diff options
Diffstat (limited to 'src/Rips_complex/example')
5 files changed, 210 insertions, 0 deletions
diff --git a/src/Rips_complex/example/CMakeLists.txt b/src/Rips_complex/example/CMakeLists.txt new file mode 100644 index 00000000..3962b15e --- /dev/null +++ b/src/Rips_complex/example/CMakeLists.txt @@ -0,0 +1,27 @@ +cmake_minimum_required(VERSION 2.6) +project(Rips_complex_examples) + +add_executable ( ripsoffreader example_rips_complex_from_off_file.cpp ) +target_link_libraries(ripsoffreader ${Boost_SYSTEM_LIBRARY}) + +add_executable ( oneskeletonripspoints example_one_skeleton_rips_from_points.cpp ) +target_link_libraries(oneskeletonripspoints ${Boost_SYSTEM_LIBRARY}) + +if (TBB_FOUND) + target_link_libraries(ripsoffreader ${TBB_LIBRARIES}) + target_link_libraries(oneskeletonripspoints ${TBB_LIBRARIES}) +endif() + +add_test(oneskeletonripspoints ${CMAKE_CURRENT_BINARY_DIR}/oneskeletonripspoints 12.0) +# Do not forget to copy test files in current binary dir +file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) +add_test(ripsoffreader_doc_12_1 ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader alphacomplexdoc.off 12.0 1 ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_1.txt) +add_test(ripsoffreader_doc_12_3 ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader alphacomplexdoc.off 12.0 3 ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_3.txt) +if (DIFF_PATH) + # Do not forget to copy test results files in current binary dir + file(COPY "one_skeleton_rips_points_for_doc.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + file(COPY "full_skeleton_rips_points_for_doc.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + + add_test(ripsoffreader_doc_12_1_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_1.txt ${CMAKE_CURRENT_BINARY_DIR}/one_skeleton_rips_points_for_doc.txt) + add_test(ripsoffreader_doc_12_3_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_3.txt ${CMAKE_CURRENT_BINARY_DIR}/full_skeleton_rips_points_for_doc.txt) +endif() diff --git a/src/Rips_complex/example/example_one_skeleton_rips_from_points.cpp b/src/Rips_complex/example/example_one_skeleton_rips_from_points.cpp new file mode 100644 index 00000000..2e63d9a6 --- /dev/null +++ b/src/Rips_complex/example/example_one_skeleton_rips_from_points.cpp @@ -0,0 +1,65 @@ +#include <gudhi/Rips_complex.h> +// to construct Rips_complex from a OFF file of points +#include <gudhi/Points_off_io.h> +// to construct a simplex_tree from rips complex +#include <gudhi/Simplex_tree.h> +#include <gudhi/distance_functions.h> + +#include <iostream> +#include <string> +#include <limits> // for std::numeric_limits + +void usage(int nbArgs, char * const progName) { + std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n"; + std::cerr << "Usage: " << progName << " threshold\n"; + std::cerr << " i.e.: " << progName << " 12.0\n"; + exit(-1); // ----- >> +} + +int main(int argc, char **argv) { + if (argc != 2) usage(argc, argv[0]); + + double threshold = atof(argv[1]); + + // Type definitions + using Point = std::vector<double>; + using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>; + using Filtration_value = Simplex_tree::Filtration_value; + using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>; + + std::vector<Point> points; + points.push_back({1.0, 1.0}); + points.push_back({7.0, 0.0}); + points.push_back({4.0, 6.0}); + points.push_back({9.0, 6.0}); + points.push_back({0.0, 14.0}); + points.push_back({2.0, 19.0}); + points.push_back({9.0, 17.0}); + + // ---------------------------------------------------------------------------- + // Init of a rips complex from points + // ---------------------------------------------------------------------------- + Rips_complex rips_complex_from_points(points, threshold, euclidean_distance<Filtration_value, Point>); + + Simplex_tree simplex; + if (rips_complex_from_points.create_complex(simplex, 1)) { + // ---------------------------------------------------------------------------- + // Display information about the one skeleton rips complex + // ---------------------------------------------------------------------------- + std::cout << "Rips complex is of dimension " << simplex.dimension() << + " - " << simplex.num_simplices() << " simplices - " << + simplex.num_vertices() << " vertices." << std::endl; + + std::cout << "Iterator on rips complex simplices in the filtration order, with [filtration value]:" << + std::endl; + for (auto f_simplex : simplex.filtration_simplex_range()) { + std::cout << " ( "; + for (auto vertex : simplex.simplex_vertex_range(f_simplex)) { + std::cout << vertex << " "; + } + std::cout << ") -> " << "[" << simplex.filtration(f_simplex) << "] "; + std::cout << std::endl; + } + } + return 0; +} 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 new file mode 100644 index 00000000..60050cea --- /dev/null +++ b/src/Rips_complex/example/example_rips_complex_from_off_file.cpp @@ -0,0 +1,72 @@ +#include <gudhi/Rips_complex.h> +// to construct Rips_complex from a OFF file of points +#include <gudhi/Points_off_io.h> +// to construct a simplex_tree from rips complex +#include <gudhi/Simplex_tree.h> +#include <gudhi/distance_functions.h> + +#include <iostream> +#include <string> + +void usage(int nbArgs, char * const progName) { + std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n"; + std::cerr << "Usage: " << progName << " filename.off threshold dim_max [ouput_file.txt]\n"; + std::cerr << " i.e.: " << progName << " ../../data/points/alphacomplexdoc.off 60.0\n"; + exit(-1); // ----- >> +} + +int main(int argc, char **argv) { + if ((argc != 4) && (argc != 5)) usage(argc, (argv[0] - 1)); + + std::string off_file_name(argv[1]); + double threshold = atof(argv[2]); + int dim_max = atoi(argv[3]); + + // Type definitions + using Point = std::vector<float>; + using Simplex_tree = Gudhi::Simplex_tree<>; + using Filtration_value = Simplex_tree::Filtration_value; + using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>; + + // ---------------------------------------------------------------------------- + // Init of a rips complex from an OFF file + // ---------------------------------------------------------------------------- + Gudhi::Points_off_reader<Point> off_reader(off_file_name); + Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold, + euclidean_distance<Filtration_value, Point>); + + std::streambuf* streambufffer; + std::ofstream ouput_file_stream; + + if (argc == 5) { + ouput_file_stream.open(std::string(argv[4])); + streambufffer = ouput_file_stream.rdbuf(); + } else { + streambufffer = std::cout.rdbuf(); + } + + Simplex_tree simplex; + if (rips_complex_from_file.create_complex(simplex, dim_max)) { + std::ostream output_stream(streambufffer); + + // ---------------------------------------------------------------------------- + // Display information about the rips complex + // ---------------------------------------------------------------------------- + output_stream << "Rips complex is of dimension " << simplex.dimension() << + " - " << simplex.num_simplices() << " simplices - " << + simplex.num_vertices() << " vertices." << std::endl; + + output_stream << "Iterator on rips complex simplices in the filtration order, with [filtration value]:" << + std::endl; + for (auto f_simplex : simplex.filtration_simplex_range()) { + output_stream << " ( "; + for (auto vertex : simplex.simplex_vertex_range(f_simplex)) { + output_stream << vertex << " "; + } + output_stream << ") -> " << "[" << simplex.filtration(f_simplex) << "] "; + output_stream << std::endl; + } + } + ouput_file_stream.close(); + return 0; +} diff --git a/src/Rips_complex/example/full_skeleton_rips_points_for_doc.txt b/src/Rips_complex/example/full_skeleton_rips_points_for_doc.txt new file mode 100644 index 00000000..319931e0 --- /dev/null +++ b/src/Rips_complex/example/full_skeleton_rips_points_for_doc.txt @@ -0,0 +1,26 @@ +Rips complex is of dimension 3 - 24 simplices - 7 vertices. +Iterator on rips complex simplices in the filtration order, with [filtration value]: + ( 0 ) -> [0] + ( 1 ) -> [0] + ( 2 ) -> [0] + ( 3 ) -> [0] + ( 4 ) -> [0] + ( 5 ) -> [0] + ( 6 ) -> [0] + ( 3 2 ) -> [5] + ( 5 4 ) -> [5.38516] + ( 2 0 ) -> [5.83095] + ( 1 0 ) -> [6.08276] + ( 3 1 ) -> [6.32456] + ( 2 1 ) -> [6.7082] + ( 2 1 0 ) -> [6.7082] + ( 3 2 1 ) -> [6.7082] + ( 6 5 ) -> [7.28011] + ( 4 2 ) -> [8.94427] + ( 3 0 ) -> [9.43398] + ( 3 1 0 ) -> [9.43398] + ( 3 2 0 ) -> [9.43398] + ( 3 2 1 0 ) -> [9.43398] + ( 6 4 ) -> [9.48683] + ( 6 5 4 ) -> [9.48683] + ( 6 3 ) -> [11] diff --git a/src/Rips_complex/example/one_skeleton_rips_points_for_doc.txt b/src/Rips_complex/example/one_skeleton_rips_points_for_doc.txt new file mode 100644 index 00000000..b0e25cc5 --- /dev/null +++ b/src/Rips_complex/example/one_skeleton_rips_points_for_doc.txt @@ -0,0 +1,20 @@ +Rips complex is of dimension 1 - 18 simplices - 7 vertices. +Iterator on rips complex simplices in the filtration order, with [filtration value]: + ( 0 ) -> [0] + ( 1 ) -> [0] + ( 2 ) -> [0] + ( 3 ) -> [0] + ( 4 ) -> [0] + ( 5 ) -> [0] + ( 6 ) -> [0] + ( 3 2 ) -> [5] + ( 5 4 ) -> [5.38516] + ( 2 0 ) -> [5.83095] + ( 1 0 ) -> [6.08276] + ( 3 1 ) -> [6.32456] + ( 2 1 ) -> [6.7082] + ( 6 5 ) -> [7.28011] + ( 4 2 ) -> [8.94427] + ( 3 0 ) -> [9.43398] + ( 6 4 ) -> [9.48683] + ( 6 3 ) -> [11] |