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author | vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2016-11-21 16:24:15 +0000 |
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committer | vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2016-11-21 16:24:15 +0000 |
commit | 1a728400187d89db914e865a979c85c7260b0b02 (patch) | |
tree | ced1be64955f9a5a75f97334923948d147acb54d /src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp | |
parent | d03c111cbb3329018d72c7ed8bea2d7ac9a57045 (diff) |
Add distance matrix rips construction (doc, code, test)
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/distance_matrix_in_rips_module@1766 636b058d-ea47-450e-bf9e-a15bfbe3eedb
Former-commit-id: 6b9bdecbaf0aca12facb023e66bdea71e8e8cd38
Diffstat (limited to 'src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp')
-rw-r--r-- | src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp | 72 |
1 files changed, 72 insertions, 0 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 new file mode 100644 index 00000000..cfada84a --- /dev/null +++ b/src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp @@ -0,0 +1,72 @@ +#include <gudhi/Rips_complex.h> +// to construct Rips_complex from a OFF file of points +#include <gudhi/reader_utils.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.csv threshold dim_max [ouput_file.txt]\n"; + std::cerr << " i.e.: " << progName << " ../../data/distance_matrix/full_square_distance_matrix.csv 1.0 3\n"; + exit(-1); // ----- >> +} + +int main(int argc, char **argv) { + if ((argc != 4) && (argc != 5)) usage(argc, (argv[0] - 1)); + + std::string csv_file_name(argv[1]); + double threshold = atof(argv[2]); + int dim_max = atoi(argv[3]); + + // Type definitions + using Simplex_tree = Gudhi::Simplex_tree<>; + using Filtration_value = Simplex_tree::Filtration_value; + using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>; + using Distance_matrix = std::vector<std::vector<Filtration_value>>; + + // ---------------------------------------------------------------------------- + // Init of a rips complex from a distance matrix in a csv file + // Default separator is ';' + // ---------------------------------------------------------------------------- + Distance_matrix distances = read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_file_name); + Rips_complex rips_complex_from_file(distances, threshold); + + 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; +} |