From 157e6fa3aa86e9de270a9f3a9b6b6acdc37abf5f Mon Sep 17 00:00:00 2001 From: cjamin Date: Wed, 31 May 2017 16:16:50 +0000 Subject: Move 2 examples from Bitmap_cubical_complex to utilities git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/add_utils_in_gudhi_v2@2492 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 40e5f550edb48780d2cf1fe322a5c1d7dd5c80b0 --- .../utilities/Bitmap_cubical_complex.cpp | 80 +++++++++++++++++++++ ...ubical_complex_periodic_boundary_conditions.cpp | 81 ++++++++++++++++++++++ .../utilities/CMakeLists.txt | 31 +++++++++ 3 files changed, 192 insertions(+) create mode 100644 src/Bitmap_cubical_complex/utilities/Bitmap_cubical_complex.cpp create mode 100644 src/Bitmap_cubical_complex/utilities/Bitmap_cubical_complex_periodic_boundary_conditions.cpp create mode 100644 src/Bitmap_cubical_complex/utilities/CMakeLists.txt (limited to 'src/Bitmap_cubical_complex/utilities') diff --git a/src/Bitmap_cubical_complex/utilities/Bitmap_cubical_complex.cpp b/src/Bitmap_cubical_complex/utilities/Bitmap_cubical_complex.cpp new file mode 100644 index 00000000..67735ba1 --- /dev/null +++ b/src/Bitmap_cubical_complex/utilities/Bitmap_cubical_complex.cpp @@ -0,0 +1,80 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Pawel Dlotko + * + * Copyright (C) 2015 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 + +// standard stuff +#include +#include +#include +#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" << + "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 example.\n" << std::endl; + + if (argc != 2) { + std::cerr << "Wrong number of parameters. Please provide the name of a file with a Perseus style bitmap at " << + "the input. The program will now terminate.\n"; + return 1; + } + + typedef Gudhi::cubical_complex::Bitmap_cubical_complex_base Bitmap_cubical_complex_base; + typedef Gudhi::cubical_complex::Bitmap_cubical_complex Bitmap_cubical_complex; + typedef Gudhi::persistent_cohomology::Field_Zp Field_Zp; + typedef Gudhi::persistent_cohomology::Persistent_cohomology Persistent_cohomology; + + Bitmap_cubical_complex b(argv[1]); + + // Compute the persistence diagram of the complex + Persistent_cohomology pcoh(b); + int p = 2; + double min_persistence = 0; + + pcoh.init_coefficients(p); // initializes the coefficient field for homology + pcoh.compute_persistent_cohomology(min_persistence); + + std::string output_file_name(argv[1]); + output_file_name += "_persistence"; + + std::size_t last_in_path = output_file_name.find_last_of("/\\"); + + if (last_in_path != std::string::npos) { + output_file_name = output_file_name.substr(last_in_path+1); + } + + std::ofstream out(output_file_name.c_str()); + pcoh.output_diagram(out); + out.close(); + + std::cout << "Result in file: " << output_file_name << "\n"; + + return 0; +} + 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 new file mode 100644 index 00000000..f8754345 --- /dev/null +++ b/src/Bitmap_cubical_complex/utilities/Bitmap_cubical_complex_periodic_boundary_conditions.cpp @@ -0,0 +1,81 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Pawel Dlotko + * + * Copyright (C) 2015 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 + +// standard stuff +#include +#include +#include + +int main(int argc, char** argv) { + std::cout << "This program computes persistent homology, by using " << + "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 " << + "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" << + " example.\n" << std::endl; + + if (argc != 2) { + std::cerr << "Wrong number of parameters. Please provide the name of a file with a Perseus style bitmap at " << + "the input. The program will now terminate.\n"; + return 1; + } + + typedef Gudhi::cubical_complex::Bitmap_cubical_complex_periodic_boundary_conditions_base Bitmap_base; + typedef Gudhi::cubical_complex::Bitmap_cubical_complex< Bitmap_base > Bitmap_cubical_complex; + + Bitmap_cubical_complex b(argv[1]); + + typedef Gudhi::persistent_cohomology::Field_Zp Field_Zp; + typedef Gudhi::persistent_cohomology::Persistent_cohomology Persistent_cohomology; + // Compute the persistence diagram of the complex + Persistent_cohomology pcoh(b, true); + + int p = 2; + double min_persistence = 0; + pcoh.init_coefficients(p); // initializes the coefficient field for homology + pcoh.compute_persistent_cohomology(min_persistence); + + std::string output_file_name(argv[1]); + output_file_name += "_persistence"; + + std::size_t last_in_path = output_file_name.find_last_of("/\\"); + + if (last_in_path != std::string::npos) { + output_file_name = output_file_name.substr(last_in_path+1); + } + + std::ofstream out(output_file_name.c_str()); + pcoh.output_diagram(out); + out.close(); + + std::cout << "Result in file: " << output_file_name << "\n"; + + return 0; +} + diff --git a/src/Bitmap_cubical_complex/utilities/CMakeLists.txt b/src/Bitmap_cubical_complex/utilities/CMakeLists.txt new file mode 100644 index 00000000..43fb8c86 --- /dev/null +++ b/src/Bitmap_cubical_complex/utilities/CMakeLists.txt @@ -0,0 +1,31 @@ +cmake_minimum_required(VERSION 2.6) +project(Bitmap_cubical_complex_utilities) + +add_executable ( Bitmap_cubical_complex Bitmap_cubical_complex.cpp ) +target_link_libraries(Bitmap_cubical_complex ${Boost_SYSTEM_LIBRARY}) +if (TBB_FOUND) + target_link_libraries(Bitmap_cubical_complex ${TBB_LIBRARIES}) +endif() + +add_test(NAME Bitmap_cubical_complex_utility_persistence_one_sphere COMMAND $ + "${CMAKE_SOURCE_DIR}/data/bitmap/CubicalOneSphere.txt") + +add_test(NAME Bitmap_cubical_complex_utility_persistence_two_sphere COMMAND $ + "${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt") + +add_executable ( Bitmap_cubical_complex_periodic_boundary_conditions Bitmap_cubical_complex_periodic_boundary_conditions.cpp ) +target_link_libraries(Bitmap_cubical_complex_periodic_boundary_conditions ${Boost_SYSTEM_LIBRARY}) +if (TBB_FOUND) + target_link_libraries(Bitmap_cubical_complex_periodic_boundary_conditions ${TBB_LIBRARIES}) +endif() + +add_test(NAME Bitmap_cubical_complex_utility_periodic_boundary_conditions_2d_torus + COMMAND $ + "${CMAKE_SOURCE_DIR}/data/bitmap/2d_torus.txt") + +add_test(NAME Bitmap_cubical_complex_utility_periodic_boundary_conditions_3d_torus + COMMAND $ + "${CMAKE_SOURCE_DIR}/data/bitmap/3d_torus.txt") + +install(TARGETS Bitmap_cubical_complex DESTINATION bin) +install(TARGETS Bitmap_cubical_complex_periodic_boundary_conditions DESTINATION bin) -- cgit v1.2.3