Merge last trunk modifications

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alpha_complex_create_complex@1649 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 7922bc81bedad2be83951857a518edb73f9ca54e

6 files changed, 38 insertions, 56 deletions

diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt
index d97d1b63..0899958c 100644
--- a/src/Persistent_cohomology/example/CMakeLists.txt
+++ b/src/Persistent_cohomology/example/CMakeLists.txt
@@ -31,9 +31,9 @@ endif()
 add_test(plain_homology ${CMAKE_CURRENT_BINARY_DIR}/plain_homology)
 add_test(persistence_from_simple_simplex_tree ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_simple_simplex_tree 1 0)
 add_test(rips_persistence_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.2 -d 3 -p 3 -m 100)
-add_test(rips_persistence_via_boundary_matrix_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence_via_boundary_matrix ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.txt -r 0.3 -d 3 -p 3 -m 100)
-add_test(persistence_from_file_3_2_0 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.st -p 2 -m 0)
-add_test(persistence_from_file_3_3_100 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.st -p 3 -m 100)
+add_test(rips_persistence_via_boundary_matrix_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence_via_boundary_matrix ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.2 -d 3 -p 3 -m 100)
+add_test(persistence_from_file_3_2_0 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc -p 2 -m 0)
+add_test(persistence_from_file_3_3_100 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc -p 3 -m 100)
    
 if(GMP_FOUND)
    if(GMPXX_FOUND)
diff --git a/src/Simplex_tree/example/CMakeLists.txt b/src/Simplex_tree/example/CMakeLists.txt
index 9314a805..e5285591 100644
--- a/src/Simplex_tree/example/CMakeLists.txt
+++ b/src/Simplex_tree/example/CMakeLists.txt
@@ -5,8 +5,10 @@ add_executable ( simplex_tree_from_cliques_of_graph simplex_tree_from_cliques_of
 if (TBB_FOUND)
   target_link_libraries(simplex_tree_from_cliques_of_graph ${TBB_LIBRARIES})
 endif()
-add_test(simplex_tree_from_cliques_of_graph_2 ${CMAKE_CURRENT_BINARY_DIR}/simplex_tree_from_cliques_of_graph ${CMAKE_SOURCE_DIR}/data/points/Klein_bottle_complex.txt 2)
-add_test(simplex_tree_from_cliques_of_graph_3 ${CMAKE_CURRENT_BINARY_DIR}/simplex_tree_from_cliques_of_graph ${CMAKE_SOURCE_DIR}/data/points/Klein_bottle_complex.txt 3)
+add_test(simplex_tree_from_cliques_of_graph_2 ${CMAKE_CURRENT_BINARY_DIR}/simplex_tree_from_cliques_of_graph
+         ${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/Klein_bottle_complex.fsc 2)
+add_test(simplex_tree_from_cliques_of_graph_3 ${CMAKE_CURRENT_BINARY_DIR}/simplex_tree_from_cliques_of_graph
+         ${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/Klein_bottle_complex.fsc 3)
 
 add_executable ( simple_simplex_tree simple_simplex_tree.cpp )
 if (TBB_FOUND)
@@ -20,10 +22,12 @@ add_test(mini_simplex_tree ${CMAKE_CURRENT_BINARY_DIR}/mini_simplex_tree)
 
 # An example with Simplex-tree using CGAL alpha_shapes_3
 if(GMP_FOUND AND CGAL_FOUND)
-  add_executable ( simplex_tree_from_alpha_shapes_3 simplex_tree_from_alpha_shapes_3.cpp )
-  target_link_libraries(simplex_tree_from_alpha_shapes_3 ${GMP_LIBRARIES} ${CGAL_LIBRARY} ${Boost_SYSTEM_LIBRARY})
+  add_executable ( alpha_shapes_3_simplex_tree_from_off_file example_alpha_shapes_3_simplex_tree_from_off_file.cpp )
+  target_link_libraries(alpha_shapes_3_simplex_tree_from_off_file ${GMP_LIBRARIES} ${CGAL_LIBRARY} ${Boost_SYSTEM_LIBRARY})
   if (TBB_FOUND)
-    target_link_libraries(simplex_tree_from_alpha_shapes_3 ${TBB_LIBRARIES})
+    target_link_libraries(alpha_shapes_3_simplex_tree_from_off_file ${TBB_LIBRARIES})
   endif()
-  add_test(simplex_tree_from_alpha_shapes_3 ${CMAKE_CURRENT_BINARY_DIR}/simplex_tree_from_alpha_shapes_3 ${CMAKE_SOURCE_DIR}/data/points/bunny_5000)
+  add_test(alpha_shapes_3_simplex_tree_from_off_file
+           ${CMAKE_CURRENT_BINARY_DIR}/alpha_shapes_3_simplex_tree_from_off_file
+           ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.off)
 endif()
diff --git a/src/Simplex_tree/example/simplex_tree_from_alpha_shapes_3.cpp b/src/Simplex_tree/example/example_alpha_shapes_3_simplex_tree_from_off_file.cpp
index 49d358ab..ff2eebcb 100644
--- a/src/Simplex_tree/example/simplex_tree_from_alpha_shapes_3.cpp
+++ b/src/Simplex_tree/example/example_alpha_shapes_3_simplex_tree_from_off_file.cpp
@@ -20,8 +20,9 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include <gudhi/graph_simplicial_complex.h>
 #include <gudhi/Simplex_tree.h>
+#include <gudhi/Points_3D_off_io.h>
+
 #include <boost/variant.hpp>
 
 #include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
@@ -118,24 +119,21 @@ int main(int argc, char * const argv[]) {
   // program args management
   if (argc != 2) {
     std::cerr << "Usage: " << argv[0]
-        << " path_to_file_graph \n";
+        << " path_to_off_file \n";
     return 0;
   }
 
   // Read points from file
-  std::string filegraph = argv[1];
-  std::list<Point> lp;
-  std::ifstream is(filegraph.c_str());
-  int n;
-  is >> n;
-#ifdef DEBUG_TRACES
-  std::cout << "Reading " << n << " points " << std::endl;
-#endif  // DEBUG_TRACES
-  Point p;
-  for (; n > 0; n--) {
-    is >> p;
-    lp.push_back(p);
+  std::string offInputFile(argv[1]);
+  // Read the OFF file (input file name given as parameter) and triangulate points
+  Gudhi::Points_3D_off_reader<Point> off_reader(offInputFile);
+  // Check the read operation was correct
+  if (!off_reader.is_valid()) {
+    std::cerr << "Unable to read file " << argv[1] << std::endl;
+    return 0;
   }
+  // Retrieve the triangulation
+  std::vector<Point> lp = off_reader.get_point_cloud();
 
   // 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);
diff --git a/src/Witness_complex/example/CMakeLists.txt b/src/Witness_complex/example/CMakeLists.txt
index 4d67e0d0..857ec819 100644
--- a/src/Witness_complex/example/CMakeLists.txt
+++ b/src/Witness_complex/example/CMakeLists.txt
@@ -3,7 +3,8 @@ 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)
diff --git a/src/Witness_complex/example/witness_complex_from_file.cpp b/src/Witness_complex/example/witness_complex_from_file.cpp
index 53207ad2..915af1ab 100644
--- a/src/Witness_complex/example/witness_complex_from_file.cpp
+++ b/src/Witness_complex/example/witness_complex_from_file.cpp
@@ -23,10 +23,10 @@
 #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/reader_utils.h>
 
 #include <iostream>
 #include <fstream>
@@ -37,49 +37,28 @@
 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";
 
diff --git a/src/cmake/modules/FindQGLViewer.cmake b/src/cmake/modules/FindQGLViewer.cmake
index 65723d67..1f3dbc1f 100644
--- a/src/cmake/modules/FindQGLViewer.cmake
+++ b/src/cmake/modules/FindQGLViewer.cmake
@@ -15,7 +15,7 @@ find_path(QGLVIEWER_INCLUDE_DIR
          )
 
 find_library(QGLVIEWER_LIBRARY_RELEASE 
-             NAMES qglviewer-qt4 qglviewer QGLViewer QGLViewer2
+             NAMES qglviewer-qt4 QGLViewer-qt4 qglviewer QGLViewer QGLViewer2
              PATHS /usr/lib
                    /usr/local/lib
                    ENV QGLVIEWERROOT