Merge from trunk

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/add_utils_in_gudhi_v2@2732 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 7872aa224ee471c05e9213b81192d304254e608a

6 files changed, 27 insertions, 49 deletions

diff --git a/src/Bottleneck_distance/benchmark/CMakeLists.txt b/src/Bottleneck_distance/benchmark/CMakeLists.txt
index 170081ce..20a4e47b 100644
--- a/src/Bottleneck_distance/benchmark/CMakeLists.txt
+++ b/src/Bottleneck_distance/benchmark/CMakeLists.txt
@@ -1,9 +1,9 @@
 cmake_minimum_required(VERSION 2.6)
 project(Bottleneck_distance_benchmark)
 
-if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
   add_executable ( bottleneck_chrono bottleneck_chrono.cpp )
   if (TBB_FOUND)
     target_link_libraries(bottleneck_chrono ${TBB_LIBRARIES})
   endif(TBB_FOUND)
-endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+endif(NOT CGAL_VERSION VERSION_LESS 4.8.1)
diff --git a/src/Bottleneck_distance/example/CMakeLists.txt b/src/Bottleneck_distance/example/CMakeLists.txt
index 93eb7b2f..b37555f9 100644
--- a/src/Bottleneck_distance/example/CMakeLists.txt
+++ b/src/Bottleneck_distance/example/CMakeLists.txt
@@ -1,7 +1,7 @@
 cmake_minimum_required(VERSION 2.6)
 project(Bottleneck_distance_examples)
 
-if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
   add_executable (bottleneck_read_file_example bottleneck_read_file_example.cpp)
   add_executable (bottleneck_basic_example bottleneck_basic_example.cpp)
 
@@ -9,5 +9,7 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
 
   install(TARGETS bottleneck_read_file_example DESTINATION bin)
   install(TARGETS bottleneck_basic_example DESTINATION bin)
-
+  if (TBB_FOUND)
+    target_link_libraries(alpha_rips_persistence_bottleneck_distance ${TBB_LIBRARIES})
+  endif(TBB_FOUND)
 endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
diff --git a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
index bde05825..24d73c57 100644
--- a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
+++ b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
@@ -20,53 +20,31 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#define CGAL_HAS_THREADS
-
 #include <gudhi/Bottleneck.h>
+#include <gudhi/reader_utils.h>
 #include <iostream>
 #include <vector>
 #include <utility>  // for pair
-#include <fstream>
-#include <sstream>
 #include <string>
-
-std::vector< std::pair<double, double> > read_diagram_from_file(const char* filename) {
-  std::ifstream in;
-  in.open(filename);
-  std::vector< std::pair<double, double> > result;
-  if (!in.is_open()) {
-    std::cerr << "File : " << filename << " do not exist. The program will now terminate \n";
-    throw "File do not exist \n";
-  }
-
-  std::string line;
-  while (!in.eof()) {
-    getline(in, line);
-    if (line.length() != 0) {
-      std::stringstream lineSS;
-      lineSS << line;
-      double beginn, endd;
-      lineSS >> beginn;
-      lineSS >> endd;
-      result.push_back(std::make_pair(beginn, endd));
-    }
-  }
-  in.close();
-  return result;
-}  // read_diagram_from_file
+#include <limits>  // for numeric_limits
 
 int main(int argc, char** argv) {
   if (argc < 3) {
-    std::cout << "To run this program please provide as an input two files with persistence diagrams. Each file " <<
-        "should contain a birth-death pair per line. Third, optional parameter is an error bound on a bottleneck" <<
-        " distance (set by default to zero). The program will now terminate \n";
+    std::cout << "To run this program please provide as an input two files with persistence diagrams. Each file" <<
+        " should contain a birth-death pair per line. Third, optional parameter is an error bound on a bottleneck" <<
+        " distance (set by default to the smallest positive double value). If you set the error bound to 0, be" <<
+        " aware this version is exact but expensive. The program will now terminate \n";
+    return -1;
   }
-  std::vector< std::pair< double, double > > diag1 = read_diagram_from_file(argv[1]);
-  std::vector< std::pair< double, double > > diag2 = read_diagram_from_file(argv[2]);
-  double tolerance = 0.;
+  std::vector<std::pair<double, double>> diag1 = Gudhi::read_persistence_intervals_in_dimension(argv[1]);
+  std::vector<std::pair<double, double>> diag2 = Gudhi::read_persistence_intervals_in_dimension(argv[2]);
+
+  double tolerance = std::numeric_limits<double>::min();
   if (argc == 4) {
     tolerance = atof(argv[3]);
   }
   double b = Gudhi::persistence_diagram::bottleneck_distance(diag1, diag2, tolerance);
   std::cout << "The distance between the diagrams is : " << b << ". The tolerance is : " << tolerance << std::endl;
+
+  return 0;
 }
diff --git a/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h
index bdc47578..a6b9b021 100644
--- a/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h
+++ b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h
@@ -44,16 +44,16 @@ struct Square_query {
   typedef Internal_point Point_d;
   typedef double FT;
   bool contains(Point_d p) const {
-    return std::abs(p.x()-c.x())<=size && std::abs(p.y()-c.y())<=size;
+    return std::abs(p.x()-c.x()) <= size && std::abs(p.y()-c.y()) <= size;
   }
-  bool inner_range_intersects(CGAL::Kd_tree_rectangle<FT,D> const&r) const {
+  bool inner_range_intersects(CGAL::Kd_tree_rectangle<FT, D> const&r) const {
     return
       r.max_coord(0) >= c.x() - size &&
       r.min_coord(0) <= c.x() + size &&
       r.max_coord(1) >= c.y() - size &&
       r.min_coord(1) <= c.y() + size;
   }
-  bool outer_range_contains(CGAL::Kd_tree_rectangle<FT,D> const&r) const {
+  bool outer_range_contains(CGAL::Kd_tree_rectangle<FT, D> const&r) const {
     return
       r.min_coord(0) >= c.x() - size &&
       r.max_coord(0) <= c.x() + size &&
@@ -146,7 +146,7 @@ inline int Neighbors_finder::pull_near(int u_point_index) {
     // Is the query point near to a V point in the plane ?
     Internal_point u_point = g.get_u_point(u_point_index);
     auto neighbor = kd_t.search_any_point(Square_query{u_point, r});
-    if(!neighbor)
+    if (!neighbor)
       return null_point_index();
     tmp = neighbor->point_index;
     auto point = g.get_v_point(tmp);
diff --git a/src/Bottleneck_distance/test/CMakeLists.txt b/src/Bottleneck_distance/test/CMakeLists.txt
index e1bbbbec..2676b82c 100644
--- a/src/Bottleneck_distance/test/CMakeLists.txt
+++ b/src/Bottleneck_distance/test/CMakeLists.txt
@@ -1,15 +1,15 @@
 cmake_minimum_required(VERSION 2.6)
 project(Bottleneck_distance_tests)
 
-if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
   include(GUDHI_test_coverage)
 
   add_executable ( Bottleneck_distance_test_unit bottleneck_unit_test.cpp )
-  target_link_libraries(Bottleneck_distance_test_unit ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+  target_link_libraries(Bottleneck_distance_test_unit ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
   if (TBB_FOUND)
     target_link_libraries(Bottleneck_distance_test_unit ${TBB_LIBRARIES})
   endif(TBB_FOUND)
 
   gudhi_add_coverage_test(Bottleneck_distance_test_unit)
 
-endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
diff --git a/src/Bottleneck_distance/utilities/CMakeLists.txt b/src/Bottleneck_distance/utilities/CMakeLists.txt
index ba4de11e..634b2479 100644
--- a/src/Bottleneck_distance/utilities/CMakeLists.txt
+++ b/src/Bottleneck_distance/utilities/CMakeLists.txt
@@ -3,10 +3,8 @@ project(Bottleneck_distance_utilities)
 
 if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
   add_executable (alpha_rips_persistence_bottleneck_distance alpha_rips_persistence_bottleneck_distance.cpp)
-  target_link_libraries(alpha_rips_persistence_bottleneck_distance ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
+  target_link_libraries(alpha_rips_persistence_bottleneck_distance ${Boost_PROGRAM_OPTIONS_LIBRARY})
   if (TBB_FOUND)
-    target_link_libraries(bottleneck_read_file_example ${TBB_LIBRARIES})
-    target_link_libraries(bottleneck_basic_example ${TBB_LIBRARIES})
     target_link_libraries(alpha_rips_persistence_bottleneck_distance ${TBB_LIBRARIES})
   endif(TBB_FOUND)