From 14f55cf58e9be168e6be635ddafebc6c86cc7eea Mon Sep 17 00:00:00 2001 From: cjamin Date: Wed, 31 May 2017 16:48:08 +0000 Subject: Convert more examples into utilities git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/add_utils_in_gudhi_v2@2494 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 54fa703f0489cba059a8df973738118f6a092f70 --- src/Persistent_cohomology/example/CMakeLists.txt | 35 --- .../example/alpha_complex_3d_helper.h | 76 ------ .../example/alpha_complex_3d_persistence.cpp | 243 ------------------- .../example/alpha_complex_persistence.cpp | 125 ---------- .../example/exact_alpha_complex_3d_persistence.cpp | 2 +- .../periodic_alpha_complex_3d_persistence.cpp | 262 --------------------- .../example/rips_distance_matrix_persistence.cpp | 144 ----------- .../example/rips_persistence.cpp | 147 ------------ .../weighted_alpha_complex_3d_persistence.cpp | 2 +- src/Persistent_cohomology/utilities/CMakeLists.txt | 56 +++++ .../utilities/alpha_complex_3d_helper.h | 76 ++++++ .../utilities/alpha_complex_3d_persistence.cpp | 243 +++++++++++++++++++ .../utilities/alpha_complex_persistence.cpp | 125 ++++++++++ .../periodic_alpha_complex_3d_persistence.cpp | 262 +++++++++++++++++++++ .../utilities/rips_distance_matrix_persistence.cpp | 144 +++++++++++ .../utilities/rips_persistence.cpp | 147 ++++++++++++ 16 files changed, 1055 insertions(+), 1034 deletions(-) delete mode 100644 src/Persistent_cohomology/example/alpha_complex_3d_helper.h delete mode 100644 src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp delete mode 100644 src/Persistent_cohomology/example/alpha_complex_persistence.cpp delete mode 100644 src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp delete mode 100644 src/Persistent_cohomology/example/rips_distance_matrix_persistence.cpp delete mode 100644 src/Persistent_cohomology/example/rips_persistence.cpp create mode 100644 src/Persistent_cohomology/utilities/CMakeLists.txt create mode 100644 src/Persistent_cohomology/utilities/alpha_complex_3d_helper.h create mode 100644 src/Persistent_cohomology/utilities/alpha_complex_3d_persistence.cpp create mode 100644 src/Persistent_cohomology/utilities/alpha_complex_persistence.cpp create mode 100644 src/Persistent_cohomology/utilities/periodic_alpha_complex_3d_persistence.cpp create mode 100644 src/Persistent_cohomology/utilities/rips_distance_matrix_persistence.cpp create mode 100644 src/Persistent_cohomology/utilities/rips_persistence.cpp (limited to 'src/Persistent_cohomology') diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt index a9884c49..eb31e050 100644 --- a/src/Persistent_cohomology/example/CMakeLists.txt +++ b/src/Persistent_cohomology/example/CMakeLists.txt @@ -7,12 +7,6 @@ target_link_libraries(plain_homology ${Boost_SYSTEM_LIBRARY}) add_executable(persistence_from_simple_simplex_tree persistence_from_simple_simplex_tree.cpp) target_link_libraries(persistence_from_simple_simplex_tree ${Boost_SYSTEM_LIBRARY}) -add_executable(rips_distance_matrix_persistence rips_distance_matrix_persistence.cpp) -target_link_libraries(rips_distance_matrix_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) - -add_executable(rips_persistence rips_persistence.cpp) -target_link_libraries(rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) - add_executable(rips_persistence_step_by_step rips_persistence_step_by_step.cpp) target_link_libraries(rips_persistence_step_by_step ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) @@ -25,8 +19,6 @@ target_link_libraries(persistence_from_file ${Boost_SYSTEM_LIBRARY} ${Boost_PROG if (TBB_FOUND) target_link_libraries(plain_homology ${TBB_LIBRARIES}) target_link_libraries(persistence_from_simple_simplex_tree ${TBB_LIBRARIES}) - target_link_libraries(rips_distance_matrix_persistence ${TBB_LIBRARIES}) - target_link_libraries(rips_persistence ${TBB_LIBRARIES}) target_link_libraries(rips_persistence_step_by_step ${TBB_LIBRARIES}) target_link_libraries(rips_persistence_via_boundary_matrix ${TBB_LIBRARIES}) target_link_libraries(persistence_from_file ${TBB_LIBRARIES}) @@ -35,10 +27,6 @@ endif() add_test(NAME Persistent_cohomology_example_plain_homology COMMAND $) add_test(NAME Persistent_cohomology_example_from_simple_simplex_tree COMMAND $ "1" "0") -add_test(NAME Persistent_cohomology_example_from_rips_distance_matrix COMMAND $ - "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" "-r" "1.0" "-d" "3" "-p" "3" "-m" "0") -add_test(NAME Persistent_cohomology_example_from_rips_on_tore_3D COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3") add_test(NAME Persistent_cohomology_example_from_rips_step_by_step_on_tore_3D COMMAND $ "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3") add_test(NAME Persistent_cohomology_example_via_boundary_matrix COMMAND $ @@ -50,8 +38,6 @@ add_test(NAME Persistent_cohomology_example_from_file_3_3_100 COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "2" "0.45") add_test(NAME Persistent_cohomology_example_exact_alpha_complex_3d COMMAND $ "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "2" "0.45") add_test(NAME Persistent_cohomology_example_weighted_alpha_complex_3d COMMAND $ "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.weights" "2" "0.45") - install(TARGETS alpha_complex_3d_persistence DESTINATION bin) install(TARGETS exact_alpha_complex_3d_persistence DESTINATION bin) install(TARGETS weighted_alpha_complex_3d_persistence DESTINATION bin) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) - add_executable (alpha_complex_persistence alpha_complex_persistence.cpp) - target_link_libraries(alpha_complex_persistence - ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) - - add_executable(periodic_alpha_complex_3d_persistence periodic_alpha_complex_3d_persistence.cpp) - target_link_libraries(periodic_alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) - add_executable(custom_persistence_sort custom_persistence_sort.cpp) target_link_libraries(custom_persistence_sort ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) if (TBB_FOUND) - target_link_libraries(alpha_complex_persistence ${TBB_LIBRARIES}) - target_link_libraries(periodic_alpha_complex_3d_persistence ${TBB_LIBRARIES}) target_link_libraries(custom_persistence_sort ${TBB_LIBRARIES}) endif(TBB_FOUND) - add_test(NAME Persistent_cohomology_example_alpha_complex COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-p" "2" "-m" "0.45") - add_test(NAME Persistent_cohomology_example_periodic_alpha_complex_3d COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off" "${CMAKE_SOURCE_DIR}/data/points/iso_cuboid_3_in_0_1.txt" "2" "0") add_test(NAME Persistent_cohomology_example_custom_persistence_sort COMMAND $) - install(TARGETS alpha_complex_persistence DESTINATION bin) - install(TARGETS periodic_alpha_complex_3d_persistence DESTINATION bin) install(TARGETS custom_persistence_sort DESTINATION bin) endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) diff --git a/src/Persistent_cohomology/example/alpha_complex_3d_helper.h b/src/Persistent_cohomology/example/alpha_complex_3d_helper.h deleted file mode 100644 index 7865e4ec..00000000 --- a/src/Persistent_cohomology/example/alpha_complex_3d_helper.h +++ /dev/null @@ -1,76 +0,0 @@ -/* 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) 2014 INRIA Saclay (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 . - */ - -#ifndef ALPHA_COMPLEX_3D_HELPER_H_ -#define ALPHA_COMPLEX_3D_HELPER_H_ - -template -Vertex_list from_cell(const Cell_handle& ch) { - Vertex_list the_list; - for (auto i = 0; i < 4; i++) { -#ifdef DEBUG_TRACES - std::cout << "from cell[" << i << "]=" << ch->vertex(i)->point() << std::endl; -#endif // DEBUG_TRACES - the_list.push_back(ch->vertex(i)); - } - return the_list; -} - -template -Vertex_list from_facet(const Facet& fct) { - Vertex_list the_list; - for (auto i = 0; i < 4; i++) { - if (fct.second != i) { -#ifdef DEBUG_TRACES - std::cout << "from facet=[" << i << "]" << fct.first->vertex(i)->point() << std::endl; -#endif // DEBUG_TRACES - the_list.push_back(fct.first->vertex(i)); - } - } - return the_list; -} - -template -Vertex_list from_edge(const Edge_3& edg) { - Vertex_list the_list; - for (auto i = 0; i < 4; i++) { - if ((edg.second == i) || (edg.third == i)) { -#ifdef DEBUG_TRACES - std::cout << "from edge[" << i << "]=" << edg.first->vertex(i)->point() << std::endl; -#endif // DEBUG_TRACES - the_list.push_back(edg.first->vertex(i)); - } - } - return the_list; -} - -template -Vertex_list from_vertex(const Vertex_handle& vh) { - Vertex_list the_list; -#ifdef DEBUG_TRACES - std::cout << "from vertex=" << vh->point() << std::endl; -#endif // DEBUG_TRACES - the_list.push_back(vh); - return the_list; -} - -#endif // ALPHA_COMPLEX_3D_HELPER_H_ diff --git a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp deleted file mode 100644 index fd227b82..00000000 --- a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp +++ /dev/null @@ -1,243 +0,0 @@ -/* 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) 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 - * 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 -#include -#include -#include - -#include -#include -#include -#include -#include -#include -#include -#include - -#include "alpha_complex_3d_helper.h" - -// Alpha_shape_3 templates type definitions -using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel; -using Vb = CGAL::Alpha_shape_vertex_base_3; -using Fb = CGAL::Alpha_shape_cell_base_3; -using Tds = CGAL::Triangulation_data_structure_3; -using Triangulation_3 = CGAL::Delaunay_triangulation_3; -using Alpha_shape_3 = CGAL::Alpha_shape_3; - -// From file type definition -using Point_3 = Kernel::Point_3; - -// filtration with alpha values needed type definition -using Alpha_value_type = Alpha_shape_3::FT; -using Object = CGAL::Object; -using Dispatch = CGAL::Dispatch_output_iterator< - CGAL::cpp11::tuple, - CGAL::cpp11::tuple >, - std::back_insert_iterator< std::vector > > >; -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; -using Vertex_list = std::list; - -// gudhi type definition -using ST = Gudhi::Simplex_tree; -using Filtration_value = ST::Filtration_value; -using Simplex_tree_vertex = ST::Vertex_handle; -using Alpha_shape_simplex_tree_map = std::map; -using Alpha_shape_simplex_tree_pair = std::pair; -using Simplex_tree_vector_vertex = std::vector< Simplex_tree_vertex >; -using PCOH = Gudhi::persistent_cohomology::Persistent_cohomology< ST, Gudhi::persistent_cohomology::Field_Zp >; - -void usage(const std::string& progName) { - std::cerr << "Usage: " << progName << - " path_to_file_graph coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n"; - exit(-1); -} - -int main(int argc, char * const argv[]) { - // program args management - if (argc != 4) { - std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n"; - usage(argv[0]); - } - - int coeff_field_characteristic = atoi(argv[2]); - - Filtration_value min_persistence = 0.0; - int returnedScanValue = sscanf(argv[3], "%f", &min_persistence); - if ((returnedScanValue == EOF) || (min_persistence < -1.0)) { - std::cerr << "Error: " << argv[3] << " is not correct\n"; - usage(argv[0]); - } - - // Read points from file - std::string offInputFile(argv[1]); - // Read the OFF file (input file name given as parameter) and triangulate points - Gudhi::Points_3D_off_reader off_reader(offInputFile); - // Check the read operation was correct - if (!off_reader.is_valid()) { - std::cerr << "Unable to read file " << offInputFile << std::endl; - usage(argv[0]); - } - - // Retrieve the triangulation - std::vector lp = off_reader.get_point_cloud(); - - // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode. - Alpha_shape_3 as(lp.begin(), lp.end(), 0, Alpha_shape_3::GENERAL); -#ifdef DEBUG_TRACES - std::cout << "Alpha shape computed in GENERAL mode" << std::endl; -#endif // DEBUG_TRACES - - // filtration with alpha values from alpha shape - std::vector the_objects; - std::vector the_alpha_values; - - Dispatch disp = CGAL::dispatch_output(std::back_inserter(the_objects), - std::back_inserter(the_alpha_values)); - - as.filtration_with_alpha_values(disp); -#ifdef DEBUG_TRACES - std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl; -#endif // DEBUG_TRACES - - Alpha_shape_3::size_type count_vertices = 0; - Alpha_shape_3::size_type count_edges = 0; - Alpha_shape_3::size_type count_facets = 0; - Alpha_shape_3::size_type count_cells = 0; - - // Loop on objects vector - Vertex_list vertex_list; - ST simplex_tree; - Alpha_shape_simplex_tree_map map_cgal_simplex_tree; - std::vector::iterator the_alpha_value_iterator = the_alpha_values.begin(); - int dim_max = 0; - Filtration_value filtration_max = 0.0; - for (auto object_iterator : the_objects) { - // Retrieve Alpha shape vertex list from object - if (const Cell_handle * cell = CGAL::object_cast(&object_iterator)) { - vertex_list = from_cell(*cell); - count_cells++; - if (dim_max < 3) { - // Cell is of dim 3 - dim_max = 3; - } - } else if (const Facet * facet = CGAL::object_cast(&object_iterator)) { - vertex_list = from_facet(*facet); - count_facets++; - if (dim_max < 2) { - // Facet is of dim 2 - dim_max = 2; - } - } else if (const Edge_3 * edge = CGAL::object_cast(&object_iterator)) { - vertex_list = from_edge(*edge); - count_edges++; - if (dim_max < 1) { - // Edge_3 is of dim 1 - dim_max = 1; - } - } else if (const Vertex_handle * vertex = CGAL::object_cast(&object_iterator)) { - count_vertices++; - vertex_list = from_vertex(*vertex); - } - // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex - Simplex_tree_vector_vertex the_simplex_tree; - for (auto the_alpha_shape_vertex : vertex_list) { - Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex); - if (the_map_iterator == map_cgal_simplex_tree.end()) { - // alpha shape not found - Simplex_tree_vertex vertex = map_cgal_simplex_tree.size(); -#ifdef DEBUG_TRACES - std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl; -#endif // DEBUG_TRACES - the_simplex_tree.push_back(vertex); - map_cgal_simplex_tree.insert(Alpha_shape_simplex_tree_pair(the_alpha_shape_vertex, vertex)); - } else { - // alpha shape found - Simplex_tree_vertex vertex = the_map_iterator->second; -#ifdef DEBUG_TRACES - std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl; -#endif // DEBUG_TRACES - the_simplex_tree.push_back(vertex); - } - } - // Construction of the simplex_tree - Filtration_value filtr = /*std::sqrt*/(*the_alpha_value_iterator); -#ifdef DEBUG_TRACES - std::cout << "filtration = " << filtr << std::endl; -#endif // DEBUG_TRACES - if (filtr > filtration_max) { - filtration_max = filtr; - } - simplex_tree.insert_simplex(the_simplex_tree, filtr); - if (the_alpha_value_iterator != the_alpha_values.end()) - ++the_alpha_value_iterator; - else - std::cout << "This shall not happen" << std::endl; - } - simplex_tree.set_filtration(filtration_max); - simplex_tree.set_dimension(dim_max); - -#ifdef DEBUG_TRACES - std::cout << "vertices \t\t" << count_vertices << std::endl; - std::cout << "edges \t\t" << count_edges << std::endl; - std::cout << "facets \t\t" << count_facets << std::endl; - std::cout << "cells \t\t" << count_cells << std::endl; - - - std::cout << "Information of the Simplex Tree: " << std::endl; - std::cout << " Number of vertices = " << simplex_tree.num_vertices() << " "; - std::cout << " Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl; - std::cout << " Dimension = " << simplex_tree.dimension() << " "; - std::cout << " filtration = " << simplex_tree.filtration() << std::endl << std::endl; -#endif // DEBUG_TRACES - -#ifdef DEBUG_TRACES - std::cout << "Iterator on vertices: " << std::endl; - for (auto vertex : simplex_tree.complex_vertex_range()) { - std::cout << vertex << " "; - } -#endif // DEBUG_TRACES - - // Sort the simplices in the order of the filtration - simplex_tree.initialize_filtration(); - - std::cout << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl; - // Compute the persistence diagram of the complex - PCOH pcoh(simplex_tree); - // initializes the coefficient field for homology - pcoh.init_coefficients(coeff_field_characteristic); - - pcoh.compute_persistent_cohomology(min_persistence); - - pcoh.output_diagram(); - - return 0; -} diff --git a/src/Persistent_cohomology/example/alpha_complex_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_persistence.cpp deleted file mode 100644 index 9e84e91f..00000000 --- a/src/Persistent_cohomology/example/alpha_complex_persistence.cpp +++ /dev/null @@ -1,125 +0,0 @@ -#include - -#include - -#include -#include -// to construct a simplex_tree from alpha complex -#include - -#include -#include -#include // for numeric_limits - -using Simplex_tree = Gudhi::Simplex_tree<>; -using Filtration_value = Simplex_tree::Filtration_value; - -void program_options(int argc, char * argv[] - , std::string & off_file_points - , std::string & output_file_diag - , Filtration_value & alpha_square_max_value - , int & coeff_field_characteristic - , Filtration_value & min_persistence); - -int main(int argc, char **argv) { - std::string off_file_points; - std::string output_file_diag; - Filtration_value alpha_square_max_value; - int coeff_field_characteristic; - Filtration_value min_persistence; - - program_options(argc, argv, off_file_points, output_file_diag, alpha_square_max_value, - coeff_field_characteristic, min_persistence); - - // ---------------------------------------------------------------------------- - // Init of an alpha complex from an OFF file - // ---------------------------------------------------------------------------- - using Kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >; - Gudhi::alpha_complex::Alpha_complex alpha_complex_from_file(off_file_points); - - Simplex_tree simplex; - if (alpha_complex_from_file.create_complex(simplex, alpha_square_max_value)) { - // ---------------------------------------------------------------------------- - // Display information about the alpha complex - // ---------------------------------------------------------------------------- - std::cout << "Simplicial complex is of dimension " << simplex.dimension() << - " - " << simplex.num_simplices() << " simplices - " << - simplex.num_vertices() << " vertices." << std::endl; - - // Sort the simplices in the order of the filtration - simplex.initialize_filtration(); - - std::cout << "Simplex_tree dim: " << simplex.dimension() << std::endl; - // Compute the persistence diagram of the complex - Gudhi::persistent_cohomology::Persistent_cohomology< Simplex_tree, - Gudhi::persistent_cohomology::Field_Zp > pcoh(simplex); - // initializes the coefficient field for homology - pcoh.init_coefficients(coeff_field_characteristic); - - pcoh.compute_persistent_cohomology(min_persistence); - - // Output the diagram in filediag - if (output_file_diag.empty()) { - pcoh.output_diagram(); - } else { - std::cout << "Result in file: " << output_file_diag << std::endl; - std::ofstream out(output_file_diag); - pcoh.output_diagram(out); - out.close(); - } - } - - return 0; -} - -void program_options(int argc, char * argv[] - , std::string & off_file_points - , std::string & output_file_diag - , Filtration_value & alpha_square_max_value - , int & coeff_field_characteristic - , Filtration_value & min_persistence) { - namespace po = boost::program_options; - po::options_description hidden("Hidden options"); - hidden.add_options() - ("input-file", po::value(&off_file_points), - "Name of file containing a point set. Format is one point per line: X1 ... Xd "); - - po::options_description visible("Allowed options", 100); - visible.add_options() - ("help,h", "produce help message") - ("output-file,o", po::value(&output_file_diag)->default_value(std::string()), - "Name of file in which the persistence diagram is written. Default print in std::cout") - ("max-alpha-square-value,r", - po::value(&alpha_square_max_value)->default_value(std::numeric_limits::infinity()), - "Maximal alpha square value for the Alpha complex construction.") - ("field-charac,p", po::value(&coeff_field_characteristic)->default_value(11), - "Characteristic p of the coefficient field Z/pZ for computing homology.") - ("min-persistence,m", po::value(&min_persistence), - "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals"); - - po::positional_options_description pos; - pos.add("input-file", 1); - - po::options_description all; - all.add(visible).add(hidden); - - po::variables_map vm; - po::store(po::command_line_parser(argc, argv). - options(all).positional(pos).run(), vm); - po::notify(vm); - - if (vm.count("help") || !vm.count("input-file")) { - std::cout << std::endl; - std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; - std::cout << "of an Alpha complex defined on a set of input points.\n \n"; - std::cout << "The output diagram contains one bar per line, written with the convention: \n"; - std::cout << " p dim b d \n"; - std::cout << "where dim is the dimension of the homological feature,\n"; - std::cout << "b and d are respectively the birth and death of the feature and \n"; - std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; - - std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; - std::cout << visible << std::endl; - std::abort(); - } -} diff --git a/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp index 8a335075..fa49dcee 100644 --- a/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp +++ b/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp @@ -40,7 +40,7 @@ #include #include -#include "alpha_complex_3d_helper.h" +#include "../utilities/alpha_complex_3d_helper.h" // Alpha_shape_3 templates type definitions using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel; diff --git a/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp deleted file mode 100644 index 8928cfc2..00000000 --- a/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp +++ /dev/null @@ -1,262 +0,0 @@ -/* 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) 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 - * 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 -#include -#include -#include -#include - -#include -#include -#include -#include -#include -#include -#include -#include -#include - -#include "alpha_complex_3d_helper.h" - -// Traits -using K = CGAL::Exact_predicates_inexact_constructions_kernel; -using PK = CGAL::Periodic_3_Delaunay_triangulation_traits_3; -// Vertex type -using DsVb = CGAL::Periodic_3_triangulation_ds_vertex_base_3<>; -using Vb = CGAL::Triangulation_vertex_base_3; -using AsVb = CGAL::Alpha_shape_vertex_base_3; -// Cell type -using DsCb = CGAL::Periodic_3_triangulation_ds_cell_base_3<>; -using Cb = CGAL::Triangulation_cell_base_3; -using AsCb = CGAL::Alpha_shape_cell_base_3; -using Tds = CGAL::Triangulation_data_structure_3; -using P3DT3 = CGAL::Periodic_3_Delaunay_triangulation_3; -using Alpha_shape_3 = CGAL::Alpha_shape_3; -using Point_3 = PK::Point_3; - -// filtration with alpha values needed type definition -using Alpha_value_type = Alpha_shape_3::FT; -using Object = CGAL::Object; -using Dispatch = CGAL::Dispatch_output_iterator< - CGAL::cpp11::tuple, - CGAL::cpp11::tuple >, - std::back_insert_iterator< std::vector > > >; -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; -using Vertex_list = std::list; - -// gudhi type definition -using ST = Gudhi::Simplex_tree; -using Filtration_value = ST::Filtration_value; -using Simplex_tree_vertex = ST::Vertex_handle; -using Alpha_shape_simplex_tree_map = std::map; -using Alpha_shape_simplex_tree_pair = std::pair; -using Simplex_tree_vector_vertex = std::vector< Simplex_tree_vertex >; -using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology< - ST, Gudhi::persistent_cohomology::Field_Zp >; - -void usage(char * const progName) { - std::cerr << "Usage: " << progName << - " path_to_file_graph path_to_iso_cuboid_3_file coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n"; - exit(-1); -} - -int main(int argc, char * const argv[]) { - // program args management - if (argc != 5) { - std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n"; - usage(argv[0]); - } - - int coeff_field_characteristic = atoi(argv[3]); - Filtration_value min_persistence = strtof(argv[4], nullptr); - - // Read points from file - std::string offInputFile(argv[1]); - // Read the OFF file (input file name given as parameter) and triangulate points - Gudhi::Points_3D_off_reader off_reader(offInputFile); - // Check the read operation was correct - if (!off_reader.is_valid()) { - std::cerr << "Unable to read file " << offInputFile << std::endl; - usage(argv[0]); - } - - // Read iso_cuboid_3 information from file - std::ifstream iso_cuboid_str(argv[2]); - 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[2] << std::endl; - usage(argv[0]); - } - - // Retrieve the triangulation - std::vector lp = off_reader.get_point_cloud(); - - // Define the periodic cube - P3DT3 pdt(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) - 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(); - 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 - // Maybe need to set it to GENERAL mode - Alpha_shape_3 as(pdt, 0, Alpha_shape_3::GENERAL); - - // filtration with alpha values from alpha shape - std::vector the_objects; - std::vector the_alpha_values; - - Dispatch disp = CGAL::dispatch_output(std::back_inserter(the_objects), - std::back_inserter(the_alpha_values)); - - as.filtration_with_alpha_values(disp); -#ifdef DEBUG_TRACES - std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl; -#endif // DEBUG_TRACES - - Alpha_shape_3::size_type count_vertices = 0; - Alpha_shape_3::size_type count_edges = 0; - Alpha_shape_3::size_type count_facets = 0; - Alpha_shape_3::size_type count_cells = 0; - - // Loop on objects vector - Vertex_list vertex_list; - ST simplex_tree; - Alpha_shape_simplex_tree_map map_cgal_simplex_tree; - std::vector::iterator the_alpha_value_iterator = the_alpha_values.begin(); - int dim_max = 0; - Filtration_value filtration_max = 0.0; - for (auto object_iterator : the_objects) { - // Retrieve Alpha shape vertex list from object - if (const Cell_handle * cell = CGAL::object_cast(&object_iterator)) { - vertex_list = from_cell(*cell); - count_cells++; - if (dim_max < 3) { - // Cell is of dim 3 - dim_max = 3; - } - } else if (const Facet * facet = CGAL::object_cast(&object_iterator)) { - vertex_list = from_facet(*facet); - count_facets++; - if (dim_max < 2) { - // Facet is of dim 2 - dim_max = 2; - } - } else if (const Edge_3 * edge = CGAL::object_cast(&object_iterator)) { - vertex_list = from_edge(*edge); - count_edges++; - if (dim_max < 1) { - // Edge_3 is of dim 1 - dim_max = 1; - } - } else if (const Alpha_shape_3::Vertex_handle * vertex = - CGAL::object_cast(&object_iterator)) { - count_vertices++; - vertex_list = from_vertex(*vertex); - } - // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex - Simplex_tree_vector_vertex the_simplex_tree; - for (auto the_alpha_shape_vertex : vertex_list) { - Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex); - if (the_map_iterator == map_cgal_simplex_tree.end()) { - // alpha shape not found - Simplex_tree_vertex vertex = map_cgal_simplex_tree.size(); -#ifdef DEBUG_TRACES - std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl; -#endif // DEBUG_TRACES - the_simplex_tree.push_back(vertex); - map_cgal_simplex_tree.insert(Alpha_shape_simplex_tree_pair(the_alpha_shape_vertex, vertex)); - } else { - // alpha shape found - Simplex_tree_vertex vertex = the_map_iterator->second; -#ifdef DEBUG_TRACES - std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl; -#endif // DEBUG_TRACES - the_simplex_tree.push_back(vertex); - } - } - // Construction of the simplex_tree - Filtration_value filtr = /*std::sqrt*/(*the_alpha_value_iterator); -#ifdef DEBUG_TRACES - std::cout << "filtration = " << filtr << std::endl; -#endif // DEBUG_TRACES - if (filtr > filtration_max) { - filtration_max = filtr; - } - simplex_tree.insert_simplex(the_simplex_tree, filtr); - if (the_alpha_value_iterator != the_alpha_values.end()) - ++the_alpha_value_iterator; - else - std::cout << "This shall not happen" << std::endl; - } - simplex_tree.set_filtration(filtration_max); - simplex_tree.set_dimension(dim_max); - -#ifdef DEBUG_TRACES - std::cout << "vertices \t\t" << count_vertices << std::endl; - std::cout << "edges \t\t" << count_edges << std::endl; - std::cout << "facets \t\t" << count_facets << std::endl; - std::cout << "cells \t\t" << count_cells << std::endl; - - - std::cout << "Information of the Simplex Tree: " << std::endl; - std::cout << " Number of vertices = " << simplex_tree.num_vertices() << " "; - std::cout << " Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl; - std::cout << " Dimension = " << simplex_tree.dimension() << " "; - std::cout << " filtration = " << simplex_tree.filtration() << std::endl << std::endl; -#endif // DEBUG_TRACES - -#ifdef DEBUG_TRACES - std::cout << "Iterator on vertices: " << std::endl; - for (auto vertex : simplex_tree.complex_vertex_range()) { - std::cout << vertex << " "; - } -#endif // DEBUG_TRACES - - // Sort the simplices in the order of the filtration - simplex_tree.initialize_filtration(); - - std::cout << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl; - // Compute the persistence diagram of the complex - Persistent_cohomology pcoh(simplex_tree, true); - // initializes the coefficient field for homology - pcoh.init_coefficients(coeff_field_characteristic); - - pcoh.compute_persistent_cohomology(min_persistence); - - pcoh.output_diagram(); - - return 0; -} diff --git a/src/Persistent_cohomology/example/rips_distance_matrix_persistence.cpp b/src/Persistent_cohomology/example/rips_distance_matrix_persistence.cpp deleted file mode 100644 index 8517e7f6..00000000 --- a/src/Persistent_cohomology/example/rips_distance_matrix_persistence.cpp +++ /dev/null @@ -1,144 +0,0 @@ -/* 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, Vincent Rouvreau - * - * Copyright (C) 2016 INRIA - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - -#include -#include -#include -#include - -#include - -#include -#include -#include // infinity - -// Types definition -using Simplex_tree = Gudhi::Simplex_tree; -using Filtration_value = Simplex_tree::Filtration_value; -using Rips_complex = Gudhi::rips_complex::Rips_complex; -using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; -using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology; -using Distance_matrix = std::vector>; - -void program_options(int argc, char * argv[] - , std::string & csv_matrix_file - , std::string & filediag - , Filtration_value & threshold - , int & dim_max - , int & p - , Filtration_value & min_persistence); - -int main(int argc, char * argv[]) { - std::string csv_matrix_file; - std::string filediag; - Filtration_value threshold; - int dim_max; - int p; - Filtration_value min_persistence; - - program_options(argc, argv, csv_matrix_file, filediag, threshold, dim_max, p, min_persistence); - - Distance_matrix distances = read_lower_triangular_matrix_from_csv_file(csv_matrix_file); - Rips_complex rips_complex_from_file(distances, threshold); - - // Construct the Rips complex in a Simplex Tree - Simplex_tree simplex_tree; - - rips_complex_from_file.create_complex(simplex_tree, dim_max); - std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n"; - std::cout << " and has dimension " << simplex_tree.dimension() << " \n"; - - // Sort the simplices in the order of the filtration - simplex_tree.initialize_filtration(); - - // Compute the persistence diagram of the complex - Persistent_cohomology pcoh(simplex_tree); - // initializes the coefficient field for homology - pcoh.init_coefficients(p); - - pcoh.compute_persistent_cohomology(min_persistence); - - // Output the diagram in filediag - if (filediag.empty()) { - pcoh.output_diagram(); - } else { - std::ofstream out(filediag); - pcoh.output_diagram(out); - out.close(); - } - return 0; -} - -void program_options(int argc, char * argv[] - , std::string & csv_matrix_file - , std::string & filediag - , Filtration_value & threshold - , int & dim_max - , int & p - , Filtration_value & min_persistence) { - namespace po = boost::program_options; - po::options_description hidden("Hidden options"); - hidden.add_options() - ("input-file", po::value(&csv_matrix_file), - "Name of file containing a distance matrix. Can be square or lower triangular matrix. Separator is ';'."); - - po::options_description visible("Allowed options", 100); - visible.add_options() - ("help,h", "produce help message") - ("output-file,o", po::value(&filediag)->default_value(std::string()), - "Name of file in which the persistence diagram is written. Default print in std::cout") - ("max-edge-length,r", - po::value(&threshold)->default_value(std::numeric_limits::infinity()), - "Maximal length of an edge for the Rips complex construction.") - ("cpx-dimension,d", po::value(&dim_max)->default_value(1), - "Maximal dimension of the Rips complex we want to compute.") - ("field-charac,p", po::value(&p)->default_value(11), - "Characteristic p of the coefficient field Z/pZ for computing homology.") - ("min-persistence,m", po::value(&min_persistence), - "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals"); - - po::positional_options_description pos; - pos.add("input-file", 1); - - po::options_description all; - all.add(visible).add(hidden); - - po::variables_map vm; - po::store(po::command_line_parser(argc, argv). - options(all).positional(pos).run(), vm); - po::notify(vm); - - if (vm.count("help") || !vm.count("input-file")) { - std::cout << std::endl; - std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; - std::cout << "of a Rips complex defined on a set of distance matrix.\n \n"; - std::cout << "The output diagram contains one bar per line, written with the convention: \n"; - std::cout << " p dim b d \n"; - std::cout << "where dim is the dimension of the homological feature,\n"; - std::cout << "b and d are respectively the birth and death of the feature and \n"; - std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; - - std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; - std::cout << visible << std::endl; - std::abort(); - } -} diff --git a/src/Persistent_cohomology/example/rips_persistence.cpp b/src/Persistent_cohomology/example/rips_persistence.cpp deleted file mode 100644 index d504798b..00000000 --- a/src/Persistent_cohomology/example/rips_persistence.cpp +++ /dev/null @@ -1,147 +0,0 @@ -/* 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): Clément Maria - * - * 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 - * 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 - -#include - -#include -#include -#include // infinity - -// Types definition -using Simplex_tree = Gudhi::Simplex_tree; -using Filtration_value = Simplex_tree::Filtration_value; -using Rips_complex = Gudhi::rips_complex::Rips_complex; -using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; -using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology; -using Point = std::vector; -using Points_off_reader = Gudhi::Points_off_reader; - -void program_options(int argc, char * argv[] - , std::string & off_file_points - , std::string & filediag - , Filtration_value & threshold - , int & dim_max - , int & p - , Filtration_value & min_persistence); - -int main(int argc, char * argv[]) { - std::string off_file_points; - std::string filediag; - Filtration_value threshold; - int dim_max; - int p; - Filtration_value min_persistence; - - program_options(argc, argv, off_file_points, filediag, threshold, dim_max, p, min_persistence); - - Points_off_reader off_reader(off_file_points); - Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold, Gudhi::Euclidean_distance()); - - // Construct the Rips complex in a Simplex Tree - Simplex_tree simplex_tree; - - rips_complex_from_file.create_complex(simplex_tree, dim_max); - std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n"; - std::cout << " and has dimension " << simplex_tree.dimension() << " \n"; - - // Sort the simplices in the order of the filtration - simplex_tree.initialize_filtration(); - - // Compute the persistence diagram of the complex - Persistent_cohomology pcoh(simplex_tree); - // initializes the coefficient field for homology - pcoh.init_coefficients(p); - - pcoh.compute_persistent_cohomology(min_persistence); - - // Output the diagram in filediag - if (filediag.empty()) { - pcoh.output_diagram(); - } else { - std::ofstream out(filediag); - pcoh.output_diagram(out); - out.close(); - } - - return 0; -} - -void program_options(int argc, char * argv[] - , std::string & off_file_points - , std::string & filediag - , Filtration_value & threshold - , int & dim_max - , int & p - , Filtration_value & min_persistence) { - namespace po = boost::program_options; - po::options_description hidden("Hidden options"); - hidden.add_options() - ("input-file", po::value(&off_file_points), - "Name of an OFF file containing a point set.\n"); - - po::options_description visible("Allowed options", 100); - visible.add_options() - ("help,h", "produce help message") - ("output-file,o", po::value(&filediag)->default_value(std::string()), - "Name of file in which the persistence diagram is written. Default print in std::cout") - ("max-edge-length,r", - po::value(&threshold)->default_value(std::numeric_limits::infinity()), - "Maximal length of an edge for the Rips complex construction.") - ("cpx-dimension,d", po::value(&dim_max)->default_value(1), - "Maximal dimension of the Rips complex we want to compute.") - ("field-charac,p", po::value(&p)->default_value(11), - "Characteristic p of the coefficient field Z/pZ for computing homology.") - ("min-persistence,m", po::value(&min_persistence), - "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals"); - - po::positional_options_description pos; - pos.add("input-file", 1); - - po::options_description all; - all.add(visible).add(hidden); - - po::variables_map vm; - po::store(po::command_line_parser(argc, argv). - options(all).positional(pos).run(), vm); - po::notify(vm); - - if (vm.count("help") || !vm.count("input-file")) { - std::cout << std::endl; - std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; - std::cout << "of a Rips complex defined on a set of input points.\n \n"; - std::cout << "The output diagram contains one bar per line, written with the convention: \n"; - std::cout << " p dim b d \n"; - std::cout << "where dim is the dimension of the homological feature,\n"; - std::cout << "b and d are respectively the birth and death of the feature and \n"; - std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; - - std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; - std::cout << visible << std::endl; - std::abort(); - } -} diff --git a/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp index 34b90933..4a2b10f3 100644 --- a/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp +++ b/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp @@ -42,7 +42,7 @@ #include #include -#include "alpha_complex_3d_helper.h" +#include "../utilities/alpha_complex_3d_helper.h" // Traits using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel; diff --git a/src/Persistent_cohomology/utilities/CMakeLists.txt b/src/Persistent_cohomology/utilities/CMakeLists.txt new file mode 100644 index 00000000..2c1e50af --- /dev/null +++ b/src/Persistent_cohomology/utilities/CMakeLists.txt @@ -0,0 +1,56 @@ +cmake_minimum_required(VERSION 2.6) +project(Persistent_cohomology_utilities) + +add_executable(rips_distance_matrix_persistence rips_distance_matrix_persistence.cpp) +target_link_libraries(rips_distance_matrix_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) + +add_executable(rips_persistence rips_persistence.cpp) +target_link_libraries(rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) + +if (TBB_FOUND) + target_link_libraries(rips_distance_matrix_persistence ${TBB_LIBRARIES}) + target_link_libraries(rips_persistence ${TBB_LIBRARIES}) +endif() + +add_test(NAME Persistent_cohomology_example_from_rips_distance_matrix COMMAND $ + "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" "-r" "1.0" "-d" "3" "-p" "3" "-m" "0") +add_test(NAME Persistent_cohomology_example_from_rips_on_tore_3D COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3") + +install(TARGETS rips_distance_matrix_persistence DESTINATION bin) +install(TARGETS rips_persistence DESTINATION bin) + +if(CGAL_FOUND) + add_executable(alpha_complex_3d_persistence alpha_complex_3d_persistence.cpp) + target_link_libraries(alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) + + if (TBB_FOUND) + target_link_libraries(alpha_complex_3d_persistence ${TBB_LIBRARIES}) + endif(TBB_FOUND) + add_test(NAME Persistent_cohomology_example_alpha_complex_3d COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "2" "0.45") + + install(TARGETS alpha_complex_3d_persistence DESTINATION bin) + + if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) + add_executable (alpha_complex_persistence alpha_complex_persistence.cpp) + target_link_libraries(alpha_complex_persistence + ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) + + add_executable(periodic_alpha_complex_3d_persistence periodic_alpha_complex_3d_persistence.cpp) + target_link_libraries(periodic_alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) + + if (TBB_FOUND) + target_link_libraries(alpha_complex_persistence ${TBB_LIBRARIES}) + target_link_libraries(periodic_alpha_complex_3d_persistence ${TBB_LIBRARIES}) + endif(TBB_FOUND) + add_test(NAME Persistent_cohomology_example_alpha_complex COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-p" "2" "-m" "0.45") + add_test(NAME Persistent_cohomology_example_periodic_alpha_complex_3d COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off" "${CMAKE_SOURCE_DIR}/data/points/iso_cuboid_3_in_0_1.txt" "2" "0") + + install(TARGETS alpha_complex_persistence DESTINATION bin) + install(TARGETS periodic_alpha_complex_3d_persistence DESTINATION bin) + + endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) +endif(CGAL_FOUND) diff --git a/src/Persistent_cohomology/utilities/alpha_complex_3d_helper.h b/src/Persistent_cohomology/utilities/alpha_complex_3d_helper.h new file mode 100644 index 00000000..7865e4ec --- /dev/null +++ b/src/Persistent_cohomology/utilities/alpha_complex_3d_helper.h @@ -0,0 +1,76 @@ +/* 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) 2014 INRIA Saclay (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 . + */ + +#ifndef ALPHA_COMPLEX_3D_HELPER_H_ +#define ALPHA_COMPLEX_3D_HELPER_H_ + +template +Vertex_list from_cell(const Cell_handle& ch) { + Vertex_list the_list; + for (auto i = 0; i < 4; i++) { +#ifdef DEBUG_TRACES + std::cout << "from cell[" << i << "]=" << ch->vertex(i)->point() << std::endl; +#endif // DEBUG_TRACES + the_list.push_back(ch->vertex(i)); + } + return the_list; +} + +template +Vertex_list from_facet(const Facet& fct) { + Vertex_list the_list; + for (auto i = 0; i < 4; i++) { + if (fct.second != i) { +#ifdef DEBUG_TRACES + std::cout << "from facet=[" << i << "]" << fct.first->vertex(i)->point() << std::endl; +#endif // DEBUG_TRACES + the_list.push_back(fct.first->vertex(i)); + } + } + return the_list; +} + +template +Vertex_list from_edge(const Edge_3& edg) { + Vertex_list the_list; + for (auto i = 0; i < 4; i++) { + if ((edg.second == i) || (edg.third == i)) { +#ifdef DEBUG_TRACES + std::cout << "from edge[" << i << "]=" << edg.first->vertex(i)->point() << std::endl; +#endif // DEBUG_TRACES + the_list.push_back(edg.first->vertex(i)); + } + } + return the_list; +} + +template +Vertex_list from_vertex(const Vertex_handle& vh) { + Vertex_list the_list; +#ifdef DEBUG_TRACES + std::cout << "from vertex=" << vh->point() << std::endl; +#endif // DEBUG_TRACES + the_list.push_back(vh); + return the_list; +} + +#endif // ALPHA_COMPLEX_3D_HELPER_H_ diff --git a/src/Persistent_cohomology/utilities/alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/utilities/alpha_complex_3d_persistence.cpp new file mode 100644 index 00000000..fd227b82 --- /dev/null +++ b/src/Persistent_cohomology/utilities/alpha_complex_3d_persistence.cpp @@ -0,0 +1,243 @@ +/* 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) 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 + * 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 +#include +#include +#include + +#include +#include +#include +#include +#include +#include +#include +#include + +#include "alpha_complex_3d_helper.h" + +// Alpha_shape_3 templates type definitions +using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel; +using Vb = CGAL::Alpha_shape_vertex_base_3; +using Fb = CGAL::Alpha_shape_cell_base_3; +using Tds = CGAL::Triangulation_data_structure_3; +using Triangulation_3 = CGAL::Delaunay_triangulation_3; +using Alpha_shape_3 = CGAL::Alpha_shape_3; + +// From file type definition +using Point_3 = Kernel::Point_3; + +// filtration with alpha values needed type definition +using Alpha_value_type = Alpha_shape_3::FT; +using Object = CGAL::Object; +using Dispatch = CGAL::Dispatch_output_iterator< + CGAL::cpp11::tuple, + CGAL::cpp11::tuple >, + std::back_insert_iterator< std::vector > > >; +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; +using Vertex_list = std::list; + +// gudhi type definition +using ST = Gudhi::Simplex_tree; +using Filtration_value = ST::Filtration_value; +using Simplex_tree_vertex = ST::Vertex_handle; +using Alpha_shape_simplex_tree_map = std::map; +using Alpha_shape_simplex_tree_pair = std::pair; +using Simplex_tree_vector_vertex = std::vector< Simplex_tree_vertex >; +using PCOH = Gudhi::persistent_cohomology::Persistent_cohomology< ST, Gudhi::persistent_cohomology::Field_Zp >; + +void usage(const std::string& progName) { + std::cerr << "Usage: " << progName << + " path_to_file_graph coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n"; + exit(-1); +} + +int main(int argc, char * const argv[]) { + // program args management + if (argc != 4) { + std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n"; + usage(argv[0]); + } + + int coeff_field_characteristic = atoi(argv[2]); + + Filtration_value min_persistence = 0.0; + int returnedScanValue = sscanf(argv[3], "%f", &min_persistence); + if ((returnedScanValue == EOF) || (min_persistence < -1.0)) { + std::cerr << "Error: " << argv[3] << " is not correct\n"; + usage(argv[0]); + } + + // Read points from file + std::string offInputFile(argv[1]); + // Read the OFF file (input file name given as parameter) and triangulate points + Gudhi::Points_3D_off_reader off_reader(offInputFile); + // Check the read operation was correct + if (!off_reader.is_valid()) { + std::cerr << "Unable to read file " << offInputFile << std::endl; + usage(argv[0]); + } + + // Retrieve the triangulation + std::vector lp = off_reader.get_point_cloud(); + + // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode. + Alpha_shape_3 as(lp.begin(), lp.end(), 0, Alpha_shape_3::GENERAL); +#ifdef DEBUG_TRACES + std::cout << "Alpha shape computed in GENERAL mode" << std::endl; +#endif // DEBUG_TRACES + + // filtration with alpha values from alpha shape + std::vector the_objects; + std::vector the_alpha_values; + + Dispatch disp = CGAL::dispatch_output(std::back_inserter(the_objects), + std::back_inserter(the_alpha_values)); + + as.filtration_with_alpha_values(disp); +#ifdef DEBUG_TRACES + std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl; +#endif // DEBUG_TRACES + + Alpha_shape_3::size_type count_vertices = 0; + Alpha_shape_3::size_type count_edges = 0; + Alpha_shape_3::size_type count_facets = 0; + Alpha_shape_3::size_type count_cells = 0; + + // Loop on objects vector + Vertex_list vertex_list; + ST simplex_tree; + Alpha_shape_simplex_tree_map map_cgal_simplex_tree; + std::vector::iterator the_alpha_value_iterator = the_alpha_values.begin(); + int dim_max = 0; + Filtration_value filtration_max = 0.0; + for (auto object_iterator : the_objects) { + // Retrieve Alpha shape vertex list from object + if (const Cell_handle * cell = CGAL::object_cast(&object_iterator)) { + vertex_list = from_cell(*cell); + count_cells++; + if (dim_max < 3) { + // Cell is of dim 3 + dim_max = 3; + } + } else if (const Facet * facet = CGAL::object_cast(&object_iterator)) { + vertex_list = from_facet(*facet); + count_facets++; + if (dim_max < 2) { + // Facet is of dim 2 + dim_max = 2; + } + } else if (const Edge_3 * edge = CGAL::object_cast(&object_iterator)) { + vertex_list = from_edge(*edge); + count_edges++; + if (dim_max < 1) { + // Edge_3 is of dim 1 + dim_max = 1; + } + } else if (const Vertex_handle * vertex = CGAL::object_cast(&object_iterator)) { + count_vertices++; + vertex_list = from_vertex(*vertex); + } + // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex + Simplex_tree_vector_vertex the_simplex_tree; + for (auto the_alpha_shape_vertex : vertex_list) { + Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex); + if (the_map_iterator == map_cgal_simplex_tree.end()) { + // alpha shape not found + Simplex_tree_vertex vertex = map_cgal_simplex_tree.size(); +#ifdef DEBUG_TRACES + std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl; +#endif // DEBUG_TRACES + the_simplex_tree.push_back(vertex); + map_cgal_simplex_tree.insert(Alpha_shape_simplex_tree_pair(the_alpha_shape_vertex, vertex)); + } else { + // alpha shape found + Simplex_tree_vertex vertex = the_map_iterator->second; +#ifdef DEBUG_TRACES + std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl; +#endif // DEBUG_TRACES + the_simplex_tree.push_back(vertex); + } + } + // Construction of the simplex_tree + Filtration_value filtr = /*std::sqrt*/(*the_alpha_value_iterator); +#ifdef DEBUG_TRACES + std::cout << "filtration = " << filtr << std::endl; +#endif // DEBUG_TRACES + if (filtr > filtration_max) { + filtration_max = filtr; + } + simplex_tree.insert_simplex(the_simplex_tree, filtr); + if (the_alpha_value_iterator != the_alpha_values.end()) + ++the_alpha_value_iterator; + else + std::cout << "This shall not happen" << std::endl; + } + simplex_tree.set_filtration(filtration_max); + simplex_tree.set_dimension(dim_max); + +#ifdef DEBUG_TRACES + std::cout << "vertices \t\t" << count_vertices << std::endl; + std::cout << "edges \t\t" << count_edges << std::endl; + std::cout << "facets \t\t" << count_facets << std::endl; + std::cout << "cells \t\t" << count_cells << std::endl; + + + std::cout << "Information of the Simplex Tree: " << std::endl; + std::cout << " Number of vertices = " << simplex_tree.num_vertices() << " "; + std::cout << " Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl; + std::cout << " Dimension = " << simplex_tree.dimension() << " "; + std::cout << " filtration = " << simplex_tree.filtration() << std::endl << std::endl; +#endif // DEBUG_TRACES + +#ifdef DEBUG_TRACES + std::cout << "Iterator on vertices: " << std::endl; + for (auto vertex : simplex_tree.complex_vertex_range()) { + std::cout << vertex << " "; + } +#endif // DEBUG_TRACES + + // Sort the simplices in the order of the filtration + simplex_tree.initialize_filtration(); + + std::cout << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl; + // Compute the persistence diagram of the complex + PCOH pcoh(simplex_tree); + // initializes the coefficient field for homology + pcoh.init_coefficients(coeff_field_characteristic); + + pcoh.compute_persistent_cohomology(min_persistence); + + pcoh.output_diagram(); + + return 0; +} diff --git a/src/Persistent_cohomology/utilities/alpha_complex_persistence.cpp b/src/Persistent_cohomology/utilities/alpha_complex_persistence.cpp new file mode 100644 index 00000000..9e84e91f --- /dev/null +++ b/src/Persistent_cohomology/utilities/alpha_complex_persistence.cpp @@ -0,0 +1,125 @@ +#include + +#include + +#include +#include +// to construct a simplex_tree from alpha complex +#include + +#include +#include +#include // for numeric_limits + +using Simplex_tree = Gudhi::Simplex_tree<>; +using Filtration_value = Simplex_tree::Filtration_value; + +void program_options(int argc, char * argv[] + , std::string & off_file_points + , std::string & output_file_diag + , Filtration_value & alpha_square_max_value + , int & coeff_field_characteristic + , Filtration_value & min_persistence); + +int main(int argc, char **argv) { + std::string off_file_points; + std::string output_file_diag; + Filtration_value alpha_square_max_value; + int coeff_field_characteristic; + Filtration_value min_persistence; + + program_options(argc, argv, off_file_points, output_file_diag, alpha_square_max_value, + coeff_field_characteristic, min_persistence); + + // ---------------------------------------------------------------------------- + // Init of an alpha complex from an OFF file + // ---------------------------------------------------------------------------- + using Kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >; + Gudhi::alpha_complex::Alpha_complex alpha_complex_from_file(off_file_points); + + Simplex_tree simplex; + if (alpha_complex_from_file.create_complex(simplex, alpha_square_max_value)) { + // ---------------------------------------------------------------------------- + // Display information about the alpha complex + // ---------------------------------------------------------------------------- + std::cout << "Simplicial complex is of dimension " << simplex.dimension() << + " - " << simplex.num_simplices() << " simplices - " << + simplex.num_vertices() << " vertices." << std::endl; + + // Sort the simplices in the order of the filtration + simplex.initialize_filtration(); + + std::cout << "Simplex_tree dim: " << simplex.dimension() << std::endl; + // Compute the persistence diagram of the complex + Gudhi::persistent_cohomology::Persistent_cohomology< Simplex_tree, + Gudhi::persistent_cohomology::Field_Zp > pcoh(simplex); + // initializes the coefficient field for homology + pcoh.init_coefficients(coeff_field_characteristic); + + pcoh.compute_persistent_cohomology(min_persistence); + + // Output the diagram in filediag + if (output_file_diag.empty()) { + pcoh.output_diagram(); + } else { + std::cout << "Result in file: " << output_file_diag << std::endl; + std::ofstream out(output_file_diag); + pcoh.output_diagram(out); + out.close(); + } + } + + return 0; +} + +void program_options(int argc, char * argv[] + , std::string & off_file_points + , std::string & output_file_diag + , Filtration_value & alpha_square_max_value + , int & coeff_field_characteristic + , Filtration_value & min_persistence) { + namespace po = boost::program_options; + po::options_description hidden("Hidden options"); + hidden.add_options() + ("input-file", po::value(&off_file_points), + "Name of file containing a point set. Format is one point per line: X1 ... Xd "); + + po::options_description visible("Allowed options", 100); + visible.add_options() + ("help,h", "produce help message") + ("output-file,o", po::value(&output_file_diag)->default_value(std::string()), + "Name of file in which the persistence diagram is written. Default print in std::cout") + ("max-alpha-square-value,r", + po::value(&alpha_square_max_value)->default_value(std::numeric_limits::infinity()), + "Maximal alpha square value for the Alpha complex construction.") + ("field-charac,p", po::value(&coeff_field_characteristic)->default_value(11), + "Characteristic p of the coefficient field Z/pZ for computing homology.") + ("min-persistence,m", po::value(&min_persistence), + "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals"); + + po::positional_options_description pos; + pos.add("input-file", 1); + + po::options_description all; + all.add(visible).add(hidden); + + po::variables_map vm; + po::store(po::command_line_parser(argc, argv). + options(all).positional(pos).run(), vm); + po::notify(vm); + + if (vm.count("help") || !vm.count("input-file")) { + std::cout << std::endl; + std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; + std::cout << "of an Alpha complex defined on a set of input points.\n \n"; + std::cout << "The output diagram contains one bar per line, written with the convention: \n"; + std::cout << " p dim b d \n"; + std::cout << "where dim is the dimension of the homological feature,\n"; + std::cout << "b and d are respectively the birth and death of the feature and \n"; + std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; + + std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; + std::cout << visible << std::endl; + std::abort(); + } +} diff --git a/src/Persistent_cohomology/utilities/periodic_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/utilities/periodic_alpha_complex_3d_persistence.cpp new file mode 100644 index 00000000..8928cfc2 --- /dev/null +++ b/src/Persistent_cohomology/utilities/periodic_alpha_complex_3d_persistence.cpp @@ -0,0 +1,262 @@ +/* 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) 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 + * 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 +#include +#include +#include +#include + +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include "alpha_complex_3d_helper.h" + +// Traits +using K = CGAL::Exact_predicates_inexact_constructions_kernel; +using PK = CGAL::Periodic_3_Delaunay_triangulation_traits_3; +// Vertex type +using DsVb = CGAL::Periodic_3_triangulation_ds_vertex_base_3<>; +using Vb = CGAL::Triangulation_vertex_base_3; +using AsVb = CGAL::Alpha_shape_vertex_base_3; +// Cell type +using DsCb = CGAL::Periodic_3_triangulation_ds_cell_base_3<>; +using Cb = CGAL::Triangulation_cell_base_3; +using AsCb = CGAL::Alpha_shape_cell_base_3; +using Tds = CGAL::Triangulation_data_structure_3; +using P3DT3 = CGAL::Periodic_3_Delaunay_triangulation_3; +using Alpha_shape_3 = CGAL::Alpha_shape_3; +using Point_3 = PK::Point_3; + +// filtration with alpha values needed type definition +using Alpha_value_type = Alpha_shape_3::FT; +using Object = CGAL::Object; +using Dispatch = CGAL::Dispatch_output_iterator< + CGAL::cpp11::tuple, + CGAL::cpp11::tuple >, + std::back_insert_iterator< std::vector > > >; +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; +using Vertex_list = std::list; + +// gudhi type definition +using ST = Gudhi::Simplex_tree; +using Filtration_value = ST::Filtration_value; +using Simplex_tree_vertex = ST::Vertex_handle; +using Alpha_shape_simplex_tree_map = std::map; +using Alpha_shape_simplex_tree_pair = std::pair; +using Simplex_tree_vector_vertex = std::vector< Simplex_tree_vertex >; +using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology< + ST, Gudhi::persistent_cohomology::Field_Zp >; + +void usage(char * const progName) { + std::cerr << "Usage: " << progName << + " path_to_file_graph path_to_iso_cuboid_3_file coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n"; + exit(-1); +} + +int main(int argc, char * const argv[]) { + // program args management + if (argc != 5) { + std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n"; + usage(argv[0]); + } + + int coeff_field_characteristic = atoi(argv[3]); + Filtration_value min_persistence = strtof(argv[4], nullptr); + + // Read points from file + std::string offInputFile(argv[1]); + // Read the OFF file (input file name given as parameter) and triangulate points + Gudhi::Points_3D_off_reader off_reader(offInputFile); + // Check the read operation was correct + if (!off_reader.is_valid()) { + std::cerr << "Unable to read file " << offInputFile << std::endl; + usage(argv[0]); + } + + // Read iso_cuboid_3 information from file + std::ifstream iso_cuboid_str(argv[2]); + 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[2] << std::endl; + usage(argv[0]); + } + + // Retrieve the triangulation + std::vector lp = off_reader.get_point_cloud(); + + // Define the periodic cube + P3DT3 pdt(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) + 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(); + 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 + // Maybe need to set it to GENERAL mode + Alpha_shape_3 as(pdt, 0, Alpha_shape_3::GENERAL); + + // filtration with alpha values from alpha shape + std::vector the_objects; + std::vector the_alpha_values; + + Dispatch disp = CGAL::dispatch_output(std::back_inserter(the_objects), + std::back_inserter(the_alpha_values)); + + as.filtration_with_alpha_values(disp); +#ifdef DEBUG_TRACES + std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl; +#endif // DEBUG_TRACES + + Alpha_shape_3::size_type count_vertices = 0; + Alpha_shape_3::size_type count_edges = 0; + Alpha_shape_3::size_type count_facets = 0; + Alpha_shape_3::size_type count_cells = 0; + + // Loop on objects vector + Vertex_list vertex_list; + ST simplex_tree; + Alpha_shape_simplex_tree_map map_cgal_simplex_tree; + std::vector::iterator the_alpha_value_iterator = the_alpha_values.begin(); + int dim_max = 0; + Filtration_value filtration_max = 0.0; + for (auto object_iterator : the_objects) { + // Retrieve Alpha shape vertex list from object + if (const Cell_handle * cell = CGAL::object_cast(&object_iterator)) { + vertex_list = from_cell(*cell); + count_cells++; + if (dim_max < 3) { + // Cell is of dim 3 + dim_max = 3; + } + } else if (const Facet * facet = CGAL::object_cast(&object_iterator)) { + vertex_list = from_facet(*facet); + count_facets++; + if (dim_max < 2) { + // Facet is of dim 2 + dim_max = 2; + } + } else if (const Edge_3 * edge = CGAL::object_cast(&object_iterator)) { + vertex_list = from_edge(*edge); + count_edges++; + if (dim_max < 1) { + // Edge_3 is of dim 1 + dim_max = 1; + } + } else if (const Alpha_shape_3::Vertex_handle * vertex = + CGAL::object_cast(&object_iterator)) { + count_vertices++; + vertex_list = from_vertex(*vertex); + } + // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex + Simplex_tree_vector_vertex the_simplex_tree; + for (auto the_alpha_shape_vertex : vertex_list) { + Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex); + if (the_map_iterator == map_cgal_simplex_tree.end()) { + // alpha shape not found + Simplex_tree_vertex vertex = map_cgal_simplex_tree.size(); +#ifdef DEBUG_TRACES + std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl; +#endif // DEBUG_TRACES + the_simplex_tree.push_back(vertex); + map_cgal_simplex_tree.insert(Alpha_shape_simplex_tree_pair(the_alpha_shape_vertex, vertex)); + } else { + // alpha shape found + Simplex_tree_vertex vertex = the_map_iterator->second; +#ifdef DEBUG_TRACES + std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl; +#endif // DEBUG_TRACES + the_simplex_tree.push_back(vertex); + } + } + // Construction of the simplex_tree + Filtration_value filtr = /*std::sqrt*/(*the_alpha_value_iterator); +#ifdef DEBUG_TRACES + std::cout << "filtration = " << filtr << std::endl; +#endif // DEBUG_TRACES + if (filtr > filtration_max) { + filtration_max = filtr; + } + simplex_tree.insert_simplex(the_simplex_tree, filtr); + if (the_alpha_value_iterator != the_alpha_values.end()) + ++the_alpha_value_iterator; + else + std::cout << "This shall not happen" << std::endl; + } + simplex_tree.set_filtration(filtration_max); + simplex_tree.set_dimension(dim_max); + +#ifdef DEBUG_TRACES + std::cout << "vertices \t\t" << count_vertices << std::endl; + std::cout << "edges \t\t" << count_edges << std::endl; + std::cout << "facets \t\t" << count_facets << std::endl; + std::cout << "cells \t\t" << count_cells << std::endl; + + + std::cout << "Information of the Simplex Tree: " << std::endl; + std::cout << " Number of vertices = " << simplex_tree.num_vertices() << " "; + std::cout << " Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl; + std::cout << " Dimension = " << simplex_tree.dimension() << " "; + std::cout << " filtration = " << simplex_tree.filtration() << std::endl << std::endl; +#endif // DEBUG_TRACES + +#ifdef DEBUG_TRACES + std::cout << "Iterator on vertices: " << std::endl; + for (auto vertex : simplex_tree.complex_vertex_range()) { + std::cout << vertex << " "; + } +#endif // DEBUG_TRACES + + // Sort the simplices in the order of the filtration + simplex_tree.initialize_filtration(); + + std::cout << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl; + // Compute the persistence diagram of the complex + Persistent_cohomology pcoh(simplex_tree, true); + // initializes the coefficient field for homology + pcoh.init_coefficients(coeff_field_characteristic); + + pcoh.compute_persistent_cohomology(min_persistence); + + pcoh.output_diagram(); + + return 0; +} diff --git a/src/Persistent_cohomology/utilities/rips_distance_matrix_persistence.cpp b/src/Persistent_cohomology/utilities/rips_distance_matrix_persistence.cpp new file mode 100644 index 00000000..8517e7f6 --- /dev/null +++ b/src/Persistent_cohomology/utilities/rips_distance_matrix_persistence.cpp @@ -0,0 +1,144 @@ +/* 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, Vincent Rouvreau + * + * Copyright (C) 2016 INRIA + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +#include +#include +#include +#include + +#include + +#include +#include +#include // infinity + +// Types definition +using Simplex_tree = Gudhi::Simplex_tree; +using Filtration_value = Simplex_tree::Filtration_value; +using Rips_complex = Gudhi::rips_complex::Rips_complex; +using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; +using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology; +using Distance_matrix = std::vector>; + +void program_options(int argc, char * argv[] + , std::string & csv_matrix_file + , std::string & filediag + , Filtration_value & threshold + , int & dim_max + , int & p + , Filtration_value & min_persistence); + +int main(int argc, char * argv[]) { + std::string csv_matrix_file; + std::string filediag; + Filtration_value threshold; + int dim_max; + int p; + Filtration_value min_persistence; + + program_options(argc, argv, csv_matrix_file, filediag, threshold, dim_max, p, min_persistence); + + Distance_matrix distances = read_lower_triangular_matrix_from_csv_file(csv_matrix_file); + Rips_complex rips_complex_from_file(distances, threshold); + + // Construct the Rips complex in a Simplex Tree + Simplex_tree simplex_tree; + + rips_complex_from_file.create_complex(simplex_tree, dim_max); + std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n"; + std::cout << " and has dimension " << simplex_tree.dimension() << " \n"; + + // Sort the simplices in the order of the filtration + simplex_tree.initialize_filtration(); + + // Compute the persistence diagram of the complex + Persistent_cohomology pcoh(simplex_tree); + // initializes the coefficient field for homology + pcoh.init_coefficients(p); + + pcoh.compute_persistent_cohomology(min_persistence); + + // Output the diagram in filediag + if (filediag.empty()) { + pcoh.output_diagram(); + } else { + std::ofstream out(filediag); + pcoh.output_diagram(out); + out.close(); + } + return 0; +} + +void program_options(int argc, char * argv[] + , std::string & csv_matrix_file + , std::string & filediag + , Filtration_value & threshold + , int & dim_max + , int & p + , Filtration_value & min_persistence) { + namespace po = boost::program_options; + po::options_description hidden("Hidden options"); + hidden.add_options() + ("input-file", po::value(&csv_matrix_file), + "Name of file containing a distance matrix. Can be square or lower triangular matrix. Separator is ';'."); + + po::options_description visible("Allowed options", 100); + visible.add_options() + ("help,h", "produce help message") + ("output-file,o", po::value(&filediag)->default_value(std::string()), + "Name of file in which the persistence diagram is written. Default print in std::cout") + ("max-edge-length,r", + po::value(&threshold)->default_value(std::numeric_limits::infinity()), + "Maximal length of an edge for the Rips complex construction.") + ("cpx-dimension,d", po::value(&dim_max)->default_value(1), + "Maximal dimension of the Rips complex we want to compute.") + ("field-charac,p", po::value(&p)->default_value(11), + "Characteristic p of the coefficient field Z/pZ for computing homology.") + ("min-persistence,m", po::value(&min_persistence), + "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals"); + + po::positional_options_description pos; + pos.add("input-file", 1); + + po::options_description all; + all.add(visible).add(hidden); + + po::variables_map vm; + po::store(po::command_line_parser(argc, argv). + options(all).positional(pos).run(), vm); + po::notify(vm); + + if (vm.count("help") || !vm.count("input-file")) { + std::cout << std::endl; + std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; + std::cout << "of a Rips complex defined on a set of distance matrix.\n \n"; + std::cout << "The output diagram contains one bar per line, written with the convention: \n"; + std::cout << " p dim b d \n"; + std::cout << "where dim is the dimension of the homological feature,\n"; + std::cout << "b and d are respectively the birth and death of the feature and \n"; + std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; + + std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; + std::cout << visible << std::endl; + std::abort(); + } +} diff --git a/src/Persistent_cohomology/utilities/rips_persistence.cpp b/src/Persistent_cohomology/utilities/rips_persistence.cpp new file mode 100644 index 00000000..d504798b --- /dev/null +++ b/src/Persistent_cohomology/utilities/rips_persistence.cpp @@ -0,0 +1,147 @@ +/* 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): Clément Maria + * + * 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 + * 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 + +#include + +#include +#include +#include // infinity + +// Types definition +using Simplex_tree = Gudhi::Simplex_tree; +using Filtration_value = Simplex_tree::Filtration_value; +using Rips_complex = Gudhi::rips_complex::Rips_complex; +using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; +using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology; +using Point = std::vector; +using Points_off_reader = Gudhi::Points_off_reader; + +void program_options(int argc, char * argv[] + , std::string & off_file_points + , std::string & filediag + , Filtration_value & threshold + , int & dim_max + , int & p + , Filtration_value & min_persistence); + +int main(int argc, char * argv[]) { + std::string off_file_points; + std::string filediag; + Filtration_value threshold; + int dim_max; + int p; + Filtration_value min_persistence; + + program_options(argc, argv, off_file_points, filediag, threshold, dim_max, p, min_persistence); + + Points_off_reader off_reader(off_file_points); + Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold, Gudhi::Euclidean_distance()); + + // Construct the Rips complex in a Simplex Tree + Simplex_tree simplex_tree; + + rips_complex_from_file.create_complex(simplex_tree, dim_max); + std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n"; + std::cout << " and has dimension " << simplex_tree.dimension() << " \n"; + + // Sort the simplices in the order of the filtration + simplex_tree.initialize_filtration(); + + // Compute the persistence diagram of the complex + Persistent_cohomology pcoh(simplex_tree); + // initializes the coefficient field for homology + pcoh.init_coefficients(p); + + pcoh.compute_persistent_cohomology(min_persistence); + + // Output the diagram in filediag + if (filediag.empty()) { + pcoh.output_diagram(); + } else { + std::ofstream out(filediag); + pcoh.output_diagram(out); + out.close(); + } + + return 0; +} + +void program_options(int argc, char * argv[] + , std::string & off_file_points + , std::string & filediag + , Filtration_value & threshold + , int & dim_max + , int & p + , Filtration_value & min_persistence) { + namespace po = boost::program_options; + po::options_description hidden("Hidden options"); + hidden.add_options() + ("input-file", po::value(&off_file_points), + "Name of an OFF file containing a point set.\n"); + + po::options_description visible("Allowed options", 100); + visible.add_options() + ("help,h", "produce help message") + ("output-file,o", po::value(&filediag)->default_value(std::string()), + "Name of file in which the persistence diagram is written. Default print in std::cout") + ("max-edge-length,r", + po::value(&threshold)->default_value(std::numeric_limits::infinity()), + "Maximal length of an edge for the Rips complex construction.") + ("cpx-dimension,d", po::value(&dim_max)->default_value(1), + "Maximal dimension of the Rips complex we want to compute.") + ("field-charac,p", po::value(&p)->default_value(11), + "Characteristic p of the coefficient field Z/pZ for computing homology.") + ("min-persistence,m", po::value(&min_persistence), + "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals"); + + po::positional_options_description pos; + pos.add("input-file", 1); + + po::options_description all; + all.add(visible).add(hidden); + + po::variables_map vm; + po::store(po::command_line_parser(argc, argv). + options(all).positional(pos).run(), vm); + po::notify(vm); + + if (vm.count("help") || !vm.count("input-file")) { + std::cout << std::endl; + std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; + std::cout << "of a Rips complex defined on a set of input points.\n \n"; + std::cout << "The output diagram contains one bar per line, written with the convention: \n"; + std::cout << " p dim b d \n"; + std::cout << "where dim is the dimension of the homological feature,\n"; + std::cout << "b and d are respectively the birth and death of the feature and \n"; + std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; + + std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; + std::cout << visible << std::endl; + std::abort(); + } +} -- cgit v1.2.3 From 0a66874247cb6ab10a2d96e22ecd5009113291d2 Mon Sep 17 00:00:00 2001 From: cjamin Date: Thu, 1 Jun 2017 08:42:39 +0000 Subject: Split and fix README file git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/add_utils_in_gudhi_v2@2496 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 0eecb1e37fd208522de15369ac8cf4c960c214c5 --- src/Persistent_cohomology/example/README | 121 +++-------------------------- src/Persistent_cohomology/utilities/README | 114 +++++++++++++++++++++++++++ 2 files changed, 125 insertions(+), 110 deletions(-) create mode 100644 src/Persistent_cohomology/utilities/README (limited to 'src/Persistent_cohomology') diff --git a/src/Persistent_cohomology/example/README b/src/Persistent_cohomology/example/README index 794b94ae..f39d9584 100644 --- a/src/Persistent_cohomology/example/README +++ b/src/Persistent_cohomology/example/README @@ -1,43 +1,14 @@ -To build the example, run in a Terminal: +To build the examples, run in a Terminal: -cd /path-to-example/ +cd /path-to-examples/ cmake . make *********************************************************************************************************************** Example of use of RIPS: -Computation of the persistent homology with Z/2Z coefficients of the Rips complex on points -sampling a Klein bottle: - -./rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 2 - -output: -2 0 0 inf -2 1 0.0983494 inf -2 1 0.104347 inf -2 2 0.138335 inf - - -Every line is of this format: p1*...*pr dim b d -where - p1*...*pr is the product of prime numbers pi such that the homology feature exists in homology with Z/piZ coefficients. - dim is the dimension of the homological feature, - b and d are respectively the birth and death of the feature and - - - -with Z/3Z coefficients: - -./rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 3 - -output: -3 0 0 inf -3 1 0.0983494 inf -3 1 0.104347 inf -3 2 0.138335 inf - -and the computation with Z/2Z and Z/3Z coefficients simultaneously: +Computation of the persistent homology with Z/2Z and Z/3Z coefficients simultaneously of the Rips complex +on points sampling a 3D torus: ./rips_multifield_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.12 -d 3 -p 2 -q 3 @@ -53,7 +24,13 @@ output: 6 0 0 0.12047 6 0 0 0.120414 -and finally the computation with all Z/pZ for 2 <= p <= 71 (20 first prime numbers): +Every line is of this format: p1*...*pr dim b d +where + p1*...*pr is the product of prime numbers pi such that the homology feature exists in homology with Z/piZ coefficients. + dim is the dimension of the homological feature, + b and d are respectively the birth and death of the feature and + +and the computation with all Z/pZ for 2 <= p <= 71 (20 first prime numbers): ./rips_multifield_persistence ../../data/points/Kl.off -r 0.25 -m 0.5 -d 3 -p 2 -q 71 @@ -69,82 +46,6 @@ output: 557940830126698960967415390 0 0 0.12047 557940830126698960967415390 0 0 0.120414 -*********************************************************************************************************************** -Example of use of ALPHA: - -For a more verbose mode, please run cmake with option "DEBUG_TRACES=TRUE" and recompile the programs. - -1) 3D special case ------------------- -Computation of the persistent homology with Z/2Z coefficients of the alpha complex on points -sampling a torus 3D: - -./alpha_complex_3d_persistence ../../data/points/tore3D_300.off 2 0.45 - -output: -Simplex_tree dim: 3 -2 0 0 inf -2 1 0.0682162 1.0001 -2 1 0.0934117 1.00003 -2 2 0.56444 1.03938 - -Here we retrieve expected Betti numbers on a tore 3D: -Betti numbers[0] = 1 -Betti numbers[1] = 2 -Betti numbers[2] = 1 - -N.B.: - alpha_complex_3d_persistence accepts only OFF files in 3D dimension. - - filtration values are alpha square values - -2) d-Dimension case -------------------- -Computation of the persistent homology with Z/2Z coefficients of the alpha complex on points -sampling a torus 3D: - -./alpha_complex_persistence -r 32 -p 2 -m 0.45 ../../data/points/tore3D_300.off - -output: -Alpha complex is of dimension 3 - 9273 simplices - 300 vertices. -Simplex_tree dim: 3 -2 0 0 inf -2 1 0.0682162 1.0001 -2 1 0.0934117 1.00003 -2 2 0.56444 1.03938 - -Here we retrieve expected Betti numbers on a tore 3D: -Betti numbers[0] = 1 -Betti numbers[1] = 2 -Betti numbers[2] = 1 - -N.B.: - alpha_complex_persistence accepts OFF files in d-Dimension. - - filtration values are alpha square values - -3) 3D periodic special case ---------------------------- -./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 - -output: -Periodic Delaunay computed. -Simplex_tree dim: 3 -3 0 0 inf -3 1 0.0025 inf -3 1 0.0025 inf -3 1 0.0025 inf -3 2 0.005 inf -3 2 0.005 inf -3 2 0.005 inf -3 3 0.0075 inf - -Here we retrieve expected Betti numbers on a tore 3D: -Betti numbers[0] = 1 -Betti numbers[1] = 3 -Betti numbers[2] = 3 -Betti numbers[3] = 1 - -N.B.: - periodic_alpha_complex_3d_persistence accepts only OFF files in 3D dimension. In this example, the periodic cube -is hard coded to { x = [0,1]; y = [0,1]; z = [0,1] } - - filtration values are alpha square values - *********************************************************************************************************************** Example of use of PLAIN HOMOLOGY: diff --git a/src/Persistent_cohomology/utilities/README b/src/Persistent_cohomology/utilities/README new file mode 100644 index 00000000..76e960da --- /dev/null +++ b/src/Persistent_cohomology/utilities/README @@ -0,0 +1,114 @@ +To build the utilities, run in a Terminal: + +cd /path-to-utilities/ +cmake . +make + +*********************************************************************************************************************** +Example of use of RIPS: + +Computation of the persistent homology with Z/2Z coefficients of the Rips complex on points +sampling a 3D torus: + +./rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 2 + +output: +2 0 0 inf +2 1 0.0983494 inf +2 1 0.104347 inf +2 2 0.138335 inf + + +Every line is of this format: p1*...*pr dim b d +where + p1*...*pr is the product of prime numbers pi such that the homology feature exists in homology with Z/piZ coefficients. + dim is the dimension of the homological feature, + b and d are respectively the birth and death of the feature and + + + +with Z/3Z coefficients: + +./rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 3 + +output: +3 0 0 inf +3 1 0.0983494 inf +3 1 0.104347 inf +3 2 0.138335 inf + +*********************************************************************************************************************** +Example of use of ALPHA: + +For a more verbose mode, please run cmake with option "DEBUG_TRACES=TRUE" and recompile the programs. + +1) 3D special case +------------------ +Computation of the persistent homology with Z/2Z coefficients of the alpha complex on points +sampling a torus 3D: + +./alpha_complex_3d_persistence ../../data/points/tore3D_300.off 2 0.45 + +output: +Simplex_tree dim: 3 +2 0 0 inf +2 1 0.0682162 1.0001 +2 1 0.0934117 1.00003 +2 2 0.56444 1.03938 + +Here we retrieve expected Betti numbers on a tore 3D: +Betti numbers[0] = 1 +Betti numbers[1] = 2 +Betti numbers[2] = 1 + +N.B.: - alpha_complex_3d_persistence accepts only OFF files in 3D dimension. + - filtration values are alpha square values + +2) d-Dimension case +------------------- +Computation of the persistent homology with Z/2Z coefficients of the alpha complex on points +sampling a torus 3D: + +./alpha_complex_persistence -r 32 -p 2 -m 0.45 ../../data/points/tore3D_300.off + +output: +Alpha complex is of dimension 3 - 9273 simplices - 300 vertices. +Simplex_tree dim: 3 +2 0 0 inf +2 1 0.0682162 1.0001 +2 1 0.0934117 1.00003 +2 2 0.56444 1.03938 + +Here we retrieve expected Betti numbers on a tore 3D: +Betti numbers[0] = 1 +Betti numbers[1] = 2 +Betti numbers[2] = 1 + +N.B.: - alpha_complex_persistence accepts OFF files in d-Dimension. + - filtration values are alpha square values + +3) 3D periodic special case +--------------------------- +./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 + +output: +Periodic Delaunay computed. +Simplex_tree dim: 3 +3 0 0 inf +3 1 0.0025 inf +3 1 0.0025 inf +3 1 0.0025 inf +3 2 0.005 inf +3 2 0.005 inf +3 2 0.005 inf +3 3 0.0075 inf + +Here we retrieve expected Betti numbers on a tore 3D: +Betti numbers[0] = 1 +Betti numbers[1] = 3 +Betti numbers[2] = 3 +Betti numbers[3] = 1 + +N.B.: - periodic_alpha_complex_3d_persistence accepts only OFF files in 3D dimension. In this example, the periodic cube +is hard coded to { x = [0,1]; y = [0,1]; z = [0,1] } + - filtration values are alpha square values -- cgit v1.2.3 From 73efba37dfcab3f9b8589cb3b0b80f6d7dd7bd0b Mon Sep 17 00:00:00 2001 From: cjamin Date: Wed, 4 Oct 2017 10:24:04 +0000 Subject: Document utilies in README files using Markdown + move/rename some utilities Only missing doc for now: Garland_heckbert git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/add_utils_in_gudhi_v2@2752 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 7ba0113762b6622130835dc9e372acfae29c2db8 --- src/Alpha_complex/utilities/CMakeLists.txt | 37 +++ src/Alpha_complex/utilities/README | 131 ++++++++++ .../utilities/alpha_complex_3d_helper.h | 76 ++++++ .../utilities/alpha_complex_3d_persistence.cpp | 242 +++++++++++++++++++ .../utilities/alpha_complex_persistence.cpp | 125 ++++++++++ .../periodic_alpha_complex_3d_persistence.cpp | 268 +++++++++++++++++++++ .../utilities/Bitmap_cubical_complex.cpp | 4 +- ...ubical_complex_periodic_boundary_conditions.cpp | 4 +- src/Bitmap_cubical_complex/utilities/README | 24 ++ src/Bottleneck_distance/utilities/README | 19 ++ src/Persistent_cohomology/utilities/CMakeLists.txt | 33 --- src/Persistent_cohomology/utilities/README | 150 ++++-------- .../utilities/alpha_complex_3d_helper.h | 76 ------ .../utilities/alpha_complex_3d_persistence.cpp | 242 ------------------- .../utilities/alpha_complex_persistence.cpp | 125 ---------- .../periodic_alpha_complex_3d_persistence.cpp | 268 --------------------- src/Witness_complex/example/CMakeLists.txt | 21 +- .../example/example_strong_witness_complex_off.cpp | 79 ++++++ .../example_witness_complex_persistence.cpp | 171 ------------- src/Witness_complex/utilities/CMakeLists.txt | 26 +- src/Witness_complex/utilities/README | 72 ++++++ .../example_strong_witness_complex_off.cpp | 79 ------ .../example_strong_witness_persistence.cpp | 171 ------------- .../utilities/strong_witness_persistence.cpp | 171 +++++++++++++ .../utilities/weak_witness_persistence.cpp | 171 +++++++++++++ src/common/utilities/README | 26 +- 26 files changed, 1506 insertions(+), 1305 deletions(-) create mode 100644 src/Alpha_complex/utilities/CMakeLists.txt create mode 100644 src/Alpha_complex/utilities/README create mode 100644 src/Alpha_complex/utilities/alpha_complex_3d_helper.h create mode 100644 src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp create mode 100644 src/Alpha_complex/utilities/alpha_complex_persistence.cpp create mode 100644 src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp create mode 100644 src/Bitmap_cubical_complex/utilities/README create mode 100644 src/Bottleneck_distance/utilities/README delete mode 100644 src/Persistent_cohomology/utilities/alpha_complex_3d_helper.h delete mode 100644 src/Persistent_cohomology/utilities/alpha_complex_3d_persistence.cpp delete mode 100644 src/Persistent_cohomology/utilities/alpha_complex_persistence.cpp delete mode 100644 src/Persistent_cohomology/utilities/periodic_alpha_complex_3d_persistence.cpp create mode 100644 src/Witness_complex/example/example_strong_witness_complex_off.cpp delete mode 100644 src/Witness_complex/example/example_witness_complex_persistence.cpp create mode 100644 src/Witness_complex/utilities/README delete mode 100644 src/Witness_complex/utilities/example_strong_witness_complex_off.cpp delete mode 100644 src/Witness_complex/utilities/example_strong_witness_persistence.cpp create mode 100644 src/Witness_complex/utilities/strong_witness_persistence.cpp create mode 100644 src/Witness_complex/utilities/weak_witness_persistence.cpp (limited to 'src/Persistent_cohomology') diff --git a/src/Alpha_complex/utilities/CMakeLists.txt b/src/Alpha_complex/utilities/CMakeLists.txt new file mode 100644 index 00000000..69dbc28a --- /dev/null +++ b/src/Alpha_complex/utilities/CMakeLists.txt @@ -0,0 +1,37 @@ +cmake_minimum_required(VERSION 2.6) +project(Alpha_complex_utilities) + +if(CGAL_FOUND) + add_executable(alpha_complex_3d_persistence alpha_complex_3d_persistence.cpp) + target_link_libraries(alpha_complex_3d_persistence ${CGAL_LIBRARY}) + + if (TBB_FOUND) + target_link_libraries(alpha_complex_3d_persistence ${TBB_LIBRARIES}) + endif(TBB_FOUND) + add_test(NAME Alpha_complex_utilities_alpha_complex_3d_persistence COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "2" "0.45") + + install(TARGETS alpha_complex_3d_persistence DESTINATION bin) + + if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) + add_executable (alpha_complex_persistence alpha_complex_persistence.cpp) + target_link_libraries(alpha_complex_persistence + ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) + + add_executable(periodic_alpha_complex_3d_persistence periodic_alpha_complex_3d_persistence.cpp) + target_link_libraries(periodic_alpha_complex_3d_persistence ${CGAL_LIBRARY}) + + if (TBB_FOUND) + target_link_libraries(alpha_complex_persistence ${TBB_LIBRARIES}) + target_link_libraries(periodic_alpha_complex_3d_persistence ${TBB_LIBRARIES}) + endif(TBB_FOUND) + add_test(NAME Alpha_complex_utilities_alpha_complex_persistence COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-p" "2" "-m" "0.45") + add_test(NAME Alpha_complex_utilities_periodic_alpha_complex_3d_persistence COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off" "${CMAKE_SOURCE_DIR}/data/points/iso_cuboid_3_in_0_1.txt" "2" "0") + + install(TARGETS alpha_complex_persistence DESTINATION bin) + install(TARGETS periodic_alpha_complex_3d_persistence DESTINATION bin) + + endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) +endif(CGAL_FOUND) diff --git a/src/Alpha_complex/utilities/README b/src/Alpha_complex/utilities/README new file mode 100644 index 00000000..30e1b187 --- /dev/null +++ b/src/Alpha_complex/utilities/README @@ -0,0 +1,131 @@ +# Alpha_complex # + +## `alpha_complex_3d_persistence` ## +This program computes the persistent homology with coefficient field Z/pZ of the 3D alpha complex built from a 3D point cloud. The output diagram contains one bar per line, written with the convention: + +`p dim b d` + +where `dim` is the dimension of the homological feature, `b` and `d` are respectively the birth and death of the feature, and `p` is the characteristic of the field *Z/pZ* used for homology coefficients (`p = p1*...*pr` is the product of prime numbers *pi* such that the homology feature exists in homology with *Z/piZ* coefficients). + +**Usage** +`alpha_complex_3d_persistence

` +where +`` is the path to the input point cloud in OFF format. +`

` is the characteristic p of the coefficient field *Z/pZ* for computing homology. It must be a stricly positive integer. +`` is the minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals. It must be a floating-point number >= -1. + +**Example** +`alpha_complex_3d_persistence ../../data/points/tore3D_300.off 2 0.45` + +outputs: +``` +Simplex_tree dim: 3 +2 0 0 inf +2 1 0.0682162 1.0001 +2 1 0.0934117 1.00003 +2 2 0.56444 1.03938 +``` + +Here we retrieve expected Betti numbers on a tore 3D: +``` +Betti numbers[0] = 1 +Betti numbers[1] = 2 +Betti numbers[2] = 1 +``` + +N.B.: +* `alpha_complex_3d_persistence` only accepts OFF files in dimension 3. +* Filtration values are alpha square values. + + + + +## `periodic_alpha_complex_3d_persistence` ## +This program computes the persistent homology with coefficient field Z/pZ of the 3D periodic alpha complex built from a 3D point cloud. The output diagram contains one bar per line, written with the convention: + +`p dim b d` + +where `dim` is the dimension of the homological feature, `b` and `d` are respectively the birth and death of the feature, and `p` is the characteristic of the field *Z/pZ* used for homology coefficients (`p = p1*...*pr` is the product of prime numbers *pi* such that the homology feature exists in homology with *Z/piZ* coefficients). + +**Usage** +`periodic_alpha_complex_3d_persistence

` +where +`` is the path to the input point cloud in OFF format. +`

` is the characteristic p of the coefficient field *Z/pZ* for computing homology. It must be a stricly positive integer. +`` is the minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals. It must be a floating-point number >= -1. + +**Example** +`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` + +outputs: +``` +Periodic Delaunay computed. +Simplex_tree dim: 3 +3 0 0 inf +3 1 0.0025 inf +3 1 0.0025 inf +3 1 0.0025 inf +3 2 0.005 inf +3 2 0.005 inf +3 2 0.005 inf +3 3 0.0075 inf +``` + +Here we retrieve expected Betti numbers on an 3D iso-oriented cuboids: +``` +Betti numbers[0] = 1 +Betti numbers[1] = 3 +Betti numbers[2] = 3 +Betti numbers[3] = 1 +``` + +N.B.: +* `periodic_alpha_complex_3d_persistence` only accepts OFF files in dimension 3. +* In this example, the periodic cube is hard coded to { x = [0,1]; y = [0,1]; z = [0,1] } +* Filtration values are alpha square values. + + + + + +## `alpha_complex_persistence` ## +This program computes the persistent homology with coefficient field Z/pZ of the dD alpha complex built from a dD point cloud. The output diagram contains one bar per line, written with the convention: + +`p dim b d` + +where `dim` is the dimension of the homological feature, `b` and `d` are respectively the birth and death of the feature, and `p` is the characteristic of the field *Z/pZ* used for homology coefficients (`p = p1*...*pr` is the product of prime numbers pi such that the homology feature exists in homology with Z/piZ coefficients). + +**Usage** +`alpha_complex_persistence [options] ` + +**Allowed options** + +* `-h [ --help ]` Produce help message +* `-o [ --output-file ]` Name of file in which the persistence diagram is written. By default, print in std::cout. +* `-r [ --max-alpha-square-value ]` (default = inf) Maximal alpha square value for the Alpha complex construction. +* `-p [ --field-charac ]` (default = 11) Characteristic p of the coefficient field Z/pZ for computing homology. +* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals. + +**Example** +`alpha_complex_persistence -r 32 -p 2 -m 0.45 ../../data/points/tore3D_300.off` + +outputs: +``` +Alpha complex is of dimension 3 - 9273 simplices - 300 vertices. +Simplex_tree dim: 3 +2 0 0 inf +2 1 0.0682162 1.0001 +2 1 0.0934117 1.00003 +2 2 0.56444 1.03938 +``` + +Here we retrieve expected Betti numbers on a tore 3D: +``` +Betti numbers[0] = 1 +Betti numbers[1] = 2 +Betti numbers[2] = 1 +``` + +N.B.: +* `alpha_complex_persistence` only accepts OFF files in dimension d. +* Filtration values are alpha square values. diff --git a/src/Alpha_complex/utilities/alpha_complex_3d_helper.h b/src/Alpha_complex/utilities/alpha_complex_3d_helper.h new file mode 100644 index 00000000..7865e4ec --- /dev/null +++ b/src/Alpha_complex/utilities/alpha_complex_3d_helper.h @@ -0,0 +1,76 @@ +/* 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) 2014 INRIA Saclay (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 . + */ + +#ifndef ALPHA_COMPLEX_3D_HELPER_H_ +#define ALPHA_COMPLEX_3D_HELPER_H_ + +template +Vertex_list from_cell(const Cell_handle& ch) { + Vertex_list the_list; + for (auto i = 0; i < 4; i++) { +#ifdef DEBUG_TRACES + std::cout << "from cell[" << i << "]=" << ch->vertex(i)->point() << std::endl; +#endif // DEBUG_TRACES + the_list.push_back(ch->vertex(i)); + } + return the_list; +} + +template +Vertex_list from_facet(const Facet& fct) { + Vertex_list the_list; + for (auto i = 0; i < 4; i++) { + if (fct.second != i) { +#ifdef DEBUG_TRACES + std::cout << "from facet=[" << i << "]" << fct.first->vertex(i)->point() << std::endl; +#endif // DEBUG_TRACES + the_list.push_back(fct.first->vertex(i)); + } + } + return the_list; +} + +template +Vertex_list from_edge(const Edge_3& edg) { + Vertex_list the_list; + for (auto i = 0; i < 4; i++) { + if ((edg.second == i) || (edg.third == i)) { +#ifdef DEBUG_TRACES + std::cout << "from edge[" << i << "]=" << edg.first->vertex(i)->point() << std::endl; +#endif // DEBUG_TRACES + the_list.push_back(edg.first->vertex(i)); + } + } + return the_list; +} + +template +Vertex_list from_vertex(const Vertex_handle& vh) { + Vertex_list the_list; +#ifdef DEBUG_TRACES + std::cout << "from vertex=" << vh->point() << std::endl; +#endif // DEBUG_TRACES + the_list.push_back(vh); + return the_list; +} + +#endif // ALPHA_COMPLEX_3D_HELPER_H_ diff --git a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp new file mode 100644 index 00000000..f63ff0f6 --- /dev/null +++ b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp @@ -0,0 +1,242 @@ +/* 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) 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 + * 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 +#include +#include +#include + +#include +#include +#include +#include +#include +#include +#include +#include + +#include "alpha_complex_3d_helper.h" + +// Alpha_shape_3 templates type definitions +using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel; +using Vb = CGAL::Alpha_shape_vertex_base_3; +using Fb = CGAL::Alpha_shape_cell_base_3; +using Tds = CGAL::Triangulation_data_structure_3; +using Triangulation_3 = CGAL::Delaunay_triangulation_3; +using Alpha_shape_3 = CGAL::Alpha_shape_3; + +// From file type definition +using Point_3 = Kernel::Point_3; + +// filtration with alpha values needed type definition +using Alpha_value_type = Alpha_shape_3::FT; +using Object = CGAL::Object; +using Dispatch = CGAL::Dispatch_output_iterator< + CGAL::cpp11::tuple, + CGAL::cpp11::tuple >, + std::back_insert_iterator< std::vector > > >; +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; +using Vertex_list = std::list; + +// gudhi type definition +using ST = Gudhi::Simplex_tree; +using Filtration_value = ST::Filtration_value; +using Simplex_tree_vertex = ST::Vertex_handle; +using Alpha_shape_simplex_tree_map = std::map; +using Alpha_shape_simplex_tree_pair = std::pair; +using Simplex_tree_vector_vertex = std::vector< Simplex_tree_vertex >; +using PCOH = Gudhi::persistent_cohomology::Persistent_cohomology< ST, Gudhi::persistent_cohomology::Field_Zp >; + +void usage(const std::string& progName) { + std::cerr << "Usage:\n" << progName << " path_to_OFF_file coeff_field_characteristic[integer " << + "> 0] min_persistence[float >= -1.0]\n"; + std::cerr << " path_to_OFF_file is the path to your points cloud in OFF format.\n"; + exit(-1); +} + +int main(int argc, char * const argv[]) { + // program args management + if (argc != 4) { + std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n"; + usage(argv[0]); + } + + int coeff_field_characteristic = atoi(argv[2]); + + Filtration_value min_persistence = 0.0; + int returnedScanValue = sscanf(argv[3], "%f", &min_persistence); + if ((returnedScanValue == EOF) || (min_persistence < -1.0)) { + std::cerr << "Error: " << argv[3] << " is not correct\n"; + usage(argv[0]); + } + + // Read points from file + std::string offInputFile(argv[1]); + // Read the OFF file (input file name given as parameter) and triangulate points + Gudhi::Points_3D_off_reader off_reader(offInputFile); + // Check the read operation was correct + if (!off_reader.is_valid()) { + std::cerr << "Unable to read file " << offInputFile << std::endl; + usage(argv[0]); + } + + // Retrieve the triangulation + std::vector lp = off_reader.get_point_cloud(); + + // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode. + Alpha_shape_3 as(lp.begin(), lp.end(), 0, Alpha_shape_3::GENERAL); +#ifdef DEBUG_TRACES + std::cout << "Alpha shape computed in GENERAL mode" << std::endl; +#endif // DEBUG_TRACES + + // filtration with alpha values from alpha shape + std::vector the_objects; + std::vector the_alpha_values; + + Dispatch disp = CGAL::dispatch_output(std::back_inserter(the_objects), + std::back_inserter(the_alpha_values)); + + as.filtration_with_alpha_values(disp); +#ifdef DEBUG_TRACES + std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl; +#endif // DEBUG_TRACES + + Alpha_shape_3::size_type count_vertices = 0; + Alpha_shape_3::size_type count_edges = 0; + Alpha_shape_3::size_type count_facets = 0; + Alpha_shape_3::size_type count_cells = 0; + + // Loop on objects vector + Vertex_list vertex_list; + ST simplex_tree; + Alpha_shape_simplex_tree_map map_cgal_simplex_tree; + std::vector::iterator the_alpha_value_iterator = the_alpha_values.begin(); + int dim_max = 0; + Filtration_value filtration_max = 0.0; + for (auto object_iterator : the_objects) { + // Retrieve Alpha shape vertex list from object + if (const Cell_handle * cell = CGAL::object_cast(&object_iterator)) { + vertex_list = from_cell(*cell); + count_cells++; + if (dim_max < 3) { + // Cell is of dim 3 + dim_max = 3; + } + } else if (const Facet * facet = CGAL::object_cast(&object_iterator)) { + vertex_list = from_facet(*facet); + count_facets++; + if (dim_max < 2) { + // Facet is of dim 2 + dim_max = 2; + } + } else if (const Edge_3 * edge = CGAL::object_cast(&object_iterator)) { + vertex_list = from_edge(*edge); + count_edges++; + if (dim_max < 1) { + // Edge_3 is of dim 1 + dim_max = 1; + } + } else if (const Vertex_handle * vertex = CGAL::object_cast(&object_iterator)) { + count_vertices++; + vertex_list = from_vertex(*vertex); + } + // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex + Simplex_tree_vector_vertex the_simplex_tree; + for (auto the_alpha_shape_vertex : vertex_list) { + Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex); + if (the_map_iterator == map_cgal_simplex_tree.end()) { + // alpha shape not found + Simplex_tree_vertex vertex = map_cgal_simplex_tree.size(); +#ifdef DEBUG_TRACES + std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl; +#endif // DEBUG_TRACES + the_simplex_tree.push_back(vertex); + map_cgal_simplex_tree.insert(Alpha_shape_simplex_tree_pair(the_alpha_shape_vertex, vertex)); + } else { + // alpha shape found + Simplex_tree_vertex vertex = the_map_iterator->second; +#ifdef DEBUG_TRACES + std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl; +#endif // DEBUG_TRACES + the_simplex_tree.push_back(vertex); + } + } + // Construction of the simplex_tree + Filtration_value filtr = /*std::sqrt*/(*the_alpha_value_iterator); +#ifdef DEBUG_TRACES + std::cout << "filtration = " << filtr << std::endl; +#endif // DEBUG_TRACES + if (filtr > filtration_max) { + filtration_max = filtr; + } + simplex_tree.insert_simplex(the_simplex_tree, filtr); + if (the_alpha_value_iterator != the_alpha_values.end()) + ++the_alpha_value_iterator; + else + std::cout << "This shall not happen" << std::endl; + } + simplex_tree.set_dimension(dim_max); + +#ifdef DEBUG_TRACES + std::cout << "vertices \t\t" << count_vertices << std::endl; + std::cout << "edges \t\t" << count_edges << std::endl; + std::cout << "facets \t\t" << count_facets << std::endl; + std::cout << "cells \t\t" << count_cells << std::endl; + + + std::cout << "Information of the Simplex Tree: " << std::endl; + std::cout << " Number of vertices = " << simplex_tree.num_vertices() << " "; + std::cout << " Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl; + std::cout << " Dimension = " << simplex_tree.dimension() << " "; +#endif // DEBUG_TRACES + +#ifdef DEBUG_TRACES + std::cout << "Iterator on vertices: " << std::endl; + for (auto vertex : simplex_tree.complex_vertex_range()) { + std::cout << vertex << " "; + } +#endif // DEBUG_TRACES + + // Sort the simplices in the order of the filtration + simplex_tree.initialize_filtration(); + + std::cout << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl; + // Compute the persistence diagram of the complex + PCOH pcoh(simplex_tree); + // initializes the coefficient field for homology + pcoh.init_coefficients(coeff_field_characteristic); + + pcoh.compute_persistent_cohomology(min_persistence); + + pcoh.output_diagram(); + + return 0; +} diff --git a/src/Alpha_complex/utilities/alpha_complex_persistence.cpp b/src/Alpha_complex/utilities/alpha_complex_persistence.cpp new file mode 100644 index 00000000..9e84e91f --- /dev/null +++ b/src/Alpha_complex/utilities/alpha_complex_persistence.cpp @@ -0,0 +1,125 @@ +#include + +#include + +#include +#include +// to construct a simplex_tree from alpha complex +#include + +#include +#include +#include // for numeric_limits + +using Simplex_tree = Gudhi::Simplex_tree<>; +using Filtration_value = Simplex_tree::Filtration_value; + +void program_options(int argc, char * argv[] + , std::string & off_file_points + , std::string & output_file_diag + , Filtration_value & alpha_square_max_value + , int & coeff_field_characteristic + , Filtration_value & min_persistence); + +int main(int argc, char **argv) { + std::string off_file_points; + std::string output_file_diag; + Filtration_value alpha_square_max_value; + int coeff_field_characteristic; + Filtration_value min_persistence; + + program_options(argc, argv, off_file_points, output_file_diag, alpha_square_max_value, + coeff_field_characteristic, min_persistence); + + // ---------------------------------------------------------------------------- + // Init of an alpha complex from an OFF file + // ---------------------------------------------------------------------------- + using Kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >; + Gudhi::alpha_complex::Alpha_complex alpha_complex_from_file(off_file_points); + + Simplex_tree simplex; + if (alpha_complex_from_file.create_complex(simplex, alpha_square_max_value)) { + // ---------------------------------------------------------------------------- + // Display information about the alpha complex + // ---------------------------------------------------------------------------- + std::cout << "Simplicial complex is of dimension " << simplex.dimension() << + " - " << simplex.num_simplices() << " simplices - " << + simplex.num_vertices() << " vertices." << std::endl; + + // Sort the simplices in the order of the filtration + simplex.initialize_filtration(); + + std::cout << "Simplex_tree dim: " << simplex.dimension() << std::endl; + // Compute the persistence diagram of the complex + Gudhi::persistent_cohomology::Persistent_cohomology< Simplex_tree, + Gudhi::persistent_cohomology::Field_Zp > pcoh(simplex); + // initializes the coefficient field for homology + pcoh.init_coefficients(coeff_field_characteristic); + + pcoh.compute_persistent_cohomology(min_persistence); + + // Output the diagram in filediag + if (output_file_diag.empty()) { + pcoh.output_diagram(); + } else { + std::cout << "Result in file: " << output_file_diag << std::endl; + std::ofstream out(output_file_diag); + pcoh.output_diagram(out); + out.close(); + } + } + + return 0; +} + +void program_options(int argc, char * argv[] + , std::string & off_file_points + , std::string & output_file_diag + , Filtration_value & alpha_square_max_value + , int & coeff_field_characteristic + , Filtration_value & min_persistence) { + namespace po = boost::program_options; + po::options_description hidden("Hidden options"); + hidden.add_options() + ("input-file", po::value(&off_file_points), + "Name of file containing a point set. Format is one point per line: X1 ... Xd "); + + po::options_description visible("Allowed options", 100); + visible.add_options() + ("help,h", "produce help message") + ("output-file,o", po::value(&output_file_diag)->default_value(std::string()), + "Name of file in which the persistence diagram is written. Default print in std::cout") + ("max-alpha-square-value,r", + po::value(&alpha_square_max_value)->default_value(std::numeric_limits::infinity()), + "Maximal alpha square value for the Alpha complex construction.") + ("field-charac,p", po::value(&coeff_field_characteristic)->default_value(11), + "Characteristic p of the coefficient field Z/pZ for computing homology.") + ("min-persistence,m", po::value(&min_persistence), + "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals"); + + po::positional_options_description pos; + pos.add("input-file", 1); + + po::options_description all; + all.add(visible).add(hidden); + + po::variables_map vm; + po::store(po::command_line_parser(argc, argv). + options(all).positional(pos).run(), vm); + po::notify(vm); + + if (vm.count("help") || !vm.count("input-file")) { + std::cout << std::endl; + std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; + std::cout << "of an Alpha complex defined on a set of input points.\n \n"; + std::cout << "The output diagram contains one bar per line, written with the convention: \n"; + std::cout << " p dim b d \n"; + std::cout << "where dim is the dimension of the homological feature,\n"; + std::cout << "b and d are respectively the birth and death of the feature and \n"; + std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; + + std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; + std::cout << visible << std::endl; + std::abort(); + } +} diff --git a/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp new file mode 100644 index 00000000..8140a3c5 --- /dev/null +++ b/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp @@ -0,0 +1,268 @@ +/* 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) 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 + * 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 +#include +#include +#include +#include + +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include "alpha_complex_3d_helper.h" + +// Traits +using K = CGAL::Exact_predicates_inexact_constructions_kernel; +using PK = CGAL::Periodic_3_Delaunay_triangulation_traits_3; +// Vertex type +using DsVb = CGAL::Periodic_3_triangulation_ds_vertex_base_3<>; +using Vb = CGAL::Triangulation_vertex_base_3; +using AsVb = CGAL::Alpha_shape_vertex_base_3; +// Cell type +using DsCb = CGAL::Periodic_3_triangulation_ds_cell_base_3<>; +using Cb = CGAL::Triangulation_cell_base_3; +using AsCb = CGAL::Alpha_shape_cell_base_3; +using Tds = CGAL::Triangulation_data_structure_3; +using P3DT3 = CGAL::Periodic_3_Delaunay_triangulation_3; +using Alpha_shape_3 = CGAL::Alpha_shape_3; +using Point_3 = PK::Point_3; + +// filtration with alpha values needed type definition +using Alpha_value_type = Alpha_shape_3::FT; +using Object = CGAL::Object; +using Dispatch = CGAL::Dispatch_output_iterator< + CGAL::cpp11::tuple, + CGAL::cpp11::tuple >, + std::back_insert_iterator< std::vector > > >; +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; +using Vertex_list = std::list; + +// gudhi type definition +using ST = Gudhi::Simplex_tree; +using Filtration_value = ST::Filtration_value; +using Simplex_tree_vertex = ST::Vertex_handle; +using Alpha_shape_simplex_tree_map = std::map; +using Alpha_shape_simplex_tree_pair = std::pair; +using Simplex_tree_vector_vertex = std::vector< Simplex_tree_vertex >; +using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology< + ST, Gudhi::persistent_cohomology::Field_Zp >; + +void usage(char * const progName) { + std::cerr << "Usage:\n" << progName << " path_to_OFF_file path_to_iso_cuboid_3_file coeff_field_characteristic[" << + "integer > 0] min_persistence[float >= -1.0]\n" << + " path_to_OFF_file is the path to your points cloud in OFF format.\n" << + " path_to_iso_cuboid_3_file is the path to the iso cuboid file with the following format :\n" << + " x_min y_min z_min x_max y_max z_max\n" << + " In this example, the periodic cube will be " << + "{ x = [x_min,x_max]; y = [y_min,y_max]; z = [z_min,z_max] }.\n" << + " For more information, please refer to\n" << + " https://doc.cgal.org/latest/Kernel_23/classCGAL_1_1Iso__cuboid__3.html\n"; + + exit(-1); +} + +int main(int argc, char * const argv[]) { + // program args management + if (argc != 5) { + std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n"; + usage(argv[0]); + } + + int coeff_field_characteristic = atoi(argv[3]); + Filtration_value min_persistence = strtof(argv[4], nullptr); + + // Read points from file + std::string offInputFile(argv[1]); + // Read the OFF file (input file name given as parameter) and triangulate points + Gudhi::Points_3D_off_reader off_reader(offInputFile); + // Check the read operation was correct + if (!off_reader.is_valid()) { + std::cerr << "Unable to read file " << offInputFile << std::endl; + usage(argv[0]); + } + + // Read iso_cuboid_3 information from file + std::ifstream iso_cuboid_str(argv[2]); + 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[2] << std::endl; + usage(argv[0]); + } + + // Retrieve the triangulation + std::vector lp = off_reader.get_point_cloud(); + + // Define the periodic cube + P3DT3 pdt(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) + 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(); + 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 + // Maybe need to set it to GENERAL mode + Alpha_shape_3 as(pdt, 0, Alpha_shape_3::GENERAL); + + // filtration with alpha values from alpha shape + std::vector the_objects; + std::vector the_alpha_values; + + Dispatch disp = CGAL::dispatch_output(std::back_inserter(the_objects), + std::back_inserter(the_alpha_values)); + + as.filtration_with_alpha_values(disp); +#ifdef DEBUG_TRACES + std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl; +#endif // DEBUG_TRACES + + Alpha_shape_3::size_type count_vertices = 0; + Alpha_shape_3::size_type count_edges = 0; + Alpha_shape_3::size_type count_facets = 0; + Alpha_shape_3::size_type count_cells = 0; + + // Loop on objects vector + Vertex_list vertex_list; + ST simplex_tree; + Alpha_shape_simplex_tree_map map_cgal_simplex_tree; + std::vector::iterator the_alpha_value_iterator = the_alpha_values.begin(); + int dim_max = 0; + Filtration_value filtration_max = 0.0; + for (auto object_iterator : the_objects) { + // Retrieve Alpha shape vertex list from object + if (const Cell_handle * cell = CGAL::object_cast(&object_iterator)) { + vertex_list = from_cell(*cell); + count_cells++; + if (dim_max < 3) { + // Cell is of dim 3 + dim_max = 3; + } + } else if (const Facet * facet = CGAL::object_cast(&object_iterator)) { + vertex_list = from_facet(*facet); + count_facets++; + if (dim_max < 2) { + // Facet is of dim 2 + dim_max = 2; + } + } else if (const Edge_3 * edge = CGAL::object_cast(&object_iterator)) { + vertex_list = from_edge(*edge); + count_edges++; + if (dim_max < 1) { + // Edge_3 is of dim 1 + dim_max = 1; + } + } else if (const Alpha_shape_3::Vertex_handle * vertex = + CGAL::object_cast(&object_iterator)) { + count_vertices++; + vertex_list = from_vertex(*vertex); + } + // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex + Simplex_tree_vector_vertex the_simplex_tree; + for (auto the_alpha_shape_vertex : vertex_list) { + Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex); + if (the_map_iterator == map_cgal_simplex_tree.end()) { + // alpha shape not found + Simplex_tree_vertex vertex = map_cgal_simplex_tree.size(); +#ifdef DEBUG_TRACES + std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl; +#endif // DEBUG_TRACES + the_simplex_tree.push_back(vertex); + map_cgal_simplex_tree.insert(Alpha_shape_simplex_tree_pair(the_alpha_shape_vertex, vertex)); + } else { + // alpha shape found + Simplex_tree_vertex vertex = the_map_iterator->second; +#ifdef DEBUG_TRACES + std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl; +#endif // DEBUG_TRACES + the_simplex_tree.push_back(vertex); + } + } + // Construction of the simplex_tree + Filtration_value filtr = /*std::sqrt*/(*the_alpha_value_iterator); +#ifdef DEBUG_TRACES + std::cout << "filtration = " << filtr << std::endl; +#endif // DEBUG_TRACES + if (filtr > filtration_max) { + filtration_max = filtr; + } + simplex_tree.insert_simplex(the_simplex_tree, filtr); + if (the_alpha_value_iterator != the_alpha_values.end()) + ++the_alpha_value_iterator; + else + std::cout << "This shall not happen" << std::endl; + } + simplex_tree.set_dimension(dim_max); + +#ifdef DEBUG_TRACES + std::cout << "vertices \t\t" << count_vertices << std::endl; + std::cout << "edges \t\t" << count_edges << std::endl; + std::cout << "facets \t\t" << count_facets << std::endl; + std::cout << "cells \t\t" << count_cells << std::endl; + + + std::cout << "Information of the Simplex Tree: " << std::endl; + std::cout << " Number of vertices = " << simplex_tree.num_vertices() << " "; + std::cout << " Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl; + std::cout << " Dimension = " << simplex_tree.dimension() << " "; +#endif // DEBUG_TRACES + +#ifdef DEBUG_TRACES + std::cout << "Iterator on vertices: " << std::endl; + for (auto vertex : simplex_tree.complex_vertex_range()) { + std::cout << vertex << " "; + } +#endif // DEBUG_TRACES + + // Sort the simplices in the order of the filtration + simplex_tree.initialize_filtration(); + + std::cout << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl; + // Compute the persistence diagram of the complex + Persistent_cohomology pcoh(simplex_tree, true); + // initializes the coefficient field for homology + pcoh.init_coefficients(coeff_field_characteristic); + + pcoh.compute_persistent_cohomology(min_persistence); + + pcoh.output_diagram(); + + return 0; +} diff --git a/src/Bitmap_cubical_complex/utilities/Bitmap_cubical_complex.cpp b/src/Bitmap_cubical_complex/utilities/Bitmap_cubical_complex.cpp index 67735ba1..e126caea 100644 --- a/src/Bitmap_cubical_complex/utilities/Bitmap_cubical_complex.cpp +++ b/src/Bitmap_cubical_complex/utilities/Bitmap_cubical_complex.cpp @@ -32,8 +32,8 @@ #include int main(int argc, char** argv) { - std::cout << "This program computes persistent homology, by using bitmap_cubical_complex class, of cubical " << - "complexes provided in text files in Perseus style (the only numbered in the first line is a dimension D of a" << + std::cout << "This program computes persistent homology, by using the Bitmap_cubical_complex_base class, of cubical " << + "complexes provided in text files in Perseus style. The only number in the first line is a dimension D of a" << "bitmap. In the lines I between 2 and D+1 there are numbers of top dimensional cells in the direction I. Let " << "N denote product of the numbers in the lines between 2 and D. In the lines D+2 to D+2+N there are " << "filtrations of top dimensional cells. We assume that the cells are in the lexicographical order. See " << diff --git a/src/Bitmap_cubical_complex/utilities/Bitmap_cubical_complex_periodic_boundary_conditions.cpp b/src/Bitmap_cubical_complex/utilities/Bitmap_cubical_complex_periodic_boundary_conditions.cpp index 122160a2..7f9296a6 100644 --- a/src/Bitmap_cubical_complex/utilities/Bitmap_cubical_complex_periodic_boundary_conditions.cpp +++ b/src/Bitmap_cubical_complex/utilities/Bitmap_cubical_complex_periodic_boundary_conditions.cpp @@ -33,9 +33,9 @@ #include int main(int argc, char** argv) { - std::cout << "This program computes persistent homology, by using " << + std::cout << "This program computes persistent homology, by using the " << "Bitmap_cubical_complex_periodic_boundary_conditions class, of cubical complexes provided in text files in " << - "Perseus style (the only numbered in the first line is a dimension D of a bitmap. In the lines I between 2 " << + "Perseus style. The only number in the first line is a dimension D of a bitmap. In the lines I between 2 " << "and D+1 there are numbers of top dimensional cells in the direction I. Let N denote product of the numbers " << "in the lines between 2 and D. In the lines D+2 to D+2+N there are filtrations of top dimensional cells. We " << "assume that the cells are in the lexicographical order. See CubicalOneSphere.txt or CubicalTwoSphere.txt for" << diff --git a/src/Bitmap_cubical_complex/utilities/README b/src/Bitmap_cubical_complex/utilities/README new file mode 100644 index 00000000..d9085635 --- /dev/null +++ b/src/Bitmap_cubical_complex/utilities/README @@ -0,0 +1,24 @@ +# Bitmap_cubical_complex # + +## `Bitmap_cubical_complex` ## +This program computes persistent homology, by using the Bitmap_cubical_complex class, of cubical complexes provided in text files in Perseus style. The only number in the first line is a dimension D of a bitmap. In the lines I between 2 and D+1 there are numbers of top dimensional cells in the direction I. Let N denote product of the numbers in the lines between 2 and D. In the lines D+2 to D+2+N there are filtrations of top dimensional cells. We assume that the cells are in the lexicographical order. + +Examples: + +* Create a Cubical Complex from the Perseus style file CubicalOneSphere.txt, computes Persistence cohomology from it and writes the results in a persistence file: +`Bitmap_cubical_complex data/bitmap/CubicalOneSphere.txt` + +* Create a Cubical Complex from the Perseus style file CubicalTwoSphere.txt, computes Persistence cohomology from it and writes the results in a persistence file: +`Bitmap_cubical_complex data/bitmap/CubicalTwoSphere.txt` + +## `Bitmap_cubical_complex_periodic_boundary_conditions` ## + +Same as above, but with periodic boundary conditions. + +Examples: + +* Create a Periodical Cubical Complex from the Perseus style file 2d_torus.txt, computes Persistence cohomology from it and writes the results in a persistence file: +`Bitmap_cubical_complex_periodic_boundary_conditions.exe data/bitmap/2d_torus.txt` + +* Create a Periodical Cubical Complex from the Perseus style file 3d_torus.txt, computes Persistence cohomology from it and writes the results in a persistence file: +`Bitmap_cubical_complex_periodic_boundary_conditions.exe data/bitmap/3d_torus.txt` diff --git a/src/Bottleneck_distance/utilities/README b/src/Bottleneck_distance/utilities/README new file mode 100644 index 00000000..4c9b0735 --- /dev/null +++ b/src/Bottleneck_distance/utilities/README @@ -0,0 +1,19 @@ +# Bottleneck_distance # + +## `alpha_rips_persistence_bottleneck_distance` ## +This program computes the persistent homology with coefficient field Z/pZ of a Rips complex defined on a set of input points. The output diagram contains one bar per line, written with the convention: + +`p dim b d` + +where `dim` is the dimension of the homological feature, `b` and `d` are respectively the birth and death of the feature, and `p` is the characteristic of the field *Z/pZ* used for homology coefficients. + +Usage: +`alpha_rips_persistence_bottleneck_distance [options] ` + +Allowed options: + +* `-h [ --help ]` Produce help message +* `-r [ --max-edge-length ]` (default = inf) Maximal length of an edge for the Rips complex construction.` +* `-d [ --cpx-dimension ]` (default = 1) Maximal dimension of the Rips complex we want to compute.` +* `-p [ --field-charac ]` (default = 11) Characteristic p of the coefficient field Z/pZ for computing homology. +* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals. \ No newline at end of file diff --git a/src/Persistent_cohomology/utilities/CMakeLists.txt b/src/Persistent_cohomology/utilities/CMakeLists.txt index c2f00da2..5b315801 100644 --- a/src/Persistent_cohomology/utilities/CMakeLists.txt +++ b/src/Persistent_cohomology/utilities/CMakeLists.txt @@ -20,37 +20,4 @@ add_test(NAME Persistent_cohomology_example_from_rips_on_tore_3D COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "2" "0.45") - - install(TARGETS alpha_complex_3d_persistence DESTINATION bin) - - if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) - add_executable (alpha_complex_persistence alpha_complex_persistence.cpp) - target_link_libraries(alpha_complex_persistence - ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) - - add_executable(periodic_alpha_complex_3d_persistence periodic_alpha_complex_3d_persistence.cpp) - target_link_libraries(periodic_alpha_complex_3d_persistence ${CGAL_LIBRARY}) - - if (TBB_FOUND) - target_link_libraries(alpha_complex_persistence ${TBB_LIBRARIES}) - target_link_libraries(periodic_alpha_complex_3d_persistence ${TBB_LIBRARIES}) - endif(TBB_FOUND) - add_test(NAME Persistent_cohomology_example_alpha_complex COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-p" "2" "-m" "0.45") - add_test(NAME Persistent_cohomology_example_periodic_alpha_complex_3d COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off" "${CMAKE_SOURCE_DIR}/data/points/iso_cuboid_3_in_0_1.txt" "2" "0") - - install(TARGETS alpha_complex_persistence DESTINATION bin) - install(TARGETS periodic_alpha_complex_3d_persistence DESTINATION bin) - - endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) endif(CGAL_FOUND) diff --git a/src/Persistent_cohomology/utilities/README b/src/Persistent_cohomology/utilities/README index 76e960da..eecee7ee 100644 --- a/src/Persistent_cohomology/utilities/README +++ b/src/Persistent_cohomology/utilities/README @@ -1,114 +1,66 @@ -To build the utilities, run in a Terminal: +# Persistent_cohomology # -cd /path-to-utilities/ -cmake . -make +## `rips_persistence` ## +This program computes the persistent homology with coefficient field *Z/pZ* of a Rips complex defined on a set of input points. The output diagram contains one bar per line, written with the convention: -*********************************************************************************************************************** -Example of use of RIPS: +`p dim b d` -Computation of the persistent homology with Z/2Z coefficients of the Rips complex on points -sampling a 3D torus: +where `dim` is the dimension of the homological feature, `b` and `d` are respectively the birth and death of the feature, and `p` is the characteristic of the field *Z/pZ* used for homology coefficients (`p = p1*...*pr` is the product of prime numbers *pi* such that the homology feature exists in homology with *Z/piZ* coefficients). -./rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 2 +**Usage** +`rips_persistence [options] ` -output: -2 0 0 inf +**Allowed options** + +* `-h [ --help ]` Produce help message +* `-r [ --max-edge-length ]` (default = inf) Maximal length of an edge for the Rips complex construction. +* `-d [ --cpx-dimension ]` (default = 1) Maximal dimension of the Rips complex we want to compute. +* `-p [ --field-charac ]` (default = 11) Characteristic p of the coefficient field Z/pZ for computing homology. +* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals. + +**Example 1 with Z/2Z coefficients** +`rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 2` + +outputs: +``` +2 0 0 inf 2 1 0.0983494 inf 2 1 0.104347 inf 2 2 0.138335 inf +``` +**Example 2 with Z/3Z coefficients** -Every line is of this format: p1*...*pr dim b d -where - p1*...*pr is the product of prime numbers pi such that the homology feature exists in homology with Z/piZ coefficients. - dim is the dimension of the homological feature, - b and d are respectively the birth and death of the feature and - +rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 3 +outputs: +``` +3 0 0 inf +3 1 0.0983494 inf +3 1 0.104347 inf +3 2 0.138335 inf +``` -with Z/3Z coefficients: -./rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 3 -output: -3 0 0 inf -3 1 0.0983494 inf -3 1 0.104347 inf -3 2 0.138335 inf - -*********************************************************************************************************************** -Example of use of ALPHA: - -For a more verbose mode, please run cmake with option "DEBUG_TRACES=TRUE" and recompile the programs. - -1) 3D special case ------------------- -Computation of the persistent homology with Z/2Z coefficients of the alpha complex on points -sampling a torus 3D: - -./alpha_complex_3d_persistence ../../data/points/tore3D_300.off 2 0.45 - -output: -Simplex_tree dim: 3 -2 0 0 inf -2 1 0.0682162 1.0001 -2 1 0.0934117 1.00003 -2 2 0.56444 1.03938 - -Here we retrieve expected Betti numbers on a tore 3D: -Betti numbers[0] = 1 -Betti numbers[1] = 2 -Betti numbers[2] = 1 - -N.B.: - alpha_complex_3d_persistence accepts only OFF files in 3D dimension. - - filtration values are alpha square values - -2) d-Dimension case -------------------- -Computation of the persistent homology with Z/2Z coefficients of the alpha complex on points -sampling a torus 3D: - -./alpha_complex_persistence -r 32 -p 2 -m 0.45 ../../data/points/tore3D_300.off - -output: -Alpha complex is of dimension 3 - 9273 simplices - 300 vertices. -Simplex_tree dim: 3 -2 0 0 inf -2 1 0.0682162 1.0001 -2 1 0.0934117 1.00003 -2 2 0.56444 1.03938 - -Here we retrieve expected Betti numbers on a tore 3D: -Betti numbers[0] = 1 -Betti numbers[1] = 2 -Betti numbers[2] = 1 - -N.B.: - alpha_complex_persistence accepts OFF files in d-Dimension. - - filtration values are alpha square values - -3) 3D periodic special case ---------------------------- -./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 - -output: -Periodic Delaunay computed. -Simplex_tree dim: 3 + +## `rips_distance_matrix_persistence` ## +Same as `rips_persistence` but taking an distance matrix as input. + +**Example** +`rips_distance_matrix_persistence data/distance_matrix/full_square_distance_matrix.csv -r 15 -d 3 -p 3 -m 0` + +outputs: +``` +The complex contains 46 simplices + and has dimension 3 3 0 0 inf -3 1 0.0025 inf -3 1 0.0025 inf -3 1 0.0025 inf -3 2 0.005 inf -3 2 0.005 inf -3 2 0.005 inf -3 3 0.0075 inf - -Here we retrieve expected Betti numbers on a tore 3D: -Betti numbers[0] = 1 -Betti numbers[1] = 3 -Betti numbers[2] = 3 -Betti numbers[3] = 1 - -N.B.: - periodic_alpha_complex_3d_persistence accepts only OFF files in 3D dimension. In this example, the periodic cube -is hard coded to { x = [0,1]; y = [0,1]; z = [0,1] } - - filtration values are alpha square values +3 0 0 8.94427 +3 0 0 7.28011 +3 0 0 6.08276 +3 0 0 5.83095 +3 0 0 5.38516 +3 0 0 5 +3 1 11 12.0416 +3 1 6.32456 6.7082 +``` diff --git a/src/Persistent_cohomology/utilities/alpha_complex_3d_helper.h b/src/Persistent_cohomology/utilities/alpha_complex_3d_helper.h deleted file mode 100644 index 7865e4ec..00000000 --- a/src/Persistent_cohomology/utilities/alpha_complex_3d_helper.h +++ /dev/null @@ -1,76 +0,0 @@ -/* 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) 2014 INRIA Saclay (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 . - */ - -#ifndef ALPHA_COMPLEX_3D_HELPER_H_ -#define ALPHA_COMPLEX_3D_HELPER_H_ - -template -Vertex_list from_cell(const Cell_handle& ch) { - Vertex_list the_list; - for (auto i = 0; i < 4; i++) { -#ifdef DEBUG_TRACES - std::cout << "from cell[" << i << "]=" << ch->vertex(i)->point() << std::endl; -#endif // DEBUG_TRACES - the_list.push_back(ch->vertex(i)); - } - return the_list; -} - -template -Vertex_list from_facet(const Facet& fct) { - Vertex_list the_list; - for (auto i = 0; i < 4; i++) { - if (fct.second != i) { -#ifdef DEBUG_TRACES - std::cout << "from facet=[" << i << "]" << fct.first->vertex(i)->point() << std::endl; -#endif // DEBUG_TRACES - the_list.push_back(fct.first->vertex(i)); - } - } - return the_list; -} - -template -Vertex_list from_edge(const Edge_3& edg) { - Vertex_list the_list; - for (auto i = 0; i < 4; i++) { - if ((edg.second == i) || (edg.third == i)) { -#ifdef DEBUG_TRACES - std::cout << "from edge[" << i << "]=" << edg.first->vertex(i)->point() << std::endl; -#endif // DEBUG_TRACES - the_list.push_back(edg.first->vertex(i)); - } - } - return the_list; -} - -template -Vertex_list from_vertex(const Vertex_handle& vh) { - Vertex_list the_list; -#ifdef DEBUG_TRACES - std::cout << "from vertex=" << vh->point() << std::endl; -#endif // DEBUG_TRACES - the_list.push_back(vh); - return the_list; -} - -#endif // ALPHA_COMPLEX_3D_HELPER_H_ diff --git a/src/Persistent_cohomology/utilities/alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/utilities/alpha_complex_3d_persistence.cpp deleted file mode 100644 index f63ff0f6..00000000 --- a/src/Persistent_cohomology/utilities/alpha_complex_3d_persistence.cpp +++ /dev/null @@ -1,242 +0,0 @@ -/* 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) 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 - * 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 -#include -#include -#include - -#include -#include -#include -#include -#include -#include -#include -#include - -#include "alpha_complex_3d_helper.h" - -// Alpha_shape_3 templates type definitions -using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel; -using Vb = CGAL::Alpha_shape_vertex_base_3; -using Fb = CGAL::Alpha_shape_cell_base_3; -using Tds = CGAL::Triangulation_data_structure_3; -using Triangulation_3 = CGAL::Delaunay_triangulation_3; -using Alpha_shape_3 = CGAL::Alpha_shape_3; - -// From file type definition -using Point_3 = Kernel::Point_3; - -// filtration with alpha values needed type definition -using Alpha_value_type = Alpha_shape_3::FT; -using Object = CGAL::Object; -using Dispatch = CGAL::Dispatch_output_iterator< - CGAL::cpp11::tuple, - CGAL::cpp11::tuple >, - std::back_insert_iterator< std::vector > > >; -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; -using Vertex_list = std::list; - -// gudhi type definition -using ST = Gudhi::Simplex_tree; -using Filtration_value = ST::Filtration_value; -using Simplex_tree_vertex = ST::Vertex_handle; -using Alpha_shape_simplex_tree_map = std::map; -using Alpha_shape_simplex_tree_pair = std::pair; -using Simplex_tree_vector_vertex = std::vector< Simplex_tree_vertex >; -using PCOH = Gudhi::persistent_cohomology::Persistent_cohomology< ST, Gudhi::persistent_cohomology::Field_Zp >; - -void usage(const std::string& progName) { - std::cerr << "Usage:\n" << progName << " path_to_OFF_file coeff_field_characteristic[integer " << - "> 0] min_persistence[float >= -1.0]\n"; - std::cerr << " path_to_OFF_file is the path to your points cloud in OFF format.\n"; - exit(-1); -} - -int main(int argc, char * const argv[]) { - // program args management - if (argc != 4) { - std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n"; - usage(argv[0]); - } - - int coeff_field_characteristic = atoi(argv[2]); - - Filtration_value min_persistence = 0.0; - int returnedScanValue = sscanf(argv[3], "%f", &min_persistence); - if ((returnedScanValue == EOF) || (min_persistence < -1.0)) { - std::cerr << "Error: " << argv[3] << " is not correct\n"; - usage(argv[0]); - } - - // Read points from file - std::string offInputFile(argv[1]); - // Read the OFF file (input file name given as parameter) and triangulate points - Gudhi::Points_3D_off_reader off_reader(offInputFile); - // Check the read operation was correct - if (!off_reader.is_valid()) { - std::cerr << "Unable to read file " << offInputFile << std::endl; - usage(argv[0]); - } - - // Retrieve the triangulation - std::vector lp = off_reader.get_point_cloud(); - - // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode. - Alpha_shape_3 as(lp.begin(), lp.end(), 0, Alpha_shape_3::GENERAL); -#ifdef DEBUG_TRACES - std::cout << "Alpha shape computed in GENERAL mode" << std::endl; -#endif // DEBUG_TRACES - - // filtration with alpha values from alpha shape - std::vector the_objects; - std::vector the_alpha_values; - - Dispatch disp = CGAL::dispatch_output(std::back_inserter(the_objects), - std::back_inserter(the_alpha_values)); - - as.filtration_with_alpha_values(disp); -#ifdef DEBUG_TRACES - std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl; -#endif // DEBUG_TRACES - - Alpha_shape_3::size_type count_vertices = 0; - Alpha_shape_3::size_type count_edges = 0; - Alpha_shape_3::size_type count_facets = 0; - Alpha_shape_3::size_type count_cells = 0; - - // Loop on objects vector - Vertex_list vertex_list; - ST simplex_tree; - Alpha_shape_simplex_tree_map map_cgal_simplex_tree; - std::vector::iterator the_alpha_value_iterator = the_alpha_values.begin(); - int dim_max = 0; - Filtration_value filtration_max = 0.0; - for (auto object_iterator : the_objects) { - // Retrieve Alpha shape vertex list from object - if (const Cell_handle * cell = CGAL::object_cast(&object_iterator)) { - vertex_list = from_cell(*cell); - count_cells++; - if (dim_max < 3) { - // Cell is of dim 3 - dim_max = 3; - } - } else if (const Facet * facet = CGAL::object_cast(&object_iterator)) { - vertex_list = from_facet(*facet); - count_facets++; - if (dim_max < 2) { - // Facet is of dim 2 - dim_max = 2; - } - } else if (const Edge_3 * edge = CGAL::object_cast(&object_iterator)) { - vertex_list = from_edge(*edge); - count_edges++; - if (dim_max < 1) { - // Edge_3 is of dim 1 - dim_max = 1; - } - } else if (const Vertex_handle * vertex = CGAL::object_cast(&object_iterator)) { - count_vertices++; - vertex_list = from_vertex(*vertex); - } - // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex - Simplex_tree_vector_vertex the_simplex_tree; - for (auto the_alpha_shape_vertex : vertex_list) { - Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex); - if (the_map_iterator == map_cgal_simplex_tree.end()) { - // alpha shape not found - Simplex_tree_vertex vertex = map_cgal_simplex_tree.size(); -#ifdef DEBUG_TRACES - std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl; -#endif // DEBUG_TRACES - the_simplex_tree.push_back(vertex); - map_cgal_simplex_tree.insert(Alpha_shape_simplex_tree_pair(the_alpha_shape_vertex, vertex)); - } else { - // alpha shape found - Simplex_tree_vertex vertex = the_map_iterator->second; -#ifdef DEBUG_TRACES - std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl; -#endif // DEBUG_TRACES - the_simplex_tree.push_back(vertex); - } - } - // Construction of the simplex_tree - Filtration_value filtr = /*std::sqrt*/(*the_alpha_value_iterator); -#ifdef DEBUG_TRACES - std::cout << "filtration = " << filtr << std::endl; -#endif // DEBUG_TRACES - if (filtr > filtration_max) { - filtration_max = filtr; - } - simplex_tree.insert_simplex(the_simplex_tree, filtr); - if (the_alpha_value_iterator != the_alpha_values.end()) - ++the_alpha_value_iterator; - else - std::cout << "This shall not happen" << std::endl; - } - simplex_tree.set_dimension(dim_max); - -#ifdef DEBUG_TRACES - std::cout << "vertices \t\t" << count_vertices << std::endl; - std::cout << "edges \t\t" << count_edges << std::endl; - std::cout << "facets \t\t" << count_facets << std::endl; - std::cout << "cells \t\t" << count_cells << std::endl; - - - std::cout << "Information of the Simplex Tree: " << std::endl; - std::cout << " Number of vertices = " << simplex_tree.num_vertices() << " "; - std::cout << " Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl; - std::cout << " Dimension = " << simplex_tree.dimension() << " "; -#endif // DEBUG_TRACES - -#ifdef DEBUG_TRACES - std::cout << "Iterator on vertices: " << std::endl; - for (auto vertex : simplex_tree.complex_vertex_range()) { - std::cout << vertex << " "; - } -#endif // DEBUG_TRACES - - // Sort the simplices in the order of the filtration - simplex_tree.initialize_filtration(); - - std::cout << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl; - // Compute the persistence diagram of the complex - PCOH pcoh(simplex_tree); - // initializes the coefficient field for homology - pcoh.init_coefficients(coeff_field_characteristic); - - pcoh.compute_persistent_cohomology(min_persistence); - - pcoh.output_diagram(); - - return 0; -} diff --git a/src/Persistent_cohomology/utilities/alpha_complex_persistence.cpp b/src/Persistent_cohomology/utilities/alpha_complex_persistence.cpp deleted file mode 100644 index 9e84e91f..00000000 --- a/src/Persistent_cohomology/utilities/alpha_complex_persistence.cpp +++ /dev/null @@ -1,125 +0,0 @@ -#include - -#include - -#include -#include -// to construct a simplex_tree from alpha complex -#include - -#include -#include -#include // for numeric_limits - -using Simplex_tree = Gudhi::Simplex_tree<>; -using Filtration_value = Simplex_tree::Filtration_value; - -void program_options(int argc, char * argv[] - , std::string & off_file_points - , std::string & output_file_diag - , Filtration_value & alpha_square_max_value - , int & coeff_field_characteristic - , Filtration_value & min_persistence); - -int main(int argc, char **argv) { - std::string off_file_points; - std::string output_file_diag; - Filtration_value alpha_square_max_value; - int coeff_field_characteristic; - Filtration_value min_persistence; - - program_options(argc, argv, off_file_points, output_file_diag, alpha_square_max_value, - coeff_field_characteristic, min_persistence); - - // ---------------------------------------------------------------------------- - // Init of an alpha complex from an OFF file - // ---------------------------------------------------------------------------- - using Kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >; - Gudhi::alpha_complex::Alpha_complex alpha_complex_from_file(off_file_points); - - Simplex_tree simplex; - if (alpha_complex_from_file.create_complex(simplex, alpha_square_max_value)) { - // ---------------------------------------------------------------------------- - // Display information about the alpha complex - // ---------------------------------------------------------------------------- - std::cout << "Simplicial complex is of dimension " << simplex.dimension() << - " - " << simplex.num_simplices() << " simplices - " << - simplex.num_vertices() << " vertices." << std::endl; - - // Sort the simplices in the order of the filtration - simplex.initialize_filtration(); - - std::cout << "Simplex_tree dim: " << simplex.dimension() << std::endl; - // Compute the persistence diagram of the complex - Gudhi::persistent_cohomology::Persistent_cohomology< Simplex_tree, - Gudhi::persistent_cohomology::Field_Zp > pcoh(simplex); - // initializes the coefficient field for homology - pcoh.init_coefficients(coeff_field_characteristic); - - pcoh.compute_persistent_cohomology(min_persistence); - - // Output the diagram in filediag - if (output_file_diag.empty()) { - pcoh.output_diagram(); - } else { - std::cout << "Result in file: " << output_file_diag << std::endl; - std::ofstream out(output_file_diag); - pcoh.output_diagram(out); - out.close(); - } - } - - return 0; -} - -void program_options(int argc, char * argv[] - , std::string & off_file_points - , std::string & output_file_diag - , Filtration_value & alpha_square_max_value - , int & coeff_field_characteristic - , Filtration_value & min_persistence) { - namespace po = boost::program_options; - po::options_description hidden("Hidden options"); - hidden.add_options() - ("input-file", po::value(&off_file_points), - "Name of file containing a point set. Format is one point per line: X1 ... Xd "); - - po::options_description visible("Allowed options", 100); - visible.add_options() - ("help,h", "produce help message") - ("output-file,o", po::value(&output_file_diag)->default_value(std::string()), - "Name of file in which the persistence diagram is written. Default print in std::cout") - ("max-alpha-square-value,r", - po::value(&alpha_square_max_value)->default_value(std::numeric_limits::infinity()), - "Maximal alpha square value for the Alpha complex construction.") - ("field-charac,p", po::value(&coeff_field_characteristic)->default_value(11), - "Characteristic p of the coefficient field Z/pZ for computing homology.") - ("min-persistence,m", po::value(&min_persistence), - "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals"); - - po::positional_options_description pos; - pos.add("input-file", 1); - - po::options_description all; - all.add(visible).add(hidden); - - po::variables_map vm; - po::store(po::command_line_parser(argc, argv). - options(all).positional(pos).run(), vm); - po::notify(vm); - - if (vm.count("help") || !vm.count("input-file")) { - std::cout << std::endl; - std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; - std::cout << "of an Alpha complex defined on a set of input points.\n \n"; - std::cout << "The output diagram contains one bar per line, written with the convention: \n"; - std::cout << " p dim b d \n"; - std::cout << "where dim is the dimension of the homological feature,\n"; - std::cout << "b and d are respectively the birth and death of the feature and \n"; - std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; - - std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; - std::cout << visible << std::endl; - std::abort(); - } -} diff --git a/src/Persistent_cohomology/utilities/periodic_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/utilities/periodic_alpha_complex_3d_persistence.cpp deleted file mode 100644 index 8140a3c5..00000000 --- a/src/Persistent_cohomology/utilities/periodic_alpha_complex_3d_persistence.cpp +++ /dev/null @@ -1,268 +0,0 @@ -/* 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) 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 - * 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 -#include -#include -#include -#include - -#include -#include -#include -#include -#include -#include -#include -#include -#include - -#include "alpha_complex_3d_helper.h" - -// Traits -using K = CGAL::Exact_predicates_inexact_constructions_kernel; -using PK = CGAL::Periodic_3_Delaunay_triangulation_traits_3; -// Vertex type -using DsVb = CGAL::Periodic_3_triangulation_ds_vertex_base_3<>; -using Vb = CGAL::Triangulation_vertex_base_3; -using AsVb = CGAL::Alpha_shape_vertex_base_3; -// Cell type -using DsCb = CGAL::Periodic_3_triangulation_ds_cell_base_3<>; -using Cb = CGAL::Triangulation_cell_base_3; -using AsCb = CGAL::Alpha_shape_cell_base_3; -using Tds = CGAL::Triangulation_data_structure_3; -using P3DT3 = CGAL::Periodic_3_Delaunay_triangulation_3; -using Alpha_shape_3 = CGAL::Alpha_shape_3; -using Point_3 = PK::Point_3; - -// filtration with alpha values needed type definition -using Alpha_value_type = Alpha_shape_3::FT; -using Object = CGAL::Object; -using Dispatch = CGAL::Dispatch_output_iterator< - CGAL::cpp11::tuple, - CGAL::cpp11::tuple >, - std::back_insert_iterator< std::vector > > >; -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; -using Vertex_list = std::list; - -// gudhi type definition -using ST = Gudhi::Simplex_tree; -using Filtration_value = ST::Filtration_value; -using Simplex_tree_vertex = ST::Vertex_handle; -using Alpha_shape_simplex_tree_map = std::map; -using Alpha_shape_simplex_tree_pair = std::pair; -using Simplex_tree_vector_vertex = std::vector< Simplex_tree_vertex >; -using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology< - ST, Gudhi::persistent_cohomology::Field_Zp >; - -void usage(char * const progName) { - std::cerr << "Usage:\n" << progName << " path_to_OFF_file path_to_iso_cuboid_3_file coeff_field_characteristic[" << - "integer > 0] min_persistence[float >= -1.0]\n" << - " path_to_OFF_file is the path to your points cloud in OFF format.\n" << - " path_to_iso_cuboid_3_file is the path to the iso cuboid file with the following format :\n" << - " x_min y_min z_min x_max y_max z_max\n" << - " In this example, the periodic cube will be " << - "{ x = [x_min,x_max]; y = [y_min,y_max]; z = [z_min,z_max] }.\n" << - " For more information, please refer to\n" << - " https://doc.cgal.org/latest/Kernel_23/classCGAL_1_1Iso__cuboid__3.html\n"; - - exit(-1); -} - -int main(int argc, char * const argv[]) { - // program args management - if (argc != 5) { - std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n"; - usage(argv[0]); - } - - int coeff_field_characteristic = atoi(argv[3]); - Filtration_value min_persistence = strtof(argv[4], nullptr); - - // Read points from file - std::string offInputFile(argv[1]); - // Read the OFF file (input file name given as parameter) and triangulate points - Gudhi::Points_3D_off_reader off_reader(offInputFile); - // Check the read operation was correct - if (!off_reader.is_valid()) { - std::cerr << "Unable to read file " << offInputFile << std::endl; - usage(argv[0]); - } - - // Read iso_cuboid_3 information from file - std::ifstream iso_cuboid_str(argv[2]); - 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[2] << std::endl; - usage(argv[0]); - } - - // Retrieve the triangulation - std::vector lp = off_reader.get_point_cloud(); - - // Define the periodic cube - P3DT3 pdt(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) - 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(); - 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 - // Maybe need to set it to GENERAL mode - Alpha_shape_3 as(pdt, 0, Alpha_shape_3::GENERAL); - - // filtration with alpha values from alpha shape - std::vector the_objects; - std::vector the_alpha_values; - - Dispatch disp = CGAL::dispatch_output(std::back_inserter(the_objects), - std::back_inserter(the_alpha_values)); - - as.filtration_with_alpha_values(disp); -#ifdef DEBUG_TRACES - std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl; -#endif // DEBUG_TRACES - - Alpha_shape_3::size_type count_vertices = 0; - Alpha_shape_3::size_type count_edges = 0; - Alpha_shape_3::size_type count_facets = 0; - Alpha_shape_3::size_type count_cells = 0; - - // Loop on objects vector - Vertex_list vertex_list; - ST simplex_tree; - Alpha_shape_simplex_tree_map map_cgal_simplex_tree; - std::vector::iterator the_alpha_value_iterator = the_alpha_values.begin(); - int dim_max = 0; - Filtration_value filtration_max = 0.0; - for (auto object_iterator : the_objects) { - // Retrieve Alpha shape vertex list from object - if (const Cell_handle * cell = CGAL::object_cast(&object_iterator)) { - vertex_list = from_cell(*cell); - count_cells++; - if (dim_max < 3) { - // Cell is of dim 3 - dim_max = 3; - } - } else if (const Facet * facet = CGAL::object_cast(&object_iterator)) { - vertex_list = from_facet(*facet); - count_facets++; - if (dim_max < 2) { - // Facet is of dim 2 - dim_max = 2; - } - } else if (const Edge_3 * edge = CGAL::object_cast(&object_iterator)) { - vertex_list = from_edge(*edge); - count_edges++; - if (dim_max < 1) { - // Edge_3 is of dim 1 - dim_max = 1; - } - } else if (const Alpha_shape_3::Vertex_handle * vertex = - CGAL::object_cast(&object_iterator)) { - count_vertices++; - vertex_list = from_vertex(*vertex); - } - // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex - Simplex_tree_vector_vertex the_simplex_tree; - for (auto the_alpha_shape_vertex : vertex_list) { - Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex); - if (the_map_iterator == map_cgal_simplex_tree.end()) { - // alpha shape not found - Simplex_tree_vertex vertex = map_cgal_simplex_tree.size(); -#ifdef DEBUG_TRACES - std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl; -#endif // DEBUG_TRACES - the_simplex_tree.push_back(vertex); - map_cgal_simplex_tree.insert(Alpha_shape_simplex_tree_pair(the_alpha_shape_vertex, vertex)); - } else { - // alpha shape found - Simplex_tree_vertex vertex = the_map_iterator->second; -#ifdef DEBUG_TRACES - std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl; -#endif // DEBUG_TRACES - the_simplex_tree.push_back(vertex); - } - } - // Construction of the simplex_tree - Filtration_value filtr = /*std::sqrt*/(*the_alpha_value_iterator); -#ifdef DEBUG_TRACES - std::cout << "filtration = " << filtr << std::endl; -#endif // DEBUG_TRACES - if (filtr > filtration_max) { - filtration_max = filtr; - } - simplex_tree.insert_simplex(the_simplex_tree, filtr); - if (the_alpha_value_iterator != the_alpha_values.end()) - ++the_alpha_value_iterator; - else - std::cout << "This shall not happen" << std::endl; - } - simplex_tree.set_dimension(dim_max); - -#ifdef DEBUG_TRACES - std::cout << "vertices \t\t" << count_vertices << std::endl; - std::cout << "edges \t\t" << count_edges << std::endl; - std::cout << "facets \t\t" << count_facets << std::endl; - std::cout << "cells \t\t" << count_cells << std::endl; - - - std::cout << "Information of the Simplex Tree: " << std::endl; - std::cout << " Number of vertices = " << simplex_tree.num_vertices() << " "; - std::cout << " Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl; - std::cout << " Dimension = " << simplex_tree.dimension() << " "; -#endif // DEBUG_TRACES - -#ifdef DEBUG_TRACES - std::cout << "Iterator on vertices: " << std::endl; - for (auto vertex : simplex_tree.complex_vertex_range()) { - std::cout << vertex << " "; - } -#endif // DEBUG_TRACES - - // Sort the simplices in the order of the filtration - simplex_tree.initialize_filtration(); - - std::cout << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl; - // Compute the persistence diagram of the complex - Persistent_cohomology pcoh(simplex_tree, true); - // initializes the coefficient field for homology - pcoh.init_coefficients(coeff_field_characteristic); - - pcoh.compute_persistent_cohomology(min_persistence); - - pcoh.output_diagram(); - - return 0; -} diff --git a/src/Witness_complex/example/CMakeLists.txt b/src/Witness_complex/example/CMakeLists.txt index f8527e0f..a8231392 100644 --- a/src/Witness_complex/example/CMakeLists.txt +++ b/src/Witness_complex/example/CMakeLists.txt @@ -14,25 +14,22 @@ install(TARGETS Witness_complex_example_nearest_landmark_table DESTINATION bin) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) add_executable( Witness_complex_example_off example_witness_complex_off.cpp ) add_executable ( Witness_complex_example_sphere example_witness_complex_sphere.cpp ) - - add_executable ( Witness_complex_example_witness_persistence example_witness_complex_persistence.cpp ) - target_link_libraries(Witness_complex_example_witness_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY}) - - if (TBB_FOUND) - target_link_libraries(Witness_complex_example_witness_persistence ${TBB_LIBRARIES}) - endif() + + add_executable( Witness_complex_example_strong_off example_strong_witness_complex_off.cpp ) + target_link_libraries(Witness_complex_example_strong_off) add_test(NAME Witness_complex_example_off_test_torus COMMAND $ "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "20" "1.0" "3") add_test(NAME Witness_complex_example_test_sphere_10 COMMAND $ "10") - add_test(NAME Witness_complex_example_test_torus_persistence - COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-l" "20" "-a" "0.5") - + add_test(NAME Witness_complex_example_strong_off_test_torus + COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "20" "1.0" "3") + install(TARGETS Witness_complex_example_off DESTINATION bin) install(TARGETS Witness_complex_example_sphere DESTINATION bin) - install(TARGETS Witness_complex_example_witness_persistence DESTINATION bin) + install(TARGETS Witness_complex_example_strong_off DESTINATION bin) + endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) diff --git a/src/Witness_complex/example/example_strong_witness_complex_off.cpp b/src/Witness_complex/example/example_strong_witness_complex_off.cpp new file mode 100644 index 00000000..0ee9ee90 --- /dev/null +++ b/src/Witness_complex/example/example_strong_witness_complex_off.cpp @@ -0,0 +1,79 @@ +/* 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): Siargey Kachanovich + * + * 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 + +#include +#include +#include +#include +#include + +using K = CGAL::Epick_d; +using Point_d = typename K::Point_d; +using Witness_complex = Gudhi::witness_complex::Euclidean_strong_witness_complex; +using Point_vector = std::vector; + +int main(int argc, char * const argv[]) { + if (argc != 5) { + std::cerr << "Usage: " << argv[0] + << " path_to_point_file number_of_landmarks max_squared_alpha limit_dimension\n"; + return 0; + } + + std::string file_name = argv[1]; + int nbL = atoi(argv[2]), lim_dim = atoi(argv[4]); + double alpha2 = atof(argv[3]); + clock_t start, end; + Gudhi::Simplex_tree<> simplex_tree; + + // Read the point file + Point_vector point_vector, landmarks; + Gudhi::Points_off_reader off_reader(file_name); + if (!off_reader.is_valid()) { + std::cerr << "Strong witness complex - Unable to read file " << file_name << "\n"; + exit(-1); // ----- >> + } + point_vector = Point_vector(off_reader.get_point_cloud()); + + std::cout << "Successfully read " << point_vector.size() << " points.\n"; + std::cout << "Ambient dimension is " << point_vector[0].dimension() << ".\n"; + + // Choose landmarks + Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks)); + + // Compute witness complex + start = clock(); + Witness_complex witness_complex(landmarks, + point_vector); + + witness_complex.create_complex(simplex_tree, alpha2, lim_dim); + end = clock(); + std::cout << "Strong witness complex took " + << static_cast(end - start) / CLOCKS_PER_SEC << " s. \n"; + std::cout << "Number of simplices is: " << simplex_tree.num_simplices() << "\n"; +} diff --git a/src/Witness_complex/example/example_witness_complex_persistence.cpp b/src/Witness_complex/example/example_witness_complex_persistence.cpp deleted file mode 100644 index a1146922..00000000 --- a/src/Witness_complex/example/example_witness_complex_persistence.cpp +++ /dev/null @@ -1,171 +0,0 @@ -/* 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): Siargey Kachanovich - * - * 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 - -#include - -#include - -#include -#include -#include // infinity - -using K = CGAL::Epick_d; -using Point_d = K::Point_d; - -using Point_vector = std::vector; -using Witness_complex = Gudhi::witness_complex::Euclidean_witness_complex; -using SimplexTree = Gudhi::Simplex_tree<>; - -using Filtration_value = SimplexTree::Filtration_value; - -using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; -using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology; - -void program_options(int argc, char * argv[] - , int & nbL - , std::string & file_name - , std::string & filediag - , Filtration_value & max_squared_alpha - , int & p - , int & dim_max - , Filtration_value & min_persistence); - -int main(int argc, char * argv[]) { - std::string file_name; - std::string filediag; - Filtration_value max_squared_alpha; - int p, nbL, lim_d; - Filtration_value min_persistence; - SimplexTree simplex_tree; - - program_options(argc, argv, nbL, file_name, filediag, max_squared_alpha, p, lim_d, min_persistence); - - // Extract the points from the file file_name - Point_vector witnesses, landmarks; - Gudhi::Points_off_reader off_reader(file_name); - if (!off_reader.is_valid()) { - std::cerr << "Witness complex - Unable to read file " << file_name << "\n"; - exit(-1); // ----- >> - } - witnesses = Point_vector(off_reader.get_point_cloud()); - std::cout << "Successfully read " << witnesses.size() << " points.\n"; - std::cout << "Ambient dimension is " << witnesses[0].dimension() << ".\n"; - - // Choose landmarks from witnesses - Gudhi::subsampling::pick_n_random_points(witnesses, nbL, std::back_inserter(landmarks)); - - // Compute witness complex - Witness_complex witness_complex(landmarks, - witnesses); - - witness_complex.create_complex(simplex_tree, max_squared_alpha, lim_d); - - std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n"; - std::cout << " and has dimension " << simplex_tree.dimension() << " \n"; - - // Sort the simplices in the order of the filtration - simplex_tree.initialize_filtration(); - - // Compute the persistence diagram of the complex - Persistent_cohomology pcoh(simplex_tree); - // initializes the coefficient field for homology - pcoh.init_coefficients(p); - - pcoh.compute_persistent_cohomology(min_persistence); - - // Output the diagram in filediag - if (filediag.empty()) { - pcoh.output_diagram(); - } else { - std::ofstream out(filediag); - pcoh.output_diagram(out); - out.close(); - } - - return 0; -} - - -void program_options(int argc, char * argv[] - , int & nbL - , std::string & file_name - , std::string & filediag - , Filtration_value & max_squared_alpha - , int & p - , int & dim_max - , Filtration_value & min_persistence) { - namespace po = boost::program_options; - - po::options_description hidden("Hidden options"); - hidden.add_options() - ("input-file", po::value(&file_name), - "Name of file containing a point set in off format."); - - Filtration_value default_alpha = std::numeric_limits::infinity(); - po::options_description visible("Allowed options", 100); - visible.add_options() - ("help,h", "produce help message") - ("landmarks,l", po::value(&nbL), - "Number of landmarks to choose from the point cloud.") - ("output-file,o", po::value(&filediag)->default_value(std::string()), - "Name of file in which the persistence diagram is written. Default print in std::cout") - ("max-sq-alpha,a", po::value(&max_squared_alpha)->default_value(default_alpha), - "Maximal squared relaxation parameter.") - ("field-charac,p", po::value(&p)->default_value(11), - "Characteristic p of the coefficient field Z/pZ for computing homology.") - ("min-persistence,m", po::value(&min_persistence)->default_value(0), - "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals") - ("cpx-dimension,d", po::value(&dim_max)->default_value(std::numeric_limits::max()), - "Maximal dimension of the weak witness complex we want to compute."); - - po::positional_options_description pos; - pos.add("input-file", 1); - - po::options_description all; - all.add(visible).add(hidden); - po::variables_map vm; - - po::store(po::command_line_parser(argc, argv). - options(all).positional(pos).run(), vm); - po::notify(vm); - - if (vm.count("help") || !vm.count("input-file")) { - std::cout << std::endl; - std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; - std::cout << "of a Weak witness complex defined on a set of input points.\n \n"; - std::cout << "The output diagram contains one bar per line, written with the convention: \n"; - std::cout << " p dim b d \n"; - std::cout << "where dim is the dimension of the homological feature,\n"; - std::cout << "b and d are respectively the birth and death of the feature and \n"; - std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; - - std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; - std::cout << visible << std::endl; - std::abort(); - } -} diff --git a/src/Witness_complex/utilities/CMakeLists.txt b/src/Witness_complex/utilities/CMakeLists.txt index 918ab864..125a41ff 100644 --- a/src/Witness_complex/utilities/CMakeLists.txt +++ b/src/Witness_complex/utilities/CMakeLists.txt @@ -3,24 +3,26 @@ project(Witness_complex_utilities) # CGAL and Eigen3 are required for Euclidean version of Witness if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) - add_executable( Witness_complex_example_strong_off example_strong_witness_complex_off.cpp ) - target_link_libraries(Witness_complex_example_strong_off) + + add_executable ( Witness_complex_strong_witness_persistence strong_witness_persistence.cpp ) + target_link_libraries(Witness_complex_strong_witness_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY}) - add_executable ( Witness_complex_example_strong_witness_persistence example_strong_witness_persistence.cpp ) - target_link_libraries(Witness_complex_example_strong_witness_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY}) + add_executable ( Witness_complex_weak_witness_persistence weak_witness_persistence.cpp ) + target_link_libraries(Witness_complex_weak_witness_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY}) if (TBB_FOUND) - target_link_libraries(Witness_complex_example_strong_witness_persistence ${TBB_LIBRARIES}) + target_link_libraries(Witness_complex_strong_witness_persistence ${TBB_LIBRARIES}) + target_link_libraries(Witness_complex_weak_witness_persistence ${TBB_LIBRARIES}) endif() - add_test(NAME Witness_complex_example_strong_off_test_torus - COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "20" "1.0" "3") - add_test(NAME Witness_complex_example_strong_test_torus_persistence - COMMAND $ + add_test(NAME Witness_complex_strong_test_torus_persistence + COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-l" "20" "-a" "0.5") + add_test(NAME Witness_complex_weak_test_torus_persistence + COMMAND $ "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-l" "20" "-a" "0.5") - install(TARGETS Witness_complex_example_strong_off DESTINATION bin) - install(TARGETS Witness_complex_example_strong_witness_persistence DESTINATION bin) + install(TARGETS Witness_complex_strong_witness_persistence DESTINATION bin) + install(TARGETS Witness_complex_weak_witness_persistence DESTINATION bin) endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) diff --git a/src/Witness_complex/utilities/README b/src/Witness_complex/utilities/README new file mode 100644 index 00000000..d8dc9ca7 --- /dev/null +++ b/src/Witness_complex/utilities/README @@ -0,0 +1,72 @@ +# Witness_complex # + +## `weak_witness_persistence` ## +This program computes the persistent homology with coefficient field *Z/pZ* of a Weak witness complex defined on a set of input points. The output diagram contains one bar per line, written with the convention: + +`p dim b d` + +where `dim` is the dimension of the homological feature, `b` and `d` are respectively the birth and death of the feature, and `p` is the characteristic of the field *Z/pZ* used for homology coefficients. + +*Usage* +`weak_witness_persistence [options] ` + +*Allowed options* + +* `-h [ --help ]` Produce help message +* `-l [ --landmarks ]` Number of landmarks to choose from the point cloud. +* `-o [ --output-file ]` Name of file in which the persistence diagram is written. By default, print in std::cout. +* `-a [ --max-sq-alpha ]` (default = inf) Maximal squared relaxation parameter. +* `-p [ --field-charac ]` (default = 11) Characteristic p of the coefficient field Z/pZ for computing homology. +* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals. +* `-d [ --cpx-dimension ]` (default = 2147483647) Maximal dimension of the weak witness complex we want to compute. + +*Example* +`weak_witness_persistence data/points/tore3D_1307.off -l 20 -a 0.5 -m 0.006` + +outputs: +``` +Successfully read 1307 points. +Ambient dimension is 3. +The complex contains 732 simplices and has dimension 8 +11 0 0 inf +11 1 0 inf +11 2 0.0275251 0.0534586 +11 1 0 0.0239952 +``` + +N.B.: output is random as the 20 landmarks are chosen randomly. + +## `strong_witness_persistence` ## +This program computes the persistent homology with coefficient field *Z/pZ* of a Strong witness complex defined on a set of input points. The output diagram contains one bar per line, written with the convention: + +`p dim b d` + +where `dim` is the dimension of the homological feature, `b` and `d` are respectively the birth and death of the feature, and `p` is the characteristic of the field *Z/pZ* used for homology coefficients. + +*Usage* +`strong_witness_persistence [options] ` + +*Allowed options* + +* `-h [ --help ]` Produce help message +* `-l [ --landmarks ]` Number of landmarks to choose from the point cloud. +* `-o [ --output-file ]` Name of file in which the persistence diagram is written. By default, print in std::cout. +* `-a [ --max-sq-alpha ]` (default = inf) Maximal squared relaxation parameter. +* `-p [ --field-charac ]` (default = 11) Characteristic p of the coefficient field Z/pZ for computing homology. +* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals. +* `-d [ --cpx-dimension ]` (default = 2147483647) Maximal dimension of the weak witness complex we want to compute. + +*Example* +`strong_witness_persistence data/points/tore3D_1307.off -l 20 -a 0.5 -m 0.06` + +outputs: +``` +Successfully read 1307 points. +Ambient dimension is 3. +The complex contains 1836 simplices and has dimension 8 +11 0 0 inf +11 1 0.00674748 inf +11 2 0.0937751 0.235354 +``` + +N.B.: output is random as the 20 landmarks are chosen randomly. diff --git a/src/Witness_complex/utilities/example_strong_witness_complex_off.cpp b/src/Witness_complex/utilities/example_strong_witness_complex_off.cpp deleted file mode 100644 index 0ee9ee90..00000000 --- a/src/Witness_complex/utilities/example_strong_witness_complex_off.cpp +++ /dev/null @@ -1,79 +0,0 @@ -/* 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): Siargey Kachanovich - * - * 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 - -#include -#include -#include -#include -#include - -using K = CGAL::Epick_d; -using Point_d = typename K::Point_d; -using Witness_complex = Gudhi::witness_complex::Euclidean_strong_witness_complex; -using Point_vector = std::vector; - -int main(int argc, char * const argv[]) { - if (argc != 5) { - std::cerr << "Usage: " << argv[0] - << " path_to_point_file number_of_landmarks max_squared_alpha limit_dimension\n"; - return 0; - } - - std::string file_name = argv[1]; - int nbL = atoi(argv[2]), lim_dim = atoi(argv[4]); - double alpha2 = atof(argv[3]); - clock_t start, end; - Gudhi::Simplex_tree<> simplex_tree; - - // Read the point file - Point_vector point_vector, landmarks; - Gudhi::Points_off_reader off_reader(file_name); - if (!off_reader.is_valid()) { - std::cerr << "Strong witness complex - Unable to read file " << file_name << "\n"; - exit(-1); // ----- >> - } - point_vector = Point_vector(off_reader.get_point_cloud()); - - std::cout << "Successfully read " << point_vector.size() << " points.\n"; - std::cout << "Ambient dimension is " << point_vector[0].dimension() << ".\n"; - - // Choose landmarks - Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks)); - - // Compute witness complex - start = clock(); - Witness_complex witness_complex(landmarks, - point_vector); - - witness_complex.create_complex(simplex_tree, alpha2, lim_dim); - end = clock(); - std::cout << "Strong witness complex took " - << static_cast(end - start) / CLOCKS_PER_SEC << " s. \n"; - std::cout << "Number of simplices is: " << simplex_tree.num_simplices() << "\n"; -} diff --git a/src/Witness_complex/utilities/example_strong_witness_persistence.cpp b/src/Witness_complex/utilities/example_strong_witness_persistence.cpp deleted file mode 100644 index f786fe7b..00000000 --- a/src/Witness_complex/utilities/example_strong_witness_persistence.cpp +++ /dev/null @@ -1,171 +0,0 @@ -/* 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): Siargey Kachanovich - * - * 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 - -#include - -#include - -#include -#include -#include // infinity - -using K = CGAL::Epick_d; -using Point_d = K::Point_d; - -using Point_vector = std::vector; -using Strong_witness_complex = Gudhi::witness_complex::Euclidean_strong_witness_complex; -using SimplexTree = Gudhi::Simplex_tree<>; - -using Filtration_value = SimplexTree::Filtration_value; - -using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; -using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology; - -void program_options(int argc, char * argv[] - , int & nbL - , std::string & file_name - , std::string & filediag - , Filtration_value & max_squared_alpha - , int & p - , int & dim_max - , Filtration_value & min_persistence); - -int main(int argc, char * argv[]) { - std::string file_name; - std::string filediag; - Filtration_value max_squared_alpha; - int p, nbL, lim_d; - Filtration_value min_persistence; - SimplexTree simplex_tree; - - program_options(argc, argv, nbL, file_name, filediag, max_squared_alpha, p, lim_d, min_persistence); - - // Extract the points from the file file_name - Point_vector witnesses, landmarks; - Gudhi::Points_off_reader off_reader(file_name); - if (!off_reader.is_valid()) { - std::cerr << "Witness complex - Unable to read file " << file_name << "\n"; - exit(-1); // ----- >> - } - witnesses = Point_vector(off_reader.get_point_cloud()); - std::cout << "Successfully read " << witnesses.size() << " points.\n"; - std::cout << "Ambient dimension is " << witnesses[0].dimension() << ".\n"; - - // Choose landmarks from witnesses - Gudhi::subsampling::pick_n_random_points(witnesses, nbL, std::back_inserter(landmarks)); - - // Compute witness complex - Strong_witness_complex strong_witness_complex(landmarks, - witnesses); - - strong_witness_complex.create_complex(simplex_tree, max_squared_alpha, lim_d); - - std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n"; - std::cout << " and has dimension " << simplex_tree.dimension() << " \n"; - - // Sort the simplices in the order of the filtration - simplex_tree.initialize_filtration(); - - // Compute the persistence diagram of the complex - Persistent_cohomology pcoh(simplex_tree); - // initializes the coefficient field for homology - pcoh.init_coefficients(p); - - pcoh.compute_persistent_cohomology(min_persistence); - - // Output the diagram in filediag - if (filediag.empty()) { - pcoh.output_diagram(); - } else { - std::ofstream out(filediag); - pcoh.output_diagram(out); - out.close(); - } - - return 0; -} - -void program_options(int argc, char * argv[] - , int & nbL - , std::string & file_name - , std::string & filediag - , Filtration_value & max_squared_alpha - , int & p - , int & dim_max - , Filtration_value & min_persistence) { - namespace po = boost::program_options; - - po::options_description hidden("Hidden options"); - hidden.add_options() - ("input-file", po::value(&file_name), - "Name of file containing a point set in off format."); - - po::options_description visible("Allowed options", 100); - Filtration_value default_alpha = std::numeric_limits::infinity(); - visible.add_options() - ("help,h", "produce help message") - ("landmarks,l", po::value(&nbL), - "Number of landmarks to choose from the point cloud.") - ("output-file,o", po::value(&filediag)->default_value(std::string()), - "Name of file in which the persistence diagram is written. Default print in std::cout") - ("max-sq-alpha,a", po::value(&max_squared_alpha)->default_value(default_alpha), - "Maximal squared relaxation parameter.") - ("field-charac,p", po::value(&p)->default_value(11), - "Characteristic p of the coefficient field Z/pZ for computing homology.") - ("min-persistence,m", po::value(&min_persistence)->default_value(0), - "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals") - ("cpx-dimension,d", po::value(&dim_max)->default_value(std::numeric_limits::max()), - "Maximal dimension of the strong witness complex we want to compute."); - - po::positional_options_description pos; - pos.add("input-file", 1); - - po::options_description all; - all.add(visible).add(hidden); - po::variables_map vm; - - po::store(po::command_line_parser(argc, argv). - options(all).positional(pos).run(), vm); - po::notify(vm); - - if (vm.count("help") || !vm.count("input-file")) { - std::cout << std::endl; - std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; - std::cout << "of a Strong witness complex defined on a set of input points.\n \n"; - std::cout << "The output diagram contains one bar per line, written with the convention: \n"; - std::cout << " p dim b d \n"; - std::cout << "where dim is the dimension of the homological feature,\n"; - std::cout << "b and d are respectively the birth and death of the feature and \n"; - std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; - - std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; - std::cout << visible << std::endl; - std::abort(); - } -} - diff --git a/src/Witness_complex/utilities/strong_witness_persistence.cpp b/src/Witness_complex/utilities/strong_witness_persistence.cpp new file mode 100644 index 00000000..f786fe7b --- /dev/null +++ b/src/Witness_complex/utilities/strong_witness_persistence.cpp @@ -0,0 +1,171 @@ +/* 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): Siargey Kachanovich + * + * 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 + +#include + +#include + +#include +#include +#include // infinity + +using K = CGAL::Epick_d; +using Point_d = K::Point_d; + +using Point_vector = std::vector; +using Strong_witness_complex = Gudhi::witness_complex::Euclidean_strong_witness_complex; +using SimplexTree = Gudhi::Simplex_tree<>; + +using Filtration_value = SimplexTree::Filtration_value; + +using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; +using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology; + +void program_options(int argc, char * argv[] + , int & nbL + , std::string & file_name + , std::string & filediag + , Filtration_value & max_squared_alpha + , int & p + , int & dim_max + , Filtration_value & min_persistence); + +int main(int argc, char * argv[]) { + std::string file_name; + std::string filediag; + Filtration_value max_squared_alpha; + int p, nbL, lim_d; + Filtration_value min_persistence; + SimplexTree simplex_tree; + + program_options(argc, argv, nbL, file_name, filediag, max_squared_alpha, p, lim_d, min_persistence); + + // Extract the points from the file file_name + Point_vector witnesses, landmarks; + Gudhi::Points_off_reader off_reader(file_name); + if (!off_reader.is_valid()) { + std::cerr << "Witness complex - Unable to read file " << file_name << "\n"; + exit(-1); // ----- >> + } + witnesses = Point_vector(off_reader.get_point_cloud()); + std::cout << "Successfully read " << witnesses.size() << " points.\n"; + std::cout << "Ambient dimension is " << witnesses[0].dimension() << ".\n"; + + // Choose landmarks from witnesses + Gudhi::subsampling::pick_n_random_points(witnesses, nbL, std::back_inserter(landmarks)); + + // Compute witness complex + Strong_witness_complex strong_witness_complex(landmarks, + witnesses); + + strong_witness_complex.create_complex(simplex_tree, max_squared_alpha, lim_d); + + std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n"; + std::cout << " and has dimension " << simplex_tree.dimension() << " \n"; + + // Sort the simplices in the order of the filtration + simplex_tree.initialize_filtration(); + + // Compute the persistence diagram of the complex + Persistent_cohomology pcoh(simplex_tree); + // initializes the coefficient field for homology + pcoh.init_coefficients(p); + + pcoh.compute_persistent_cohomology(min_persistence); + + // Output the diagram in filediag + if (filediag.empty()) { + pcoh.output_diagram(); + } else { + std::ofstream out(filediag); + pcoh.output_diagram(out); + out.close(); + } + + return 0; +} + +void program_options(int argc, char * argv[] + , int & nbL + , std::string & file_name + , std::string & filediag + , Filtration_value & max_squared_alpha + , int & p + , int & dim_max + , Filtration_value & min_persistence) { + namespace po = boost::program_options; + + po::options_description hidden("Hidden options"); + hidden.add_options() + ("input-file", po::value(&file_name), + "Name of file containing a point set in off format."); + + po::options_description visible("Allowed options", 100); + Filtration_value default_alpha = std::numeric_limits::infinity(); + visible.add_options() + ("help,h", "produce help message") + ("landmarks,l", po::value(&nbL), + "Number of landmarks to choose from the point cloud.") + ("output-file,o", po::value(&filediag)->default_value(std::string()), + "Name of file in which the persistence diagram is written. Default print in std::cout") + ("max-sq-alpha,a", po::value(&max_squared_alpha)->default_value(default_alpha), + "Maximal squared relaxation parameter.") + ("field-charac,p", po::value(&p)->default_value(11), + "Characteristic p of the coefficient field Z/pZ for computing homology.") + ("min-persistence,m", po::value(&min_persistence)->default_value(0), + "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals") + ("cpx-dimension,d", po::value(&dim_max)->default_value(std::numeric_limits::max()), + "Maximal dimension of the strong witness complex we want to compute."); + + po::positional_options_description pos; + pos.add("input-file", 1); + + po::options_description all; + all.add(visible).add(hidden); + po::variables_map vm; + + po::store(po::command_line_parser(argc, argv). + options(all).positional(pos).run(), vm); + po::notify(vm); + + if (vm.count("help") || !vm.count("input-file")) { + std::cout << std::endl; + std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; + std::cout << "of a Strong witness complex defined on a set of input points.\n \n"; + std::cout << "The output diagram contains one bar per line, written with the convention: \n"; + std::cout << " p dim b d \n"; + std::cout << "where dim is the dimension of the homological feature,\n"; + std::cout << "b and d are respectively the birth and death of the feature and \n"; + std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; + + std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; + std::cout << visible << std::endl; + std::abort(); + } +} + diff --git a/src/Witness_complex/utilities/weak_witness_persistence.cpp b/src/Witness_complex/utilities/weak_witness_persistence.cpp new file mode 100644 index 00000000..a1146922 --- /dev/null +++ b/src/Witness_complex/utilities/weak_witness_persistence.cpp @@ -0,0 +1,171 @@ +/* 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): Siargey Kachanovich + * + * 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 + +#include + +#include + +#include +#include +#include // infinity + +using K = CGAL::Epick_d; +using Point_d = K::Point_d; + +using Point_vector = std::vector; +using Witness_complex = Gudhi::witness_complex::Euclidean_witness_complex; +using SimplexTree = Gudhi::Simplex_tree<>; + +using Filtration_value = SimplexTree::Filtration_value; + +using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; +using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology; + +void program_options(int argc, char * argv[] + , int & nbL + , std::string & file_name + , std::string & filediag + , Filtration_value & max_squared_alpha + , int & p + , int & dim_max + , Filtration_value & min_persistence); + +int main(int argc, char * argv[]) { + std::string file_name; + std::string filediag; + Filtration_value max_squared_alpha; + int p, nbL, lim_d; + Filtration_value min_persistence; + SimplexTree simplex_tree; + + program_options(argc, argv, nbL, file_name, filediag, max_squared_alpha, p, lim_d, min_persistence); + + // Extract the points from the file file_name + Point_vector witnesses, landmarks; + Gudhi::Points_off_reader off_reader(file_name); + if (!off_reader.is_valid()) { + std::cerr << "Witness complex - Unable to read file " << file_name << "\n"; + exit(-1); // ----- >> + } + witnesses = Point_vector(off_reader.get_point_cloud()); + std::cout << "Successfully read " << witnesses.size() << " points.\n"; + std::cout << "Ambient dimension is " << witnesses[0].dimension() << ".\n"; + + // Choose landmarks from witnesses + Gudhi::subsampling::pick_n_random_points(witnesses, nbL, std::back_inserter(landmarks)); + + // Compute witness complex + Witness_complex witness_complex(landmarks, + witnesses); + + witness_complex.create_complex(simplex_tree, max_squared_alpha, lim_d); + + std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n"; + std::cout << " and has dimension " << simplex_tree.dimension() << " \n"; + + // Sort the simplices in the order of the filtration + simplex_tree.initialize_filtration(); + + // Compute the persistence diagram of the complex + Persistent_cohomology pcoh(simplex_tree); + // initializes the coefficient field for homology + pcoh.init_coefficients(p); + + pcoh.compute_persistent_cohomology(min_persistence); + + // Output the diagram in filediag + if (filediag.empty()) { + pcoh.output_diagram(); + } else { + std::ofstream out(filediag); + pcoh.output_diagram(out); + out.close(); + } + + return 0; +} + + +void program_options(int argc, char * argv[] + , int & nbL + , std::string & file_name + , std::string & filediag + , Filtration_value & max_squared_alpha + , int & p + , int & dim_max + , Filtration_value & min_persistence) { + namespace po = boost::program_options; + + po::options_description hidden("Hidden options"); + hidden.add_options() + ("input-file", po::value(&file_name), + "Name of file containing a point set in off format."); + + Filtration_value default_alpha = std::numeric_limits::infinity(); + po::options_description visible("Allowed options", 100); + visible.add_options() + ("help,h", "produce help message") + ("landmarks,l", po::value(&nbL), + "Number of landmarks to choose from the point cloud.") + ("output-file,o", po::value(&filediag)->default_value(std::string()), + "Name of file in which the persistence diagram is written. Default print in std::cout") + ("max-sq-alpha,a", po::value(&max_squared_alpha)->default_value(default_alpha), + "Maximal squared relaxation parameter.") + ("field-charac,p", po::value(&p)->default_value(11), + "Characteristic p of the coefficient field Z/pZ for computing homology.") + ("min-persistence,m", po::value(&min_persistence)->default_value(0), + "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals") + ("cpx-dimension,d", po::value(&dim_max)->default_value(std::numeric_limits::max()), + "Maximal dimension of the weak witness complex we want to compute."); + + po::positional_options_description pos; + pos.add("input-file", 1); + + po::options_description all; + all.add(visible).add(hidden); + po::variables_map vm; + + po::store(po::command_line_parser(argc, argv). + options(all).positional(pos).run(), vm); + po::notify(vm); + + if (vm.count("help") || !vm.count("input-file")) { + std::cout << std::endl; + std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; + std::cout << "of a Weak witness complex defined on a set of input points.\n \n"; + std::cout << "The output diagram contains one bar per line, written with the convention: \n"; + std::cout << " p dim b d \n"; + std::cout << "where dim is the dimension of the homological feature,\n"; + std::cout << "b and d are respectively the birth and death of the feature and \n"; + std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; + + std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; + std::cout << visible << std::endl; + std::abort(); + } +} diff --git a/src/common/utilities/README b/src/common/utilities/README index dc841521..18fa8cc4 100644 --- a/src/common/utilities/README +++ b/src/common/utilities/README @@ -1,19 +1,19 @@ -======================= off_file_from_shape_generator ================================== +# Pointset generator # -Example of use : +## `off_file_from_shape_generator` ## -*** on|in sphere|cube|curve|torus|klein generator +Generates a pointset and save it in an OFF file. Command-line is: +`off_file_from_shape_generator on|in sphere|cube|curve|torus|klein ...` -./off_file_from_shape_generator on sphere onSphere.off 1000 3 15.2 +Warning: "on cube" generator is not available! - => generates a onSphere.off file with 1000 points randomized on a sphere of dimension 3 and radius 15.2 +Examples: -./off_file_from_shape_generator in sphere inSphere.off 100 2 +* Generate an onSphere.off file with 1000 points randomized on a sphere of dimension 3 and radius 15.2: +`off_file_from_shape_generator on sphere onSphere.off 1000 3 15.2` + +* Generate an inSphere.off file with 100 points randomized in a sphere of dimension 2 (circle) and radius 1.0 (default): +`off_file_from_shape_generator in sphere inSphere.off 100 2` - => generates a inSphere.off file with 100 points randomized in a sphere of dimension 2 (circle) and radius 1.0 (default) - -./off_file_from_shape_generator in cube inCube.off 10000 3 5.8 - - => generates a inCube.off file with 10000 points randomized in a cube of dimension 3 and side 5.8 - -!! Warning: hypegenerator on cube is not available !! +* Generates a inCube.off file with 10000 points randomized in a cube of dimension 3 and side 5.8: +`off_file_from_shape_generator in cube inCube.off 10000 3 5.8` -- cgit v1.2.3 From e678542b5578e32bb931605b2ea0f8ae763ec6b8 Mon Sep 17 00:00:00 2001 From: cjamin Date: Wed, 4 Oct 2017 13:12:13 +0000 Subject: Fix some CMakeLists.txt files git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/add_utils_in_gudhi_v2@2753 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: f895fab289a0c508ded97fcc5d9c8f5dd3670224 --- src/Bottleneck_distance/example/CMakeLists.txt | 12 +++++++----- src/Contraction/utilities/CMakeLists.txt | 1 + src/Persistent_cohomology/utilities/CMakeLists.txt | 2 -- 3 files changed, 8 insertions(+), 7 deletions(-) (limited to 'src/Persistent_cohomology') diff --git a/src/Bottleneck_distance/example/CMakeLists.txt b/src/Bottleneck_distance/example/CMakeLists.txt index b37555f9..6a602dbb 100644 --- a/src/Bottleneck_distance/example/CMakeLists.txt +++ b/src/Bottleneck_distance/example/CMakeLists.txt @@ -2,14 +2,16 @@ cmake_minimum_required(VERSION 2.6) project(Bottleneck_distance_examples) if (NOT CGAL_VERSION VERSION_LESS 4.8.1) - add_executable (bottleneck_read_file_example bottleneck_read_file_example.cpp) add_executable (bottleneck_basic_example bottleneck_basic_example.cpp) + add_executable (bottleneck_read_file_example bottleneck_read_file_example.cpp) add_test(NAME Bottleneck_distance_example_basic COMMAND $) + add_test(NAME Bottleneck_read_file_example + COMMAND $ + "${CMAKE_SOURCE_DIR}/data/persistence_diagram/first.pers" "${CMAKE_SOURCE_DIR}/data/persistence_diagram/second.pers") + install(TARGETS bottleneck_read_file_example DESTINATION bin) install(TARGETS bottleneck_basic_example DESTINATION bin) - if (TBB_FOUND) - target_link_libraries(alpha_rips_persistence_bottleneck_distance ${TBB_LIBRARIES}) - endif(TBB_FOUND) -endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) + +endif (NOT CGAL_VERSION VERSION_LESS 4.8.1) diff --git a/src/Contraction/utilities/CMakeLists.txt b/src/Contraction/utilities/CMakeLists.txt index a18783ef..36efd99a 100644 --- a/src/Contraction/utilities/CMakeLists.txt +++ b/src/Contraction/utilities/CMakeLists.txt @@ -2,5 +2,6 @@ cmake_minimum_required(VERSION 2.6) project(Contraction_utilities) add_executable(GarlandHeckbert Garland_heckbert.cpp) +target_link_libraries(GarlandHeckbert ${Boost_TIMER_LIBRARY}) install(TARGETS GarlandHeckbert DESTINATION bin) diff --git a/src/Persistent_cohomology/utilities/CMakeLists.txt b/src/Persistent_cohomology/utilities/CMakeLists.txt index 5b315801..9a506b3f 100644 --- a/src/Persistent_cohomology/utilities/CMakeLists.txt +++ b/src/Persistent_cohomology/utilities/CMakeLists.txt @@ -19,5 +19,3 @@ add_test(NAME Persistent_cohomology_example_from_rips_on_tore_3D COMMAND $ Date: Thu, 5 Oct 2017 08:26:50 +0000 Subject: Move some utils + update doc so that utilities are shown as examples git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/add_utils_in_gudhi_v2@2756 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: a707d174a382da7efad3d12a73bb66d2c90da599 --- src/Doxyfile | 3 +- .../doc/Intro_persistent_cohomology.h | 20 +-- src/Persistent_cohomology/utilities/CMakeLists.txt | 21 --- src/Persistent_cohomology/utilities/README | 66 --------- .../utilities/rips_distance_matrix_persistence.cpp | 144 -------------------- .../utilities/rips_persistence.cpp | 147 --------------------- src/Rips_complex/utilities/CMakeLists.txt | 21 +++ src/Rips_complex/utilities/README | 66 +++++++++ .../utilities/rips_distance_matrix_persistence.cpp | 144 ++++++++++++++++++++ src/Rips_complex/utilities/rips_persistence.cpp | 147 +++++++++++++++++++++ src/common/doc/main_page.h | 54 ++++---- 11 files changed, 415 insertions(+), 418 deletions(-) delete mode 100644 src/Persistent_cohomology/utilities/CMakeLists.txt delete mode 100644 src/Persistent_cohomology/utilities/README delete mode 100644 src/Persistent_cohomology/utilities/rips_distance_matrix_persistence.cpp delete mode 100644 src/Persistent_cohomology/utilities/rips_persistence.cpp create mode 100644 src/Rips_complex/utilities/CMakeLists.txt create mode 100644 src/Rips_complex/utilities/README create mode 100644 src/Rips_complex/utilities/rips_distance_matrix_persistence.cpp create mode 100644 src/Rips_complex/utilities/rips_persistence.cpp (limited to 'src/Persistent_cohomology') diff --git a/src/Doxyfile b/src/Doxyfile index 7f5975eb..7b506e42 100644 --- a/src/Doxyfile +++ b/src/Doxyfile @@ -819,7 +819,8 @@ EXCLUDE_SYMBOLS = # command). EXAMPLE_PATH = biblio/ \ - example/ + example/ \ + utilities/ # If the value of the EXAMPLE_PATH tag contains directories, you can use the # EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and diff --git a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h index e17e5926..576a1af8 100644 --- a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h +++ b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h @@ -143,8 +143,8 @@ namespace persistent_cohomology { We provide several example files: run these examples with -h for details on their use, and read the README file. -\li -Persistent_cohomology/rips_persistence.cpp computes the Rips complex of a point cloud and outputs its persistence +\li +Rips_complex/rips_persistence.cpp computes the Rips complex of a point cloud and outputs its persistence diagram. \code $> ./rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 3 \endcode \code The complex contains 177838 simplices @@ -158,12 +158,12 @@ diagram. Persistent_cohomology/rips_multifield_persistence.cpp computes the Rips complex of a point cloud and outputs its persistence diagram with a family of field coefficients. -\li -Persistent_cohomology/rips_distance_matrix_persistence.cpp computes the Rips complex of a distance matrix and +\li +Rips_complex/rips_distance_matrix_persistence.cpp computes the Rips complex of a distance matrix and outputs its persistence diagram. -\li -Persistent_cohomology/alpha_complex_3d_persistence.cpp computes the persistent homology with +\li +Alpha_complex/alpha_complex_3d_persistence.cpp computes the persistent homology with \f$\mathbb{Z}/2\mathbb{Z}\f$ coefficients of the alpha complex on points sampling from an OFF file. \code $> ./alpha_complex_3d_persistence ../../data/points/tore3D_300.off 2 0.45 \endcode \code Simplex_tree dim: 3 @@ -194,8 +194,8 @@ and a weights file. 2 1 0.0934117 1.00003 2 2 0.56444 1.03938 \endcode -\li -Persistent_cohomology/alpha_complex_persistence.cpp computes the persistent homology with +\li +Alpha_complex/alpha_complex_persistence.cpp computes the persistent homology with \f$\mathbb{Z}/p\mathbb{Z}\f$ coefficients of the alpha complex on points sampling from an OFF file. \code $> ./alpha_complex_persistence -r 32 -p 2 -m 0.45 ../../data/points/tore3D_300.off \endcode \code Alpha complex is of dimension 3 - 9273 simplices - 300 vertices. @@ -205,8 +205,8 @@ Simplex_tree dim: 3 2 1 0.0934117 1.00003 2 2 0.56444 1.03938 \endcode -\li -Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp computes the persistent homology with +\li +Alpha_complex/periodic_alpha_complex_3d_persistence.cpp computes the persistent homology with \f$\mathbb{Z}/2\mathbb{Z}\f$ coefficients of the periodic alpha complex on points sampling from an OFF file. \code $> ./periodic_alpha_complex_3d_persistence ../../data/points/grid_10_10_10_in_0_1.off 3 1.0 \endcode \code Periodic Delaunay computed. diff --git a/src/Persistent_cohomology/utilities/CMakeLists.txt b/src/Persistent_cohomology/utilities/CMakeLists.txt deleted file mode 100644 index 9a506b3f..00000000 --- a/src/Persistent_cohomology/utilities/CMakeLists.txt +++ /dev/null @@ -1,21 +0,0 @@ -cmake_minimum_required(VERSION 2.6) -project(Persistent_cohomology_utilities) - -add_executable(rips_distance_matrix_persistence rips_distance_matrix_persistence.cpp) -target_link_libraries(rips_distance_matrix_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY}) - -add_executable(rips_persistence rips_persistence.cpp) -target_link_libraries(rips_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY}) - -if (TBB_FOUND) - target_link_libraries(rips_distance_matrix_persistence ${TBB_LIBRARIES}) - target_link_libraries(rips_persistence ${TBB_LIBRARIES}) -endif() - -add_test(NAME Persistent_cohomology_example_from_rips_distance_matrix COMMAND $ - "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" "-r" "1.0" "-d" "3" "-p" "3" "-m" "0") -add_test(NAME Persistent_cohomology_example_from_rips_on_tore_3D COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3") - -install(TARGETS rips_distance_matrix_persistence DESTINATION bin) -install(TARGETS rips_persistence DESTINATION bin) diff --git a/src/Persistent_cohomology/utilities/README b/src/Persistent_cohomology/utilities/README deleted file mode 100644 index eecee7ee..00000000 --- a/src/Persistent_cohomology/utilities/README +++ /dev/null @@ -1,66 +0,0 @@ -# Persistent_cohomology # - -## `rips_persistence` ## -This program computes the persistent homology with coefficient field *Z/pZ* of a Rips complex defined on a set of input points. The output diagram contains one bar per line, written with the convention: - -`p dim b d` - -where `dim` is the dimension of the homological feature, `b` and `d` are respectively the birth and death of the feature, and `p` is the characteristic of the field *Z/pZ* used for homology coefficients (`p = p1*...*pr` is the product of prime numbers *pi* such that the homology feature exists in homology with *Z/piZ* coefficients). - -**Usage** -`rips_persistence [options] ` - -**Allowed options** - -* `-h [ --help ]` Produce help message -* `-r [ --max-edge-length ]` (default = inf) Maximal length of an edge for the Rips complex construction. -* `-d [ --cpx-dimension ]` (default = 1) Maximal dimension of the Rips complex we want to compute. -* `-p [ --field-charac ]` (default = 11) Characteristic p of the coefficient field Z/pZ for computing homology. -* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals. - -**Example 1 with Z/2Z coefficients** -`rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 2` - -outputs: -``` -2 0 0 inf -2 1 0.0983494 inf -2 1 0.104347 inf -2 2 0.138335 inf -``` - -**Example 2 with Z/3Z coefficients** - -rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 3 - -outputs: -``` -3 0 0 inf -3 1 0.0983494 inf -3 1 0.104347 inf -3 2 0.138335 inf -``` - - - - -## `rips_distance_matrix_persistence` ## -Same as `rips_persistence` but taking an distance matrix as input. - -**Example** -`rips_distance_matrix_persistence data/distance_matrix/full_square_distance_matrix.csv -r 15 -d 3 -p 3 -m 0` - -outputs: -``` -The complex contains 46 simplices - and has dimension 3 -3 0 0 inf -3 0 0 8.94427 -3 0 0 7.28011 -3 0 0 6.08276 -3 0 0 5.83095 -3 0 0 5.38516 -3 0 0 5 -3 1 11 12.0416 -3 1 6.32456 6.7082 -``` diff --git a/src/Persistent_cohomology/utilities/rips_distance_matrix_persistence.cpp b/src/Persistent_cohomology/utilities/rips_distance_matrix_persistence.cpp deleted file mode 100644 index d38808c7..00000000 --- a/src/Persistent_cohomology/utilities/rips_distance_matrix_persistence.cpp +++ /dev/null @@ -1,144 +0,0 @@ -/* 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, Vincent Rouvreau - * - * Copyright (C) 2016 INRIA - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - -#include -#include -#include -#include - -#include - -#include -#include -#include // infinity - -// Types definition -using Simplex_tree = Gudhi::Simplex_tree; -using Filtration_value = Simplex_tree::Filtration_value; -using Rips_complex = Gudhi::rips_complex::Rips_complex; -using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; -using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology; -using Distance_matrix = std::vector>; - -void program_options(int argc, char * argv[] - , std::string & csv_matrix_file - , std::string & filediag - , Filtration_value & threshold - , int & dim_max - , int & p - , Filtration_value & min_persistence); - -int main(int argc, char * argv[]) { - std::string csv_matrix_file; - std::string filediag; - Filtration_value threshold; - int dim_max; - int p; - Filtration_value min_persistence; - - program_options(argc, argv, csv_matrix_file, filediag, threshold, dim_max, p, min_persistence); - - Distance_matrix distances = Gudhi::read_lower_triangular_matrix_from_csv_file(csv_matrix_file); - Rips_complex rips_complex_from_file(distances, threshold); - - // Construct the Rips complex in a Simplex Tree - Simplex_tree simplex_tree; - - rips_complex_from_file.create_complex(simplex_tree, dim_max); - std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n"; - std::cout << " and has dimension " << simplex_tree.dimension() << " \n"; - - // Sort the simplices in the order of the filtration - simplex_tree.initialize_filtration(); - - // Compute the persistence diagram of the complex - Persistent_cohomology pcoh(simplex_tree); - // initializes the coefficient field for homology - pcoh.init_coefficients(p); - - pcoh.compute_persistent_cohomology(min_persistence); - - // Output the diagram in filediag - if (filediag.empty()) { - pcoh.output_diagram(); - } else { - std::ofstream out(filediag); - pcoh.output_diagram(out); - out.close(); - } - return 0; -} - -void program_options(int argc, char * argv[] - , std::string & csv_matrix_file - , std::string & filediag - , Filtration_value & threshold - , int & dim_max - , int & p - , Filtration_value & min_persistence) { - namespace po = boost::program_options; - po::options_description hidden("Hidden options"); - hidden.add_options() - ("input-file", po::value(&csv_matrix_file), - "Name of file containing a distance matrix. Can be square or lower triangular matrix. Separator is ';'."); - - po::options_description visible("Allowed options", 100); - visible.add_options() - ("help,h", "produce help message") - ("output-file,o", po::value(&filediag)->default_value(std::string()), - "Name of file in which the persistence diagram is written. Default print in std::cout") - ("max-edge-length,r", - po::value(&threshold)->default_value(std::numeric_limits::infinity()), - "Maximal length of an edge for the Rips complex construction.") - ("cpx-dimension,d", po::value(&dim_max)->default_value(1), - "Maximal dimension of the Rips complex we want to compute.") - ("field-charac,p", po::value(&p)->default_value(11), - "Characteristic p of the coefficient field Z/pZ for computing homology.") - ("min-persistence,m", po::value(&min_persistence), - "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals"); - - po::positional_options_description pos; - pos.add("input-file", 1); - - po::options_description all; - all.add(visible).add(hidden); - - po::variables_map vm; - po::store(po::command_line_parser(argc, argv). - options(all).positional(pos).run(), vm); - po::notify(vm); - - if (vm.count("help") || !vm.count("input-file")) { - std::cout << std::endl; - std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; - std::cout << "of a Rips complex defined on a set of distance matrix.\n \n"; - std::cout << "The output diagram contains one bar per line, written with the convention: \n"; - std::cout << " p dim b d \n"; - std::cout << "where dim is the dimension of the homological feature,\n"; - std::cout << "b and d are respectively the birth and death of the feature and \n"; - std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; - - std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; - std::cout << visible << std::endl; - std::abort(); - } -} diff --git a/src/Persistent_cohomology/utilities/rips_persistence.cpp b/src/Persistent_cohomology/utilities/rips_persistence.cpp deleted file mode 100644 index d504798b..00000000 --- a/src/Persistent_cohomology/utilities/rips_persistence.cpp +++ /dev/null @@ -1,147 +0,0 @@ -/* 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): Clément Maria - * - * 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 - * 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 - -#include - -#include -#include -#include // infinity - -// Types definition -using Simplex_tree = Gudhi::Simplex_tree; -using Filtration_value = Simplex_tree::Filtration_value; -using Rips_complex = Gudhi::rips_complex::Rips_complex; -using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; -using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology; -using Point = std::vector; -using Points_off_reader = Gudhi::Points_off_reader; - -void program_options(int argc, char * argv[] - , std::string & off_file_points - , std::string & filediag - , Filtration_value & threshold - , int & dim_max - , int & p - , Filtration_value & min_persistence); - -int main(int argc, char * argv[]) { - std::string off_file_points; - std::string filediag; - Filtration_value threshold; - int dim_max; - int p; - Filtration_value min_persistence; - - program_options(argc, argv, off_file_points, filediag, threshold, dim_max, p, min_persistence); - - Points_off_reader off_reader(off_file_points); - Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold, Gudhi::Euclidean_distance()); - - // Construct the Rips complex in a Simplex Tree - Simplex_tree simplex_tree; - - rips_complex_from_file.create_complex(simplex_tree, dim_max); - std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n"; - std::cout << " and has dimension " << simplex_tree.dimension() << " \n"; - - // Sort the simplices in the order of the filtration - simplex_tree.initialize_filtration(); - - // Compute the persistence diagram of the complex - Persistent_cohomology pcoh(simplex_tree); - // initializes the coefficient field for homology - pcoh.init_coefficients(p); - - pcoh.compute_persistent_cohomology(min_persistence); - - // Output the diagram in filediag - if (filediag.empty()) { - pcoh.output_diagram(); - } else { - std::ofstream out(filediag); - pcoh.output_diagram(out); - out.close(); - } - - return 0; -} - -void program_options(int argc, char * argv[] - , std::string & off_file_points - , std::string & filediag - , Filtration_value & threshold - , int & dim_max - , int & p - , Filtration_value & min_persistence) { - namespace po = boost::program_options; - po::options_description hidden("Hidden options"); - hidden.add_options() - ("input-file", po::value(&off_file_points), - "Name of an OFF file containing a point set.\n"); - - po::options_description visible("Allowed options", 100); - visible.add_options() - ("help,h", "produce help message") - ("output-file,o", po::value(&filediag)->default_value(std::string()), - "Name of file in which the persistence diagram is written. Default print in std::cout") - ("max-edge-length,r", - po::value(&threshold)->default_value(std::numeric_limits::infinity()), - "Maximal length of an edge for the Rips complex construction.") - ("cpx-dimension,d", po::value(&dim_max)->default_value(1), - "Maximal dimension of the Rips complex we want to compute.") - ("field-charac,p", po::value(&p)->default_value(11), - "Characteristic p of the coefficient field Z/pZ for computing homology.") - ("min-persistence,m", po::value(&min_persistence), - "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals"); - - po::positional_options_description pos; - pos.add("input-file", 1); - - po::options_description all; - all.add(visible).add(hidden); - - po::variables_map vm; - po::store(po::command_line_parser(argc, argv). - options(all).positional(pos).run(), vm); - po::notify(vm); - - if (vm.count("help") || !vm.count("input-file")) { - std::cout << std::endl; - std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; - std::cout << "of a Rips complex defined on a set of input points.\n \n"; - std::cout << "The output diagram contains one bar per line, written with the convention: \n"; - std::cout << " p dim b d \n"; - std::cout << "where dim is the dimension of the homological feature,\n"; - std::cout << "b and d are respectively the birth and death of the feature and \n"; - std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; - - std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; - std::cout << visible << std::endl; - std::abort(); - } -} diff --git a/src/Rips_complex/utilities/CMakeLists.txt b/src/Rips_complex/utilities/CMakeLists.txt new file mode 100644 index 00000000..baa571fa --- /dev/null +++ b/src/Rips_complex/utilities/CMakeLists.txt @@ -0,0 +1,21 @@ +cmake_minimum_required(VERSION 2.6) +project(Rips_complex_utilities) + +add_executable(rips_distance_matrix_persistence rips_distance_matrix_persistence.cpp) +target_link_libraries(rips_distance_matrix_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY}) + +add_executable(rips_persistence rips_persistence.cpp) +target_link_libraries(rips_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY}) + +if (TBB_FOUND) + target_link_libraries(rips_distance_matrix_persistence ${TBB_LIBRARIES}) + target_link_libraries(rips_persistence ${TBB_LIBRARIES}) +endif() + +add_test(NAME Rips_complex_utility_from_rips_distance_matrix COMMAND $ + "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" "-r" "1.0" "-d" "3" "-p" "3" "-m" "0") +add_test(NAME Rips_complex_utility_from_rips_on_tore_3D COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3") + +install(TARGETS rips_distance_matrix_persistence DESTINATION bin) +install(TARGETS rips_persistence DESTINATION bin) diff --git a/src/Rips_complex/utilities/README b/src/Rips_complex/utilities/README new file mode 100644 index 00000000..ddb7860f --- /dev/null +++ b/src/Rips_complex/utilities/README @@ -0,0 +1,66 @@ +# Rips_complex # + +## `rips_persistence` ## +This program computes the persistent homology with coefficient field *Z/pZ* of a Rips complex defined on a set of input points. The output diagram contains one bar per line, written with the convention: + +`p dim b d` + +where `dim` is the dimension of the homological feature, `b` and `d` are respectively the birth and death of the feature, and `p` is the characteristic of the field *Z/pZ* used for homology coefficients (`p = p1*...*pr` is the product of prime numbers *pi* such that the homology feature exists in homology with *Z/piZ* coefficients). + +**Usage** +`rips_persistence [options] ` + +**Allowed options** + +* `-h [ --help ]` Produce help message +* `-r [ --max-edge-length ]` (default = inf) Maximal length of an edge for the Rips complex construction. +* `-d [ --cpx-dimension ]` (default = 1) Maximal dimension of the Rips complex we want to compute. +* `-p [ --field-charac ]` (default = 11) Characteristic p of the coefficient field Z/pZ for computing homology. +* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals. + +**Example 1 with Z/2Z coefficients** +`rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 2` + +outputs: +``` +2 0 0 inf +2 1 0.0983494 inf +2 1 0.104347 inf +2 2 0.138335 inf +``` + +**Example 2 with Z/3Z coefficients** + +rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 3 + +outputs: +``` +3 0 0 inf +3 1 0.0983494 inf +3 1 0.104347 inf +3 2 0.138335 inf +``` + + + + +## `rips_distance_matrix_persistence` ## +Same as `rips_persistence` but taking an distance matrix as input. + +**Example** +`rips_distance_matrix_persistence data/distance_matrix/full_square_distance_matrix.csv -r 15 -d 3 -p 3 -m 0` + +outputs: +``` +The complex contains 46 simplices + and has dimension 3 +3 0 0 inf +3 0 0 8.94427 +3 0 0 7.28011 +3 0 0 6.08276 +3 0 0 5.83095 +3 0 0 5.38516 +3 0 0 5 +3 1 11 12.0416 +3 1 6.32456 6.7082 +``` diff --git a/src/Rips_complex/utilities/rips_distance_matrix_persistence.cpp b/src/Rips_complex/utilities/rips_distance_matrix_persistence.cpp new file mode 100644 index 00000000..d38808c7 --- /dev/null +++ b/src/Rips_complex/utilities/rips_distance_matrix_persistence.cpp @@ -0,0 +1,144 @@ +/* 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, Vincent Rouvreau + * + * Copyright (C) 2016 INRIA + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +#include +#include +#include +#include + +#include + +#include +#include +#include // infinity + +// Types definition +using Simplex_tree = Gudhi::Simplex_tree; +using Filtration_value = Simplex_tree::Filtration_value; +using Rips_complex = Gudhi::rips_complex::Rips_complex; +using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; +using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology; +using Distance_matrix = std::vector>; + +void program_options(int argc, char * argv[] + , std::string & csv_matrix_file + , std::string & filediag + , Filtration_value & threshold + , int & dim_max + , int & p + , Filtration_value & min_persistence); + +int main(int argc, char * argv[]) { + std::string csv_matrix_file; + std::string filediag; + Filtration_value threshold; + int dim_max; + int p; + Filtration_value min_persistence; + + program_options(argc, argv, csv_matrix_file, filediag, threshold, dim_max, p, min_persistence); + + Distance_matrix distances = Gudhi::read_lower_triangular_matrix_from_csv_file(csv_matrix_file); + Rips_complex rips_complex_from_file(distances, threshold); + + // Construct the Rips complex in a Simplex Tree + Simplex_tree simplex_tree; + + rips_complex_from_file.create_complex(simplex_tree, dim_max); + std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n"; + std::cout << " and has dimension " << simplex_tree.dimension() << " \n"; + + // Sort the simplices in the order of the filtration + simplex_tree.initialize_filtration(); + + // Compute the persistence diagram of the complex + Persistent_cohomology pcoh(simplex_tree); + // initializes the coefficient field for homology + pcoh.init_coefficients(p); + + pcoh.compute_persistent_cohomology(min_persistence); + + // Output the diagram in filediag + if (filediag.empty()) { + pcoh.output_diagram(); + } else { + std::ofstream out(filediag); + pcoh.output_diagram(out); + out.close(); + } + return 0; +} + +void program_options(int argc, char * argv[] + , std::string & csv_matrix_file + , std::string & filediag + , Filtration_value & threshold + , int & dim_max + , int & p + , Filtration_value & min_persistence) { + namespace po = boost::program_options; + po::options_description hidden("Hidden options"); + hidden.add_options() + ("input-file", po::value(&csv_matrix_file), + "Name of file containing a distance matrix. Can be square or lower triangular matrix. Separator is ';'."); + + po::options_description visible("Allowed options", 100); + visible.add_options() + ("help,h", "produce help message") + ("output-file,o", po::value(&filediag)->default_value(std::string()), + "Name of file in which the persistence diagram is written. Default print in std::cout") + ("max-edge-length,r", + po::value(&threshold)->default_value(std::numeric_limits::infinity()), + "Maximal length of an edge for the Rips complex construction.") + ("cpx-dimension,d", po::value(&dim_max)->default_value(1), + "Maximal dimension of the Rips complex we want to compute.") + ("field-charac,p", po::value(&p)->default_value(11), + "Characteristic p of the coefficient field Z/pZ for computing homology.") + ("min-persistence,m", po::value(&min_persistence), + "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals"); + + po::positional_options_description pos; + pos.add("input-file", 1); + + po::options_description all; + all.add(visible).add(hidden); + + po::variables_map vm; + po::store(po::command_line_parser(argc, argv). + options(all).positional(pos).run(), vm); + po::notify(vm); + + if (vm.count("help") || !vm.count("input-file")) { + std::cout << std::endl; + std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; + std::cout << "of a Rips complex defined on a set of distance matrix.\n \n"; + std::cout << "The output diagram contains one bar per line, written with the convention: \n"; + std::cout << " p dim b d \n"; + std::cout << "where dim is the dimension of the homological feature,\n"; + std::cout << "b and d are respectively the birth and death of the feature and \n"; + std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; + + std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; + std::cout << visible << std::endl; + std::abort(); + } +} diff --git a/src/Rips_complex/utilities/rips_persistence.cpp b/src/Rips_complex/utilities/rips_persistence.cpp new file mode 100644 index 00000000..d504798b --- /dev/null +++ b/src/Rips_complex/utilities/rips_persistence.cpp @@ -0,0 +1,147 @@ +/* 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): Clément Maria + * + * 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 + * 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 + +#include + +#include +#include +#include // infinity + +// Types definition +using Simplex_tree = Gudhi::Simplex_tree; +using Filtration_value = Simplex_tree::Filtration_value; +using Rips_complex = Gudhi::rips_complex::Rips_complex; +using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; +using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology; +using Point = std::vector; +using Points_off_reader = Gudhi::Points_off_reader; + +void program_options(int argc, char * argv[] + , std::string & off_file_points + , std::string & filediag + , Filtration_value & threshold + , int & dim_max + , int & p + , Filtration_value & min_persistence); + +int main(int argc, char * argv[]) { + std::string off_file_points; + std::string filediag; + Filtration_value threshold; + int dim_max; + int p; + Filtration_value min_persistence; + + program_options(argc, argv, off_file_points, filediag, threshold, dim_max, p, min_persistence); + + Points_off_reader off_reader(off_file_points); + Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold, Gudhi::Euclidean_distance()); + + // Construct the Rips complex in a Simplex Tree + Simplex_tree simplex_tree; + + rips_complex_from_file.create_complex(simplex_tree, dim_max); + std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n"; + std::cout << " and has dimension " << simplex_tree.dimension() << " \n"; + + // Sort the simplices in the order of the filtration + simplex_tree.initialize_filtration(); + + // Compute the persistence diagram of the complex + Persistent_cohomology pcoh(simplex_tree); + // initializes the coefficient field for homology + pcoh.init_coefficients(p); + + pcoh.compute_persistent_cohomology(min_persistence); + + // Output the diagram in filediag + if (filediag.empty()) { + pcoh.output_diagram(); + } else { + std::ofstream out(filediag); + pcoh.output_diagram(out); + out.close(); + } + + return 0; +} + +void program_options(int argc, char * argv[] + , std::string & off_file_points + , std::string & filediag + , Filtration_value & threshold + , int & dim_max + , int & p + , Filtration_value & min_persistence) { + namespace po = boost::program_options; + po::options_description hidden("Hidden options"); + hidden.add_options() + ("input-file", po::value(&off_file_points), + "Name of an OFF file containing a point set.\n"); + + po::options_description visible("Allowed options", 100); + visible.add_options() + ("help,h", "produce help message") + ("output-file,o", po::value(&filediag)->default_value(std::string()), + "Name of file in which the persistence diagram is written. Default print in std::cout") + ("max-edge-length,r", + po::value(&threshold)->default_value(std::numeric_limits::infinity()), + "Maximal length of an edge for the Rips complex construction.") + ("cpx-dimension,d", po::value(&dim_max)->default_value(1), + "Maximal dimension of the Rips complex we want to compute.") + ("field-charac,p", po::value(&p)->default_value(11), + "Characteristic p of the coefficient field Z/pZ for computing homology.") + ("min-persistence,m", po::value(&min_persistence), + "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals"); + + po::positional_options_description pos; + pos.add("input-file", 1); + + po::options_description all; + all.add(visible).add(hidden); + + po::variables_map vm; + po::store(po::command_line_parser(argc, argv). + options(all).positional(pos).run(), vm); + po::notify(vm); + + if (vm.count("help") || !vm.count("input-file")) { + std::cout << std::endl; + std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; + std::cout << "of a Rips complex defined on a set of input points.\n \n"; + std::cout << "The output diagram contains one bar per line, written with the convention: \n"; + std::cout << " p dim b d \n"; + std::cout << "where dim is the dimension of the homological feature,\n"; + std::cout << "b and d are respectively the birth and death of the feature and \n"; + std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; + + std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; + std::cout << visible << std::endl; + std::abort(); + } +} diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h index cee0c28b..466236ad 100644 --- a/src/common/doc/main_page.h +++ b/src/common/doc/main_page.h @@ -271,8 +271,8 @@ make doxygen * * The following examples/utilities require the Computational Geometry Algorithms * Library (CGAL \cite cgal:eb-15b) and will not be built if CGAL is not installed: - * \li - * Persistent_cohomology/alpha_complex_3d_persistence.cpp + * \li + * Alpha_complex/alpha_complex_3d_persistence.cpp * \li * Persistent_cohomology/exact_alpha_complex_3d_persistence.cpp * \li @@ -289,10 +289,10 @@ make doxygen * Alpha_complex/Alpha_complex_from_off.cpp * \li * Alpha_complex/Alpha_complex_from_points.cpp - * \li - * Persistent_cohomology/alpha_complex_persistence.cpp - * \li - * Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp + * \li + * Alpha_complex/alpha_complex_persistence.cpp + * \li + * Alpha_complex/periodic_alpha_complex_3d_persistence.cpp * \li * Persistent_cohomology/custom_persistence_sort.cpp * @@ -329,12 +329,12 @@ make doxygen * Alpha_complex/Alpha_complex_from_off.cpp * \li * Alpha_complex/Alpha_complex_from_points.cpp + * \li + * Alpha_complex/alpha_complex_persistence.cpp + * \li + * Alpha_complex/periodic_alpha_complex_3d_persistence.cpp * \li * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp - * \li - * Persistent_cohomology/alpha_complex_persistence.cpp - * \li - * Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp * \li * Persistent_cohomology/custom_persistence_sort.cpp * \li @@ -364,26 +364,24 @@ make doxygen * Alpha_complex/Alpha_complex_from_off.cpp * \li * Alpha_complex/Alpha_complex_from_points.cpp + * \li + * Alpha_complex/alpha_complex_3d_persistence.cpp + * \li + * Alpha_complex/alpha_complex_persistence.cpp + * \li + * Alpha_complex/periodic_alpha_complex_3d_persistence.cpp * \li * Bitmap_cubical_complex/Bitmap_cubical_complex.cpp * \li * Bitmap_cubical_complex/Bitmap_cubical_complex_periodic_boundary_conditions.cpp * \li * Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp - * \li - * Persistent_cohomology/alpha_complex_3d_persistence.cpp - * \li - * Persistent_cohomology/alpha_complex_persistence.cpp * \li * Simplex_tree/simple_simplex_tree.cpp * \li * Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp * \li * Simplex_tree/simplex_tree_from_cliques_of_graph.cpp - * \li - * Persistent_cohomology/alpha_complex_3d_persistence.cpp - * \li - * Persistent_cohomology/alpha_complex_persistence.cpp * \li * Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp * \li @@ -392,26 +390,24 @@ make doxygen * Persistent_cohomology/persistence_from_simple_simplex_tree.cpp * \li * Persistent_cohomology/plain_homology.cpp - * \li - * Persistent_cohomology/rips_distance_matrix_persistence.cpp * \li * Persistent_cohomology/rips_multifield_persistence.cpp - * \li - * Persistent_cohomology/rips_persistence.cpp * \li * Persistent_cohomology/rips_persistence_step_by_step.cpp * \li * Persistent_cohomology/exact_alpha_complex_3d_persistence.cpp * \li * Persistent_cohomology/weighted_alpha_complex_3d_persistence.cpp - * \li - * Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp * \li * Persistent_cohomology/custom_persistence_sort.cpp * \li * Rips_complex/example_one_skeleton_rips_from_points.cpp * \li * Rips_complex/example_rips_complex_from_off_file.cpp + * \li + * Rips_complex/rips_distance_matrix_persistence.cpp + * \li + * Rips_complex/rips_persistence.cpp * * \section Contributions Bug reports and contributions * Please help us improving the quality of the GUDHI library. You may report bugs or suggestions to: @@ -436,6 +432,9 @@ make doxygen /*! @file Examples * @example Alpha_complex/Alpha_complex_from_off.cpp * @example Alpha_complex/Alpha_complex_from_points.cpp + * @example Alpha_complex/alpha_complex_3d_persistence.cpp + * @example Alpha_complex/alpha_complex_persistence.cpp + * @example Alpha_complex/periodic_alpha_complex_3d_persistence.cpp * @example Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp * @example Bottleneck_distance/bottleneck_basic_example.cpp * @example Bottleneck_distance/bottleneck_read_file_example.cpp @@ -446,22 +445,19 @@ make doxygen * @example common/example_CGAL_points_off_reader.cpp * @example Contraction/Garland_heckbert.cpp * @example Contraction/Rips_contraction.cpp - * @example Persistent_cohomology/alpha_complex_3d_persistence.cpp - * @example Persistent_cohomology/alpha_complex_persistence.cpp * @example Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp * @example Persistent_cohomology/exact_alpha_complex_3d_persistence.cpp * @example Persistent_cohomology/weighted_alpha_complex_3d_persistence.cpp - * @example Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp * @example Persistent_cohomology/persistence_from_file.cpp * @example Persistent_cohomology/persistence_from_simple_simplex_tree.cpp * @example Persistent_cohomology/plain_homology.cpp * @example Persistent_cohomology/rips_multifield_persistence.cpp - * @example Persistent_cohomology/rips_distance_matrix_persistence.cpp - * @example Persistent_cohomology/rips_persistence.cpp * @example Persistent_cohomology/custom_persistence_sort.cpp * @example Persistent_cohomology/rips_persistence_step_by_step.cpp * @example Rips_complex/example_one_skeleton_rips_from_points.cpp * @example Rips_complex/example_rips_complex_from_off_file.cpp + * @example Rips_complex/rips_persistence.cpp + * @example Rips_complex/rips_distance_matrix_persistence.cpp * @example Simplex_tree/mini_simplex_tree.cpp * @example Simplex_tree/simple_simplex_tree.cpp * @example Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp -- cgit v1.2.3 From 048108b77120bf7b607a5093977b1da294bc472b Mon Sep 17 00:00:00 2001 From: cjamin Date: Wed, 15 Nov 2017 14:50:29 +0000 Subject: Move 2 more examples into utilities git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/add_utils_in_gudhi_v2@2883 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: b9fd71a4833c84640be2a0f792f1eaea5109874d --- src/Alpha_complex/utilities/CMakeLists.txt | 13 + .../exact_alpha_complex_3d_persistence.cpp | 244 +++++++++++++++++++ .../weighted_alpha_complex_3d_persistence.cpp | 267 +++++++++++++++++++++ src/Persistent_cohomology/example/CMakeLists.txt | 17 -- .../example/exact_alpha_complex_3d_persistence.cpp | 244 ------------------- .../weighted_alpha_complex_3d_persistence.cpp | 267 --------------------- 6 files changed, 524 insertions(+), 528 deletions(-) create mode 100644 src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp create mode 100644 src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp delete mode 100644 src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp delete mode 100644 src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp (limited to 'src/Persistent_cohomology') diff --git a/src/Alpha_complex/utilities/CMakeLists.txt b/src/Alpha_complex/utilities/CMakeLists.txt index 69dbc28a..120ca416 100644 --- a/src/Alpha_complex/utilities/CMakeLists.txt +++ b/src/Alpha_complex/utilities/CMakeLists.txt @@ -4,14 +4,27 @@ project(Alpha_complex_utilities) if(CGAL_FOUND) add_executable(alpha_complex_3d_persistence alpha_complex_3d_persistence.cpp) target_link_libraries(alpha_complex_3d_persistence ${CGAL_LIBRARY}) + add_executable(exact_alpha_complex_3d_persistence exact_alpha_complex_3d_persistence.cpp) + target_link_libraries(exact_alpha_complex_3d_persistence ${CGAL_LIBRARY}) + add_executable(weighted_alpha_complex_3d_persistence weighted_alpha_complex_3d_persistence.cpp) + target_link_libraries(weighted_alpha_complex_3d_persistence ${CGAL_LIBRARY}) if (TBB_FOUND) target_link_libraries(alpha_complex_3d_persistence ${TBB_LIBRARIES}) + target_link_libraries(exact_alpha_complex_3d_persistence ${TBB_LIBRARIES}) + target_link_libraries(weighted_alpha_complex_3d_persistence ${TBB_LIBRARIES}) endif(TBB_FOUND) + add_test(NAME Alpha_complex_utilities_alpha_complex_3d_persistence COMMAND $ "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "2" "0.45") + add_test(NAME Persistent_cohomology_example_exact_alpha_complex_3d COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "2" "0.45") + add_test(NAME Persistent_cohomology_example_weighted_alpha_complex_3d COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.weights" "2" "0.45") install(TARGETS alpha_complex_3d_persistence DESTINATION bin) + install(TARGETS exact_alpha_complex_3d_persistence DESTINATION bin) + install(TARGETS weighted_alpha_complex_3d_persistence DESTINATION bin) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) add_executable (alpha_complex_persistence alpha_complex_persistence.cpp) diff --git a/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp new file mode 100644 index 00000000..8ce68406 --- /dev/null +++ b/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp @@ -0,0 +1,244 @@ +/* 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) 2014 INRIA Saclay (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 +#include +#include +#include + +#include +#include +#include +#include +#include +#include +#include +#include + +#include "../utilities/alpha_complex_3d_helper.h" + +// Alpha_shape_3 templates type definitions +using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel; +using Exact_tag = CGAL::Tag_true; +using Vb = CGAL::Alpha_shape_vertex_base_3; +using Fb = CGAL::Alpha_shape_cell_base_3; +using Tds = CGAL::Triangulation_data_structure_3; +using Triangulation_3 = CGAL::Delaunay_triangulation_3; +using Alpha_shape_3 = CGAL::Alpha_shape_3; + +// From file type definition +using Point_3 = Kernel::Point_3; + +// filtration with alpha values needed type definition +using Alpha_value_type = Alpha_shape_3::FT; +using Object = CGAL::Object; +using Dispatch = CGAL::Dispatch_output_iterator< + CGAL::cpp11::tuple, + CGAL::cpp11::tuple >, + std::back_insert_iterator< std::vector > > >; +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; +using Vertex_list = std::list; + +// gudhi type definition +using ST = Gudhi::Simplex_tree; +using Filtration_value = ST::Filtration_value; +using Simplex_tree_vertex = ST::Vertex_handle; +using Alpha_shape_simplex_tree_map = std::map; +using Alpha_shape_simplex_tree_pair = std::pair; +using Simplex_tree_vector_vertex = std::vector< Simplex_tree_vertex >; +using PCOH = Gudhi::persistent_cohomology::Persistent_cohomology< ST, Gudhi::persistent_cohomology::Field_Zp >; + +void usage(char * const progName) { + std::cerr << "Usage:\n" << progName << " path_to_OFF_file coeff_field_characteristic[integer " << + "> 0] min_persistence[float >= -1.0]\n"; + std::cerr << " path_to_OFF_file is the path to your points cloud in OFF format.\n"; + exit(-1); +} + +int main(int argc, char * const argv[]) { + // program args management + if (argc != 4) { + std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n"; + usage(argv[0]); + } + + int coeff_field_characteristic = atoi(argv[2]); + + Filtration_value min_persistence = 0.0; + int returnedScanValue = sscanf(argv[3], "%f", &min_persistence); + if ((returnedScanValue == EOF) || (min_persistence < -1.0)) { + std::cerr << "Error: " << argv[3] << " is not correct\n"; + usage(argv[0]); + } + + // Read points from file + std::string offInputFile(argv[1]); + // Read the OFF file (input file name given as parameter) and triangulate points + Gudhi::Points_3D_off_reader off_reader(offInputFile); + // Check the read operation was correct + if (!off_reader.is_valid()) { + std::cerr << "Unable to read file " << offInputFile << std::endl; + usage(argv[0]); + } + + // Retrieve the triangulation + std::vector lp = off_reader.get_point_cloud(); + + // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode. + Alpha_shape_3 as(lp.begin(), lp.end(), 0, Alpha_shape_3::GENERAL); +#ifdef DEBUG_TRACES + std::cout << "Alpha shape computed in GENERAL mode" << std::endl; +#endif // DEBUG_TRACES + + // filtration with alpha values from alpha shape + std::vector the_objects; + std::vector the_alpha_values; + + Dispatch disp = CGAL::dispatch_output(std::back_inserter(the_objects), + std::back_inserter(the_alpha_values)); + + as.filtration_with_alpha_values(disp); +#ifdef DEBUG_TRACES + std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl; +#endif // DEBUG_TRACES + + Alpha_shape_3::size_type count_vertices = 0; + Alpha_shape_3::size_type count_edges = 0; + Alpha_shape_3::size_type count_facets = 0; + Alpha_shape_3::size_type count_cells = 0; + + // Loop on objects vector + Vertex_list vertex_list; + ST simplex_tree; + Alpha_shape_simplex_tree_map map_cgal_simplex_tree; + std::vector::iterator the_alpha_value_iterator = the_alpha_values.begin(); + int dim_max = 0; + Filtration_value filtration_max = 0.0; + for (auto object_iterator : the_objects) { + // Retrieve Alpha shape vertex list from object + if (const Cell_handle * cell = CGAL::object_cast(&object_iterator)) { + vertex_list = from_cell(*cell); + count_cells++; + if (dim_max < 3) { + // Cell is of dim 3 + dim_max = 3; + } + } else if (const Facet * facet = CGAL::object_cast(&object_iterator)) { + vertex_list = from_facet(*facet); + count_facets++; + if (dim_max < 2) { + // Facet is of dim 2 + dim_max = 2; + } + } else if (const Edge_3 * edge = CGAL::object_cast(&object_iterator)) { + vertex_list = from_edge(*edge); + count_edges++; + if (dim_max < 1) { + // Edge_3 is of dim 1 + dim_max = 1; + } + } else if (const Vertex_handle * vertex = CGAL::object_cast(&object_iterator)) { + count_vertices++; + vertex_list = from_vertex(*vertex); + } + // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex + Simplex_tree_vector_vertex the_simplex_tree; + for (auto the_alpha_shape_vertex : vertex_list) { + Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex); + if (the_map_iterator == map_cgal_simplex_tree.end()) { + // alpha shape not found + Simplex_tree_vertex vertex = map_cgal_simplex_tree.size(); +#ifdef DEBUG_TRACES + std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl; +#endif // DEBUG_TRACES + the_simplex_tree.push_back(vertex); + map_cgal_simplex_tree.insert(Alpha_shape_simplex_tree_pair(the_alpha_shape_vertex, vertex)); + } else { + // alpha shape found + Simplex_tree_vertex vertex = the_map_iterator->second; +#ifdef DEBUG_TRACES + std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl; +#endif // DEBUG_TRACES + the_simplex_tree.push_back(vertex); + } + } + // Construction of the simplex_tree + // you can also use the_alpha_value_iterator->exact() + Filtration_value filtr = /*std::sqrt*/CGAL::to_double(the_alpha_value_iterator->exact()); +#ifdef DEBUG_TRACES + std::cout << "filtration = " << filtr << std::endl; +#endif // DEBUG_TRACES + if (filtr > filtration_max) { + filtration_max = filtr; + } + simplex_tree.insert_simplex(the_simplex_tree, filtr); + if (the_alpha_value_iterator != the_alpha_values.end()) + ++the_alpha_value_iterator; + else + std::cout << "This shall not happen" << std::endl; + } + simplex_tree.set_dimension(dim_max); + +#ifdef DEBUG_TRACES + std::cout << "vertices \t\t" << count_vertices << std::endl; + std::cout << "edges \t\t" << count_edges << std::endl; + std::cout << "facets \t\t" << count_facets << std::endl; + std::cout << "cells \t\t" << count_cells << std::endl; + + + std::cout << "Information of the Simplex Tree: " << std::endl; + std::cout << " Number of vertices = " << simplex_tree.num_vertices() << " "; + std::cout << " Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl; + std::cout << " Dimension = " << simplex_tree.dimension() << " "; +#endif // DEBUG_TRACES + +#ifdef DEBUG_TRACES + std::cout << "Iterator on vertices: " << std::endl; + for (auto vertex : simplex_tree.complex_vertex_range()) { + std::cout << vertex << " "; + } +#endif // DEBUG_TRACES + + // Sort the simplices in the order of the filtration + simplex_tree.initialize_filtration(); + + std::cout << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl; + // Compute the persistence diagram of the complex + PCOH pcoh(simplex_tree); + // initializes the coefficient field for homology + pcoh.init_coefficients(coeff_field_characteristic); + + pcoh.compute_persistent_cohomology(min_persistence); + + pcoh.output_diagram(); + + return 0; +} diff --git a/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp new file mode 100644 index 00000000..a4ecf9da --- /dev/null +++ b/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp @@ -0,0 +1,267 @@ +/* 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) 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 + * 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 +#include +#include +#include +#include + +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include "../utilities/alpha_complex_3d_helper.h" + +// Traits +using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel; +using Gt = CGAL::Regular_triangulation_euclidean_traits_3; +using Vb = CGAL::Alpha_shape_vertex_base_3; +using Fb = CGAL::Alpha_shape_cell_base_3; +using Tds = CGAL::Triangulation_data_structure_3; +using Triangulation_3 = CGAL::Regular_triangulation_3; +using Alpha_shape_3 = CGAL::Alpha_shape_3; + +// From file type definition +using Point_3 = Gt::Bare_point; +using Weighted_point_3 = Gt::Weighted_point; + +// filtration with alpha values needed type definition +using Alpha_value_type = Alpha_shape_3::FT; +using Object = CGAL::Object; +using Dispatch = CGAL::Dispatch_output_iterator< + CGAL::cpp11::tuple, + CGAL::cpp11::tuple >, + std::back_insert_iterator< std::vector > > >; +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; +using Vertex_list = std::list; + +// gudhi type definition +using ST = Gudhi::Simplex_tree; +using Filtration_value = ST::Filtration_value; +using Simplex_tree_vertex = ST::Vertex_handle; +using Alpha_shape_simplex_tree_map = std::map; +using Alpha_shape_simplex_tree_pair = std::pair; +using Simplex_tree_vector_vertex = std::vector< Simplex_tree_vertex >; +using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology< + ST, Gudhi::persistent_cohomology::Field_Zp >; + +void usage(char * const progName) { + std::cerr << "Usage:\n" << progName << " path_to_OFF_file path_to_weight_file coeff_field_characteristic[integer " << + "> 0] min_persistence[float >= -1.0]\n"; + std::cerr << " path_to_OFF_file is the path to your points cloud in OFF format.\n"; + std::cerr << " path_to_weight_file is the path to the weights of your points cloud (one value per line.)\n"; + std::cerr << " Weights values are explained on CGAL documentation:\n"; + std::cerr << " https://doc.cgal.org/latest/Alpha_shapes_3/index.html#title0\n"; + std::cerr << " https://doc.cgal.org/latest/Triangulation_3/index.html#Triangulation3secclassRegulartriangulation\n"; + exit(-1); +} + +int main(int argc, char * const argv[]) { + // program args management + if (argc != 5) { + std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n"; + usage(argv[0]); + } + + int coeff_field_characteristic = atoi(argv[3]); + Filtration_value min_persistence = strtof(argv[4], nullptr); + + // Read points from file + std::string offInputFile(argv[1]); + // Read the OFF file (input file name given as parameter) and triangulate points + Gudhi::Points_3D_off_reader off_reader(offInputFile); + // Check the read operation was correct + if (!off_reader.is_valid()) { + std::cerr << "Unable to read file " << offInputFile << std::endl; + usage(argv[0]); + } + + // Retrieve the triangulation + std::vector lp = off_reader.get_point_cloud(); + + // Read weights information from file + std::ifstream weights_ifstr(argv[2]); + std::vector wp; + if (weights_ifstr.good()) { + 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())) { + wp.push_back(Weighted_point_3(lp[index], weight)); + index++; + } + if (index != lp.size()) { + std::cerr << "Bad number of weights in file " << argv[2] << std::endl; + usage(argv[0]); + } + } else { + std::cerr << "Unable to read file " << argv[2] << std::endl; + usage(argv[0]); + } + + // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode. + Alpha_shape_3 as(wp.begin(), wp.end(), 0, Alpha_shape_3::GENERAL); +#ifdef DEBUG_TRACES + std::cout << "Alpha shape computed in GENERAL mode" << std::endl; +#endif // DEBUG_TRACES + + // filtration with alpha values from alpha shape + std::vector the_objects; + std::vector the_alpha_values; + + Dispatch disp = CGAL::dispatch_output(std::back_inserter(the_objects), + std::back_inserter(the_alpha_values)); + + as.filtration_with_alpha_values(disp); +#ifdef DEBUG_TRACES + std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl; +#endif // DEBUG_TRACES + + Alpha_shape_3::size_type count_vertices = 0; + Alpha_shape_3::size_type count_edges = 0; + Alpha_shape_3::size_type count_facets = 0; + Alpha_shape_3::size_type count_cells = 0; + + // Loop on objects vector + Vertex_list vertex_list; + ST simplex_tree; + Alpha_shape_simplex_tree_map map_cgal_simplex_tree; + std::vector::iterator the_alpha_value_iterator = the_alpha_values.begin(); + int dim_max = 0; + Filtration_value filtration_max = 0.0; + for (auto object_iterator : the_objects) { + // Retrieve Alpha shape vertex list from object + if (const Cell_handle * cell = CGAL::object_cast(&object_iterator)) { + vertex_list = from_cell(*cell); + count_cells++; + if (dim_max < 3) { + // Cell is of dim 3 + dim_max = 3; + } + } else if (const Facet * facet = CGAL::object_cast(&object_iterator)) { + vertex_list = from_facet(*facet); + count_facets++; + if (dim_max < 2) { + // Facet is of dim 2 + dim_max = 2; + } + } else if (const Edge_3 * edge = CGAL::object_cast(&object_iterator)) { + vertex_list = from_edge(*edge); + count_edges++; + if (dim_max < 1) { + // Edge_3 is of dim 1 + dim_max = 1; + } + } else if (const Alpha_shape_3::Vertex_handle * vertex = + CGAL::object_cast(&object_iterator)) { + count_vertices++; + vertex_list = from_vertex(*vertex); + } + // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex + Simplex_tree_vector_vertex the_simplex_tree; + for (auto the_alpha_shape_vertex : vertex_list) { + Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex); + if (the_map_iterator == map_cgal_simplex_tree.end()) { + // alpha shape not found + Simplex_tree_vertex vertex = map_cgal_simplex_tree.size(); +#ifdef DEBUG_TRACES + std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl; +#endif // DEBUG_TRACES + the_simplex_tree.push_back(vertex); + map_cgal_simplex_tree.insert(Alpha_shape_simplex_tree_pair(the_alpha_shape_vertex, vertex)); + } else { + // alpha shape found + Simplex_tree_vertex vertex = the_map_iterator->second; +#ifdef DEBUG_TRACES + std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl; +#endif // DEBUG_TRACES + the_simplex_tree.push_back(vertex); + } + } + // Construction of the simplex_tree + Filtration_value filtr = /*std::sqrt*/(*the_alpha_value_iterator); +#ifdef DEBUG_TRACES + std::cout << "filtration = " << filtr << std::endl; +#endif // DEBUG_TRACES + if (filtr > filtration_max) { + filtration_max = filtr; + } + simplex_tree.insert_simplex(the_simplex_tree, filtr); + if (the_alpha_value_iterator != the_alpha_values.end()) + ++the_alpha_value_iterator; + else + std::cout << "This shall not happen" << std::endl; + } + simplex_tree.set_dimension(dim_max); + +#ifdef DEBUG_TRACES + std::cout << "vertices \t\t" << count_vertices << std::endl; + std::cout << "edges \t\t" << count_edges << std::endl; + std::cout << "facets \t\t" << count_facets << std::endl; + std::cout << "cells \t\t" << count_cells << std::endl; + + + std::cout << "Information of the Simplex Tree: " << std::endl; + std::cout << " Number of vertices = " << simplex_tree.num_vertices() << " "; + std::cout << " Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl; + std::cout << " Dimension = " << simplex_tree.dimension() << " "; +#endif // DEBUG_TRACES + +#ifdef DEBUG_TRACES + std::cout << "Iterator on vertices: " << std::endl; + for (auto vertex : simplex_tree.complex_vertex_range()) { + std::cout << vertex << " "; + } +#endif // DEBUG_TRACES + + // Sort the simplices in the order of the filtration + simplex_tree.initialize_filtration(); + + std::cout << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl; + // Compute the persistence diagram of the complex + Persistent_cohomology pcoh(simplex_tree, true); + // initializes the coefficient field for homology + pcoh.init_coefficients(coeff_field_characteristic); + + pcoh.compute_persistent_cohomology(min_persistence); + + pcoh.output_diagram(); + + return 0; +} diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt index 98ed753d..18e2913b 100644 --- a/src/Persistent_cohomology/example/CMakeLists.txt +++ b/src/Persistent_cohomology/example/CMakeLists.txt @@ -55,23 +55,6 @@ if(GMP_FOUND) endif(GMP_FOUND) if(CGAL_FOUND) - add_executable(exact_alpha_complex_3d_persistence exact_alpha_complex_3d_persistence.cpp) - target_link_libraries(exact_alpha_complex_3d_persistence ${CGAL_LIBRARY}) - add_executable(weighted_alpha_complex_3d_persistence weighted_alpha_complex_3d_persistence.cpp) - target_link_libraries(weighted_alpha_complex_3d_persistence ${CGAL_LIBRARY}) - - if (TBB_FOUND) - target_link_libraries(exact_alpha_complex_3d_persistence ${TBB_LIBRARIES}) - target_link_libraries(weighted_alpha_complex_3d_persistence ${TBB_LIBRARIES}) - endif(TBB_FOUND) - add_test(NAME Persistent_cohomology_example_exact_alpha_complex_3d COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "2" "0.45") - add_test(NAME Persistent_cohomology_example_weighted_alpha_complex_3d COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.weights" "2" "0.45") - - install(TARGETS exact_alpha_complex_3d_persistence DESTINATION bin) - install(TARGETS weighted_alpha_complex_3d_persistence DESTINATION bin) - if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) add_executable(custom_persistence_sort custom_persistence_sort.cpp) target_link_libraries(custom_persistence_sort ${CGAL_LIBRARY}) diff --git a/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp deleted file mode 100644 index 8ce68406..00000000 --- a/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp +++ /dev/null @@ -1,244 +0,0 @@ -/* 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) 2014 INRIA Saclay (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 -#include -#include -#include - -#include -#include -#include -#include -#include -#include -#include -#include - -#include "../utilities/alpha_complex_3d_helper.h" - -// Alpha_shape_3 templates type definitions -using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel; -using Exact_tag = CGAL::Tag_true; -using Vb = CGAL::Alpha_shape_vertex_base_3; -using Fb = CGAL::Alpha_shape_cell_base_3; -using Tds = CGAL::Triangulation_data_structure_3; -using Triangulation_3 = CGAL::Delaunay_triangulation_3; -using Alpha_shape_3 = CGAL::Alpha_shape_3; - -// From file type definition -using Point_3 = Kernel::Point_3; - -// filtration with alpha values needed type definition -using Alpha_value_type = Alpha_shape_3::FT; -using Object = CGAL::Object; -using Dispatch = CGAL::Dispatch_output_iterator< - CGAL::cpp11::tuple, - CGAL::cpp11::tuple >, - std::back_insert_iterator< std::vector > > >; -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; -using Vertex_list = std::list; - -// gudhi type definition -using ST = Gudhi::Simplex_tree; -using Filtration_value = ST::Filtration_value; -using Simplex_tree_vertex = ST::Vertex_handle; -using Alpha_shape_simplex_tree_map = std::map; -using Alpha_shape_simplex_tree_pair = std::pair; -using Simplex_tree_vector_vertex = std::vector< Simplex_tree_vertex >; -using PCOH = Gudhi::persistent_cohomology::Persistent_cohomology< ST, Gudhi::persistent_cohomology::Field_Zp >; - -void usage(char * const progName) { - std::cerr << "Usage:\n" << progName << " path_to_OFF_file coeff_field_characteristic[integer " << - "> 0] min_persistence[float >= -1.0]\n"; - std::cerr << " path_to_OFF_file is the path to your points cloud in OFF format.\n"; - exit(-1); -} - -int main(int argc, char * const argv[]) { - // program args management - if (argc != 4) { - std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n"; - usage(argv[0]); - } - - int coeff_field_characteristic = atoi(argv[2]); - - Filtration_value min_persistence = 0.0; - int returnedScanValue = sscanf(argv[3], "%f", &min_persistence); - if ((returnedScanValue == EOF) || (min_persistence < -1.0)) { - std::cerr << "Error: " << argv[3] << " is not correct\n"; - usage(argv[0]); - } - - // Read points from file - std::string offInputFile(argv[1]); - // Read the OFF file (input file name given as parameter) and triangulate points - Gudhi::Points_3D_off_reader off_reader(offInputFile); - // Check the read operation was correct - if (!off_reader.is_valid()) { - std::cerr << "Unable to read file " << offInputFile << std::endl; - usage(argv[0]); - } - - // Retrieve the triangulation - std::vector lp = off_reader.get_point_cloud(); - - // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode. - Alpha_shape_3 as(lp.begin(), lp.end(), 0, Alpha_shape_3::GENERAL); -#ifdef DEBUG_TRACES - std::cout << "Alpha shape computed in GENERAL mode" << std::endl; -#endif // DEBUG_TRACES - - // filtration with alpha values from alpha shape - std::vector the_objects; - std::vector the_alpha_values; - - Dispatch disp = CGAL::dispatch_output(std::back_inserter(the_objects), - std::back_inserter(the_alpha_values)); - - as.filtration_with_alpha_values(disp); -#ifdef DEBUG_TRACES - std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl; -#endif // DEBUG_TRACES - - Alpha_shape_3::size_type count_vertices = 0; - Alpha_shape_3::size_type count_edges = 0; - Alpha_shape_3::size_type count_facets = 0; - Alpha_shape_3::size_type count_cells = 0; - - // Loop on objects vector - Vertex_list vertex_list; - ST simplex_tree; - Alpha_shape_simplex_tree_map map_cgal_simplex_tree; - std::vector::iterator the_alpha_value_iterator = the_alpha_values.begin(); - int dim_max = 0; - Filtration_value filtration_max = 0.0; - for (auto object_iterator : the_objects) { - // Retrieve Alpha shape vertex list from object - if (const Cell_handle * cell = CGAL::object_cast(&object_iterator)) { - vertex_list = from_cell(*cell); - count_cells++; - if (dim_max < 3) { - // Cell is of dim 3 - dim_max = 3; - } - } else if (const Facet * facet = CGAL::object_cast(&object_iterator)) { - vertex_list = from_facet(*facet); - count_facets++; - if (dim_max < 2) { - // Facet is of dim 2 - dim_max = 2; - } - } else if (const Edge_3 * edge = CGAL::object_cast(&object_iterator)) { - vertex_list = from_edge(*edge); - count_edges++; - if (dim_max < 1) { - // Edge_3 is of dim 1 - dim_max = 1; - } - } else if (const Vertex_handle * vertex = CGAL::object_cast(&object_iterator)) { - count_vertices++; - vertex_list = from_vertex(*vertex); - } - // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex - Simplex_tree_vector_vertex the_simplex_tree; - for (auto the_alpha_shape_vertex : vertex_list) { - Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex); - if (the_map_iterator == map_cgal_simplex_tree.end()) { - // alpha shape not found - Simplex_tree_vertex vertex = map_cgal_simplex_tree.size(); -#ifdef DEBUG_TRACES - std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl; -#endif // DEBUG_TRACES - the_simplex_tree.push_back(vertex); - map_cgal_simplex_tree.insert(Alpha_shape_simplex_tree_pair(the_alpha_shape_vertex, vertex)); - } else { - // alpha shape found - Simplex_tree_vertex vertex = the_map_iterator->second; -#ifdef DEBUG_TRACES - std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl; -#endif // DEBUG_TRACES - the_simplex_tree.push_back(vertex); - } - } - // Construction of the simplex_tree - // you can also use the_alpha_value_iterator->exact() - Filtration_value filtr = /*std::sqrt*/CGAL::to_double(the_alpha_value_iterator->exact()); -#ifdef DEBUG_TRACES - std::cout << "filtration = " << filtr << std::endl; -#endif // DEBUG_TRACES - if (filtr > filtration_max) { - filtration_max = filtr; - } - simplex_tree.insert_simplex(the_simplex_tree, filtr); - if (the_alpha_value_iterator != the_alpha_values.end()) - ++the_alpha_value_iterator; - else - std::cout << "This shall not happen" << std::endl; - } - simplex_tree.set_dimension(dim_max); - -#ifdef DEBUG_TRACES - std::cout << "vertices \t\t" << count_vertices << std::endl; - std::cout << "edges \t\t" << count_edges << std::endl; - std::cout << "facets \t\t" << count_facets << std::endl; - std::cout << "cells \t\t" << count_cells << std::endl; - - - std::cout << "Information of the Simplex Tree: " << std::endl; - std::cout << " Number of vertices = " << simplex_tree.num_vertices() << " "; - std::cout << " Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl; - std::cout << " Dimension = " << simplex_tree.dimension() << " "; -#endif // DEBUG_TRACES - -#ifdef DEBUG_TRACES - std::cout << "Iterator on vertices: " << std::endl; - for (auto vertex : simplex_tree.complex_vertex_range()) { - std::cout << vertex << " "; - } -#endif // DEBUG_TRACES - - // Sort the simplices in the order of the filtration - simplex_tree.initialize_filtration(); - - std::cout << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl; - // Compute the persistence diagram of the complex - PCOH pcoh(simplex_tree); - // initializes the coefficient field for homology - pcoh.init_coefficients(coeff_field_characteristic); - - pcoh.compute_persistent_cohomology(min_persistence); - - pcoh.output_diagram(); - - return 0; -} diff --git a/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp deleted file mode 100644 index a4ecf9da..00000000 --- a/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp +++ /dev/null @@ -1,267 +0,0 @@ -/* 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) 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 - * 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 -#include -#include -#include -#include - -#include -#include -#include -#include -#include -#include -#include -#include -#include - -#include "../utilities/alpha_complex_3d_helper.h" - -// Traits -using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel; -using Gt = CGAL::Regular_triangulation_euclidean_traits_3; -using Vb = CGAL::Alpha_shape_vertex_base_3; -using Fb = CGAL::Alpha_shape_cell_base_3; -using Tds = CGAL::Triangulation_data_structure_3; -using Triangulation_3 = CGAL::Regular_triangulation_3; -using Alpha_shape_3 = CGAL::Alpha_shape_3; - -// From file type definition -using Point_3 = Gt::Bare_point; -using Weighted_point_3 = Gt::Weighted_point; - -// filtration with alpha values needed type definition -using Alpha_value_type = Alpha_shape_3::FT; -using Object = CGAL::Object; -using Dispatch = CGAL::Dispatch_output_iterator< - CGAL::cpp11::tuple, - CGAL::cpp11::tuple >, - std::back_insert_iterator< std::vector > > >; -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; -using Vertex_list = std::list; - -// gudhi type definition -using ST = Gudhi::Simplex_tree; -using Filtration_value = ST::Filtration_value; -using Simplex_tree_vertex = ST::Vertex_handle; -using Alpha_shape_simplex_tree_map = std::map; -using Alpha_shape_simplex_tree_pair = std::pair; -using Simplex_tree_vector_vertex = std::vector< Simplex_tree_vertex >; -using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology< - ST, Gudhi::persistent_cohomology::Field_Zp >; - -void usage(char * const progName) { - std::cerr << "Usage:\n" << progName << " path_to_OFF_file path_to_weight_file coeff_field_characteristic[integer " << - "> 0] min_persistence[float >= -1.0]\n"; - std::cerr << " path_to_OFF_file is the path to your points cloud in OFF format.\n"; - std::cerr << " path_to_weight_file is the path to the weights of your points cloud (one value per line.)\n"; - std::cerr << " Weights values are explained on CGAL documentation:\n"; - std::cerr << " https://doc.cgal.org/latest/Alpha_shapes_3/index.html#title0\n"; - std::cerr << " https://doc.cgal.org/latest/Triangulation_3/index.html#Triangulation3secclassRegulartriangulation\n"; - exit(-1); -} - -int main(int argc, char * const argv[]) { - // program args management - if (argc != 5) { - std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n"; - usage(argv[0]); - } - - int coeff_field_characteristic = atoi(argv[3]); - Filtration_value min_persistence = strtof(argv[4], nullptr); - - // Read points from file - std::string offInputFile(argv[1]); - // Read the OFF file (input file name given as parameter) and triangulate points - Gudhi::Points_3D_off_reader off_reader(offInputFile); - // Check the read operation was correct - if (!off_reader.is_valid()) { - std::cerr << "Unable to read file " << offInputFile << std::endl; - usage(argv[0]); - } - - // Retrieve the triangulation - std::vector lp = off_reader.get_point_cloud(); - - // Read weights information from file - std::ifstream weights_ifstr(argv[2]); - std::vector wp; - if (weights_ifstr.good()) { - 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())) { - wp.push_back(Weighted_point_3(lp[index], weight)); - index++; - } - if (index != lp.size()) { - std::cerr << "Bad number of weights in file " << argv[2] << std::endl; - usage(argv[0]); - } - } else { - std::cerr << "Unable to read file " << argv[2] << std::endl; - usage(argv[0]); - } - - // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode. - Alpha_shape_3 as(wp.begin(), wp.end(), 0, Alpha_shape_3::GENERAL); -#ifdef DEBUG_TRACES - std::cout << "Alpha shape computed in GENERAL mode" << std::endl; -#endif // DEBUG_TRACES - - // filtration with alpha values from alpha shape - std::vector the_objects; - std::vector the_alpha_values; - - Dispatch disp = CGAL::dispatch_output(std::back_inserter(the_objects), - std::back_inserter(the_alpha_values)); - - as.filtration_with_alpha_values(disp); -#ifdef DEBUG_TRACES - std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl; -#endif // DEBUG_TRACES - - Alpha_shape_3::size_type count_vertices = 0; - Alpha_shape_3::size_type count_edges = 0; - Alpha_shape_3::size_type count_facets = 0; - Alpha_shape_3::size_type count_cells = 0; - - // Loop on objects vector - Vertex_list vertex_list; - ST simplex_tree; - Alpha_shape_simplex_tree_map map_cgal_simplex_tree; - std::vector::iterator the_alpha_value_iterator = the_alpha_values.begin(); - int dim_max = 0; - Filtration_value filtration_max = 0.0; - for (auto object_iterator : the_objects) { - // Retrieve Alpha shape vertex list from object - if (const Cell_handle * cell = CGAL::object_cast(&object_iterator)) { - vertex_list = from_cell(*cell); - count_cells++; - if (dim_max < 3) { - // Cell is of dim 3 - dim_max = 3; - } - } else if (const Facet * facet = CGAL::object_cast(&object_iterator)) { - vertex_list = from_facet(*facet); - count_facets++; - if (dim_max < 2) { - // Facet is of dim 2 - dim_max = 2; - } - } else if (const Edge_3 * edge = CGAL::object_cast(&object_iterator)) { - vertex_list = from_edge(*edge); - count_edges++; - if (dim_max < 1) { - // Edge_3 is of dim 1 - dim_max = 1; - } - } else if (const Alpha_shape_3::Vertex_handle * vertex = - CGAL::object_cast(&object_iterator)) { - count_vertices++; - vertex_list = from_vertex(*vertex); - } - // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex - Simplex_tree_vector_vertex the_simplex_tree; - for (auto the_alpha_shape_vertex : vertex_list) { - Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex); - if (the_map_iterator == map_cgal_simplex_tree.end()) { - // alpha shape not found - Simplex_tree_vertex vertex = map_cgal_simplex_tree.size(); -#ifdef DEBUG_TRACES - std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl; -#endif // DEBUG_TRACES - the_simplex_tree.push_back(vertex); - map_cgal_simplex_tree.insert(Alpha_shape_simplex_tree_pair(the_alpha_shape_vertex, vertex)); - } else { - // alpha shape found - Simplex_tree_vertex vertex = the_map_iterator->second; -#ifdef DEBUG_TRACES - std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl; -#endif // DEBUG_TRACES - the_simplex_tree.push_back(vertex); - } - } - // Construction of the simplex_tree - Filtration_value filtr = /*std::sqrt*/(*the_alpha_value_iterator); -#ifdef DEBUG_TRACES - std::cout << "filtration = " << filtr << std::endl; -#endif // DEBUG_TRACES - if (filtr > filtration_max) { - filtration_max = filtr; - } - simplex_tree.insert_simplex(the_simplex_tree, filtr); - if (the_alpha_value_iterator != the_alpha_values.end()) - ++the_alpha_value_iterator; - else - std::cout << "This shall not happen" << std::endl; - } - simplex_tree.set_dimension(dim_max); - -#ifdef DEBUG_TRACES - std::cout << "vertices \t\t" << count_vertices << std::endl; - std::cout << "edges \t\t" << count_edges << std::endl; - std::cout << "facets \t\t" << count_facets << std::endl; - std::cout << "cells \t\t" << count_cells << std::endl; - - - std::cout << "Information of the Simplex Tree: " << std::endl; - std::cout << " Number of vertices = " << simplex_tree.num_vertices() << " "; - std::cout << " Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl; - std::cout << " Dimension = " << simplex_tree.dimension() << " "; -#endif // DEBUG_TRACES - -#ifdef DEBUG_TRACES - std::cout << "Iterator on vertices: " << std::endl; - for (auto vertex : simplex_tree.complex_vertex_range()) { - std::cout << vertex << " "; - } -#endif // DEBUG_TRACES - - // Sort the simplices in the order of the filtration - simplex_tree.initialize_filtration(); - - std::cout << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl; - // Compute the persistence diagram of the complex - Persistent_cohomology pcoh(simplex_tree, true); - // initializes the coefficient field for homology - pcoh.init_coefficients(coeff_field_characteristic); - - pcoh.compute_persistent_cohomology(min_persistence); - - pcoh.output_diagram(); - - return 0; -} -- cgit v1.2.3 From 1b895dd0d76cbe13b92b68b7198f58631678200f Mon Sep 17 00:00:00 2001 From: cjamin Date: Thu, 16 Nov 2017 11:54:36 +0000 Subject: Add missing includes git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/add_utils_in_gudhi_v2@2890 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 9ddda864abff7b9509984dcbc657225ea1c80b1a --- src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp | 2 ++ src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp | 2 ++ src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp | 2 ++ src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp | 2 ++ .../example/weighted_periodic_alpha_complex_3d_persistence.cpp | 2 ++ .../example/example_alpha_shapes_3_simplex_tree_from_off_file.cpp | 2 ++ 6 files changed, 12 insertions(+) (limited to 'src/Persistent_cohomology') diff --git a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp index f2085ab2..28daca5e 100644 --- a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp +++ b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp @@ -30,6 +30,8 @@ #include #include #include +#include +#include #include #include diff --git a/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp index 7919c7fd..c69482ab 100644 --- a/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp +++ b/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp @@ -30,6 +30,8 @@ #include #include #include +#include +#include #include #include 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 10b62f75..b480a9ec 100644 --- a/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp +++ b/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp @@ -31,6 +31,8 @@ #include #include #include +#include +#include #include #include diff --git a/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp index 293170f7..91747a8c 100644 --- a/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp +++ b/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp @@ -31,6 +31,8 @@ #include #include #include +#include +#include #include #include diff --git a/src/Persistent_cohomology/example/weighted_periodic_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/weighted_periodic_alpha_complex_3d_persistence.cpp index 13634ff7..67d830dc 100644 --- a/src/Persistent_cohomology/example/weighted_periodic_alpha_complex_3d_persistence.cpp +++ b/src/Persistent_cohomology/example/weighted_periodic_alpha_complex_3d_persistence.cpp @@ -30,6 +30,8 @@ #include #include #include +#include +#include #include #include diff --git a/src/Simplex_tree/example/example_alpha_shapes_3_simplex_tree_from_off_file.cpp b/src/Simplex_tree/example/example_alpha_shapes_3_simplex_tree_from_off_file.cpp index ff2eebcb..d8289ba9 100644 --- a/src/Simplex_tree/example/example_alpha_shapes_3_simplex_tree_from_off_file.cpp +++ b/src/Simplex_tree/example/example_alpha_shapes_3_simplex_tree_from_off_file.cpp @@ -28,6 +28,8 @@ #include #include #include +#include +#include #include #include -- cgit v1.2.3 From 9b05f9dadd25f2a5f1051044b2e00ebfc6e9b0a5 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Wed, 22 Nov 2017 09:57:46 +0000 Subject: Merge graph_expansion_blocker fix from cech_complex branch git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2932 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: c6397609dbf92cad0fdd6c0fc5365b96657edec9 --- .../example/rips_persistence_step_by_step.cpp | 59 +----- src/Simplex_tree/example/CMakeLists.txt | 10 + .../example/cech_complex_cgal_mini_sphere_3d.cpp | 234 +++++++++++++++++++++ src/Simplex_tree/include/gudhi/Simplex_tree.h | 26 ++- .../include/gudhi/graph_simplicial_complex.h | 63 ++++++ 5 files changed, 323 insertions(+), 69 deletions(-) create mode 100644 src/Simplex_tree/example/cech_complex_cgal_mini_sphere_3d.cpp (limited to 'src/Persistent_cohomology') diff --git a/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp b/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp index 554eeba6..c1de0ef8 100644 --- a/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp +++ b/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp @@ -45,14 +45,7 @@ using Simplex_tree = Gudhi::Simplex_tree; using Vertex_handle = Simplex_tree::Vertex_handle; using Filtration_value = Simplex_tree::Filtration_value; -using Graph_t = boost::adjacency_list < boost::vecS, boost::vecS, boost::undirectedS -, boost::property < vertex_filtration_t, Filtration_value > -, boost::property < edge_filtration_t, Filtration_value > ->; -using Edge_t = std::pair< Vertex_handle, Vertex_handle >; - -template< typename InputPointRange, typename Distance > -Graph_t compute_proximity_graph(InputPointRange &points, Filtration_value threshold, Distance distance); +using Proximity_graph = Gudhi::Proximity_graph; using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology; @@ -81,8 +74,9 @@ int main(int argc, char * argv[]) { Points_off_reader off_reader(off_file_points); // Compute the proximity graph of the points - Graph_t prox_graph = compute_proximity_graph(off_reader.get_point_cloud(), threshold - , Gudhi::Euclidean_distance()); + Proximity_graph prox_graph = Gudhi::compute_proximity_graph(off_reader.get_point_cloud(), + threshold, + Gudhi::Euclidean_distance()); // Construct the Rips complex in a Simplex Tree Simplex_tree st; @@ -170,48 +164,3 @@ void program_options(int argc, char * argv[] std::abort(); } } - -/** Output the proximity graph of the points. - * - * If points contains n elements, the proximity graph is the graph - * with n vertices, and an edge [u,v] iff the distance function between - * points u and v is smaller than threshold. - * - * The type PointCloud furnishes .begin() and .end() methods, that return - * iterators with value_type Point. - */ -template< typename InputPointRange, typename Distance > -Graph_t compute_proximity_graph(InputPointRange &points, Filtration_value threshold, Distance distance) { - std::vector< Edge_t > edges; - std::vector< Filtration_value > edges_fil; - - Vertex_handle idx_u, idx_v; - Filtration_value fil; - idx_u = 0; - for (auto it_u = points.begin(); it_u != points.end(); ++it_u) { - idx_v = idx_u + 1; - for (auto it_v = it_u + 1; it_v != points.end(); ++it_v, ++idx_v) { - fil = distance(*it_u, *it_v); - if (fil <= threshold) { - edges.emplace_back(idx_u, idx_v); - edges_fil.push_back(fil); - } - } - ++idx_u; - } - - Graph_t skel_graph(edges.begin() - , edges.end() - , edges_fil.begin() - , idx_u); // number of points labeled from 0 to idx_u-1 - - auto vertex_prop = boost::get(vertex_filtration_t(), skel_graph); - - boost::graph_traits::vertex_iterator vi, vi_end; - for (std::tie(vi, vi_end) = boost::vertices(skel_graph); - vi != vi_end; ++vi) { - boost::put(vertex_prop, *vi, 0.); - } - - return skel_graph; -} diff --git a/src/Simplex_tree/example/CMakeLists.txt b/src/Simplex_tree/example/CMakeLists.txt index 8bc4ad53..b33b2d05 100644 --- a/src/Simplex_tree/example/CMakeLists.txt +++ b/src/Simplex_tree/example/CMakeLists.txt @@ -34,6 +34,16 @@ if(GMP_FOUND AND CGAL_FOUND) "${CMAKE_SOURCE_DIR}/data/points/bunny_5000.off") install(TARGETS Simplex_tree_example_alpha_shapes_3_from_off DESTINATION bin) + + add_executable ( Simplex_tree_example_cech_complex_cgal_mini_sphere_3d cech_complex_cgal_mini_sphere_3d.cpp ) + target_link_libraries(Simplex_tree_example_cech_complex_cgal_mini_sphere_3d ${Boost_PROGRAM_OPTIONS_LIBRARY} ${CGAL_LIBRARY}) + if (TBB_FOUND) + target_link_libraries(Simplex_tree_example_cech_complex_cgal_mini_sphere_3d ${TBB_LIBRARIES}) + endif() + add_test(NAME Simplex_tree_example_cech_complex_cgal_mini_sphere_3d COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" -r 0.3 -d 3) + + install(TARGETS Simplex_tree_example_alpha_shapes_3_from_off DESTINATION bin) endif() add_executable ( Simplex_tree_example_graph_expansion_with_blocker graph_expansion_with_blocker.cpp ) diff --git a/src/Simplex_tree/example/cech_complex_cgal_mini_sphere_3d.cpp b/src/Simplex_tree/example/cech_complex_cgal_mini_sphere_3d.cpp new file mode 100644 index 00000000..217e251f --- /dev/null +++ b/src/Simplex_tree/example/cech_complex_cgal_mini_sphere_3d.cpp @@ -0,0 +1,234 @@ +/* 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): Clément Maria + * + * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (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 +#include +#include + +#include + +#include +#include +#include // infinity +#include // for pair +#include + +// ------------------------------------------------------------------------------- +// cech_complex_cgal_mini_sphere_3d is an example of each step that is required to +// build a Cech over a Simplex_tree. Please refer to cech_persistence to see +// how to do the same thing with the Cech_complex wrapper for less detailed +// steps. +// ------------------------------------------------------------------------------- + +// Types definition +using Simplex_tree = Gudhi::Simplex_tree<>; +using Vertex_handle = Simplex_tree::Vertex_handle; +using Simplex_handle = Simplex_tree::Simplex_handle; +using Filtration_value = Simplex_tree::Filtration_value; +using Siblings = Simplex_tree::Siblings; +using Graph_t = boost::adjacency_list < boost::vecS, boost::vecS, boost::undirectedS +, boost::property < Gudhi::vertex_filtration_t, Filtration_value > +, boost::property < Gudhi::edge_filtration_t, Filtration_value > +>; +using Edge_t = std::pair< Vertex_handle, Vertex_handle >; + +using Kernel = CGAL::Epick_d< CGAL::Dimension_tag<3> >; +using Point = Kernel::Point_d; +using Traits = CGAL::Min_sphere_of_points_d_traits_d; +using Min_sphere = CGAL::Min_sphere_of_spheres_d; + +using Points_off_reader = Gudhi::Points_off_reader; + +class Cech_blocker { + public: + bool operator()(Simplex_handle sh) { + std::vector points; +#if DEBUG_TRACES + std::cout << "Cech_blocker on ["; +#endif // DEBUG_TRACES + for (auto vertex : simplex_tree_.simplex_vertex_range(sh)) { + points.push_back(point_cloud_[vertex]); +#if DEBUG_TRACES + std::cout << vertex << ", "; +#endif // DEBUG_TRACES + } + Min_sphere ms(points.begin(),points.end()); + Filtration_value radius = ms.radius(); +#if DEBUG_TRACES + std::cout << "] - radius = " << radius << " - returns " << (radius > threshold_) << std::endl; +#endif // DEBUG_TRACES + simplex_tree_.assign_filtration(sh, radius); + return (radius > threshold_); + } + Cech_blocker(Simplex_tree& simplex_tree, Filtration_value threshold, const std::vector& point_cloud) + : simplex_tree_(simplex_tree), + threshold_(threshold), + point_cloud_(point_cloud) { } + private: + Simplex_tree simplex_tree_; + Filtration_value threshold_; + std::vector point_cloud_; +}; + +template< typename InputPointRange> +Graph_t compute_proximity_graph(InputPointRange &points, Filtration_value threshold); + +void program_options(int argc, char * argv[] + , std::string & off_file_points + , Filtration_value & threshold + , int & dim_max); + +int main(int argc, char * argv[]) { + std::string off_file_points; + Filtration_value threshold; + int dim_max; + + program_options(argc, argv, off_file_points, threshold, dim_max); + + // Extract the points from the file filepoints + Points_off_reader off_reader(off_file_points); + + // Compute the proximity graph of the points + Graph_t prox_graph = compute_proximity_graph(off_reader.get_point_cloud(), threshold); + + //Min_sphere sph1(off_reader.get_point_cloud()[0], off_reader.get_point_cloud()[1], off_reader.get_point_cloud()[2]); + // Construct the Rips complex in a Simplex Tree + Simplex_tree st; + // insert the proximity graph in the simplex tree + st.insert_graph(prox_graph); + // expand the graph until dimension dim_max + st.expansion_with_blockers(dim_max, Cech_blocker(st, threshold, off_reader.get_point_cloud())); + + std::cout << "The complex contains " << st.num_simplices() << " simplices \n"; + std::cout << " and has dimension " << st.dimension() << " \n"; + + // Sort the simplices in the order of the filtration + st.initialize_filtration(); + +#if DEBUG_TRACES + std::cout << "********************************************************************\n"; + // Display the Simplex_tree - Can not be done in the middle of 2 inserts + std::cout << "* The complex contains " << st.num_simplices() << " simplices - dimension=" << st.dimension() << "\n"; + std::cout << "* Iterator on Simplices in the filtration, with [filtration value]:\n"; + for (auto f_simplex : st.filtration_simplex_range()) { + std::cout << " " << "[" << st.filtration(f_simplex) << "] "; + for (auto vertex : st.simplex_vertex_range(f_simplex)) { + std::cout << static_cast(vertex) << " "; + } + std::cout << std::endl; + } +#endif // DEBUG_TRACES + return 0; +} + +void program_options(int argc, char * argv[] + , std::string & off_file_points + , Filtration_value & threshold + , int & dim_max) { + namespace po = boost::program_options; + po::options_description hidden("Hidden options"); + hidden.add_options() + ("input-file", po::value(&off_file_points), + "Name of an OFF file containing a 3d point set.\n"); + + po::options_description visible("Allowed options", 100); + visible.add_options() + ("help,h", "produce help message") + ("max-edge-length,r", + po::value(&threshold)->default_value(std::numeric_limits::infinity()), + "Maximal length of an edge for the Cech complex construction.") + ("cpx-dimension,d", po::value(&dim_max)->default_value(1), + "Maximal dimension of the Cech complex we want to compute."); + + po::positional_options_description pos; + pos.add("input-file", 1); + + po::options_description all; + all.add(visible).add(hidden); + + po::variables_map vm; + po::store(po::command_line_parser(argc, argv). + options(all).positional(pos).run(), vm); + po::notify(vm); + + if (vm.count("help") || !vm.count("input-file")) { + std::cout << std::endl; + std::cout << "Construct a Cech complex defined on a set of input points.\n \n"; + + std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; + std::cout << visible << std::endl; + std::abort(); + } +} + +/** Output the proximity graph of the points. + * + * If points contains n elements, the proximity graph is the graph + * with n vertices, and an edge [u,v] iff the distance function between + * points u and v is smaller than threshold. + * + * The type PointCloud furnishes .begin() and .end() methods, that return + * iterators with value_type Point. + */ +template< typename InputPointRange> +Graph_t compute_proximity_graph(InputPointRange &points, Filtration_value threshold) { + std::vector< Edge_t > edges; + std::vector< Filtration_value > edges_fil; + + Kernel k; + Vertex_handle idx_u, idx_v; + Filtration_value fil; + idx_u = 0; + for (auto it_u = points.begin(); it_u != points.end(); ++it_u) { + idx_v = idx_u + 1; + for (auto it_v = it_u + 1; it_v != points.end(); ++it_v, ++idx_v) { + fil = k.squared_distance_d_object()(*it_u, *it_v); + // For Cech Complex, threshold is a radius (distance /2) + fil = std::sqrt(fil) / 2.; + if (fil <= threshold) { + edges.emplace_back(idx_u, idx_v); + edges_fil.push_back(fil); + } + } + ++idx_u; + } + + Graph_t skel_graph(edges.begin() + , edges.end() + , edges_fil.begin() + , idx_u); // number of points labeled from 0 to idx_u-1 + + auto vertex_prop = boost::get(Gudhi::vertex_filtration_t(), skel_graph); + + boost::graph_traits::vertex_iterator vi, vi_end; + for (std::tie(vi, vi_end) = boost::vertices(skel_graph); + vi != vi_end; ++vi) { + boost::put(vertex_prop, *vi, 0.); + } + + return skel_graph; +} diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h index 7da767cb..5d8a90ee 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h @@ -1145,7 +1145,7 @@ class Simplex_tree { Siblings * new_sib = new Siblings(siblings, // oncles simplex->first, // parent boost::adaptors::reverse(intersection)); // boost::container::ordered_unique_range_t - std::vector blocked_new_sib_list; + std::vector blocked_new_sib_vertex_list; // As all intersections are inserted, we can call the blocker function on all new_sib members for (auto new_sib_member = new_sib->members().begin(); new_sib_member != new_sib->members().end(); @@ -1153,17 +1153,19 @@ class Simplex_tree { bool blocker_result = block_simplex(new_sib_member); // new_sib member has been blocked by the blocker function // add it to the list to be removed - do not perform it while looping on it - if (blocker_result) - blocked_new_sib_list.push_back(new_sib_member); + if (blocker_result) { + blocked_new_sib_vertex_list.push_back(new_sib_member->first); + } } - bool removed = false; - for (auto& blocked_new_sib_member : blocked_new_sib_list){ - removed = removed || remove_maximal_simplex(blocked_new_sib_member); - } - if (removed) { + if (blocked_new_sib_vertex_list.size() == new_sib->members().size()) { + // Specific case where all have to be deleted + delete new_sib; // ensure the children property simplex->second.assign_children(siblings); } else { + for (auto& blocked_new_sib_member : blocked_new_sib_vertex_list) { + new_sib->members().erase(blocked_new_sib_member); + } // ensure recursive call simplex->second.assign_children(new_sib); siblings_expansion_with_blockers(new_sib, max_dim, k - 1, block_simplex); @@ -1338,16 +1340,14 @@ class Simplex_tree { public: /** \brief Remove a maximal simplex. * @param[in] sh Simplex handle on the maximal simplex to remove. - * @return a boolean value that is an implementation detail, and that the user is supposed to ignore * \pre Please check the simplex has no coface before removing it. * \exception std::invalid_argument In debug mode, if sh has children. - * \post Be aware that removing is shifting data in a flat_map (`initialize_filtration()` to be done). + * \post Be aware that removing is shifting data in a flat_map (initialize_filtration to be done). * \post Note that the dimension of the simplicial complex may be lower after calling `remove_maximal_simplex()` * than it was before. However, `upper_bound_dimension()` will return the old value, which remains a valid upper * bound. If you care, you can call `dimension()` to recompute the exact dimension. - * \internal @return true if the leaf's branch has no other leaves (branch's children has been re-assigned), false otherwise. */ - bool remove_maximal_simplex(Simplex_handle sh) { + void remove_maximal_simplex(Simplex_handle sh) { // Guarantee the simplex has no children GUDHI_CHECK(!has_children(sh), std::invalid_argument("Simplex_tree::remove_maximal_simplex - argument has children")); @@ -1365,9 +1365,7 @@ class Simplex_tree { delete child; // dimension may need to be lowered dimension_to_be_lowered_ = true; - return true; } - return false; } private: diff --git a/src/common/include/gudhi/graph_simplicial_complex.h b/src/common/include/gudhi/graph_simplicial_complex.h index 5fe7c826..d84421b2 100644 --- a/src/common/include/gudhi/graph_simplicial_complex.h +++ b/src/common/include/gudhi/graph_simplicial_complex.h @@ -28,6 +28,9 @@ #include // for pair<> #include #include +#include // for std::tie + +namespace Gudhi { /* Edge tag for Boost PropertyGraph. */ struct edge_filtration_t { @@ -39,4 +42,64 @@ struct vertex_filtration_t { typedef boost::vertex_property_tag kind; }; +template +using Proximity_graph = typename boost::adjacency_list < boost::vecS, boost::vecS, boost::undirectedS +, boost::property < vertex_filtration_t, typename SimplicialComplexForProximityGraph::Filtration_value > +, boost::property < edge_filtration_t, typename SimplicialComplexForProximityGraph::Filtration_value >>; + +/** \brief Computes the proximity graph of the points. + * + * If points contains n elements, the proximity graph is the graph with n vertices, and an edge [u,v] iff the + * distance function between points u and v is smaller than threshold. + * + * \tparam ForwardPointRange furnishes `.begin()` and `.end()` methods. + * + * \tparam Distance furnishes `operator()(const Point& p1, const Point& p2)`, where + * `Point` is a point from the `ForwardPointRange`, and that returns a `Filtration_value`. + */ +template< typename SimplicialComplexForProximityGraph + , typename ForwardPointRange + , typename Distance > +Proximity_graph compute_proximity_graph( + const ForwardPointRange& points, + typename SimplicialComplexForProximityGraph::Filtration_value threshold, + Distance distance) { + using Vertex_handle = typename SimplicialComplexForProximityGraph::Vertex_handle; + using Filtration_value = typename SimplicialComplexForProximityGraph::Filtration_value; + + std::vector> edges; + std::vector< Filtration_value > edges_fil; + std::map< Vertex_handle, Filtration_value > vertices; + + Vertex_handle idx_u, idx_v; + Filtration_value fil; + idx_u = 0; + for (auto it_u = points.begin(); it_u != points.end(); ++it_u) { + idx_v = idx_u + 1; + for (auto it_v = it_u + 1; it_v != points.end(); ++it_v, ++idx_v) { + fil = distance(*it_u, *it_v); + if (fil <= threshold) { + edges.emplace_back(idx_u, idx_v); + edges_fil.push_back(fil); + } + } + ++idx_u; + } + + // Points are labeled from 0 to idx_u-1 + Proximity_graph skel_graph(edges.begin(), edges.end(), edges_fil.begin(), idx_u); + + auto vertex_prop = boost::get(vertex_filtration_t(), skel_graph); + + typename boost::graph_traits>::vertex_iterator vi, vi_end; + for (std::tie(vi, vi_end) = boost::vertices(skel_graph); + vi != vi_end; ++vi) { + boost::put(vertex_prop, *vi, 0.); + } + + return skel_graph; +} + +} // namespace Gudhi + #endif // GRAPH_SIMPLICIAL_COMPLEX_H_ -- cgit v1.2.3 From e898db7707f6f4cd45a4759a3ebf6688d8eb826e Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Wed, 20 Dec 2017 22:17:22 +0000 Subject: Merge 1_fold_cover_periodic_alpha_complexes branch git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@3093 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 16709f47787220b4bb4a96936b211c932b03102d --- data/points/iso_cuboid_3_in_0_10.txt | 1 + data/points/shifted_sphere.off | 1002 ++++++++++++++++++++ data/points/shifted_sphere.weights | 1000 +++++++++++++++++++ .../periodic_alpha_complex_3d_persistence.cpp | 14 +- ...ghted_periodic_alpha_complex_3d_persistence.cpp | 46 +- .../doc/Intro_persistent_cohomology.h | 32 +- 6 files changed, 2078 insertions(+), 17 deletions(-) create mode 100644 data/points/iso_cuboid_3_in_0_10.txt create mode 100644 data/points/shifted_sphere.off create mode 100644 data/points/shifted_sphere.weights (limited to 'src/Persistent_cohomology') 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 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//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 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..f7a89454 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 * @@ -113,6 +114,24 @@ int main(int argc, char* const argv[]) { // Retrieve the points std::vector 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.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]); + } + //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_weigth = 0.015625 * (x_max-x_min) * (x_max-x_min); + // Read weights information from file std::ifstream weights_ifstr(argv[2]); std::vector wp; @@ -122,6 +141,14 @@ int main(int argc, char* const argv[]) { 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_weigth) + { + std::cerr << "At line " << (index + 1) << ", the weight (" << weight + << ") is more or equal to maximal possible weight (" << maximal_possible_weigth + << ") = 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 +161,18 @@ 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/Persistent_cohomology/doc/Intro_persistent_cohomology.h b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h index 62bbbfc5..5059bc33 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 Alpha_complex/alpha_complex_3d_persistence.cpp 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 $> ./alpha_complex_3d_persistence ../../data/points/tore3D_300.off -p 2 -m 0.45 \endcode \code Simplex_tree dim: 3 2 0 0 inf 2 1 0.0682162 1.0001 @@ -177,7 +177,7 @@ Alpha_complex/exact_alpha_complex_3d_persistence.cpp computes the persistent \f$\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 $> ./exact_alpha_complex_3d_persistence ../../data/points/sphere3D_pts_on_grid.off -p 2 -m 0.1 \endcode \code Simplex_tree dim: 3 2 0 0 inf 2 2 0.0002 0.2028 \endcode @@ -187,7 +187,7 @@ Alpha_complex/weighted_alpha_complex_3d_persistence.cpp computes the persist \f$\mathbb{Z}/2\mathbb{Z}\f$ coefficients of the weighted alpha complex on points sampling from an OFF file and a weights file. \code $> ./weighted_alpha_complex_3d_persistence ../../data/points/tore3D_300.off -../../data/points/tore3D_300.weights 2 0.45 \endcode +../../data/points/tore3D_300.weights -p 2 -m 0.45 \endcode \code Simplex_tree dim: 3 2 0 -1 inf 2 1 -0.931784 0.000103311 @@ -208,8 +208,10 @@ Simplex_tree dim: 3 \li Alpha_complex/periodic_alpha_complex_3d_persistence.cpp computes the persistent homology with \f$\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 $> ./periodic_alpha_complex_3d_persistence ../../data/points/grid_10_10_10_in_0_1.off -../../data/points/iso_cuboid_3_in_0_1.txt 3 1.0 \endcode +../../data/points/iso_cuboid_3_in_0_1.txt -p 3 -m 1.0 \endcode \code Periodic Delaunay computed. Simplex_tree dim: 3 3 0 0 inf @@ -221,6 +223,28 @@ Simplex_tree dim: 3 3 2 0.005 inf 3 3 0.0075 inf \endcode +\li +Persistent_cohomology/weighted_periodic_alpha_complex_3d_persistence.cpp computes the persistent homology with +\f$\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:
+(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 diameter of +the cuboid.
+(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.
+\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 Persistent_cohomology/plain_homology.cpp computes the plain homology of a simple simplicial complex without filtration values. -- cgit v1.2.3 From f6e028d90a036e357485a977edd8b3a6010b762b Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Thu, 21 Dec 2017 19:08:54 +0000 Subject: Code review fix : Bad cmake utility name, file read check, non negative weight check git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@3095 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 09c0342e7c06f69b62f01c3ba8330a99b963399c --- src/Alpha_complex/utilities/CMakeLists.txt | 2 +- .../weighted_periodic_alpha_complex_3d_persistence.cpp | 16 ++++++++++------ .../doc/Intro_persistent_cohomology.h | 3 +-- 3 files changed, 12 insertions(+), 9 deletions(-) (limited to 'src/Persistent_cohomology') 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 $ + add_test(NAME Alpha_complex_utilities_weigted_periodic_alpha_complex_3d COMMAND $ "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off" "${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/weighted_periodic_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/weighted_periodic_alpha_complex_3d_persistence.cpp index f7a89454..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 @@ -117,8 +117,12 @@ int main(int argc, char* const argv[]) { // 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; + 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]); @@ -130,21 +134,21 @@ int main(int argc, char* const argv[]) { exit(-1); } - double maximal_possible_weigth = 0.015625 * (x_max-x_min) * (x_max-x_min); + 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 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_weigth) + if ((weight >= maximal_possible_weight) || (weight < 0)) { std::cerr << "At line " << (index + 1) << ", the weight (" << weight - << ") is more or equal to maximal possible weight (" << maximal_possible_weigth + << ") 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); } diff --git a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h index 5059bc33..ceaea505 100644 --- a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h +++ b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h @@ -228,8 +228,7 @@ Persistent_cohomology/weighted_periodic_alpha_complex_3d_persistence.cpp com \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:
(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 diameter of -the cuboid.
+Note that the weight of each single point have to be bounded by 1/64 times the square of the cuboid edge length.
(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.
\code $> ./weighted_periodic_alpha_complex_3d_persistence ../../data/points/shifted_sphere.off -- cgit v1.2.3 From b674e9a5fae8bdbb22eadb9a7c0013ce84451743 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 26 Jan 2018 14:55:28 +0000 Subject: Move documentation Copyright in footer Removed from each module git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@3167 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 7595f2d18cdc3773bbd96fa9fed414876ff9fdc7 --- src/Alpha_complex/doc/Intro_alpha_complex.h | 4 +--- src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h | 1 - src/Contraction/include/gudhi/Edge_contraction.h | 4 ---- src/Nerve_GIC/doc/Intro_graph_induced_complex.h | 1 - .../doc/Persistence_representations_doc.h | 1 - src/Persistent_cohomology/doc/Intro_persistent_cohomology.h | 1 - src/Rips_complex/doc/Intro_rips_complex.h | 2 -- src/Simplex_tree/doc/Intro_simplex_tree.h | 1 - src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h | 3 --- src/Spatial_searching/doc/Intro_spatial_searching.h | 2 -- src/Subsampling/doc/Intro_subsampling.h | 2 -- src/Tangential_complex/doc/Intro_tangential_complex.h | 2 -- src/Witness_complex/doc/Witness_complex_doc.h | 3 --- src/common/doc/footer.html | 10 ++-------- 14 files changed, 3 insertions(+), 34 deletions(-) (limited to 'src/Persistent_cohomology') diff --git a/src/Alpha_complex/doc/Intro_alpha_complex.h b/src/Alpha_complex/doc/Intro_alpha_complex.h index cf1a946a..a08663ca 100644 --- a/src/Alpha_complex/doc/Intro_alpha_complex.h +++ b/src/Alpha_complex/doc/Intro_alpha_complex.h @@ -31,7 +31,7 @@ namespace alpha_complex { /** \defgroup alpha_complex Alpha complex * * \author Vincent Rouvreau - * + * * @{ * * \section definition Definition @@ -195,8 +195,6 @@ namespace alpha_complex { * * \include Alpha_complex/alphaoffreader_for_doc_32.txt * - * \copyright GNU General Public License v3. - * \verbatim Contact: gudhi-users@lists.gforge.inria.fr \endverbatim */ /** @} */ // end defgroup alpha_complex diff --git a/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h b/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h index ee84e201..a5d7b60f 100644 --- a/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h +++ b/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h @@ -105,7 +105,6 @@ namespace cubical_complex { * \section BitmapExamples Examples * End user programs are available in example/Bitmap_cubical_complex and utilities/Bitmap_cubical_complex folders. * - * \copyright GNU General Public License v3. */ /** @} */ // end defgroup cubical_complex diff --git a/src/Contraction/include/gudhi/Edge_contraction.h b/src/Contraction/include/gudhi/Edge_contraction.h index 61f2d945..cf9a2c27 100644 --- a/src/Contraction/include/gudhi/Edge_contraction.h +++ b/src/Contraction/include/gudhi/Edge_contraction.h @@ -210,7 +210,6 @@ int main (int argc, char *argv[]) } \endcode - \verbatim ./example/Contraction/RipsContraction ../../data/SO3_10000.off 0.3 [ 50%] [100%] Built target SkeletonBlockerIteration @@ -223,9 +222,6 @@ Time to simplify and enumerate simplices: 3.166621s wall, 3.150000s user + 0.010000s system = 3.160000s CPU (99.8%) \endverbatim - - -\copyright GNU General Public License v3. */ /** @} */ // end defgroup } // namespace contraction diff --git a/src/Nerve_GIC/doc/Intro_graph_induced_complex.h b/src/Nerve_GIC/doc/Intro_graph_induced_complex.h index 344cb031..f2409087 100644 --- a/src/Nerve_GIC/doc/Intro_graph_induced_complex.h +++ b/src/Nerve_GIC/doc/Intro_graph_induced_complex.h @@ -176,7 +176,6 @@ namespace cover_complex { * * \image html "funcGICvisu.jpg" "Visualization with neato" * - * \copyright GNU General Public License v3. */ /** @} */ // end defgroup cover_complex diff --git a/src/Persistence_representations/doc/Persistence_representations_doc.h b/src/Persistence_representations/doc/Persistence_representations_doc.h index 978fb5bd..d781211a 100644 --- a/src/Persistence_representations/doc/Persistence_representations_doc.h +++ b/src/Persistence_representations/doc/Persistence_representations_doc.h @@ -250,7 +250,6 @@ namespace Persistence_representations { absolute value of differences between coordinates. A scalar product is a sum of products of values at the corresponding positions of two vectors. - \copyright GNU General Public License v3. */ /** @} */ // end defgroup Persistence_representations diff --git a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h index ceaea505..4dbe82c7 100644 --- a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h +++ b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h @@ -248,7 +248,6 @@ Simplex_tree dim: 3 Persistent_cohomology/plain_homology.cpp computes the plain homology of a simple simplicial complex without filtration values. - \copyright GNU General Public License v3. */ } // namespace persistent_cohomology diff --git a/src/Rips_complex/doc/Intro_rips_complex.h b/src/Rips_complex/doc/Intro_rips_complex.h index 124dfec9..8c517516 100644 --- a/src/Rips_complex/doc/Intro_rips_complex.h +++ b/src/Rips_complex/doc/Intro_rips_complex.h @@ -146,8 +146,6 @@ namespace rips_complex { * * \include Rips_complex/full_skeleton_rips_for_doc.txt * - * \copyright GNU General Public License v3. - * \verbatim Contact: gudhi-users@lists.gforge.inria.fr \endverbatim */ /** @} */ // end defgroup rips_complex diff --git a/src/Simplex_tree/doc/Intro_simplex_tree.h b/src/Simplex_tree/doc/Intro_simplex_tree.h index 769491d9..6b80d1c9 100644 --- a/src/Simplex_tree/doc/Intro_simplex_tree.h +++ b/src/Simplex_tree/doc/Intro_simplex_tree.h @@ -79,7 +79,6 @@ Number of vertices = 10 Number of simplices = 98 \endcode * 1 incidence relations in a complex. It is consequently faster when accessing the boundary of a simplex, but is less * compact and harder to construct from scratch. * - * \copyright GNU General Public License v3. * @} */ diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h index 32fe411c..aca2aa57 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h @@ -239,9 +239,6 @@ their collaboration to write the two initial papers about this data-structure and also Dominique for leaving him use a prototype. - -\copyright GNU General Public License v3. - @} */ } // namespace skeleton_blocker diff --git a/src/Spatial_searching/doc/Intro_spatial_searching.h b/src/Spatial_searching/doc/Intro_spatial_searching.h index 1ee5e92e..52ed65e4 100644 --- a/src/Spatial_searching/doc/Intro_spatial_searching.h +++ b/src/Spatial_searching/doc/Intro_spatial_searching.h @@ -50,8 +50,6 @@ namespace spatial_searching { * * \include Spatial_searching/example_spatial_searching.cpp * - * \copyright GNU General Public License v3. - * \verbatim Contact: gudhi-users@lists.gforge.inria.fr \endverbatim */ /** @} */ // end defgroup spatial_searching diff --git a/src/Subsampling/doc/Intro_subsampling.h b/src/Subsampling/doc/Intro_subsampling.h index c84616dd..ab9cdc37 100644 --- a/src/Subsampling/doc/Intro_subsampling.h +++ b/src/Subsampling/doc/Intro_subsampling.h @@ -58,8 +58,6 @@ namespace subsampling { * This example outputs a subset of 100 points picked randomly. * * \include Subsampling/example_pick_n_random_points.cpp - * \copyright GNU General Public License v3. - * \verbatim Contact: gudhi-users@lists.gforge.inria.fr \endverbatim */ /** @} */ // end defgroup subsampling diff --git a/src/Tangential_complex/doc/Intro_tangential_complex.h b/src/Tangential_complex/doc/Intro_tangential_complex.h index 3d687c1d..00e00c52 100644 --- a/src/Tangential_complex/doc/Intro_tangential_complex.h +++ b/src/Tangential_complex/doc/Intro_tangential_complex.h @@ -107,8 +107,6 @@ dimensions are known at compile-time. \include Tangential_complex/example_with_perturb.cpp -\copyright GNU General Public License v3. -\verbatim Contact: gudhi-users@lists.gforge.inria.fr \endverbatim */ /** @} */ // end defgroup tangential_complex diff --git a/src/Witness_complex/doc/Witness_complex_doc.h b/src/Witness_complex/doc/Witness_complex_doc.h index 5d5c0735..62203054 100644 --- a/src/Witness_complex/doc/Witness_complex_doc.h +++ b/src/Witness_complex/doc/Witness_complex_doc.h @@ -117,9 +117,6 @@ int main(int argc, char * const argv[]) { \include Witness_complex/example_nearest_landmark_table.cpp - \copyright GNU General Public License v3. - - */ #endif // WITNESS_COMPLEX_DOC_H_ diff --git a/src/common/doc/footer.html b/src/common/doc/footer.html index 7b4cdc5c..a557922b 100644 --- a/src/common/doc/footer.html +++ b/src/common/doc/footer.html @@ -6,24 +6,18 @@ $projectname  Version $projectnumber  - $projectbrief + - Copyright : GPL v3 $generatedby - doxygen $doxygenversion + Doxygen $doxygenversion - -
tralala -$generatedby   -doxygen - $doxygenversion -
- -- cgit v1.2.3