Modification for Porquerolles Workshop

Bar_code_persistence and alpha_complex_persistence


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alphashapes@893 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 63d2d21d5ff7c9a94a67eafc326bf8a561bf8166

3 files changed, 106 insertions, 7 deletions

diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt
index ea69352e..74c2e778 100644
--- a/src/Persistent_cohomology/example/CMakeLists.txt
+++ b/src/Persistent_cohomology/example/CMakeLists.txt
@@ -39,6 +39,50 @@ if(GMPXX_FOUND AND GMP_FOUND)
      target_link_libraries(alpha_shapes_persistence ${Boost_SYSTEM_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES} ${CGAL_LIBRARY})
      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)
+
+
+
+
+  if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
+    message(STATUS "CGAL version: ${CGAL_VERSION}.")
+
+    include( ${CGAL_USE_FILE} )
+     # In CMakeLists.txt, when include(${CGAL_USE_FILE}), CXX_FLAGS are overwritten.
+    # cf. http://doc.cgal.org/latest/Manual/installation.html#title40
+    # A workaround is to add "-std=c++11" again.
+    # A fix would be to use https://cmake.org/cmake/help/v3.1/prop_gbl/CMAKE_CXX_KNOWN_FEATURES.html 
+    # or even better https://cmake.org/cmake/help/v3.1/variable/CMAKE_CXX_STANDARD.html
+    # but it implies to use cmake version 3.1 at least.
+    if(NOT MSVC)
+      include(CheckCXXCompilerFlag)
+      CHECK_CXX_COMPILER_FLAG(-std=c++11 COMPILER_SUPPORTS_CXX11)
+      if(COMPILER_SUPPORTS_CXX11)
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
+      endif()
+    endif()
+    # - End of workaround
+
+    find_package(Eigen3 3.1.0)
+    if (EIGEN3_FOUND)
+      message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.")
+      include( ${EIGEN3_USE_FILE} )
+      if (CMAKE_BUILD_TYPE MATCHES Debug)
+        # For programs to be more verbose
+        add_definitions(-DDEBUG_TRACES)
+      endif()
+      
+      add_executable (alphacomplexpersistence alpha_complex_persistence.cpp)
+      target_link_libraries(alphacomplexpersistence  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+
+    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 ()
+
+
+
    endif()
    
 endif()
diff --git a/src/Persistent_cohomology/example/alpha_complex_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_persistence.cpp
new file mode 100644
index 00000000..fbadf673
--- /dev/null
+++ b/src/Persistent_cohomology/example/alpha_complex_persistence.cpp
@@ -0,0 +1,55 @@
+#include <iostream>
+#include <string>
+
+// to construct a Delaunay_triangulation from a OFF file
+#include <gudhi/Delaunay_triangulation_off_io.h>
+#include <gudhi/Alpha_complex.h>
+#include <gudhi/Persistent_cohomology.h>
+
+void usage(char * const progName) {
+  std::cerr << "Usage: " << progName << " filename.off alpha_square_max_value[double] " <<
+      "coeff_field_characteristic[integer > 0] min_persistence[double >= -1.0]" << std::endl;
+  std::cerr << "       i.e.: " << progName << " ../../data/points/alphacomplexdoc.off 60.0 2 0.02" << std::endl;
+  exit(-1); // ----- >>
+}
+
+int main(int argc, char **argv) {
+  if (argc != 5) {
+    std::cerr << "Error: Number of arguments (" << argc << ") is not correct" << std::endl;
+    usage(argv[0]);
+  }
+
+  std::string off_file_name(argv[1]);
+  double alpha_square_max_value = atof(argv[2]);
+  int coeff_field_characteristic = atoi(argv[3]);
+  double min_persistence = atof(argv[4]);
+  
+  // ----------------------------------------------------------------------------
+  // Init of an alpha complex from an OFF file
+  // ----------------------------------------------------------------------------
+  typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kernel;
+  Gudhi::alphacomplex::Alpha_complex<Kernel> alpha_complex_from_file(off_file_name, alpha_square_max_value);
+
+  // ----------------------------------------------------------------------------
+  // Display information about the alpha complex
+  // ----------------------------------------------------------------------------
+  std::cout << "Alpha complex is of dimension " << alpha_complex_from_file.dimension() <<
+      " - " << alpha_complex_from_file.num_simplices() << " simplices - " <<
+      alpha_complex_from_file.num_vertices() << " vertices." << std::endl;
+
+  // Sort the simplices in the order of the filtration
+  alpha_complex_from_file.initialize_filtration();
+
+  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::Field_Zp > pcoh(alpha_complex_from_file);
+  // initializes the coefficient field for homology
+  pcoh.init_coefficients(coeff_field_characteristic);
+
+  pcoh.compute_persistent_cohomology(min_persistence);
+
+  pcoh.output_diagram();
+
+  return 0;
+}
diff --git a/src/Persistent_cohomology/example/alpha_shapes_persistence.cpp b/src/Persistent_cohomology/example/alpha_shapes_persistence.cpp
index 6d5eebcf..235ea141 100644
--- a/src/Persistent_cohomology/example/alpha_shapes_persistence.cpp
+++ b/src/Persistent_cohomology/example/alpha_shapes_persistence.cpp
@@ -124,6 +124,12 @@ void usage(char * const progName) {
 }
 
 int main(int argc, char * const argv[]) {
+  // program args management
+  if (argc != 4) {
+    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);
   if ((returnedScanValue == EOF) || (coeff_field_characteristic <= 0)) {
@@ -138,12 +144,6 @@ int main(int argc, char * const argv[]) {
     usage(argv[0]);
   }
 
-  // program args management
-  if (argc != 4) {
-    std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n";
-    usage(argv[0]);
-  }
-
   // Read points from file
   std::string filegraph = argv[1];
   std::list<Point_3> lp;
@@ -239,7 +239,7 @@ int main(int argc, char * const argv[]) {
       }
     }
     // Construction of the simplex_tree
-    Filtration_value filtr = std::sqrt(*the_alpha_value_iterator);
+    Filtration_value filtr = /*std::sqrt*/(*the_alpha_value_iterator);
 #ifdef DEBUG_TRACES
     std::cout << "filtration = " << filtr << std::endl;
 #endif  // DEBUG_TRACES