diff options
Diffstat (limited to 'src/Bitmap_cubical_complex/example')
4 files changed, 246 insertions, 0 deletions
diff --git a/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex.cpp b/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex.cpp new file mode 100644 index 00000000..7c7e8ac5 --- /dev/null +++ b/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex.cpp @@ -0,0 +1,72 @@ +/* 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 <sstream> +#include <vector> + +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; + + int p = 2; + double min_persistence = 0; + + 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); + pcoh.init_coefficients(p); // initializes the coefficient field for homology + pcoh.compute_persistent_cohomology(min_persistence); + + std::stringstream ss; + ss << argv[1] << "_persistence"; + std::ofstream out(ss.str().c_str()); + pcoh.output_diagram(out); + out.close(); + + std::cout << "Result in file: " << ss.str().c_str() << "\n"; + + return 0; +} + diff --git a/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex_periodic_boundary_conditions.cpp b/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex_periodic_boundary_conditions.cpp new file mode 100644 index 00000000..2c5d7fd3 --- /dev/null +++ b/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex_periodic_boundary_conditions.cpp @@ -0,0 +1,74 @@ +/* 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> + +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; + + int p = 2; + double min_persistence = 0; + + 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); + pcoh.init_coefficients(p); // initializes the coefficient field for homology + pcoh.compute_persistent_cohomology(min_persistence); + + std::stringstream ss; + ss << argv[1] << "_persistence"; + std::ofstream out(ss.str().c_str()); + pcoh.output_diagram(out); + out.close(); + + std::cout << "Result in file: " << ss.str().c_str() << "\n"; + + return 0; +} + diff --git a/src/Bitmap_cubical_complex/example/CMakeLists.txt b/src/Bitmap_cubical_complex/example/CMakeLists.txt new file mode 100644 index 00000000..8f9cfa80 --- /dev/null +++ b/src/Bitmap_cubical_complex/example/CMakeLists.txt @@ -0,0 +1,17 @@ +cmake_minimum_required(VERSION 2.6) +project(GUDHIBitmap) + +add_executable ( Bitmap_cubical_complex Bitmap_cubical_complex.cpp ) +target_link_libraries(Bitmap_cubical_complex ${Boost_SYSTEM_LIBRARY}) +add_test(Bitmap_cubical_complex_one_sphere ${CMAKE_CURRENT_BINARY_DIR}/Bitmap_cubical_complex ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalOneSphere.txt) +add_test(Bitmap_cubical_complex_two_sphere ${CMAKE_CURRENT_BINARY_DIR}/Bitmap_cubical_complex ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt) + +add_executable ( Random_bitmap_cubical_complex Random_bitmap_cubical_complex.cpp ) +target_link_libraries(Random_bitmap_cubical_complex ${Boost_SYSTEM_LIBRARY}) +add_test(Random_bitmap_cubical_complex ${CMAKE_CURRENT_BINARY_DIR}/Random_bitmap_cubical_complex 2 100 100) + +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}) +add_test(Bitmap_cubical_complex_periodic_2d_torus ${CMAKE_CURRENT_BINARY_DIR}/Bitmap_cubical_complex_periodic_boundary_conditions ${CMAKE_SOURCE_DIR}/data/bitmap/2d_torus.txt) +add_test(Bitmap_cubical_complex_periodic_3d_torus ${CMAKE_CURRENT_BINARY_DIR}/Bitmap_cubical_complex_periodic_boundary_conditions ${CMAKE_SOURCE_DIR}/data/bitmap/3d_torus.txt) + diff --git a/src/Bitmap_cubical_complex/example/Random_bitmap_cubical_complex.cpp b/src/Bitmap_cubical_complex/example/Random_bitmap_cubical_complex.cpp new file mode 100644 index 00000000..416ad8f2 --- /dev/null +++ b/src/Bitmap_cubical_complex/example/Random_bitmap_cubical_complex.cpp @@ -0,0 +1,83 @@ +/* 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/>. + */ + + +// for persistence algorithm +#include <gudhi/reader_utils.h> +#include <gudhi/Bitmap_cubical_complex.h> +#include <gudhi/Persistent_cohomology.h> + +// standard stuff +#include <iostream> +#include <sstream> +#include <vector> + +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; + + int p = 2; + double min_persistence = 0; + + if (argc < 3) { + std::cerr << "Wrong number of parameters, the program will now terminate\n"; + return 1; + } + + 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]); + sizes.push_back(sizeInThisDimension); + multipliers *= sizeInThisDimension; + } + + std::vector< double > data; + for (size_t i = 0; i != multipliers; ++i) { + data.push_back(rand() / static_cast<double>(RAND_MAX)); + } + + 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; + Bitmap_cubical_complex b(sizes, data); + + // Compute the persistence diagram of the complex + typedef Gudhi::persistent_cohomology::Field_Zp Field_Zp; + typedef Gudhi::persistent_cohomology::Persistent_cohomology<Bitmap_cubical_complex, Field_Zp> Persistent_cohomology; + Persistent_cohomology pcoh(b); + pcoh.init_coefficients(p); // initializes the coefficient field for homology + pcoh.compute_persistent_cohomology(min_persistence); + + std::stringstream ss; + ss << "randomComplex_persistence"; + std::ofstream out(ss.str().c_str()); + pcoh.output_diagram(out); + out.close(); + + return 0; +} + |