diff options
Diffstat (limited to 'src/Alpha_complex/example')
5 files changed, 94 insertions, 17 deletions
diff --git a/src/Alpha_complex/example/Alpha_complex_from_off.cpp b/src/Alpha_complex/example/Alpha_complex_from_off.cpp index d411e90a..220a66de 100644 --- a/src/Alpha_complex/example/Alpha_complex_from_off.cpp +++ b/src/Alpha_complex/example/Alpha_complex_from_off.cpp @@ -2,8 +2,6 @@ // to construct a simplex_tree from alpha complex #include <gudhi/Simplex_tree.h> -#include <CGAL/Epick_d.h> - #include <iostream> #include <string> @@ -23,22 +21,21 @@ int main(int argc, char **argv) { // ---------------------------------------------------------------------------- // 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); + Gudhi::alpha_complex::Alpha_complex<> alpha_complex_from_file(off_file_name); - std::streambuf* streambufffer; + std::streambuf* streambuffer; std::ofstream ouput_file_stream; if (argc == 4) { ouput_file_stream.open(std::string(argv[3])); - streambufffer = ouput_file_stream.rdbuf(); + streambuffer = ouput_file_stream.rdbuf(); } else { - streambufffer = std::cout.rdbuf(); + streambuffer = std::cout.rdbuf(); } Gudhi::Simplex_tree<> simplex; if (alpha_complex_from_file.create_complex(simplex, alpha_square_max_value)) { - std::ostream output_stream(streambufffer); + std::ostream output_stream(streambuffer); // ---------------------------------------------------------------------------- // Display information about the alpha complex diff --git a/src/Alpha_complex/example/Alpha_complex_from_points.cpp b/src/Alpha_complex/example/Alpha_complex_from_points.cpp index 981aa470..6526ca3a 100644 --- a/src/Alpha_complex/example/Alpha_complex_from_points.cpp +++ b/src/Alpha_complex/example/Alpha_complex_from_points.cpp @@ -2,12 +2,13 @@ // to construct a simplex_tree from alpha complex #include <gudhi/Simplex_tree.h> -#include <CGAL/Epick_d.h> +#include <CGAL/Epeck_d.h> #include <iostream> #include <vector> -using Kernel = CGAL::Epick_d< CGAL::Dimension_tag<2> >; +// Explicit dimension 2 Epeck_d kernel +using Kernel = CGAL::Epeck_d< CGAL::Dimension_tag<2> >; using Point = Kernel::Point_d; using Vector_of_points = std::vector<Point>; diff --git a/src/Alpha_complex/example/CMakeLists.txt b/src/Alpha_complex/example/CMakeLists.txt index b069b443..b0337934 100644 --- a/src/Alpha_complex/example/CMakeLists.txt +++ b/src/Alpha_complex/example/CMakeLists.txt @@ -5,9 +5,12 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) 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}) + add_executable ( Alpha_complex_example_fast_from_off Fast_alpha_complex_from_off.cpp ) + target_link_libraries(Alpha_complex_example_fast_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}) + target_link_libraries(Alpha_complex_example_fast_from_off ${TBB_LIBRARIES}) endif() add_test(NAME Alpha_complex_example_from_points COMMAND $<TARGET_FILE:Alpha_complex_example_from_points>) @@ -16,7 +19,13 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) "${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) + + add_test(NAME Alpha_complex_example_fast_from_off_60 COMMAND $<TARGET_FILE:Alpha_complex_example_fast_from_off> + "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" "60.0" "${CMAKE_CURRENT_BINARY_DIR}/fastalphaoffreader_result_60.txt") + add_test(NAME Alpha_complex_example_fast_from_off_32 COMMAND $<TARGET_FILE:Alpha_complex_example_fast_from_off> + "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" "32.0" "${CMAKE_CURRENT_BINARY_DIR}/fastalphaoffreader_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}/) @@ -25,6 +34,11 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) ${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) + + add_test(Alpha_complex_example_fast_from_off_60_diff_files ${DIFF_PATH} + ${CMAKE_CURRENT_BINARY_DIR}/fastalphaoffreader_result_60.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_60.txt) + add_test(Alpha_complex_example_fast_from_off_32_diff_files ${DIFF_PATH} + ${CMAKE_CURRENT_BINARY_DIR}/fastalphaoffreader_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 ) diff --git a/src/Alpha_complex/example/Fast_alpha_complex_from_off.cpp b/src/Alpha_complex/example/Fast_alpha_complex_from_off.cpp new file mode 100644 index 00000000..f181005a --- /dev/null +++ b/src/Alpha_complex/example/Fast_alpha_complex_from_off.cpp @@ -0,0 +1,65 @@ +#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])}; + + // WARNING : CGAL::Epick_d is fast but not safe (unlike CGAL::Epeck_d) + // (i.e. when the points are on a grid) + using Fast_kernel = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>; + // ---------------------------------------------------------------------------- + // Init of an alpha complex from an OFF file + // ---------------------------------------------------------------------------- + Gudhi::alpha_complex::Alpha_complex<Fast_kernel> alpha_complex_from_file(off_file_name); + + std::streambuf* streambuffer; + std::ofstream ouput_file_stream; + + if (argc == 4) { + ouput_file_stream.open(std::string(argv[3])); + streambuffer = ouput_file_stream.rdbuf(); + } else { + streambuffer = std::cout.rdbuf(); + } + + Gudhi::Simplex_tree<> simplex; + if (alpha_complex_from_file.create_complex(simplex, alpha_square_max_value)) { + std::ostream output_stream(streambuffer); + + // ---------------------------------------------------------------------------- + // 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/Weighted_alpha_complex_3d_from_points.cpp b/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp index ac11b68c..fcf80802 100644 --- a/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp +++ b/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp @@ -10,7 +10,7 @@ // 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 Bare_point = Weighted_alpha_complex_3d::Bare_point_3; using Weighted_point = Weighted_alpha_complex_3d::Weighted_point_3; int main(int argc, char **argv) { @@ -18,11 +18,11 @@ 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.)); + weighted_points.push_back(Weighted_point(Bare_point(1, -1, -1), 4.)); + weighted_points.push_back(Weighted_point(Bare_point(-1, 1, -1), 4.)); + weighted_points.push_back(Weighted_point(Bare_point(-1, -1, 1), 4.)); + weighted_points.push_back(Weighted_point(Bare_point(1, 1, 1), 4.)); + weighted_points.push_back(Weighted_point(Bare_point(2, 2, 2), 1.)); // ---------------------------------------------------------------------------- // Init of an alpha complex from the list of points |