diff options
Diffstat (limited to 'ripser.cpp')
-rw-r--r-- | ripser.cpp | 187 |
1 files changed, 94 insertions, 93 deletions
@@ -98,32 +98,34 @@ std::vector<coefficient_t> multiplicative_inverse_vector(const coefficient_t m) return inverse; } +index_t get_next_vertex(index_t& v, const index_t idx, const index_t k, const binomial_coeff_table& binomial_coeff) { + if (binomial_coeff(v, k) > idx) { + index_t count = v; + while (count > 0) { + index_t i = v; + index_t step = count >> 1; + i -= step; + if (binomial_coeff(i, k) > idx) { + v = --i; + count -= step + 1; + } else + count = step; + } + } + assert(binomial_coeff(v, k) <= idx); + assert(binomial_coeff(v + 1, k) > idx); + return v; +} + template <typename OutputIterator> -OutputIterator get_simplex_vertices(index_t idx, const index_t dim, index_t n, +OutputIterator get_simplex_vertices(index_t idx, const index_t dim, index_t v, const binomial_coeff_table& binomial_coeff, OutputIterator out) { - --n; - + --v; for (index_t k = dim + 1; k > 0; --k) { - if (binomial_coeff(n, k) > idx) { - index_t count = n; - while (count > 0) { - index_t i = n; - index_t step = count >> 1; - i -= step; - if (binomial_coeff(i, k) > idx) { - n = --i; - count -= step + 1; - } else - count = step; - } - } - assert(binomial_coeff(n, k) <= idx); - assert(binomial_coeff(n + 1, k) > idx); - - *out++ = n; - idx -= binomial_coeff(n, k); + get_next_vertex(v, idx, k, binomial_coeff); + *out++ = v; + idx -= binomial_coeff(v, k); } - return out; } @@ -165,7 +167,7 @@ typedef index_t entry_t; const index_t get_index(entry_t i) { return i; } index_t get_coefficient(entry_t i) { return 1; } entry_t make_entry(index_t _index, coefficient_t _value) { return entry_t(_index); } -void set_coefficient(index_t& e, const coefficient_t c) { e = c; } +void set_coefficient(index_t& e, const coefficient_t c) { } #endif @@ -175,7 +177,11 @@ template <typename Entry> struct smaller_index { bool operator()(const Entry& a, const Entry& b) { return get_index(a) < get_index(b); } }; -typedef std::pair<value_t, index_t> diameter_index_t; +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>(p) {} +}; value_t get_diameter(diameter_index_t i) { return i.first; } index_t get_index(diameter_index_t i) { return i.second; } @@ -184,6 +190,12 @@ 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, e) {} diameter_entry_t() : diameter_entry_t(0) {} + 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(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(diameter_index_t _diameter_index) : diameter_entry_t(_diameter_index, 1) {} }; const entry_t& get_entry(const diameter_entry_t& p) { return p.second; } @@ -192,12 +204,6 @@ const index_t get_index(const diameter_entry_t& p) { return get_index(get_entry( const coefficient_t get_coefficient(const diameter_entry_t& p) { return get_coefficient(get_entry(p)); } const value_t& get_diameter(const diameter_entry_t& p) { return p.first; } void set_coefficient(diameter_entry_t& p, const coefficient_t c) { set_coefficient(get_entry(p), c); } -diameter_entry_t make_diameter_entry(value_t _diameter, index_t _index, coefficient_t _coefficient) { - return std::make_pair(_diameter, make_entry(_index, _coefficient)); -} -diameter_entry_t make_diameter_entry(diameter_index_t _diameter_index, coefficient_t _coefficient) { - return std::make_pair(get_diameter(_diameter_index), make_entry(get_index(_diameter_index), _coefficient)); -} template <typename Entry> struct greater_diameter_or_smaller_index { bool operator()(const Entry& a, const Entry& b) { @@ -242,14 +248,23 @@ public: } }; -class simplex_coboundary_enumerator { +template <class DistanceMatrix> class simplex_coboundary_enumerator { private: index_t idx_below, idx_above, v, k; + std::vector<index_t> vertices; + const diameter_entry_t simplex; + const coefficient_t modulus; + const DistanceMatrix& dist; const binomial_coeff_table& binomial_coeff; public: - simplex_coboundary_enumerator(index_t _idx, index_t _dim, index_t _n, const binomial_coeff_table& _binomial_coeff) - : idx_below(_idx), idx_above(0), v(_n - 1), k(_dim + 1), binomial_coeff(_binomial_coeff) {} + simplex_coboundary_enumerator(const diameter_entry_t _simplex, index_t _dim, index_t _n, + const coefficient_t _modulus, const DistanceMatrix& _dist, + const binomial_coeff_table& _binomial_coeff) + : simplex(_simplex), idx_below(get_index(_simplex)), idx_above(0), v(_n - 1), k(_dim + 1), modulus(_modulus), + binomial_coeff(_binomial_coeff), dist(_dist), vertices(_dim + 1) { + get_simplex_vertices(get_index(_simplex), _dim, _n, binomial_coeff, vertices.begin()); + } bool has_next() { while ((v != -1) && (binomial_coeff(v, k) <= idx_below)) { @@ -263,10 +278,13 @@ public: return v != -1; } - std::pair<entry_t, index_t> next() { - auto result = std::make_pair(make_entry(idx_above + binomial_coeff(v, k + 1) + idx_below, k & 1 ? -1 : 1), v); - --v; - return result; + index_t next_index() { return idx_above + binomial_coeff(v--, k + 1) + idx_below; } + + diameter_entry_t next() { + value_t coface_diameter = get_diameter(simplex); + for (index_t w : vertices) coface_diameter = std::max(coface_diameter, dist(v, w)); + coefficient_t coface_coefficient = (k & 1 ? -1 + modulus : 1) * get_coefficient(simplex) % modulus; + return diameter_entry_t(coface_diameter, idx_above + binomial_coeff(v--, k + 1) + idx_below, coface_coefficient); } }; @@ -484,6 +502,11 @@ void assemble_columns_to_reduce(std::vector<diameter_index_t>& columns_to_reduce if (pivot_column_index.find(index) == pivot_column_index.end()) { value_t diameter = comp.diameter(index); if (diameter <= threshold) columns_to_reduce.push_back(std::make_pair(diameter, index)); +#ifdef INDICATE_PROGRESS + if ((index + 1) % 1000 == 0) + std::cout << "\033[K" + << "assembled " << columns_to_reduce.size() << " out of " << (index + 1) << "/" << num_simplices << " columns" << std::flush << "\r"; +#endif } } @@ -501,9 +524,10 @@ void assemble_columns_to_reduce(std::vector<diameter_index_t>& columns_to_reduce template <typename DistanceMatrix, typename ComparatorCofaces, typename Comparator> void compute_pairs(std::vector<diameter_index_t>& columns_to_reduce, hash_map<index_t, index_t>& pivot_column_index, - const DistanceMatrix& dist, const ComparatorCofaces& comp, const Comparator& comp_prev, index_t dim, - index_t n, value_t threshold, coefficient_t modulus, + index_t dim, index_t n, value_t threshold, coefficient_t modulus, const std::vector<coefficient_t>& multiplicative_inverse, + const DistanceMatrix& dist, + const ComparatorCofaces& comp, const Comparator& comp_prev, const binomial_coeff_table& binomial_coeff) { #ifdef PRINT_PERSISTENCE_PAIRS @@ -511,7 +535,7 @@ void compute_pairs(std::vector<diameter_index_t>& columns_to_reduce, hash_map<in #endif #ifdef ASSEMBLE_REDUCTION_MATRIX - compressed_sparse_matrix<diameter_entry_t> reduction_matrix; + compressed_sparse_matrix<diameter_entry_t> reduction_coefficients; #else #ifdef USE_COEFFICIENTS std::vector<diameter_entry_t> reduction_coefficients; @@ -519,7 +543,6 @@ void compute_pairs(std::vector<diameter_index_t>& columns_to_reduce, hash_map<in #endif std::vector<diameter_entry_t> coface_entries; - std::vector<index_t> vertices; for (index_t i = 0; i < columns_to_reduce.size(); ++i) { auto column_to_reduce = columns_to_reduce[i]; @@ -546,15 +569,15 @@ void compute_pairs(std::vector<diameter_index_t>& columns_to_reduce, hash_map<in // 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 = make_diameter_entry(0, -1, -1 + modulus); + diameter_entry_t pivot(0, -1, -1 + modulus); #ifdef ASSEMBLE_REDUCTION_MATRIX - // initialize reduction_matrix as identity matrix - reduction_matrix.append_column(); - reduction_matrix.push_back(make_diameter_entry(column_to_reduce, 1)); + // initialize reduction_coefficients as identity matrix + reduction_coefficients.append_column(); + reduction_coefficients.push_back(diameter_entry_t(column_to_reduce, 1)); #else #ifdef USE_COEFFICIENTS - reduction_coefficients.push_back(make_diameter_entry(column_to_reduce, 1)); + reduction_coefficients.push_back(diameter_entry_t(column_to_reduce, 1)); #endif #endif @@ -564,52 +587,33 @@ void compute_pairs(std::vector<diameter_index_t>& columns_to_reduce, hash_map<in const coefficient_t factor = modulus - get_coefficient(pivot); #ifdef ASSEMBLE_REDUCTION_MATRIX - for (auto it = reduction_matrix.cbegin(j); it != reduction_matrix.cend(j); ++it) -#endif - { -#ifdef ASSEMBLE_REDUCTION_MATRIX - const auto& simplex = *it; + auto coeffs_begin = reduction_coefficients.cbegin(j), coeffs_end = reduction_coefficients.cend(j); #else #ifdef USE_COEFFICIENTS - const auto& simplex = reduction_coefficients[j]; + auto coeffs_begin = &reduction_coefficients[j], coeffs_end = &reduction_coefficients[j] + 1; #else - const auto& simplex = columns_to_reduce[j]; + auto coeffs_begin = &columns_to_reduce[j], coeffs_end = &columns_to_reduce[j] + 1; #endif #endif - coefficient_t simplex_coefficient = get_coefficient(simplex) * factor % modulus; + for (auto it = coeffs_begin; it != coeffs_end; ++it) + { + diameter_entry_t simplex = *it; + set_coefficient(simplex, get_coefficient(simplex) * factor % modulus); #ifdef ASSEMBLE_REDUCTION_MATRIX - reduction_column.push( - make_diameter_entry(get_diameter(simplex), get_index(simplex), simplex_coefficient)); + reduction_column.push(simplex); #endif - vertices.clear(); - get_simplex_vertices(get_index(simplex), dim, n, binomial_coeff, std::back_inserter(vertices)); - coface_entries.clear(); - simplex_coboundary_enumerator cofaces(get_index(simplex), dim, n, binomial_coeff); + simplex_coboundary_enumerator<decltype(dist)> cofaces(simplex, dim, n, modulus, dist, binomial_coeff); while (cofaces.has_next()) { - auto coface_descriptor = cofaces.next(); - entry_t coface = coface_descriptor.first; - index_t covertex = coface_descriptor.second; - index_t coface_index = get_index(coface); - value_t coface_diameter = get_diameter(simplex); - for (index_t v : vertices) { coface_diameter = std::max(coface_diameter, dist(v, covertex)); } - assert(comp.diameter(coface_index) == coface_diameter); - - if (coface_diameter <= threshold) { - coefficient_t coface_coefficient = - (get_coefficient(coface) + modulus) * simplex_coefficient % modulus; - assert(coface_coefficient >= 0); - - diameter_entry_t coface_entry = - make_diameter_entry(coface_diameter, coface_index, coface_coefficient); - coface_entries.push_back(coface_entry); - - if (might_be_apparent_pair && (get_diameter(simplex) == coface_diameter)) { - if (pivot_column_index.find(coface_index) == pivot_column_index.end()) { - pivot = coface_entry; + 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; @@ -656,25 +660,22 @@ void compute_pairs(std::vector<diameter_index_t>& columns_to_reduce, hash_map<in #endif #ifdef ASSEMBLE_REDUCTION_MATRIX - // replace current column of reduction_matrix (with a single diagonal 1 entry) + // replace current column of reduction_coefficients (with a single diagonal 1 entry) // by reduction_column (possibly with a different entry on the diagonal) - reduction_matrix.pop_back(); + reduction_coefficients.pop_back(); while (true) { diameter_entry_t e = pop_pivot(reduction_column, modulus); - index_t index = get_index(e); - if (index == -1) break; + if (get_index(e) == -1) break; #ifdef USE_COEFFICIENTS - const coefficient_t coefficient = inverse * get_coefficient(e) % modulus; - assert(coefficient > 0); -#else - const coefficient_t coefficient = 1; + set_coefficient(e, inverse * get_coefficient(e) % modulus); + assert(get_coefficient(e) > 0); #endif - reduction_matrix.push_back(make_diameter_entry(get_diameter(e), index, coefficient)); + reduction_coefficients.push_back(e); } #else #ifdef USE_COEFFICIENTS reduction_coefficients.pop_back(); - reduction_coefficients.push_back(make_diameter_entry(column_to_reduce, inverse)); + reduction_coefficients.push_back(diameter_entry_t(column_to_reduce, inverse)); #endif #endif break; @@ -910,7 +911,7 @@ int main(int argc, char** argv) { rips_filtration_comparator<decltype(dist)> comp(dist, 1, binomial_coeff); for (index_t index = binomial_coeff(n, 2); index-- > 0;) { value_t diameter = comp.diameter(index); - if (diameter <= threshold) edges.push_back(diameter_index_t(diameter, index)); + if (diameter <= threshold) edges.push_back(std::make_pair(diameter, index)); } std::sort(edges.rbegin(), edges.rend(), greater_diameter_or_smaller_index<diameter_index_t>()); @@ -948,8 +949,8 @@ int main(int argc, char** argv) { hash_map<index_t, index_t> pivot_column_index; pivot_column_index.reserve(columns_to_reduce.size()); - compute_pairs(columns_to_reduce, pivot_column_index, dist, comp, comp_prev, dim, n, threshold, modulus, - multiplicative_inverse, binomial_coeff); + compute_pairs(columns_to_reduce, pivot_column_index, dim, n, threshold, modulus, multiplicative_inverse, + dist, comp, comp_prev, binomial_coeff); if (dim < dim_max) { assemble_columns_to_reduce(columns_to_reduce, pivot_column_index, comp, dim, n, threshold, binomial_coeff); |