diff options
Diffstat (limited to 'src/common/include')
| -rw-r--r-- | src/common/include/gudhi/reader_utils.h | 78 |
1 files changed, 76 insertions, 2 deletions
diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h index 97a87edd..f1684d78 100644 --- a/src/common/include/gudhi/reader_utils.h +++ b/src/common/include/gudhi/reader_utils.h @@ -2,7 +2,7 @@ * (Geometric Understanding in Higher Dimensions) is a generic C++ * library for computational topology. * - * Author(s): Clement Maria, Pawel Dlotko + * Author(s): Clement Maria, Pawel Dlotko, Clement Jamin * * Copyright (C) 2014 INRIA * @@ -24,7 +24,9 @@ #define READER_UTILS_H_ #include <gudhi/graph_simplicial_complex.h> +#include <gudhi/Debug_utils.h> +#include <boost/function_output_iterator.hpp> #include <boost/graph/adjacency_list.hpp> #include <iostream> @@ -92,7 +94,10 @@ template< typename Graph_t, typename Filtration_value, typename Vertex_handle > Graph_t read_graph(std::string file_name) { std::ifstream in_(file_name.c_str(), std::ios::in); if (!in_.is_open()) { - std::cerr << "Unable to open file " << file_name << std::endl; + std::string error_str("read_graph - Unable to open file "); + error_str.append(file_name); + std::cerr << error_str << std::endl; + throw std::invalid_argument(error_str); } typedef std::pair< Vertex_handle, Vertex_handle > Edge_t; @@ -295,4 +300,73 @@ std::vector< std::vector< Filtration_value > > read_lower_triangular_matrix_from return result; } // read_lower_triangular_matrix_from_csv_file +/** +Reads a file containing persistence intervals. +Each line might contain 2, 3 or 4 values: [[field] dimension] birth death +The output iterator `out` is used this way: `*out++ = std::make_tuple(dim, birth, death);` +where `dim` is an `int`, `birth` a `double`, and `death` a `double`. +Note: the function does not check that birth <= death. +**/ +template <typename OutputIterator> +void read_persistence_intervals_and_dimension(std::string const& filename, OutputIterator out) { + + std::ifstream in(filename); + if (!in.is_open()) { + std::string error_str("read_persistence_intervals_and_dimension - Unable to open file "); + error_str.append(filename); + std::cerr << error_str << std::endl; + throw std::invalid_argument(error_str); + } + + while (!in.eof()) { + std::string line; + getline(in, line); + if (line.length() != 0 && line[0] != '#') { + double numbers[4]; + int n = sscanf(line.c_str(), "%lf %lf %lf %lf", &numbers[0], &numbers[1], &numbers[2], &numbers[3]); + if (n >= 2) { + //int field = (n == 4 ? static_cast<int>(numbers[0]) : -1); + int dim = (n >= 3 ? static_cast<int>(numbers[n - 3]) : -1); + *out++ = std::make_tuple(dim, numbers[n - 2], numbers[n - 1]); + } + } + } +} // read_persistence_diagram_from_file + +/** +Reads a file containing persistence intervals. +Each line might contain 2, 3 or 4 values: [[field] dimension] birth death +The return value is an `std::map<dim, std::vector<std::pair<birth, death>>>` +where `dim` is an `int`, `birth` a `double`, and `death` a `double`. +Note: the function does not check that birth <= death. +**/ +inline std::map<int, std::vector<std::pair<double, double>>> read_persistence_intervals_grouped_by_dimension(std::string const& filename) { + + std::map<int, std::vector<std::pair<double, double>>> ret; + read_persistence_intervals_and_dimension( + filename, + boost::make_function_output_iterator([&ret](std::tuple<int, double, double> t) { ret[get<0>(t)].push_back(std::make_pair(get<1>(t), get<2>(t))); })); + return ret; +} // read_persistence_diagram_from_file + + +/** +Reads a file containing persistence intervals. +Each line might contain 2, 3 or 4 values: [[field] dimension] birth death +If `only_this_dim` = -1, dimension is ignored and all lines are returned. +If `only_this_dim` is >= 0, only the lines where dimension = `only_this_dim` +(or where dimension is not specified) are returned. +The return value is an `std::vector<std::pair<birth, death>>` +where `dim` is an `int`, `birth` a `double`, and `death` a `double`. +Note: the function does not check that birth <= death. +**/ +inline std::vector<std::pair<double, double>> read_persistence_intervals_in_dimension(std::string const& filename, int only_this_dim = -1) { + + std::vector<std::pair<double, double>> ret; + read_persistence_intervals_and_dimension( + filename, + boost::make_function_output_iterator([&ret](std::tuple<int, double, double> t) { ret.emplace_back(get<1>(t), get<2>(t)); })); + return ret; +} // read_persistence_diagram_from_file + #endif // READER_UTILS_H_ |