diff options
Diffstat (limited to 'src/Alpha_complex/example')
8 files changed, 349 insertions, 0 deletions
diff --git a/src/Alpha_complex/example/Alpha_complex_3d_from_points.cpp b/src/Alpha_complex/example/Alpha_complex_3d_from_points.cpp new file mode 100644 index 00000000..0e359a27 --- /dev/null +++ b/src/Alpha_complex/example/Alpha_complex_3d_from_points.cpp @@ -0,0 +1,56 @@ +#include <gudhi/Alpha_complex_3d.h> +// to construct a simplex_tree from alpha complex +#include <gudhi/Simplex_tree.h> + +#include <iostream> +#include <string> +#include <vector> +#include <limits> // for numeric limits + +using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::SAFE, false, false>; +using Point = Alpha_complex_3d::Point_3; +using Vector_of_points = std::vector<Point>; + +int main(int argc, char **argv) { + if (argc != 1) { + std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n"; + std::cerr << "Usage: " << (argv[0] - 1) << " \n"; + exit(-1); // ----- >> + } + + // ---------------------------------------------------------------------------- + // Init of a list of points from a small molecule + // ---------------------------------------------------------------------------- + Vector_of_points points; + points.push_back(Point(1, -1, -1)); + points.push_back(Point(-1, 1, -1)); + points.push_back(Point(-1, -1, 1)); + points.push_back(Point(1, 1, 1)); + points.push_back(Point(2, 2, 2)); + + // ---------------------------------------------------------------------------- + // Init of an alpha complex from the list of points + // ---------------------------------------------------------------------------- + Alpha_complex_3d alpha_complex_from_points(points); + + Gudhi::Simplex_tree<> simplex; + if (alpha_complex_from_points.create_complex(simplex)) { + // ---------------------------------------------------------------------------- + // Display information about the alpha complex + // ---------------------------------------------------------------------------- + std::cout << "Alpha complex is of dimension " << simplex.dimension() << " - " << simplex.num_simplices() + << " simplices - " << simplex.num_vertices() << " vertices." << std::endl; + + std::cout << "Iterator on alpha 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/Alpha_complex/example/Alpha_complex_from_off.cpp b/src/Alpha_complex/example/Alpha_complex_from_off.cpp new file mode 100644 index 00000000..d411e90a --- /dev/null +++ b/src/Alpha_complex/example/Alpha_complex_from_off.cpp @@ -0,0 +1,63 @@ +#include <gudhi/Alpha_complex.h> +// to construct a simplex_tree from alpha complex +#include <gudhi/Simplex_tree.h> + +#include <CGAL/Epick_d.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 alpha_square_max_value [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 != 3) && (argc != 4)) usage(argc, (argv[0] - 1)); + + std::string off_file_name {argv[1]}; + double alpha_square_max_value {atof(argv[2])}; + + // ---------------------------------------------------------------------------- + // Init of an alpha complex from an OFF file + // ---------------------------------------------------------------------------- + using Kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >; + Gudhi::alpha_complex::Alpha_complex<Kernel> alpha_complex_from_file(off_file_name); + + std::streambuf* streambufffer; + std::ofstream ouput_file_stream; + + if (argc == 4) { + ouput_file_stream.open(std::string(argv[3])); + streambufffer = ouput_file_stream.rdbuf(); + } else { + streambufffer = std::cout.rdbuf(); + } + + Gudhi::Simplex_tree<> simplex; + if (alpha_complex_from_file.create_complex(simplex, alpha_square_max_value)) { + std::ostream output_stream(streambufffer); + + // ---------------------------------------------------------------------------- + // Display information about the alpha complex + // ---------------------------------------------------------------------------- + output_stream << "Alpha complex is of dimension " << simplex.dimension() << + " - " << simplex.num_simplices() << " simplices - " << + simplex.num_vertices() << " vertices." << std::endl; + + output_stream << "Iterator on alpha 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/Alpha_complex/example/Alpha_complex_from_points.cpp b/src/Alpha_complex/example/Alpha_complex_from_points.cpp new file mode 100644 index 00000000..981aa470 --- /dev/null +++ b/src/Alpha_complex/example/Alpha_complex_from_points.cpp @@ -0,0 +1,52 @@ +#include <gudhi/Alpha_complex.h> +// to construct a simplex_tree from alpha complex +#include <gudhi/Simplex_tree.h> + +#include <CGAL/Epick_d.h> + +#include <iostream> +#include <vector> + +using Kernel = CGAL::Epick_d< CGAL::Dimension_tag<2> >; +using Point = Kernel::Point_d; +using Vector_of_points = std::vector<Point>; + +int main() { + // ---------------------------------------------------------------------------- + // Init of a list of points + // ---------------------------------------------------------------------------- + Vector_of_points points; + points.push_back(Point(1.0, 1.0)); + points.push_back(Point(7.0, 0.0)); + points.push_back(Point(4.0, 6.0)); + points.push_back(Point(9.0, 6.0)); + points.push_back(Point(0.0, 14.0)); + points.push_back(Point(2.0, 19.0)); + points.push_back(Point(9.0, 17.0)); + + // ---------------------------------------------------------------------------- + // Init of an alpha complex from the list of points + // ---------------------------------------------------------------------------- + Gudhi::alpha_complex::Alpha_complex<Kernel> alpha_complex_from_points(points); + + Gudhi::Simplex_tree<> simplex; + if (alpha_complex_from_points.create_complex(simplex)) { + // ---------------------------------------------------------------------------- + // Display information about the alpha complex + // ---------------------------------------------------------------------------- + std::cout << "Alpha complex is of dimension " << simplex.dimension() << + " - " << simplex.num_simplices() << " simplices - " << + simplex.num_vertices() << " vertices." << std::endl; + + std::cout << "Iterator on alpha 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/Alpha_complex/example/CMakeLists.txt b/src/Alpha_complex/example/CMakeLists.txt new file mode 100644 index 00000000..b069b443 --- /dev/null +++ b/src/Alpha_complex/example/CMakeLists.txt @@ -0,0 +1,46 @@ +project(Alpha_complex_examples) + +if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) + add_executable ( Alpha_complex_example_from_points Alpha_complex_from_points.cpp ) + target_link_libraries(Alpha_complex_example_from_points ${CGAL_LIBRARY}) + add_executable ( Alpha_complex_example_from_off Alpha_complex_from_off.cpp ) + target_link_libraries(Alpha_complex_example_from_off ${CGAL_LIBRARY}) + if (TBB_FOUND) + target_link_libraries(Alpha_complex_example_from_points ${TBB_LIBRARIES}) + target_link_libraries(Alpha_complex_example_from_off ${TBB_LIBRARIES}) + endif() + + add_test(NAME Alpha_complex_example_from_points COMMAND $<TARGET_FILE:Alpha_complex_example_from_points>) + + add_test(NAME Alpha_complex_example_from_off_60 COMMAND $<TARGET_FILE:Alpha_complex_example_from_off> + "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" "60.0" "${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_60.txt") + add_test(NAME Alpha_complex_example_from_off_32 COMMAND $<TARGET_FILE:Alpha_complex_example_from_off> + "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" "32.0" "${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_32.txt") + if (DIFF_PATH) + # Do not forget to copy test results files in current binary dir + file(COPY "alphaoffreader_for_doc_32.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + file(COPY "alphaoffreader_for_doc_60.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + + add_test(Alpha_complex_example_from_off_60_diff_files ${DIFF_PATH} + ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_60.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_60.txt) + add_test(Alpha_complex_example_from_off_32_diff_files ${DIFF_PATH} + ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_32.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_32.txt) + endif() + + add_executable ( Alpha_complex_example_weighted_3d_from_points Weighted_alpha_complex_3d_from_points.cpp ) + target_link_libraries(Alpha_complex_example_weighted_3d_from_points ${CGAL_LIBRARY}) + if (TBB_FOUND) + target_link_libraries(Alpha_complex_example_weighted_3d_from_points ${TBB_LIBRARIES}) + endif() + add_test(NAME Alpha_complex_example_weighted_3d_from_points + COMMAND $<TARGET_FILE:Alpha_complex_example_weighted_3d_from_points>) + + add_executable ( Alpha_complex_example_3d_from_points Alpha_complex_3d_from_points.cpp ) + target_link_libraries(Alpha_complex_example_3d_from_points ${CGAL_LIBRARY}) + if (TBB_FOUND) + target_link_libraries(Alpha_complex_example_3d_from_points ${TBB_LIBRARIES}) + endif() + add_test(NAME Alpha_complex_example_3d_from_points + COMMAND $<TARGET_FILE:Alpha_complex_example_3d_from_points>) + +endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) diff --git a/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp b/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp new file mode 100644 index 00000000..ac11b68c --- /dev/null +++ b/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp @@ -0,0 +1,52 @@ +#include <gudhi/Alpha_complex_3d.h> +// to construct a simplex_tree from alpha complex +#include <gudhi/Simplex_tree.h> + +#include <iostream> +#include <string> +#include <vector> +#include <limits> // for numeric limits + +// Complexity = FAST, weighted = true, periodic = false +using Weighted_alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::SAFE, true, false>; +using Point = Weighted_alpha_complex_3d::Point_3; +using Weighted_point = Weighted_alpha_complex_3d::Weighted_point_3; + +int main(int argc, char **argv) { + // ---------------------------------------------------------------------------- + // Init of a list of points and weights from a small molecule + // ---------------------------------------------------------------------------- + std::vector<Weighted_point> weighted_points; + weighted_points.push_back(Weighted_point(Point(1, -1, -1), 4.)); + weighted_points.push_back(Weighted_point(Point(-1, 1, -1), 4.)); + weighted_points.push_back(Weighted_point(Point(-1, -1, 1), 4.)); + weighted_points.push_back(Weighted_point(Point(1, 1, 1), 4.)); + weighted_points.push_back(Weighted_point(Point(2, 2, 2), 1.)); + + // ---------------------------------------------------------------------------- + // Init of an alpha complex from the list of points + // ---------------------------------------------------------------------------- + Weighted_alpha_complex_3d alpha_complex_from_points(weighted_points); + + Gudhi::Simplex_tree<> simplex; + if (alpha_complex_from_points.create_complex(simplex)) { + // ---------------------------------------------------------------------------- + // Display information about the alpha complex + // ---------------------------------------------------------------------------- + std::cout << "Alpha complex is of dimension " << simplex.dimension() << " - " << simplex.num_simplices() + << " simplices - " << simplex.num_vertices() << " vertices." << std::endl; + + std::cout << "Iterator on alpha 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/Alpha_complex/example/alphaoffreader_for_doc_32.txt b/src/Alpha_complex/example/alphaoffreader_for_doc_32.txt new file mode 100644 index 00000000..13183e86 --- /dev/null +++ b/src/Alpha_complex/example/alphaoffreader_for_doc_32.txt @@ -0,0 +1,22 @@ +Alpha complex is of dimension 2 - 20 simplices - 7 vertices. +Iterator on alpha 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 ) -> [6.25] + ( 5 4 ) -> [7.25] + ( 2 0 ) -> [8.5] + ( 1 0 ) -> [9.25] + ( 3 1 ) -> [10] + ( 2 1 ) -> [11.25] + ( 3 2 1 ) -> [12.5] + ( 2 1 0 ) -> [12.9959] + ( 6 5 ) -> [13.25] + ( 4 2 ) -> [20] + ( 6 4 ) -> [22.7367] + ( 6 5 4 ) -> [22.7367] + ( 6 3 ) -> [30.25] diff --git a/src/Alpha_complex/example/alphaoffreader_for_doc_60.txt b/src/Alpha_complex/example/alphaoffreader_for_doc_60.txt new file mode 100644 index 00000000..71f29a00 --- /dev/null +++ b/src/Alpha_complex/example/alphaoffreader_for_doc_60.txt @@ -0,0 +1,27 @@ +Alpha complex is of dimension 2 - 25 simplices - 7 vertices. +Iterator on alpha 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 ) -> [6.25] + ( 5 4 ) -> [7.25] + ( 2 0 ) -> [8.5] + ( 1 0 ) -> [9.25] + ( 3 1 ) -> [10] + ( 2 1 ) -> [11.25] + ( 3 2 1 ) -> [12.5] + ( 2 1 0 ) -> [12.9959] + ( 6 5 ) -> [13.25] + ( 4 2 ) -> [20] + ( 6 4 ) -> [22.7367] + ( 6 5 4 ) -> [22.7367] + ( 6 3 ) -> [30.25] + ( 6 2 ) -> [36.5] + ( 6 3 2 ) -> [36.5] + ( 6 4 2 ) -> [37.2449] + ( 4 0 ) -> [59.7107] + ( 4 2 0 ) -> [59.7107] diff --git a/src/Alpha_complex/example/weightedalpha3dfrompoints_for_doc.txt b/src/Alpha_complex/example/weightedalpha3dfrompoints_for_doc.txt new file mode 100644 index 00000000..7a09998d --- /dev/null +++ b/src/Alpha_complex/example/weightedalpha3dfrompoints_for_doc.txt @@ -0,0 +1,31 @@ +Alpha complex is of dimension 3 - 29 simplices - 5 vertices. +Iterator on alpha complex simplices in the filtration order, with [filtration value]: + ( 0 ) -> [-4] + ( 1 ) -> [-4] + ( 2 ) -> [-4] + ( 3 ) -> [-4] + ( 1 0 ) -> [-2] + ( 2 0 ) -> [-2] + ( 2 1 ) -> [-2] + ( 3 0 ) -> [-2] + ( 3 1 ) -> [-2] + ( 3 2 ) -> [-2] + ( 2 1 0 ) -> [-1.33333] + ( 3 1 0 ) -> [-1.33333] + ( 3 2 0 ) -> [-1.33333] + ( 3 2 1 ) -> [-1.33333] + ( 3 2 1 0 ) -> [-1] + ( 4 ) -> [-1] + ( 4 2 ) -> [-1] + ( 4 0 ) -> [23] + ( 4 1 ) -> [23] + ( 4 2 0 ) -> [23] + ( 4 2 1 ) -> [23] + ( 4 3 ) -> [23] + ( 4 3 2 ) -> [23] + ( 4 1 0 ) -> [95] + ( 4 2 1 0 ) -> [95] + ( 4 3 0 ) -> [95] + ( 4 3 1 ) -> [95] + ( 4 3 2 0 ) -> [95] + ( 4 3 2 1 ) -> [95] |