diff options
77 files changed, 3046 insertions, 1237 deletions
diff --git a/data/persistence_diagram/simple_diagram.txt b/data/persistence_diagram/simple_diagram.txt deleted file mode 100644 index 2f199fd4..00000000 --- a/data/persistence_diagram/simple_diagram.txt +++ /dev/null @@ -1,4 +0,0 @@ -1 2 -3 4 -5 6 -7 8
\ No newline at end of file diff --git a/data/points/KleinBottle5D.off b/data/points/KleinBottle5D.off index b578593c..b578593c 100755..100644 --- a/data/points/KleinBottle5D.off +++ b/data/points/KleinBottle5D.off diff --git a/data/points/human.off b/data/points/human.off index f9f79a3f..f9f79a3f 100755..100644 --- a/data/points/human.off +++ b/data/points/human.off diff --git a/data/points/iso_cuboid_3_in_0_10.txt b/data/points/iso_cuboid_3_in_0_10.txt new file mode 100644 index 00000000..d4bd2233 --- /dev/null +++ b/data/points/iso_cuboid_3_in_0_10.txt @@ -0,0 +1 @@ +0.0 0.0 0.0 10.0 10.0 10.0 diff --git a/data/points/shifted_sphere.off b/data/points/shifted_sphere.off new file mode 100644 index 00000000..54051bb1 --- /dev/null +++ b/data/points/shifted_sphere.off @@ -0,0 +1,1002 @@ +OFF +1000 0 0 +9.30846 0.674959 0.354663 +0.319662 1.44971 1.83394 +9.65204 0.108855 0.71069 +0.436642 0.138375 0.741799 +0.0632498 0.127158 1.4832 +9.82265 1.72038 0.329397 +9.68531 1.67209 1.6711 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<gudhi/Unitary_tests_utils.h> // Use dynamic_dimension_tag for the user to be able to set dimension typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kernel_d; @@ -96,10 +97,6 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(Alpha_complex_from_OFF_file, TestedKernel, list_of BOOST_CHECK(simplex_tree_59.num_simplices() == 23); } -bool are_almost_the_same(float a, float b) { - return std::fabs(a - b) < std::numeric_limits<float>::epsilon(); -} - // Use static dimension_tag for the user not to be able to set dimension typedef CGAL::Epick_d< CGAL::Dimension_tag<4> > Kernel_4; typedef Kernel_4::Point_d Point_4; @@ -166,16 +163,16 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_from_points) { for (auto f_simplex : simplex_tree.filtration_simplex_range()) { switch (simplex_tree.dimension(f_simplex)) { case 0: - BOOST_CHECK(are_almost_the_same(simplex_tree.filtration(f_simplex), 0.0)); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(simplex_tree.filtration(f_simplex), 0.0); break; case 1: - BOOST_CHECK(are_almost_the_same(simplex_tree.filtration(f_simplex), 1.0/2.0)); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(simplex_tree.filtration(f_simplex), 1.0/2.0); break; case 2: - BOOST_CHECK(are_almost_the_same(simplex_tree.filtration(f_simplex), 2.0/3.0)); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(simplex_tree.filtration(f_simplex), 2.0/3.0); break; case 3: - BOOST_CHECK(are_almost_the_same(simplex_tree.filtration(f_simplex), 3.0/4.0)); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(simplex_tree.filtration(f_simplex), 3.0/4.0); break; default: BOOST_CHECK(false); // Shall not happen @@ -239,10 +236,10 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_from_points) { for (auto f_simplex : simplex_tree.filtration_simplex_range()) { switch (simplex_tree.dimension(f_simplex)) { case 0: - BOOST_CHECK(are_almost_the_same(simplex_tree.filtration(f_simplex), 0.0)); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(simplex_tree.filtration(f_simplex), 0.0); break; case 1: - BOOST_CHECK(are_almost_the_same(simplex_tree.filtration(f_simplex), 1.0/2.0)); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(simplex_tree.filtration(f_simplex), 1.0/2.0); break; default: BOOST_CHECK(false); // Shall not happen diff --git a/src/Alpha_complex/utilities/CMakeLists.txt b/src/Alpha_complex/utilities/CMakeLists.txt index 79d9e7dd..a2dfac20 100644 --- a/src/Alpha_complex/utilities/CMakeLists.txt +++ b/src/Alpha_complex/utilities/CMakeLists.txt @@ -54,7 +54,7 @@ if(CGAL_FOUND) target_link_libraries(weighted_periodic_alpha_complex_3d_persistence ${TBB_LIBRARIES}) endif(TBB_FOUND) - add_test(NAME Persistent_cohomology_example_weigted_periodic_alpha_complex_3d COMMAND $<TARGET_FILE:weighted_periodic_alpha_complex_3d_persistence> + add_test(NAME Alpha_complex_utilities_weigted_periodic_alpha_complex_3d COMMAND $<TARGET_FILE:weighted_periodic_alpha_complex_3d_persistence> "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off" "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.weights" "${CMAKE_SOURCE_DIR}/data/points/iso_cuboid_3_in_0_1.txt" "3" "1.0") diff --git a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp index f4a14ae3..1070d17b 100644 --- a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp +++ b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp @@ -20,9 +20,13 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ +#include <boost/version.hpp> #include <boost/program_options.hpp> #include <boost/variant.hpp> + +#if BOOST_VERSION >= 105400 #include <boost/container/static_vector.hpp> +#endif #include <gudhi/Simplex_tree.h> #include <gudhi/Persistent_cohomology.h> @@ -66,7 +70,12 @@ using Cell_handle = Alpha_shape_3::Cell_handle; using Facet = Alpha_shape_3::Facet; using Edge_3 = Alpha_shape_3::Edge; using Vertex_handle = Alpha_shape_3::Vertex_handle; + +#if BOOST_VERSION >= 105400 using Vertex_list = boost::container::static_vector<Alpha_shape_3::Vertex_handle, 4>; +#else +using Vertex_list = std::vector<Alpha_shape_3::Vertex_handle>; +#endif // gudhi type definition using ST = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>; diff --git a/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp index 6993b0ad..ac72dcc4 100644 --- a/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp +++ b/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp @@ -3,6 +3,7 @@ * library for computational topology. * * Author(s): Vincent Rouvreau + * Pawel Dlotko - 2017 - Swansea University, UK * * Copyright (C) 2014 INRIA * @@ -112,6 +113,12 @@ int main(int argc, char **argv) { std::cerr << "Unable to read file " << cuboid_file << std::endl; exit(-1); } + //Checking if the cuboid is the same in x,y and z direction. If not, CGAL will not process it. + if ((x_max-x_min != y_max-y_min) || (x_max-x_min != z_max-z_min) || (z_max-z_min != y_max-y_min)) + { + std::cerr << "The size of the cuboid in every directions is not the same." << std::endl; + exit(-1); + } // Retrieve the points std::vector<Point_3> lp = off_reader.get_point_cloud(); @@ -121,7 +128,12 @@ int main(int argc, char **argv) { // Heuristic for inserting large point sets (if pts is reasonably large) pdt.insert(lp.begin(), lp.end(), true); // As pdt won't be modified anymore switch to 1-sheeted cover if possible - if (pdt.is_triangulation_in_1_sheet()) pdt.convert_to_1_sheeted_covering(); + if (pdt.is_triangulation_in_1_sheet()) { + pdt.convert_to_1_sheeted_covering(); + } else { + std::cerr << "ERROR: we were not able to construct a triangulation within a single periodic domain." << std::endl; + exit(-1); + } std::cout << "Periodic Delaunay computed." << std::endl; // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode. This is the default mode diff --git a/src/Alpha_complex/utilities/weighted_periodic_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/weighted_periodic_alpha_complex_3d_persistence.cpp index 282b9180..0fe8931f 100644 --- a/src/Alpha_complex/utilities/weighted_periodic_alpha_complex_3d_persistence.cpp +++ b/src/Alpha_complex/utilities/weighted_periodic_alpha_complex_3d_persistence.cpp @@ -3,6 +3,7 @@ * library for computational topology. * * Author(s): Vincent Rouvreau + * Pawel Dlotko - 2017 - Swansea University, UK * * Copyright (C) 2014 INRIA * @@ -113,15 +114,45 @@ int main(int argc, char* const argv[]) { // Retrieve the points std::vector<Point_3> lp = off_reader.get_point_cloud(); + // Read iso_cuboid_3 information from file + std::ifstream iso_cuboid_str(argv[3]); + double x_min, y_min, z_min, x_max, y_max, z_max; + if (iso_cuboid_str.is_open()) { + if (!(iso_cuboid_str >> x_min >> y_min >> z_min >> x_max >> y_max >> z_max)) { + std::cerr << argv[3] << " - Bad file format." << std::endl; + usage(argv[0]); + } + + } else { + std::cerr << "Unable to read file " << argv[3] << std::endl; + usage(argv[0]); + } + //Checking if the cuboid is the same in x,y and z direction. If not, CGAL will not process it. + if ((x_max-x_min != y_max-y_min) || (x_max-x_min != z_max-z_min) || (z_max-z_min != y_max-y_min)) + { + std::cerr << "The size of the cuboid in every directions is not the same." << std::endl; + exit(-1); + } + + double maximal_possible_weight = 0.015625 * (x_max-x_min) * (x_max-x_min); + // Read weights information from file std::ifstream weights_ifstr(argv[2]); std::vector<Weighted_point_3> wp; - if (weights_ifstr.good()) { + if (weights_ifstr.is_open()) { double weight = 0.0; std::size_t index = 0; wp.reserve(lp.size()); // Attempt read the weight in a double format, return false if it fails while ((weights_ifstr >> weight) && (index < lp.size())) { + if ((weight >= maximal_possible_weight) || (weight < 0)) + { + std::cerr << "At line " << (index + 1) << ", the weight (" << weight + << ") is negative or more than or equal to maximal possible weight (" << maximal_possible_weight + << ") = 1/64*cuboid length squared, which is not an acceptable input." << std::endl; + exit(-1); + } + wp.push_back(Weighted_point_3(lp[index], weight)); index++; } @@ -134,23 +165,18 @@ int main(int argc, char* const argv[]) { usage(argv[0]); } - // Read iso_cuboid_3 information from file - std::ifstream iso_cuboid_str(argv[3]); - double x_min, y_min, z_min, x_max, y_max, z_max; - if (iso_cuboid_str.good()) { - iso_cuboid_str >> x_min >> y_min >> z_min >> x_max >> y_max >> z_max; - } else { - std::cerr << "Unable to read file " << argv[3] << std::endl; - usage(argv[0]); - } - // Define the periodic cube P3RT3 prt(PK::Iso_cuboid_3(x_min, y_min, z_min, x_max, y_max, z_max)); // Heuristic for inserting large point sets (if pts is reasonably large) prt.insert(wp.begin(), wp.end(), true); // As prt won't be modified anymore switch to 1-sheeted cover if possible - if (prt.is_triangulation_in_1_sheet()) prt.convert_to_1_sheeted_covering(); - std::cout << "Periodic Delaunay computed." << std::endl; + if (prt.is_triangulation_in_1_sheet()) { + prt.convert_to_1_sheeted_covering(); + } else { + std::cerr << "ERROR: we were not able to construct a triangulation within a single periodic domain." << std::endl; + exit(-1); + } + std::cout << "Weighted Periodic Delaunay computed." << std::endl; // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode. This is the default mode // Maybe need to set it to GENERAL mode diff --git a/src/Persistence_representations/doc/Persistence_representations_doc.h b/src/Persistence_representations/doc/Persistence_representations_doc.h index c77e75e2..978fb5bd 100644 --- a/src/Persistence_representations/doc/Persistence_representations_doc.h +++ b/src/Persistence_representations/doc/Persistence_representations_doc.h @@ -83,8 +83,8 @@ namespace Persistence_representations { \li Persistence vectors (allow averaging, computation of distances, scalar products, vectorizations and real value characteristics). \li Persistence diagrams / barcodes (allow computation of distances, vectorizations and real value characteristics). - - + + Note that at the while functionalities like averaging, distances and scalar products are fixed, there is no canonical way of vectorizing and computing real valued characteristics of objects. Therefore the vectorizations and computation of real value characteristics procedures are quite likely to evolve in the furthering @@ -139,7 +139,8 @@ namespace Persistence_representations { possible ways to proceed: \li Use non exact representation on a grid described in the Section \ref sec_landscapes_on_grid. - \li Compute just a number of initial nonzero landscapes. This option is available from C++ level as a last parameter of the constructor of persistence landscape (set by default to std::numeric_limits<size_t>::max()). + \li Compute just a number of initial nonzero landscapes. This option is available from C++ level as a last parameter of + the constructor of persistence landscape (set by default to std::numeric_limits<size_t>::max()). diff --git a/src/Persistence_representations/example/CMakeLists.txt b/src/Persistence_representations/example/CMakeLists.txt index 7788b603..b8ce8ea6 100644 --- a/src/Persistence_representations/example/CMakeLists.txt +++ b/src/Persistence_representations/example/CMakeLists.txt @@ -1,8 +1,6 @@ cmake_minimum_required(VERSION 2.6) project(Persistence_representations_example) -file(COPY "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/") - add_executable ( Persistence_representations_example_landscape_on_grid persistence_landscape_on_grid.cpp ) target_link_libraries(Persistence_representations_example_landscape_on_grid ${Boost_SYSTEM_LIBRARY}) add_test(NAME Persistence_representations_example_landscape_on_grid @@ -17,7 +15,7 @@ add_executable ( Persistence_representations_example_intervals persistence_inter target_link_libraries(Persistence_representations_example_intervals ${Boost_SYSTEM_LIBRARY}) add_test(NAME Persistence_representations_example_intervals COMMAND $<TARGET_FILE:Persistence_representations_example_intervals> - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") + "${CMAKE_SOURCE_DIR}/data/persistence_diagram/first.pers") add_executable ( Persistence_representations_example_vectors persistence_vectors.cpp ) target_link_libraries(Persistence_representations_example_vectors ${Boost_SYSTEM_LIBRARY}) diff --git a/src/Persistence_representations/example/persistence_vectors.cpp b/src/Persistence_representations/example/persistence_vectors.cpp index 59eca152..834ae644 100644 --- a/src/Persistence_representations/example/persistence_vectors.cpp +++ b/src/Persistence_representations/example/persistence_vectors.cpp @@ -30,7 +30,7 @@ #include <utility> using Vector_distances_in_diagram = - Gudhi::Persistence_representations::Vector_distances_in_diagram<Gudhi::Euclidean_distance>; + Gudhi::Persistence_representations::Vector_distances_in_diagram<Gudhi::Euclidean_distance>; int main(int argc, char** argv) { // create two simple vectors with birth--death pairs: diff --git a/src/Persistence_representations/include/gudhi/PSSK.h b/src/Persistence_representations/include/gudhi/PSSK.h index e2d4225e..630f5623 100644 --- a/src/Persistence_representations/include/gudhi/PSSK.h +++ b/src/Persistence_representations/include/gudhi/PSSK.h @@ -121,10 +121,10 @@ void PSSK::construct(const std::vector<std::pair<double, double> >& intervals_, for (size_t pt_nr = 0; pt_nr != intervals_.size(); ++pt_nr) { // compute the value of intervals_[pt_nr] in the grid: - int x_grid = static_cast<int>((intervals_[pt_nr].first - this->min_) / - (this->max_ - this->min_) * number_of_pixels); - int y_grid = static_cast<int>((intervals_[pt_nr].second - this->min_) / - (this->max_ - this->min_) * number_of_pixels); + int x_grid = + static_cast<int>((intervals_[pt_nr].first - this->min_) / (this->max_ - this->min_) * number_of_pixels); + int y_grid = + static_cast<int>((intervals_[pt_nr].second - this->min_) / (this->max_ - this->min_) * number_of_pixels); if (dbg) { std::cerr << "point : " << intervals_[pt_nr].first << " , " << intervals_[pt_nr].second << std::endl; diff --git a/src/Persistence_representations/include/gudhi/Persistence_heat_maps.h b/src/Persistence_representations/include/gudhi/Persistence_heat_maps.h index 04dd78ad..a80c3c40 100644 --- a/src/Persistence_representations/include/gudhi/Persistence_heat_maps.h +++ b/src/Persistence_representations/include/gudhi/Persistence_heat_maps.h @@ -582,10 +582,10 @@ void Persistence_heat_maps<Scalling_of_kernels>::construct(const std::vector<std for (size_t pt_nr = 0; pt_nr != intervals_.size(); ++pt_nr) { // compute the value of intervals_[pt_nr] in the grid: - int x_grid = static_cast<int>((intervals_[pt_nr].first - this->min_) / - (this->max_ - this->min_) * number_of_pixels); - int y_grid = static_cast<int>((intervals_[pt_nr].second - this->min_) / - (this->max_ - this->min_) * number_of_pixels); + int x_grid = + static_cast<int>((intervals_[pt_nr].first - this->min_) / (this->max_ - this->min_) * number_of_pixels); + int y_grid = + static_cast<int>((intervals_[pt_nr].second - this->min_) / (this->max_ - this->min_) * number_of_pixels); if (dbg) { std::cerr << "point : " << intervals_[pt_nr].first << " , " << intervals_[pt_nr].second << std::endl; @@ -743,10 +743,10 @@ void Persistence_heat_maps<Scalling_of_kernels>::compute_percentage_of_active( template <typename Scalling_of_kernels> void Persistence_heat_maps<Scalling_of_kernels>::plot(const char* filename) const { std::ofstream out; - std::stringstream ss; - ss << filename << "_GnuplotScript"; + std::stringstream gnuplot_script; + gnuplot_script << filename << "_GnuplotScript"; - out.open(ss.str().c_str()); + out.open(gnuplot_script.str().c_str()); out << "plot '-' matrix with image" << std::endl; for (size_t i = 0; i != this->heat_map.size(); ++i) { for (size_t j = 0; j != this->heat_map[i].size(); ++j) { @@ -755,8 +755,8 @@ void Persistence_heat_maps<Scalling_of_kernels>::plot(const char* filename) cons out << std::endl; } out.close(); - std::cout << "Gnuplot script have been created. Open gnuplot and type load \'" << ss.str().c_str() - << "\' to see the picture." << std::endl; + std::cout << "To visualize, install gnuplot and type the command: gnuplot -persist -e \"load \'" + << gnuplot_script.str().c_str() << "\'\"" << std::endl; } template <typename Scalling_of_kernels> @@ -797,8 +797,7 @@ void Persistence_heat_maps<Scalling_of_kernels>::load_from_file(const char* file std::string temp; std::getline(in, temp); - - while (!in.eof()) { + while (in.good()) { std::getline(in, temp); std::stringstream lineSS; lineSS << temp; diff --git a/src/Persistence_representations/include/gudhi/Persistence_intervals.h b/src/Persistence_representations/include/gudhi/Persistence_intervals.h index 525d58a3..3d04d8b7 100644 --- a/src/Persistence_representations/include/gudhi/Persistence_intervals.h +++ b/src/Persistence_representations/include/gudhi/Persistence_intervals.h @@ -167,10 +167,10 @@ class Persistence_intervals { // this program create a gnuplot script file that allows to plot persistence diagram. std::ofstream out; - std::ostringstream nameSS; - nameSS << filename << "_GnuplotScript"; - std::string nameStr = nameSS.str(); - out.open(nameStr); + std::stringstream gnuplot_script; + gnuplot_script << filename << "_GnuplotScript"; + + out.open(gnuplot_script.str().c_str()); std::pair<double, double> min_max_values = this->get_x_range(); if (min_x == max_x) { @@ -195,8 +195,8 @@ class Persistence_intervals { out.close(); - std::cout << "Gnuplot script to visualize persistence diagram written to the file: " << nameStr << ". Type load '" - << nameStr << "' in gnuplot to visualize." << std::endl; + std::cout << "To visualize, install gnuplot and type the command: gnuplot -persist -e \"load \'" + << gnuplot_script.str().c_str() << "\'\"" << std::endl; } /** @@ -402,9 +402,8 @@ std::vector<double> Persistence_intervals::characteristic_function_of_diagram(do } for (size_t pos = beginIt; pos != endIt; ++pos) { - result[pos] += - ((x_max - x_min) / static_cast<double>(number_of_bins)) * - (this->intervals[i].second - this->intervals[i].first); + result[pos] += ((x_max - x_min) / static_cast<double>(number_of_bins)) * + (this->intervals[i].second - this->intervals[i].first); } if (dbg) { std::cerr << "Result at this stage \n"; diff --git a/src/Persistence_representations/include/gudhi/Persistence_intervals_with_distances.h b/src/Persistence_representations/include/gudhi/Persistence_intervals_with_distances.h index d5ab04b4..79908883 100644 --- a/src/Persistence_representations/include/gudhi/Persistence_intervals_with_distances.h +++ b/src/Persistence_representations/include/gudhi/Persistence_intervals_with_distances.h @@ -26,7 +26,6 @@ #include <gudhi/Persistence_intervals.h> #include <gudhi/Bottleneck.h> - #include <limits> namespace Gudhi { @@ -47,7 +46,7 @@ class Persistence_intervals_with_distances : public Persistence_intervals { * The last parameter, tolerance, it is an additiv error of the approimation, set by default to zero. **/ double distance(const Persistence_intervals_with_distances& second, double power = std::numeric_limits<double>::max(), - double tolerance = 0) const { + double tolerance = (std::numeric_limits<double>::min)()) const { if (power >= std::numeric_limits<double>::max()) { return Gudhi::persistence_diagram::bottleneck_distance(this->intervals, second.intervals, tolerance); } else { diff --git a/src/Persistence_representations/include/gudhi/Persistence_landscape.h b/src/Persistence_representations/include/gudhi/Persistence_landscape.h index 5c300112..c5aa7867 100644 --- a/src/Persistence_representations/include/gudhi/Persistence_landscape.h +++ b/src/Persistence_representations/include/gudhi/Persistence_landscape.h @@ -79,14 +79,16 @@ class Persistence_landscape { /** * Constructor that takes as an input a vector of birth-death pairs. **/ - Persistence_landscape(const std::vector<std::pair<double, double> >& p, size_t number_of_levels = std::numeric_limits<size_t>::max() ); + Persistence_landscape(const std::vector<std::pair<double, double> >& p, + size_t number_of_levels = std::numeric_limits<size_t>::max()); /** * Constructor that reads persistence intervals from file and creates persistence landscape. The format of the *input file is the following: in each line we put birth-death pair. Last line is assumed * to be empty. Even if the points within a line are not ordered, they will be ordered while the input is read. **/ - Persistence_landscape(const char* filename, size_t dimension = std::numeric_limits<unsigned>::max() , size_t number_of_levels = std::numeric_limits<size_t>::max() ); + Persistence_landscape(const char* filename, size_t dimension = std::numeric_limits<unsigned>::max(), + size_t number_of_levels = std::numeric_limits<size_t>::max()); /** * This procedure loads a landscape from file. It erase all the data that was previously stored in this landscape. @@ -285,7 +287,7 @@ class Persistence_landscape { *distance, we need to take its absolute value. This is the purpose of this procedure. **/ Persistence_landscape abs(); - + Persistence_landscape* new_abs(); /** @@ -453,7 +455,8 @@ class Persistence_landscape { size_t number_of_functions_for_vectorization; size_t number_of_functions_for_projections_to_reals; - void construct_persistence_landscape_from_barcode(const std::vector<std::pair<double, double> >& p , size_t number_of_levels = std::numeric_limits<size_t>::max()); + void construct_persistence_landscape_from_barcode(const std::vector<std::pair<double, double> >& p, + size_t number_of_levels = std::numeric_limits<size_t>::max()); Persistence_landscape multiply_lanscape_by_real_number_not_overwrite(double x) const; void multiply_lanscape_by_real_number_overwrite(double x); friend double compute_maximal_distance_non_symmetric(const Persistence_landscape& pl1, @@ -473,7 +476,7 @@ Persistence_landscape::Persistence_landscape(const char* filename, size_t dimens } else { barcode = read_persistence_intervals_in_one_dimension_from_file(filename); } - this->construct_persistence_landscape_from_barcode(barcode,number_of_levels); + this->construct_persistence_landscape_from_barcode(barcode, number_of_levels); this->set_up_numbers_of_functions_for_vectorization_and_projections_to_reals(); } @@ -506,14 +509,14 @@ bool Persistence_landscape::operator==(const Persistence_landscape& rhs) const { return true; } -Persistence_landscape::Persistence_landscape(const std::vector<std::pair<double, double> >& p,size_t number_of_levels) { - this->construct_persistence_landscape_from_barcode(p,number_of_levels); +Persistence_landscape::Persistence_landscape(const std::vector<std::pair<double, double> >& p, + size_t number_of_levels) { + this->construct_persistence_landscape_from_barcode(p, number_of_levels); this->set_up_numbers_of_functions_for_vectorization_and_projections_to_reals(); } void Persistence_landscape::construct_persistence_landscape_from_barcode( - const std::vector<std::pair<double, double> >& p, size_t number_of_levels) - { + const std::vector<std::pair<double, double> >& p, size_t number_of_levels) { bool dbg = false; if (dbg) { std::cerr << "Persistence_landscape::Persistence_landscape( const std::vector< std::pair< double , double > >& p )" @@ -648,12 +651,11 @@ void Persistence_landscape::construct_persistence_landscape_from_barcode( lambda_n.erase(std::unique(lambda_n.begin(), lambda_n.end()), lambda_n.end()); this->land.push_back(lambda_n); - + ++number_of_levels_in_the_landscape; - if ( number_of_levels == number_of_levels_in_the_landscape ) - { - break; - } + if (number_of_levels == number_of_levels_in_the_landscape) { + break; + } } } @@ -857,58 +859,47 @@ Persistence_landscape Persistence_landscape::abs() { return result; } +Persistence_landscape* Persistence_landscape::new_abs() { + Persistence_landscape* result = new Persistence_landscape(*this); + for (size_t level = 0; level != this->land.size(); ++level) { + if (AbsDbg) { + std::cout << "level: " << level << std::endl; + } + std::vector<std::pair<double, double> > lambda_n; + lambda_n.push_back(std::make_pair(-std::numeric_limits<int>::max(), 0)); + for (size_t i = 1; i != this->land[level].size(); ++i) { + if (AbsDbg) { + std::cout << "this->land[" << level << "][" << i << "] : " << this->land[level][i].first << " " + << this->land[level][i].second << std::endl; + } + // if a line segment between this->land[level][i-1] and this->land[level][i] crosses the x-axis, then we have to + // add one landscape point t o result + if ((this->land[level][i - 1].second) * (this->land[level][i].second) < 0) { + double zero = + find_zero_of_a_line_segment_between_those_two_points(this->land[level][i - 1], this->land[level][i]); -Persistence_landscape* Persistence_landscape::new_abs() -{ - Persistence_landscape* result = new Persistence_landscape(*this); - for (size_t level = 0; level != this->land.size(); ++level) - { - if (AbsDbg) - { - std::cout << "level: " << level << std::endl; - } - std::vector<std::pair<double, double> > lambda_n; - lambda_n.push_back(std::make_pair(-std::numeric_limits<int>::max(), 0)); - for (size_t i = 1; i != this->land[level].size(); ++i) - { - if (AbsDbg) - { - std::cout << "this->land[" << level << "][" << i << "] : " << this->land[level][i].first << " " - << this->land[level][i].second << std::endl; - } - // if a line segment between this->land[level][i-1] and this->land[level][i] crosses the x-axis, then we have to - // add one landscape point t o result - if ((this->land[level][i - 1].second) * (this->land[level][i].second) < 0) { - double zero = - find_zero_of_a_line_segment_between_those_two_points(this->land[level][i - 1], this->land[level][i]); - - lambda_n.push_back(std::make_pair(zero, 0)); - lambda_n.push_back(std::make_pair(this->land[level][i].first, fabs(this->land[level][i].second))); - if (AbsDbg) - { - std::cout << "Adding pair : (" << zero << ",0)" << std::endl; - std::cout << "In the same step adding pair : (" << this->land[level][i].first << "," - << fabs(this->land[level][i].second) << ") " << std::endl; - std::cin.ignore(); - } - } - else - { - lambda_n.push_back(std::make_pair(this->land[level][i].first, fabs(this->land[level][i].second))); - if (AbsDbg) - { - std::cout << "Adding pair : (" << this->land[level][i].first << "," << fabs(this->land[level][i].second) - << ") " << std::endl; - std::cin.ignore(); - } - } - } - result->land.push_back(lambda_n); - } - return result; + lambda_n.push_back(std::make_pair(zero, 0)); + lambda_n.push_back(std::make_pair(this->land[level][i].first, fabs(this->land[level][i].second))); + if (AbsDbg) { + std::cout << "Adding pair : (" << zero << ",0)" << std::endl; + std::cout << "In the same step adding pair : (" << this->land[level][i].first << "," + << fabs(this->land[level][i].second) << ") " << std::endl; + std::cin.ignore(); + } + } else { + lambda_n.push_back(std::make_pair(this->land[level][i].first, fabs(this->land[level][i].second))); + if (AbsDbg) { + std::cout << "Adding pair : (" << this->land[level][i].first << "," << fabs(this->land[level][i].second) + << ") " << std::endl; + std::cin.ignore(); + } + } + } + result->land.push_back(lambda_n); + } + return result; } - Persistence_landscape Persistence_landscape::multiply_lanscape_by_real_number_not_overwrite(double x) const { std::vector<std::vector<std::pair<double, double> > > result(this->land.size()); for (size_t dim = 0; dim != this->land.size(); ++dim) { @@ -954,7 +945,7 @@ void Persistence_landscape::load_landscape_from_file(const char* filename) { std::vector<std::pair<double, double> > landscapeAtThisLevel; bool isThisAFirsLine = true; - while (!in.eof()) { + while (in.good()) { getline(in, line); if (!(line.length() == 0 || line[0] == '#')) { std::stringstream lineSS; @@ -1340,10 +1331,9 @@ void Persistence_landscape::plot(const char* filename, double xRangeBegin, doubl // this program create a gnuplot script file that allows to plot persistence diagram. std::ofstream out; - std::ostringstream nameSS; - nameSS << filename << "_GnuplotScript"; - std::string nameStr = nameSS.str(); - out.open(nameStr); + std::ostringstream gnuplot_script; + gnuplot_script << filename << "_GnuplotScript"; + out.open(gnuplot_script.str().c_str()); if ((xRangeBegin != std::numeric_limits<double>::max()) || (xRangeEnd != std::numeric_limits<double>::max()) || (yRangeBegin != std::numeric_limits<double>::max()) || (yRangeEnd != std::numeric_limits<double>::max())) { @@ -1376,8 +1366,8 @@ void Persistence_landscape::plot(const char* filename, double xRangeBegin, doubl } out << "EOF" << std::endl; } - std::cout << "Gnuplot script to visualize persistence diagram written to the file: " << nameStr << ". Type load '" - << nameStr << "' in gnuplot to visualize." << std::endl; + std::cout << "To visualize, install gnuplot and type the command: gnuplot -persist -e \"load \'" + << gnuplot_script.str().c_str() << "\'\"" << std::endl; } } // namespace Persistence_representations diff --git a/src/Persistence_representations/include/gudhi/Persistence_landscape_on_grid.h b/src/Persistence_representations/include/gudhi/Persistence_landscape_on_grid.h index 4ceb9bf6..84fd22ed 100644 --- a/src/Persistence_representations/include/gudhi/Persistence_landscape_on_grid.h +++ b/src/Persistence_representations/include/gudhi/Persistence_landscape_on_grid.h @@ -1207,10 +1207,9 @@ void Persistence_landscape_on_grid::plot(const char* filename, double min_x, dou // this program create a gnuplot script file that allows to plot persistence diagram. std::ofstream out; - std::ostringstream nameSS; - nameSS << filename << "_GnuplotScript"; - std::string nameStr = nameSS.str(); - out.open(nameStr); + std::ostringstream gnuplot_script; + gnuplot_script << filename << "_GnuplotScript"; + out.open(gnuplot_script.str().c_str()); if (min_x == max_x) { std::pair<double, double> min_max = compute_minimum_maximum(); @@ -1241,7 +1240,6 @@ void Persistence_landscape_on_grid::plot(const char* filename, double min_x, dou out << "plot "; for (size_t lambda = from; lambda != to; ++lambda) { - // out << " '-' using 1:2 title 'l" << lambda << "' with lp"; out << " '-' using 1:2 notitle with lp"; if (lambda + 1 != to) { out << ", \\"; @@ -1261,8 +1259,8 @@ void Persistence_landscape_on_grid::plot(const char* filename, double min_x, dou } out << "EOF" << std::endl; } - std::cout << "Gnuplot script to visualize persistence diagram written to the file: " << nameStr << ". Type load '" - << nameStr << "' in gnuplot to visualize." << std::endl; + std::cout << "To visualize, install gnuplot and type the command: gnuplot -persist -e \"load \'" + << gnuplot_script.str().c_str() << "\'\"" << std::endl; } template <typename T> diff --git a/src/Persistence_representations/include/gudhi/Persistence_vectors.h b/src/Persistence_representations/include/gudhi/Persistence_vectors.h index 0fb49eee..63577e46 100644 --- a/src/Persistence_representations/include/gudhi/Persistence_vectors.h +++ b/src/Persistence_representations/include/gudhi/Persistence_vectors.h @@ -201,7 +201,8 @@ class Vector_distances_in_diagram { } out << std::endl; out.close(); - std::cout << "To visualize, open gnuplot and type: load \'" << gnuplot_script.str().c_str() << "\'" << std::endl; + std::cout << "To visualize, install gnuplot and type the command: gnuplot -persist -e \"load \'" + << gnuplot_script.str().c_str() << "\'\"" << std::endl; } /** @@ -617,9 +618,7 @@ void Vector_distances_in_diagram<F>::load_from_file(const char* filename) { } double number; - while (true) { - in >> number; - if (in.eof()) break; + while (in >> number) { this->sorted_vector_of_distances.push_back(number); } in.close(); diff --git a/src/Persistence_representations/include/gudhi/read_persistence_from_file.h b/src/Persistence_representations/include/gudhi/read_persistence_from_file.h index 770da15b..450c223c 100644 --- a/src/Persistence_representations/include/gudhi/read_persistence_from_file.h +++ b/src/Persistence_representations/include/gudhi/read_persistence_from_file.h @@ -50,81 +50,73 @@ namespace Persistence_representations { * The procedure returns vector of persistence pairs. **/ std::vector<std::pair<double, double> > read_persistence_intervals_in_one_dimension_from_file( - std::string const& filename, int dimension = -1, double what_to_substitute_for_infinite_bar = -1) { + std::string const& filename, int dimension = -1, double what_to_substitute_for_infinite_bar = -1) { bool dbg = false; std::string line; - std::vector<std::pair<double, double> > barcode_initial = read_persistence_intervals_in_dimension(filename,(int)dimension); + std::vector<std::pair<double, double> > barcode_initial = + read_persistence_intervals_in_dimension(filename, (int)dimension); std::vector<std::pair<double, double> > final_barcode; - final_barcode.reserve( barcode_initial.size() ); - - if ( dbg ) - { - std::cerr << "Here are the intervals that we read from the file : \n"; - for ( size_t i = 0 ; i != barcode_initial.size() ; ++i ) - { - std::cout << barcode_initial[i].first << " " << barcode_initial[i].second << std::endl; - } - getchar(); + final_barcode.reserve(barcode_initial.size()); + + if (dbg) { + std::cerr << "Here are the intervals that we read from the file : \n"; + for (size_t i = 0; i != barcode_initial.size(); ++i) { + std::cout << barcode_initial[i].first << " " << barcode_initial[i].second << std::endl; + } + getchar(); } - - for ( size_t i = 0 ; i != barcode_initial.size() ; ++i ) - { - if ( dbg ) - { - std::cout << "COnsidering interval : " << barcode_initial[i].first << " " << barcode_initial[i].second << std::endl; - } - // if ( barcode_initial[i].first == barcode_initial[i].second ) - //{ - // if ( dbg )std::cout << "It has zero length \n"; - // continue;//zero length intervals are not relevant, so we skip all of them. - //} - - if ( barcode_initial[i].first > barcode_initial[i].second )//note that in this case barcode_initial[i].second != std::numeric_limits<double>::infinity() - { - if ( dbg )std::cout << "Swap and enter \n"; - //swap them to make sure that birth < death - final_barcode.push_back( std::pair<double,double>( barcode_initial[i].second , barcode_initial[i].first ) ); - continue; - } - else - { - if ( barcode_initial[i].second != std::numeric_limits<double>::infinity() ) - { - if ( dbg )std::cout << "Simply enters\n"; - //in this case, due to the previous conditions we know that barcode_initial[i].first < barcode_initial[i].second, so we put them as they are - final_barcode.push_back( std::pair<double,double>( barcode_initial[i].first , barcode_initial[i].second ) ); - } - } - - if ( (barcode_initial[i].second == std::numeric_limits<double>::infinity() ) && ( what_to_substitute_for_infinite_bar != -1 ) ) - { - if ( barcode_initial[i].first < what_to_substitute_for_infinite_bar )//if only birth < death. - { - final_barcode.push_back( std::pair<double,double>( barcode_initial[i].first , what_to_substitute_for_infinite_bar ) ); - } - } - else - { - //if the variable what_to_substitute_for_infinite_bar is not set, then we ignore all the infinite bars. - } + + for (size_t i = 0; i != barcode_initial.size(); ++i) { + if (dbg) { + std::cout << "COnsidering interval : " << barcode_initial[i].first << " " << barcode_initial[i].second + << std::endl; + } + // if ( barcode_initial[i].first == barcode_initial[i].second ) + //{ + // if ( dbg )std::cout << "It has zero length \n"; + // continue;//zero length intervals are not relevant, so we skip all of them. + //} + + if (barcode_initial[i].first > + barcode_initial[i] + .second) // note that in this case barcode_initial[i].second != std::numeric_limits<double>::infinity() + { + if (dbg) std::cout << "Swap and enter \n"; + // swap them to make sure that birth < death + final_barcode.push_back(std::pair<double, double>(barcode_initial[i].second, barcode_initial[i].first)); + continue; + } else { + if (barcode_initial[i].second != std::numeric_limits<double>::infinity()) { + if (dbg) std::cout << "Simply enters\n"; + // in this case, due to the previous conditions we know that barcode_initial[i].first < + // barcode_initial[i].second, so we put them as they are + final_barcode.push_back(std::pair<double, double>(barcode_initial[i].first, barcode_initial[i].second)); + } + } + + if ((barcode_initial[i].second == std::numeric_limits<double>::infinity()) && + (what_to_substitute_for_infinite_bar != -1)) { + if (barcode_initial[i].first < what_to_substitute_for_infinite_bar) // if only birth < death. + { + final_barcode.push_back( + std::pair<double, double>(barcode_initial[i].first, what_to_substitute_for_infinite_bar)); + } + } else { + // if the variable what_to_substitute_for_infinite_bar is not set, then we ignore all the infinite bars. + } } - - - if ( dbg ) - { - std::cerr << "Here are the final bars that we are sending further : \n"; - for ( size_t i = 0 ; i != final_barcode.size() ; ++i ) - { - std::cout << final_barcode[i].first << " " << final_barcode[i].second << std::endl; - } - std::cerr << "final_barcode.size() : " << final_barcode.size() << std::endl; - getchar(); + + if (dbg) { + std::cerr << "Here are the final bars that we are sending further : \n"; + for (size_t i = 0; i != final_barcode.size(); ++i) { + std::cout << final_barcode[i].first << " " << final_barcode[i].second << std::endl; + } + std::cerr << "final_barcode.size() : " << final_barcode.size() << std::endl; + getchar(); } - - - - return final_barcode; + + return final_barcode; } // read_persistence_intervals_in_one_dimension_from_file } // namespace Persistence_representations diff --git a/src/Persistence_representations/test/persistence_heat_maps_test.cpp b/src/Persistence_representations/test/persistence_heat_maps_test.cpp index 1f1502f5..e36108b7 100644 --- a/src/Persistence_representations/test/persistence_heat_maps_test.cpp +++ b/src/Persistence_representations/test/persistence_heat_maps_test.cpp @@ -25,12 +25,15 @@ #include <boost/test/unit_test.hpp> #include <gudhi/reader_utils.h> #include <gudhi/Persistence_heat_maps.h> +#include <gudhi/Unitary_tests_utils.h> #include <iostream> using namespace Gudhi; using namespace Gudhi::Persistence_representations; +double epsilon = 0.0005; + BOOST_AUTO_TEST_CASE(check_construction_of_heat_maps) { std::vector<std::vector<double> > filter = create_Gaussian_filter(100, 1); Persistence_heat_maps<constant_scaling_function> p("data/file_with_diagram", filter, false, 1000, 0, 1); @@ -139,28 +142,15 @@ BOOST_AUTO_TEST_CASE(check_distance_for_heat_maps) { Persistence_heat_maps<constant_scaling_function> q("data/file_with_diagram_1", filter, false, 1000, 0, 1); Persistence_heat_maps<constant_scaling_function> r("data/file_with_diagram_2", filter, false, 1000, 0, 1); - // cerr << p.distance( p ) << endl; - // cerr << p.distance( q ) << endl; - // cerr << p.distance( r ) << endl; - // cerr << q.distance( p ) << endl; - // cerr << q.distance( q ) << endl; - // cerr << q.distance( r ) << endl; - // cerr << r.distance( p ) << endl; - // cerr << r.distance( q ) << endl; - // cerr << r.distance( r ) << endl; - // 0 624.183 415.815 - // 624.183 0 528.06Z - // 415.815 528.066 0 - - BOOST_CHECK(fabs(p.distance(p) - 0) < 0.0005); - BOOST_CHECK(fabs(p.distance(q) - 624.183) < 0.0005); - BOOST_CHECK(fabs(p.distance(r) - 415.815) < 0.0005); - BOOST_CHECK(fabs(q.distance(p) - 624.183) < 0.0005); - BOOST_CHECK(fabs(q.distance(q) - 0) < 0.0005); - BOOST_CHECK(fabs(q.distance(r) - 528.066) < 0.0005); - BOOST_CHECK(fabs(r.distance(p) - 415.815) < 0.0005); - BOOST_CHECK(fabs(r.distance(q) - 528.066) < 0.0005); - BOOST_CHECK(fabs(r.distance(r) - 0) < 0.0005); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(p.distance(p), 0., epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(p.distance(q), 624.183, epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(p.distance(r), 415.815, epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(q.distance(p), 624.183, epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(q.distance(q), 0., epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(q.distance(r), 528.066, epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(r.distance(p), 415.815, epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(r.distance(q), 528.066, epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(r.distance(r), 0., epsilon); } BOOST_AUTO_TEST_CASE(check_projections_to_R_for_heat_maps) { @@ -169,13 +159,9 @@ BOOST_AUTO_TEST_CASE(check_projections_to_R_for_heat_maps) { Persistence_heat_maps<constant_scaling_function> q("data/file_with_diagram_1", filter, false, 1000, 0, 1); Persistence_heat_maps<constant_scaling_function> r("data/file_with_diagram_2", filter, false, 1000, 0, 1); - // cerr << p.project_to_R(0) << endl; - // cerr << q.project_to_R(0) << endl; - // cerr << r.project_to_R(0) << endl; - - BOOST_CHECK(fabs(p.project_to_R(0) - 44.3308) < 0.0005); - BOOST_CHECK(fabs(q.project_to_R(0) - 650.568) < 0.0005); - BOOST_CHECK(fabs(r.project_to_R(0) - 429.287) < 0.0005); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(p.project_to_R(0), 44.3308, epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(q.project_to_R(0), 650.568, epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(r.project_to_R(0), 429.287, epsilon); } BOOST_AUTO_TEST_CASE(check_scalar_products_for_heat_maps) { @@ -184,25 +170,15 @@ BOOST_AUTO_TEST_CASE(check_scalar_products_for_heat_maps) { Persistence_heat_maps<constant_scaling_function> q("data/file_with_diagram_1", filter, false, 1000, 0, 1); Persistence_heat_maps<constant_scaling_function> r("data/file_with_diagram_2", filter, false, 1000, 0, 1); - // cerr << p.compute_scalar_product( p ) << endl; - // cerr << p.compute_scalar_product( q ) << endl; - // cerr << p.compute_scalar_product( r ) << endl; - // cerr << q.compute_scalar_product( p ) << endl; - // cerr << q.compute_scalar_product( q ) << endl; - // cerr << q.compute_scalar_product( r ) << endl; - // cerr << r.compute_scalar_product( p ) << endl; - // cerr << r.compute_scalar_product( q ) << endl; - // cerr << r.compute_scalar_product( r ) << endl; - - BOOST_CHECK(fabs(p.compute_scalar_product(p) - 0.0345687) < 0.0005); - BOOST_CHECK(fabs(p.compute_scalar_product(q) - 0.0509357) < 0.0005); - BOOST_CHECK(fabs(p.compute_scalar_product(r) - 0.0375608) < 0.0005); - BOOST_CHECK(fabs(q.compute_scalar_product(p) - 0.0509357) < 0.0005); - BOOST_CHECK(fabs(q.compute_scalar_product(q) - 1.31293) < 0.0005); - BOOST_CHECK(fabs(q.compute_scalar_product(r) - 0.536799) < 0.0005); - BOOST_CHECK(fabs(r.compute_scalar_product(p) - 0.0375608) < 0.0005); - BOOST_CHECK(fabs(r.compute_scalar_product(q) - 0.536799) < 0.0005); - BOOST_CHECK(fabs(r.compute_scalar_product(r) - 0.672907) < 0.0005); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(p.compute_scalar_product(p), 0.0345687, epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(p.compute_scalar_product(q), 0.0509357, epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(p.compute_scalar_product(r), 0.0375608, epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(q.compute_scalar_product(p), 0.0509357, epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(q.compute_scalar_product(q), 1.31293, epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(q.compute_scalar_product(r), 0.536799, epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(r.compute_scalar_product(p), 0.0375608, epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(r.compute_scalar_product(q), 0.536799, epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(r.compute_scalar_product(r), 0.672907, epsilon); } BOOST_AUTO_TEST_CASE(check_arythmetic_operations_for_heat_maps) { diff --git a/src/Persistence_representations/test/persistence_intervals_test.cpp b/src/Persistence_representations/test/persistence_intervals_test.cpp index 545330c4..f555e243 100644 --- a/src/Persistence_representations/test/persistence_intervals_test.cpp +++ b/src/Persistence_representations/test/persistence_intervals_test.cpp @@ -25,25 +25,20 @@ #include <boost/test/unit_test.hpp> #include <gudhi/reader_utils.h> #include "gudhi/Persistence_intervals.h" +#include <gudhi/common_persistence_representations.h> +#include <gudhi/Unitary_tests_utils.h> #include <iostream> using namespace Gudhi; using namespace Gudhi::Persistence_representations; -double epsilon = 0.0000005; - -// cout << "Left most end of the interval : " << min_max_.first << std::endl; -// cout << "Right most end of the interval : " << min_max_.second << std::endl; BOOST_AUTO_TEST_CASE(check_min_max_function) { - std::cerr << "First test \n"; Persistence_intervals p("data/file_with_diagram"); std::pair<double, double> min_max_ = p.get_x_range(); - // cout << min_max_.first << " " << min_max_.second << std::endl;getchar(); - - BOOST_CHECK(fabs(min_max_.first - 0.0290362) <= epsilon); - BOOST_CHECK(fabs(min_max_.second - 0.994537) <= epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(min_max_.first, 0.0290362, Gudhi::Persistence_representations::epsi); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(min_max_.second, 0.994537, Gudhi::Persistence_representations::epsi); } BOOST_AUTO_TEST_CASE(check_length_of_dominant_intervals) { @@ -61,7 +56,8 @@ BOOST_AUTO_TEST_CASE(check_length_of_dominant_intervals) { dominant_intervals_length.push_back(0.700468); dominant_intervals_length.push_back(0.622177); for (size_t i = 0; i != dominant_ten_intervals_length.size(); ++i) { - BOOST_CHECK(fabs(dominant_ten_intervals_length[i] - dominant_intervals_length[i]) <= epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(dominant_ten_intervals_length[i], dominant_intervals_length[i], + Gudhi::Persistence_representations::epsi); } } BOOST_AUTO_TEST_CASE(check_dominant_intervals) { @@ -81,8 +77,10 @@ BOOST_AUTO_TEST_CASE(check_dominant_intervals) { templ.push_back(std::pair<double, double>(0.267421, 0.889597)); for (size_t i = 0; i != ten_dominant_intervals.size(); ++i) { - BOOST_CHECK(fabs(ten_dominant_intervals[i].first - templ[i].first) <= epsilon); - BOOST_CHECK(fabs(ten_dominant_intervals[i].second - templ[i].second) <= epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(ten_dominant_intervals[i].first, templ[i].first, + Gudhi::Persistence_representations::epsi); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(ten_dominant_intervals[i].second, templ[i].second, + Gudhi::Persistence_representations::epsi); } } @@ -102,7 +100,7 @@ BOOST_AUTO_TEST_CASE(check_histogram_of_lengths) { template_histogram.push_back(1); template_histogram.push_back(1); for (size_t i = 0; i != histogram.size(); ++i) { - BOOST_CHECK(fabs(histogram[i] - template_histogram[i]) <= epsilon); + BOOST_CHECK(histogram[i] == template_histogram[i]); } } @@ -123,7 +121,7 @@ BOOST_AUTO_TEST_CASE(check_cumulative_histograms_of_lengths) { template_cumulative_histogram.push_back(45); for (size_t i = 0; i != cumulative_histogram.size(); ++i) { - BOOST_CHECK(fabs(cumulative_histogram[i] - template_cumulative_histogram[i]) <= epsilon); + BOOST_CHECK(cumulative_histogram[i] == template_cumulative_histogram[i]); } } BOOST_AUTO_TEST_CASE(check_characteristic_function_of_diagram) { @@ -143,15 +141,8 @@ BOOST_AUTO_TEST_CASE(check_characteristic_function_of_diagram) { template_char_funct_diag.push_back(0.0676303); for (size_t i = 0; i != char_funct_diag.size(); ++i) { - // cout << char_funct_diag[i] << std::endl; - if (fabs(char_funct_diag[i] - template_char_funct_diag[i]) >= 0.0001) { - std::cout << "Boost test fail check_characteristic_function_of_diagram : " << std::endl; - std::cerr << char_funct_diag[i] << " " << template_char_funct_diag[i] << std::endl; - std::cerr << fabs(char_funct_diag[i] - template_char_funct_diag[i]) << std::endl; - std::cerr << 0.0001 << std::endl; - //getchar(); - } - BOOST_CHECK(fabs(char_funct_diag[i] - template_char_funct_diag[i]) <= 0.0001); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(char_funct_diag[i], template_char_funct_diag[i], + Gudhi::Persistence_representations::epsi); } } @@ -174,110 +165,109 @@ BOOST_AUTO_TEST_CASE(check_cumulative_characteristic_function_of_diagram) { template_char_funct_diag_cumul.push_back(9.48386); for (size_t i = 0; i != cumul_char_funct_diag.size(); ++i) { - // cout << cumul_char_funct_diag[i] << std::endl; - BOOST_CHECK(fabs(cumul_char_funct_diag[i] - template_char_funct_diag_cumul[i]) <= 0.0001); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(cumul_char_funct_diag[i], template_char_funct_diag_cumul[i], + Gudhi::Persistence_representations::epsi); } } BOOST_AUTO_TEST_CASE(check_compute_persistent_betti_numbers) { Persistence_intervals p("data/file_with_diagram"); - std::vector<std::pair<double, double> > pbns; - pbns.push_back(std::pair<double, double>(0.0290362, 1)); - pbns.push_back(std::pair<double, double>(0.0307676, 2)); - pbns.push_back(std::pair<double, double>(0.0366312, 3)); - pbns.push_back(std::pair<double, double>(0.0544614, 4)); - pbns.push_back(std::pair<double, double>(0.0920033, 5)); - pbns.push_back(std::pair<double, double>(0.104599, 6)); - pbns.push_back(std::pair<double, double>(0.114718, 7)); - pbns.push_back(std::pair<double, double>(0.117379, 8)); - pbns.push_back(std::pair<double, double>(0.123493, 9)); - pbns.push_back(std::pair<double, double>(0.133638, 10)); - pbns.push_back(std::pair<double, double>(0.137798, 9)); - pbns.push_back(std::pair<double, double>(0.149798, 10)); - pbns.push_back(std::pair<double, double>(0.155421, 11)); - pbns.push_back(std::pair<double, double>(0.158443, 12)); - pbns.push_back(std::pair<double, double>(0.176956, 13)); - pbns.push_back(std::pair<double, double>(0.183234, 12)); - pbns.push_back(std::pair<double, double>(0.191069, 13)); - pbns.push_back(std::pair<double, double>(0.191333, 14)); - pbns.push_back(std::pair<double, double>(0.191836, 15)); - pbns.push_back(std::pair<double, double>(0.192675, 16)); - pbns.push_back(std::pair<double, double>(0.208564, 17)); - pbns.push_back(std::pair<double, double>(0.218425, 18)); - pbns.push_back(std::pair<double, double>(0.219902, 17)); - pbns.push_back(std::pair<double, double>(0.23233, 16)); - pbns.push_back(std::pair<double, double>(0.234558, 17)); - pbns.push_back(std::pair<double, double>(0.237166, 16)); - pbns.push_back(std::pair<double, double>(0.247352, 17)); - pbns.push_back(std::pair<double, double>(0.267421, 18)); - pbns.push_back(std::pair<double, double>(0.268093, 19)); - pbns.push_back(std::pair<double, double>(0.278734, 18)); - pbns.push_back(std::pair<double, double>(0.284722, 19)); - pbns.push_back(std::pair<double, double>(0.284998, 20)); - pbns.push_back(std::pair<double, double>(0.294069, 21)); - pbns.push_back(std::pair<double, double>(0.306293, 22)); - pbns.push_back(std::pair<double, double>(0.322361, 21)); - pbns.push_back(std::pair<double, double>(0.323152, 22)); - pbns.push_back(std::pair<double, double>(0.371021, 23)); - pbns.push_back(std::pair<double, double>(0.372395, 24)); - pbns.push_back(std::pair<double, double>(0.387744, 25)); - pbns.push_back(std::pair<double, double>(0.435537, 26)); - pbns.push_back(std::pair<double, double>(0.462911, 25)); - pbns.push_back(std::pair<double, double>(0.483569, 26)); - pbns.push_back(std::pair<double, double>(0.489209, 25)); - pbns.push_back(std::pair<double, double>(0.517115, 24)); - pbns.push_back(std::pair<double, double>(0.522197, 23)); - pbns.push_back(std::pair<double, double>(0.532665, 22)); - pbns.push_back(std::pair<double, double>(0.545262, 23)); - pbns.push_back(std::pair<double, double>(0.587227, 22)); - pbns.push_back(std::pair<double, double>(0.593036, 23)); - pbns.push_back(std::pair<double, double>(0.602647, 24)); - pbns.push_back(std::pair<double, double>(0.605044, 25)); - pbns.push_back(std::pair<double, double>(0.621962, 24)); - pbns.push_back(std::pair<double, double>(0.629449, 23)); - pbns.push_back(std::pair<double, double>(0.636719, 22)); - pbns.push_back(std::pair<double, double>(0.64957, 21)); - pbns.push_back(std::pair<double, double>(0.650781, 22)); - pbns.push_back(std::pair<double, double>(0.654951, 23)); - pbns.push_back(std::pair<double, double>(0.683489, 24)); - pbns.push_back(std::pair<double, double>(0.687172, 23)); - pbns.push_back(std::pair<double, double>(0.69703, 22)); - pbns.push_back(std::pair<double, double>(0.701174, 21)); - pbns.push_back(std::pair<double, double>(0.717623, 22)); - pbns.push_back(std::pair<double, double>(0.722023, 21)); - pbns.push_back(std::pair<double, double>(0.722298, 20)); - pbns.push_back(std::pair<double, double>(0.725347, 19)); - pbns.push_back(std::pair<double, double>(0.73071, 18)); - pbns.push_back(std::pair<double, double>(0.758355, 17)); - pbns.push_back(std::pair<double, double>(0.770913, 18)); - pbns.push_back(std::pair<double, double>(0.790833, 17)); - pbns.push_back(std::pair<double, double>(0.821211, 16)); - pbns.push_back(std::pair<double, double>(0.849305, 17)); - pbns.push_back(std::pair<double, double>(0.853669, 16)); - pbns.push_back(std::pair<double, double>(0.866659, 15)); - pbns.push_back(std::pair<double, double>(0.872896, 16)); - pbns.push_back(std::pair<double, double>(0.889597, 15)); - pbns.push_back(std::pair<double, double>(0.900231, 14)); - pbns.push_back(std::pair<double, double>(0.903847, 13)); - pbns.push_back(std::pair<double, double>(0.906299, 12)); - pbns.push_back(std::pair<double, double>(0.910852, 11)); - pbns.push_back(std::pair<double, double>(0.93453, 10)); - pbns.push_back(std::pair<double, double>(0.944757, 9)); - pbns.push_back(std::pair<double, double>(0.947812, 8)); - pbns.push_back(std::pair<double, double>(0.959154, 7)); - pbns.push_back(std::pair<double, double>(0.975654, 6)); - pbns.push_back(std::pair<double, double>(0.976719, 5)); - pbns.push_back(std::pair<double, double>(0.977343, 4)); - pbns.push_back(std::pair<double, double>(0.980129, 3)); - pbns.push_back(std::pair<double, double>(0.987842, 2)); - pbns.push_back(std::pair<double, double>(0.990127, 1)); - pbns.push_back(std::pair<double, double>(0.994537, 0)); + std::vector<std::pair<double, size_t> > pbns; + pbns.push_back(std::pair<double, size_t>(0.0290362, 1)); + pbns.push_back(std::pair<double, size_t>(0.0307676, 2)); + pbns.push_back(std::pair<double, size_t>(0.0366312, 3)); + pbns.push_back(std::pair<double, size_t>(0.0544614, 4)); + pbns.push_back(std::pair<double, size_t>(0.0920033, 5)); + pbns.push_back(std::pair<double, size_t>(0.104599, 6)); + pbns.push_back(std::pair<double, size_t>(0.114718, 7)); + pbns.push_back(std::pair<double, size_t>(0.117379, 8)); + pbns.push_back(std::pair<double, size_t>(0.123493, 9)); + pbns.push_back(std::pair<double, size_t>(0.133638, 10)); + pbns.push_back(std::pair<double, size_t>(0.137798, 9)); + pbns.push_back(std::pair<double, size_t>(0.149798, 10)); + pbns.push_back(std::pair<double, size_t>(0.155421, 11)); + pbns.push_back(std::pair<double, size_t>(0.158443, 12)); + pbns.push_back(std::pair<double, size_t>(0.176956, 13)); + pbns.push_back(std::pair<double, size_t>(0.183234, 12)); + pbns.push_back(std::pair<double, size_t>(0.191069, 13)); + pbns.push_back(std::pair<double, size_t>(0.191333, 14)); + pbns.push_back(std::pair<double, size_t>(0.191836, 15)); + pbns.push_back(std::pair<double, size_t>(0.192675, 16)); + pbns.push_back(std::pair<double, size_t>(0.208564, 17)); + pbns.push_back(std::pair<double, size_t>(0.218425, 18)); + pbns.push_back(std::pair<double, size_t>(0.219902, 17)); + pbns.push_back(std::pair<double, size_t>(0.23233, 16)); + pbns.push_back(std::pair<double, size_t>(0.234558, 17)); + pbns.push_back(std::pair<double, size_t>(0.237166, 16)); + pbns.push_back(std::pair<double, size_t>(0.247352, 17)); + pbns.push_back(std::pair<double, size_t>(0.267421, 18)); + pbns.push_back(std::pair<double, size_t>(0.268093, 19)); + pbns.push_back(std::pair<double, size_t>(0.278734, 18)); + pbns.push_back(std::pair<double, size_t>(0.284722, 19)); + pbns.push_back(std::pair<double, size_t>(0.284998, 20)); + pbns.push_back(std::pair<double, size_t>(0.294069, 21)); + pbns.push_back(std::pair<double, size_t>(0.306293, 22)); + pbns.push_back(std::pair<double, size_t>(0.322361, 21)); + pbns.push_back(std::pair<double, size_t>(0.323152, 22)); + pbns.push_back(std::pair<double, size_t>(0.371021, 23)); + pbns.push_back(std::pair<double, size_t>(0.372395, 24)); + pbns.push_back(std::pair<double, size_t>(0.387744, 25)); + pbns.push_back(std::pair<double, size_t>(0.435537, 26)); + pbns.push_back(std::pair<double, size_t>(0.462911, 25)); + pbns.push_back(std::pair<double, size_t>(0.483569, 26)); + pbns.push_back(std::pair<double, size_t>(0.489209, 25)); + pbns.push_back(std::pair<double, size_t>(0.517115, 24)); + pbns.push_back(std::pair<double, size_t>(0.522197, 23)); + pbns.push_back(std::pair<double, size_t>(0.532665, 22)); + pbns.push_back(std::pair<double, size_t>(0.545262, 23)); + pbns.push_back(std::pair<double, size_t>(0.587227, 22)); + pbns.push_back(std::pair<double, size_t>(0.593036, 23)); + pbns.push_back(std::pair<double, size_t>(0.602647, 24)); + pbns.push_back(std::pair<double, size_t>(0.605044, 25)); + pbns.push_back(std::pair<double, size_t>(0.621962, 24)); + pbns.push_back(std::pair<double, size_t>(0.629449, 23)); + pbns.push_back(std::pair<double, size_t>(0.636719, 22)); + pbns.push_back(std::pair<double, size_t>(0.64957, 21)); + pbns.push_back(std::pair<double, size_t>(0.650781, 22)); + pbns.push_back(std::pair<double, size_t>(0.654951, 23)); + pbns.push_back(std::pair<double, size_t>(0.683489, 24)); + pbns.push_back(std::pair<double, size_t>(0.687172, 23)); + pbns.push_back(std::pair<double, size_t>(0.69703, 22)); + pbns.push_back(std::pair<double, size_t>(0.701174, 21)); + pbns.push_back(std::pair<double, size_t>(0.717623, 22)); + pbns.push_back(std::pair<double, size_t>(0.722023, 21)); + pbns.push_back(std::pair<double, size_t>(0.722298, 20)); + pbns.push_back(std::pair<double, size_t>(0.725347, 19)); + pbns.push_back(std::pair<double, size_t>(0.73071, 18)); + pbns.push_back(std::pair<double, size_t>(0.758355, 17)); + pbns.push_back(std::pair<double, size_t>(0.770913, 18)); + pbns.push_back(std::pair<double, size_t>(0.790833, 17)); + pbns.push_back(std::pair<double, size_t>(0.821211, 16)); + pbns.push_back(std::pair<double, size_t>(0.849305, 17)); + pbns.push_back(std::pair<double, size_t>(0.853669, 16)); + pbns.push_back(std::pair<double, size_t>(0.866659, 15)); + pbns.push_back(std::pair<double, size_t>(0.872896, 16)); + pbns.push_back(std::pair<double, size_t>(0.889597, 15)); + pbns.push_back(std::pair<double, size_t>(0.900231, 14)); + pbns.push_back(std::pair<double, size_t>(0.903847, 13)); + pbns.push_back(std::pair<double, size_t>(0.906299, 12)); + pbns.push_back(std::pair<double, size_t>(0.910852, 11)); + pbns.push_back(std::pair<double, size_t>(0.93453, 10)); + pbns.push_back(std::pair<double, size_t>(0.944757, 9)); + pbns.push_back(std::pair<double, size_t>(0.947812, 8)); + pbns.push_back(std::pair<double, size_t>(0.959154, 7)); + pbns.push_back(std::pair<double, size_t>(0.975654, 6)); + pbns.push_back(std::pair<double, size_t>(0.976719, 5)); + pbns.push_back(std::pair<double, size_t>(0.977343, 4)); + pbns.push_back(std::pair<double, size_t>(0.980129, 3)); + pbns.push_back(std::pair<double, size_t>(0.987842, 2)); + pbns.push_back(std::pair<double, size_t>(0.990127, 1)); + pbns.push_back(std::pair<double, size_t>(0.994537, 0)); std::vector<std::pair<double, size_t> > pbns_new = p.compute_persistent_betti_numbers(); for (size_t i = 0; i != pbns.size(); ++i) { - // cout << pbns_new[i].first << "," << pbns_new[i].second << std::endl; - BOOST_CHECK(fabs(pbns[i].first - pbns_new[i].first) <= epsilon); - BOOST_CHECK(fabs(pbns[i].second - pbns_new[i].second) <= epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(pbns[i].first, pbns_new[i].first, Gudhi::Persistence_representations::epsi); + BOOST_CHECK(pbns[i].second == pbns_new[i].second); } } @@ -297,7 +287,6 @@ BOOST_AUTO_TEST_CASE(check_k_n_n) { knn_template.push_back(0.786945); for (size_t i = 0; i != knn.size(); ++i) { - // cout << knn[i] << std::endl; - BOOST_CHECK(fabs(knn[i] - knn_template[i]) <= 0.000005); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(knn[i], knn_template[i], Gudhi::Persistence_representations::epsi); } } diff --git a/src/Persistence_representations/test/persistence_intervals_with_distances_test.cpp b/src/Persistence_representations/test/persistence_intervals_with_distances_test.cpp index 7b70eee3..631e4d70 100644 --- a/src/Persistence_representations/test/persistence_intervals_with_distances_test.cpp +++ b/src/Persistence_representations/test/persistence_intervals_with_distances_test.cpp @@ -24,8 +24,9 @@ #define BOOST_TEST_MODULE "Persistence_intervals_with_distances_test" #include <boost/test/unit_test.hpp> #include <gudhi/reader_utils.h> -#include "gudhi/Persistence_intervals_with_distances.h" -#include "gudhi/common_persistence_representations.h" +#include <gudhi/Persistence_intervals_with_distances.h> +#include <gudhi/common_persistence_representations.h> +#include <gudhi/Unitary_tests_utils.h> #include <iostream> @@ -38,9 +39,7 @@ BOOST_AUTO_TEST_CASE(check_bottleneck_distances_computation) { double dist = p.distance(q); - // std::cout << "dist : " << dist << std::endl; - - BOOST_CHECK(almost_equal(dist, 0.389043)); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(dist, 0.389043, Gudhi::Persistence_representations::epsi); } BOOST_AUTO_TEST_CASE(check_default_parameters_in_distance) { @@ -51,11 +50,7 @@ BOOST_AUTO_TEST_CASE(check_default_parameters_in_distance) { double max_parameter_distance = p.distance(q, std::numeric_limits<double>::max()); double inf_parameter_distance = p.distance(q, std::numeric_limits<double>::infinity()); - // std::cout << "default_parameter_distance : " << default_parameter_distance << std::endl; - // std::cout << "max_parameter_distance : " << max_parameter_distance << std::endl; - // std::cout << "inf_parameter_distance : " << inf_parameter_distance << std::endl; - - BOOST_CHECK(default_parameter_distance == max_parameter_distance); - BOOST_CHECK(inf_parameter_distance == max_parameter_distance); - BOOST_CHECK(inf_parameter_distance == max_parameter_distance); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(default_parameter_distance, max_parameter_distance); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(inf_parameter_distance, max_parameter_distance); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(inf_parameter_distance, max_parameter_distance); } diff --git a/src/Persistence_representations/test/persistence_lanscapes_on_grid_test.cpp b/src/Persistence_representations/test/persistence_lanscapes_on_grid_test.cpp index 6b1608fe..130ac8cc 100644 --- a/src/Persistence_representations/test/persistence_lanscapes_on_grid_test.cpp +++ b/src/Persistence_representations/test/persistence_lanscapes_on_grid_test.cpp @@ -25,12 +25,15 @@ #include <boost/test/unit_test.hpp> #include <gudhi/reader_utils.h> #include <gudhi/Persistence_landscape_on_grid.h> +#include <gudhi/Unitary_tests_utils.h> #include <iostream> using namespace Gudhi; using namespace Gudhi::Persistence_representations; +double epsilon = 0.0005; + BOOST_AUTO_TEST_CASE(check_construction_of_landscape) { Persistence_landscape_on_grid l("data/file_with_diagram_1", 100, std::numeric_limits<unsigned short>::max()); l.print_to_file("landscape_from_file_with_diagram_1"); @@ -53,16 +56,14 @@ BOOST_AUTO_TEST_CASE(check_construction_of_landscape_using_only_ten_levels) { std::vector<double> v2 = g.vectorize(level); BOOST_CHECK(v1.size() == v2.size()); for (size_t i = 0; i != v1.size(); ++i) { - BOOST_CHECK(v1[i] == v2[i]); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(v1[i], v2[i]); } } } BOOST_AUTO_TEST_CASE(check_computations_of_integrals) { Persistence_landscape_on_grid p("data/file_with_diagram_1", 100, std::numeric_limits<unsigned short>::max()); - double integral = p.compute_integral_of_landscape(); - // cerr << "integral : " << integral << endl;getchar(); - BOOST_CHECK(fabs(integral - 27.343) <= 0.00005); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(p.compute_integral_of_landscape(), 27.343, epsilon); } BOOST_AUTO_TEST_CASE(check_computations_of_integrals_for_each_level_separatelly) { @@ -92,9 +93,8 @@ BOOST_AUTO_TEST_CASE(check_computations_of_integrals_for_each_level_separatelly) integrals_fir_different_levels.push_back(0.202633); for (size_t level = 0; level != integrals_fir_different_levels.size(); ++level) { - double integral = p.compute_integral_of_landscape(level); - // cerr << integral << endl; - BOOST_CHECK(fabs(integral - integrals_fir_different_levels[level]) <= 0.00005); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(p.compute_integral_of_landscape(level), integrals_fir_different_levels[level], + epsilon); } } @@ -109,9 +109,8 @@ BOOST_AUTO_TEST_CASE(check_computations_of_integrals_of_powers_of_landscape) { integrals_fir_different_powers.push_back(0.23011); for (size_t power = 0; power != 5; ++power) { - double integral = p.compute_integral_of_landscape(power); - // cerr << integral << endl; - BOOST_CHECK(fabs(integral - integrals_fir_different_powers[power]) <= 0.00001); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(p.compute_integral_of_landscape(power), integrals_fir_different_powers[power], + epsilon); } } @@ -145,8 +144,8 @@ BOOST_AUTO_TEST_CASE(check_computations_of_values_on_different_points) { double x = 0.0012321; double dx = 0.05212; for (size_t i = 0; i != 10; ++i) { - BOOST_CHECK(almost_equal(p.compute_value_at_a_given_point(0, x), results_level_0[i])); - BOOST_CHECK(almost_equal(p.compute_value_at_a_given_point(10, x), results_level_10[i])); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(p.compute_value_at_a_given_point(0, x), results_level_0[i], epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(p.compute_value_at_a_given_point(10, x), results_level_10[i], epsilon); x += dx; } } @@ -179,37 +178,27 @@ BOOST_AUTO_TEST_CASE(check_computations_of_maxima_and_norms) { Persistence_landscape_on_grid second("data/file_with_diagram_2", 0., 1., 100); Persistence_landscape_on_grid sum = p + second; - // cerr << p.compute_maximum() << endl; - // cerr << p.compute_norm_of_landscape(1) << endl; - // cerr << p.compute_norm_of_landscape(2) << endl; - // cerr << p.compute_norm_of_landscape(3) << endl; - // cerr << compute_distance_of_landscapes_on_grid(p,sum,1) << endl; - // cerr << compute_distance_of_landscapes_on_grid(p,sum,2) << endl; - // cerr << compute_distance_of_landscapes_on_grid(p,sum,std::numeric_limits<double>::max()) << endl; - - BOOST_CHECK(fabs(p.compute_maximum() - 0.46) <= 0.00001); - BOOST_CHECK(fabs(p.compute_norm_of_landscape(1) - 27.3373) <= 0.00001); - BOOST_CHECK(fabs(p.compute_norm_of_landscape(2) - 1.84143) <= 0.00001); - BOOST_CHECK(fabs(p.compute_norm_of_landscape(3) - 0.927067) <= 0.00001); - BOOST_CHECK(fabs(compute_distance_of_landscapes_on_grid(p, sum, 1) - 16.8519) <= 0.00005); - BOOST_CHECK(fabs(compute_distance_of_landscapes_on_grid(p, sum, 2) - 1.44542) <= 0.00001); - BOOST_CHECK(fabs(compute_distance_of_landscapes_on_grid(p, sum, std::numeric_limits<double>::max()) - 0.45) <= - 0.00001); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(p.compute_maximum(), 0.46, epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(p.compute_norm_of_landscape(1), 27.3373, epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(p.compute_norm_of_landscape(2), 1.84143, epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(p.compute_norm_of_landscape(3), 0.927067, epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(compute_distance_of_landscapes_on_grid(p, sum, 1), 16.8519, epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(compute_distance_of_landscapes_on_grid(p, sum, 2), 1.44542, epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(compute_distance_of_landscapes_on_grid(p, sum, std::numeric_limits<double>::max()), + 0.45, epsilon); } BOOST_AUTO_TEST_CASE(check_default_parameters_of_distances) { - std::vector<std::pair<double, double> > diag = - read_persistence_intervals_in_dimension("data/file_with_diagram"); + std::vector<std::pair<double, double> > diag = read_persistence_intervals_in_dimension("data/file_with_diagram"); Persistence_landscape_on_grid p(diag, 0., 1., 100); - std::vector<std::pair<double, double> > diag1 = - read_persistence_intervals_in_dimension("data/file_with_diagram_1"); + std::vector<std::pair<double, double> > diag1 = read_persistence_intervals_in_dimension("data/file_with_diagram_1"); Persistence_landscape_on_grid q(diag1, 0., 1., 100); double dist_numeric_limit_max = p.distance(q, std::numeric_limits<double>::max()); double dist_infinity = p.distance(q, std::numeric_limits<double>::infinity()); - BOOST_CHECK(dist_numeric_limit_max == dist_infinity); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(dist_numeric_limit_max, dist_infinity); } BOOST_AUTO_TEST_CASE(check_computations_of_averages) { @@ -226,16 +215,15 @@ BOOST_AUTO_TEST_CASE(check_computations_of_averages) { BOOST_AUTO_TEST_CASE(check_computations_of_distances) { Persistence_landscape_on_grid p("data/file_with_diagram", 0., 1., 10000); Persistence_landscape_on_grid q("data/file_with_diagram_1", 0., 1., 10000); - BOOST_CHECK(fabs(p.distance(q) - 25.5779) <= 0.00005); - BOOST_CHECK(fabs(p.distance(q, 2) - 2.04891) <= 0.00001); - BOOST_CHECK(fabs(p.distance(q, std::numeric_limits<double>::max()) - 0.359) <= 0.00001); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(p.distance(q), 25.5779, epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(p.distance(q, 2), 2.04891, epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(p.distance(q, std::numeric_limits<double>::max()), 0.359, epsilon); } BOOST_AUTO_TEST_CASE(check_computations_of_scalar_product) { Persistence_landscape_on_grid p("data/file_with_diagram", 0., 1., 10000); Persistence_landscape_on_grid q("data/file_with_diagram_1", 0., 1., 10000); - // std::cerr << p.compute_scalar_product( q ) << std::endl; - BOOST_CHECK(almost_equal(p.compute_scalar_product(q), 0.754367)); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(p.compute_scalar_product(q), 0.754367, epsilon); } // Below I am storing the code used to generate tests for that functionality. diff --git a/src/Persistence_representations/test/persistence_lanscapes_test.cpp b/src/Persistence_representations/test/persistence_lanscapes_test.cpp index 81adb6fa..e98ef894 100644 --- a/src/Persistence_representations/test/persistence_lanscapes_test.cpp +++ b/src/Persistence_representations/test/persistence_lanscapes_test.cpp @@ -25,6 +25,7 @@ #include <boost/test/unit_test.hpp> #include <gudhi/reader_utils.h> #include <gudhi/Persistence_landscape.h> +#include <gudhi/Unitary_tests_utils.h> #include <iostream> #include <limits> @@ -32,14 +33,14 @@ using namespace Gudhi; using namespace Gudhi::Persistence_representations; -double epsilon = 0.0000005; +double epsilon = 0.0005; -BOOST_AUTO_TEST_CASE(check_construction_of_landscape) { +BOOST_AUTO_TEST_CASE(check_construction_of_landscape) { std::vector<std::pair<double, double> > diag = - read_persistence_intervals_in_one_dimension_from_file("data/file_with_diagram"); + read_persistence_intervals_in_one_dimension_from_file("data/file_with_diagram"); Persistence_landscape p(diag); - Persistence_landscape q; - q.load_landscape_from_file("data/file_with_landscape_from_file_with_diagram"); + Persistence_landscape q; + q.load_landscape_from_file("data/file_with_landscape_from_file_with_diagram"); BOOST_CHECK(p == q); } @@ -47,19 +48,15 @@ BOOST_AUTO_TEST_CASE(check_construction_of_landscape_form_gudhi_style_file) { Persistence_landscape p("data/persistence_file_with_four_entries_per_line", 1); // p.print_to_file("persistence_file_with_four_entries_per_line_landscape"); Persistence_landscape q; - q.load_landscape_from_file("data/persistence_file_with_four_entries_per_line_landscape"); + q.load_landscape_from_file("data/persistence_file_with_four_entries_per_line_landscape"); BOOST_CHECK(p == q); } - - BOOST_AUTO_TEST_CASE(check_computations_of_integrals) { std::vector<std::pair<double, double> > diag = read_persistence_intervals_in_one_dimension_from_file("data/file_with_diagram"); Persistence_landscape p(diag); - double integral = p.compute_integral_of_landscape(); - // cerr << integral << " " << 2.34992 << endl; - BOOST_CHECK(fabs(integral - 2.34992) <= 0.00001); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(p.compute_integral_of_landscape(), 2.34992, epsilon); } BOOST_AUTO_TEST_CASE(check_computations_of_integrals_for_each_level_separatelly) { @@ -67,37 +64,37 @@ BOOST_AUTO_TEST_CASE(check_computations_of_integrals_for_each_level_separatelly) read_persistence_intervals_in_one_dimension_from_file("data/file_with_diagram"); Persistence_landscape p(diag); - std::vector<double> integrals_fir_different_levels; - integrals_fir_different_levels.push_back(0.216432); - integrals_fir_different_levels.push_back(0.204763); - integrals_fir_different_levels.push_back(0.188793); - integrals_fir_different_levels.push_back(0.178856); - integrals_fir_different_levels.push_back(0.163142); - integrals_fir_different_levels.push_back(0.155015); - integrals_fir_different_levels.push_back(0.143046); - integrals_fir_different_levels.push_back(0.133765); - integrals_fir_different_levels.push_back(0.123531); - integrals_fir_different_levels.push_back(0.117393); - integrals_fir_different_levels.push_back(0.111269); - integrals_fir_different_levels.push_back(0.104283); - integrals_fir_different_levels.push_back(0.0941308); - integrals_fir_different_levels.push_back(0.0811208); - integrals_fir_different_levels.push_back(0.0679001); - integrals_fir_different_levels.push_back(0.0580801); - integrals_fir_different_levels.push_back(0.0489647); - integrals_fir_different_levels.push_back(0.0407936); - integrals_fir_different_levels.push_back(0.0342599); - integrals_fir_different_levels.push_back(0.02896); - integrals_fir_different_levels.push_back(0.0239881); - integrals_fir_different_levels.push_back(0.0171792); - integrals_fir_different_levels.push_back(0.0071511); - integrals_fir_different_levels.push_back(0.00462067); - integrals_fir_different_levels.push_back(0.00229033); - integrals_fir_different_levels.push_back(0.000195296); + std::vector<double> integrals_for_different_levels; + integrals_for_different_levels.push_back(0.216432); + integrals_for_different_levels.push_back(0.204763); + integrals_for_different_levels.push_back(0.188793); + integrals_for_different_levels.push_back(0.178856); + integrals_for_different_levels.push_back(0.163142); + integrals_for_different_levels.push_back(0.155015); + integrals_for_different_levels.push_back(0.143046); + integrals_for_different_levels.push_back(0.133765); + integrals_for_different_levels.push_back(0.123531); + integrals_for_different_levels.push_back(0.117393); + integrals_for_different_levels.push_back(0.111269); + integrals_for_different_levels.push_back(0.104283); + integrals_for_different_levels.push_back(0.0941308); + integrals_for_different_levels.push_back(0.0811208); + integrals_for_different_levels.push_back(0.0679001); + integrals_for_different_levels.push_back(0.0580801); + integrals_for_different_levels.push_back(0.0489647); + integrals_for_different_levels.push_back(0.0407936); + integrals_for_different_levels.push_back(0.0342599); + integrals_for_different_levels.push_back(0.02896); + integrals_for_different_levels.push_back(0.0239881); + integrals_for_different_levels.push_back(0.0171792); + integrals_for_different_levels.push_back(0.0071511); + integrals_for_different_levels.push_back(0.00462067); + integrals_for_different_levels.push_back(0.00229033); + integrals_for_different_levels.push_back(0.000195296); for (size_t level = 0; level != p.size(); ++level) { - double integral = p.compute_integral_of_a_level_of_a_landscape(level); - BOOST_CHECK(fabs(integral - integrals_fir_different_levels[level]) <= 0.00001); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(p.compute_integral_of_a_level_of_a_landscape(level), + integrals_for_different_levels[level], epsilon); } } @@ -106,16 +103,16 @@ BOOST_AUTO_TEST_CASE(check_computations_of_integrals_of_powers_of_landscape) { read_persistence_intervals_in_one_dimension_from_file("data/file_with_diagram"); Persistence_landscape p(diag); - std::vector<double> integrals_fir_different_powers; - integrals_fir_different_powers.push_back(17.1692); - integrals_fir_different_powers.push_back(2.34992); - integrals_fir_different_powers.push_back(0.49857); - integrals_fir_different_powers.push_back(0.126405); - integrals_fir_different_powers.push_back(0.0355235); + std::vector<double> integrals_for_different_powers; + integrals_for_different_powers.push_back(17.1692); + integrals_for_different_powers.push_back(2.34992); + integrals_for_different_powers.push_back(0.49857); + integrals_for_different_powers.push_back(0.126405); + integrals_for_different_powers.push_back(0.0355235); for (size_t power = 0; power != 5; ++power) { - double integral = p.compute_integral_of_landscape((double)power); - BOOST_CHECK(fabs(integral - integrals_fir_different_powers[power]) <= 0.00005); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(p.compute_integral_of_landscape((double)power), + integrals_for_different_powers[power], epsilon); } } @@ -124,18 +121,18 @@ BOOST_AUTO_TEST_CASE(check_computations_of_values_on_different_points) { read_persistence_intervals_in_one_dimension_from_file("data/file_with_diagram"); Persistence_landscape p(diag); - BOOST_CHECK(fabs(p.compute_value_at_a_given_point(1, 0.0)) <= 0.00001); - BOOST_CHECK(fabs(p.compute_value_at_a_given_point(1, 0.1) - 0.0692324) <= 0.00001); - BOOST_CHECK(fabs(p.compute_value_at_a_given_point(1, 0.2) - 0.163369) <= 0.00001); - BOOST_CHECK(fabs(p.compute_value_at_a_given_point(1, 0.3) - 0.217115) <= 0.00001); - BOOST_CHECK(fabs(p.compute_value_at_a_given_point(2, 0.0)) <= 0.00001); - BOOST_CHECK(fabs(p.compute_value_at_a_given_point(2, 0.1) - 0.0633688) <= 0.00001); - BOOST_CHECK(fabs(p.compute_value_at_a_given_point(2, 0.2) - 0.122361) <= 0.00001); - BOOST_CHECK(fabs(p.compute_value_at_a_given_point(2, 0.3) - 0.195401) <= 0.00001); - BOOST_CHECK(fabs(p.compute_value_at_a_given_point(3, 0.0)) <= 0.00001); - BOOST_CHECK(fabs(p.compute_value_at_a_given_point(3, 0.1) - 0.0455386) <= 0.00001); - BOOST_CHECK(fabs(p.compute_value_at_a_given_point(3, 0.2) - 0.0954012) <= 0.00001); - BOOST_CHECK(fabs(p.compute_value_at_a_given_point(3, 0.3) - 0.185282) <= 0.00001); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(p.compute_value_at_a_given_point(1, 0.0), 0., epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(p.compute_value_at_a_given_point(1, 0.1), 0.0692324, epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(p.compute_value_at_a_given_point(1, 0.2), 0.163369, epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(p.compute_value_at_a_given_point(1, 0.3), 0.217115, epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(p.compute_value_at_a_given_point(2, 0.0), 0., epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(p.compute_value_at_a_given_point(2, 0.1), 0.0633688, epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(p.compute_value_at_a_given_point(2, 0.2), 0.122361, epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(p.compute_value_at_a_given_point(2, 0.3), 0.195401, epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(p.compute_value_at_a_given_point(3, 0.0), 0., epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(p.compute_value_at_a_given_point(3, 0.1), 0.0455386, epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(p.compute_value_at_a_given_point(3, 0.2), 0.0954012, epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(p.compute_value_at_a_given_point(3, 0.3), 0.185282, epsilon); } BOOST_AUTO_TEST_CASE(check_computations_sum_differences_and_multiplications) { @@ -171,13 +168,14 @@ BOOST_AUTO_TEST_CASE(check_computations_of_maxima_and_norms) { second.load_landscape_from_file("data/file_with_landscape_from_file_with_diagram_1"); Persistence_landscape sum = p + second; - BOOST_CHECK(fabs(p.compute_maximum() - 0.431313) <= 0.00001); - BOOST_CHECK(fabs(p.compute_norm_of_landscape(1) - 2.34992) <= 0.00001); - BOOST_CHECK(fabs(p.compute_norm_of_landscape(2) - 0.706095) <= 0.00001); - BOOST_CHECK(fabs(p.compute_norm_of_landscape(3) - 0.501867) <= 0.00001); - BOOST_CHECK(fabs(compute_distance_of_landscapes(p, sum, 1) - 27.9323) <= 0.00005); - BOOST_CHECK(fabs(compute_distance_of_landscapes(p, sum, 2) - 2.35199) <= 0.00001); - BOOST_CHECK(fabs(compute_distance_of_landscapes(p, sum, std::numeric_limits<double>::max()) - 0.464478) <= 0.00001); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(p.compute_maximum(), 0.431313, epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(p.compute_norm_of_landscape(1), 2.34992, epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(p.compute_norm_of_landscape(2), 0.706095, epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(p.compute_norm_of_landscape(3), 0.501867, epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(compute_distance_of_landscapes(p, sum, 1), 27.9323, epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(compute_distance_of_landscapes(p, sum, 2), 2.35199, epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(compute_distance_of_landscapes(p, sum, std::numeric_limits<double>::max()), 0.464478, + epsilon); } BOOST_AUTO_TEST_CASE(check_default_parameters_of_distances) { @@ -192,7 +190,7 @@ BOOST_AUTO_TEST_CASE(check_default_parameters_of_distances) { double dist_numeric_limit_max = p.distance(q, std::numeric_limits<double>::max()); double dist_infinity = p.distance(q, std::numeric_limits<double>::infinity()); - BOOST_CHECK(dist_numeric_limit_max == dist_infinity); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(dist_numeric_limit_max, dist_infinity); } BOOST_AUTO_TEST_CASE(check_computations_of_averages) { @@ -217,13 +215,9 @@ BOOST_AUTO_TEST_CASE(check_computations_of_distances) { std::vector<std::pair<double, double> > diag2 = read_persistence_intervals_in_one_dimension_from_file("data/file_with_diagram_1"); Persistence_landscape q(diag2); - std::cout << "p.distance(q) = " << p.distance(q) << std::endl; - BOOST_CHECK(fabs(p.distance(q) - 25.5824) <= 0.00005); - std::cout << "p.distance(q, 2) = " << p.distance(q, 2) << std::endl; - BOOST_CHECK(fabs(p.distance(q, 2) - 2.1264) <= 0.0001); - std::cout << "p.distance(q, std::numeric_limits<double>::max()) = " << - p.distance(q, std::numeric_limits<double>::max()) << std::endl; - BOOST_CHECK(fabs(p.distance(q, std::numeric_limits<double>::max()) - 0.359068) <= 0.00001); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(p.distance(q), 25.5824, epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(p.distance(q, 2), 2.1264, epsilon); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(p.distance(q, std::numeric_limits<double>::max()), 0.359068, epsilon); } BOOST_AUTO_TEST_CASE(check_computations_of_scalar_product) { @@ -233,33 +227,9 @@ BOOST_AUTO_TEST_CASE(check_computations_of_scalar_product) { std::vector<std::pair<double, double> > diag2 = read_persistence_intervals_in_one_dimension_from_file("data/file_with_diagram_1"); Persistence_landscape q(diag2); - BOOST_CHECK(fabs(p.compute_scalar_product(q) - 0.754498) <= 0.00001); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(p.compute_scalar_product(q), 0.754498, epsilon); } - - - - - - - - - - - - - - - - - - - - - - - - // Below I am storing the code used to generate tests for that functionality. /* if ( argc != 2 ) diff --git a/src/Persistence_representations/test/read_persistence_from_file_test.cpp b/src/Persistence_representations/test/read_persistence_from_file_test.cpp index 76d7cdb0..276b92ab 100644 --- a/src/Persistence_representations/test/read_persistence_from_file_test.cpp +++ b/src/Persistence_representations/test/read_persistence_from_file_test.cpp @@ -21,7 +21,7 @@ */ #define BOOST_TEST_DYN_LINK -#define BOOST_TEST_MODULE "Persistence_representations" +#define BOOST_TEST_MODULE "read_persistence_from_file_test" #include <boost/test/unit_test.hpp> #include <gudhi/read_persistence_from_file.h> @@ -30,8 +30,6 @@ using namespace Gudhi; using namespace Gudhi::Persistence_representations; - - BOOST_AUTO_TEST_CASE(test_read_file_with_four_elements_per_line) { std::vector<std::pair<double, double> > what_we_should_get; what_we_should_get.push_back(std::make_pair(0, 2)); @@ -39,7 +37,7 @@ BOOST_AUTO_TEST_CASE(test_read_file_with_four_elements_per_line) { what_we_should_get.push_back(std::make_pair(10, 90)); what_we_should_get.push_back(std::make_pair(4, 4)); std::vector<std::pair<double, double> > what_we_get = read_persistence_intervals_in_one_dimension_from_file( - "data/persistence_file_with_four_entries_per_line", 1, 1000); + "data/persistence_file_with_four_entries_per_line", 1, 1000); // for ( size_t i = 0 ; i != what_we_get.size() ; ++i ) //{ @@ -76,7 +74,6 @@ BOOST_AUTO_TEST_CASE(test_read_file_with_three_elements_per_line) { } } - BOOST_AUTO_TEST_CASE(test_read_file_with_two_elements_per_line) { std::vector<std::pair<double, double> > what_we_should_get; what_we_should_get.push_back(std::make_pair(4, 10)); @@ -84,12 +81,11 @@ BOOST_AUTO_TEST_CASE(test_read_file_with_two_elements_per_line) { what_we_should_get.push_back(std::make_pair(0, 1)); what_we_should_get.push_back(std::make_pair(1, 4)); - std::vector<std::pair<double, double> > what_we_get = - read_persistence_intervals_in_one_dimension_from_file("data/persistence_file_with_two_entries_per_line", -1, 9999); + std::vector<std::pair<double, double> > what_we_get = read_persistence_intervals_in_one_dimension_from_file( + "data/persistence_file_with_two_entries_per_line", -1, 9999); BOOST_CHECK(what_we_should_get.size() == what_we_get.size()); for (size_t i = 0; i != what_we_get.size(); ++i) { BOOST_CHECK(what_we_should_get[i] == what_we_get[i]); } } - diff --git a/src/Persistence_representations/test/vector_representation_test.cpp b/src/Persistence_representations/test/vector_representation_test.cpp index 3f3e2abe..c545dce7 100644 --- a/src/Persistence_representations/test/vector_representation_test.cpp +++ b/src/Persistence_representations/test/vector_representation_test.cpp @@ -26,7 +26,7 @@ #include <iostream> #define BOOST_TEST_DYN_LINK -#define BOOST_TEST_MODULE "Persistence_representations" +#define BOOST_TEST_MODULE "vector_representation_test" #include <boost/test/unit_test.hpp> #include <gudhi/reader_utils.h> #include <vector> @@ -295,12 +295,10 @@ BOOST_AUTO_TEST_CASE(check_distance_computations) { } BOOST_AUTO_TEST_CASE(check_default_parameters_of_distances) { - std::vector<std::pair<double, double> > diag = - read_persistence_intervals_in_dimension("data/file_with_diagram"); + std::vector<std::pair<double, double> > diag = read_persistence_intervals_in_dimension("data/file_with_diagram"); Vector_distances_in_diagram<Euclidean_distance> p(diag, 100); - std::vector<std::pair<double, double> > diag1 = - read_persistence_intervals_in_dimension("data/file_with_diagram_1"); + std::vector<std::pair<double, double> > diag1 = read_persistence_intervals_in_dimension("data/file_with_diagram_1"); Vector_distances_in_diagram<Euclidean_distance> q(diag1, 100); double dist_numeric_limit_max = p.distance(q, std::numeric_limits<double>::max()); diff --git a/src/Persistence_representations/utilities/CMakeLists.txt b/src/Persistence_representations/utilities/CMakeLists.txt index 66524666..137eb0c1 100644 --- a/src/Persistence_representations/utilities/CMakeLists.txt +++ b/src/Persistence_representations/utilities/CMakeLists.txt @@ -1,6 +1,53 @@ +# Copy files, otherwise result files are created in sources +file(COPY "${CMAKE_SOURCE_DIR}/data/persistence_diagram/first.pers" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/") +file(COPY "${CMAKE_SOURCE_DIR}/data/persistence_diagram/second.pers" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/") + +function(add_persistence_representation_creation_utility creation_utility) + add_executable ( ${creation_utility} ${creation_utility}.cpp ) + + # as the function is called in a subdirectory level, need to '../' to find persistence files + # ARGN will add all the other arguments (except creation_utility) sent to the CMake functions + add_test(NAME Persistence_representation_utilities_${creation_utility} COMMAND $<TARGET_FILE:${creation_utility}> + ${ARGN} "${CMAKE_CURRENT_BINARY_DIR}/../first.pers" + "${CMAKE_CURRENT_BINARY_DIR}/../second.pers") +endfunction(add_persistence_representation_creation_utility) + +function(add_persistence_representation_plot_utility plot_utility tool_extension) + add_executable ( ${plot_utility} ${plot_utility}.cpp ) + + # as the function is called in a subdirectory level, need to '../' to find persistence heat maps files + add_test(NAME Persistence_representation_utilities_${plot_utility}_first COMMAND $<TARGET_FILE:${plot_utility}> + "${CMAKE_CURRENT_BINARY_DIR}/../first.pers${tool_extension}") + #add_test(NAME Persistence_representation_utilities_${plot_utility}_second COMMAND $<TARGET_FILE:${plot_utility}> + # "${CMAKE_CURRENT_BINARY_DIR}/../second.pers${tool_extension}") + if(GNUPLOT_PATH) + add_test(NAME Persistence_representation_utilities_${plot_utility}_first_gnuplot COMMAND ${GNUPLOT_PATH} + "-e" "load '${CMAKE_CURRENT_BINARY_DIR}/../first.pers${tool_extension}_GnuplotScript'") + #add_test(NAME Persistence_representation_utilities_${plot_utility}_second_gnuplot COMMAND ${GNUPLOT_PATH} + # "-e" "load '${CMAKE_CURRENT_BINARY_DIR}/../second.pers${tool_extension}_GnuplotScript'") + endif() +endfunction(add_persistence_representation_plot_utility) + +function(add_persistence_representation_function_utility function_utility tool_extension) + add_executable ( ${function_utility} ${function_utility}.cpp ) + + # ARGV2 is an optional argument + if (${ARGV2}) + # as the function is called in a subdirectory level, need to '../' to find persistence heat maps files + add_test(NAME Persistence_representation_utilities_${function_utility} COMMAND $<TARGET_FILE:${function_utility}> + "${ARGV2}" + "${CMAKE_CURRENT_BINARY_DIR}/../first.pers${tool_extension}" + "${CMAKE_CURRENT_BINARY_DIR}/../second.pers${tool_extension}") + else() + # as the function is called in a subdirectory level, need to '../' to find persistence heat maps files + add_test(NAME Persistence_representation_utilities_${function_utility} COMMAND $<TARGET_FILE:${function_utility}> + "${CMAKE_CURRENT_BINARY_DIR}/../first.pers${tool_extension}" + "${CMAKE_CURRENT_BINARY_DIR}/../second.pers${tool_extension}") + endif() +endfunction(add_persistence_representation_function_utility) + add_subdirectory(persistence_heat_maps) add_subdirectory(persistence_intervals) add_subdirectory(persistence_landscapes) add_subdirectory(persistence_landscapes_on_grid) add_subdirectory(persistence_vectors) - diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_heat_maps/CMakeLists.txt index 0dd63852..386e9fa5 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/CMakeLists.txt +++ b/src/Persistence_representations/utilities/persistence_heat_maps/CMakeLists.txt @@ -1,63 +1,15 @@ cmake_minimum_required(VERSION 2.6) project(Persistence_representations_heat_maps_utilities) -file(COPY "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/") - -add_executable ( create_persistence_heat_maps create_persistence_heat_maps.cpp ) -target_link_libraries(create_persistence_heat_maps ${Boost_SYSTEM_LIBRARY}) - -add_test(NAME create_persistence_heat_maps COMMAND $<TARGET_FILE:create_persistence_heat_maps> - "10" "-1" "-1" "4" "-1" "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") - - -add_executable ( create_pssk create_pssk.cpp ) -target_link_libraries(create_pssk ${Boost_SYSTEM_LIBRARY}) - -add_test(NAME create_pssk COMMAND $<TARGET_FILE:create_pssk> - "10" "-1" "-1" "4" "-1" "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") - -add_executable ( create_p_h_m_weighted_by_distance_from_diagonal create_p_h_m_weighted_by_distance_from_diagonal.cpp ) -target_link_libraries(create_p_h_m_weighted_by_distance_from_diagonal ${Boost_SYSTEM_LIBRARY}) - -add_test(NAME create_p_h_m_weighted_by_distance_from_diagonal COMMAND $<TARGET_FILE:create_p_h_m_weighted_by_distance_from_diagonal> - "10" "-1" "-1" "4" "-1" "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") - -add_executable ( create_p_h_m_weighted_by_squared_diag_distance create_p_h_m_weighted_by_squared_diag_distance.cpp ) -target_link_libraries(create_p_h_m_weighted_by_squared_diag_distance ${Boost_SYSTEM_LIBRARY}) - -add_test(NAME create_p_h_m_weighted_by_squared_diag_distance COMMAND $<TARGET_FILE:create_p_h_m_weighted_by_squared_diag_distance> - "10" "-1" "-1" "4" "-1" "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") - -add_executable ( create_p_h_m_weighted_by_arctan_of_their_persistence create_p_h_m_weighted_by_arctan_of_their_persistence.cpp ) -target_link_libraries(create_p_h_m_weighted_by_arctan_of_their_persistence ${Boost_SYSTEM_LIBRARY}) - -add_test(NAME create_p_h_m_weighted_by_arctan_of_their_persistence COMMAND $<TARGET_FILE:create_p_h_m_weighted_by_arctan_of_their_persistence> - "10" "-1" "-1" "4" "-1" "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") - -add_executable ( average_persistence_heat_maps average_persistence_heat_maps.cpp ) -target_link_libraries(average_persistence_heat_maps ${Boost_SYSTEM_LIBRARY}) - -add_test(NAME average_persistence_heat_maps COMMAND $<TARGET_FILE:average_persistence_heat_maps> - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt" - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") - -add_executable ( plot_persistence_heat_map plot_persistence_heat_map.cpp ) -target_link_libraries(plot_persistence_heat_map ${Boost_SYSTEM_LIBRARY}) - -add_test(NAME plot_persistence_heat_map COMMAND $<TARGET_FILE:plot_persistence_heat_map> - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") - -add_executable ( compute_distance_of_persistence_heat_maps compute_distance_of_persistence_heat_maps.cpp ) -target_link_libraries(compute_distance_of_persistence_heat_maps ${Boost_SYSTEM_LIBRARY}) - -add_test(NAME compute_distance_of_persistence_heat_maps COMMAND $<TARGET_FILE:compute_distance_of_persistence_heat_maps> - "1" - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt" - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") - -add_executable ( compute_scalar_product_of_persistence_heat_maps compute_scalar_product_of_persistence_heat_maps.cpp ) -target_link_libraries(compute_scalar_product_of_persistence_heat_maps ${Boost_SYSTEM_LIBRARY}) - -add_test(NAME compute_scalar_product_of_persistence_heat_maps COMMAND $<TARGET_FILE:compute_scalar_product_of_persistence_heat_maps> - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt" - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") +add_persistence_representation_creation_utility(create_pssk "10" "-1" "-1" "4" "-1") +add_persistence_representation_creation_utility(create_p_h_m_weighted_by_arctan_of_their_persistence "10" "-1" "-1" "4" "-1") +add_persistence_representation_creation_utility(create_p_h_m_weighted_by_distance_from_diagonal "10" "-1" "-1" "4" "-1") +add_persistence_representation_creation_utility(create_p_h_m_weighted_by_squared_diag_distance "10" "-1" "-1" "4" "-1") +# Need to set grid min and max for further average, distance and scalar_product +add_persistence_representation_creation_utility(create_persistence_heat_maps "10" "0" "35" "10" "-1") + +add_persistence_representation_plot_utility(plot_persistence_heat_map ".mps") + +add_persistence_representation_function_utility(average_persistence_heat_maps ".mps") +add_persistence_representation_function_utility(compute_distance_of_persistence_heat_maps ".mps" "1") +add_persistence_representation_function_utility(compute_scalar_product_of_persistence_heat_maps ".mps") diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/average_persistence_heat_maps.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/average_persistence_heat_maps.cpp index 4e81375a..6739e0b6 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/average_persistence_heat_maps.cpp +++ b/src/Persistence_representations/utilities/persistence_heat_maps/average_persistence_heat_maps.cpp @@ -29,21 +29,20 @@ using constant_scaling_function = Gudhi::Persistence_representations::constant_s using Persistence_heat_maps = Gudhi::Persistence_representations::Persistence_heat_maps<constant_scaling_function>; int main(int argc, char** argv) { - std::cout << "This program computes average persistence landscape of persistence landscapes created based on " - "persistence diagrams provided as an input. Please call this program with the names of files with " - "persistence diagrams \n"; - std::vector<const char*> filenames; + std::cout << "This program computes average of persistence heat maps stored in files (the files needs to be " + << "created beforehand).\n" + << "The parameters of this programs are names of files with persistence heat maps.\n"; - if (argc == 1) { - std::cout << "No input files given, the program will now terminate \n"; + if (argc < 3) { + std::cout << "Wrong number of parameters, the program will now terminate \n"; return 1; } + std::vector<const char*> filenames; for (int i = 1; i < argc; ++i) { filenames.push_back(argv[i]); } - std::cout << "Creating persistence landscapes...\n"; std::vector<Persistence_heat_maps*> maps; for (size_t i = 0; i != filenames.size(); ++i) { Persistence_heat_maps* l = new Persistence_heat_maps; @@ -53,13 +52,12 @@ int main(int argc, char** argv) { Persistence_heat_maps av; av.compute_average(maps); - av.print_to_file("average.mps"); for (size_t i = 0; i != filenames.size(); ++i) { delete maps[i]; } - std::cout << "Done \n"; + std::cout << "Average can be found in 'average.mps' file\n"; return 0; } diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp index befb0837..ed8278a2 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp +++ b/src/Persistence_representations/utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp @@ -31,11 +31,11 @@ using constant_scaling_function = Gudhi::Persistence_representations::constant_s using Persistence_heat_maps = Gudhi::Persistence_representations::Persistence_heat_maps<constant_scaling_function>; int main(int argc, char** argv) { - std::cout << "This program computes distance of persistence heat maps stored in a file (the file needs to be created " - "beforehand). \n"; - std::cout << "The first parameter of a program is an integer p. The program compute L^p distance of the two heat " - "maps. For L^infty distance choose p = -1. \n"; - std::cout << "The remaining parameters of this program are names of files with persistence heat maps.\n"; + std::cout << "This program computes distance of persistence heat maps stored in files (the files needs to be " + << "created beforehand).\n" + << "The first parameter of a program is an integer p. The program compute L^p distance of the two heat " + << "maps. For L^infty distance choose p = -1. \n" + << "The remaining parameters of this program are names of files with persistence heat maps.\n"; if (argc < 3) { std::cout << "Wrong number of parameters, the program will now terminate \n"; @@ -78,7 +78,7 @@ int main(int argc, char** argv) { // and now output the result to the screen and a file: std::ofstream out; - out.open("distance"); + out.open("distance.mps"); for (size_t i = 0; i != distance.size(); ++i) { for (size_t j = 0; j != distance.size(); ++j) { std::cout << distance[i][j] << " "; @@ -89,5 +89,6 @@ int main(int argc, char** argv) { } out.close(); + std::cout << "Distance can be found in 'distance.mps' file\n"; return 0; } diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp index c684a336..63626853 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp +++ b/src/Persistence_representations/utilities/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp @@ -30,9 +30,14 @@ using constant_scaling_function = Gudhi::Persistence_representations::constant_s using Persistence_heat_maps = Gudhi::Persistence_representations::Persistence_heat_maps<constant_scaling_function>; int main(int argc, char** argv) { - std::cout << "This program computes scalar product of persistence landscapes stored in a file (the file needs to be " - "created beforehand). \n"; - std::cout << "The parameters of this programs are names of files with persistence landscapes.\n"; + std::cout << "This program computes scalar product of persistence heat maps stored in a file (the file needs to be " + << "created beforehand). \n" + << "The parameters of this programs are names of files with persistence heat maps.\n"; + + if (argc < 3) { + std::cout << "Wrong number of parameters, the program will now terminate \n"; + return 1; + } std::vector<const char*> filenames; for (int i = 1; i < argc; ++i) { @@ -64,7 +69,7 @@ int main(int argc, char** argv) { // and now output the result to the screen and a file: std::ofstream out; - out.open("scalar_product"); + out.open("scalar_product.mps"); for (size_t i = 0; i != scalar_product.size(); ++i) { for (size_t j = 0; j != scalar_product.size(); ++j) { std::cout << scalar_product[i][j] << " "; @@ -75,5 +80,6 @@ int main(int argc, char** argv) { } out.close(); + std::cout << "Distance can be found in 'scalar_product.mps' file\n"; return 0; } diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp index 2bf185a3..b4a1daa5 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp +++ b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp @@ -29,25 +29,25 @@ using arc_tan_of_persistence_of_point = Gudhi::Persistence_representations::arc_tan_of_persistence_of_point; using Persistence_heat_maps = - Gudhi::Persistence_representations::Persistence_heat_maps<arc_tan_of_persistence_of_point>; + Gudhi::Persistence_representations::Persistence_heat_maps<arc_tan_of_persistence_of_point>; int main(int argc, char** argv) { - std::cout << "This program creates persistence heat map of diagrams provided as an input. The Gaussian kernels are " - "weighted by the arc tangential of their persistence.\n"; - std::cout << "The first parameter of a program is an integer, a size of a grid.\n"; - std::cout << "The second and third parameters are min and max of the grid. If you want those numbers to be computed " - "based on the data, set them both to -1 \n"; - std::cerr << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number " - "of pixels \n"; - std::cout << "The fifth parameter of this program is a dimension of persistence that will be used in creation of the " - "persistence heat maps."; - std::cout << "If our input files contain persistence pairs of various dimension, as a fifth parameter of the " - "procedure please provide the dimension of persistence you want to use."; - std::cout << "If in your file there are only birth-death pairs of the same dimension, set the first parameter to -1." - << std::endl; - std::cout << "The remaining parameters are the names of files with persistence diagrams. \n"; + std::cout << "This program creates persistence heat map files (*.mps) of persistence diagrams files (*.pers) " + << "provided as an input.The Gaussian kernels are weighted by the arc tangential of their persistence.\n" + << "The first parameter of a program is an integer, a size of a grid.\n" + << "The second and third parameters are min and max of the grid. If you want those numbers to be computed " + << "based on the data, set them both to -1 \n" + << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number " + << "of pixels.\n" + << "The fifth parameter of this program is a dimension of persistence that will be used in creation of " + << "the persistence heat maps." + << "If your input files contains persistence pairs of various dimension, as a fifth parameter of the " + << "procedure please provide the dimension of persistence you want to use." + << "If in your files there are only birth-death pairs of the same dimension, set the fifth parameter to " + << "-1.\n" + << "The remaining parameters are the names of files with persistence diagrams. \n"; - if (argc < 5) { + if (argc < 7) { std::cout << "Wrong parameter list, the program will now terminate \n"; return 1; } @@ -68,9 +68,7 @@ int main(int argc, char** argv) { filenames.push_back(argv[i]); } - std::cout << "Creating persistence heat maps...\n"; std::vector<std::vector<double> > filter = Gudhi::Persistence_representations::create_Gaussian_filter(stdiv, 1); - for (size_t i = 0; i != filenames.size(); ++i) { std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl; Persistence_heat_maps l(filenames[i], filter, false, size_of_grid, min_, max_, dimension); @@ -79,6 +77,5 @@ int main(int argc, char** argv) { ss << filenames[i] << ".mps"; l.print_to_file(ss.str().c_str()); } - std::cout << "Done \n"; return 0; } diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp index ec9477f1..c50f9ddb 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp +++ b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp @@ -28,26 +28,26 @@ #include <vector> using distance_from_diagonal_scaling = Gudhi::Persistence_representations::distance_from_diagonal_scaling; -using Persistence_heat_maps = - Gudhi::Persistence_representations::Persistence_heat_maps<distance_from_diagonal_scaling>; +using Persistence_heat_maps = Gudhi::Persistence_representations::Persistence_heat_maps<distance_from_diagonal_scaling>; int main(int argc, char** argv) { - std::cout << "This program creates persistence heat map of diagrams provided as an input. The Gaussian kernels are " - "weighted by the distance of a center from the diagonal.\n"; - std::cout << "The first parameter of a program is an integer, a size of a grid.\n"; - std::cout << "The second and third parameters are min and max of the grid. If you want those numbers to be computed " - "based on the data, set them both to -1 \n"; - std::cerr << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number " - "of pixels \n"; - std::cout << "The fifth parameter of this program is a dimension of persistence that will be used in creation of the " - "persistence heat maps."; - std::cout << "If our input files contain persistence pairs of various dimension, as a fifth parameter of the " - "procedure please provide the dimension of persistence you want to use."; - std::cout << "If in your file there are only birth-death pairs of the same dimension, set the first parameter to -1." - << std::endl; - std::cout << "The remaining parameters are the names of files with persistence diagrams. \n"; + std::cout << "This program creates persistence heat map files (*.mps) of persistence diagrams files (*.pers) " + << "provided as an input.The Gaussian kernels are weighted by the distance of a center from the " + << "diagonal.\n" + << "The first parameter of a program is an integer, a size of a grid.\n" + << "The second and third parameters are min and max of the grid. If you want those numbers to be computed " + << "based on the data, set them both to -1 \n" + << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number " + << "of pixels.\n" + << "The fifth parameter of this program is a dimension of persistence that will be used in creation of " + << "the persistence heat maps." + << "If your input files contains persistence pairs of various dimension, as a fifth parameter of the " + << "procedure please provide the dimension of persistence you want to use." + << "If in your files there are only birth-death pairs of the same dimension, set the fifth parameter to " + << "-1.\n" + << "The remaining parameters are the names of files with persistence diagrams. \n"; - if (argc < 5) { + if (argc < 7) { std::cout << "Wrong parameter list, the program will now terminate \n"; return 1; } @@ -68,9 +68,7 @@ int main(int argc, char** argv) { filenames.push_back(argv[i]); } - std::cout << "Creating persistence heat maps...\n"; std::vector<std::vector<double> > filter = Gudhi::Persistence_representations::create_Gaussian_filter(stdiv, 1); - for (size_t i = 0; i != filenames.size(); ++i) { std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl; Persistence_heat_maps l(filenames[i], filter, false, size_of_grid, min_, max_, dimension); @@ -79,6 +77,5 @@ int main(int argc, char** argv) { ss << filenames[i] << ".mps"; l.print_to_file(ss.str().c_str()); } - std::cout << "Done \n"; return 0; } diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp index ffec8b3d..59ff3c24 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp +++ b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp @@ -28,27 +28,28 @@ #include <vector> using squared_distance_from_diagonal_scaling = - Gudhi::Persistence_representations::squared_distance_from_diagonal_scaling; + Gudhi::Persistence_representations::squared_distance_from_diagonal_scaling; using Persistence_heat_maps = - Gudhi::Persistence_representations::Persistence_heat_maps<squared_distance_from_diagonal_scaling>; + Gudhi::Persistence_representations::Persistence_heat_maps<squared_distance_from_diagonal_scaling>; int main(int argc, char** argv) { - std::cout << "This program creates persistence heat map of diagrams provided as an input. The Gaussian kernels are " - "weighted by the square of distance of a center from the diagonal.\n"; - std::cout << "The first parameter of a program is an integer, a size of a grid.\n"; - std::cout << "The second and third parameters are min and max of the grid. If you want those numbers to be computed " - "based on the data, set them both to -1 \n"; - std::cerr << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number " - "of pixels \n"; - std::cout << "The fifth parameter of this program is a dimension of persistence that will be used in creation of the " - "persistence heat maps."; - std::cout << "If our input files contain persistence pairs of various dimension, as a fifth parameter of the " - "procedure please provide the dimension of persistence you want to use."; - std::cout << "If in your file there are only birth-death pairs of the same dimension, set the first parameter to -1." - << std::endl; - std::cout << "The remaining parameters are the names of files with persistence diagrams. \n"; + std::cout << "This program creates persistence heat map files (*.mps) of persistence diagrams files (*.pers) " + << "provided as an input.The Gaussian kernels are weighted by the square of distance of a center from the " + << "diagonal.\n" + << "The first parameter of a program is an integer, a size of a grid.\n" + << "The second and third parameters are min and max of the grid. If you want those numbers to be computed " + << "based on the data, set them both to -1 \n" + << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number " + << "of pixels.\n" + << "The fifth parameter of this program is a dimension of persistence that will be used in creation of " + << "the persistence heat maps." + << "If your input files contains persistence pairs of various dimension, as a fifth parameter of the " + << "procedure please provide the dimension of persistence you want to use." + << "If in your files there are only birth-death pairs of the same dimension, set the fifth parameter to " + << "-1.\n" + << "The remaining parameters are the names of files with persistence diagrams. \n"; - if (argc < 5) { + if (argc < 7) { std::cout << "Wrong parameter list, the program will now terminate \n"; return 1; } @@ -69,9 +70,7 @@ int main(int argc, char** argv) { filenames.push_back(argv[i]); } - std::cout << "Creating persistence heat maps...\n"; std::vector<std::vector<double> > filter = Gudhi::Persistence_representations::create_Gaussian_filter(stdiv, 1); - for (size_t i = 0; i != filenames.size(); ++i) { std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl; Persistence_heat_maps l(filenames[i], filter, false, size_of_grid, min_, max_, dimension); @@ -80,6 +79,5 @@ int main(int argc, char** argv) { ss << filenames[i] << ".mps"; l.print_to_file(ss.str().c_str()); } - std::cout << "Done \n"; return 0; } diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp index db2f0008..25cd1067 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp +++ b/src/Persistence_representations/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp @@ -31,21 +31,22 @@ using constant_scaling_function = Gudhi::Persistence_representations::constant_s using Persistence_heat_maps = Gudhi::Persistence_representations::Persistence_heat_maps<constant_scaling_function>; int main(int argc, char** argv) { - std::cout << "This program creates persistence heat map of diagrams provided as an input.\n"; - std::cout << "The first parameter of a program is an integer, a size of a grid.\n"; - std::cout << "The second and third parameters are min and max of the grid. If you want those numbers to be computed " - "based on the data, set them both to -1 \n"; - std::cerr << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number " - "of pixels \n"; + std::cout << "This program creates persistence heat map files (*.mps) of persistence diagrams files (*.pers) " + << "provided as an input.\n" + << "The first parameter of a program is an integer, a size of a grid.\n" + << "The second and third parameters are min and max of the grid. If you want those numbers to be computed " + << "based on the data, set them both to -1 \n" + << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number " + << "of pixels.\n" + << "The fifth parameter of this program is a dimension of persistence that will be used in creation of " + << "the persistence heat maps." + << "If your input files contains persistence pairs of various dimension, as a fifth parameter of the " + << "procedure please provide the dimension of persistence you want to use." + << "If in your files there are only birth-death pairs of the same dimension, set the fifth parameter to " + << "-1.\n" + << "The remaining parameters are the names of files with persistence diagrams. \n"; - std::cout << "The fifth parameter of this program is a dimension of persistence that will be used in creation of the " - "persistence heat maps."; - std::cout << "If your input file contains persistence pairs of various dimension, as a fifth parameter of the " - "procedure please provide the dimension of persistence you want to use."; - std::cout << "If in your file there are only birth-death pairs of the same dimension, set the first parameter to -1." - << std::endl; - std::cout << "The remaining parameters are the names of files with persistence diagrams. \n"; - if (argc < 5) { + if (argc < 7) { std::cout << "Wrong parameter list, the program will now terminate \n"; return 1; } @@ -64,17 +65,14 @@ int main(int argc, char** argv) { filenames.push_back(argv[i]); } - std::cout << "Creating persistence heat maps...\n"; std::vector<std::vector<double> > filter = Gudhi::Persistence_representations::create_Gaussian_filter(stdiv, 1); - for (size_t i = 0; i != filenames.size(); ++i) { - std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl; + std::cout << "Creating a heat map based on file : " << filenames[i] << std::endl; Persistence_heat_maps l(filenames[i], filter, false, size_of_grid, min_, max_, dimension); std::stringstream ss; ss << filenames[i] << ".mps"; l.print_to_file(ss.str().c_str()); } - std::cout << "Done \n"; return 0; } diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/create_pssk.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/create_pssk.cpp index 6aefbb00..97ddb8f0 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/create_pssk.cpp +++ b/src/Persistence_representations/utilities/persistence_heat_maps/create_pssk.cpp @@ -30,21 +30,22 @@ using PSSK = Gudhi::Persistence_representations::PSSK; int main(int argc, char** argv) { - std::cout << "This program creates PSSK of diagrams provided as an input.\n"; - std::cout << "The first parameter of a program is an integer, a size of a grid.\n"; - std::cout << "The second and third parameters are min and max of the grid. If you want those numbers to be computed " - "based on the data, set them both to -1 \n"; - std::cerr << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number " - "of pixels \n"; - std::cout << "The fifth parameter of this program is a dimension of persistence that will be used in creation of the " - "persistence heat maps."; - std::cout << "If our input files contain persistence pairs of various dimension, as a fifth parameter of the " - "procedure please provide the dimension of persistence you want to use."; - std::cout << "If in your file there are only birth-death pairs of the same dimension, set the first parameter to -1." - << std::endl; - std::cout << "The remaining parameters are the names of files with persistence diagrams. \n"; + std::cout << "This program creates PSSK files (*.pssk) of persistence diagrams files (*.pers) " + << "provided as an input.\n" + << "The first parameter of a program is an integer, a size of a grid.\n" + << "The second and third parameters are min and max of the grid. If you want those numbers to be computed " + << "based on the data, set them both to -1 \n" + << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number " + << "of pixels.\n" + << "The fifth parameter of this program is a dimension of persistence that will be used in creation of " + << "the PSSK." + << "If your input files contains persistence pairs of various dimension, as a fifth parameter of the " + << "procedure please provide the dimension of persistence you want to use." + << "If in your files there are only birth-death pairs of the same dimension, set the first parameter to " + << "-1.\n" + << "The remaining parameters are the names of files with persistence diagrams. \n"; - if (argc < 5) { + if (argc < 7) { std::cout << "Wrong parameter list, the program will now terminate \n"; return 1; } @@ -65,17 +66,14 @@ int main(int argc, char** argv) { filenames.push_back(argv[i]); } - std::cout << "Creating persistence heat maps...\n"; std::vector<std::vector<double> > filter = Gudhi::Persistence_representations::create_Gaussian_filter(stdiv, 1); - for (size_t i = 0; i != filenames.size(); ++i) { - std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl; + std::cout << "Creating a PSSK based on a file : " << filenames[i] << std::endl; PSSK l(filenames[i], filter, size_of_grid, min_, max_, dimension); std::stringstream ss; ss << filenames[i] << ".pssk"; l.print_to_file(ss.str().c_str()); } - std::cout << "Done \n"; return 0; } diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/plot_persistence_heat_map.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/plot_persistence_heat_map.cpp index a7c9f2d8..63711d83 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/plot_persistence_heat_map.cpp +++ b/src/Persistence_representations/utilities/persistence_heat_maps/plot_persistence_heat_map.cpp @@ -29,8 +29,12 @@ using constant_scaling_function = Gudhi::Persistence_representations::constant_s using Persistence_heat_maps = Gudhi::Persistence_representations::Persistence_heat_maps<constant_scaling_function>; int main(int argc, char** argv) { - std::cout << "This program plot persistence landscape stored in a file (the file needs to be created beforehand). " - "Please call the code with the name of a landscape file \n"; + std::cout << "This program creates a gnuplot script from a persistence heat maps stored in a file (the file needs " + << "to be created beforehand). Please call the code with the name of a single heat maps file \n"; + if (argc != 2) { + std::cout << "Wrong parameter list, the program will now terminate \n"; + return 1; + } Persistence_heat_maps l; l.load_from_file(argv[1]); l.plot(argv[1]); diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/simple_diagram.txt.mps b/src/Persistence_representations/utilities/persistence_heat_maps/simple_diagram.txt.mps deleted file mode 100644 index b7643887..00000000 --- a/src/Persistence_representations/utilities/persistence_heat_maps/simple_diagram.txt.mps +++ /dev/null @@ -1,11 +0,0 @@ -0.93 8.0707 -0.0492104 0.03889 0.0190956 0.00603584 0.00131569 0.000120934 2.10152e-05 0 0 0 -0.0650745 0.0539306 0.0296488 0.011745 0.00357642 0.000695928 0.000120934 0 0 0 -0.0572665 0.0559446 0.0409942 0.0230905 0.00937173 0.00242903 0.000422102 0 0 0 -0.0409942 0.0559656 0.0573874 0.0408475 0.0192639 0.00628964 0.00178718 0.000422102 0.000120934 2.10152e-05 -0.0296488 0.0540515 0.0657704 0.0519133 0.0283092 0.0132056 0.00628964 0.00242903 0.000695928 0.000120934 -0.0190956 0.0393121 0.0516395 0.0465955 0.0359385 0.0283092 0.0192639 0.00937173 0.00357642 0.00131569 -0.00847814 0.0188418 0.0281882 0.0358964 0.0465955 0.0519133 0.0408475 0.0230905 0.011745 0.00603584 -0.00242903 0.00628964 0.0132056 0.0281882 0.0516395 0.0657704 0.0573874 0.0409942 0.0296488 0.0190956 -0.000422102 0.00178718 0.00628964 0.0188418 0.0393121 0.0540515 0.0559656 0.0559446 0.0539306 0.03889 -0 0.000422102 0.00242903 0.00847814 0.0190956 0.0296488 0.0409942 0.0572665 0.0650745 0.0492104 diff --git a/src/Persistence_representations/utilities/persistence_intervals/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_intervals/CMakeLists.txt index 105b7efb..897e12a3 100644 --- a/src/Persistence_representations/utilities/persistence_intervals/CMakeLists.txt +++ b/src/Persistence_representations/utilities/persistence_intervals/CMakeLists.txt @@ -1,46 +1,32 @@ cmake_minimum_required(VERSION 2.6) project(Persistence_representations_intervals_utilities) -file(COPY "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/") -add_executable ( plot_persistence_intervals plot_persistence_intervals.cpp ) -target_link_libraries( plot_persistence_intervals ${Boost_SYSTEM_LIBRARY}) - -add_test(NAME plot_persistence_intervals COMMAND $<TARGET_FILE:plot_persistence_intervals> - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") - -add_executable ( compute_birth_death_range_in_persistence_diagram compute_birth_death_range_in_persistence_diagram.cpp ) -target_link_libraries( compute_birth_death_range_in_persistence_diagram ${Boost_SYSTEM_LIBRARY}) - -add_test(NAME compute_birth_death_range_in_persistence_diagram COMMAND $<TARGET_FILE:compute_birth_death_range_in_persistence_diagram> - "-1" "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") +add_executable ( plot_histogram_of_intervals_lengths plot_histogram_of_intervals_lengths.cpp ) -add_executable ( compute_number_of_dominant_intervals compute_number_of_dominant_intervals.cpp ) -target_link_libraries( compute_number_of_dominant_intervals ${Boost_SYSTEM_LIBRARY}) +add_test(NAME plot_histogram_of_intervals_lengths COMMAND $<TARGET_FILE:plot_histogram_of_intervals_lengths> + "${CMAKE_CURRENT_BINARY_DIR}/../first.pers" "-1") -add_test(NAME compute_number_of_dominant_intervals COMMAND $<TARGET_FILE:compute_number_of_dominant_intervals> - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt" "-1" "2") +add_persistence_representation_plot_utility(plot_persistence_intervals "") +add_persistence_representation_plot_utility(plot_persistence_Betti_numbers "") -add_executable ( plot_histogram_of_intervals_lengths plot_histogram_of_intervals_lengths.cpp ) -target_link_libraries( plot_histogram_of_intervals_lengths ${Boost_SYSTEM_LIBRARY}) +add_persistence_representation_creation_utility(compute_birth_death_range_in_persistence_diagram "-1") -add_test(NAME plot_histogram_of_intervals_lengths COMMAND $<TARGET_FILE:plot_histogram_of_intervals_lengths> - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt" "2") -add_executable ( plot_persistence_Betti_numbers plot_persistence_Betti_numbers.cpp ) -target_link_libraries( plot_persistence_Betti_numbers ${Boost_SYSTEM_LIBRARY}) +add_executable ( compute_number_of_dominant_intervals compute_number_of_dominant_intervals.cpp ) +add_test(NAME Persistence_representation_utilities_compute_number_of_dominant_intervals + COMMAND $<TARGET_FILE:compute_number_of_dominant_intervals> + "${CMAKE_CURRENT_BINARY_DIR}/../first.pers" "-1" "2") -add_test(NAME plot_persistence_Betti_numbers COMMAND $<TARGET_FILE:plot_persistence_Betti_numbers> - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) add_executable ( compute_bottleneck_distance compute_bottleneck_distance.cpp ) - target_link_libraries( compute_bottleneck_distance ${Boost_SYSTEM_LIBRARY}) if (TBB_FOUND) target_link_libraries(compute_bottleneck_distance ${TBB_LIBRARIES}) endif(TBB_FOUND) - - add_test(NAME compute_bottleneck_distance COMMAND $<TARGET_FILE:compute_bottleneck_distance> - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt" - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") + add_test(NAME Persistence_representation_utilities_compute_bottleneck_distance + COMMAND $<TARGET_FILE:compute_bottleneck_distance> + "-1" + "${CMAKE_CURRENT_BINARY_DIR}/../first.pers" + "${CMAKE_CURRENT_BINARY_DIR}/../second.pers") endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) diff --git a/src/Persistence_representations/utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp b/src/Persistence_representations/utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp index 66fa31ca..9102da79 100644 --- a/src/Persistence_representations/utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp +++ b/src/Persistence_representations/utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp @@ -20,7 +20,6 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ -#include <gudhi/reader_utils.h> #include <gudhi/Persistence_intervals.h> #include <iostream> @@ -31,16 +30,21 @@ using Persistence_intervals = Gudhi::Persistence_representations::Persistence_intervals; int main(int argc, char** argv) { - std::cout << "This program compute the range of birth and death times of persistence pairs in diagrams provided as " - "an input. \n"; - std::cout << "The first parameter of the program is the dimension of persistence to be used. If your file contains "; - std::cout << "the information about dimension of persistence pairs, please provide here the dimension of persistence " - "pairs you want to use. If your input files consist only "; - std::cout << "of birth-death pairs, please set this first parameter to -1 \n"; - std::cout << "The remaining parameters of the program are the names of files with persistence diagrams. \n"; + std::cout << "This program computes the range of birth and death times of persistence pairs in diagrams provided as " + << "an input.\n" + << "The first parameter is the dimension of persistence to be used to create persistence intervals. " + << "If your file contains the information about dimension of persistence pairs, please provide here the " + << "dimension of persistence pairs you want to use. " + << "If your input files consist only of birth-death pairs, please set this first parameter to -1.\n" + << "The remaining parameters of the program are the names of files with persistence diagrams.\n"; + + if (argc < 3) { + std::cout << "Wrong parameter list, the program will now terminate \n"; + return 1; + } - int dim = atoi(argv[1]); unsigned dimension = std::numeric_limits<unsigned>::max(); + int dim = atoi(argv[1]); if (dim >= 0) { dimension = (unsigned)dim; } diff --git a/src/Persistence_representations/utilities/persistence_intervals/compute_bottleneck_distance.cpp b/src/Persistence_representations/utilities/persistence_intervals/compute_bottleneck_distance.cpp index 0b1b526d..c8290845 100644 --- a/src/Persistence_representations/utilities/persistence_intervals/compute_bottleneck_distance.cpp +++ b/src/Persistence_representations/utilities/persistence_intervals/compute_bottleneck_distance.cpp @@ -21,7 +21,6 @@ */ #include <gudhi/Persistence_intervals_with_distances.h> -#include <gudhi/read_persistence_from_file.h> #include <iostream> #include <sstream> @@ -31,21 +30,21 @@ using Persistence_intervals_with_distances = Gudhi::Persistence_representations::Persistence_intervals_with_distances; int main(int argc, char** argv) { - std::cout << "This program compute the bottleneck distance of persistence diagrams stored in a files. \n"; - std::cout << "The first parameter of the program is the dimension of persistence to be used to construct persistence " - "landscapes. If your file contains "; - std::cout << "the information about dimension of persistence pairs, please provide here the dimension of persistence " - "pairs you want to use. If your input files consist only "; - std::cout << "of birth-death pairs, please set this first parameter to -1 \n"; - std::cout << "The remaining parameters of this programs are names of files with persistence diagrams.\n"; + std::cout << "This program computes the bottleneck distance of persistence pairs in diagrams provided as " + << "an input.\n" + << "The first parameter is the dimension of persistence to be used to create persistence intervals. " + << "If your file contains the information about dimension of persistence pairs, please provide here the " + << "dimension of persistence pairs you want to use. " + << "If your input files consist only of birth-death pairs, please set this first parameter to -1.\n" + << "The remaining parameters of the program are the names of files with persistence diagrams.\n"; if (argc < 3) { std::cout << "Wrong number of parameters, the program will now terminate \n"; return 1; } - int dim = atoi(argv[1]); unsigned dimension = std::numeric_limits<unsigned>::max(); + int dim = atoi(argv[1]); if (dim >= 0) { dimension = (unsigned)dim; } @@ -80,7 +79,7 @@ int main(int argc, char** argv) { // and now output the result to the screen and a file: std::ofstream out; - out.open("distance"); + out.open("distance.itv"); for (size_t i = 0; i != distance.size(); ++i) { for (size_t j = 0; j != distance.size(); ++j) { std::cout << distance[i][j] << " "; @@ -91,5 +90,6 @@ int main(int argc, char** argv) { } out.close(); + std::cout << "Distance can be found in 'distance.itv' file\n"; return 0; } diff --git a/src/Persistence_representations/utilities/persistence_intervals/compute_number_of_dominant_intervals.cpp b/src/Persistence_representations/utilities/persistence_intervals/compute_number_of_dominant_intervals.cpp index 1286ca57..b3d126f0 100644 --- a/src/Persistence_representations/utilities/persistence_intervals/compute_number_of_dominant_intervals.cpp +++ b/src/Persistence_representations/utilities/persistence_intervals/compute_number_of_dominant_intervals.cpp @@ -20,7 +20,6 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ -#include <gudhi/reader_utils.h> #include <gudhi/Persistence_intervals.h> #include <iostream> diff --git a/src/Persistence_representations/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp b/src/Persistence_representations/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp index d68f4584..ccb5b645 100644 --- a/src/Persistence_representations/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp +++ b/src/Persistence_representations/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp @@ -20,7 +20,6 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ -#include <gudhi/reader_utils.h> #include <gudhi/Persistence_intervals.h> #include <iostream> @@ -31,30 +30,34 @@ using Persistence_intervals = Gudhi::Persistence_representations::Persistence_intervals; int main(int argc, char** argv) { - std::cout << "This program compute a histogram of barcode's length. A number of bins in the histogram is a parameter " - "of this program. \n"; - if (argc != 3) { + std::cout << "This program computes a histogram of barcode's length. A number of bins in the histogram is a " + << "parameter of this program. \n"; + if ((argc != 3) && (argc != 4)) { std::cout << "To run this program, please provide the name of a file with persistence diagram and number of " - "dominant intervals you would like to get \n"; - std::cout << "The third parameter of a program is the dimension of the persistence that is to be used. If your " - "file contains only birth-death pairs, you can skip this parameter\n"; + << "dominant intervals you would like to get. Set a negative number dominant intervals value " + << "If your file contains only birth-death pairs.\n" + << "The third parameter is the dimension of the persistence that is to be used. If your " + << "file contains only birth-death pairs, you can skip this parameter\n"; return 1; } - unsigned dimension = std::numeric_limits<unsigned>::max(); - int dim = -1; - if (argc > 2) { - dim = atoi(argv[2]); + + unsigned dominant_interval_number = std::numeric_limits<unsigned>::max(); + int nbr = atoi(argv[2]); + if (nbr >= 0) { + dominant_interval_number = static_cast<unsigned>(nbr); } - if (dim >= 0) { - dimension = (unsigned)dim; + + int persistence_dimension = -1; + if (argc == 4) { + persistence_dimension = atoi(argv[3]); } - Persistence_intervals p(argv[1], dimension); - std::vector<std::pair<double, double> > dominant_intervals = p.dominant_intervals(atoi(argv[2])); + Persistence_intervals p(argv[1], dominant_interval_number); + std::vector<std::pair<double, double> > dominant_intervals = p.dominant_intervals(persistence_dimension); std::vector<size_t> histogram = p.histogram_of_lengths(10); std::stringstream gnuplot_script; - gnuplot_script << argv[1] << "_Gnuplot_script"; + gnuplot_script << argv[1] << "_GnuplotScript"; std::ofstream out; out.open(gnuplot_script.str().c_str()); @@ -66,7 +69,9 @@ int main(int argc, char** argv) { out << histogram[i] << std::endl; } out << std::endl; - std::cout << "To visualize, open gnuplot and type: load \'" << gnuplot_script.str().c_str() << "\'" << std::endl; out.close(); + + std::cout << "To visualize, install gnuplot and type the command: gnuplot -persist -e \"load \'" + << gnuplot_script.str().c_str() << "\'\"" << std::endl; return 0; } diff --git a/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_Betti_numbers.cpp b/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_Betti_numbers.cpp index da2b9319..b433c2b3 100644 --- a/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_Betti_numbers.cpp +++ b/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_Betti_numbers.cpp @@ -20,7 +20,6 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ -#include <gudhi/reader_utils.h> #include <gudhi/Persistence_intervals.h> #include <iostream> @@ -31,29 +30,24 @@ using Persistence_intervals = Gudhi::Persistence_representations::Persistence_intervals; int main(int argc, char** argv) { - std::cout << "This program compute a plot of persistence Betti numbers. The input parameter is a file with " - "persistence intervals. \n"; - std::cout << "The second optional parameter of a program is the dimension of the persistence that is to be used. If " - "your file contains only birth-death pairs, you can skip this parameter\n"; - if (argc < 2) { - std::cout << "To run this program, please provide the name of a file with persistence diagram and number of " - "dominant intervals you would like to get \n"; + if ((argc != 3) && (argc != 2)) { + std::cout << "This program creates a gnuplot script of Betti numbers from a single persistence diagram file" + << "(*.pers).\n" + << "To run this program, please provide the name of a file with persistence diagram.\n" + << "The second optional parameter of a program is the dimension of the persistence that is to be used. " + << "If your file contains only birth-death pairs, you can skip this parameter.\n"; return 1; } + unsigned dimension = std::numeric_limits<unsigned>::max(); int dim = -1; - if (argc > 2) { + if (argc == 3) { dim = atoi(argv[2]); } if (dim >= 0) { dimension = (unsigned)dim; } - std::stringstream gnuplot_script; - gnuplot_script << argv[1] << "_Gnuplot_script"; - std::ofstream out; - out.open(gnuplot_script.str().c_str()); - Persistence_intervals p(argv[1], dimension); std::vector<std::pair<double, size_t> > pbns = p.compute_persistent_betti_numbers(); @@ -69,6 +63,11 @@ int main(int argc, char** argv) { xRangeEnd += (xRangeEnd - xRangeBegin) / 100.0; yRangeEnd += yRangeEnd / 100; + std::stringstream gnuplot_script; + gnuplot_script << argv[1] << "_GnuplotScript"; + std::ofstream out; + out.open(gnuplot_script.str().c_str()); + out << "set xrange [" << xRangeBegin << " : " << xRangeEnd << "]" << std::endl; out << "set yrange [" << yRangeBegin << " : " << yRangeEnd << "]" << std::endl; out << "plot '-' using 1:2 notitle with lp " << std::endl; @@ -81,7 +80,8 @@ int main(int argc, char** argv) { out << std::endl; out.close(); - std::cout << "To visualize, open gnuplot and type: load \'" << gnuplot_script.str().c_str() << "\'" << std::endl; + std::cout << "To visualize, install gnuplot and type the command: gnuplot -persist -e \"load \'" + << gnuplot_script.str().c_str() << "\'\"" << std::endl; return 0; } diff --git a/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_intervals.cpp b/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_intervals.cpp index e7d29e84..33387802 100644 --- a/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_intervals.cpp +++ b/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_intervals.cpp @@ -20,9 +20,7 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ -#include <gudhi/reader_utils.h> #include <gudhi/Persistence_intervals.h> -#include <gudhi/read_persistence_from_file.h> #include <iostream> #include <limits> @@ -32,15 +30,16 @@ using Persistence_intervals = Gudhi::Persistence_representations::Persistence_intervals; int main(int argc, char** argv) { - if (argc < 2) { - std::cout << "To run this program, please provide the name of a file with persistence diagram \n"; - std::cout << "The second optional parameter of a program is the dimension of the persistence that is to be used. " - "If your file contains only birth-death pairs, you can skip this parameter\n"; + if ((argc != 3) && (argc != 2)) { + std::cout << "This program creates a gnuplot script from a single persistence diagram file (*.pers).\n" + << "To run this program, please provide the name of a file with persistence diagram.\n" + << "The second optional parameter of a program is the dimension of the persistence that is to be used. " + << "If your file contains only birth-death pairs, you can skip this parameter.\n"; return 1; } unsigned dimension = std::numeric_limits<unsigned>::max(); int dim = -1; - if (argc > 2) { + if (argc == 3) { dim = atoi(argv[2]); } if (dim >= 0) { diff --git a/src/Persistence_representations/utilities/persistence_landscapes/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_landscapes/CMakeLists.txt index baf8de3c..d7087ed8 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes/CMakeLists.txt +++ b/src/Persistence_representations/utilities/persistence_landscapes/CMakeLists.txt @@ -1,38 +1,10 @@ cmake_minimum_required(VERSION 2.6) -project(Persistence_representations_lanscapes_utilities) +project(Persistence_representations_landscapes_utilities) -file(COPY "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/") +add_persistence_representation_creation_utility(create_landscapes "-1") -add_executable ( create_landscapes create_landscapes.cpp ) -target_link_libraries(create_landscapes ${Boost_SYSTEM_LIBRARY}) +add_persistence_representation_plot_utility(plot_landscapes ".land") -# Will create simple_diagram.txt.land -add_test(NAME create_landscapes COMMAND $<TARGET_FILE:create_landscapes> - "-1" "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") - -add_executable ( average_landscapes average_landscapes.cpp ) -target_link_libraries(average_landscapes ${Boost_SYSTEM_LIBRARY}) - -add_test(NAME average_landscapes COMMAND $<TARGET_FILE:average_landscapes> - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt" - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") - -add_executable ( plot_landscapes plot_landscapes.cpp ) -target_link_libraries(plot_landscapes ${Boost_SYSTEM_LIBRARY}) - -add_test(NAME plot_landscapes COMMAND $<TARGET_FILE:plot_landscapes> - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") - -add_executable ( compute_distance_of_landscapes compute_distance_of_landscapes.cpp ) -target_link_libraries(compute_distance_of_landscapes ${Boost_SYSTEM_LIBRARY}) - -add_test(NAME compute_distance_of_landscapes COMMAND $<TARGET_FILE:compute_distance_of_landscapes> - "1" "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.land" - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.land") - -add_executable ( compute_scalar_product_of_landscapes compute_scalar_product_of_landscapes.cpp ) -target_link_libraries(compute_scalar_product_of_landscapes ${Boost_SYSTEM_LIBRARY}) - -add_test(NAME compute_scalar_product_of_landscapes COMMAND $<TARGET_FILE:compute_scalar_product_of_landscapes> - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.land" - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.land") +add_persistence_representation_function_utility(average_landscapes ".land") +add_persistence_representation_function_utility(compute_distance_of_landscapes ".land" "1") +add_persistence_representation_function_utility(compute_scalar_product_of_landscapes ".land") diff --git a/src/Persistence_representations/utilities/persistence_landscapes/average_landscapes.cpp b/src/Persistence_representations/utilities/persistence_landscapes/average_landscapes.cpp index 526130e9..1a59be8c 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes/average_landscapes.cpp +++ b/src/Persistence_representations/utilities/persistence_landscapes/average_landscapes.cpp @@ -28,14 +28,13 @@ using Persistence_landscape = Gudhi::Persistence_representations::Persistence_landscape; int main(int argc, char** argv) { - std::cout << "This program computes average persistence landscape of persistence landscapes created based on " - "persistence diagrams provided as an input (you must create them first).\n"; - std::cout << "Please call this program with the names of files with persistence landscapes. The program will create " - "a persistence landscape which will be their average \n"; + std::cout << "This program computes average of persistence landscapes stored in files (the files needs to be " + << "created beforehand).\n" + << "The parameters of this programs are names of files with persistence landscapes.\n"; std::vector<const char*> filenames; - if (argc == 1) { - std::cout << "No input files given, the program will now terminate \n"; + if (argc < 3) { + std::cout << "Wrong number of parameters, the program will now terminate \n"; return 1; } @@ -43,7 +42,6 @@ int main(int argc, char** argv) { filenames.push_back(argv[i]); } - std::cout << "Creating persistence landscapes...\n"; std::vector<Persistence_landscape*> lands; for (size_t i = 0; i != filenames.size(); ++i) { Persistence_landscape* l = new Persistence_landscape; @@ -60,7 +58,6 @@ int main(int argc, char** argv) { delete lands[i]; } - std::cout << "Done \n"; - + std::cout << "Average can be found in 'average.land' file\n"; return 0; } diff --git a/src/Persistence_representations/utilities/persistence_landscapes/compute_distance_of_landscapes.cpp b/src/Persistence_representations/utilities/persistence_landscapes/compute_distance_of_landscapes.cpp index b3881d6a..5062f521 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes/compute_distance_of_landscapes.cpp +++ b/src/Persistence_representations/utilities/persistence_landscapes/compute_distance_of_landscapes.cpp @@ -30,11 +30,11 @@ using Persistence_landscape = Gudhi::Persistence_representations::Persistence_landscape; int main(int argc, char** argv) { - std::cout << "This program compute distance of persistence landscapes stored in a file (the file needs to be created " - "beforehand). \n"; - std::cout << "The first parameter of a program is an integer p. The program compute L^p distance of the given " - "landscapes. For L^infty distance choose p = -1. \n"; - std::cout << "The remaining parameters of this programs are names of files with persistence landscapes."; + std::cout << "This program computes distance of persistence landscapes stored in files (the files needs to be " + << "created beforehand).\n" + << "The first parameter of a program is an integer p. The program compute L^p distance of the two heat " + << "maps. For L^infty distance choose p = -1. \n" + << "The remaining parameters of this program are names of files with persistence landscapes.\n"; if (argc < 3) { std::cout << "Wrong number of parameters, the program will now terminate \n"; @@ -54,7 +54,6 @@ int main(int argc, char** argv) { std::vector<Persistence_landscape> landscaspes; landscaspes.reserve(filenames.size()); for (size_t file_no = 0; file_no != filenames.size(); ++file_no) { - std::cout << "Loading persistence landscape from a file : " << filenames[file_no] << std::endl; Persistence_landscape l; l.load_landscape_from_file(filenames[file_no]); landscaspes.push_back(l); @@ -78,7 +77,7 @@ int main(int argc, char** argv) { // and now output the result to the screen and a file: std::ofstream out; - out.open("distance"); + out.open("distance.land"); for (size_t i = 0; i != distance.size(); ++i) { for (size_t j = 0; j != distance.size(); ++j) { std::cout << distance[i][j] << " "; @@ -89,5 +88,6 @@ int main(int argc, char** argv) { } out.close(); + std::cout << "Distance can be found in 'distance.land' file\n"; return 0; } diff --git a/src/Persistence_representations/utilities/persistence_landscapes/compute_scalar_product_of_landscapes.cpp b/src/Persistence_representations/utilities/persistence_landscapes/compute_scalar_product_of_landscapes.cpp index 8dad7b4d..5b5e9fa3 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes/compute_scalar_product_of_landscapes.cpp +++ b/src/Persistence_representations/utilities/persistence_landscapes/compute_scalar_product_of_landscapes.cpp @@ -29,9 +29,14 @@ using Persistence_landscape = Gudhi::Persistence_representations::Persistence_landscape; int main(int argc, char** argv) { - std::cout << "This program compute scalar product of persistence landscapes stored in a file (the file needs to be " - "created beforehand). \n"; - std::cout << "The parameters of this programs are names of files with persistence landscapes.\n"; + std::cout << "This program computes scalar product of persistence landscapes stored in a file (the file needs to be " + << "created beforehand). \n" + << "The parameters of this programs are names of files with persistence landscapes.\n"; + + if (argc < 3) { + std::cout << "Wrong number of parameters, the program will now terminate \n"; + return 1; + } std::vector<const char*> filenames; for (int i = 1; i < argc; ++i) { @@ -40,7 +45,6 @@ int main(int argc, char** argv) { std::vector<Persistence_landscape> landscaspes; landscaspes.reserve(filenames.size()); for (size_t file_no = 0; file_no != filenames.size(); ++file_no) { - std::cout << "Reading persistence landscape from a file : " << filenames[file_no] << std::endl; Persistence_landscape l; l.load_landscape_from_file(filenames[file_no]); landscaspes.push_back(l); @@ -64,7 +68,7 @@ int main(int argc, char** argv) { // and now output the result to the screen and a file: std::ofstream out; - out.open("scalar_product"); + out.open("scalar_product.land"); for (size_t i = 0; i != scalar_product.size(); ++i) { for (size_t j = 0; j != scalar_product.size(); ++j) { std::cout << scalar_product[i][j] << " "; @@ -75,5 +79,6 @@ int main(int argc, char** argv) { } out.close(); + std::cout << "Distance can be found in 'scalar_product.land' file\n"; return 0; } diff --git a/src/Persistence_representations/utilities/persistence_landscapes/create_landscapes.cpp b/src/Persistence_representations/utilities/persistence_landscapes/create_landscapes.cpp index 325081d1..6030e994 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes/create_landscapes.cpp +++ b/src/Persistence_representations/utilities/persistence_landscapes/create_landscapes.cpp @@ -30,13 +30,20 @@ using Persistence_landscape = Gudhi::Persistence_representations::Persistence_landscape; int main(int argc, char** argv) { - std::cout << "This program creates persistence landscapes of diagrams provided as an input. \n"; - std::cout << "The first parameter of the program is the dimension of persistence to be used to construct persistence " - "landscapes. If your file contains "; - std::cout << "the information about dimension of persistence pairs, please provide here the dimension of persistence " - "pairs you want to use. If your input files consist only "; - std::cout << "of birth-death pairs, please set this first parameter to -1 \n"; - std::cout << "The remaining parameters of the program are the names of files with persistence diagrams. \n"; + std::cout << "This program creates persistence landscapes files (*.land) of persistence diagrams files (*.pers) " + << "provided as an input.\n" + << "The first parameter of this program is a dimension of persistence that will be used in creation of " + << "the persistence heat maps." + << "If your input files contains persistence pairs of various dimension, as a first parameter of the " + << "procedure please provide the dimension of persistence you want to use." + << "If in your files there are only birth-death pairs of the same dimension, set the first parameter to " + << "-1.\n" + << "The remaining parameters are the names of files with persistence diagrams. \n"; + + if (argc < 3) { + std::cout << "Wrong parameter list, the program will now terminate \n"; + return 1; + } std::vector<const char*> filenames; int dim = atoi(argv[1]); unsigned dimension = std::numeric_limits<unsigned>::max(); @@ -47,13 +54,12 @@ int main(int argc, char** argv) { filenames.push_back(argv[i]); } - std::cout << "Creating persistence landscapes...\n"; for (size_t i = 0; i != filenames.size(); ++i) { + std::cout << "Creating a landscape based on file : " << filenames[i] << std::endl; Persistence_landscape l(filenames[i], dimension); std::stringstream ss; ss << filenames[i] << ".land"; l.print_to_file(ss.str().c_str()); } - std::cout << "Done \n"; return 0; } diff --git a/src/Persistence_representations/utilities/persistence_landscapes/plot_landscapes.cpp b/src/Persistence_representations/utilities/persistence_landscapes/plot_landscapes.cpp index ebdb20a1..c797a7a8 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes/plot_landscapes.cpp +++ b/src/Persistence_representations/utilities/persistence_landscapes/plot_landscapes.cpp @@ -28,16 +28,16 @@ using Persistence_landscape = Gudhi::Persistence_representations::Persistence_landscape; int main(int argc, char** argv) { - std::cout << "This program plot persistence landscape stored in a file (the file needs to be created beforehand). " - "Please call the code with the name of a landscape file \n"; + std::cout << "This program creates a gnuplot script from a persistence landscape stored in a file (the file needs " + << "to be created beforehand). Please call the code with the name of a single landscape file.\n"; + if (argc != 2) { + std::cout << "Wrong parameter list, the program will now terminate \n"; + return 1; + } + Persistence_landscape l; l.load_landscape_from_file(argv[1]); - - std::stringstream ss; - ss << argv[1] << "_gnuplot_script"; - l.plot(ss.str().c_str()); - - std::cout << "Done \n"; + l.plot(argv[1]); return 0; } diff --git a/src/Persistence_representations/utilities/persistence_landscapes/simple_diagram.txt.land b/src/Persistence_representations/utilities/persistence_landscapes/simple_diagram.txt.land deleted file mode 100644 index b99d2f62..00000000 --- a/src/Persistence_representations/utilities/persistence_landscapes/simple_diagram.txt.land +++ /dev/null @@ -1,13 +0,0 @@ -#lambda_0 -1 0 -1.5 0.5 -2 0 -3 0 -3.5 0.5 -4 0 -5 0 -5.5 0.5 -6 0 -7 0 -7.5 0.5 -8 0 diff --git a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/CMakeLists.txt index 55a4fd50..c5ea4bbf 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/CMakeLists.txt +++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/CMakeLists.txt @@ -1,38 +1,11 @@ cmake_minimum_required(VERSION 2.6) project(Persistence_representations_lanscapes_on_grid_utilities) -file(COPY "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/") +# Need to set grid min and max for further average, distance and scalar_product +add_persistence_representation_creation_utility(create_landscapes_on_grid "100" "0" "35" "-1") -add_executable ( create_landscapes_on_grid create_landscapes_on_grid.cpp ) -target_link_libraries(create_landscapes_on_grid ${Boost_SYSTEM_LIBRARY}) +add_persistence_representation_plot_utility(plot_landscapes_on_grid ".g_land") -# Will create simple_diagram.txt.land -add_test(NAME create_landscapes_on_grid COMMAND $<TARGET_FILE:create_landscapes_on_grid> - "100" "-1" "-1" "-1" "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") - -add_executable ( average_landscapes_on_grid average_landscapes_on_grid.cpp ) -target_link_libraries(average_landscapes_on_grid ${Boost_SYSTEM_LIBRARY}) - -add_test(NAME average_landscapes_on_grid COMMAND $<TARGET_FILE:average_landscapes_on_grid> - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.g_land" - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.g_land") - -add_executable ( plot_landscapes_on_grid plot_landscapes_on_grid.cpp ) -target_link_libraries(plot_landscapes_on_grid ${Boost_SYSTEM_LIBRARY}) - -add_test(NAME plot_landscapes_on_grid COMMAND $<TARGET_FILE:plot_landscapes_on_grid> - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.g_land") - -add_executable ( compute_distance_of_landscapes_on_grid compute_distance_of_landscapes_on_grid.cpp ) -target_link_libraries(compute_distance_of_landscapes_on_grid ${Boost_SYSTEM_LIBRARY}) - -add_test(NAME compute_distance_of_landscapes_on_grid COMMAND $<TARGET_FILE:compute_distance_of_landscapes_on_grid> - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.g_land" - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.g_land") - -add_executable ( compute_scalar_product_of_landscapes_on_grid compute_scalar_product_of_landscapes_on_grid.cpp ) -target_link_libraries(compute_scalar_product_of_landscapes_on_grid ${Boost_SYSTEM_LIBRARY}) - -add_test(NAME compute_scalar_product_of_landscapes_on_grid COMMAND $<TARGET_FILE:compute_scalar_product_of_landscapes_on_grid> - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.g_land" - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.g_land") +add_persistence_representation_function_utility(average_landscapes_on_grid ".g_land") +add_persistence_representation_function_utility(compute_distance_of_landscapes_on_grid ".g_land" "1") +add_persistence_representation_function_utility(compute_scalar_product_of_landscapes_on_grid ".g_land") diff --git a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp index d50118a0..0b098d1a 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp +++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp @@ -28,21 +28,20 @@ using Persistence_landscape_on_grid = Gudhi::Persistence_representations::Persistence_landscape_on_grid; int main(int argc, char** argv) { - std::cout << "This program computes average persistence landscape on grid of persistence landscapes on grid created " - "based on persistence diagrams provided as an input. Please call this program with the names of files " - "with persistence diagrams \n"; - std::vector<const char*> filenames; + std::cout << "This program computes average of persistence landscapes on grid stored in files (the files needs to " + << "be created beforehand).\n" + << "The parameters of this programs are names of files with persistence landscapes on grid.\n"; - if (argc == 1) { - std::cout << "No input files given, the program will now terminate \n"; + if (argc < 3) { + std::cout << "Wrong number of parameters, the program will now terminate \n"; return 1; } + std::vector<const char*> filenames; for (int i = 1; i < argc; ++i) { filenames.push_back(argv[i]); } - std::cout << "Creating persistence landscapes...\n"; std::vector<Persistence_landscape_on_grid*> lands; for (size_t i = 0; i != filenames.size(); ++i) { Persistence_landscape_on_grid* l = new Persistence_landscape_on_grid; @@ -59,7 +58,6 @@ int main(int argc, char** argv) { delete lands[i]; } - std::cout << "Done \n"; - + std::cout << "Average can be found in 'average.g_land' file\n"; return 0; } diff --git a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp index 859c6991..fd0fcd15 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp +++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp @@ -30,11 +30,11 @@ using Persistence_landscape_on_grid = Gudhi::Persistence_representations::Persistence_landscape_on_grid; int main(int argc, char** argv) { - std::cout << "This program compute distance of persistence landscapes on grid stored in a file (the file needs to be " - "created beforehand). \n"; - std::cout << "The first parameter of a program is an integer p. The program compute L^p distance of the landscapes " - "on grid. For L^infty distance choose p = -1. \n"; - std::cout << "The remaining parameters of this programs are names of files with persistence landscapes on grid.\n"; + std::cout << "This program computes distance of persistence landscapes on grid stored in files (the files needs to " + << "be created beforehand).\n" + << "The first parameter of a program is an integer p. The program compute L^p distance of the two heat " + << "maps. For L^infty distance choose p = -1. \n" + << "The remaining parameters of this program are names of files with persistence landscapes on grid.\n"; if (argc < 3) { std::cout << "Wrong number of parameters, the program will now terminate \n"; @@ -77,7 +77,7 @@ int main(int argc, char** argv) { // and now output the result to the screen and a file: std::ofstream out; - out.open("distance"); + out.open("distance.g_land"); for (size_t i = 0; i != distance.size(); ++i) { for (size_t j = 0; j != distance.size(); ++j) { std::cout << distance[i][j] << " "; @@ -88,5 +88,6 @@ int main(int argc, char** argv) { } out.close(); + std::cout << "Distance can be found in 'distance.g_land' file\n"; return 0; } diff --git a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp index e95bf8ad..01de3dee 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp +++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp @@ -29,9 +29,15 @@ using Persistence_landscape_on_grid = Gudhi::Persistence_representations::Persistence_landscape_on_grid; int main(int argc, char** argv) { - std::cout << "This program compute scalar product of persistence landscapes on grid stored in a file (the file needs " - "to be created beforehand). \n"; - std::cout << "The parameters of this programs are names of files with persistence landscapes on grid.\n"; + std::cout + << "This program computes scalar product of persistence landscapes on grid stored in a file (the file needs to " + << "be created beforehand). \n" + << "The parameters of this programs are names of files with persistence landscapes on grid.\n"; + + if (argc < 3) { + std::cout << "Wrong number of parameters, the program will now terminate \n"; + return 1; + } std::vector<const char*> filenames; for (int i = 1; i < argc; ++i) { @@ -63,7 +69,7 @@ int main(int argc, char** argv) { // and now output the result to the screen and a file: std::ofstream out; - out.open("scalar_product"); + out.open("scalar_product.g_land"); for (size_t i = 0; i != scalar_product.size(); ++i) { for (size_t j = 0; j != scalar_product.size(); ++j) { std::cout << scalar_product[i][j] << " "; @@ -74,5 +80,6 @@ int main(int argc, char** argv) { } out.close(); + std::cout << "Distance can be found in 'scalar_product.g_land' file\n"; return 0; } diff --git a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp index 8d747c14..78e8ef57 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp +++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp @@ -30,18 +30,20 @@ using Persistence_landscape_on_grid = Gudhi::Persistence_representations::Persistence_landscape_on_grid; int main(int argc, char** argv) { - std::cout << "This program creates persistence landscape on grid of diagrams provided as an input.\n"; - std::cout << "The first parameter of a program is an integer, a size of a grid.\n"; - std::cout << "The second and third parameters are min and max of the grid. If you want those numbers to be computed " - "based on the data, set them both to -1 \n"; - std::cout << "The fourth parameter of the program is the dimension of persistence to be used to construct " - "persistence landscape on a grid. If your file contains "; - std::cout << "the information about dimension of birth-death pairs, please provide here the dimension of intervals " - "you want to use. If your input files consist only "; - std::cout << "of birth-death pairs, please set the fourth parameter to -1 \n"; - std::cout << "The remaining parameters are the names of files with persistence diagrams. \n"; + std::cout << "This program creates persistence landscapes on grid files (*.g_land) of persistence diagrams files " + << "(*.pers) provided as an input.\n" + << "The first parameter of a program is an integer, a size of a grid.\n" + << "The second and third parameters are min and max of the grid. If you want those numbers to be computed " + << "based on the data, set them both to -1 \n" + << "The fourth parameter of this program is a dimension of persistence that will be used in creation of " + << "the persistence heat maps." + << "If your input files contains persistence pairs of various dimension, as a fourth parameter of the " + << "procedure please provide the dimension of persistence you want to use." + << "If in your files there are only birth-death pairs of the same dimension, set the fourth parameter to " + << "-1.\n" + << "The remaining parameters are the names of files with persistence diagrams. \n"; - if (argc < 5) { + if (argc < 6) { std::cout << "Wrong parameter list, the program will now terminate \n"; return 1; } @@ -60,7 +62,6 @@ int main(int argc, char** argv) { filenames.push_back(argv[i]); } - std::cout << "Creating persistence landscapes...\n"; for (size_t i = 0; i != filenames.size(); ++i) { std::cout << "Creating persistence landscape on a grid based on a file : " << filenames[i] << std::endl; Persistence_landscape_on_grid l; @@ -74,6 +75,5 @@ int main(int argc, char** argv) { ss << filenames[i] << ".g_land"; l.print_to_file(ss.str().c_str()); } - std::cout << "Done \n"; return 0; } diff --git a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp index 42822a01..dddb3615 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp +++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp @@ -28,20 +28,17 @@ using Persistence_landscape_on_grid = Gudhi::Persistence_representations::Persistence_landscape_on_grid; int main(int argc, char** argv) { - std::cout << "This program plot persistence landscape on grid stored in a file (the file needs to be created " - "beforehand). Please call the code with the name of a landscape on grid file \n"; - if (argc == 1) { - std::cout << "Wrong parameters of a program call, the program will now terminate \n"; + std::cout << "This program creates a gnuplot script from a persistence landscape on grid stored in a file (the file " + << "needs to be created beforehand). Please call the code with the name of a single landscape on grid file" + << ".\n"; + if (argc != 2) { + std::cout << "Wrong parameter list, the program will now terminate \n"; return 1; } + Persistence_landscape_on_grid l; l.load_landscape_from_file(argv[1]); - - std::stringstream ss; - ss << argv[1] << "_gnuplot_script"; - l.plot(ss.str().c_str()); - - std::cout << "Done \n"; + l.plot(argv[1]); return 0; } diff --git a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/simple_diagram.txt.g_land b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/simple_diagram.txt.g_land deleted file mode 100644 index dc53b932..00000000 --- a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/simple_diagram.txt.g_land +++ /dev/null @@ -1,104 +0,0 @@ -1 -8 -101 - -0.07 -0.14 -0.21 -0.28 -0.35 -0.42 -0.49 -0.42 -0.35 -0.28 -0.21 -0.14 -0.07 - - - - - - - - - - - - - - - -0.07 -0.14 -0.21 -0.28 -0.35 -0.42 -0.49 -0.42 -0.35 -0.28 -0.21 -0.14 -0.07 - - - - - - - - - - - - - - - - -0.07 -0.14 -0.21 -0.28 -0.35 -0.42 -0.49 -0.42 -0.35 -0.28 -0.21 -0.14 -0.07 - - - - - - - - - - - - - - - -0.07 -0.14 -0.21 -0.28 -0.35 -0.42 -0.49 -0.42 -0.35 -0.28 -0.21 -0.14 -0.07 - - diff --git a/src/Persistence_representations/utilities/persistence_vectors/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_vectors/CMakeLists.txt index e3d1013b..a401c955 100644 --- a/src/Persistence_representations/utilities/persistence_vectors/CMakeLists.txt +++ b/src/Persistence_representations/utilities/persistence_vectors/CMakeLists.txt @@ -1,38 +1,10 @@ cmake_minimum_required(VERSION 2.6) project(Persistence_vectors_utilities) -file(COPY "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/") +add_persistence_representation_creation_utility(create_persistence_vectors "-1") -add_executable ( create_persistence_vectors create_persistence_vectors.cpp ) -target_link_libraries(create_persistence_vectors ${Boost_SYSTEM_LIBRARY}) +add_persistence_representation_plot_utility(plot_persistence_vectors ".vect") -# Will create simple_diagram.txt.vect -add_test(NAME create_persistence_vectors COMMAND $<TARGET_FILE:create_persistence_vectors> - "-1" "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") - -add_executable ( average_persistence_vectors average_persistence_vectors.cpp ) -target_link_libraries(average_persistence_vectors ${Boost_SYSTEM_LIBRARY}) - -add_test(NAME average_persistence_vectors COMMAND $<TARGET_FILE:average_persistence_vectors> - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.vect" - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.vect") - -add_executable ( compute_distance_of_persistence_vectors compute_distance_of_persistence_vectors.cpp ) -target_link_libraries(compute_distance_of_persistence_vectors ${Boost_SYSTEM_LIBRARY}) - -add_test(NAME compute_distance_of_persistence_vectors COMMAND $<TARGET_FILE:compute_distance_of_persistence_vectors> - "-1" "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.vect" - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.vect") - -add_executable ( compute_scalar_product_of_persistence_vectors compute_scalar_product_of_persistence_vectors.cpp ) -target_link_libraries(compute_scalar_product_of_persistence_vectors ${Boost_SYSTEM_LIBRARY}) - -add_test(NAME compute_scalar_product_of_persistence_vectors COMMAND $<TARGET_FILE:compute_scalar_product_of_persistence_vectors> - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.vect" - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.vect") - -add_executable ( plot_persistence_vectors plot_persistence_vectors.cpp ) -target_link_libraries(plot_persistence_vectors ${Boost_SYSTEM_LIBRARY}) - -add_test(NAME plot_persistence_vectors COMMAND $<TARGET_FILE:plot_persistence_vectors> - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.vect") +add_persistence_representation_function_utility(average_persistence_vectors ".vect") +add_persistence_representation_function_utility(compute_distance_of_persistence_vectors ".vect" "1") +add_persistence_representation_function_utility(compute_scalar_product_of_persistence_vectors ".vect") diff --git a/src/Persistence_representations/utilities/persistence_vectors/average_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/average_persistence_vectors.cpp index 366ee2bc..0144e76f 100644 --- a/src/Persistence_representations/utilities/persistence_vectors/average_persistence_vectors.cpp +++ b/src/Persistence_representations/utilities/persistence_vectors/average_persistence_vectors.cpp @@ -26,25 +26,23 @@ #include <vector> using Euclidean_distance = Gudhi::Euclidean_distance; -using Vector_distances_in_diagram = - Gudhi::Persistence_representations::Vector_distances_in_diagram<Euclidean_distance>; +using Vector_distances_in_diagram = Gudhi::Persistence_representations::Vector_distances_in_diagram<Euclidean_distance>; int main(int argc, char** argv) { - std::cout << "This program computes average persistence vector of persistence vectors created based on persistence " - "diagrams provided as an input. \n"; - std::cout << "Please call this program with the names of files with persistence diagrams \n"; - std::vector<const char*> filenames; + std::cout << "This program computes average of persistence vectors stored in files (the files needs to " + << "be created beforehand).\n" + << "The parameters of this programs are names of files with persistence vectors.\n"; - if (argc == 1) { - std::cout << "No input files given, the program will now terminate \n"; + if (argc < 3) { + std::cout << "Wrong number of parameters, the program will now terminate \n"; return 1; } + std::vector<const char*> filenames; for (int i = 1; i < argc; ++i) { filenames.push_back(argv[i]); } - std::cout << "Reading persistence vectors...\n"; std::vector<Vector_distances_in_diagram*> lands; for (size_t i = 0; i != filenames.size(); ++i) { Vector_distances_in_diagram* l = new Vector_distances_in_diagram; diff --git a/src/Persistence_representations/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp index 3aed297e..7e66d25e 100644 --- a/src/Persistence_representations/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp +++ b/src/Persistence_representations/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp @@ -28,8 +28,7 @@ #include <vector> using Euclidean_distance = Gudhi::Euclidean_distance; -using Vector_distances_in_diagram = - Gudhi::Persistence_representations::Vector_distances_in_diagram<Euclidean_distance>; +using Vector_distances_in_diagram = Gudhi::Persistence_representations::Vector_distances_in_diagram<Euclidean_distance>; int main(int argc, char** argv) { std::cout << "This program compute distance of persistence vectors stored in a file (the file needs to be created " @@ -79,7 +78,7 @@ int main(int argc, char** argv) { // and now output the result to the screen and a file: std::ofstream out; - out.open("distance"); + out.open("distance.vect"); for (size_t i = 0; i != distance.size(); ++i) { for (size_t j = 0; j != distance.size(); ++j) { std::cout << distance[i][j] << " "; @@ -90,5 +89,6 @@ int main(int argc, char** argv) { } out.close(); + std::cout << "Distance can be found in 'distance.vect' file\n"; return 0; } diff --git a/src/Persistence_representations/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp index d9ad4360..303c6e3e 100644 --- a/src/Persistence_representations/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp +++ b/src/Persistence_representations/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp @@ -28,13 +28,17 @@ #include <vector> using Euclidean_distance = Gudhi::Euclidean_distance; -using Vector_distances_in_diagram = - Gudhi::Persistence_representations::Vector_distances_in_diagram<Euclidean_distance>; +using Vector_distances_in_diagram = Gudhi::Persistence_representations::Vector_distances_in_diagram<Euclidean_distance>; int main(int argc, char** argv) { - std::cout << "This program compute scalar product of persistence vectors stored in a file (the file needs to be " - "created beforehand). \n"; - std::cout << "The parameters of this programs are names of files with persistence vectors.\n"; + std::cout << "This program computes scalar product of persistence vectors stored in a file (the file needs to " + << "be created beforehand). \n" + << "The parameters of this programs are names of files with persistence vectors.\n"; + + if (argc < 3) { + std::cout << "Wrong number of parameters, the program will now terminate \n"; + return 1; + } std::vector<const char*> filenames; for (int i = 1; i < argc; ++i) { @@ -66,7 +70,7 @@ int main(int argc, char** argv) { // and now output the result to the screen and a file: std::ofstream out; - out.open("scalar_product"); + out.open("scalar_product.vect"); for (size_t i = 0; i != scalar_product.size(); ++i) { for (size_t j = 0; j != scalar_product.size(); ++j) { std::cout << scalar_product[i][j] << " "; @@ -76,5 +80,7 @@ int main(int argc, char** argv) { out << std::endl; } out.close(); + + std::cout << "Distance can be found in 'scalar_product.vect' file\n"; return 0; } diff --git a/src/Persistence_representations/utilities/persistence_vectors/create_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/create_persistence_vectors.cpp index b618ca67..cc5e5393 100644 --- a/src/Persistence_representations/utilities/persistence_vectors/create_persistence_vectors.cpp +++ b/src/Persistence_representations/utilities/persistence_vectors/create_persistence_vectors.cpp @@ -28,17 +28,24 @@ #include <vector> using Euclidean_distance = Gudhi::Euclidean_distance; -using Vector_distances_in_diagram = - Gudhi::Persistence_representations::Vector_distances_in_diagram<Euclidean_distance>; +using Vector_distances_in_diagram = Gudhi::Persistence_representations::Vector_distances_in_diagram<Euclidean_distance>; int main(int argc, char** argv) { - std::cout << "This program creates persistence vectors of diagrams provided as an input. The first parameter of this " - "program is a dimension of persistence "; - std::cout << " that will be used in creation of the persistence vectors. If our input files contain persistence " - "pairs of various dimension, as a second parameter of the "; - std::cout << " procedure please provide the dimension of persistence you want to use. If in your file there are only " - "birth-death pairs of the same dimension, set the first parameter to -1." - << std::endl; + std::cout << "This program creates persistence vectors files (*.vect) of persistence diagrams files (*.pers) " + << "provided as an input.\n" + << "The first parameter of this program is a dimension of persistence that will be used in creation of " + << "the persistence heat maps." + << "If your input files contains persistence pairs of various dimension, as a first parameter of the " + << "procedure please provide the dimension of persistence you want to use." + << "If in your files there are only birth-death pairs of the same dimension, set the first parameter to " + << "-1.\n" + << "The remaining parameters are the names of files with persistence diagrams. \n"; + + if (argc < 3) { + std::cout << "Wrong parameter list, the program will now terminate \n"; + return 1; + } + std::cout << "The remaining parameters are the names of files with persistence diagrams. \n"; int dim = atoi(argv[1]); unsigned dimension = std::numeric_limits<unsigned>::max(); @@ -58,6 +65,5 @@ int main(int argc, char** argv) { ss << filenames[i] << ".vect"; l.print_to_file(ss.str().c_str()); } - std::cout << "Done \n"; return 0; } diff --git a/src/Persistence_representations/utilities/persistence_vectors/plot_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/plot_persistence_vectors.cpp index e52b8f7d..aa33107d 100644 --- a/src/Persistence_representations/utilities/persistence_vectors/plot_persistence_vectors.cpp +++ b/src/Persistence_representations/utilities/persistence_vectors/plot_persistence_vectors.cpp @@ -26,8 +26,7 @@ #include <sstream> using Euclidean_distance = Gudhi::Euclidean_distance; -using Vector_distances_in_diagram = - Gudhi::Persistence_representations::Vector_distances_in_diagram<Euclidean_distance>; +using Vector_distances_in_diagram = Gudhi::Persistence_representations::Vector_distances_in_diagram<Euclidean_distance>; int main(int argc, char** argv) { std::cout << "This program create a Gnuplot script to plot persistence vector. Please call this program with the " diff --git a/src/Persistence_representations/utilities/persistence_vectors/simple_diagram.txt.vect b/src/Persistence_representations/utilities/persistence_vectors/simple_diagram.txt.vect deleted file mode 100644 index 1d4eeaaf..00000000 --- a/src/Persistence_representations/utilities/persistence_vectors/simple_diagram.txt.vect +++ /dev/null @@ -1 +0,0 @@ -0.707107 0.707107 0.707107 0.707107 0.707107 0.707107 0.707107 0.707107 0.707107 0.707107
\ No newline at end of file diff --git a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h index 62bbbfc5..ceaea505 100644 --- a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h +++ b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h @@ -165,7 +165,7 @@ outputs its persistence diagram. \li <a href="_alpha_complex_2alpha_complex_3d_persistence_8cpp-example.html"> Alpha_complex/alpha_complex_3d_persistence.cpp</a> computes the persistent homology with \f$\mathbb{Z}/2\mathbb{Z}\f$ coefficients of the alpha complex on points sampling from an OFF file. -\code $> ./alpha_complex_3d_persistence ../../data/points/tore3D_300.off 2 0.45 \endcode +\code $> ./alpha_complex_3d_persistence ../../data/points/tore3D_300.off -p 2 -m 0.45 \endcode \code Simplex_tree dim: 3 2 0 0 inf 2 1 0.0682162 1.0001 @@ -177,7 +177,7 @@ Alpha_complex/exact_alpha_complex_3d_persistence.cpp</a> computes the persistent \f$\mathbb{Z}/2\mathbb{Z}\f$ coefficients of the alpha complex on points sampling from an OFF file. Here, as CGAL computes the exact values, it is slower, but it is necessary when points are on a grid for instance. -\code $> ./exact_alpha_complex_3d_persistence ../../data/points/sphere3D_pts_on_grid.off 2 0.1 \endcode +\code $> ./exact_alpha_complex_3d_persistence ../../data/points/sphere3D_pts_on_grid.off -p 2 -m 0.1 \endcode \code Simplex_tree dim: 3 2 0 0 inf 2 2 0.0002 0.2028 \endcode @@ -187,7 +187,7 @@ Alpha_complex/weighted_alpha_complex_3d_persistence.cpp</a> computes the persist \f$\mathbb{Z}/2\mathbb{Z}\f$ coefficients of the weighted alpha complex on points sampling from an OFF file and a weights file. \code $> ./weighted_alpha_complex_3d_persistence ../../data/points/tore3D_300.off -../../data/points/tore3D_300.weights 2 0.45 \endcode +../../data/points/tore3D_300.weights -p 2 -m 0.45 \endcode \code Simplex_tree dim: 3 2 0 -1 inf 2 1 -0.931784 0.000103311 @@ -208,8 +208,10 @@ Simplex_tree dim: 3 \li <a href="_alpha_complex_2periodic_alpha_complex_3d_persistence_8cpp-example.html"> Alpha_complex/periodic_alpha_complex_3d_persistence.cpp</a> computes the persistent homology with \f$\mathbb{Z}/2\mathbb{Z}\f$ coefficients of the periodic alpha complex on points sampling from an OFF file. +The second parameter is a \ref FileFormatsIsoCuboid file with coordinates of the periodic cuboid. +Note that the lengths of the sides of the periodic cuboid have to be the same. \code $> ./periodic_alpha_complex_3d_persistence ../../data/points/grid_10_10_10_in_0_1.off -../../data/points/iso_cuboid_3_in_0_1.txt 3 1.0 \endcode +../../data/points/iso_cuboid_3_in_0_1.txt -p 3 -m 1.0 \endcode \code Periodic Delaunay computed. Simplex_tree dim: 3 3 0 0 inf @@ -221,6 +223,27 @@ Simplex_tree dim: 3 3 2 0.005 inf 3 3 0.0075 inf \endcode +\li <a href="_persistent_cohomology_2weighted_periodic_alpha_complex_3d_persistence_8cpp-example.html"> +Persistent_cohomology/weighted_periodic_alpha_complex_3d_persistence.cpp</a> computes the persistent homology with +\f$\mathbb{Z}/2\mathbb{Z}\f$ coefficients of the periodic alpha complex on weighted points from an OFF file. The +additional parameters of this program are:<br> +(a) The file with the weights of points. The file consist of a sequence of numbers (as many as points). +Note that the weight of each single point have to be bounded by 1/64 times the square of the cuboid edge length.<br> +(b) A \ref FileFormatsIsoCuboid file with coordinates of the periodic cuboid. +Note that the lengths of the sides of the periodic cuboid have to be the same.<br> +\code $> ./weighted_periodic_alpha_complex_3d_persistence ../../data/points/shifted_sphere.off +../../data/points/shifted_sphere.weights ../../data/points/iso_cuboid_3_in_0_10.txt 3 1.0 \endcode +\code Weighted Periodic Delaunay computed. +Simplex_tree dim: 3 +3 0 -0.0001 inf +3 1 16.0264 inf +3 1 16.0273 inf +3 1 16.0303 inf +3 2 36.8635 inf +3 2 36.8704 inf +3 2 36.8838 inf +3 3 58.6783 inf \endcode + \li <a href="_persistent_cohomology_2plain_homology_8cpp-example.html"> Persistent_cohomology/plain_homology.cpp</a> computes the plain homology of a simple simplicial complex without filtration values. diff --git a/src/Rips_complex/test/test_rips_complex.cpp b/src/Rips_complex/test/test_rips_complex.cpp index fc83f5f7..89afbc25 100644 --- a/src/Rips_complex/test/test_rips_complex.cpp +++ b/src/Rips_complex/test/test_rips_complex.cpp @@ -36,6 +36,7 @@ #include <gudhi/Simplex_tree.h> #include <gudhi/distance_functions.h> #include <gudhi/reader_utils.h> +#include <gudhi/Unitary_tests_utils.h> // Type definitions using Point = std::vector<double>; @@ -44,10 +45,6 @@ using Filtration_value = Simplex_tree::Filtration_value; using Rips_complex = Gudhi::rips_complex::Rips_complex<Simplex_tree::Filtration_value>; using Distance_matrix = std::vector<std::vector<Filtration_value>>; -bool are_almost_the_same(float a, float b) { - return std::fabs(a - b) < std::numeric_limits<float>::epsilon(); -} - BOOST_AUTO_TEST_CASE(RIPS_DOC_OFF_file) { // ---------------------------------------------------------------------------- // @@ -92,7 +89,7 @@ BOOST_AUTO_TEST_CASE(RIPS_DOC_OFF_file) { std::cout << ") - distance =" << Gudhi::Euclidean_distance()(vp.at(0), vp.at(1)) << " - filtration =" << st.filtration(f_simplex) << std::endl; BOOST_CHECK(vp.size() == 2); - BOOST_CHECK(are_almost_the_same(st.filtration(f_simplex), Gudhi::Euclidean_distance()(vp.at(0), vp.at(1)))); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(st.filtration(f_simplex), Gudhi::Euclidean_distance()(vp.at(0), vp.at(1))); } } @@ -113,14 +110,14 @@ BOOST_AUTO_TEST_CASE(RIPS_DOC_OFF_file) { Simplex_tree::Filtration_value f12 = st2.filtration(st2.find({1, 2})); Simplex_tree::Filtration_value f012 = st2.filtration(st2.find({0, 1, 2})); std::cout << "f012= " << f012 << " | f01= " << f01 << " - f02= " << f02 << " - f12= " << f12 << std::endl; - BOOST_CHECK(are_almost_the_same(f012, std::max(f01, std::max(f02,f12)))); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(f012, std::max(f01, std::max(f02,f12))); Simplex_tree::Filtration_value f45 = st2.filtration(st2.find({4, 5})); Simplex_tree::Filtration_value f56 = st2.filtration(st2.find({5, 6})); Simplex_tree::Filtration_value f46 = st2.filtration(st2.find({4, 6})); Simplex_tree::Filtration_value f456 = st2.filtration(st2.find({4, 5, 6})); std::cout << "f456= " << f456 << " | f45= " << f45 << " - f56= " << f56 << " - f46= " << f46 << std::endl; - BOOST_CHECK(are_almost_the_same(f456, std::max(f45, std::max(f56,f46)))); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(f456, std::max(f45, std::max(f56,f46))); const int DIMENSION_3 = 3; Simplex_tree st3; @@ -140,7 +137,7 @@ BOOST_AUTO_TEST_CASE(RIPS_DOC_OFF_file) { Simplex_tree::Filtration_value f0123 = st3.filtration(st3.find({0, 1, 2, 3})); std::cout << "f0123= " << f0123 << " | f012= " << f012 << " - f123= " << f123 << " - f013= " << f013 << " - f023= " << f023 << std::endl; - BOOST_CHECK(are_almost_the_same(f0123, std::max(f012, std::max(f123, std::max(f013, f023))))); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(f0123, std::max(f012, std::max(f123, std::max(f013, f023)))); } @@ -219,12 +216,12 @@ BOOST_AUTO_TEST_CASE(Rips_complex_from_points) { std::cout << "dimension(" << st.dimension(f_simplex) << ") - f = " << st.filtration(f_simplex) << std::endl; switch (st.dimension(f_simplex)) { case 0: - BOOST_CHECK(are_almost_the_same(st.filtration(f_simplex), 0.0)); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(st.filtration(f_simplex), 0.0); break; case 1: case 2: case 3: - BOOST_CHECK(are_almost_the_same(st.filtration(f_simplex), 2.0)); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(st.filtration(f_simplex), 2.0); break; default: BOOST_CHECK(false); // Shall not happen @@ -276,7 +273,7 @@ BOOST_AUTO_TEST_CASE(Rips_doc_csv_file) { } std::cout << ") - filtration =" << st.filtration(f_simplex) << std::endl; BOOST_CHECK(vvh.size() == 2); - BOOST_CHECK(are_almost_the_same(st.filtration(f_simplex), distances[vvh.at(0)][vvh.at(1)])); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(st.filtration(f_simplex), distances[vvh.at(0)][vvh.at(1)]); } } @@ -297,14 +294,14 @@ BOOST_AUTO_TEST_CASE(Rips_doc_csv_file) { Simplex_tree::Filtration_value f12 = st2.filtration(st2.find({1, 2})); Simplex_tree::Filtration_value f012 = st2.filtration(st2.find({0, 1, 2})); std::cout << "f012= " << f012 << " | f01= " << f01 << " - f02= " << f02 << " - f12= " << f12 << std::endl; - BOOST_CHECK(are_almost_the_same(f012, std::max(f01, std::max(f02,f12)))); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(f012, std::max(f01, std::max(f02,f12))); Simplex_tree::Filtration_value f45 = st2.filtration(st2.find({4, 5})); Simplex_tree::Filtration_value f56 = st2.filtration(st2.find({5, 6})); Simplex_tree::Filtration_value f46 = st2.filtration(st2.find({4, 6})); Simplex_tree::Filtration_value f456 = st2.filtration(st2.find({4, 5, 6})); std::cout << "f456= " << f456 << " | f45= " << f45 << " - f56= " << f56 << " - f46= " << f46 << std::endl; - BOOST_CHECK(are_almost_the_same(f456, std::max(f45, std::max(f56,f46)))); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(f456, std::max(f45, std::max(f56,f46))); const int DIMENSION_3 = 3; Simplex_tree st3; @@ -324,7 +321,7 @@ BOOST_AUTO_TEST_CASE(Rips_doc_csv_file) { Simplex_tree::Filtration_value f0123 = st3.filtration(st3.find({0, 1, 2, 3})); std::cout << "f0123= " << f0123 << " | f012= " << f012 << " - f123= " << f123 << " - f013= " << f013 << " - f023= " << f023 << std::endl; - BOOST_CHECK(are_almost_the_same(f0123, std::max(f012, std::max(f123, std::max(f013, f023))))); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(f0123, std::max(f012, std::max(f123, std::max(f013, f023)))); } diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h index 92add101..7456cb1f 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h @@ -49,6 +49,7 @@ #include <initializer_list> #include <algorithm> // for std::max #include <cstdint> // for std::uint32_t +#include <iterator> // for std::distance namespace Gudhi { @@ -106,8 +107,9 @@ class Simplex_tree { }; struct Key_simplex_base_dummy { Key_simplex_base_dummy() {} - void assign_key(Simplex_key) { } - Simplex_key key() const { assert(false); return -1; } + // Undefined so it will not link + void assign_key(Simplex_key); + Simplex_key key() const; }; typedef typename std::conditional<Options::store_key, Key_simplex_base_real, Key_simplex_base_dummy>::type Key_simplex_base; @@ -121,7 +123,7 @@ class Simplex_tree { }; struct Filtration_simplex_base_dummy { Filtration_simplex_base_dummy() {} - void assign_filtration(Filtration_value f) { assert(f == 0); } + void assign_filtration(Filtration_value GUDHI_CHECK_code(f)) { GUDHI_CHECK(f == 0, "filtration value specified for a complex that does not store them"); } Filtration_value filtration() const { return 0; } }; typedef typename std::conditional<Options::store_filtration, Filtration_simplex_base_real, @@ -679,75 +681,67 @@ class Simplex_tree { */ template<class InputVertexRange = std::initializer_list<Vertex_handle>> std::pair<Simplex_handle, bool> insert_simplex_and_subfaces(const InputVertexRange& Nsimplex, - Filtration_value filtration = 0) { + Filtration_value filtration = 0) { auto first = std::begin(Nsimplex); auto last = std::end(Nsimplex); if (first == last) - return std::pair<Simplex_handle, bool>(null_simplex(), true); // ----->> + return { null_simplex(), true }; // ----->> // Copy before sorting - std::vector<Vertex_handle> copy(first, last); + thread_local std::vector<Vertex_handle> copy; + copy.clear(); + copy.insert(copy.end(), first, last); std::sort(std::begin(copy), std::end(copy)); GUDHI_CHECK_code( for (Vertex_handle v : copy) GUDHI_CHECK(v != null_vertex(), "cannot use the dummy null_vertex() as a real vertex"); ) - std::vector<std::vector<Vertex_handle>> to_be_inserted; - std::vector<std::vector<Vertex_handle>> to_be_propagated; - return rec_insert_simplex_and_subfaces(copy, to_be_inserted, to_be_propagated, filtration); + return insert_simplex_and_subfaces_sorted(copy, filtration); } private: - std::pair<Simplex_handle, bool> rec_insert_simplex_and_subfaces(std::vector<Vertex_handle>& the_simplex, - std::vector<std::vector<Vertex_handle>>& to_be_inserted, - std::vector<std::vector<Vertex_handle>>& to_be_propagated, - Filtration_value filtration = 0.0) { - std::pair<Simplex_handle, bool> insert_result; - if (the_simplex.size() > 1) { - // Get and remove last vertex - Vertex_handle last_vertex = the_simplex.back(); - the_simplex.pop_back(); - // Recursive call after last vertex removal - insert_result = rec_insert_simplex_and_subfaces(the_simplex, to_be_inserted, to_be_propagated, filtration); - - // Concatenation of to_be_inserted and to_be_propagated - to_be_inserted.insert(to_be_inserted.begin(), to_be_propagated.begin(), to_be_propagated.end()); - to_be_propagated = to_be_inserted; - - // to_be_inserted treatment - for (auto& simplex_tbi : to_be_inserted) { - simplex_tbi.push_back(last_vertex); - } - std::vector<Vertex_handle> last_simplex(1, last_vertex); - to_be_inserted.insert(to_be_inserted.begin(), last_simplex); - // i.e. (0,1,2) => - // [to_be_inserted | to_be_propagated] = [(1) (0,1) | (0)] - // [to_be_inserted | to_be_propagated] = [(2) (0,2) (1,2) (0,1,2) | (0) (1) (0,1)] - // N.B. : it is important the last inserted to be the highest in dimension - // in order to return the "last" insert_simplex result - - // insert all to_be_inserted - for (auto& simplex_tbi : to_be_inserted) { - insert_result = insert_vertex_vector(simplex_tbi, filtration); - } - } else if (the_simplex.size() == 1) { - // When reaching the end of recursivity, vector of simplices shall be empty and filled on back recursive - if ((to_be_inserted.size() != 0) || (to_be_propagated.size() != 0)) { - std::cerr << "Simplex_tree::rec_insert_simplex_and_subfaces - Error vector not empty\n"; - exit(-1); + /// Same as insert_simplex_and_subfaces but assumes that the range of vertices is sorted + template<class ForwardVertexRange = std::initializer_list<Vertex_handle>> + std::pair<Simplex_handle, bool> insert_simplex_and_subfaces_sorted(const ForwardVertexRange& Nsimplex, Filtration_value filt = 0) { + auto first = std::begin(Nsimplex); + auto last = std::end(Nsimplex); + if (first == last) + return { null_simplex(), true }; // FIXME: false would make more sense to me. + GUDHI_CHECK(std::is_sorted(first, last), "simplex vertices listed in unsorted order"); + // Update dimension if needed. We could wait to see if the insertion succeeds, but I doubt there is much to gain. + dimension_ = (std::max)(dimension_, static_cast<int>(std::distance(first, last)) - 1); + return rec_insert_simplex_and_subfaces_sorted(root(), first, last, filt); + } + // To insert {1,2,3,4}, we insert {2,3,4} twice, once at the root, and once below 1. + template<class ForwardVertexIterator> + std::pair<Simplex_handle, bool> rec_insert_simplex_and_subfaces_sorted(Siblings* sib, ForwardVertexIterator first, ForwardVertexIterator last, Filtration_value filt) { + // An alternative strategy would be: + // - try to find the complete simplex, if found (and low filtration) exit + // - insert all the vertices at once in sib + // - loop over those (new or not) simplices, with a recursive call(++first, last) + Vertex_handle vertex_one = *first; + auto&& dict = sib->members(); + auto insertion_result = dict.emplace(vertex_one, Node(sib, filt)); + Simplex_handle simplex_one = insertion_result.first; + bool one_is_new = insertion_result.second; + if (!one_is_new) { + if (filtration(simplex_one) > filt) { + assign_filtration(simplex_one, filt); + } else { + // FIXME: this interface makes no sense, and it doesn't seem to be tested. + insertion_result.first = null_simplex(); } - std::vector<Vertex_handle> first_simplex(1, the_simplex.back()); - // i.e. (0,1,2) => [to_be_inserted | to_be_propagated] = [(0) | ] - to_be_inserted.push_back(first_simplex); - - insert_result = insert_vertex_vector(first_simplex, filtration); - } else { - std::cerr << "Simplex_tree::rec_insert_simplex_and_subfaces - Recursivity error\n"; - exit(-1); } - return insert_result; + if (++first == last) return insertion_result; + if (!has_children(simplex_one)) + // TODO: have special code here, we know we are building the whole subtree from scratch. + simplex_one->second.assign_children(new Siblings(sib, vertex_one)); + auto res = rec_insert_simplex_and_subfaces_sorted(simplex_one->second.children(), first, last, filt); + // No need to continue if the full simplex was already there with a low enough filtration value. + if (res.first != null_simplex()) rec_insert_simplex_and_subfaces_sorted(sib, first, last, filt); + return res; } public: @@ -1165,7 +1159,7 @@ class Simplex_tree { to_be_inserted=false; break; } - filt = std::max(filt, filtration(border_child)); + filt = (std::max)(filt, filtration(border_child)); } if (to_be_inserted) { intersection.emplace_back(next->first, Node(nullptr, filt)); @@ -1361,7 +1355,7 @@ class Simplex_tree { if (sh_dimension >= dimension_) // Stop browsing as soon as the dimension is reached, no need to go furter return false; - new_dimension = std::max(new_dimension, sh_dimension); + new_dimension = (std::max)(new_dimension, sh_dimension); } dimension_ = new_dimension; return true; diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h index 7e0a454d..ab7346d4 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h @@ -23,6 +23,8 @@ #ifndef SIMPLEX_TREE_SIMPLEX_TREE_ITERATORS_H_ #define SIMPLEX_TREE_SIMPLEX_TREE_ITERATORS_H_ +#include <gudhi/Debug_utils.h> + #include <boost/iterator/iterator_facade.hpp> #include <boost/version.hpp> #if BOOST_VERSION >= 105600 @@ -109,11 +111,18 @@ class Simplex_tree_boundary_simplex_iterator : public boost::iterator_facade< : last_(sh->first), sib_(nullptr), st_(st) { + // Only check once at the beginning instead of for every increment, as this is expensive. + if (SimplexTree::Options::contiguous_vertices) + GUDHI_CHECK(st_->contiguous_vertices(), "The set of vertices is not { 0, ..., n } without holes"); Siblings * sib = st->self_siblings(sh); next_ = sib->parent(); sib_ = sib->oncles(); if (sib_ != nullptr) { - sh_ = sib_->find(next_); + if (SimplexTree::Options::contiguous_vertices && sib_->oncles() == nullptr) + // Only relevant for edges + sh_ = sib_->members_.begin()+next_; + else + sh_ = sib_->find(next_); } else { sh_ = st->null_simplex(); } // vertex: == end() @@ -140,14 +149,19 @@ class Simplex_tree_boundary_simplex_iterator : public boost::iterator_facade< Siblings * for_sib = sib_; Siblings * new_sib = sib_->oncles(); auto rit = suffix_.rbegin(); - if (SimplexTree::Options::contiguous_vertices && new_sib == nullptr && rit != suffix_.rend()) { - // We reached the root, use a short-cut to find a vertex. We could also - // optimize finding the second vertex of a segment, but people are - // expected to call endpoints(). - assert(st_->contiguous_vertices()); - sh_ = for_sib->members_.begin()+*rit; - for_sib = sh_->second.children(); - ++rit; + if (SimplexTree::Options::contiguous_vertices && new_sib == nullptr) { + // We reached the root, use a short-cut to find a vertex. + if (rit == suffix_.rend()) { + // Segment, this vertex is the last boundary simplex + sh_ = for_sib->members_.begin()+last_; + sib_ = nullptr; + return; + } else { + // Dim >= 2, initial step of the descent + sh_ = for_sib->members_.begin()+*rit; + for_sib = sh_->second.children(); + ++rit; + } } for (; rit != suffix_.rend(); ++rit) { sh_ = for_sib->find(*rit); diff --git a/src/cmake/modules/GUDHI_test_coverage.cmake b/src/cmake/modules/GUDHI_test_coverage.cmake index ce171a0e..bea5b2d6 100644 --- a/src/cmake/modules/GUDHI_test_coverage.cmake +++ b/src/cmake/modules/GUDHI_test_coverage.cmake @@ -8,7 +8,19 @@ if (GPROF_PATH) set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg") endif() +if (DEBUG_TRACES) + # Make CTest more verbose with DEBUG_TRACES - no XML output + set(GUDHI_UT_LOG_LEVEL "--log_level=all") + set(GUDHI_UT_REPORT_LEVEL "--report_level=detailed") +else() + set(GUDHI_UT_LOG_FORMAT "--log_format=XML") + set(GUDHI_UT_LOG_SINK "--log_sink=${CMAKE_BINARY_DIR}/${unitary_test}_UT.xml") + set(GUDHI_UT_LOG_LEVEL "--log_level=test_suite") + set(GUDHI_UT_REPORT_LEVEL "--report_level=no") +endif() + function(gudhi_add_coverage_test unitary_test) add_test(NAME ${unitary_test} COMMAND $<TARGET_FILE:${unitary_test}> - "--log_format=XML" "--log_sink=${CMAKE_BINARY_DIR}/${unitary_test}_UT.xml" "--log_level=test_suite" "--report_level=no") + ${GUDHI_UT_LOG_FORMAT} ${GUDHI_UT_LOG_SINK} + ${GUDHI_UT_LOG_LEVEL} ${GUDHI_UT_REPORT_LEVEL}) endfunction() diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake index 8269c3bf..419c2581 100644 --- a/src/cmake/modules/GUDHI_third_party_libraries.cmake +++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake @@ -1,6 +1,6 @@ # This files manage third party libraries required by GUDHI -find_package(Boost REQUIRED COMPONENTS system filesystem unit_test_framework program_options thread) +find_package(Boost 1.48.0 REQUIRED COMPONENTS system filesystem unit_test_framework program_options thread) if(NOT Boost_FOUND) message(FATAL_ERROR "NOTICE: This program requires Boost and will not be compiled.") @@ -85,7 +85,6 @@ FIND_PROGRAM( GCOVR_PATH gcovr ) if (GCOVR_PATH) message("gcovr found in ${GCOVR_PATH}") endif() -# Required programs for unitary tests purpose FIND_PROGRAM( GPROF_PATH gprof ) if (GPROF_PATH) message("gprof found in ${GPROF_PATH}") @@ -94,6 +93,10 @@ FIND_PROGRAM( DIFF_PATH diff ) if (DIFF_PATH) message("diff found in ${DIFF_PATH}") endif() +FIND_PROGRAM( GNUPLOT_PATH gnuplot ) +if (GNUPLOT_PATH) + message("gnuplot found in ${GNUPLOT_PATH}") +endif() # BOOST ISSUE result_of vs C++11 add_definitions(-DBOOST_RESULT_OF_USE_DECLTYPE) diff --git a/src/common/include/gudhi/Debug_utils.h b/src/common/include/gudhi/Debug_utils.h index 8ed3b7b3..90d3cf47 100644 --- a/src/common/include/gudhi/Debug_utils.h +++ b/src/common/include/gudhi/Debug_utils.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (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 @@ -32,7 +32,7 @@ // GUDHI_CHECK throw an exception if expression is false in debug mode, but does nothing in release mode // Could assert in release mode, but cmake sets NDEBUG (for "NO DEBUG") in this mode, means assert does nothing. #ifdef GUDHI_DEBUG - #define GUDHI_CHECK(expression, excpt) if ((expression) == 0) throw excpt + #define GUDHI_CHECK(expression, excpt) ((expression) ? (void) 0 : (throw excpt)) #define GUDHI_CHECK_code(CODE) CODE #else #define GUDHI_CHECK(expression, excpt) (void) 0 diff --git a/src/common/include/gudhi/Unitary_tests_utils.h b/src/common/include/gudhi/Unitary_tests_utils.h new file mode 100644 index 00000000..7ae5d356 --- /dev/null +++ b/src/common/include/gudhi/Unitary_tests_utils.h @@ -0,0 +1,39 @@ +/* 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) 2017 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/>. + */ +#ifndef UNITARY_TESTS_UTILS_H_ +#define UNITARY_TESTS_UTILS_H_ + +#include <boost/test/unit_test.hpp> + +#include <iostream> + +template<typename FloatingType > +void GUDHI_TEST_FLOAT_EQUALITY_CHECK(FloatingType a, FloatingType b, + FloatingType epsilon = std::numeric_limits<FloatingType>::epsilon()) { +#ifdef DEBUG_TRACES + std::cout << "GUDHI_TEST_FLOAT_EQUALITY_CHECK - " << a << " versus " << b + << " | diff = " << std::fabs(a - b) << " - epsilon = " << epsilon << std::endl; +#endif + BOOST_CHECK(std::fabs(a - b) < epsilon); +} + +#endif // UNITARY_TESTS_UTILS_H_ |