diff options
Diffstat (limited to 'ripser.cpp')
| -rw-r--r-- | ripser.cpp | 300 |
1 files changed, 159 insertions, 141 deletions
@@ -130,25 +130,21 @@ void set_coefficient(entry_t& e, const coefficient_t c) {} const entry_t& get_entry(const entry_t& e) { return e; } -class diameter_index_t : public std::pair<value_t, index_t> { -public: - diameter_index_t() : std::pair<value_t, index_t>() {} - diameter_index_t(std::pair<value_t, index_t>&& p) : std::pair<value_t, index_t>(std::move(p)) {} -}; +typedef std::pair<value_t, index_t> diameter_index_t; value_t get_diameter(const diameter_index_t& i) { return i.first; } index_t get_index(const diameter_index_t& i) { return i.second; } class diameter_entry_t : public std::pair<value_t, entry_t> { public: - diameter_entry_t(std::pair<value_t, entry_t> p) : std::pair<value_t, entry_t>(p) {} - diameter_entry_t(entry_t&& e) : std::pair<value_t, entry_t>(0, std::move(e)) {} - diameter_entry_t() : diameter_entry_t(entry_t()) {} + diameter_entry_t() {} + diameter_entry_t(const entry_t& e) : std::pair<value_t, entry_t>(0, e) {} diameter_entry_t(value_t _diameter, index_t _index, coefficient_t _coefficient) : std::pair<value_t, entry_t>(_diameter, make_entry(_index, _coefficient)) {} diameter_entry_t(const diameter_index_t& _diameter_index, coefficient_t _coefficient) : std::pair<value_t, entry_t>(get_diameter(_diameter_index), make_entry(get_index(_diameter_index), _coefficient)) {} - diameter_entry_t(const diameter_index_t& _diameter_index) : diameter_entry_t(_diameter_index, 1) {} + diameter_entry_t(const diameter_index_t& _diameter_index) + : diameter_entry_t(_diameter_index, 1) {} }; const entry_t& get_entry(const diameter_entry_t& p) { return p.second; } @@ -233,10 +229,8 @@ public: euclidean_distance_matrix(std::vector<std::vector<value_t>>&& _points) : points(std::move(_points)) { - for (auto p: points) { - assert(p.size() == points.front().size()); - } - } + for (auto p : points) { assert(p.size() == points.front().size()); } + } value_t operator()(const index_t i, const index_t j) const { assert(i < points.size()); @@ -368,12 +362,6 @@ 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)); -} - class ripser { compressed_lower_distance_matrix dist; index_t dim_max, n; @@ -382,6 +370,7 @@ class ripser { const binomial_coeff_table binomial_coeff; std::vector<coefficient_t> multiplicative_inverse; mutable std::vector<index_t> vertices; + mutable std::vector<diameter_entry_t> coface_entries; public: ripser(compressed_lower_distance_matrix&& _dist, index_t _dim_max, value_t _threshold, @@ -512,6 +501,44 @@ public: #endif } + template <typename Column, typename Iterator> + diameter_entry_t add_coboundary_and_get_pivot(Iterator column_begin, Iterator column_end, + coefficient_t factor_column_to_add, +#ifdef ASSEMBLE_REDUCTION_MATRIX + Column& working_reduction_column, +#endif + Column& working_coboundary, const index_t& dim, + hash_map<index_t, index_t>& pivot_column_index, + bool& might_be_apparent_pair) { + for (auto it = column_begin; it != column_end; ++it) { + diameter_entry_t simplex = *it; + set_coefficient(simplex, get_coefficient(simplex) * factor_column_to_add % modulus); + +#ifdef ASSEMBLE_REDUCTION_MATRIX + working_reduction_column.push(simplex); +#endif + + coface_entries.clear(); + simplex_coboundary_enumerator cofaces(simplex, dim, *this); + while (cofaces.has_next()) { + diameter_entry_t coface = cofaces.next(); + if (get_diameter(coface) <= threshold) { + coface_entries.push_back(coface); + if (might_be_apparent_pair && (get_diameter(simplex) == get_diameter(coface))) { + if (pivot_column_index.find(get_index(coface)) == + pivot_column_index.end()) { + return coface; + } + might_be_apparent_pair = false; + } + } + } + for (auto coface : coface_entries) working_coboundary.push(coface); + } + + return get_pivot(working_coboundary, modulus); + } + void compute_pairs(std::vector<diameter_index_t>& columns_to_reduce, hash_map<index_t, index_t>& pivot_column_index, index_t dim) { @@ -520,22 +547,23 @@ public: #endif #ifdef ASSEMBLE_REDUCTION_MATRIX - compressed_sparse_matrix<diameter_entry_t> reduction_coefficients; + compressed_sparse_matrix<diameter_entry_t> reduction_matrix; #else #ifdef USE_COEFFICIENTS - std::vector<diameter_entry_t> reduction_coefficients; + std::vector<diameter_entry_t> reduction_matrix; #endif #endif std::vector<diameter_entry_t> coface_entries; - for (index_t i = 0; i < columns_to_reduce.size(); ++i) { - auto column_to_reduce = columns_to_reduce[i]; + for (index_t index_column_to_reduce = 0; index_column_to_reduce < columns_to_reduce.size(); + ++index_column_to_reduce) { + auto column_to_reduce = columns_to_reduce[index_column_to_reduce]; #ifdef ASSEMBLE_REDUCTION_MATRIX std::priority_queue<diameter_entry_t, std::vector<diameter_entry_t>, greater_diameter_or_smaller_index<diameter_entry_t>> - reduction_column; + working_reduction_column; #endif std::priority_queue<diameter_entry_t, std::vector<diameter_entry_t>, @@ -545,169 +573,149 @@ public: value_t diameter = get_diameter(column_to_reduce); #ifdef INDICATE_PROGRESS - if ((i + 1) % 1000000 == 0) + if ((index_column_to_reduce + 1) % 1000000 == 0) std::cout << "\033[K" - << "reducing column " << i + 1 << "/" << columns_to_reduce.size() - << " (diameter " << diameter << ")" << std::flush << "\r"; + << "reducing column " << index_column_to_reduce + 1 << "/" + << columns_to_reduce.size() << " (diameter " << diameter << ")" + << std::flush << "\r"; #endif - index_t j = i; + index_t index_column_to_add = index_column_to_reduce; - // start with a dummy pivot entry with coefficient -1 in order to initialize - // working_coboundary with the coboundary of the simplex with index column_to_reduce - diameter_entry_t pivot(0, -1, -1 + modulus); + diameter_entry_t pivot; + + // start with factor 1 in order to initialize working_coboundary + // with the coboundary of the simplex with index column_to_reduce + coefficient_t factor_column_to_add = 1; #ifdef ASSEMBLE_REDUCTION_MATRIX - // initialize reduction_coefficients as identity matrix - reduction_coefficients.append_column(); + // initialize reduction_matrix as identity matrix + reduction_matrix.append_column(); #endif #ifdef USE_COEFFICIENTS - reduction_coefficients.push_back(diameter_entry_t(column_to_reduce, 1)); + reduction_matrix.push_back(diameter_entry_t(column_to_reduce, 1)); #endif - bool might_be_apparent_pair = (i == j); - - do { - const coefficient_t factor = modulus - get_coefficient(pivot); + bool might_be_apparent_pair = (index_column_to_reduce == index_column_to_add); + while (true) { #ifdef ASSEMBLE_REDUCTION_MATRIX #ifdef USE_COEFFICIENTS - auto coeffs_begin = reduction_coefficients.cbegin(j), - coeffs_end = reduction_coefficients.cend(j); + auto reduction_column_begin = reduction_matrix.cbegin(index_column_to_add), + reduction_column_end = reduction_matrix.cend(index_column_to_add); #else std::vector<diameter_entry_t> coeffs; - coeffs.push_back(columns_to_reduce[j]); - for (auto it = reduction_coefficients.cbegin(j); - it != reduction_coefficients.cend(j); ++it) + coeffs.push_back(columns_to_reduce[index_column_to_add]); + for (auto it = reduction_matrix.cbegin(index_column_to_add); + it != reduction_matrix.cend(index_column_to_add); ++it) coeffs.push_back(*it); - auto coeffs_begin = coeffs.begin(), coeffs_end = coeffs.end(); + auto reduction_column_begin = coeffs.begin(), reduction_column_end = coeffs.end(); #endif #else #ifdef USE_COEFFICIENTS - auto coeffs_begin = &reduction_coefficients[j], - coeffs_end = &reduction_coefficients[j] + 1; + auto reduction_column_begin = &reduction_matrix[index_column_to_add], + reduction_column_end = &reduction_matrix[index_column_to_add] + 1; #else - auto coeffs_begin = &columns_to_reduce[j], coeffs_end = &columns_to_reduce[j] + 1; + auto reduction_column_begin = &columns_to_reduce[index_column_to_add], + reduction_column_end = &columns_to_reduce[index_column_to_add] + 1; #endif #endif - for (auto it = coeffs_begin; it != coeffs_end; ++it) { - diameter_entry_t simplex = *it; - set_coefficient(simplex, get_coefficient(simplex) * factor % modulus); - + pivot = add_coboundary_and_get_pivot( + reduction_column_begin, reduction_column_end, factor_column_to_add, #ifdef ASSEMBLE_REDUCTION_MATRIX - reduction_column.push(simplex); -#endif - - coface_entries.clear(); - simplex_coboundary_enumerator cofaces(simplex, dim, *this); - while (cofaces.has_next()) { - diameter_entry_t coface = cofaces.next(); - if (get_diameter(coface) <= threshold) { - coface_entries.push_back(coface); - if (might_be_apparent_pair && - (get_diameter(simplex) == get_diameter(coface))) { - if (pivot_column_index.find(get_index(coface)) == - pivot_column_index.end()) { - pivot = coface; - goto found_persistence_pair; - } - might_be_apparent_pair = false; - } - } - } - for (auto coface : coface_entries) working_coboundary.push(coface); - } - - pivot = get_pivot(working_coboundary, modulus); + working_reduction_column, +#endif + working_coboundary, dim, pivot_column_index, might_be_apparent_pair); if (get_index(pivot) != -1) { auto pair = pivot_column_index.find(get_index(pivot)); if (pair != pivot_column_index.end()) { - j = pair->second; - continue; - } - } else { + index_column_to_add = pair->second; + factor_column_to_add = modulus - get_coefficient(pivot); + } else { #ifdef PRINT_PERSISTENCE_PAIRS + value_t death = get_diameter(pivot); + if (diameter != death) { #ifdef INDICATE_PROGRESS - std::cout << "\033[K"; -#endif -// std::cout << " [" << diameter << ", )" << std::endl << std::flush; - std::cout << " [" << diameter << ", ): {"; - auto cocycle = reduction_column; - while (get_index(pivot = get_pivot(cocycle, modulus)) != -1) { - vertices.clear(); - get_simplex_vertices(get_index(pivot), dim, n, std::back_inserter(vertices)); - std::cout << vertices; -#ifdef USE_COEFFICIENTS - std::cout << ":" << get_coefficient(pivot); -#endif - cocycle.pop(); - if (get_index(pivot = get_pivot(cocycle, modulus)) != -1) std::cout << ", "; - } - std::cout << "}" << std::endl; + std::cout << "\033[K"; #endif - break; - } - - found_persistence_pair: -#ifdef PRINT_PERSISTENCE_PAIRS - value_t death = get_diameter(pivot); - if (diameter != death) { -#ifdef INDICATE_PROGRESS - std::cout << "\033[K"; -#endif -// std::cout << " [" << diameter << "," << death << ")" << std::endl << std::flush; - std::cout << " [" << diameter << "," << death << "): {"; - auto cocycle = reduction_column; - diameter_entry_t e; - while (get_index(e = get_pivot(cocycle, modulus)) != -1) { - vertices.clear(); - get_simplex_vertices(get_index(e), dim, n, std::back_inserter(vertices)); - std::cout << vertices; + // std::cout << " [" << diameter << "," << death << ")" << std::endl << std::flush; + std::cout << " [" << diameter << "," << death << "): {"; + auto cocycle = working_reduction_column; + diameter_entry_t e; + while (get_index(e = get_pivot(cocycle, modulus)) != -1) { + vertices.clear(); + get_simplex_vertices(get_index(e), dim, n, std::back_inserter(vertices)); + std::cout << vertices; #ifdef USE_COEFFICIENTS - std::cout << ":" << get_coefficient(pivot); + std::cout << ":" << get_coefficient(pivot); #endif - cocycle.pop(); - if (get_index(e = get_pivot(cocycle, modulus)) != -1) std::cout << ", "; - } - std::cout << "}" << std::endl; - } + cocycle.pop(); + if (get_index(e = get_pivot(cocycle, modulus)) != -1) std::cout << ", "; + } + std::cout << "}" << std::endl; + } #endif - - pivot_column_index.insert(std::make_pair(get_index(pivot), i)); + pivot_column_index.insert( + std::make_pair(get_index(pivot), index_column_to_reduce)); #ifdef USE_COEFFICIENTS - const coefficient_t inverse = multiplicative_inverse[get_coefficient(pivot)]; + const coefficient_t inverse = + multiplicative_inverse[get_coefficient(pivot)]; #endif #ifdef ASSEMBLE_REDUCTION_MATRIX -// replace current column of reduction_coefficients (with a single diagonal 1 entry) -// by reduction_column (possibly with a different entry on the diagonal) + // replace current column of reduction_matrix (with a single diagonal 1 + // entry) by reduction_column (possibly with a different entry on the + // diagonal) #ifdef USE_COEFFICIENTS - reduction_coefficients.pop_back(); + reduction_matrix.pop_back(); #else - pop_pivot(reduction_column, modulus); + pop_pivot(working_reduction_column, modulus); #endif - while (true) { - diameter_entry_t e = pop_pivot(reduction_column, modulus); - if (get_index(e) == -1) break; + while (true) { + diameter_entry_t e = pop_pivot(working_reduction_column, modulus); + if (get_index(e) == -1) break; #ifdef USE_COEFFICIENTS - set_coefficient(e, inverse * get_coefficient(e) % modulus); - assert(get_coefficient(e) > 0); + set_coefficient(e, inverse * get_coefficient(e) % modulus); + assert(get_coefficient(e) > 0); #endif - reduction_coefficients.push_back(e); - } + reduction_matrix.push_back(e); + } #else #ifdef USE_COEFFICIENTS - reduction_coefficients.pop_back(); - reduction_coefficients.push_back(diameter_entry_t(column_to_reduce, inverse)); + reduction_matrix.pop_back(); + reduction_matrix.push_back(diameter_entry_t(column_to_reduce, inverse)); +#endif +#endif + break; + } + } else { +#ifdef PRINT_PERSISTENCE_PAIRS +#ifdef INDICATE_PROGRESS + std::cout << "\033[K"; +#endif + // std::cout << " [" << diameter << ", )" << std::endl << std::flush; + std::cout << " [" << diameter << ", ): {"; + auto cocycle = working_reduction_column; + while (get_index(pivot = get_pivot(cocycle, modulus)) != -1) { + vertices.clear(); + get_simplex_vertices(get_index(pivot), dim, n, std::back_inserter(vertices)); + std::cout << vertices; +#ifdef USE_COEFFICIENTS + std::cout << ":" << get_coefficient(pivot); #endif + cocycle.pop(); + if (get_index(pivot = get_pivot(cocycle, modulus)) != -1) std::cout << ", "; + } + std::cout << "}" << std::endl; #endif - break; - } while (true); + break; + } + } } #ifdef INDICATE_PROGRESS @@ -884,7 +892,7 @@ int main(int argc, char** argv) { file_format format = DISTANCE_MATRIX; index_t dim_max = 1; - value_t threshold = std::numeric_limits<value_t>::max(); + value_t threshold = std::numeric_limits<value_t>::infinity(); #ifdef USE_COEFFICIENTS coefficient_t modulus = 2; @@ -945,9 +953,19 @@ int main(int argc, char** argv) { std::cout << "distance matrix with " << dist.size() << " points" << std::endl; - auto value_range = std::minmax_element(dist.distances.begin(), dist.distances.end()); - std::cout << "value range: [" << *value_range.first << "," << *value_range.second << "]" - << std::endl; + value_t min = std::numeric_limits<value_t>::infinity(), + max = -std::numeric_limits<value_t>::infinity(); + + for (auto d : dist.distances) { + if (d != std::numeric_limits<value_t>::infinity()) { + min = std::min(min, d); + max = std::max(max, d); + } else { + threshold = std::min(threshold, std::numeric_limits<value_t>::max()); + } + } + + std::cout << "value range: [" << min << "," << max << "]" << std::endl; ripser(std::move(dist), dim_max, threshold, modulus).compute_barcodes(); } |