diff options
| author | Ulrich Bauer <mail@ulrich-bauer.org> | 2018-02-15 11:24:52 +0100 |
|---|---|---|
| committer | Ulrich Bauer <mail@ulrich-bauer.org> | 2018-02-15 11:24:52 +0100 |
| commit | 2c2c04796ca1e2aca8575d975755be58311a380a (patch) | |
| tree | 4ae306217f30875899081d09bf2b014b02cd4556 | |
| parent | 23a262f1b59eacd7a3ef01589101e64290cd7128 (diff) | |
| parent | 0ed8c7932825572e49fa5abd50f2338cb66d7fd0 (diff) | |
Merge commit '0ed8c7932825572e49fa5abd50f2338cb66d7fd0' into sparse-distance-matrix
# Conflicts:
# ripser.cpp
| -rw-r--r-- | benchmarks/sphere_3_192/eirene.dim_1.out.txt | 173 | ||||
| -rw-r--r-- | benchmarks/sphere_3_192/eirene.dim_2.out.txt | 173 | ||||
| -rw-r--r-- | benchmarks/sphere_3_192/run_eirene.sh | 7 | ||||
| -rw-r--r-- | ripser.cpp | 217 |
4 files changed, 467 insertions, 103 deletions
diff --git a/benchmarks/sphere_3_192/eirene.dim_1.out.txt b/benchmarks/sphere_3_192/eirene.dim_1.out.txt new file mode 100644 index 0000000..3f205e1 --- /dev/null +++ b/benchmarks/sphere_3_192/eirene.dim_1.out.txt @@ -0,0 +1,173 @@ + + +Eirene Library for Homological Algebra +Copyright (C) 2016, 2017 Gregory Henselman +www.gregoryhenselman.org + +Eirene is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +Eirene 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 General Public License for more details. + +You should have received a copy of the GNU General Public License +along with Eirene. If not, see <http://www.gnu.org/licenses/>. + + +WELCOME TO EIRENE! +v0.3.5 + +Please help us document Eirene's recent work! Bibtex entries and +contact information for teaching and outreach can be found at the +Eirene homepage, http://gregoryhenselman.org/eirene. + + +Please Note: MultivariateStats.jl may not be installed. This package is required for +some operations pertaining to multidimensional scaling, but is not required. +To install, enter the following at the Julia prompt: + +Pkg.add("MultivariateStats") +using MultivariateStats + + +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +in __persistF2#19__ at /Users/uli/Source/Eirene0_3_5/Eirene0_3_5.jl +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +in __persistF2#19__ at /Users/uli/Source/Eirene0_3_5/Eirene0_3_5.jl +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +in __persistF2#19__ at /Users/uli/Source/Eirene0_3_5/Eirene0_3_5.jl +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +in __persistF2#19__ at /Users/uli/Source/Eirene0_3_5/Eirene0_3_5.jl +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +in __persistF2#19__ at /Users/uli/Source/Eirene0_3_5/Eirene0_3_5.jl +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +in __persistF2#19__ at /Users/uli/Source/Eirene0_3_5/Eirene0_3_5.jl +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +in ezlabel at /Users/uli/Source/Eirene0_3_5/Eirene0_3_5.jl +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +in ezlabel at /Users/uli/Source/Eirene0_3_5/Eirene0_3_5.jl +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +in ezlabel at /Users/uli/Source/Eirene0_3_5/Eirene0_3_5.jl +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +in ezlabel at /Users/uli/Source/Eirene0_3_5/Eirene0_3_5.jl +Constructed Morse boundary operator, columns indexed by cells of dimension 1 +elapsed time: 5.240448941 seconds +Constructed Morse boundary operator, columns indexed by cells of dimension 1 +Constructed Morse boundary operator, columns indexed by cells of dimension 2 +Constructed Morse boundary operator, columns indexed by cells of dimension 3 +elapsed time: 2.614149242 seconds + 22.13 real 21.22 user 1.07 sys + 632369152 maximum resident set size + 0 average shared memory size + 0 average unshared data size + 0 average unshared stack size + 263754 page reclaims + 0 page faults + 0 swaps + 59 block input operations + 0 block output operations + 0 messages sent + 0 messages received + 5 signals received + 120 voluntary context switches + 165216 involuntary context switches diff --git a/benchmarks/sphere_3_192/eirene.dim_2.out.txt b/benchmarks/sphere_3_192/eirene.dim_2.out.txt new file mode 100644 index 0000000..acfb3db --- /dev/null +++ b/benchmarks/sphere_3_192/eirene.dim_2.out.txt @@ -0,0 +1,173 @@ + + +Eirene Library for Homological Algebra +Copyright (C) 2016, 2017 Gregory Henselman +www.gregoryhenselman.org + +Eirene is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +Eirene 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 General Public License for more details. + +You should have received a copy of the GNU General Public License +along with Eirene. If not, see <http://www.gnu.org/licenses/>. + + +WELCOME TO EIRENE! +v0.3.5 + +Please help us document Eirene's recent work! Bibtex entries and +contact information for teaching and outreach can be found at the +Eirene homepage, http://gregoryhenselman.org/eirene. + + +Please Note: MultivariateStats.jl may not be installed. This package is required for +some operations pertaining to multidimensional scaling, but is not required. +To install, enter the following at the Julia prompt: + +Pkg.add("MultivariateStats") +using MultivariateStats + + +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +in __persistF2#19__ at /Users/uli/Source/Eirene0_3_5/Eirene0_3_5.jl +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +in __persistF2#19__ at /Users/uli/Source/Eirene0_3_5/Eirene0_3_5.jl +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +in __persistF2#19__ at /Users/uli/Source/Eirene0_3_5/Eirene0_3_5.jl +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +in __persistF2#19__ at /Users/uli/Source/Eirene0_3_5/Eirene0_3_5.jl +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +in __persistF2#19__ at /Users/uli/Source/Eirene0_3_5/Eirene0_3_5.jl +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +in __persistF2#19__ at /Users/uli/Source/Eirene0_3_5/Eirene0_3_5.jl +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +in ezlabel at /Users/uli/Source/Eirene0_3_5/Eirene0_3_5.jl +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +in ezlabel at /Users/uli/Source/Eirene0_3_5/Eirene0_3_5.jl +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +in ezlabel at /Users/uli/Source/Eirene0_3_5/Eirene0_3_5.jl +WARNING: Base.String is deprecated, use AbstractString instead. + likely near no file:0 +in ezlabel at /Users/uli/Source/Eirene0_3_5/Eirene0_3_5.jl +Constructed Morse boundary operator, columns indexed by cells of dimension 1 +elapsed time: 5.023364429 seconds +Constructed Morse boundary operator, columns indexed by cells of dimension 1 +Constructed Morse boundary operator, columns indexed by cells of dimension 2 +Constructed Morse boundary operator, columns indexed by cells of dimension 3 +elapsed time: 13.676510239 seconds + 33.14 real 30.90 user 2.37 sys +1508073472 maximum resident set size + 0 average shared memory size + 0 average unshared data size + 0 average unshared stack size + 810601 page reclaims + 0 page faults + 0 swaps + 0 block input operations + 0 block output operations + 0 messages sent + 0 messages received + 5 signals received + 46 voluntary context switches + 195015 involuntary context switches diff --git a/benchmarks/sphere_3_192/run_eirene.sh b/benchmarks/sphere_3_192/run_eirene.sh new file mode 100644 index 0000000..4d76795 --- /dev/null +++ b/benchmarks/sphere_3_192/run_eirene.sh @@ -0,0 +1,7 @@ +/usr/bin/time -l julia --load /Users/uli/Source/Eirene0_3_5/Eirene0_3_5.jl --eval \ +'p = readdlm("/Users/uli/Bitbucket/phat-paper/benchmark/point cloud/sphere_3_192_points.dat"); eirene(p, rowsare="points", bettimax=0); eirene(p, rowsare="points", bettimax=1);' \ +2>&1 | tee eirene.dim_1.out.txt + +/usr/bin/time -l julia --load /Users/uli/Source/Eirene0_3_5/Eirene0_3_5.jl --eval \ +'p = readdlm("/Users/uli/Bitbucket/phat-paper/benchmark/point cloud/sphere_3_192_points.dat"); eirene(p, rowsare="points", bettimax=0); eirene(p, rowsare="points", bettimax=2);' \ +2>&1 | tee eirene.dim_2.out.txt @@ -128,19 +128,14 @@ 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) @@ -400,6 +395,7 @@ template <typename DistanceMatrix> class ripser { 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: ripser(DistanceMatrix&& _dist, index_t _dim_max, value_t _threshold, float _ratio, @@ -498,7 +494,44 @@ public: #endif } - template <typename BoundaryEnumerator> + 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) { @@ -507,22 +540,23 @@ 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>, @@ -532,142 +566,120 @@ 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; + + diameter_entry_t pivot; - // 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); + // 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); + working_reduction_column, #endif - - coface_entries.clear(); - BoundaryEnumerator 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_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 { -#ifdef PRINT_PERSISTENCE_PAIRS -#ifdef INDICATE_PROGRESS - std::cout << "\033[K"; -#endif - std::cout << " [" << diameter << ", )" << std::endl << std::flush; -#endif - break; - } - - found_persistence_pair: + 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 ((float)death / diameter > ratio) { + value_t death = get_diameter(pivot); + if (diameter != death) { #ifdef INDICATE_PROGRESS - std::cout << "\033[K"; + std::cout << "\033[K"; #endif - std::cout << " [" << diameter << "," << death << ")" << std::endl << std::flush; - } + std::cout << " [" << diameter << "," << death << ")" << std::endl + << std::flush; + } #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; - } while (true); + break; + } + } else { +#ifdef PRINT_PERSISTENCE_PAIRS + std::cout << " [" << diameter << ", )" << std::endl << std::flush; +#endif + break; + } + } } #ifdef INDICATE_PROGRESS @@ -687,8 +699,7 @@ public: hash_map<index_t, index_t> pivot_column_index; pivot_column_index.reserve(columns_to_reduce.size()); - compute_pairs<simplex_coboundary_enumerator>(columns_to_reduce, pivot_column_index, - dim); + compute_pairs(columns_to_reduce, pivot_column_index, dim); if (dim < dim_max) { assemble_columns_to_reduce(simplices, columns_to_reduce, pivot_column_index, |