Merge last trunk modifications

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/get_persistence@1298 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: bd50f9840b3ef3b3ef7593e81cbd7d6d22b845e3

13 files changed, 50 insertions, 38 deletions

diff --git a/data/points/generator/CMakeLists.txt b/data/points/generator/CMakeLists.txt
index c01a380d..f892aa50 100644
--- a/data/points/generator/CMakeLists.txt
+++ b/data/points/generator/CMakeLists.txt
@@ -9,8 +9,9 @@ if(CGAL_FOUND)
     if (EIGEN3_FOUND)
       include( ${EIGEN3_USE_FILE} )
       include_directories (BEFORE "../../include")
-
+	  
       add_executable ( hypergenerator hypergenerator.cpp )
+      target_link_libraries(hypergenerator ${Boost_SYSTEM_LIBRARY})
       add_test(hypergenerator_on_sphere_3000_10_5.0 ${CMAKE_CURRENT_BINARY_DIR}/hypergenerator on sphere onSphere.off 3000 10 5.0)
       add_test(hypergenerator_on_sphere_10000_3 ${CMAKE_CURRENT_BINARY_DIR}/hypergenerator on sphere onSphere.off 10000 3)
       add_test(hypergenerator_in_sphere_7000_12_10.8 ${CMAKE_CURRENT_BINARY_DIR}/hypergenerator in sphere inSphere.off 7000 12 10.8)
diff --git a/data/points/iso_cuboid_3_in_0_1.txt b/data/points/iso_cuboid_3_in_0_1.txt
new file mode 100644
index 00000000..17f3c37b
--- /dev/null
+++ b/data/points/iso_cuboid_3_in_0_1.txt
@@ -0,0 +1 @@
+0.0 0.0 0.0 1.0 1.0 1.0
diff --git a/src/Alpha_complex/example/CMakeLists.txt b/src/Alpha_complex/example/CMakeLists.txt
index f1346867..c1439f70 100644
--- a/src/Alpha_complex/example/CMakeLists.txt
+++ b/src/Alpha_complex/example/CMakeLists.txt
@@ -13,12 +13,12 @@ if(CGAL_FOUND)
       include( ${EIGEN3_USE_FILE} )
 
       add_executable ( alphapoints Alpha_complex_from_points.cpp )
-      target_link_libraries(alphapoints  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+      target_link_libraries(alphapoints  ${Boost_SYSTEM_LIBRARY} ${Boost_THREAD_LIBRARY} ${CGAL_LIBRARY})
       add_executable ( alphaoffreader Alpha_complex_from_off.cpp )
-      target_link_libraries(alphaoffreader  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+      target_link_libraries(alphaoffreader  ${Boost_SYSTEM_LIBRARY} ${Boost_THREAD_LIBRARY} ${CGAL_LIBRARY})
       if (TBB_FOUND)
-        target_link_libraries(alphapoints ${TBB_RELEASE_LIBRARY})
-        target_link_libraries(alphaoffreader ${TBB_RELEASE_LIBRARY})
+        target_link_libraries(alphapoints ${TBB_LIBRARIES})
+        target_link_libraries(alphaoffreader ${TBB_LIBRARIES})
       endif()
 
       add_test(alphapoints ${CMAKE_CURRENT_BINARY_DIR}/alphapoints)
diff --git a/src/Alpha_complex/test/CMakeLists.txt b/src/Alpha_complex/test/CMakeLists.txt
index e24588d7..f8d6d789 100644
--- a/src/Alpha_complex/test/CMakeLists.txt
+++ b/src/Alpha_complex/test/CMakeLists.txt
@@ -25,7 +25,7 @@ if(CGAL_FOUND)
       add_executable ( AlphaComplexUT Alpha_complex_unit_test.cpp )
       target_link_libraries(AlphaComplexUT  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
       if (TBB_FOUND)
-        target_link_libraries(AlphaComplexUT ${TBB_RELEASE_LIBRARY})
+        target_link_libraries(AlphaComplexUT ${TBB_LIBRARIES})
       endif()
 
       # Do not forget to copy test files in current binary dir
diff --git a/src/Bitmap_cubical_complex/example/CMakeLists.txt b/src/Bitmap_cubical_complex/example/CMakeLists.txt
index ad86b763..48b5d22f 100644
--- a/src/Bitmap_cubical_complex/example/CMakeLists.txt
+++ b/src/Bitmap_cubical_complex/example/CMakeLists.txt
@@ -4,7 +4,7 @@ project(GUDHIBitmap)
 add_executable ( Bitmap_cubical_complex Bitmap_cubical_complex.cpp )
 target_link_libraries(Bitmap_cubical_complex ${Boost_SYSTEM_LIBRARY})
 if (TBB_FOUND)
-  target_link_libraries(Bitmap_cubical_complex ${TBB_RELEASE_LIBRARY})
+  target_link_libraries(Bitmap_cubical_complex ${TBB_LIBRARIES})
 endif()
 add_test(Bitmap_cubical_complex_one_sphere ${CMAKE_CURRENT_BINARY_DIR}/Bitmap_cubical_complex ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalOneSphere.txt)
 add_test(Bitmap_cubical_complex_two_sphere ${CMAKE_CURRENT_BINARY_DIR}/Bitmap_cubical_complex ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt)
@@ -12,14 +12,14 @@ add_test(Bitmap_cubical_complex_two_sphere ${CMAKE_CURRENT_BINARY_DIR}/Bitmap_cu
 add_executable ( Random_bitmap_cubical_complex Random_bitmap_cubical_complex.cpp )
 target_link_libraries(Random_bitmap_cubical_complex ${Boost_SYSTEM_LIBRARY})
 if (TBB_FOUND)
-  target_link_libraries(Random_bitmap_cubical_complex ${TBB_RELEASE_LIBRARY})
+  target_link_libraries(Random_bitmap_cubical_complex ${TBB_LIBRARIES})
 endif()
 add_test(Random_bitmap_cubical_complex ${CMAKE_CURRENT_BINARY_DIR}/Random_bitmap_cubical_complex 2 100 100)
 
 add_executable ( Bitmap_cubical_complex_periodic_boundary_conditions Bitmap_cubical_complex_periodic_boundary_conditions.cpp )
 target_link_libraries(Bitmap_cubical_complex_periodic_boundary_conditions ${Boost_SYSTEM_LIBRARY})
 if (TBB_FOUND)
-  target_link_libraries(Bitmap_cubical_complex_periodic_boundary_conditions ${TBB_RELEASE_LIBRARY})
+  target_link_libraries(Bitmap_cubical_complex_periodic_boundary_conditions ${TBB_LIBRARIES})
 endif()
 add_test(Bitmap_cubical_complex_periodic_2d_torus ${CMAKE_CURRENT_BINARY_DIR}/Bitmap_cubical_complex_periodic_boundary_conditions ${CMAKE_SOURCE_DIR}/data/bitmap/2d_torus.txt)
 add_test(Bitmap_cubical_complex_periodic_3d_torus ${CMAKE_CURRENT_BINARY_DIR}/Bitmap_cubical_complex_periodic_boundary_conditions ${CMAKE_SOURCE_DIR}/data/bitmap/3d_torus.txt)
diff --git a/src/Bitmap_cubical_complex/test/CMakeLists.txt b/src/Bitmap_cubical_complex/test/CMakeLists.txt
index 0e5340c7..d8c44035 100644
--- a/src/Bitmap_cubical_complex/test/CMakeLists.txt
+++ b/src/Bitmap_cubical_complex/test/CMakeLists.txt
@@ -13,7 +13,7 @@ endif()
 add_executable ( BitmapCCUT Bitmap_test.cpp )
 target_link_libraries(BitmapCCUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
 if (TBB_FOUND)
-  target_link_libraries(BitmapCCUT ${TBB_RELEASE_LIBRARY})
+  target_link_libraries(BitmapCCUT ${TBB_LIBRARIES})
 endif()
 
 # Unitary tests
diff --git a/src/GudhUI/CMakeLists.txt b/src/GudhUI/CMakeLists.txt
index a7e64319..a43294ea 100644
--- a/src/GudhUI/CMakeLists.txt
+++ b/src/GudhUI/CMakeLists.txt
@@ -58,7 +58,7 @@ if ( CGAL_FOUND AND QT4_FOUND AND OPENGL_FOUND AND QGLVIEWER_FOUND )
   target_link_libraries( GudhUI ${QT_LIBRARIES} ${QGLVIEWER_LIBRARIES} )
   target_link_libraries( GudhUI ${OPENGL_gl_LIBRARY} ${OPENGL_glu_LIBRARY} )	
 if (TBB_FOUND)
-  target_link_libraries( GudhUI ${TBB_RELEASE_LIBRARY})
+  target_link_libraries( GudhUI ${TBB_LIBRARIES})
 endif()
 
 ###############################################################################
diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt
index 186a6c33..9582e19b 100644
--- a/src/Persistent_cohomology/example/CMakeLists.txt
+++ b/src/Persistent_cohomology/example/CMakeLists.txt
@@ -21,11 +21,11 @@ add_executable(persistence_from_file persistence_from_file.cpp)
 target_link_libraries(persistence_from_file ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
 
 if (TBB_FOUND)
-  target_link_libraries(plain_homology ${TBB_RELEASE_LIBRARY})
-  target_link_libraries(persistence_from_simple_simplex_tree ${TBB_RELEASE_LIBRARY})
-  target_link_libraries(rips_persistence ${TBB_RELEASE_LIBRARY})
-  target_link_libraries(rips_persistence_via_boundary_matrix ${TBB_RELEASE_LIBRARY})
-  target_link_libraries(persistence_from_file ${TBB_RELEASE_LIBRARY})
+  target_link_libraries(plain_homology ${TBB_LIBRARIES})
+  target_link_libraries(persistence_from_simple_simplex_tree ${TBB_LIBRARIES})
+  target_link_libraries(rips_persistence ${TBB_LIBRARIES})
+  target_link_libraries(rips_persistence_via_boundary_matrix ${TBB_LIBRARIES})
+  target_link_libraries(persistence_from_file ${TBB_LIBRARIES})
 endif()
 
 add_test(plain_homology ${CMAKE_CURRENT_BINARY_DIR}/plain_homology)
@@ -44,8 +44,8 @@ if(GMPXX_FOUND AND GMP_FOUND)
    add_executable ( performance_rips_persistence performance_rips_persistence.cpp )
    target_link_libraries(performance_rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
    if (TBB_FOUND)
-     target_link_libraries(rips_multifield_persistence ${TBB_RELEASE_LIBRARY})
-     target_link_libraries(performance_rips_persistence ${TBB_RELEASE_LIBRARY})
+     target_link_libraries(rips_multifield_persistence ${TBB_LIBRARIES})
+     target_link_libraries(performance_rips_persistence ${TBB_LIBRARIES})
    endif()
 
    add_test(rips_multifield_persistence_2_71 ${CMAKE_CURRENT_BINARY_DIR}/rips_multifield_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.2 -d 3 -p 2 -q 71 -m 100)
@@ -55,7 +55,7 @@ if(GMPXX_FOUND AND GMP_FOUND)
     target_link_libraries(alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES} ${CGAL_LIBRARY})
 
     if (TBB_FOUND)
-      target_link_libraries(alpha_complex_3d_persistence ${TBB_RELEASE_LIBRARY})
+      target_link_libraries(alpha_complex_3d_persistence ${TBB_LIBRARIES})
     endif()
     add_test(alpha_complex_3d_persistence_2_0_5 ${CMAKE_CURRENT_BINARY_DIR}/alpha_complex_3d_persistence ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off 2 0.45)
 
@@ -78,12 +78,12 @@ if(GMPXX_FOUND AND GMP_FOUND)
         target_link_libraries(custom_persistence_sort ${Boost_SYSTEM_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES} ${CGAL_LIBRARY})
 
         if (TBB_FOUND)
-          target_link_libraries(alpha_complex_persistence ${TBB_RELEASE_LIBRARY})
-          target_link_libraries(periodic_alpha_complex_3d_persistence ${TBB_RELEASE_LIBRARY})
-          target_link_libraries(custom_persistence_sort ${TBB_RELEASE_LIBRARY})
+          target_link_libraries(alpha_complex_persistence ${TBB_LIBRARIES})
+          target_link_libraries(periodic_alpha_complex_3d_persistence ${TBB_LIBRARIES})
+          target_link_libraries(custom_persistence_sort ${TBB_LIBRARIES})
         endif()
         add_test(alpha_complex_persistence_2_0_45 ${CMAKE_CURRENT_BINARY_DIR}/alpha_complex_persistence ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -m 0.45 -p 2)
-        add_test(periodic_alpha_complex_3d_persistence_2_0 ${CMAKE_CURRENT_BINARY_DIR}/periodic_alpha_complex_3d_persistence ${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off 2 0)
+        add_test(periodic_alpha_complex_3d_persistence_2_0 ${CMAKE_CURRENT_BINARY_DIR}/periodic_alpha_complex_3d_persistence ${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off ${CMAKE_SOURCE_DIR}/data/points/iso_cuboid_3_in_0_1.txt 2 0)
         add_test(custom_persistence_sort ${CMAKE_CURRENT_BINARY_DIR}/custom_persistence_sort)
 
       else()
diff --git a/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp
index b8e1097d..a199fea1 100644
--- a/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp
+++ b/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp
@@ -125,28 +125,28 @@ Vertex_list from(const Alpha_shape_3::Vertex_handle& vh) {
 
 void usage(char * const progName) {
   std::cerr << "Usage: " << progName <<
-      " path_to_file_graph coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n";
+      " path_to_file_graph path_to_iso_cuboid_3_file coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n";
   exit(-1);
 }
 
 int main(int argc, char * const argv[]) {
   // program args management
-  if (argc != 4) {
+  if (argc != 5) {
     std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n";
     usage(argv[0]);
   }
 
   int coeff_field_characteristic = 0;
-  int returnedScanValue = sscanf(argv[2], "%d", &coeff_field_characteristic);
+  int returnedScanValue = sscanf(argv[3], "%d", &coeff_field_characteristic);
   if ((returnedScanValue == EOF) || (coeff_field_characteristic <= 0)) {
-    std::cerr << "Error: " << argv[2] << " is not correct\n";
+    std::cerr << "Error: " << argv[3] << " is not correct\n";
     usage(argv[0]);
   }
 
   Filtration_value min_persistence = 0.0;
-  returnedScanValue = sscanf(argv[3], "%lf", &min_persistence);
+  returnedScanValue = sscanf(argv[4], "%lf", &min_persistence);
   if ((returnedScanValue == EOF) || (min_persistence < -1.0)) {
-    std::cerr << "Error: " << argv[3] << " is not correct\n";
+    std::cerr << "Error: " << argv[4] << " is not correct\n";
     usage(argv[0]);
   }
 
@@ -160,11 +160,21 @@ int main(int argc, char * const argv[]) {
     usage(argv[0]);
   }
 
+  // Read iso_cuboid_3 information from file
+  std::ifstream iso_cuboid_str(argv[2]);
+  double x_min, y_min, z_min, x_max, y_max, z_max;
+  if (iso_cuboid_str.good()) {
+    iso_cuboid_str >> x_min >> y_min >> z_min >> x_max >> y_max >> z_max;
+  } else {
+    std::cerr << "Unable to read file " << argv[2] << std::endl;
+    usage(argv[0]);
+  }
+
   // Retrieve the triangulation
   std::vector<Point_3> lp = off_reader.get_point_cloud();
 
   // Define the periodic cube
-  P3DT3 pdt(PK::Iso_cuboid_3(0, 0, 0, 1, 1, 1));
+  P3DT3 pdt(PK::Iso_cuboid_3(x_min, y_min, z_min, x_max, y_max, z_max));
   // Heuristic for inserting large point sets (if pts is reasonably large)
   pdt.insert(lp.begin(), lp.end(), true);
   // As pdt won't be modified anymore switch to 1-sheeted cover if possible
diff --git a/src/Persistent_cohomology/test/CMakeLists.txt b/src/Persistent_cohomology/test/CMakeLists.txt
index a034031a..b50430f9 100644
--- a/src/Persistent_cohomology/test/CMakeLists.txt
+++ b/src/Persistent_cohomology/test/CMakeLists.txt
@@ -15,8 +15,8 @@ target_link_libraries(PersistentCohomologyUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNI
 add_executable ( BettiNumbersUT betti_numbers_unit_test.cpp )
 target_link_libraries(BettiNumbersUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
 if (TBB_FOUND)
-  target_link_libraries(PersistentCohomologyUT ${TBB_RELEASE_LIBRARY})
-  target_link_libraries(BettiNumbersUT ${TBB_RELEASE_LIBRARY})
+  target_link_libraries(PersistentCohomologyUT ${TBB_LIBRARIES})
+  target_link_libraries(BettiNumbersUT ${TBB_LIBRARIES})
 endif()
 
 # Unitary tests
@@ -35,7 +35,7 @@ if(GMPXX_FOUND AND GMP_FOUND)
   add_executable ( PersistentCohomologyMultiFieldUT persistent_cohomology_unit_test_multi_field.cpp )
 target_link_libraries(PersistentCohomologyMultiFieldUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
 if (TBB_FOUND)
-  target_link_libraries(PersistentCohomologyMultiFieldUT ${TBB_RELEASE_LIBRARY})
+  target_link_libraries(PersistentCohomologyMultiFieldUT ${TBB_LIBRARIES})
 endif()
 
   # Unitary tests
diff --git a/src/Simplex_tree/example/CMakeLists.txt b/src/Simplex_tree/example/CMakeLists.txt
index 89a4e053..30a34b20 100644
--- a/src/Simplex_tree/example/CMakeLists.txt
+++ b/src/Simplex_tree/example/CMakeLists.txt
@@ -3,14 +3,14 @@ project(GUDHISimplexTreeFromFile)
 
 add_executable ( simplex_tree_from_cliques_of_graph simplex_tree_from_cliques_of_graph.cpp )
 if (TBB_FOUND)
-  target_link_libraries(simplex_tree_from_cliques_of_graph ${TBB_RELEASE_LIBRARY})
+  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_executable ( simple_simplex_tree simple_simplex_tree.cpp )
 if (TBB_FOUND)
-  target_link_libraries(simple_simplex_tree ${TBB_RELEASE_LIBRARY})
+  target_link_libraries(simple_simplex_tree ${TBB_LIBRARIES})
 endif()
 add_test(simple_simplex_tree ${CMAKE_CURRENT_BINARY_DIR}/simple_simplex_tree)
 
@@ -23,7 +23,7 @@ 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})
   if (TBB_FOUND)
-    target_link_libraries(simplex_tree_from_alpha_shapes_3 ${TBB_RELEASE_LIBRARY})
+    target_link_libraries(simplex_tree_from_alpha_shapes_3 ${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)
 endif()
diff --git a/src/Simplex_tree/test/CMakeLists.txt b/src/Simplex_tree/test/CMakeLists.txt
index 609d8669..d6755c49 100644
--- a/src/Simplex_tree/test/CMakeLists.txt
+++ b/src/Simplex_tree/test/CMakeLists.txt
@@ -13,7 +13,7 @@ endif()
 add_executable ( SimplexTreeUT simplex_tree_unit_test.cpp )
 target_link_libraries(SimplexTreeUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
 if (TBB_FOUND)
-  target_link_libraries(SimplexTreeUT ${TBB_RELEASE_LIBRARY})
+  target_link_libraries(SimplexTreeUT ${TBB_LIBRARIES})
 endif()
 
 # Do not forget to copy test files in current binary dir
diff --git a/src/common/example/CGAL_points_off_reader.cpp b/src/common/example/CGAL_points_off_reader.cpp
index 997b47c1..d1ca166d 100644
--- a/src/common/example/CGAL_points_off_reader.cpp
+++ b/src/common/example/CGAL_points_off_reader.cpp
@@ -9,7 +9,7 @@
 #include <vector>
 
 using Kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >;
-using Point_d = typename Kernel::Point_d;
+using Point_d = Kernel::Point_d;
 
 void usage(char * const progName) {
   std::cerr << "Usage: " << progName << " inputFile.off" << std::endl;