Merge last trunk modifications and fix new rips interface

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/gudhi_stat@2299 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 1e836cba1a372f609e94b66b6db512817a3d875e

5 files changed, 43 insertions, 34 deletions

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/Simplex_tree/example/mini_simplex_tree.cpp b/src/Simplex_tree/example/mini_simplex_tree.cpp
index 7e48aaaf..ad99df23 100644
--- a/src/Simplex_tree/example/mini_simplex_tree.cpp
+++ b/src/Simplex_tree/example/mini_simplex_tree.cpp
@@ -24,19 +24,18 @@
 #include <iostream>
 #include <initializer_list>
 
-using namespace Gudhi;
-
-struct MyOptions : Simplex_tree_options_full_featured {
+struct MyOptions : Gudhi::Simplex_tree_options_full_featured {
   // Not doing persistence, so we don't need those
   static const bool store_key = false;
   static const bool store_filtration = false;
   // I have few vertices
   typedef short Vertex_handle;
 };
-typedef Simplex_tree<MyOptions> ST;
+
+using ST = Gudhi::Simplex_tree<MyOptions>;
 
 // Dictionary should be private, but for now this is the easiest way.
-static_assert(sizeof(ST::Dictionary::value_type) < sizeof(Simplex_tree<>::Dictionary::value_type),
+static_assert(sizeof(ST::Dictionary::value_type) < sizeof(Gudhi::Simplex_tree<>::Dictionary::value_type),
     "Not storing the filtration and key should save some space");
 
 int main() {
diff --git a/src/Simplex_tree/example/simple_simplex_tree.cpp b/src/Simplex_tree/example/simple_simplex_tree.cpp
index 5146b906..60f9a35e 100644
--- a/src/Simplex_tree/example/simple_simplex_tree.cpp
+++ b/src/Simplex_tree/example/simple_simplex_tree.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Vincent Rouvreau
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (France)
+ *    Copyright (C) 2014
  *
  *    This program is free software: you can redistribute it and/or modify
  *    it under the terms of the GNU General Public License as published by
@@ -27,10 +27,11 @@
 #include <utility>  // for pair
 #include <vector>
 
-using namespace Gudhi;
-
-typedef std::vector< Vertex_handle > typeVectorVertex;
-typedef std::pair< Simplex_tree<>::Simplex_handle, bool > typePairSimplexBool;
+using Simplex_tree = Gudhi::Simplex_tree<>;
+using Vertex_handle = Simplex_tree::Vertex_handle;
+using Filtration_value = Simplex_tree::Filtration_value;
+using typeVectorVertex = std::vector< Vertex_handle >;
+using typePairSimplexBool = std::pair< Simplex_tree::Simplex_handle, bool >;
 
 int main(int argc, char * const argv[]) {
   const Filtration_value FIRST_FILTRATION_VALUE = 0.1;
@@ -42,7 +43,7 @@ int main(int argc, char * const argv[]) {
   std::cout << "********************************************************************" << std::endl;
   std::cout << "EXAMPLE OF SIMPLE INSERTION" << std::endl;
   // Construct the Simplex Tree
-  Simplex_tree<> simplexTree;
+  Simplex_tree simplexTree;
 
   /* Simplex to be inserted:  */
   /*    1                     */
@@ -212,7 +213,7 @@ int main(int argc, char * const argv[]) {
   // ------------------------------------------------------------------------------------------------------------------
   // Find in the simplex_tree
   // ------------------------------------------------------------------------------------------------------------------
-  Simplex_tree<>::Simplex_handle simplexFound = simplexTree.find(secondSimplexVector);
+  Simplex_tree::Simplex_handle simplexFound = simplexTree.find(secondSimplexVector);
   std::cout << "**************IS THE SIMPLEX {1} IN THE SIMPLEX TREE ?\n";
   if (simplexFound != simplexTree.null_simplex())
     std::cout << "***+ YES IT IS!\n";
diff --git a/src/Simplex_tree/example/simplex_tree_from_cliques_of_graph.cpp b/src/Simplex_tree/example/simplex_tree_from_cliques_of_graph.cpp
index 58085014..d1b8b2de 100644
--- a/src/Simplex_tree/example/simplex_tree_from_cliques_of_graph.cpp
+++ b/src/Simplex_tree/example/simplex_tree_from_cliques_of_graph.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Clément Maria
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (France)
+ *    Copyright (C) 2014  INRIA
  *
  *    This program is free software: you can redistribute it and/or modify
  *    it under the terms of the GNU General Public License as published by
@@ -26,9 +26,16 @@
 #include <iostream>
 #include <ctime>
 #include <string>
+#include <utility>  // for std::pair
 
 using namespace Gudhi;
 
+typedef int Vertex_handle;
+typedef double Filtration_value;
+typedef boost::adjacency_list < boost::vecS, boost::vecS, boost::undirectedS,
+                                boost::property < vertex_filtration_t, Filtration_value >,
+                                boost::property < edge_filtration_t, Filtration_value > > Graph_t;
+
 int main(int argc, char * const argv[]) {
   if (argc != 3) {
     std::cerr << "Usage: " << argv[0]
@@ -43,7 +50,7 @@ int main(int argc, char * const argv[]) {
   Simplex_tree<> st;
 
   start = clock();
-  auto g = read_graph(filegraph);
+  auto g = read_graph<Graph_t, Filtration_value, Vertex_handle>(filegraph);
   // insert the graph in the simplex tree as 1-skeleton
   st.insert_graph(g);
   end = clock();