diff options
Diffstat (limited to 'src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp')
| -rw-r--r-- | src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp | 212 |
1 files changed, 212 insertions, 0 deletions
diff --git a/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp b/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp new file mode 100644 index 00000000..a1c106d5 --- /dev/null +++ b/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp @@ -0,0 +1,212 @@ +#include <iostream> +#include <string> +#include <algorithm> +#include <utility> // std::pair, std::make_pair +#include <cmath> // float comparison +#include <limits> +#include <cstdint> // for std::uint8_t + +#define BOOST_TEST_DYN_LINK +#define BOOST_TEST_MODULE "persistent_cohomology" +#include <boost/test/unit_test.hpp> + +#include <gudhi/graph_simplicial_complex.h> +#include <gudhi/reader_utils.h> +#include <gudhi/Simplex_tree.h> +#include <gudhi/Persistent_cohomology.h> + +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::cout << "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<Simplex_tree<>, 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::cout << "********************************************************************" << std::endl; + std::cout << "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::cout << 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::cout << "str_rips_persistence=" << str_rips_persistence << std::endl; + + std::cout << "********************************************************************" << std::endl; + std::cout << "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::cout << "str_rips_persistence=" << str_rips_persistence << std::endl; + + std::cout << "********************************************************************" << std::endl; + std::cout << "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::cout << "str_rips_persistence=" << str_rips_persistence << std::endl; + + std::cout << "********************************************************************" << std::endl; + std::cout << "TEST OF RIPS_PERSISTENT_COHOMOLOGY_SINGLE_FIELD DIM=" << dimension << " MIN_PERS=Inf" << std::endl; + + str_rips_persistence = test_rips_persistence(dimension, (std::numeric_limits<int>::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::cout << "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 <CODE>std::numeric_limits<std::uint8_t>::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<MiniSTOptions>; +using Mini_st_persistence = + Gudhi::persistent_cohomology::Persistent_cohomology<Mini_simplex_tree, Gudhi::persistent_cohomology::Field_Zp>; + +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<MiniSTOptions::Simplex_key>::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<MiniSTOptions::Simplex_key>::max()); + // Class for homology computation + BOOST_CHECK_THROW(Mini_st_persistence pcoh2(st), std::out_of_range); + +} |