From 9899ae167f281d10b1684dfcd02c6838c5bf28df Mon Sep 17 00:00:00 2001 From: Gard Spreemann Date: Fri, 2 Feb 2018 13:51:45 +0100 Subject: GUDHI 2.1.0 as released by upstream in a tarball. --- .../persistence_intervals/CMakeLists.txt | 32 ++++++++ ...te_birth_death_range_in_persistence_diagram.cpp | 68 ++++++++++++++++ .../compute_bottleneck_distance.cpp | 95 ++++++++++++++++++++++ .../compute_number_of_dominant_intervals.cpp | 54 ++++++++++++ .../plot_histogram_of_intervals_lengths.cpp | 77 ++++++++++++++++++ .../plot_persistence_Betti_numbers.cpp | 87 ++++++++++++++++++++ .../plot_persistence_intervals.cpp | 53 ++++++++++++ 7 files changed, 466 insertions(+) create mode 100644 utilities/Persistence_representations/persistence_intervals/CMakeLists.txt create mode 100644 utilities/Persistence_representations/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp create mode 100644 utilities/Persistence_representations/persistence_intervals/compute_bottleneck_distance.cpp create mode 100644 utilities/Persistence_representations/persistence_intervals/compute_number_of_dominant_intervals.cpp create mode 100644 utilities/Persistence_representations/persistence_intervals/plot_histogram_of_intervals_lengths.cpp create mode 100644 utilities/Persistence_representations/persistence_intervals/plot_persistence_Betti_numbers.cpp create mode 100644 utilities/Persistence_representations/persistence_intervals/plot_persistence_intervals.cpp (limited to 'utilities/Persistence_representations/persistence_intervals') diff --git a/utilities/Persistence_representations/persistence_intervals/CMakeLists.txt b/utilities/Persistence_representations/persistence_intervals/CMakeLists.txt new file mode 100644 index 00000000..897e12a3 --- /dev/null +++ b/utilities/Persistence_representations/persistence_intervals/CMakeLists.txt @@ -0,0 +1,32 @@ +cmake_minimum_required(VERSION 2.6) +project(Persistence_representations_intervals_utilities) + + +add_executable ( plot_histogram_of_intervals_lengths plot_histogram_of_intervals_lengths.cpp ) + +add_test(NAME plot_histogram_of_intervals_lengths COMMAND $ + "${CMAKE_CURRENT_BINARY_DIR}/../first.pers" "-1") + +add_persistence_representation_plot_utility(plot_persistence_intervals "") +add_persistence_representation_plot_utility(plot_persistence_Betti_numbers "") + +add_persistence_representation_creation_utility(compute_birth_death_range_in_persistence_diagram "-1") + + +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 $ + "${CMAKE_CURRENT_BINARY_DIR}/../first.pers" "-1" "2") + + +if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) + add_executable ( compute_bottleneck_distance compute_bottleneck_distance.cpp ) + if (TBB_FOUND) + target_link_libraries(compute_bottleneck_distance ${TBB_LIBRARIES}) + endif(TBB_FOUND) + add_test(NAME Persistence_representation_utilities_compute_bottleneck_distance + COMMAND $ + "-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/utilities/Persistence_representations/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp b/utilities/Persistence_representations/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp new file mode 100644 index 00000000..9102da79 --- /dev/null +++ b/utilities/Persistence_representations/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp @@ -0,0 +1,68 @@ +/* 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): Pawel Dlotko + * + * Copyright (C) 2016 INRIA (France) + * + * 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 . + */ + +#include + +#include +#include +#include +#include + +using Persistence_intervals = Gudhi::Persistence_representations::Persistence_intervals; + +int main(int argc, char** argv) { + 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; + } + + unsigned dimension = std::numeric_limits::max(); + int dim = atoi(argv[1]); + if (dim >= 0) { + dimension = (unsigned)dim; + } + std::vector filenames; + for (int i = 2; i < argc; ++i) { + filenames.push_back(argv[i]); + } + + double min_ = std::numeric_limits::max(); + double max_ = -std::numeric_limits::max(); + + for (size_t file_no = 0; file_no != filenames.size(); ++file_no) { + std::cout << "Creating diagram based on a file : " << filenames[file_no] << std::endl; + Persistence_intervals p(filenames[file_no], dimension); + std::pair min_max_ = p.get_x_range(); + if (min_max_.first < min_) min_ = min_max_.first; + if (min_max_.second > max_) max_ = min_max_.second; + } + std::cout << "Birth-death range : min: " << min_ << ", max: " << max_ << std::endl; + return 0; +} diff --git a/utilities/Persistence_representations/persistence_intervals/compute_bottleneck_distance.cpp b/utilities/Persistence_representations/persistence_intervals/compute_bottleneck_distance.cpp new file mode 100644 index 00000000..c8290845 --- /dev/null +++ b/utilities/Persistence_representations/persistence_intervals/compute_bottleneck_distance.cpp @@ -0,0 +1,95 @@ +/* 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): Pawel Dlotko + * + * Copyright (C) 2016 INRIA (France) + * + * 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 . + */ + +#include + +#include +#include +#include +#include + +using Persistence_intervals_with_distances = Gudhi::Persistence_representations::Persistence_intervals_with_distances; + +int main(int argc, char** argv) { + 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; + } + + unsigned dimension = std::numeric_limits::max(); + int dim = atoi(argv[1]); + if (dim >= 0) { + dimension = (unsigned)dim; + } + + std::vector filenames; + for (int i = 2; i < argc; ++i) { + filenames.push_back(argv[i]); + } + + // reading the persistence intervals: + std::vector persistence_intervals; + for (size_t i = 0; i != filenames.size(); ++i) { + Persistence_intervals_with_distances pers(filenames[i], dimension); + persistence_intervals.push_back(pers); + } + + // and now we will compute the scalar product of landscapes. + + // first we prepare an array: + std::vector > distance(filenames.size()); + for (size_t i = 0; i != filenames.size(); ++i) { + std::vector v(filenames.size(), 0); + distance[i] = v; + } + + // and now we can compute the distances: + for (size_t i = 0; i != persistence_intervals.size(); ++i) { + for (size_t j = i + 1; j != persistence_intervals.size(); ++j) { + distance[i][j] = distance[j][i] = persistence_intervals[i].distance(persistence_intervals[j]); + } + } + + // and now output the result to the screen and a file: + std::ofstream out; + 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] << " "; + out << distance[i][j] << " "; + } + std::cout << std::endl; + out << std::endl; + } + out.close(); + + std::cout << "Distance can be found in 'distance.itv' file\n"; + return 0; +} diff --git a/utilities/Persistence_representations/persistence_intervals/compute_number_of_dominant_intervals.cpp b/utilities/Persistence_representations/persistence_intervals/compute_number_of_dominant_intervals.cpp new file mode 100644 index 00000000..b3d126f0 --- /dev/null +++ b/utilities/Persistence_representations/persistence_intervals/compute_number_of_dominant_intervals.cpp @@ -0,0 +1,54 @@ +/* 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): Pawel Dlotko + * + * Copyright (C) 2016 INRIA (France) + * + * 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 . + */ + +#include + +#include +#include +#include +#include + +using Persistence_intervals = Gudhi::Persistence_representations::Persistence_intervals; + +int main(int argc, char** argv) { + std::cout << "This program compute the dominant intervals. A number of intervals to be displayed is a parameter of " + "this program. \n"; + if (argc != 4) { + std::cout << "To run this program, please provide the name of a file with persistence diagram, dimension of " + "intervals that should be taken into account (if your file contains only persistence pairs in a " + "single dimension, set it up to -1) and number of dominant intervals you would like to get \n"; + return 1; + } + int dim = atoi(argv[2]); + unsigned dimension = std::numeric_limits::max(); + if (dim >= 0) { + dimension = (unsigned)dim; + } + Persistence_intervals p(argv[1], dimension); + std::vector > dominant_intervals = p.dominant_intervals(atoi(argv[3])); + std::cout << "Here are the dominant intervals : " << std::endl; + for (size_t i = 0; i != dominant_intervals.size(); ++i) { + std::cout << " " << dominant_intervals[i].first << "," << dominant_intervals[i].second << " " << std::endl; + } + + return 0; +} diff --git a/utilities/Persistence_representations/persistence_intervals/plot_histogram_of_intervals_lengths.cpp b/utilities/Persistence_representations/persistence_intervals/plot_histogram_of_intervals_lengths.cpp new file mode 100644 index 00000000..ccb5b645 --- /dev/null +++ b/utilities/Persistence_representations/persistence_intervals/plot_histogram_of_intervals_lengths.cpp @@ -0,0 +1,77 @@ +/* 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): Pawel Dlotko + * + * Copyright (C) 2016 INRIA (France) + * + * 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 . + */ + +#include + +#include +#include +#include +#include + +using Persistence_intervals = Gudhi::Persistence_representations::Persistence_intervals; + +int main(int argc, char** argv) { + 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. 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 dominant_interval_number = std::numeric_limits::max(); + int nbr = atoi(argv[2]); + if (nbr >= 0) { + dominant_interval_number = static_cast(nbr); + } + + int persistence_dimension = -1; + if (argc == 4) { + persistence_dimension = atoi(argv[3]); + } + + Persistence_intervals p(argv[1], dominant_interval_number); + std::vector > dominant_intervals = p.dominant_intervals(persistence_dimension); + std::vector histogram = p.histogram_of_lengths(10); + + std::stringstream gnuplot_script; + gnuplot_script << argv[1] << "_GnuplotScript"; + std::ofstream out; + out.open(gnuplot_script.str().c_str()); + + out << "set style data histogram" << std::endl; + out << "set style histogram cluster gap 1" << std::endl; + out << "set style fill solid border -1" << std::endl; + out << "plot '-' notitle" << std::endl; + for (size_t i = 0; i != histogram.size(); ++i) { + out << histogram[i] << std::endl; + } + out << 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/utilities/Persistence_representations/persistence_intervals/plot_persistence_Betti_numbers.cpp b/utilities/Persistence_representations/persistence_intervals/plot_persistence_Betti_numbers.cpp new file mode 100644 index 00000000..b433c2b3 --- /dev/null +++ b/utilities/Persistence_representations/persistence_intervals/plot_persistence_Betti_numbers.cpp @@ -0,0 +1,87 @@ +/* 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): Pawel Dlotko + * + * Copyright (C) 2016 INRIA (France) + * + * 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 . + */ + +#include + +#include +#include +#include +#include + +using Persistence_intervals = Gudhi::Persistence_representations::Persistence_intervals; + +int main(int argc, char** argv) { + 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::max(); + int dim = -1; + if (argc == 3) { + dim = atoi(argv[2]); + } + if (dim >= 0) { + dimension = (unsigned)dim; + } + + Persistence_intervals p(argv[1], dimension); + std::vector > pbns = p.compute_persistent_betti_numbers(); + + // set up the ranges so that we see the image well. + double xRangeBegin = pbns[0].first; + double xRangeEnd = pbns[pbns.size() - 1].first; + double yRangeBegin = 0; + double yRangeEnd = 0; + for (size_t i = 0; i != pbns.size(); ++i) { + if (pbns[i].second > yRangeEnd) yRangeEnd = pbns[i].second; + } + xRangeBegin -= (xRangeEnd - xRangeBegin) / 100.0; + 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; + double previous_y = 0; + for (size_t i = 0; i != pbns.size(); ++i) { + out << pbns[i].first << " " << previous_y << std::endl; + out << pbns[i].first << " " << pbns[i].second << std::endl; + previous_y = pbns[i].second; + } + out << 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/utilities/Persistence_representations/persistence_intervals/plot_persistence_intervals.cpp b/utilities/Persistence_representations/persistence_intervals/plot_persistence_intervals.cpp new file mode 100644 index 00000000..33387802 --- /dev/null +++ b/utilities/Persistence_representations/persistence_intervals/plot_persistence_intervals.cpp @@ -0,0 +1,53 @@ +/* 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): Pawel Dlotko + * + * Copyright (C) 2016 INRIA (France) + * + * 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 . + */ + +#include + +#include +#include +#include +#include + +using Persistence_intervals = Gudhi::Persistence_representations::Persistence_intervals; + +int main(int argc, char** argv) { + 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::max(); + int dim = -1; + if (argc == 3) { + dim = atoi(argv[2]); + } + if (dim >= 0) { + dimension = (unsigned)dim; + } + std::vector > intervals = + Gudhi::Persistence_representations::read_persistence_intervals_in_one_dimension_from_file(argv[1], dimension); + Persistence_intervals b(intervals); + b.plot(argv[1]); + return 0; +} -- cgit v1.2.3