diff options
Diffstat (limited to 'example/Bottleneck_distance')
| -rw-r--r-- | example/Bottleneck_distance/CMakeLists.txt | 34 | ||||
| -rw-r--r-- | example/Bottleneck_distance/README | 19 | ||||
| -rw-r--r-- | example/Bottleneck_distance/bottleneck_read_file_example.cpp | 50 |
3 files changed, 28 insertions, 75 deletions
diff --git a/example/Bottleneck_distance/CMakeLists.txt b/example/Bottleneck_distance/CMakeLists.txt index eac617db..6095d6eb 100644 --- a/example/Bottleneck_distance/CMakeLists.txt +++ b/example/Bottleneck_distance/CMakeLists.txt @@ -2,37 +2,21 @@ 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 (alpha_rips_persistence_bottleneck_distance alpha_rips_persistence_bottleneck_distance.cpp) + target_link_libraries(alpha_rips_persistence_bottleneck_distance ${Boost_PROGRAM_OPTIONS_LIBRARY}) if (TBB_FOUND) - target_link_libraries(bottleneck_read_file_example ${TBB_LIBRARIES}) + target_link_libraries(alpha_rips_persistence_bottleneck_distance ${TBB_LIBRARIES}) target_link_libraries(bottleneck_basic_example ${TBB_LIBRARIES}) endif(TBB_FOUND) - + add_test(NAME Bottleneck_distance_example_basic COMMAND $<TARGET_FILE:bottleneck_basic_example>) - - add_test(NAME Bottleneck_read_file_example - COMMAND $<TARGET_FILE:bottleneck_read_file_example> - "${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) - -endif (NOT CGAL_VERSION VERSION_LESS 4.8.1) - -# Eigen3 and CGAL > 4.7.0 is required for alpha complex -# CGAL > 4.8.1 is required for bottleneck distance => -if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) - add_executable (alpha_rips_persistence_bottleneck_distance alpha_rips_persistence_bottleneck_distance.cpp) - target_link_libraries(alpha_rips_persistence_bottleneck_distance ${Boost_PROGRAM_OPTIONS_LIBRARY}) - add_test(NAME Bottleneck_distance_example_alpha_rips_persistence_bottleneck - COMMAND $<TARGET_FILE:alpha_rips_persistence_bottleneck_distance> - "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.15" "-m" "0.12" "-d" "3" "-p" "3") + COMMAND $<TARGET_FILE:alpha_rips_persistence_bottleneck_distance> + "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.15" "-m" "0.12" "-d" "3" "-p" "3") + install(TARGETS bottleneck_basic_example DESTINATION bin) install(TARGETS alpha_rips_persistence_bottleneck_distance 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/example/Bottleneck_distance/README b/example/Bottleneck_distance/README new file mode 100644 index 00000000..01bcd74a --- /dev/null +++ b/example/Bottleneck_distance/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 birth death`
+
+where `dim` is the dimension of the homological feature, `birth` and `death` 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] <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.
diff --git a/example/Bottleneck_distance/bottleneck_read_file_example.cpp b/example/Bottleneck_distance/bottleneck_read_file_example.cpp deleted file mode 100644 index 24d73c57..00000000 --- a/example/Bottleneck_distance/bottleneck_read_file_example.cpp +++ /dev/null @@ -1,50 +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. - * - * Authors: Francois Godi, small modifications by Pawel Dlotko - * - * Copyright (C) 2015 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/Bottleneck.h> -#include <gudhi/reader_utils.h> -#include <iostream> -#include <vector> -#include <utility> // for pair -#include <string> -#include <limits> // for numeric_limits - -int main(int argc, char** argv) { - if (argc < 3) { - std::cout << "To run this program please provide as an input two files with persistence diagrams. Each file" << - " should contain a birth-death pair per line. Third, optional parameter is an error bound on a bottleneck" << - " distance (set by default to the smallest positive double value). If you set the error bound to 0, be" << - " aware this version is exact but expensive. The program will now terminate \n"; - return -1; - } - std::vector<std::pair<double, double>> diag1 = Gudhi::read_persistence_intervals_in_dimension(argv[1]); - std::vector<std::pair<double, double>> diag2 = Gudhi::read_persistence_intervals_in_dimension(argv[2]); - - double tolerance = std::numeric_limits<double>::min(); - if (argc == 4) { - tolerance = atof(argv[3]); - } - double b = Gudhi::persistence_diagram::bottleneck_distance(diag1, diag2, tolerance); - std::cout << "The distance between the diagrams is : " << b << ". The tolerance is : " << tolerance << std::endl; - - return 0; -} |