From 1129608c2add6f15538b3e281d75119f0e1bc8b0 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 8 Aug 2017 12:48:40 +0000 Subject: Fix bug in read_persistence_intervals_in_dimension for only_this_dim Add unitary tests for read_persistence Add .clang-format to clang format new files git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2601 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 28e870973f9ebd686d503246202fa6d6a549e9e3 --- src/common/include/gudhi/reader_utils.h | 93 +++++++++++++++------------------ 1 file changed, 43 insertions(+), 50 deletions(-) (limited to 'src/common/include') diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h index f1684d78..bda93f4f 100644 --- a/src/common/include/gudhi/reader_utils.h +++ b/src/common/include/gudhi/reader_utils.h @@ -1,5 +1,5 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ * library for computational topology. * * Author(s): Clement Maria, Pawel Dlotko, Clement Jamin @@ -36,6 +36,7 @@ #include #include #include // for pair +#include // for std::make_tuple // Keep this file tag for Doxygen to parse the code, otherwise, functions are not documented. // It is required for global functions and variables. @@ -52,7 +53,7 @@ * X21 X22 ... X2d
* etc
*/ -inline void read_points(std::string file_name, std::vector< std::vector< double > > & points) { +inline void read_points(std::string file_name, std::vector>& points) { std::ifstream in_file(file_name.c_str(), std::ios::in); if (!in_file.is_open()) { std::cerr << "Unable to open file " << file_name << std::endl; @@ -62,14 +63,13 @@ inline void read_points(std::string file_name, std::vector< std::vector< double std::string line; double x; while (getline(in_file, line)) { - std::vector< double > point; + std::vector point; std::istringstream iss(line); while (iss >> x) { point.push_back(x); } // Check for empty lines - if (!point.empty()) - points.push_back(point); + if (!point.empty()) points.push_back(point); } in_file.close(); } @@ -90,7 +90,7 @@ inline void read_points(std::string file_name, std::vector< std::vector< double * Every simplex must appear exactly once. * Simplices of dimension more than 1 are ignored. */ -template< typename Graph_t, typename Filtration_value, typename Vertex_handle > +template Graph_t read_graph(std::string file_name) { std::ifstream in_(file_name.c_str(), std::ios::in); if (!in_.is_open()) { @@ -100,10 +100,10 @@ Graph_t read_graph(std::string file_name) { throw std::invalid_argument(error_str); } - typedef std::pair< Vertex_handle, Vertex_handle > Edge_t; - std::vector< Edge_t > edges; - std::vector< Filtration_value > edges_fil; - std::map< Vertex_handle, Filtration_value > vertices; + typedef std::pair Edge_t; + std::vector edges; + std::vector edges_fil; + std::map vertices; std::string line; int dim; @@ -113,8 +113,7 @@ Graph_t read_graph(std::string file_name) { std::istringstream iss(line); while (iss >> dim) { switch (dim) { - case 0: - { + case 0: { iss >> u; iss >> fil; vertices[u] = fil; @@ -123,8 +122,7 @@ Graph_t read_graph(std::string file_name) { } break; } - case 1: - { + case 1: { iss >> u; iss >> v; iss >> fil; @@ -132,16 +130,13 @@ Graph_t read_graph(std::string file_name) { edges_fil.push_back(fil); break; } - default: - { - break; - } + default: { break; } } } } in_.close(); - if ((size_t) (max_h + 1) != vertices.size()) { + if ((size_t)(max_h + 1) != vertices.size()) { std::cerr << "Error: vertices must be labeled from 0 to n-1 \n"; } @@ -169,8 +164,8 @@ Graph_t read_graph(std::string file_name) { * Every simplex must appear exactly once. * Simplices of dimension more than 1 are ignored. */ -template< typename Vertex_handle, typename Filtration_value > -bool read_simplex(std::istream & in_, std::vector< Vertex_handle > & simplex, Filtration_value & fil) { +template +bool read_simplex(std::istream& in_, std::vector& simplex, Filtration_value& fil) { int dim = 0; if (!(in_ >> dim)) return false; Vertex_handle v; @@ -194,8 +189,8 @@ bool read_simplex(std::istream & in_, std::vector< Vertex_handle > & simplex, Fi * The key of a simplex is its position in the filtration order and also the number of its row in the file. * Dimi ki1 ki2 ... kiDimi Fili means that the ith simplex in the filtration has dimension Dimi, filtration value * fil1 and simplices with key ki1 ... kiDimi in its boundary.*/ -template< typename Simplex_key, typename Filtration_value > -bool read_hasse_simplex(std::istream & in_, std::vector< Simplex_key > & boundary, Filtration_value & fil) { +template +bool read_hasse_simplex(std::istream& in_, std::vector& boundary, Filtration_value& fil) { int dim; if (!(in_ >> dim)) return false; if (dim == 0) { @@ -214,7 +209,7 @@ bool read_hasse_simplex(std::istream & in_, std::vector< Simplex_key > & boundar /** * @brief Read a lower triangular distance matrix from a csv file. We assume that the .csv store the whole * (square) matrix. - * + * * @author Pawel Dlotko * * Square matrix file format:
@@ -231,13 +226,13 @@ bool read_hasse_simplex(std::istream & in_, std::vector< Simplex_key > & boundar * Dj1;Dj2;...;Dj(j-1);
* **/ -template< typename Filtration_value > -std::vector< std::vector< Filtration_value > > read_lower_triangular_matrix_from_csv_file(const std::string& filename, - const char separator = ';') { +template +std::vector> read_lower_triangular_matrix_from_csv_file(const std::string& filename, + const char separator = ';') { #ifdef DEBUG_TRACES std::cout << "Using procedure read_lower_triangular_matrix_from_csv_file \n"; #endif // DEBUG_TRACES - std::vector< std::vector< Filtration_value > > result; + std::vector> result; std::ifstream in; in.open(filename.c_str()); if (!in.is_open()) { @@ -248,7 +243,7 @@ std::vector< std::vector< Filtration_value > > read_lower_triangular_matrix_from // the first line is emtpy, so we ignore it: std::getline(in, line); - std::vector< Filtration_value > values_in_this_line; + std::vector values_in_this_line; result.push_back(values_in_this_line); int number_of_line = 0; @@ -256,11 +251,10 @@ std::vector< std::vector< Filtration_value > > read_lower_triangular_matrix_from // first, read the file line by line to a string: while (std::getline(in, line)) { // if line is empty, break - if (line.size() == 0) - break; + if (line.size() == 0) break; // if the last element of a string is comma: - if (line[ line.size() - 1 ] == separator) { + if (line[line.size() - 1] == separator) { // then shrink the string by one line.pop_back(); } @@ -273,7 +267,7 @@ std::vector< std::vector< Filtration_value > > read_lower_triangular_matrix_from // and now read the doubles. int number_of_entry = 0; - std::vector< Filtration_value > values_in_this_line; + std::vector values_in_this_line; while (iss.good()) { double entry; iss >> entry; @@ -282,7 +276,7 @@ std::vector< std::vector< Filtration_value > > read_lower_triangular_matrix_from } ++number_of_entry; } - if (!values_in_this_line.empty())result.push_back(values_in_this_line); + if (!values_in_this_line.empty()) result.push_back(values_in_this_line); ++number_of_line; } in.close(); @@ -309,7 +303,6 @@ Note: the function does not check that birth <= death. **/ template 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 "); @@ -325,13 +318,12 @@ void read_persistence_intervals_and_dimension(std::string const& filename, Outpu 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(numbers[0]) : -1); int dim = (n >= 3 ? static_cast(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. @@ -340,33 +332,34 @@ The return value is an `std::map>>` where `dim` is an `int`, `birth` a `double`, and `death` a `double`. Note: the function does not check that birth <= death. **/ -inline std::map>> read_persistence_intervals_grouped_by_dimension(std::string const& filename) { - +inline std::map>> read_persistence_intervals_grouped_by_dimension( + std::string const& filename) { std::map>> ret; read_persistence_intervals_and_dimension( - filename, - boost::make_function_output_iterator([&ret](std::tuple t) { ret[get<0>(t)].push_back(std::make_pair(get<1>(t), get<2>(t))); })); + filename, boost::make_function_output_iterator([&ret](std::tuple 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` +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>` where `dim` is an `int`, `birth` a `double`, and `death` a `double`. Note: the function does not check that birth <= death. **/ -inline std::vector> read_persistence_intervals_in_dimension(std::string const& filename, int only_this_dim = -1) { - +inline std::vector> read_persistence_intervals_in_dimension(std::string const& filename, + int only_this_dim = -1) { std::vector> ret; read_persistence_intervals_and_dimension( - filename, - boost::make_function_output_iterator([&ret](std::tuple t) { ret.emplace_back(get<1>(t), get<2>(t)); })); + filename, boost::make_function_output_iterator([only_this_dim, &ret](std::tuple t) { + if (only_this_dim == get<0>(t) || only_this_dim == -1) ret.emplace_back(get<1>(t), get<2>(t)); + })); return ret; -} // read_persistence_diagram_from_file +} #endif // READER_UTILS_H_ -- cgit v1.2.3