diff options
Diffstat (limited to 'example/Bitmap_cubical_complex')
4 files changed, 9 insertions, 198 deletions
diff --git a/example/Bitmap_cubical_complex/Bitmap_cubical_complex.cpp b/example/Bitmap_cubical_complex/Bitmap_cubical_complex.cpp deleted file mode 100644 index 67735ba1..00000000 --- a/example/Bitmap_cubical_complex/Bitmap_cubical_complex.cpp +++ /dev/null @@ -1,80 +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 - * - * 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 <http://www.gnu.org/licenses/>. - */ - - -#include <gudhi/reader_utils.h> -#include <gudhi/Bitmap_cubical_complex.h> -#include <gudhi/Persistent_cohomology.h> - -// standard stuff -#include <iostream> -#include <string> -#include <vector> -#include <cstddef> - -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<double> Bitmap_cubical_complex_base; - typedef Gudhi::cubical_complex::Bitmap_cubical_complex<Bitmap_cubical_complex_base> Bitmap_cubical_complex; - typedef Gudhi::persistent_cohomology::Field_Zp Field_Zp; - typedef Gudhi::persistent_cohomology::Persistent_cohomology<Bitmap_cubical_complex, Field_Zp> 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/example/Bitmap_cubical_complex/Bitmap_cubical_complex_periodic_boundary_conditions.cpp b/example/Bitmap_cubical_complex/Bitmap_cubical_complex_periodic_boundary_conditions.cpp deleted file mode 100644 index 122160a2..00000000 --- a/example/Bitmap_cubical_complex/Bitmap_cubical_complex_periodic_boundary_conditions.cpp +++ /dev/null @@ -1,82 +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 - * - * 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 <http://www.gnu.org/licenses/>. - */ - - -#include <gudhi/reader_utils.h> -#include <gudhi/Bitmap_cubical_complex.h> -#include <gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h> -#include <gudhi/Persistent_cohomology.h> - -// standard stuff -#include <iostream> -#include <sstream> -#include <vector> -#include <string> - -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<double> 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<Bitmap_cubical_complex, Field_Zp> 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/example/Bitmap_cubical_complex/CMakeLists.txt b/example/Bitmap_cubical_complex/CMakeLists.txt index a0401619..99304aa4 100644 --- a/example/Bitmap_cubical_complex/CMakeLists.txt +++ b/example/Bitmap_cubical_complex/CMakeLists.txt @@ -1,17 +1,6 @@ cmake_minimum_required(VERSION 2.6) project(Bitmap_cubical_complex_examples) -add_executable ( Bitmap_cubical_complex Bitmap_cubical_complex.cpp ) -if (TBB_FOUND) - target_link_libraries(Bitmap_cubical_complex ${TBB_LIBRARIES}) -endif() - -add_test(NAME Bitmap_cubical_complex_example_persistence_one_sphere COMMAND $<TARGET_FILE:Bitmap_cubical_complex> - "${CMAKE_SOURCE_DIR}/data/bitmap/CubicalOneSphere.txt") - -add_test(NAME Bitmap_cubical_complex_example_persistence_two_sphere COMMAND $<TARGET_FILE:Bitmap_cubical_complex> - "${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt") - add_executable ( Random_bitmap_cubical_complex Random_bitmap_cubical_complex.cpp ) if (TBB_FOUND) target_link_libraries(Random_bitmap_cubical_complex ${TBB_LIBRARIES}) @@ -19,19 +8,4 @@ endif() add_test(NAME Bitmap_cubical_complex_example_random COMMAND $<TARGET_FILE:Random_bitmap_cubical_complex> "2" "100" "100") -add_executable ( Bitmap_cubical_complex_periodic_boundary_conditions Bitmap_cubical_complex_periodic_boundary_conditions.cpp ) -if (TBB_FOUND) - target_link_libraries(Bitmap_cubical_complex_periodic_boundary_conditions ${TBB_LIBRARIES}) -endif() - -add_test(NAME Bitmap_cubical_complex_example_periodic_boundary_conditions_2d_torus - COMMAND $<TARGET_FILE:Bitmap_cubical_complex_periodic_boundary_conditions> - "${CMAKE_SOURCE_DIR}/data/bitmap/2d_torus.txt") - -add_test(NAME Bitmap_cubical_complex_example_periodic_boundary_conditions_3d_torus - COMMAND $<TARGET_FILE:Bitmap_cubical_complex_periodic_boundary_conditions> - "${CMAKE_SOURCE_DIR}/data/bitmap/3d_torus.txt") - -install(TARGETS Bitmap_cubical_complex DESTINATION bin) install(TARGETS Random_bitmap_cubical_complex DESTINATION bin) -install(TARGETS Bitmap_cubical_complex_periodic_boundary_conditions DESTINATION bin) diff --git a/example/Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp b/example/Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp index 16ad65a0..f70558f2 100644 --- a/example/Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp +++ b/example/Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp @@ -20,7 +20,6 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ - // for persistence algorithm #include <gudhi/reader_utils.h> #include <gudhi/Bitmap_cubical_complex.h> @@ -34,10 +33,11 @@ int main(int argc, char** argv) { srand(time(0)); - std::cout << "This program computes persistent homology, by using bitmap_cubical_complex class, of cubical " << - "complexes. The first parameter of the program is the dimension D of the bitmap. The next D parameters are " << - "number of top dimensional cubes in each dimension of the bitmap. The program will create random cubical " << - "complex of that sizes and compute persistent homology of it." << std::endl; + std::cout + << "This program computes persistent homology, by using bitmap_cubical_complex class, of cubical " + << "complexes. The first parameter of the program is the dimension D of the bitmap. The next D parameters are " + << "number of top dimensional cubes in each dimension of the bitmap. The program will create random cubical " + << "complex of that sizes and compute persistent homology of it." << std::endl; int p = 2; double min_persistence = 0; @@ -47,16 +47,16 @@ int main(int argc, char** argv) { return 1; } - size_t dimensionOfBitmap = (size_t) atoi(argv[1]); - std::vector< unsigned > sizes; + size_t dimensionOfBitmap = (size_t)atoi(argv[1]); + std::vector<unsigned> sizes; size_t multipliers = 1; for (size_t dim = 0; dim != dimensionOfBitmap; ++dim) { - unsigned sizeInThisDimension = (unsigned) atoi(argv[2 + dim]); + unsigned sizeInThisDimension = (unsigned)atoi(argv[2 + dim]); sizes.push_back(sizeInThisDimension); multipliers *= sizeInThisDimension; } - std::vector< double > data; + std::vector<double> data; for (size_t i = 0; i != multipliers; ++i) { data.push_back(rand() / static_cast<double>(RAND_MAX)); } @@ -80,4 +80,3 @@ int main(int argc, char** argv) { return 0; } - |