Rename namespaces according to convention

+ Missing Boost_THREAD_LIBRARY
+ Useless typename
+ Use TBB_LIBRARIES

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/fix_naming@1274 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 5c02ec481b62ef52b40d849e76e3d333e2ca4e7c

4 files changed, 32 insertions, 22 deletions

diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt
index f85c50f9..a0af11c1 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/alpha_complex_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_persistence.cpp
index 17fb84d2..cb181936 100644
--- a/src/Persistent_cohomology/example/alpha_complex_persistence.cpp
+++ b/src/Persistent_cohomology/example/alpha_complex_persistence.cpp
@@ -30,7 +30,7 @@ int main(int argc, char **argv) {
   // Init of an alpha complex from an OFF file
   // ----------------------------------------------------------------------------
   using Kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >;
-  Gudhi::alphacomplex::Alpha_complex<Kernel> alpha_complex_from_file(off_file_points, alpha_square_max_value);
+  Gudhi::alpha_complex::Alpha_complex<Kernel> alpha_complex_from_file(off_file_points, alpha_square_max_value);
 
   // ----------------------------------------------------------------------------
   // Display information about the alpha complex
@@ -44,7 +44,7 @@ int main(int argc, char **argv) {
 
   std::cout << "Simplex_tree dim: " << alpha_complex_from_file.dimension() << std::endl;
   // Compute the persistence diagram of the complex
-  Gudhi::persistent_cohomology::Persistent_cohomology< Gudhi::alphacomplex::Alpha_complex<Kernel>,
+  Gudhi::persistent_cohomology::Persistent_cohomology< Gudhi::alpha_complex::Alpha_complex<Kernel>,
       Gudhi::persistent_cohomology::Field_Zp > pcoh(alpha_complex_from_file);
   // initializes the coefficient field for homology
   pcoh.init_coefficients(coeff_field_characteristic);
diff --git a/src/Persistent_cohomology/example/custom_persistence_sort.cpp b/src/Persistent_cohomology/example/custom_persistence_sort.cpp
index d591a0d0..9af38611 100644
--- a/src/Persistent_cohomology/example/custom_persistence_sort.cpp
+++ b/src/Persistent_cohomology/example/custom_persistence_sort.cpp
@@ -37,7 +37,7 @@
 
 using Kernel = CGAL::Epick_d< CGAL::Dimension_tag<3> >;
 using Point = Kernel::Point_d;
-using Alpha_complex = Gudhi::alphacomplex::Alpha_complex<Kernel>;
+using Alpha_complex = Gudhi::alpha_complex::Alpha_complex<Kernel>;
 
 std::vector<Point> random_points() {
   // Instanciate a random point generator
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