diff options
Diffstat (limited to 'src/common')
| -rw-r--r-- | src/common/doc/main_page.h | 48 | ||||
| -rw-r--r-- | src/common/example/example_CGAL_3D_points_off_reader.cpp | 2 | ||||
| -rw-r--r-- | src/common/example/example_CGAL_points_off_reader.cpp | 2 | ||||
| -rw-r--r-- | src/common/include/gudhi/distance_functions.h | 34 | ||||
| -rw-r--r-- | src/common/include/gudhi/graph_simplicial_complex.h | 59 | ||||
| -rw-r--r-- | src/common/include/gudhi/reader_utils.h | 166 | ||||
| -rw-r--r-- | src/common/test/CMakeLists.txt | 9 | ||||
| -rw-r--r-- | src/common/test/test_distance_matrix_reader.cpp | 85 | ||||
| -rw-r--r-- | src/common/test/test_points_off_reader.cpp | 2 |
9 files changed, 288 insertions, 119 deletions
diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h index 5fb75002..116aba09 100644 --- a/src/common/doc/main_page.h +++ b/src/common/doc/main_page.h @@ -56,6 +56,24 @@ <b>User manual:</b> \ref cubical_complex - <b>Reference manual:</b> Gudhi::cubical_complex::Bitmap_cubical_complex </td> </tr> + \subsection RipsComplexDataStructure Rips complex + \image html "rips_complex_representation.png" "Rips complex representation" +<table border="0"> + <tr> + <td width="25%"> + <b>Author:</b> Clément Maria, Pawel Dlotko, Vincent Rouvreau<br> + <b>Introduced in:</b> GUDHI 1.4.0<br> + <b>Copyright:</b> GPL v3<br> + </td> + <td width="75%"> + Rips_complex is a simplicial complex constructed from a one skeleton graph.<br> + The filtration value of each edge is computed from a user-given distance function and is inserted until a + user-given threshold value.<br> + This complex can be built from a point cloud and a distance function, or from a distance matrix.<br> + <b>User manual:</b> \ref rips_complex - <b>Reference manual:</b> Gudhi::rips_complex::Rips_complex + </td> + </tr> +</table> </table> \subsection SimplexTreeDataStructure Simplex tree \image html "Simplex_tree_representation.png" "Simplex tree representation" @@ -223,8 +241,6 @@ make \endverbatim * * The following example requires the <a target="_blank" href="http://gmplib.org/">GNU Multiple Precision Arithmetic * Library</a> (GMP) and will not be built if GMP is not installed: - * \li <a href="_persistent_cohomology_2performance_rips_persistence_8cpp-example.html"> - * Persistent_cohomology/performance_rips_persistence.cpp</a> * \li <a href="_persistent_cohomology_2rips_multifield_persistence_8cpp-example.html"> * Persistent_cohomology/rips_multifield_persistence.cpp</a> * @@ -261,9 +277,11 @@ make \endverbatim * Persistent_cohomology/custom_persistence_sort.cpp</a> * * The following example requires CGAL version ≥ 4.8.0: - * \li <a href="_bottleneck_distance_2_bottleneck_example_8cpp-example.html"> - * - * Bottleneck_distance/bottleneck_example.cpp</a> + * \li <a href="_bottleneck_distance_2_bottleneck_basic_example_8cpp-example.html"> + * Bottleneck_distance/bottleneck_basic_example.cpp</a> + * \li <a href="_bottleneck_distance_2_bottleneck_read_file_example_8cpp-example.html"> + * Bottleneck_distance/bottleneck_read_file_example.cpp</a> + * * \subsection eigen3 Eigen3 * The \ref alpha_complex data structure and few examples requires * <a target="_blank" href="http://eigen.tuxfamily.org/">Eigen3</a> is a C++ template library for linear algebra: @@ -275,8 +293,6 @@ make \endverbatim * Alpha_complex/Alpha_complex_from_off.cpp</a> * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html"> * Alpha_complex/Alpha_complex_from_points.cpp</a> - * \li <a href="_bottleneck_distance_2_bottleneck_example_8cpp-example.html"> - * Bottleneck_distance/bottleneck_example.cpp</a> * \li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html"> * Persistent_cohomology/alpha_complex_persistence.cpp</a> * \li <a href="_persistent_cohomology_2periodic_alpha_complex_3d_persistence_8cpp-example.html"> @@ -318,22 +334,28 @@ make \endverbatim * Persistent_cohomology/alpha_complex_persistence.cpp</a> * \li <a href="_persistent_cohomology_2rips_persistence_via_boundary_matrix_8cpp-example.html"> * Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp</a> - * \li <a href="_persistent_cohomology_2performance_rips_persistence_8cpp-example.html"> - * Persistent_cohomology/performance_rips_persistence.cpp</a> * \li <a href="_persistent_cohomology_2persistence_from_file_8cpp-example.html"> * Persistent_cohomology/persistence_from_file.cpp</a> * \li <a href="_persistent_cohomology_2persistence_from_simple_simplex_tree_8cpp-example.html"> * Persistent_cohomology/persistence_from_simple_simplex_tree.cpp</a> * \li <a href="_persistent_cohomology_2plain_homology_8cpp-example.html"> * Persistent_cohomology/plain_homology.cpp</a> + * \li <a href="_persistent_cohomology_2rips_distance_matrix_persistence_8cpp-example.html"> + * Persistent_cohomology/rips_distance_matrix_persistence.cpp</a> * \li <a href="_persistent_cohomology_2rips_multifield_persistence_8cpp-example.html"> * Persistent_cohomology/rips_multifield_persistence.cpp</a> * \li <a href="_persistent_cohomology_2rips_persistence_8cpp-example.html"> * Persistent_cohomology/rips_persistence.cpp</a> + * \li <a href="_persistent_cohomology_2rips_persistence_step_by_step_8cpp-example.html"> + * Persistent_cohomology/rips_persistence_step_by_step.cpp</a> * \li <a href="_persistent_cohomology_2periodic_alpha_complex_3d_persistence_8cpp-example.html"> * Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp</a> * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html"> * Persistent_cohomology/custom_persistence_sort.cpp</a> + * \li <a href="_rips_complex_2example_one_skeleton_rips_from_points_8cpp-example.html"> + * Rips_complex/example_one_skeleton_rips_from_points.cpp</a> + * \li <a href="_rips_complex_2example_rips_complex_from_off_file_8cpp-example.html"> + * Rips_complex/example_rips_complex_from_off_file.cpp</a> * * \section Contributions Bug reports and contributions * Please help us improving the quality of the GUDHI library. You may report bugs or suggestions to: @@ -358,7 +380,8 @@ make \endverbatim /*! @file Examples * @example Alpha_complex/Alpha_complex_from_off.cpp * @example Alpha_complex/Alpha_complex_from_points.cpp - * @example Bottleneck_distance/bottleneck_example.cpp + * @example Bottleneck_distance/bottleneck_basic_example.cpp + * @example Bottleneck_distance/bottleneck_read_file_example.cpp * @example Bitmap_cubical_complex/Bitmap_cubical_complex.cpp * @example Bitmap_cubical_complex/Bitmap_cubical_complex_periodic_boundary_conditions.cpp * @example Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp @@ -369,14 +392,17 @@ make \endverbatim * @example Persistent_cohomology/alpha_complex_3d_persistence.cpp * @example Persistent_cohomology/alpha_complex_persistence.cpp * @example Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp - * @example Persistent_cohomology/performance_rips_persistence.cpp * @example Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp * @example Persistent_cohomology/persistence_from_file.cpp * @example Persistent_cohomology/persistence_from_simple_simplex_tree.cpp * @example Persistent_cohomology/plain_homology.cpp * @example Persistent_cohomology/rips_multifield_persistence.cpp + * @example Persistent_cohomology/rips_distance_matrix_persistence.cpp * @example Persistent_cohomology/rips_persistence.cpp * @example Persistent_cohomology/custom_persistence_sort.cpp + * @example Persistent_cohomology/rips_persistence_step_by_step.cpp + * @example Rips_complex/example_one_skeleton_rips_from_points.cpp + * @example Rips_complex/example_rips_complex_from_off_file.cpp * @example Simplex_tree/mini_simplex_tree.cpp * @example Simplex_tree/simple_simplex_tree.cpp * @example Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp diff --git a/src/common/example/example_CGAL_3D_points_off_reader.cpp b/src/common/example/example_CGAL_3D_points_off_reader.cpp index d48bb17d..665b7a29 100644 --- a/src/common/example/example_CGAL_3D_points_off_reader.cpp +++ b/src/common/example/example_CGAL_3D_points_off_reader.cpp @@ -32,7 +32,7 @@ int main(int argc, char **argv) { // Retrieve the triangulation std::vector<Point_3> point_cloud = off_reader.get_point_cloud(); - int n {0}; + int n {}; for (auto point : point_cloud) { ++n; std::cout << "Point[" << n << "] = (" << point[0] << ", " << point[1] << ", " << point[2] << ")\n"; diff --git a/src/common/example/example_CGAL_points_off_reader.cpp b/src/common/example/example_CGAL_points_off_reader.cpp index 4522174a..8c6a6b54 100644 --- a/src/common/example/example_CGAL_points_off_reader.cpp +++ b/src/common/example/example_CGAL_points_off_reader.cpp @@ -34,7 +34,7 @@ int main(int argc, char **argv) { // Retrieve the triangulation std::vector<Point_d> point_cloud = off_reader.get_point_cloud(); - int n {0}; + int n {}; for (auto point : point_cloud) { std::cout << "Point[" << n << "] = "; for (std::size_t i {0}; i < point.size(); i++) diff --git a/src/common/include/gudhi/distance_functions.h b/src/common/include/gudhi/distance_functions.h index cd518581..5891ef0e 100644 --- a/src/common/include/gudhi/distance_functions.h +++ b/src/common/include/gudhi/distance_functions.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 INRIA * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -25,19 +25,25 @@ #include <cmath> // for std::sqrt -/* Compute the Euclidean distance between two Points given - * by a range of coordinates. The points are assumed to have - * the same dimension. */ -template< typename Point > -double euclidean_distance(Point &p1, Point &p2) { - double dist = 0.; - auto it1 = p1.begin(); - auto it2 = p2.begin(); - for (; it1 != p1.end(); ++it1, ++it2) { - double tmp = *it1 - *it2; - dist += tmp*tmp; +/** @file + * @brief Global distance functions + */ + +/** @brief Compute the Euclidean distance between two Points given by a range of coordinates. The points are assumed to + * have the same dimension. */ +class Euclidean_distance { + public: + template< typename Point > + auto operator()(const Point& p1, const Point& p2) -> typename std::decay<decltype(*std::begin(p1))>::type { + auto it1 = p1.begin(); + auto it2 = p2.begin(); + typename Point::value_type dist = 0.; + for (; it1 != p1.end(); ++it1, ++it2) { + typename Point::value_type tmp = (*it1) - (*it2); + dist += tmp*tmp; + } + return std::sqrt(dist); } - return std::sqrt(dist); -} +}; #endif // DISTANCE_FUNCTIONS_H_ diff --git a/src/common/include/gudhi/graph_simplicial_complex.h b/src/common/include/gudhi/graph_simplicial_complex.h index 042ef516..5fe7c826 100644 --- a/src/common/include/gudhi/graph_simplicial_complex.h +++ b/src/common/include/gudhi/graph_simplicial_complex.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 INRIA * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -39,61 +39,4 @@ struct vertex_filtration_t { typedef boost::vertex_property_tag kind; }; -typedef int Vertex_handle; -typedef double Filtration_value; -typedef boost::adjacency_list < boost::vecS, boost::vecS, boost::undirectedS -, boost::property < vertex_filtration_t, Filtration_value > -, boost::property < edge_filtration_t, Filtration_value > -> Graph_t; -typedef std::pair< Vertex_handle, Vertex_handle > Edge_t; - -/** \brief Output the proximity graph of the points. - * - * If points contains n elements, the proximity graph is the graph - * with n vertices, and an edge [u,v] iff the distance function between - * points u and v is smaller than threshold. - * - * The type PointCloud furnishes .begin() and .end() methods, that return - * iterators with value_type Point. - */ -template< typename PointCloud -, typename Point > -Graph_t compute_proximity_graph(PointCloud &points - , Filtration_value threshold - , Filtration_value distance(Point p1, Point p2)) { - std::vector< Edge_t > edges; - std::vector< Filtration_value > edges_fil; - std::map< Vertex_handle, Filtration_value > vertices; - - Vertex_handle idx_u, idx_v; - Filtration_value fil; - idx_u = 0; - for (auto it_u = points.begin(); it_u != points.end(); ++it_u) { - idx_v = idx_u + 1; - for (auto it_v = it_u + 1; it_v != points.end(); ++it_v, ++idx_v) { - fil = distance(*it_u, *it_v); - if (fil <= threshold) { - edges.emplace_back(idx_u, idx_v); - edges_fil.push_back(fil); - } - } - ++idx_u; - } - - Graph_t skel_graph(edges.begin() - , edges.end() - , edges_fil.begin() - , idx_u); // number of points labeled from 0 to idx_u-1 - - auto vertex_prop = boost::get(vertex_filtration_t(), skel_graph); - - boost::graph_traits<Graph_t>::vertex_iterator vi, vi_end; - for (std::tie(vi, vi_end) = boost::vertices(skel_graph); - vi != vi_end; ++vi) { - boost::put(vertex_prop, *vi, 0.); - } - - return skel_graph; -} - #endif // GRAPH_SIMPLICIAL_COMPLEX_H_ diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h index 899f9df6..97a87edd 100644 --- a/src/common/include/gudhi/reader_utils.h +++ b/src/common/include/gudhi/reader_utils.h @@ -2,9 +2,9 @@ * (Geometric Understanding in Higher Dimensions) is a generic C++ * library for computational topology. * - * Author(s): Clément Maria + * Author(s): Clement Maria, Pawel Dlotko * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 INRIA * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -30,18 +30,25 @@ #include <iostream> #include <fstream> #include <map> -#include <limits> // for numeric_limits<> +#include <limits> // for numeric_limits #include <string> #include <vector> +#include <utility> // for pair + +// Keep this file tag for Doxygen to parse the code, otherwise, functions are not documented. +// It is required for global functions and variables. + +/** @file + * @brief This file includes common file reader for GUDHI + */ /** - * \brief Read a set of points to turn it - * into a vector< vector<double> > by filling points + * @brief Read a set of points to turn it into a vector< vector<double> > by filling points. * - * File format: 1 point per line - * X11 X12 ... X1d - * X21 X22 ... X2d - * etc + * File format: 1 point per line<br> + * X11 X12 ... X1d<br> + * X21 X22 ... X2d<br> + * etc<br> */ inline void read_points(std::string file_name, std::vector< std::vector< double > > & points) { std::ifstream in_file(file_name.c_str(), std::ios::in); @@ -66,23 +73,29 @@ inline void read_points(std::string file_name, std::vector< std::vector< double } /** - * \brief Read a graph from a file. + * @brief Read a graph from a file. + * + * \tparam Graph_t Type for the return graph. Must be constructible from iterators on pairs of Vertex_handle + * \tparam Filtration_value Type for the value of the read filtration + * \tparam Vertex_handle Type for the value of the read vertices * - * File format: 1 simplex per line - * Dim1 X11 X12 ... X1d Fil1 - * Dim2 X21 X22 ... X2d Fil2 - * etc + * File format: 1 simplex per line<br> + * Dim1 X11 X12 ... X1d Fil1<br> + * Dim2 X21 X22 ... X2d Fil2<br> + * etc<br> * * The vertices must be labeled from 0 to n-1. * Every simplex must appear exactly once. * Simplices of dimension more than 1 are ignored. */ -inline Graph_t read_graph(std::string file_name) { +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; } + 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; @@ -130,7 +143,7 @@ inline Graph_t read_graph(std::string file_name) { Graph_t skel_graph(edges.begin(), edges.end(), edges_fil.begin(), vertices.size()); auto vertex_prop = boost::get(vertex_filtration_t(), skel_graph); - boost::graph_traits<Graph_t>::vertex_iterator vi, vi_end; + typename boost::graph_traits<Graph_t>::vertex_iterator vi, vi_end; auto v_it = vertices.begin(); for (std::tie(vi, vi_end) = boost::vertices(skel_graph); vi != vi_end; ++vi, ++v_it) { boost::put(vertex_prop, *vi, v_it->second); @@ -140,12 +153,12 @@ inline Graph_t read_graph(std::string file_name) { } /** - * \brief Read a face from a file. + * @brief Read a face from a file. * - * File format: 1 simplex per line - * Dim1 X11 X12 ... X1d Fil1 - * Dim2 X21 X22 ... X2d Fil2 - * etc + * File format: 1 simplex per line<br> + * Dim1 X11 X12 ... X1d Fil1<br> + * Dim2 X21 X22 ... X2d Fil2<br> + * etc<br> * * The vertices must be labeled from 0 to n-1. * Every simplex must appear exactly once. @@ -166,18 +179,16 @@ bool read_simplex(std::istream & in_, std::vector< Vertex_handle > & simplex, Fi } /** - * \brief Read a hasse simplex from a file. - * - * File format: 1 simplex per line - * Dim1 k11 k12 ... k1Dim1 Fil1 - * Dim2 k21 k22 ... k2Dim2 Fil2 - * etc - * - * 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.*/ + * @brief Read a hasse simplex from a file. + * + * File format: 1 simplex per line<br> + * Dim1 k11 k12 ... k1Dim1 Fil1<br> + * Dim2 k21 k22 ... k2Dim2 Fil2<br> + * etc<br> + * + * 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) { int dim; @@ -195,4 +206,93 @@ bool read_hasse_simplex(std::istream & in_, std::vector< Simplex_key > & boundar return true; } +/** + * @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:<br> + * 0;D12;...;D1j<br> + * D21;0;...;D2j<br> + * ...<br> + * Dj1;Dj2;...;0<br> + * + * lower matrix file format:<br> + * 0<br> + * D21;<br> + * D31;D32;<br> + * ...<br> + * Dj1;Dj2;...;Dj(j-1);<br> + * + **/ +template< typename Filtration_value > +std::vector< std::vector< Filtration_value > > 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::ifstream in; + in.open(filename.c_str()); + if (!in.is_open()) { + return result; + } + + std::string line; + + // the first line is emtpy, so we ignore it: + std::getline(in, line); + std::vector< Filtration_value > values_in_this_line; + result.push_back(values_in_this_line); + + int number_of_line = 0; + + // 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 the last element of a string is comma: + if (line[ line.size() - 1 ] == separator) { + // then shrink the string by one + line.pop_back(); + } + + // replace all commas with spaces + std::replace(line.begin(), line.end(), separator, ' '); + + // put the new line to a stream + std::istringstream iss(line); + // and now read the doubles. + + int number_of_entry = 0; + std::vector< Filtration_value > values_in_this_line; + while (iss.good()) { + double entry; + iss >> entry; + if (number_of_entry <= number_of_line) { + values_in_this_line.push_back(entry); + } + ++number_of_entry; + } + if (!values_in_this_line.empty())result.push_back(values_in_this_line); + ++number_of_line; + } + in.close(); + +#ifdef DEBUG_TRACES + std::cerr << "Here is the matrix we read : \n"; + for (size_t i = 0; i != result.size(); ++i) { + for (size_t j = 0; j != result[i].size(); ++j) { + std::cerr << result[i][j] << " "; + } + std::cerr << std::endl; + } +#endif // DEBUG_TRACES + + return result; +} // read_lower_triangular_matrix_from_csv_file + #endif // READER_UTILS_H_ diff --git a/src/common/test/CMakeLists.txt b/src/common/test/CMakeLists.txt index 7ccdb752..baa24539 100644 --- a/src/common/test/CMakeLists.txt +++ b/src/common/test/CMakeLists.txt @@ -13,12 +13,21 @@ endif() add_executable ( poffreader_UT test_points_off_reader.cpp ) target_link_libraries(poffreader_UT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) +add_executable ( distancematrixreader_UT test_distance_matrix_reader.cpp ) +target_link_libraries(distancematrixreader_UT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) + # Do not forget to copy test files in current binary dir file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) +file(COPY "${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) +file(COPY "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) # Unitary tests add_test(poffreader_UT ${CMAKE_CURRENT_BINARY_DIR}/poffreader_UT # XML format for Jenkins xUnit plugin --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/poffreader_UT.xml --log_level=test_suite --report_level=no) +add_test(distancematrixreader_UT ${CMAKE_CURRENT_BINARY_DIR}/distancematrixreader_UT + # XML format for Jenkins xUnit plugin + --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/distancematrixreader_UT.xml --log_level=test_suite --report_level=no) + diff --git a/src/common/test/test_distance_matrix_reader.cpp b/src/common/test/test_distance_matrix_reader.cpp new file mode 100644 index 00000000..95a73bd9 --- /dev/null +++ b/src/common/test/test_distance_matrix_reader.cpp @@ -0,0 +1,85 @@ +/* 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): Vincent Rouvreau + * + * Copyright (C) 2016 INRIA + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +#include <gudhi/reader_utils.h> + +#include <iostream> +#include <string> +#include <vector> + +#define BOOST_TEST_DYN_LINK +#define BOOST_TEST_MODULE "distance_matrix_reader" +#include <boost/test/unit_test.hpp> + +using Distance_matrix = std::vector<std::vector<double>>; + +BOOST_AUTO_TEST_CASE( lower_triangular_distance_matrix ) +{ + Distance_matrix from_lower_triangular; + // Read lower_triangular_distance_matrix.csv file where the separator is a ',' + from_lower_triangular = read_lower_triangular_matrix_from_csv_file<double>("lower_triangular_distance_matrix.csv", + ','); + for (auto& i : from_lower_triangular) { + for (auto j : i) { + std::cout << j << " "; + } + std::cout << std::endl; + } + std::cout << "from_lower_triangular size = " << from_lower_triangular.size() << std::endl; + BOOST_CHECK(from_lower_triangular.size() == 5); + + for (std::size_t i = 0; i < from_lower_triangular.size(); i++) { + std::cout << "from_lower_triangular[" << i << "] size = " << from_lower_triangular[i].size() << std::endl; + BOOST_CHECK(from_lower_triangular[i].size() == i); + } + std::vector<double> expected = {1}; + BOOST_CHECK(from_lower_triangular[1] == expected); + + expected = {2,3}; + BOOST_CHECK(from_lower_triangular[2] == expected); + + expected = {4,5,6}; + BOOST_CHECK(from_lower_triangular[3] == expected); + + expected = {7,8,9,10}; + BOOST_CHECK(from_lower_triangular[4] == expected); + +} + +BOOST_AUTO_TEST_CASE( full_square_distance_matrix ) +{ + Distance_matrix from_full_square; + // Read full_square_distance_matrix.csv file where the separator is the default one ';' + from_full_square = read_lower_triangular_matrix_from_csv_file<double>("full_square_distance_matrix.csv"); + for (auto& i : from_full_square) { + for (auto j : i) { + std::cout << j << " "; + } + std::cout << std::endl; + } + std::cout << "from_full_square size = " << from_full_square.size() << std::endl; + BOOST_CHECK(from_full_square.size() == 7); + for (std::size_t i = 0; i < from_full_square.size(); i++) { + std::cout << "from_full_square[" << i << "] size = " << from_full_square[i].size() << std::endl; + BOOST_CHECK(from_full_square[i].size() == i); + } +} diff --git a/src/common/test/test_points_off_reader.cpp b/src/common/test/test_points_off_reader.cpp index b4f71182..0a78d190 100644 --- a/src/common/test/test_points_off_reader.cpp +++ b/src/common/test/test_points_off_reader.cpp @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2015 INRIA Saclay (France) + * Copyright (C) 2015 * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by |