From a4cbfdacbce7d813d5e48298e8a6b31e12c2670c Mon Sep 17 00:00:00 2001 From: "hub.wag@gmail.com" Date: Tue, 2 Apr 2013 20:24:37 +0000 Subject: Added bit-tree pivot representation. It's available from the command line tool and included in self-test. git-svn-id: https://phat.googlecode.com/svn/branches/bit-tree@19 8e3bb3c2-eed4-f18f-5264-0b6c94e6926d --- src/phat.cpp | 37 ++++--- src/self_test.cpp | 323 ++++++++++++++++++++++++++++-------------------------- 2 files changed, 192 insertions(+), 168 deletions(-) (limited to 'src') diff --git a/src/phat.cpp b/src/phat.cpp index a98827c..6757d3c 100644 --- a/src/phat.cpp +++ b/src/phat.cpp @@ -21,15 +21,16 @@ #include #include #include -#include +#include +#include #include -#include +#include #include #include -enum Representation_type {VEC_VEC, VEC_SET, SPARSE_PIVOT, FULL_PIVOT}; +enum Representation_type {VEC_VEC, VEC_SET, SPARSE_PIVOT, FULL_PIVOT, BIT_TREE_PIVOT}; enum Algorithm_type {STANDARD, TWIST, ROW, CHUNK }; void print_help() { @@ -42,23 +43,23 @@ void print_help() { std::cerr << "--help -- prints this screen" << std::endl; std::cerr << "--verbose -- verbose output" << std::endl; std::cerr << "--dualize -- use dualization approach" << std::endl; - std::cerr << "--vec-vec, --vec-set, --full-pivot, --sparse-pivot -- selects a representation data structure for boundary matrices (default is '--sparse-pivot')" << std::endl; + std::cerr << "--vec-vec, --vec-set, --full-pivot, --sparse-pivot, --bit-tree-pivot -- selects a representation data structure for boundary matrices (default is '--sparse-pivot')" << std::endl; std::cerr << "--standard, --twist, --chunk, --row -- selects a reduction algorithm (default is '--twist')" << std::endl; } void print_help_and_exit() { print_help(); exit( EXIT_FAILURE ); -} +} void parse_command_line( int argc, char** argv, bool& use_binary, Representation_type& rep_type, Algorithm_type& reduction, std::string& input_filename, std::string& output_filename, bool& verbose, bool& dualize ) { - + if( argc < 3 ) print_help_and_exit(); input_filename = argv[ argc - 2 ]; output_filename = argv[ argc - 1 ]; - + for( int idx = 1; idx < argc - 2; idx++ ) { const std::string option = argv[ idx ]; @@ -68,6 +69,7 @@ void parse_command_line( int argc, char** argv, bool& use_binary, Representation else if( option == "--vec-vec" ) rep_type = VEC_VEC; else if( option == "--vec-set" ) rep_type = VEC_SET; else if( option == "--full-pivot" ) rep_type = FULL_PIVOT; + else if( option == "--bit-tree-pivot" ) rep_type = BIT_TREE_PIVOT; else if( option == "--sparse-pivot" ) rep_type = SPARSE_PIVOT; else if( option == "--standard" ) reduction = STANDARD; else if( option == "--twist" ) reduction = TWIST; @@ -79,13 +81,13 @@ void parse_command_line( int argc, char** argv, bool& use_binary, Representation } } -#define LOG(msg) if( verbose ) std::cout << msg << std::endl; +#define LOG(msg) if( verbose ) std::cout << msg << std::endl; template void generic_compute_pairing( std::string input_filename, std::string output_filename, - bool use_binary, - bool verbose, + bool use_binary, + bool verbose, bool dualize ) { phat::boundary_matrix< Representation > matrix; @@ -93,7 +95,7 @@ void generic_compute_pairing( std::string input_filename, double read_timer = omp_get_wtime(); if( use_binary ) { - LOG( "Reading input file " << input_filename << " in binary mode" ) + LOG( "Reading input file " << input_filename << " in binary mode" ) read_successful = matrix.load_binary( input_filename ); } else { LOG( "Reading input file " << input_filename << " in ascii mode" ) @@ -111,7 +113,7 @@ void generic_compute_pairing( std::string input_filename, LOG( "Computing persistence pairs ..." ) if( dualize ) phat::compute_persistence_pairs_dualized< Algorithm > ( pairs, matrix ); - else + else phat::compute_persistence_pairs < Algorithm > ( pairs, matrix ); LOG( "Computing persistence pairs took " << omp_get_wtime() - pairs_timer <<"s" ) @@ -124,12 +126,12 @@ void generic_compute_pairing( std::string input_filename, pairs.save_ascii( output_filename ); } LOG( "Writing output file took " << omp_get_wtime() - write_timer <<"s" ) - + } #define CALL_GENERIC_CODE(rep,alg) generic_compute_pairing < rep, alg >( input_filename, output_filename, use_binary, verbose, dualize ); -int main( int argc, char** argv ) +int main( int argc, char** argv ) { bool use_binary = true; // interpret input as binary or ascii file Representation_type rep_type = SPARSE_PIVOT; // representation class @@ -163,6 +165,13 @@ int main( int argc, char** argv ) case CHUNK: CALL_GENERIC_CODE(phat::full_pivot_column, phat::chunk_reduction) break; } break; + case BIT_TREE_PIVOT: switch( reduction ) { + case STANDARD: CALL_GENERIC_CODE(phat::bit_tree_pivot_column, phat::standard_reduction) break; + case TWIST: CALL_GENERIC_CODE(phat::bit_tree_pivot_column, phat::twist_reduction) break; + case ROW: CALL_GENERIC_CODE(phat::bit_tree_pivot_column, phat::row_reduction) break; + case CHUNK: CALL_GENERIC_CODE(phat::bit_tree_pivot_column, phat::chunk_reduction) break; + } break; + case SPARSE_PIVOT: switch( reduction ) { case STANDARD: CALL_GENERIC_CODE(phat::sparse_pivot_column, phat::standard_reduction) break; case TWIST: CALL_GENERIC_CODE(phat::sparse_pivot_column, phat::twist_reduction) break; diff --git a/src/self_test.cpp b/src/self_test.cpp index 4764874..b3cddc2 100644 --- a/src/self_test.cpp +++ b/src/self_test.cpp @@ -1,154 +1,169 @@ -/* Copyright 2013 IST Austria - Contributed by: Ulrich Bauer, Michael Kerber, Jan Reininghaus - - This file is part of PHAT. - - PHAT is free software: you can redistribute it and/or modify - it under the terms of the GNU Lesser General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - PHAT 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 Lesser General Public License for more details. - - You should have received a copy of the GNU Lesser General Public License - along with PHAT. If not, see . */ - -#include - -#include -#include -#include -#include - -#include -#include -#include -#include - -int main( int argc, char** argv ) -{ - std::string test_data = argc > 1 ? argv[ 1 ] : "examples/torus.bin"; - - typedef phat::sparse_pivot_column Sparse; - typedef phat::full_pivot_column Full; - typedef phat::vector_vector Vec_vec; - typedef phat::vector_set Vec_set; - - std::cout << "Reading test data " << test_data << " in binary format ..." << std::endl; - phat::boundary_matrix< Full > boundary_matrix; - if( !boundary_matrix.load_binary( test_data ) ) { - std::cerr << "Error: test data " << test_data << " not found!" << std::endl; - return EXIT_FAILURE; - } - - bool error = false; - std::cout << "Comparing representations using Chunk algorithm ..." << std::endl; - { - std::cout << "Running Chunk - Sparse ..." << std::endl; - phat::persistence_pairs sparse_pairs; - phat::boundary_matrix< Sparse > sparse_boundary_matrix = boundary_matrix; - phat::compute_persistence_pairs< phat::chunk_reduction >( sparse_pairs, sparse_boundary_matrix ); - - std::cout << "Running Chunk - Full ..." << std::endl; - phat::persistence_pairs full_pairs; - phat::boundary_matrix< Full > full_boundary_matrix = boundary_matrix; - phat::compute_persistence_pairs< phat::chunk_reduction >( full_pairs, full_boundary_matrix ); - - std::cout << "Running Chunk - Vec_vec ..." << std::endl; - phat::persistence_pairs vec_vec_pairs; - phat::boundary_matrix< Vec_vec > vec_vec_boundary_matrix = boundary_matrix; - phat::compute_persistence_pairs< phat::chunk_reduction >( vec_vec_pairs, vec_vec_boundary_matrix ); - - std::cout << "Running Chunk - Vec_set ..." << std::endl; - phat::persistence_pairs vec_set_pairs; - phat::boundary_matrix< Vec_set > vec_set_boundary_matrix = boundary_matrix; - phat::compute_persistence_pairs< phat::chunk_reduction >( vec_set_pairs, vec_set_boundary_matrix ); - - if( sparse_pairs != full_pairs ) { - std::cerr << "Error: sparse and full differ!" << std::endl; - error = true; - } - if( full_pairs != vec_vec_pairs ) { - std::cerr << "Error: full and vec_vec differ!" << std::endl; - error = true; - } - if( vec_vec_pairs != vec_set_pairs ) { - std::cerr << "Error: vec_vec and vec_set differ!" << std::endl; - error = true; - } - if( vec_set_pairs != sparse_pairs ) { - std::cerr << "Error: vec_set and sparse differ!" << std::endl; - error = true; - } - - if( error ) return EXIT_FAILURE; - else std::cout << "All results are identical (as they should be)" << std::endl; - } - - std::cout << "Comparing algorithms using full_pivot_column representation ..." << std::endl; - { - std::cout << "Running Twist - Full ..." << std::endl; - phat::persistence_pairs twist_pairs; - phat::boundary_matrix< Full > twist_boundary_matrix = boundary_matrix; - phat::compute_persistence_pairs< phat::twist_reduction >( twist_pairs, twist_boundary_matrix ); - - std::cout << "Running Standard - Full ..." << std::endl; - phat::persistence_pairs std_pairs; - phat::boundary_matrix< Full > std_boundary_matrix = boundary_matrix; - phat::compute_persistence_pairs< phat::standard_reduction >( std_pairs, std_boundary_matrix ); - - std::cout << "Running Chunk - Full ..." << std::endl; - phat::persistence_pairs chunk_pairs; - phat::boundary_matrix< Full > chunk_boundary_matrix = boundary_matrix; - phat::compute_persistence_pairs< phat::chunk_reduction >( chunk_pairs, chunk_boundary_matrix ); - - std::cout << "Running Row - Full ..." << std::endl; - phat::persistence_pairs row_pairs; - phat::boundary_matrix< Full > row_boundary_matrix = boundary_matrix; - phat::compute_persistence_pairs< phat::row_reduction >( row_pairs, row_boundary_matrix ); - - if( twist_pairs != std_pairs ) { - std::cerr << "Error: twist and standard differ!" << std::endl; - error = true; - } - if( std_pairs != chunk_pairs ) { - std::cerr << "Error: standard and chunk differ!" << std::endl; - error = true; - } - if( chunk_pairs != row_pairs ) { - std::cerr << "Error: chunk and row differ!" << std::endl; - error = true; - } - if( row_pairs != twist_pairs ) { - std::cerr << "Error: row and twist differ!" << std::endl; - error = true; - } - - if( error ) return EXIT_FAILURE; - else std::cout << "All results are identical (as they should be)" << std::endl; - } - - std::cout << "Comparing primal and dual approach using Chunk - Full ..." << std::endl; - { - phat::persistence_pairs primal_pairs; - phat::boundary_matrix< Full > primal_boundary_matrix = boundary_matrix; - phat::compute_persistence_pairs< phat::chunk_reduction >( primal_pairs, primal_boundary_matrix ); - - phat::persistence_pairs dual_pairs; - phat::boundary_matrix< Full > dual_boundary_matrix = boundary_matrix; - phat::compute_persistence_pairs_dualized< phat::chunk_reduction >( dual_pairs, dual_boundary_matrix ); - - if( primal_pairs != dual_pairs ) { - std::cerr << "Error: primal and dual differ!" << std::endl; - error = true; - } - - if( error ) return EXIT_FAILURE; - else std::cout << "All results are identical (as they should be)" << std::endl; - } - - return EXIT_SUCCESS; -} +/* Copyright 2013 IST Austria + Contributed by: Ulrich Bauer, Michael Kerber, Jan Reininghaus + + This file is part of PHAT. + + PHAT is free software: you can redistribute it and/or modify + it under the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + PHAT 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 Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public License + along with PHAT. If not, see . */ + +#include + +#include +#include +#include +#include +#include + +#include +#include +#include +#include + +int main( int argc, char** argv ) +{ + std::string test_data = argc > 1 ? argv[ 1 ] : "torus.bin"; + + typedef phat::sparse_pivot_column Sparse; + typedef phat::full_pivot_column Full; + typedef phat::bit_tree_pivot_column BitTree; + typedef phat::vector_vector Vec_vec; + typedef phat::vector_set Vec_set; + + std::cout << "Reading test data " << test_data << " in binary format ..." << std::endl; + phat::boundary_matrix< Full > boundary_matrix; + if( !boundary_matrix.load_binary( test_data ) ) { + std::cerr << "Error: test data " << test_data << " not found!" << std::endl; + return EXIT_FAILURE; + } + + bool error = false; + std::cout << "Comparing representations using Chunk algorithm ..." << std::endl; + { + std::cout << "Running Chunk - Sparse ..." << std::endl; + phat::persistence_pairs sparse_pairs; + phat::boundary_matrix< Sparse > sparse_boundary_matrix = boundary_matrix; + phat::compute_persistence_pairs< phat::chunk_reduction >( sparse_pairs, sparse_boundary_matrix ); + + std::cout << "Running Chunk - Full ..." << std::endl; + phat::persistence_pairs full_pairs; + phat::boundary_matrix< Full > full_boundary_matrix = boundary_matrix; + phat::compute_persistence_pairs< phat::chunk_reduction >( full_pairs, full_boundary_matrix ); + + std::cout << "Running Chunk - BitTree ..." << std::endl; + phat::persistence_pairs bit_tree_pairs; + phat::boundary_matrix< BitTree > bit_tree_boundary_matrix = boundary_matrix; + phat::compute_persistence_pairs< phat::chunk_reduction >( bit_tree_pairs, bit_tree_boundary_matrix ); + + std::cout << "Running Chunk - Vec_vec ..." << std::endl; + phat::persistence_pairs vec_vec_pairs; + phat::boundary_matrix< Vec_vec > vec_vec_boundary_matrix = boundary_matrix; + phat::compute_persistence_pairs< phat::chunk_reduction >( vec_vec_pairs, vec_vec_boundary_matrix ); + + std::cout << "Running Chunk - Vec_set ..." << std::endl; + phat::persistence_pairs vec_set_pairs; + phat::boundary_matrix< Vec_set > vec_set_boundary_matrix = boundary_matrix; + phat::compute_persistence_pairs< phat::chunk_reduction >( vec_set_pairs, vec_set_boundary_matrix ); + + if( sparse_pairs != full_pairs ) { + std::cerr << "Error: sparse and full differ!" << std::endl; + error = true; + } + if( full_pairs != vec_vec_pairs ) { + std::cerr << "Error: full and vec_vec differ!" << std::endl; + error = true; + } + if( vec_vec_pairs != vec_set_pairs ) { + std::cerr << "Error: vec_vec and vec_set differ!" << std::endl; + error = true; + } + if( vec_set_pairs != sparse_pairs ) { + std::cerr << "Error: vec_set and sparse differ!" << std::endl; + error = true; + } + if( bit_tree_pairs != sparse_pairs ) { + std::cerr << "Error: bit_tree and sparse differ!" << std::endl; + error = true; + } + if( bit_tree_pairs != vec_set_pairs ) { + std::cerr << "Error: bit_tree and vec_vec differ!" << std::endl; + error = true; + } + + if( error ) return EXIT_FAILURE; + else std::cout << "All results are identical (as they should be)" << std::endl; + } + + std::cout << "Comparing algorithms using full_pivot_column representation ..." << std::endl; + { + std::cout << "Running Twist - Full ..." << std::endl; + phat::persistence_pairs twist_pairs; + phat::boundary_matrix< Full > twist_boundary_matrix = boundary_matrix; + phat::compute_persistence_pairs< phat::twist_reduction >( twist_pairs, twist_boundary_matrix ); + + std::cout << "Running Standard - Full ..." << std::endl; + phat::persistence_pairs std_pairs; + phat::boundary_matrix< Full > std_boundary_matrix = boundary_matrix; + phat::compute_persistence_pairs< phat::standard_reduction >( std_pairs, std_boundary_matrix ); + + std::cout << "Running Chunk - Full ..." << std::endl; + phat::persistence_pairs chunk_pairs; + phat::boundary_matrix< Full > chunk_boundary_matrix = boundary_matrix; + phat::compute_persistence_pairs< phat::chunk_reduction >( chunk_pairs, chunk_boundary_matrix ); + + std::cout << "Running Row - Full ..." << std::endl; + phat::persistence_pairs row_pairs; + phat::boundary_matrix< Full > row_boundary_matrix = boundary_matrix; + phat::compute_persistence_pairs< phat::row_reduction >( row_pairs, row_boundary_matrix ); + + if( twist_pairs != std_pairs ) { + std::cerr << "Error: twist and standard differ!" << std::endl; + error = true; + } + if( std_pairs != chunk_pairs ) { + std::cerr << "Error: standard and chunk differ!" << std::endl; + error = true; + } + if( chunk_pairs != row_pairs ) { + std::cerr << "Error: chunk and row differ!" << std::endl; + error = true; + } + if( row_pairs != twist_pairs ) { + std::cerr << "Error: row and twist differ!" << std::endl; + error = true; + } + + if( error ) return EXIT_FAILURE; + else std::cout << "All results are identical (as they should be)" << std::endl; + } + + std::cout << "Comparing primal and dual approach using Chunk - Full ..." << std::endl; + { + phat::persistence_pairs primal_pairs; + phat::boundary_matrix< Full > primal_boundary_matrix = boundary_matrix; + phat::compute_persistence_pairs< phat::chunk_reduction >( primal_pairs, primal_boundary_matrix ); + + phat::persistence_pairs dual_pairs; + phat::boundary_matrix< Full > dual_boundary_matrix = boundary_matrix; + phat::compute_persistence_pairs_dualized< phat::chunk_reduction >( dual_pairs, dual_boundary_matrix ); + + if( primal_pairs != dual_pairs ) { + std::cerr << "Error: primal and dual differ!" << std::endl; + error = true; + } + + if( error ) return EXIT_FAILURE; + else std::cout << "All results are identical (as they should be)" << std::endl; + } + + return EXIT_SUCCESS; +} -- cgit v1.2.3