#include #include #include #include // std::pair, std::make_pair #include // float comparison #include #include // for std::uint8_t #define BOOST_TEST_DYN_LINK #define BOOST_TEST_MODULE "persistent_cohomology" #include #include #include #include #include using namespace Gudhi; using namespace Gudhi::persistent_cohomology; using namespace boost::unit_test; typedef Simplex_tree<> typeST; std::string test_rips_persistence(int coefficient, int min_persistence) { // file is copied in CMakeLists.txt std::ifstream simplex_tree_stream; simplex_tree_stream.open("simplex_tree_file_for_unit_test.txt"); typeST st; simplex_tree_stream >> st; simplex_tree_stream.close(); // Display the Simplex_tree std::clog << "The complex contains " << st.num_simplices() << " simplices" << " - dimension= " << st.dimension() << std::endl; // Check BOOST_CHECK(st.num_simplices() == 98); BOOST_CHECK(st.dimension() == 3); // Sort the simplices in the order of the filtration st.initialize_filtration(); // Compute the persistence diagram of the complex Persistent_cohomology, Field_Zp> pcoh(st); pcoh.init_coefficients( coefficient ); // initializes the coefficient field for homology // Check infinite rips pcoh.compute_persistent_cohomology( min_persistence ); // Minimal lifetime of homology feature to be recorded. std::ostringstream ossInfinite; pcoh.output_diagram(ossInfinite); std::string strInfinite = ossInfinite.str(); return strInfinite; } void test_rips_persistence_in_dimension(int dimension) { std::string value0(" 0 0.02 1.12"); std::string value1(" 0 0.03 1.13"); std::string value2(" 0 0.04 1.14"); std::string value3(" 0 0.05 1.15"); std::string value4(" 0 0.06 1.16"); std::string value5(" 0 0.07 1.17"); std::string value6(" 0 0.08 1.18"); std::string value7(" 0 0.09 1.19"); std::string value8(" 0 0 inf" ); std::string value9(" 0 0.01 inf" ); value0.insert(0,std::to_string(dimension)); value1.insert(0,std::to_string(dimension)); value2.insert(0,std::to_string(dimension)); value3.insert(0,std::to_string(dimension)); value4.insert(0,std::to_string(dimension)); value5.insert(0,std::to_string(dimension)); value6.insert(0,std::to_string(dimension)); value7.insert(0,std::to_string(dimension)); value8.insert(0,std::to_string(dimension)); value9.insert(0,std::to_string(dimension)); std::clog << "********************************************************************" << std::endl; std::clog << "TEST OF RIPS_PERSISTENT_COHOMOLOGY_SINGLE_FIELD DIM=" << dimension << " MIN_PERS=0" << std::endl; std::string str_rips_persistence = test_rips_persistence(dimension, 0); std::clog << str_rips_persistence << std::endl; BOOST_CHECK(str_rips_persistence.find(value0) != std::string::npos); // Check found BOOST_CHECK(str_rips_persistence.find(value1) != std::string::npos); // Check found BOOST_CHECK(str_rips_persistence.find(value2) != std::string::npos); // Check found BOOST_CHECK(str_rips_persistence.find(value3) != std::string::npos); // Check found BOOST_CHECK(str_rips_persistence.find(value4) != std::string::npos); // Check found BOOST_CHECK(str_rips_persistence.find(value5) != std::string::npos); // Check found BOOST_CHECK(str_rips_persistence.find(value6) != std::string::npos); // Check found BOOST_CHECK(str_rips_persistence.find(value7) != std::string::npos); // Check found BOOST_CHECK(str_rips_persistence.find(value8) != std::string::npos); // Check found BOOST_CHECK(str_rips_persistence.find(value9) != std::string::npos); // Check found std::clog << "str_rips_persistence=" << str_rips_persistence << std::endl; std::clog << "********************************************************************" << std::endl; std::clog << "TEST OF RIPS_PERSISTENT_COHOMOLOGY_SINGLE_FIELD DIM=" << dimension << " MIN_PERS=1" << std::endl; str_rips_persistence = test_rips_persistence(dimension, 1); BOOST_CHECK(str_rips_persistence.find(value0) != std::string::npos); // Check found BOOST_CHECK(str_rips_persistence.find(value1) != std::string::npos); // Check found BOOST_CHECK(str_rips_persistence.find(value2) != std::string::npos); // Check found BOOST_CHECK(str_rips_persistence.find(value3) != std::string::npos); // Check found BOOST_CHECK(str_rips_persistence.find(value4) != std::string::npos); // Check found BOOST_CHECK(str_rips_persistence.find(value5) != std::string::npos); // Check found BOOST_CHECK(str_rips_persistence.find(value6) != std::string::npos); // Check found BOOST_CHECK(str_rips_persistence.find(value7) != std::string::npos); // Check found BOOST_CHECK(str_rips_persistence.find(value8) != std::string::npos); // Check found BOOST_CHECK(str_rips_persistence.find(value9) != std::string::npos); // Check found std::clog << "str_rips_persistence=" << str_rips_persistence << std::endl; std::clog << "********************************************************************" << std::endl; std::clog << "TEST OF RIPS_PERSISTENT_COHOMOLOGY_SINGLE_FIELD DIM=" << dimension << " MIN_PERS=2" << std::endl; str_rips_persistence = test_rips_persistence(dimension, 2); BOOST_CHECK(str_rips_persistence.find(value0) == std::string::npos); // Check not found BOOST_CHECK(str_rips_persistence.find(value1) == std::string::npos); // Check not found BOOST_CHECK(str_rips_persistence.find(value2) == std::string::npos); // Check not found BOOST_CHECK(str_rips_persistence.find(value3) == std::string::npos); // Check not found BOOST_CHECK(str_rips_persistence.find(value4) == std::string::npos); // Check not found BOOST_CHECK(str_rips_persistence.find(value5) == std::string::npos); // Check not found BOOST_CHECK(str_rips_persistence.find(value6) == std::string::npos); // Check not found BOOST_CHECK(str_rips_persistence.find(value7) == std::string::npos); // Check not found BOOST_CHECK(str_rips_persistence.find(value8) != std::string::npos); // Check found BOOST_CHECK(str_rips_persistence.find(value9) != std::string::npos); // Check found std::clog << "str_rips_persistence=" << str_rips_persistence << std::endl; std::clog << "********************************************************************" << std::endl; std::clog << "TEST OF RIPS_PERSISTENT_COHOMOLOGY_SINGLE_FIELD DIM=" << dimension << " MIN_PERS=Inf" << std::endl; str_rips_persistence = test_rips_persistence(dimension, (std::numeric_limits::max)()); BOOST_CHECK(str_rips_persistence.find(value0) == std::string::npos); // Check not found BOOST_CHECK(str_rips_persistence.find(value1) == std::string::npos); // Check not found BOOST_CHECK(str_rips_persistence.find(value2) == std::string::npos); // Check not found BOOST_CHECK(str_rips_persistence.find(value3) == std::string::npos); // Check not found BOOST_CHECK(str_rips_persistence.find(value4) == std::string::npos); // Check not found BOOST_CHECK(str_rips_persistence.find(value5) == std::string::npos); // Check not found BOOST_CHECK(str_rips_persistence.find(value6) == std::string::npos); // Check not found BOOST_CHECK(str_rips_persistence.find(value7) == std::string::npos); // Check not found BOOST_CHECK(str_rips_persistence.find(value8) != std::string::npos); // Check found BOOST_CHECK(str_rips_persistence.find(value9) != std::string::npos); // Check found std::clog << "str_rips_persistence=" << str_rips_persistence << std::endl; } BOOST_AUTO_TEST_CASE( rips_persistent_cohomology_single_field_dim_1 ) { test_rips_persistence_in_dimension(1); } BOOST_AUTO_TEST_CASE( rips_persistent_cohomology_single_field_dim_2 ) { test_rips_persistence_in_dimension(2); } BOOST_AUTO_TEST_CASE( rips_persistent_cohomology_single_field_dim_3 ) { test_rips_persistence_in_dimension(3); } BOOST_AUTO_TEST_CASE( rips_persistent_cohomology_single_field_dim_5 ) { test_rips_persistence_in_dimension(5); } // TODO(VR): not working from 6 // std::string str_rips_persistence = test_rips_persistence(6, 0); // TODO(VR): division by zero // std::string str_rips_persistence = test_rips_persistence(0, 0); /** SimplexTree minimal options to test the limits. * * Maximum number of simplices to compute persistence is

std::numeric_limits::max()<\CODE> = 256.*/
struct MiniSTOptions {
  typedef linear_indexing_tag Indexing_tag;
  typedef short Vertex_handle;
  typedef double Filtration_value;
  // Maximum number of simplices to compute persistence is 2^8 - 1 = 255. One is reserved for null_key
  typedef std::uint8_t Simplex_key;
  static const bool store_key = true;
  static const bool store_filtration = false;
  static const bool contiguous_vertices = false;
};

using Mini_simplex_tree = Gudhi::Simplex_tree;
using Mini_st_persistence =
    Gudhi::persistent_cohomology::Persistent_cohomology;

BOOST_AUTO_TEST_CASE( persistence_constructor_exception )
{
  Mini_simplex_tree st;

  // To make number of simplices = 255
  const short simplex_0[] = {0, 1, 2, 3, 4, 5, 6, 7};
  st.insert_simplex_and_subfaces(simplex_0);

  // Sort the simplices in the order of the filtration
  st.initialize_filtration();

  BOOST_CHECK(st.num_simplices() <= std::numeric_limits::max());
  // Class for homology computation
  BOOST_CHECK_NO_THROW(Mini_st_persistence pcoh(st));

  st.insert_simplex({8});
  BOOST_CHECK(st.num_simplices() > std::numeric_limits::max());
  // Class for homology computation
  BOOST_CHECK_THROW(Mini_st_persistence pcoh2(st), std::out_of_range);

}