Merge of alpha complex feature from trunk

Add Eigen3 in installation
Add alpha complex in introduction
All examples directory moved to example (was example/common, example/Alpha_complex)


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/Doxygen_for_GUDHI_1.3.0@1110 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 0b88a4f2b102e2189f4b916b8358ffb2458a72f0

1 files changed, 46 insertions, 36 deletions

diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt
index 9702a5f9..2f94ed15 100644
--- a/src/Persistent_cohomology/example/CMakeLists.txt
+++ b/src/Persistent_cohomology/example/CMakeLists.txt
@@ -7,37 +7,31 @@ add_definitions( -DBOOST_ALL_DYN_LINK )
 
 add_executable(plain_homology plain_homology.cpp)
 target_link_libraries(plain_homology ${Boost_SYSTEM_LIBRARY})
-if (TBB_FOUND)
-  target_link_libraries(plain_homology ${TBB_RELEASE_LIBRARY})
-endif()
-add_test(plain_homology ${CMAKE_CURRENT_BINARY_DIR}/plain_homology)
 
 add_executable(persistence_from_simple_simplex_tree persistence_from_simple_simplex_tree.cpp)
 target_link_libraries(persistence_from_simple_simplex_tree ${Boost_SYSTEM_LIBRARY})
-if (TBB_FOUND)
-  target_link_libraries(persistence_from_simple_simplex_tree ${TBB_RELEASE_LIBRARY})
-endif()
-add_test(persistence_from_simple_simplex_tree ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_simple_simplex_tree 1 0)
 
 add_executable(rips_persistence rips_persistence.cpp)
 target_link_libraries(rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
-if (TBB_FOUND)
-  target_link_libraries(rips_persistence ${TBB_RELEASE_LIBRARY})
-endif()
-add_test(rips_persistence_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.2 -d 3 -p 3 -m 100)
-   
+
 add_executable(parallel_rips_persistence parallel_rips_persistence.cpp)
 target_link_libraries(parallel_rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
-if (TBB_FOUND)
-  target_link_libraries(parallel_rips_persistence ${TBB_RELEASE_LIBRARY})
-endif()
-add_test(parallel_rips_persistence_3 ${CMAKE_CURRENT_BINARY_DIR}/parallel_rips_persistence ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.txt -r 0.3 -d 3 -p 3 -m 100)
-   
+
 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(parallel_rips_persistence ${TBB_RELEASE_LIBRARY})
   target_link_libraries(persistence_from_file ${TBB_RELEASE_LIBRARY})
 endif()
+
+add_test(plain_homology ${CMAKE_CURRENT_BINARY_DIR}/plain_homology)
+add_test(persistence_from_simple_simplex_tree ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_simple_simplex_tree 1 0)
+add_test(rips_persistence_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.2 -d 3 -p 3 -m 100)
+add_test(parallel_rips_persistence_3 ${CMAKE_CURRENT_BINARY_DIR}/parallel_rips_persistence ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.txt -r 0.3 -d 3 -p 3 -m 100)
 add_test(persistence_from_file_3_2_0 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.st -p 2 -m 0)
 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)
    
@@ -47,29 +41,45 @@ if(GMPXX_FOUND AND GMP_FOUND)
 
    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})
-   if (TBB_FOUND)
-     target_link_libraries(rips_multifield_persistence ${TBB_RELEASE_LIBRARY})
-   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)
-
    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})
    endif()
 
-   if(CGAL_FOUND)
-     if (CMAKE_BUILD_TYPE MATCHES Debug)
-       # For programs to be more verbose
-       add_definitions(-DDEBUG_TRACES)
-     endif()
-     add_executable(alpha_shapes_persistence alpha_shapes_persistence.cpp)
-     target_link_libraries(alpha_shapes_persistence ${Boost_SYSTEM_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES} ${CGAL_LIBRARY})
-     if (TBB_FOUND)
-       target_link_libraries(alpha_shapes_persistence ${TBB_RELEASE_LIBRARY})
-     endif()
-     add_test(alpha_shapes_persistence_2_0_5 ${CMAKE_CURRENT_BINARY_DIR}/alpha_shapes_persistence ${CMAKE_SOURCE_DIR}/data/points/bunny_5000 2 0.5)
-     #add_test(alpha_shapes_persistence_3_3_100 ${CMAKE_CURRENT_BINARY_DIR}/alpha_shapes_persistence ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.st -p 3 -m 100)
-   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)
+
+  if(CGAL_FOUND)
+    add_executable(alpha_complex_3d_persistence alpha_complex_3d_persistence.cpp)
+    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})
+    endif()
+    add_test(alpha_complex_3d_persistence_2_0_5 ${CMAKE_CURRENT_BINARY_DIR}/alpha_complex_3d_persistence ${CMAKE_SOURCE_DIR}/data/points/bunny_5000 2 0.5)
+
+    if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
+      message(STATUS "CGAL version: ${CGAL_VERSION}.")
+
+      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 (TBB_FOUND)
+          target_link_libraries(alpha_complex_persistence ${TBB_RELEASE_LIBRARY})
+        endif()
+
+      else()
+        message(WARNING "Eigen3 not found. Version 3.1.0 is required for Alpha shapes feature.")
+      endif()
+    else()
+      message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile Alpha shapes feature. Version 4.6.0 is required.")
+    endif ()
+  else()
+    # message(WARNING "CGAL not found.")
+  endif()
    
 endif()