From 39ffc7af64543f0b2ce17487771afbd010a97349 Mon Sep 17 00:00:00 2001 From: pdlotko Date: Fri, 27 Nov 2015 14:16:44 +0000 Subject: Adding changes to the cubcial complex class according to Marc and Vincent's comments. git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bitmap@930 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: cb9134a5c18fae3e2e63bbaf8329dd168d08d3b3 --- .../example/Bitmap_cubical_complex.cpp | 147 ++++++++--------- src/Bitmap_cubical_complex/example/CMakeLists.txt | 2 +- .../example/Random_bitmap_cubical_complex.cpp | 174 +++++++++++---------- 3 files changed, 170 insertions(+), 153 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 37c16618..31da3609 100644 --- a/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex.cpp +++ b/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex.cpp @@ -1,71 +1,76 @@ -/* 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 Sophia-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 - -#include - -// standard stuff -#include -#include - -using namespace Gudhi; -using namespace Gudhi::persistent_cohomology; -using namespace std; - -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 numbed in the first line is a dimension D of a cubical " - "complex. 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 cubical complex at the " - "input. The program will now terminate.\n"; - return 1; - } - - Bitmap_cubical_complex b(argv[1]); - - - // Compute the persistence diagram of the complex - persistent_cohomology::Persistent_cohomology< Bitmap_cubical_complex, Field_Zp > pcoh(b); - pcoh.init_coefficients(p); // initializes 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 . + */ + + +//for persistence algorithm +#include +#include +#include + + +using namespace Gudhi; +using namespace Gudhi::Cubical_complex; +using namespace Gudhi::persistent_cohomology; + +//standard stuff +#include +#include + +using namespace std; + +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; + + 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 b( argv[1] ); + + + // Compute the persistence diagram of the complex + persistent_cohomology::Persistent_cohomology< Bitmap_cubical_complex, Field_Zp > pcoh(b); + 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; +} diff --git a/src/Bitmap_cubical_complex/example/CMakeLists.txt b/src/Bitmap_cubical_complex/example/CMakeLists.txt index 05ef1319..dd252a79 100644 --- a/src/Bitmap_cubical_complex/example/CMakeLists.txt +++ b/src/Bitmap_cubical_complex/example/CMakeLists.txt @@ -1,5 +1,5 @@ cmake_minimum_required(VERSION 2.6) -project(GUDHISimplexTreeFromFile) +project(GUDHIBitmap) add_executable ( Bitmap_cubical_complex Bitmap_cubical_complex.cpp ) target_link_libraries(Bitmap_cubical_complex ${Boost_SYSTEM_LIBRARY}) 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 ac7557ce..60cfc113 100644 --- a/src/Bitmap_cubical_complex/example/Random_bitmap_cubical_complex.cpp +++ b/src/Bitmap_cubical_complex/example/Random_bitmap_cubical_complex.cpp @@ -1,81 +1,93 @@ -/* 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 - -#include - -// standard stuff -#include -#include -#include -#include -#include - -using namespace Gudhi; -using namespace Gudhi::persistent_cohomology; -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 cubical complex. The next D parameters are number " - "of top dimensional cubes in each dimension of the cubical complex. The program will create random cubical " - "complex of that sizes and compute persistent homology of it." << endl; - - int p = 2; - double min_persistence = 0; - - 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 b(sizes, data); - - // Compute the persistence diagram of the complex - persistent_cohomology::Persistent_cohomology< Bitmap_cubical_complex, Field_Zp > pcoh(b); - pcoh.init_coefficients(p); // initializes the coefficient field for homology - pcoh.compute_persistent_cohomology(min_persistence); - - stringstream ss; - ss << "randomComplex_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 . + */ + + +//for persistence algorithm +#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 ) +{ + 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 b( sizes , data ); + + + // Compute the persistence diagram of the complex + persistent_cohomology::Persistent_cohomology< Bitmap_cubical_complex, 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((char*)ss.str().c_str()); + pcoh.output_diagram(out); + out.close(); + + return 0; +} -- cgit v1.2.3