diff options
Diffstat (limited to 'src/Rips_complex')
5 files changed, 22 insertions, 15 deletions
diff --git a/src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp b/src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp index 9e182f1e..b7040453 100644 --- a/src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp +++ b/src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp @@ -35,19 +35,19 @@ int main(int argc, char **argv) { Distance_matrix distances = Gudhi::read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_file_name); Rips_complex rips_complex_from_file(distances, threshold); - std::streambuf* streambufffer; + std::streambuf* streambuffer; std::ofstream ouput_file_stream; if (argc == 5) { ouput_file_stream.open(std::string(argv[4])); - streambufffer = ouput_file_stream.rdbuf(); + streambuffer = ouput_file_stream.rdbuf(); } else { - streambufffer = std::cout.rdbuf(); + streambuffer = std::cout.rdbuf(); } Simplex_tree stree; rips_complex_from_file.create_complex(stree, dim_max); - std::ostream output_stream(streambufffer); + std::ostream output_stream(streambuffer); // ---------------------------------------------------------------------------- // Display information about the Rips complex diff --git a/src/Rips_complex/example/example_rips_complex_from_off_file.cpp b/src/Rips_complex/example/example_rips_complex_from_off_file.cpp index de2e4ea4..36b468a7 100644 --- a/src/Rips_complex/example/example_rips_complex_from_off_file.cpp +++ b/src/Rips_complex/example/example_rips_complex_from_off_file.cpp @@ -34,19 +34,19 @@ int main(int argc, char **argv) { Gudhi::Points_off_reader<Point> off_reader(off_file_name); Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold, Gudhi::Euclidean_distance()); - std::streambuf* streambufffer; + std::streambuf* streambuffer; std::ofstream ouput_file_stream; if (argc == 5) { ouput_file_stream.open(std::string(argv[4])); - streambufffer = ouput_file_stream.rdbuf(); + streambuffer = ouput_file_stream.rdbuf(); } else { - streambufffer = std::cout.rdbuf(); + streambuffer = std::cout.rdbuf(); } Simplex_tree stree; rips_complex_from_file.create_complex(stree, dim_max); - std::ostream output_stream(streambufffer); + std::ostream output_stream(streambuffer); // ---------------------------------------------------------------------------- // Display information about the Rips complex diff --git a/src/Rips_complex/test/CMakeLists.txt b/src/Rips_complex/test/CMakeLists.txt index 745d953c..b359584e 100644 --- a/src/Rips_complex/test/CMakeLists.txt +++ b/src/Rips_complex/test/CMakeLists.txt @@ -1,9 +1,8 @@ project(Rips_complex_tests) -include(GUDHI_test_coverage) +include(GUDHI_boost_test) add_executable ( Rips_complex_test_unit test_rips_complex.cpp ) -target_link_libraries(Rips_complex_test_unit ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) if (TBB_FOUND) target_link_libraries(Rips_complex_test_unit ${TBB_LIBRARIES}) endif() @@ -12,4 +11,4 @@ endif() file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) file(COPY "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) -gudhi_add_coverage_test(Rips_complex_test_unit) +gudhi_add_boost_test(Rips_complex_test_unit) diff --git a/src/Rips_complex/utilities/ripscomplex.md b/src/Rips_complex/utilities/ripscomplex.md index 03838085..61f31e3c 100644 --- a/src/Rips_complex/utilities/ripscomplex.md +++ b/src/Rips_complex/utilities/ripscomplex.md @@ -99,6 +99,7 @@ where `dim` is the dimension of the homological feature, `birth` and `death` are * `-h [ --help ]` Produce help message * `-o [ --output-file ]` Name of file in which the persistence diagram is written. Default print in standard output. +* `-r [ --max-edge-length ]` (default = inf) Maximal length of an edge for the Rips complex construction. * `-e [ --approximation ]` (default = .5) Epsilon, where the sparse Rips complex is a (1+epsilon)/(1-epsilon)-approximation of the Rips complex. * `-d [ --cpx-dimension ]` (default = INT_MAX) Maximal dimension of the Rips complex we want to compute. * `-p [ --field-charac ]` (default = 11) Characteristic p of the coefficient field Z/pZ for computing homology. diff --git a/src/Rips_complex/utilities/sparse_rips_persistence.cpp b/src/Rips_complex/utilities/sparse_rips_persistence.cpp index 1a86eafe..cefd8a67 100644 --- a/src/Rips_complex/utilities/sparse_rips_persistence.cpp +++ b/src/Rips_complex/utilities/sparse_rips_persistence.cpp @@ -28,21 +28,24 @@ using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomolog using Point = std::vector<double>; using Points_off_reader = Gudhi::Points_off_reader<Point>; -void program_options(int argc, char* argv[], std::string& off_file_points, std::string& filediag, double& epsilon, +void program_options(int argc, char* argv[], std::string& off_file_points, std::string& filediag, + Filtration_value& threshold, double& epsilon, int& dim_max, int& p, Filtration_value& min_persistence); int main(int argc, char* argv[]) { std::string off_file_points; std::string filediag; + Filtration_value threshold; double epsilon; int dim_max; int p; Filtration_value min_persistence; - program_options(argc, argv, off_file_points, filediag, epsilon, dim_max, p, min_persistence); + program_options(argc, argv, off_file_points, filediag, threshold, epsilon, dim_max, p, min_persistence); Points_off_reader off_reader(off_file_points); - Sparse_rips sparse_rips(off_reader.get_point_cloud(), Gudhi::Euclidean_distance(), epsilon); + Sparse_rips sparse_rips(off_reader.get_point_cloud(), Gudhi::Euclidean_distance(), epsilon, + -std::numeric_limits<Filtration_value>::infinity(), threshold); // Construct the Rips complex in a Simplex Tree Simplex_tree simplex_tree; @@ -73,7 +76,8 @@ int main(int argc, char* argv[]) { return 0; } -void program_options(int argc, char* argv[], std::string& off_file_points, std::string& filediag, double& epsilon, +void program_options(int argc, char* argv[], std::string& off_file_points, std::string& filediag, + Filtration_value& threshold, double& epsilon, int& dim_max, int& p, Filtration_value& min_persistence) { namespace po = boost::program_options; po::options_description hidden("Hidden options"); @@ -84,6 +88,9 @@ void program_options(int argc, char* argv[], std::string& off_file_points, std:: visible.add_options()("help,h", "produce help message")( "output-file,o", po::value<std::string>(&filediag)->default_value(std::string()), "Name of file in which the persistence diagram is written. Default print in std::cout")( + "max-edge-length,r", + po::value<Filtration_value>(&threshold)->default_value(std::numeric_limits<Filtration_value>::infinity()), + "Maximal length of an edge for the Rips complex construction.")( "approximation,e", po::value<double>(&epsilon)->default_value(.5), "Epsilon, where the sparse Rips complex is a (1+epsilon)-approximation of the Rips complex.")( "cpx-dimension,d", po::value<int>(&dim_max)->default_value(std::numeric_limits<int>::max()), |