From 7fe2c44c56e4fbd176131f31bc4338932f7a9d32 Mon Sep 17 00:00:00 2001 From: pdlotko Date: Fri, 5 Feb 2016 12:24:49 +0000 Subject: Over here I have linkd phat with Gudhi. So far it is done only for cubical complexes, but since I am ONLY using Filtration_simplex_iterator, there should be no problem to have it run with any other class we have. git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bitmap@1004 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: ddb3e2c5fa0c2a816e7435c57d32c0644f8163d2 --- ...ubical_complex_periodic_boundary_conditions.cpp | 159 +++++++++++---------- src/Bitmap_cubical_complex/example/CMakeLists.txt | 2 + .../example/Compute_persistence_with_phat.cpp | 60 ++++++++ 3 files changed, 146 insertions(+), 75 deletions(-) create mode 100644 src/Bitmap_cubical_complex/example/Compute_persistence_with_phat.cpp (limited to 'src/Bitmap_cubical_complex') 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 3d80c96d..df01240b 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 @@ -1,75 +1,84 @@ - /* 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 -#include -#include -#include - -using namespace std; - -int main( int argc , char** argv ) -{ - 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] ); - - - // 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(); - - return 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 . + */ + + +#include +#include +#include +#include + +using namespace Gudhi; +using namespace Gudhi::Cubical_complex; +using namespace Gudhi::persistent_cohomology; + +//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; +} diff --git a/src/Bitmap_cubical_complex/example/CMakeLists.txt b/src/Bitmap_cubical_complex/example/CMakeLists.txt index 26796e9d..fbd1b28b 100644 --- a/src/Bitmap_cubical_complex/example/CMakeLists.txt +++ b/src/Bitmap_cubical_complex/example/CMakeLists.txt @@ -13,3 +13,5 @@ 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_executable ( Compute_persistence_with_phat Compute_persistence_with_phat.cpp ) +target_link_libraries(Compute_persistence_with_phat ${Boost_SYSTEM_LIBRARY}) \ No newline at end of file diff --git a/src/Bitmap_cubical_complex/example/Compute_persistence_with_phat.cpp b/src/Bitmap_cubical_complex/example/Compute_persistence_with_phat.cpp new file mode 100644 index 00000000..fe9be33e --- /dev/null +++ b/src/Bitmap_cubical_complex/example/Compute_persistence_with_phat.cpp @@ -0,0 +1,60 @@ + + /* 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 +#include + +using namespace Gudhi; +using namespace Gudhi::Cubical_complex; + +//standard stuff +#include +#include +#include + +using namespace std; + + +int main( int argc , char** argv ) +{ + 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_base > b( argv[1] ); + cerr << "Cubical complex created \n"; + + + Compute_persistence_with_phat< Bitmap_cubical_complex< Bitmap_cubical_complex_base > , double > phat(&b); + phat::persistence_pairs pairs = phat.compute_persistence_pairs_dualized_chunk_reduction(); + std::pair< std::vector< std::vector > , std::vector< std::vector< std::pair > > > persistence = phat.get_the_intervals( pairs ); + writeBettiNumbersAndPersistenceIntervalsToFile( "phat_persistence" , persistence ); + + return 0; +} -- cgit v1.2.3