Merge from trunk

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/subsampling_and_spatialsearching@1413 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: bb7801bb78feccf12ff73c6e82511806753db8dd

5 files changed, 36 insertions, 47 deletions

diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt
index c37b4229..bae652c5 100644
--- a/src/Persistent_cohomology/example/CMakeLists.txt
+++ b/src/Persistent_cohomology/example/CMakeLists.txt
@@ -1,5 +1,5 @@
 cmake_minimum_required(VERSION 2.6)
-project(GUDHIExPersCohom)
+project(Persistent_cohomology_examples)
 
 # problem with Visual Studio link on Boost program_options
 add_definitions( -DBOOST_ALL_NO_LIB )
@@ -36,11 +36,7 @@ add_test(persistence_from_file_3_2_0 ${CMAKE_CURRENT_BINARY_DIR}/persistence_fro
 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)
    
 if(GMP_FOUND)
-   message("GMP_LIBRARIES = ${GMP_LIBRARIES}")
-
    if(GMPXX_FOUND)
-      message("GMPXX_LIBRARIES = ${GMPXX_LIBRARIES}")
-
    add_executable(rips_multifield_persistence rips_multifield_persistence.cpp )
    target_link_libraries(rips_multifield_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
    add_executable ( performance_rips_persistence performance_rips_persistence.cpp )
@@ -56,49 +52,42 @@ else()
   # message(WARNING "GMP not found.")
 endif(GMP_FOUND)
 
-  if(CGAL_FOUND)
-    add_executable(alpha_complex_3d_persistence alpha_complex_3d_persistence.cpp)
-    target_link_libraries(alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
-
-    if (TBB_FOUND)
-      target_link_libraries(alpha_complex_3d_persistence ${TBB_LIBRARIES})
-    endif(TBB_FOUND)
-    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)
-
+if(CGAL_FOUND)
+  add_executable(alpha_complex_3d_persistence alpha_complex_3d_persistence.cpp)
+  target_link_libraries(alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
 
-    if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
-      message(STATUS "CGAL version: ${CGAL_VERSION}.")
+  if (TBB_FOUND)
+    target_link_libraries(alpha_complex_3d_persistence ${TBB_LIBRARIES})
+  endif(TBB_FOUND)
+  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)
 
-      find_package(Eigen3 3.1.0)
-      if (EIGEN3_FOUND)
-        message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.")
-        include( ${EIGEN3_USE_FILE} )
 
-        add_executable (alpha_complex_persistence alpha_complex_persistence.cpp)
-        target_link_libraries(alpha_complex_persistence  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
+  if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
+    if (EIGEN3_FOUND)
+      add_executable (alpha_complex_persistence alpha_complex_persistence.cpp)
+      target_link_libraries(alpha_complex_persistence  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
 
-        add_executable(periodic_alpha_complex_3d_persistence periodic_alpha_complex_3d_persistence.cpp)
-        target_link_libraries(periodic_alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+      add_executable(periodic_alpha_complex_3d_persistence periodic_alpha_complex_3d_persistence.cpp)
+      target_link_libraries(periodic_alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
 
-        add_executable(custom_persistence_sort custom_persistence_sort.cpp)
-        target_link_libraries(custom_persistence_sort ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+      add_executable(custom_persistence_sort custom_persistence_sort.cpp)
+      target_link_libraries(custom_persistence_sort ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
 
-        if (TBB_FOUND)
-          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(TBB_FOUND)
-        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 ${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)
+      if (TBB_FOUND)
+        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(TBB_FOUND)
+      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 ${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()
-        message(WARNING "Eigen3 not found. Version 3.1.0 is required for Alpha shapes feature.")
-      endif(EIGEN3_FOUND)
     else()
-      message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile Alpha shapes feature. Version 4.6.0 is required.")
-    endif ()
+      message(WARNING "Eigen3 not found. Version 3.1.0 is required for Alpha complex persistence examples.")
+    endif(EIGEN3_FOUND)
   else()
-    # message(WARNING "CGAL not found.")
-  endif(CGAL_FOUND)
-   
+    message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile Alpha complex persistence examples. Version 4.7.0 is required.")
+  endif ()
+else()
+  # message(WARNING "CGAL not found.")
+endif(CGAL_FOUND)
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/test/CMakeLists.txt b/src/Persistent_cohomology/test/CMakeLists.txt
index 18d85eda..a21f39c4 100644
--- a/src/Persistent_cohomology/test/CMakeLists.txt
+++ b/src/Persistent_cohomology/test/CMakeLists.txt
@@ -1,5 +1,5 @@
 cmake_minimum_required(VERSION 2.6)
-project(GUDHIPersistentCohomologyUT)
+project(Persistent_cohomology_tests)
 
 if (GCOVR_PATH)
   # for gcovr to make coverage reports - Corbera Jenkins plugin
diff --git a/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp b/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp
index 194b3e74..5c54ed5f 100644
--- a/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp
+++ b/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp
@@ -43,7 +43,7 @@ std::string test_rips_persistence(int coefficient, int min_persistence) {
   st.initialize_filtration();
 
   // Compute the persistence diagram of the complex
-  persistent_cohomology::Persistent_cohomology<Simplex_tree<>, Field_Zp> pcoh(st);
+  Persistent_cohomology<Simplex_tree<>, Field_Zp> pcoh(st);
 
   pcoh.init_coefficients( coefficient );  // initializes the coefficient field for homology
   // Check infinite rips