diff options
author | cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2017-10-05 08:26:50 +0000 |
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committer | cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2017-10-05 08:26:50 +0000 |
commit | 300914816e3e5d347efd9eaa5d06c236ad81511e (patch) | |
tree | be2b6484191bd40bfaf66c634889fcb91466282f /src/Persistent_cohomology | |
parent | b2160d53d6b94979cb62c0369e62aad83a4cb8c7 (diff) |
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
Diffstat (limited to 'src/Persistent_cohomology')
5 files changed, 10 insertions, 388 deletions
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 <a href="_persistent_cohomology_2rips_persistence_8cpp-example.html"> -Persistent_cohomology/rips_persistence.cpp</a> computes the Rips complex of a point cloud and outputs its persistence +\li <a href="_rips_complex_2rips_persistence_8cpp-example.html"> +Rips_complex/rips_persistence.cpp</a> computes the Rips complex of a point cloud and outputs its persistence diagram. \code $> ./rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 3 \endcode \code The complex contains 177838 simplices @@ -158,12 +158,12 @@ diagram. Persistent_cohomology/rips_multifield_persistence.cpp</a> computes the Rips complex of a point cloud and outputs its persistence diagram with a family of field coefficients. -\li <a href="_persistent_cohomology_2rips_distance_matrix_persistence_8cpp-example.html"> -Persistent_cohomology/rips_distance_matrix_persistence.cpp</a> computes the Rips complex of a distance matrix and +\li <a href="_rips_complex_2rips_distance_matrix_persistence_8cpp-example.html"> +Rips_complex/rips_distance_matrix_persistence.cpp</a> computes the Rips complex of a distance matrix and outputs its persistence diagram. -\li <a href="_persistent_cohomology_2alpha_complex_3d_persistence_8cpp-example.html"> -Persistent_cohomology/alpha_complex_3d_persistence.cpp</a> computes the persistent homology with +\li <a href="_alpha_complex_2alpha_complex_3d_persistence_8cpp-example.html"> +Alpha_complex/alpha_complex_3d_persistence.cpp</a> computes the persistent homology with \f$\mathbb{Z}/2\mathbb{Z}\f$ coefficients of the alpha complex on points sampling from an OFF file. \code $> ./alpha_complex_3d_persistence ../../data/points/tore3D_300.off 2 0.45 \endcode \code Simplex_tree dim: 3 @@ -194,8 +194,8 @@ and a weights file. 2 1 0.0934117 1.00003 2 2 0.56444 1.03938 \endcode -\li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html"> -Persistent_cohomology/alpha_complex_persistence.cpp</a> computes the persistent homology with +\li <a href="_alpha_complex_2alpha_complex_persistence_8cpp-example.html"> +Alpha_complex/alpha_complex_persistence.cpp</a> computes the persistent homology with \f$\mathbb{Z}/p\mathbb{Z}\f$ coefficients of the alpha complex on points sampling from an OFF file. \code $> ./alpha_complex_persistence -r 32 -p 2 -m 0.45 ../../data/points/tore3D_300.off \endcode \code Alpha complex is of dimension 3 - 9273 simplices - 300 vertices. @@ -205,8 +205,8 @@ Simplex_tree dim: 3 2 1 0.0934117 1.00003 2 2 0.56444 1.03938 \endcode -\li <a href="_persistent_cohomology_2periodic_alpha_complex_3d_persistence_8cpp-example.html"> -Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp</a> computes the persistent homology with +\li <a href="_alpha_complex_2periodic_alpha_complex_3d_persistence_8cpp-example.html"> +Alpha_complex/periodic_alpha_complex_3d_persistence.cpp</a> computes the persistent homology with \f$\mathbb{Z}/2\mathbb{Z}\f$ coefficients of the periodic alpha complex on points sampling from an OFF file. \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 $<TARGET_FILE:rips_distance_matrix_persistence> - "${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 $<TARGET_FILE:rips_persistence> - "${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] <OFF input file>` - -**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 <http://www.gnu.org/licenses/>. - */ - -#include <gudhi/Rips_complex.h> -#include <gudhi/Simplex_tree.h> -#include <gudhi/Persistent_cohomology.h> -#include <gudhi/reader_utils.h> - -#include <boost/program_options.hpp> - -#include <string> -#include <vector> -#include <limits> // infinity - -// Types definition -using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>; -using Filtration_value = Simplex_tree::Filtration_value; -using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>; -using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; -using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp >; -using Distance_matrix = std::vector<std::vector<Filtration_value>>; - -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<Filtration_value>(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<std::string>(&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<std::string>(&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<Filtration_value>(&threshold)->default_value(std::numeric_limits<Filtration_value>::infinity()), - "Maximal length of an edge for the Rips complex construction.") - ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(1), - "Maximal dimension of the Rips complex we want to compute.") - ("field-charac,p", po::value<int>(&p)->default_value(11), - "Characteristic p of the coefficient field Z/pZ for computing homology.") - ("min-persistence,m", po::value<Filtration_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 <http://www.gnu.org/licenses/>. - */ - -#include <gudhi/Rips_complex.h> -#include <gudhi/distance_functions.h> -#include <gudhi/Simplex_tree.h> -#include <gudhi/Persistent_cohomology.h> -#include <gudhi/Points_off_io.h> - -#include <boost/program_options.hpp> - -#include <string> -#include <vector> -#include <limits> // infinity - -// Types definition -using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>; -using Filtration_value = Simplex_tree::Filtration_value; -using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>; -using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; -using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp >; -using Point = std::vector<double>; -using Points_off_reader = Gudhi::Points_off_reader<Point>; - -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<std::string>(&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<std::string>(&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<Filtration_value>(&threshold)->default_value(std::numeric_limits<Filtration_value>::infinity()), - "Maximal length of an edge for the Rips complex construction.") - ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(1), - "Maximal dimension of the Rips complex we want to compute.") - ("field-charac,p", po::value<int>(&p)->default_value(11), - "Characteristic p of the coefficient field Z/pZ for computing homology.") - ("min-persistence,m", po::value<Filtration_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(); - } -} |