diff options
| -rw-r--r-- | ripser.cpp | 174 |
1 files changed, 170 insertions, 4 deletions
@@ -192,6 +192,22 @@ public: size_t size() const { return rows.size(); } }; +class sparse_distance_matrix { +public: + std::vector<std::vector<diameter_index_t>> neighbors; + + template <typename DistanceMatrix> + sparse_distance_matrix(const DistanceMatrix& mat, value_t threshold) : neighbors(mat.size()) { + + for (index_t i = 0; i < size(); ++i) + for (index_t j = 0; j < size(); ++j) + if (i != j && mat(i, j) <= threshold) + neighbors[i].push_back(std::make_pair(mat(i, j), j)); + } + + size_t size() const { return neighbors.size(); } +}; + template <> void compressed_distance_matrix<LOWER_TRIANGULAR>::init_rows() { value_t* pointer = &distances[0]; for (index_t i = 1; i < size(); ++i) { @@ -355,6 +371,12 @@ public: } }; +template <typename Heap> +void push_entry(Heap& column, index_t i, coefficient_t c, value_t diameter) { + entry_t e = make_entry(i, c); + column.push(std::make_pair(diameter, e)); +} + template <typename DistanceMatrix> class ripser { DistanceMatrix dist; index_t n, dim_max; @@ -364,6 +386,8 @@ template <typename DistanceMatrix> class ripser { const binomial_coeff_table binomial_coeff; std::vector<coefficient_t> multiplicative_inverse; mutable std::vector<index_t> vertices; + mutable std::vector<std::vector<diameter_index_t>::const_reverse_iterator> neighbor_it; + mutable std::vector<std::vector<diameter_index_t>::const_reverse_iterator> neighbor_end; mutable std::vector<diameter_entry_t> coface_entries; public: @@ -392,6 +416,10 @@ public: return v; } + index_t get_edge_index(const index_t i, const index_t j) const { + return binomial_coeff(i, 2) + j; + } + template <typename OutputIterator> OutputIterator get_simplex_vertices(index_t idx, const index_t dim, index_t v, OutputIterator out) const { @@ -713,6 +741,81 @@ public: } }; +template <> class ripser<sparse_distance_matrix>::simplex_coboundary_enumerator { +private: + const ripser& parent; + + index_t idx_below, idx_above, v, k, max_vertex_below; + const diameter_entry_t simplex; + const coefficient_t modulus; + const sparse_distance_matrix& dist; + const binomial_coeff_table& binomial_coeff; + + std::vector<index_t>& vertices; + std::vector<std::vector<diameter_index_t>::const_reverse_iterator>& neighbor_it; + std::vector<std::vector<diameter_index_t>::const_reverse_iterator>& neighbor_end; + diameter_index_t x; + +public: + simplex_coboundary_enumerator(const diameter_entry_t _simplex, index_t _dim, + const ripser& _parent) + : parent(_parent), idx_below(get_index(_simplex)), idx_above(0), v(parent.n - 1), + k(_dim + 1), max_vertex_below(parent.n - 1), simplex(_simplex), modulus(parent.modulus), + dist(parent.dist), binomial_coeff(parent.binomial_coeff), vertices(parent.vertices), + neighbor_it(parent.neighbor_it), neighbor_end(parent.neighbor_end) { + + neighbor_it.clear(); + neighbor_end.clear(); + vertices.clear(); + + parent.get_simplex_vertices(idx_below, _dim, parent.n, std::back_inserter(vertices)); + + for (auto v : vertices) { + neighbor_it.push_back(dist.neighbors[v].rbegin()); + neighbor_end.push_back(dist.neighbors[v].rend()); + } + } + + bool has_next(bool all_cofaces = true) { + for (auto &it0 = neighbor_it[0], &end0 = neighbor_end[0]; it0 != end0; ++it0) { + x = *it0; + for (size_t idx = 1; idx < neighbor_it.size(); ++idx) { + auto &it = neighbor_it[idx], end = neighbor_end[idx]; + while (get_index(*it) > get_index(x)) + if (++it == end) return false; + auto y = *it; + if (get_index(y) != get_index(x)) + goto continue_outer; + else + x = std::max(x, y); + } + return all_cofaces || !(k > 0 && parent.get_next_vertex(max_vertex_below, idx_below, + k) > get_index(x)); + continue_outer:; + } + return false; + } + + diameter_entry_t next() { + ++neighbor_it[0]; + + while (k > 0 && parent.get_next_vertex(max_vertex_below, idx_below, k) > get_index(x)) { + idx_below -= binomial_coeff(max_vertex_below, k); + idx_above += binomial_coeff(max_vertex_below, k + 1); + --k; + } + + value_t coface_diameter = std::max(get_diameter(simplex), get_diameter(x)); + + coefficient_t coface_coefficient = + (k & 1 ? -1 + modulus : 1) * get_coefficient(simplex) % modulus; + + return diameter_entry_t(coface_diameter, + idx_above + binomial_coeff(get_index(x), k + 1) + idx_below, + coface_coefficient); + } +}; + template <> std::vector<diameter_index_t> ripser<compressed_lower_distance_matrix>::get_edges() { std::vector<diameter_index_t> edges; for (index_t index = binomial_coeff(n, 2); index-- > 0;) { @@ -722,6 +825,16 @@ template <> std::vector<diameter_index_t> ripser<compressed_lower_distance_matri return edges; } +template <> std::vector<diameter_index_t> ripser<sparse_distance_matrix>::get_edges() { + std::vector<diameter_index_t> edges; + for (index_t i = 0; i < n; ++i) + for (auto n : dist.neighbors[i]) { + index_t j = get_index(n); + if (i > j) edges.push_back(std::make_pair(get_diameter(n), get_edge_index(i, j))); + } + return edges; +} + template <> void ripser<compressed_lower_distance_matrix>::assemble_columns_to_reduce( std::vector<diameter_index_t>& simplices, std::vector<diameter_index_t>& columns_to_reduce, @@ -760,6 +873,49 @@ void ripser<compressed_lower_distance_matrix>::assemble_columns_to_reduce( #endif } +template <> +void ripser<sparse_distance_matrix>::assemble_columns_to_reduce( + std::vector<diameter_index_t>& simplices, std::vector<diameter_index_t>& columns_to_reduce, + hash_map<index_t, index_t>& pivot_column_index, index_t dim) { + +#ifdef INDICATE_PROGRESS + std::cout << "\033[K" + << "assembling columns" << std::flush << "\r"; +#endif + + --dim; + columns_to_reduce.clear(); + + std::vector<diameter_index_t> next_simplices; + + for (diameter_index_t simplex : simplices) { + simplex_coboundary_enumerator cofaces(simplex, dim, *this); + + while (cofaces.has_next(false)) { + auto coface = cofaces.next(); + + next_simplices.push_back(std::make_pair(get_diameter(coface), get_index(coface))); + + if (pivot_column_index.find(get_index(coface)) == pivot_column_index.end()) + columns_to_reduce.push_back( + std::make_pair(get_diameter(coface), get_index(coface))); + } + } + + simplices.swap(next_simplices); + +#ifdef INDICATE_PROGRESS + std::cout << "\033[K" + << "sorting " << columns_to_reduce.size() << " columns" << std::flush << "\r"; +#endif + + std::sort(columns_to_reduce.begin(), columns_to_reduce.end(), + greater_diameter_or_smaller_index<diameter_index_t>()); +#ifdef INDICATE_PROGRESS + std::cout << "\033[K"; +#endif +} + enum file_format { LOWER_DISTANCE_MATRIX, UPPER_DISTANCE_MATRIX, @@ -928,7 +1084,7 @@ int main(int argc, char** argv) { file_format format = DISTANCE_MATRIX; index_t dim_max = 1; - value_t threshold = std::numeric_limits<value_t>::infinity(); + value_t threshold = std::numeric_limits<value_t>::max(); float ratio = 1; @@ -1016,7 +1172,17 @@ int main(int argc, char** argv) { std::cout << "value range: [" << min << "," << max_finite << "]" << std::endl; - std::cout << "distance matrix with " << dist.size() << " points" << std::endl; - ripser<compressed_lower_distance_matrix>(std::move(dist), dim_max, threshold, ratio, modulus) - .compute_barcodes(); + if (threshold >= max) { + std::cout << "distance matrix with " << dist.size() << " points" << std::endl; + ripser<compressed_lower_distance_matrix>(std::move(dist), dim_max, threshold, ratio, + modulus) + .compute_barcodes(); + } else { + std::cout << "sparse distance matrix with " << dist.size() << " points and " << num_edges + << " entries" << std::endl; + + ripser<sparse_distance_matrix>(sparse_distance_matrix(std::move(dist), threshold), dim_max, + threshold, ratio, modulus) + .compute_barcodes(); + } } |