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Diffstat (limited to 'matching/include/phat/compute_persistence_pairs.h')
| -rw-r--r-- | matching/include/phat/compute_persistence_pairs.h | 128 |
1 files changed, 128 insertions, 0 deletions
diff --git a/matching/include/phat/compute_persistence_pairs.h b/matching/include/phat/compute_persistence_pairs.h new file mode 100644 index 0000000..48be65c --- /dev/null +++ b/matching/include/phat/compute_persistence_pairs.h @@ -0,0 +1,128 @@ +/* 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 <http://www.gnu.org/licenses/>. */ + +#pragma once + +#include <phat/persistence_pairs.h> +#include <phat/boundary_matrix.h> +#include <phat/helpers/dualize.h> +#include <phat/algorithms/twist_reduction.h> + +namespace phat { + // Extracts persistence pairs in separate dimensions from a reduced + // boundary matrix representing ``double`` filtration. The pairs + // give persistent relative homology of the pair of filtrations. + // TODO: Use it with standard reduction algorithm (no template option). + template< typename ReductionAlgorithm, typename Representation > + void compute_relative_persistence_pairs(std::vector<persistence_pairs>& pairs, boundary_matrix<Representation>& boundary_matrix, const std::map<int, int>& L) { + ReductionAlgorithm reduce; + reduce(boundary_matrix); + std::map<int, bool> free; + std::map<int, int> invL; + for (std::map<int, int>::const_iterator it = L.begin(); it != L.end(); ++it) { invL[it->second] = it->first; } + for (std::vector<persistence_pairs>::iterator it = pairs.begin(); it != pairs.end(); ++it) { it->clear(); } + for (index idx = 0; idx < boundary_matrix.get_num_cols(); ++idx) { + int dimension = boundary_matrix.get_dim(idx); + if (L.find(idx) != L.end()) { ++dimension; } + free[idx] = true; + if (!boundary_matrix.is_empty(idx)) { + index birth = boundary_matrix.get_max_index(idx); + index death = idx; + pairs[dimension-1].append_pair(birth, death); + free[birth] = false; + free[death] = false; + } else { + // This is an L-simplex and a (dimension+1)-dimensional cycle + if (L.find(idx) != L.end()) { + assert(dimension < pairs.size()); + pairs[dimension].append_pair(idx, -1); + } + } + } + for (std::map<int, bool>::iterator it = free.begin(); it != free.end(); ++it) { + if (it->second) { + int dimension = boundary_matrix.get_dim(it->first); + if (invL.find(it->first) == invL.end() && L.find(it->first) == L.end()) { + assert(dimension < pairs.size()); + pairs[dimension].append_pair(it->first, -1); + } + } + } + } + + // Extracts persistence pairs in separate dimensions; expects a d-dimensional vector of persistent_pairs + template< typename ReductionAlgorithm, typename Representation > + void compute_persistence_pairs(std::vector<persistence_pairs>& pairs, boundary_matrix<Representation>& boundary_matrix) { + ReductionAlgorithm reduce; + reduce(boundary_matrix); + std::map<int, bool> free; + for (std::vector<persistence_pairs>::iterator it = pairs.begin(); it != pairs.end(); ++it) { it->clear(); } + for (index idx = 0; idx < boundary_matrix.get_num_cols(); ++idx) { + int dimension = boundary_matrix.get_dim(idx); + free[idx] = true; + if (!boundary_matrix.is_empty(idx)) { + index birth = boundary_matrix.get_max_index(idx); + index death = idx; + pairs[dimension-1].append_pair(birth, death); + // Cannot be of the form (a, infinity) + free[birth] = false; + free[death] = false; + } + } + for (std::map<int, bool>::iterator it = free.begin(); it != free.end(); ++it) { + if (it->second) { + int dimension = boundary_matrix.get_dim(it->first); + pairs[dimension].append_pair(it->first, -1); + } + } + } + + template< typename ReductionAlgorithm, typename Representation > + void compute_persistence_pairs( persistence_pairs& pairs, boundary_matrix< Representation >& boundary_matrix ) { + ReductionAlgorithm reduce; + reduce( boundary_matrix ); + pairs.clear(); + for( index idx = 0; idx < boundary_matrix.get_num_cols(); idx++ ) { + if( !boundary_matrix.is_empty( idx ) ) { + index birth = boundary_matrix.get_max_index( idx ); + index death = idx; + pairs.append_pair( birth, death ); + } + } + } + + template< typename ReductionAlgorithm, typename Representation > + void compute_persistence_pairs_dualized( persistence_pairs& pairs, boundary_matrix< Representation >& boundary_matrix ) { + + dualize( boundary_matrix ); + compute_persistence_pairs< ReductionAlgorithm >( pairs, boundary_matrix ); + dualize_persistence_pairs( pairs, boundary_matrix.get_num_cols() ); + } + + template< typename Representation > + void compute_persistence_pairs( persistence_pairs& pairs, boundary_matrix< Representation >& boundary_matrix ) { + phat::compute_persistence_pairs< twist_reduction >( pairs, boundary_matrix ); + } + + + template< typename Representation > + void compute_persistence_pairs_dualized( persistence_pairs& pairs, boundary_matrix< Representation >& boundary_matrix ) { + compute_persistence_pairs_dualized< twist_reduction >( pairs, boundary_matrix ); + } + +} |