From d1a3b2267b7e638b5d868720cf46987641b22132 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 29 Mar 2016 16:05:12 +0000 Subject: Merge VR_bitmap git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bitmap@1074 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 4c9ac225ffcfb924371c72fccc44cbd6ecb3d6e3 --- .../example/Bitmap_cubical_complex.cpp | 107 +++++++------- ...ubical_complex_periodic_boundary_conditions.cpp | 134 ++++++++--------- src/Bitmap_cubical_complex/example/CMakeLists.txt | 11 +- .../example/Random_bitmap_cubical_complex.cpp | 159 ++++++++++----------- 4 files changed, 193 insertions(+), 218 deletions(-) (limited to 'src/Bitmap_cubical_complex/example') diff --git a/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex.cpp b/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex.cpp index 4c30ee85..7c7e8ac5 100644 --- a/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex.cpp +++ b/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex.cpp @@ -1,73 +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 . - */ +/* 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 - -using namespace Gudhi; -using namespace Gudhi::Cubical_complex; -using namespace Gudhi::persistent_cohomology; - -//standard stuff +// standard stuff #include #include #include -using namespace std; +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; -int main( int argc , char** argv ) -{ - 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." << 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; + } - int p = 2; - double min_persistence = 0; + 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; - if ( argc != 2 ) - { - cout << "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; - } + Bitmap_cubical_complex b(argv[1]); - Bitmap_cubical_complex< Bitmap_cubical_complex_base > 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); - // Compute the persistence diagram of the complex - persistent_cohomology::Persistent_cohomology< Bitmap_cubical_complex< Bitmap_cubical_complex_base >, Field_Zp > pcoh(b); - pcoh.init_coefficients( p ); //initilizes the coefficient field for homology + std::stringstream ss; + ss << argv[1] << "_persistence"; + std::ofstream out(ss.str().c_str()); + pcoh.output_diagram(out); + out.close(); - pcoh.compute_persistent_cohomology( min_persistence ); + std::cout << "Result in file: " << ss.str().c_str() << "\n"; - stringstream ss; - ss << argv[1] << "_persistence"; - std::ofstream out((char*)ss.str().c_str()); - pcoh.output_diagram(out); - out.close(); - - return 0; + 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 index df01240b..2c5d7fd3 100644 --- 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 @@ -1,24 +1,24 @@ - /* 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 . - */ +/* 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 @@ -26,59 +26,49 @@ #include #include -using namespace Gudhi; -using namespace Gudhi::Cubical_complex; -using namespace Gudhi::persistent_cohomology; - -//standard stuff +// standard stuff #include #include #include -using namespace std; - -int main( int argc , char** argv ) -{ - clock_t beginOfProgram = clock(); - - 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." << endl; - - int p = 2; - double min_persistence = 0; - - if ( argc != 2 ) - { - cout << "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; - } - - Bitmap_cubical_complex< Bitmap_cubical_complex_periodic_boundary_conditions_base > b( argv[1] ); - - cerr << "Here \n"; - - clock_t endCreateBitmap = clock(); - double elapsed_secsCreateBitmap = double(endCreateBitmap - beginOfProgram) / CLOCKS_PER_SEC; - cerr << "Time of creation of bitmap : " << elapsed_secsCreateBitmap << endl; - - - - // Compute the persistence diagram of the complex - persistent_cohomology::Persistent_cohomology< Bitmap_cubical_complex< Bitmap_cubical_complex_periodic_boundary_conditions_base >, Field_Zp > pcoh(b,true); - pcoh.init_coefficients( p ); //initilizes the coefficient field for homology - pcoh.compute_persistent_cohomology( min_persistence ); - - - stringstream ss; - ss << argv[1] << "_persistence"; - std::ofstream out((char*)ss.str().c_str()); - pcoh.output_diagram(out); - out.close(); - - clock_t endOfProgram = clock(); - double elapsed_secsOfProgram = double(endOfProgram - beginOfProgram) / CLOCKS_PER_SEC; - cerr << "Overall execution time : " << elapsed_secsOfProgram << endl; - return 0; +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 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); + 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 index 088e6fbd..8f9cfa80 100644 --- a/src/Bitmap_cubical_complex/example/CMakeLists.txt +++ b/src/Bitmap_cubical_complex/example/CMakeLists.txt @@ -3,8 +3,8 @@ 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 ${CMAKE_CURRENT_BINARY_DIR}/Bitmap_cubical_complex ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalOneSphere.txt) -add_test(Bitmap_cubical_complex ${CMAKE_CURRENT_BINARY_DIR}/Bitmap_cubical_complex ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt) +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}) @@ -12,9 +12,6 @@ add_test(Random_bitmap_cubical_complex ${CMAKE_CURRENT_BINARY_DIR}/Random_bitmap 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) -#add_executable ( Compute_persistence_with_phat Compute_persistence_with_phat.cpp ) -#target_link_libraries(Compute_persistence_with_phat ${Boost_SYSTEM_LIBRARY}) - -#add_executable ( periodic_boundary_conditions_phat periodic_boundary_conditions_phat.cpp ) -#target_link_libraries(periodic_boundary_conditions_phat ${Boost_SYSTEM_LIBRARY}) \ No newline at end of file diff --git a/src/Bitmap_cubical_complex/example/Random_bitmap_cubical_complex.cpp b/src/Bitmap_cubical_complex/example/Random_bitmap_cubical_complex.cpp index 8b7f6a04..416ad8f2 100644 --- a/src/Bitmap_cubical_complex/example/Random_bitmap_cubical_complex.cpp +++ b/src/Bitmap_cubical_complex/example/Random_bitmap_cubical_complex.cpp @@ -1,94 +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 . - */ - - -//for persistence algorithm +/* 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 . + */ + + +// for persistence algorithm #include #include #include - -using namespace Gudhi; -using namespace Gudhi::Cubical_complex; -using namespace Gudhi::persistent_cohomology; - -//standard stuff +// standard stuff #include #include #include -using namespace std; - -int main( int argc , char** argv ) -{ - srand( time(0) ); - - 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." << endl; - - int p = 2; - double min_persistence = 0; - - if ( argc < 3 ) - { - 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()/(double)RAND_MAX ); - } - - Bitmap_cubical_complex< Bitmap_cubical_complex_base > b( sizes , data ); - - - - - - // Compute the persistence diagram of the complex - persistent_cohomology::Persistent_cohomology< Bitmap_cubical_complex< Bitmap_cubical_complex_base >, Field_Zp > pcoh(b); - pcoh.init_coefficients( p ); //initilizes the coefficient field for homology - pcoh.compute_persistent_cohomology( min_persistence ); - - - stringstream ss; - ss << "randomComplex_persistence"; - std::ofstream out(ss.str().c_str()); - pcoh.output_diagram(out); - out.close(); - - return 0; +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(RAND_MAX)); + } + + typedef Gudhi::Cubical_complex::Bitmap_cubical_complex_base Bitmap_cubical_complex_base; + typedef Gudhi::Cubical_complex::Bitmap_cubical_complex 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 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; } + -- cgit v1.2.3