795965ae78511e8dd4

3 files changed, 12 insertions, 75 deletions

diff --git a/src/Witness_complex/example/CMakeLists.txt b/src/Witness_complex/example/CMakeLists.txt
index d6a958b7..4d67e0d0 100644
--- a/src/Witness_complex/example/CMakeLists.txt
+++ b/src/Witness_complex/example/CMakeLists.txt
@@ -1,5 +1,5 @@
 cmake_minimum_required(VERSION 2.6)
-project(GUDHIWitnessComplex)
+project(Witness_complex_examples)
 
 # A simple example
    add_executable( witness_complex_from_file witness_complex_from_file.cpp )
@@ -7,51 +7,10 @@ project(GUDHIWitnessComplex)
 
 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)   
-      add_executable ( relaxed_witness_persistence relaxed_witness_persistence.cpp )
-      target_link_libraries(relaxed_witness_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
-      add_test( relaxed_witness_persistence_10 ${CMAKE_CURRENT_BINARY_DIR}/relaxed_witness_persistence 10)   
-      add_executable ( a0_persistence a0_persistence.cpp )
-      target_link_libraries(a0_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
-      add_test( a0_persistence_10 ${CMAKE_CURRENT_BINARY_DIR}/a0_persistence 10)
-      add_executable ( bench_rwit bench_rwit.cpp )
-      target_link_libraries(bench_rwit ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
-                  
-      add_executable ( relaxed_delaunay relaxed_delaunay.cpp )
-      target_link_libraries(relaxed_delaunay ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
-      add_test( relaxed_delaunay_10 ${CMAKE_CURRENT_BINARY_DIR}/relaxed_delaunay 10)   
-      add_executable ( generate_torus generate_torus.cpp )
-    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 77109512..53207ad2 100644
--- a/src/Witness_complex/example/witness_complex_from_file.cpp
+++ b/src/Witness_complex/example/witness_complex_from_file.cpp
@@ -34,14 +34,9 @@
 #include <string>
 #include <vector>
 
-using namespace Gudhi;
-using namespace Gudhi::witness_complex;
-
 typedef std::vector< Vertex_handle > typeVectorVertex;
 typedef std::vector< std::vector <double> > Point_Vector;
 
-typedef Witness_complex< Simplex_tree<> > WitnessComplex;
-
 /**
  * \brief Customized version of read_points
  * which takes into account a possible nbP first line
@@ -68,17 +63,6 @@ read_points_cust(std::string file_name, std::vector< std::vector< double > > & p
   in_file.close();
 }
 
-/** Write a gnuplot readable file.
- *  Data range is a random access range of pairs (arg, value)
- */
-template < typename Data_range >
-void write_data(Data_range & data, std::string filename) {
-  std::ofstream ofs(filename, std::ofstream::out);
-  for (auto entry : data)
-    ofs << entry.first << ", " << entry.second << "\n";
-  ofs.close();
-}
-
 int main(int argc, char * const argv[]) {
   if (argc != 3) {
     std::cerr << "Usage: " << argv[0]
@@ -91,7 +75,7 @@ int main(int argc, char * const argv[]) {
   clock_t start, end;
 
   // Construct the Simplex Tree
-  Simplex_tree<> simplex_tree;
+  Gudhi::Simplex_tree<> simplex_tree;
 
   // Read the point file
   Point_Vector point_vector;
@@ -109,7 +93,7 @@ int main(int argc, char * const argv[]) {
 
   // Compute witness complex
   start = clock();
-  WitnessComplex(knn, simplex_tree, nbL, point_vector[0].size());
+  Gudhi::witness_complex::witness_complex(knn, nbL, point_vector[0].size(), simplex_tree);
   end = clock();
   std::cout << "Witness complex 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 1ff35bff..b26c9f36 100644
--- a/src/Witness_complex/example/witness_complex_sphere.cpp
+++ b/src/Witness_complex/example/witness_complex_sphere.cpp
@@ -39,13 +39,6 @@
 
 #include "generators.h"
 
-using namespace Gudhi;
-using namespace Gudhi::witness_complex;
-
-typedef std::vector< Vertex_handle > typeVectorVertex;
-
-typedef Witness_complex< Simplex_tree<> > WitnessComplex;
-
 /** Write a gnuplot readable file.
  *  Data range is a random access range of pairs (arg, value)
  */
@@ -60,15 +53,15 @@ void write_data(Data_range & data, std::string filename) {
 int main(int argc, char * const argv[]) {
   if (argc != 2) {
     std::cerr << "Usage: " << argv[0]
-        << " nbL \n";
+        << " number_of_landmarks \n";
     return 0;
   }
 
-  int nbL = atoi(argv[1]);
+  int number_of_landmarks = atoi(argv[1]);
   clock_t start, end;
 
   // Construct the Simplex Tree
-  Simplex_tree<> simplex_tree;
+  Gudhi::Simplex_tree<> simplex_tree;
 
   std::vector< std::pair<int, double> > l_time;
 
@@ -82,14 +75,15 @@ 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, nbL, knn);
+    Gudhi::witness_complex::landmark_choice_by_random_point(point_vector, number_of_landmarks, knn);
 
     // Compute witness complex
-    WitnessComplex(knn, simplex_tree, nbL, point_vector[0].size());
+    Gudhi::witness_complex::witness_complex(knn, number_of_landmarks, point_vector[0].size(), simplex_tree);
     end = clock();
     double time = static_cast<double>(end - start) / CLOCKS_PER_SEC;
-    std::cout << "Witness complex for " << nbL << " landmarks took "
+    std::cout << "Witness complex for " << number_of_landmarks << " landmarks took "
         << time << " s. \n";
+    std::cout << "Number of simplices is: " << simplex_tree.num_simplices() << "\n";
     l_time.push_back(std::make_pair(nbP, time));
   }
   write_data(l_time, "w_time.dat");