diff --git a/Makefile b/Makefile index d2b8065..13f2097 100644 --- a/Makefile +++ b/Makefile @@ -5,7 +5,7 @@ all: ripser ripser-coeff ripser-reduction ripser-coeff-reduction ripser-debug ripser: ripser.cpp - c++ -std=c++11 ripser.cpp -o ripser -Ofast -D NDEBUG + c++ -std=c++11 ripser.cpp -o ripser -Ofast -D NDEBUG -D PRINT_PERSISTENCE_PAIRS -D INDICATE_PROGRESS ripser-coeff: ripser.cpp c++ -std=c++11 ripser.cpp -o ripser-coeff -Ofast -D NDEBUG -D USE_COEFFICIENTS @@ -21,7 +21,8 @@ ripser-debug: ripser.cpp clean: - rm -rf ripser ripser-coeff ripser-reduction ripser-coeff-reduction ripser-debug emscripten pnacl && NACL_SDK_ROOT=~/Source/nacl_sdk/pepper_49/ make -f Makefile_pnacl clean + yes| rm ripser ripser-coeff ripser-reduction ripser-coeff-reduction ripser-debug emscripten pnacl + #&& NACL_SDK_ROOT=~/Source/nacl_sdk/pepper_49/ make -f Makefile_pnacl clean live: pnacl emscripten diff --git a/README.md b/README.md index 0c5a2e6..e64fea1 100644 --- a/README.md +++ b/README.md @@ -25,6 +25,7 @@ Input formats currently supported by Ripser: - comma-separated values full distance matrix - [DIPHA] distance matrix data - point cloud data + - sparse space-separated lower triangular matrix. Each line corresponds to a row. Row n consists of pairs (k dist(n,k)), where n>k. This especially means that the first line is empty. All missing values are presumed infinite. See the examples. When using sparse matrices, the threshold is ignored -- use a python filter. Ripser's efficiency is based on a few important concepts and principles: @@ -109,4 +110,4 @@ Ripser is licensed under the [LGPL] 3.0. Please contact the author if you want t [Perseus]: [GUDHI]: [sparsehash]: -[LGPL]: \ No newline at end of file +[LGPL]: diff --git a/examples/sphere_3_192.lower_distance_matrix.sparse.threshold1.0 b/examples/sphere_3_192.lower_distance_matrix.sparse.threshold1.0 new file mode 100644 index 0000000..9fa004e --- /dev/null +++ b/examples/sphere_3_192.lower_distance_matrix.sparse.threshold1.0 @@ -0,0 +1,192 @@ + + +1 0.920778 +1 0.375817 2 0.586113 + +0 0.916373 +0 0.185211 +0 0.693814 5 0.524761 6 0.804527 +4 0.588045 +1 0.693387 3 1.00594 4 0.6561 8 0.401576 +0 0.855067 5 0.613495 6 0.941014 7 0.200333 +4 0.231179 8 0.792794 9 0.863212 +2 0.617515 3 0.864858 + +0 0.65706 4 0.922642 6 0.63549 11 0.789805 +1 0.53904 2 0.857563 3 0.448892 5 0.94607 +8 1.01434 +2 0.757279 10 0.950995 13 0.680141 +2 0.881271 12 1.00568 13 0.439355 17 0.502416 +2 0.708398 12 0.796307 13 0.66447 17 0.571517 18 0.237316 +1 0.932799 2 0.354112 3 0.593158 12 0.943208 15 0.661629 17 0.638039 18 0.956103 19 0.858389 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0.798539 108 0.362091 109 0.916357 117 0.670412 119 0.973392 121 0.640264 122 0.502107 127 0.795666 130 0.904383 132 0.786051 133 0.652644 138 0.58391 145 0.318032 152 0.501741 155 0.915282 156 0.282169 160 0.672854 161 0.555513 166 0.442195 172 0.512494 174 0.615148 175 0.936448 180 0.289189 182 0.737167 +1 0.896623 4 0.37503 8 0.319493 9 0.300811 11 0.598504 21 0.852879 23 0.827768 32 0.350411 34 0.791829 35 0.474698 40 0.90083 46 0.922667 59 0.98348 64 0.0623736 65 1.01992 70 0.395439 71 0.750722 77 0.832212 78 0.911284 86 0.990593 87 0.942176 105 0.704996 106 0.193791 109 0.326021 114 0.85952 116 0.978233 117 0.961461 118 0.830641 127 0.427842 128 0.749144 135 0.895137 136 0.65551 146 0.441412 156 0.999399 159 0.930062 160 0.691812 162 0.90912 167 0.734848 170 0.842151 172 0.734402 173 1.01339 178 0.530526 +8 0.958819 16 0.337858 21 0.916493 24 0.399021 30 0.598872 35 0.820359 46 0.828041 48 0.941399 51 0.78639 55 0.859683 60 1.00932 65 0.343083 70 0.89222 72 0.796295 79 0.436881 81 0.874153 82 0.710567 89 0.915402 90 0.964869 92 0.498205 93 0.254889 98 0.599498 114 0.726884 115 0.764341 118 0.519516 123 0.0387451 124 0.862032 125 0.562445 131 0.635227 135 0.902801 136 0.702928 141 0.946703 144 0.925803 146 0.848376 147 0.351856 149 0.893449 158 0.98121 159 0.468227 165 0.9875 167 0.957447 168 0.736627 170 0.768119 171 0.191661 173 0.445665 178 0.964628 181 0.964335 +1 0.900839 4 0.245934 8 0.489582 9 0.4329 11 0.454411 21 0.999809 23 0.684183 32 0.411091 34 0.655235 35 0.63294 46 0.972809 59 0.845693 64 0.127383 70 0.568523 71 0.637235 77 0.75986 78 0.758403 86 0.864984 87 0.831876 105 0.613456 106 0.330803 109 0.203812 117 0.826439 118 0.994721 127 0.24509 128 0.69513 130 0.963268 135 0.931262 136 0.782477 146 0.610353 150 0.989314 156 0.834335 160 0.562895 162 0.888605 167 0.88537 170 0.913555 172 0.558634 176 0.977006 178 0.697272 183 1.00268 184 0.186722 +0 0.739957 6 0.710923 7 0.577658 10 0.549427 13 0.744679 17 0.986533 26 0.804739 28 0.779298 31 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174 0.603754 175 0.630084 179 0.847796 180 0.974209 182 0.188963 183 0.825768 \ No newline at end of file diff --git a/ripser.cpp b/ripser.cpp index 5791676..8ca3063 100644 --- a/ripser.cpp +++ b/ripser.cpp @@ -58,6 +58,34 @@ template class hash_map : public google::sparse_hash_map class hash_map : public std::unordered_map {}; #endif +#ifdef INDICATE_PROGRESS +#ifndef INICATE_STATS + #define INDICATE_STATS +#endif +const uint32_t display_q = 1<<12; +bool line_kill = false; +inline void kill_line(){ + if(line_kill){ + std::cout << "\r\033[K"; + line_kill = false; + } +} +#else +#define kill_line() +#endif + +#ifdef INDICATE_STATS +#include + +std::chrono::time_point time_0; +void print_runtime(){ + auto now = std::chrono::high_resolution_clock::now(); + auto tt = std::chrono::duration_cast(now - time_0); + char buff[20]; + sprintf(buff, "[%04d.%06ds] ", tt.count()/1000000, tt.count()%1000000); + std::cout << buff; +} +#endif typedef float value_t; // typedef uint16_t value_t; @@ -269,6 +297,44 @@ class sparse_distance_matrix { } size_t size() const { return neighbors.size(); } + + sparse_distance_matrix(std::istream& input ){ + std::string line; + value_t value; + index_t idx; + std::vector lens; + for (int i = 0; std::getline(input, line); ++i) { + std::vector nbv; + neighbors.push_back(nbv); + int len = 0; + std::istringstream s(line); + while(s >> idx && s>> value){ + neighbors[i].push_back(std::make_pair(value, idx)); + len++; + } + lens.push_back(len); + } + for(index_t i = 0; i < lens.size(); i++){ + for(index_t j = 0; j < lens[i]; j++){ + auto other = neighbors[i][j]; + neighbors[get_index(other)].push_back(std::make_pair(get_diameter(other), i)); + } + } + } + void print(){ + //For testing. The output of this can be parsed again. + //std::cout << "Sparse distance matrix of size " << neighbors.size() << std::endl; + for(int i = 0; i < neighbors.size(); i++){ + // std::cout << "Line " << i << std::endl; + for(auto ed: neighbors[i]){ + if(get_index(ed)< i) + std::cout<< get_index(ed) << " " << get_diameter(ed) << " "; + else + break; + } + std::cout << std::endl; + } + } }; template <> void compressed_distance_matrix::init_rows() { @@ -636,9 +702,10 @@ template class ripser { columns_to_reduce.clear(); -#ifdef INDICATE_PROGRESS - std::cout << "\033[K" - << "assembling " << num_simplices << " columns" << std::flush << "\r"; + +#ifdef INDICATE_STATS + print_runtime(); + std::cout << "assembling " << num_simplices << " columns" << std::flush << "\n"; #endif for (index_t index = 0; index < num_simplices; ++index) { @@ -647,25 +714,26 @@ template class ripser { 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"; + if ((index + 1) % display_q == 0){ + std::cout << "\r\033[Kassembled " << columns_to_reduce.size() << " out of " + << (index + 1) << "/" << num_simplices << " columns" << std::flush; + } #endif } } -#ifdef INDICATE_PROGRESS - std::cout << "\033[K" - << "sorting " << num_simplices << " columns" << std::flush << "\r"; + +#ifdef INDICATE_STATS + kill_line(); + print_runtime(); + std::cout << "assembled " << columns_to_reduce.size() << " columns out of " + << num_simplices << "\n"; + print_runtime(); + std::cout << "sorting " << columns_to_reduce.size() << " columns\n" << std::flush; #endif std::sort(columns_to_reduce.begin(), columns_to_reduce.end(), greater_diameter_or_smaller_index()); -#ifdef INDICATE_PROGRESS - std::cout << "\033[K"; -#endif } void assemble_sparse_columns_to_reduce(std::vector& simplices, @@ -673,9 +741,11 @@ template class ripser { hash_map& pivot_column_index, index_t dim) { -#ifdef INDICATE_PROGRESS - std::cout << "\033[K" - << "assembling columns" << std::flush << "\r"; + +#ifdef INDICATE_STATS + print_runtime(); + std::cout << "assembling columns\n" << std::flush; + index_t i = 0; #endif --dim; @@ -688,7 +758,13 @@ template class ripser { while (cofaces.has_next(false)) { auto coface = cofaces.next(); - +#ifdef INDICATE_PROGRESS + if (++i % display_q == 0){ + std::cout << "\r\033[Kassembled " << columns_to_reduce.size() + << " columns" << std::flush; + line_kill = true; + } +#endif 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()) @@ -699,25 +775,33 @@ template class ripser { simplices.swap(next_simplices); -#ifdef INDICATE_PROGRESS - std::cout << "\033[K" - << "sorting " << columns_to_reduce.size() << " columns" << std::flush << "\r"; + +#ifdef INDICATE_STATS + kill_line(); + print_runtime(); + std::cout << "assembled " << columns_to_reduce.size() << " columns out of " + << simplices.size() << " simplices" << std::flush << "\n"; + print_runtime(); + std::cout << "sorting " << columns_to_reduce.size() << " columns" << std::flush << "\n"; #endif std::sort(columns_to_reduce.begin(), columns_to_reduce.end(), greater_diameter_or_smaller_index()); -#ifdef INDICATE_PROGRESS - std::cout << "\033[K"; -#endif + } template void compute_pairs(std::vector& columns_to_reduce, hash_map& pivot_column_index, index_t dim) { - + kill_line(); #ifdef PRINT_PERSISTENCE_PAIRS std::cout << "persistence intervals in dim " << dim << ":" << std::endl; #endif +#ifdef INDICATE_STATS + print_runtime(); + std::cout << "reducing "<< columns_to_reduce.size() <<" columns" << std::endl; + index_t num_apparent = 0, num_non_apparent = 0; +#endif #ifdef __native_client__ pp::VarDictionary var_dict; var_dict.Set("type", pp::Var("dim")); @@ -754,10 +838,12 @@ template class ripser { value_t diameter = get_diameter(column_to_reduce); #ifdef INDICATE_PROGRESS - //if ((i + 1) % 1000 == 0) - std::cout << "\033[K" - << "reducing column " << i + 1 << "/" << columns_to_reduce.size() + if ((i + 1) % display_q == 0){ + std::cout << "\r\033[Kreducing column " << i + 1 << "/" << columns_to_reduce.size() << " (diameter " << diameter << ")" << std::flush << "\r"; + line_kill = true; + } + #endif index_t j = i; @@ -819,9 +905,15 @@ template class ripser { if (pivot_column_index.find(get_index(coface)) == pivot_column_index.end()) { pivot = coface; +#ifdef INDICATE_STATS + num_apparent ++; +#endif goto found_persistence_pair; } might_be_apparent_pair = false; +#ifdef INDICATE_STATS + num_non_apparent++; +#endif } } } @@ -839,10 +931,8 @@ template class ripser { } } else { #ifdef PRINT_PERSISTENCE_PAIRS -#ifdef INDICATE_PROGRESS - std::cout << "\033[K"; -#endif - std::cout << " [" << diameter << ", )" << std::endl << std::flush; + kill_line(); + std::cout << "dim "<< dim <<": [" << diameter << ", )" << std::endl << std::flush; #endif #ifdef __native_client__ pp::VarDictionary var_dict; @@ -862,10 +952,8 @@ template class ripser { value_t death = get_diameter(pivot); if (diameter != death) { #ifdef PRINT_PERSISTENCE_PAIRS -#ifdef INDICATE_PROGRESS - std::cout << "\033[K"; -#endif - std::cout << " [" << diameter << "," << death << ")" << std::endl; + kill_line(); + std::cout << "dim "<< dim << ": [" << diameter << "," << death << ")" << std::endl; #endif #ifdef __native_client__ pp::VarDictionary var_dict; @@ -916,9 +1004,15 @@ template class ripser { } while (true); } -#ifdef INDICATE_PROGRESS - std::cout << "\033[K"; + +#ifdef INDICATE_STATS + kill_line(); + print_runtime(); + std::cout << "reduced "<< columns_to_reduce.size() <<" columns. "<< num_apparent + << " apparent, " << num_non_apparent << " non-apparent (" + << float(num_non_apparent)/float(num_apparent+num_non_apparent) <<")" << std::endl; #endif + kill_line(); } void compute_barcodes(); @@ -933,7 +1027,8 @@ enum file_format { DISTANCE_MATRIX, POINT_CLOUD, DIPHA, - RIPSER + RIPSER, + LOWER_SPARSE }; template T read(std::istream& s) { @@ -962,9 +1057,11 @@ compressed_lower_distance_matrix read_point_cloud(std::istream& input_stream) { index_t n = eucl_dist.size(); -#ifdef INDICATE_PROGRESS + +#ifdef INDICATE_STATS + print_runtime(); std::cout << "point cloud with " << n << " points in dimension " - << eucl_dist.points.front().size() << std::endl; + << eucl_dist.points.front().size() << std::endl; #endif #ifdef __native_client__ pp::VarDictionary var_dict; @@ -1089,7 +1186,9 @@ void print_usage_and_exit(int exit_code) { << " distance (full distance matrix)" << std::endl << " point-cloud (point cloud in Euclidean space)" << std::endl << " dipha (distance matrix in DIPHA file format)" << std::endl - << " ripser (distance matrix in Ripser binary file format)" + << " ripser (distance matrix in Ripser binary file format)\n" + << " lower-sparse (sparse lower triangular distance matrix)" + << std::endl << " --dim compute persistent homology up to dimension " << std::endl << " --threshold compute Rips complexes up to diameter " << std::endl @@ -1104,7 +1203,10 @@ void print_usage_and_exit(int exit_code) { #ifndef __EMSCRIPTEN__ #ifndef __native_client__ int main(int argc, char** argv) { - + std::cout<< "starting ripser\n" <::max()) + ripser(std::move(dist), dim_max, threshold, modulus) + .compute_barcodes(); + else{ + ripser(sparse_distance_matrix(std::move(dist), threshold), dim_max, + threshold, modulus) + .compute_barcodes(); + } + } + else{ + ripser(sparse_distance_matrix(filename ? file_stream : std::cin), dim_max, + threshold, modulus) + .compute_barcodes(); + } +} - compressed_lower_distance_matrix dist = read_file(filename ? file_stream : std::cin, format); - - auto value_range = std::minmax_element(dist.distances.begin(), dist.distances.end()); - -#ifdef INDICATE_PROGRESS - std::cout << "distance matrix with " << dist.size() << " points" << std::endl; - std::cout << "value range: [" << *value_range.first << "," << *value_range.second << "]" - << std::endl; -#endif - - if (threshold == std::numeric_limits::max()) - ripser(std::move(dist), dim_max, threshold, modulus) - .compute_barcodes(); - else - ripser(sparse_distance_matrix(std::move(dist), threshold), dim_max, - threshold, modulus) - .compute_barcodes(); -} #endif #endif @@ -1276,7 +1381,8 @@ template <> void ripser::compute_barcodes() { } template <> void ripser::compute_barcodes() { - + //for debugging and testing: + //dist.print(); std::vector columns_to_reduce; std::vector simplices; @@ -1314,7 +1420,7 @@ template <> void ripser::compute_barcodes() { if (u != v) { if (get_diameter(e) != 0) { #ifdef PRINT_PERSISTENCE_PAIRS - std::cout << " [0," << get_diameter(e) << ")" << std::endl; + std::cout << "dim 0: [0," << get_diameter(e) << ")" << std::endl; #endif #ifdef __native_client__ pp::VarDictionary var_dict; @@ -1338,7 +1444,7 @@ template <> void ripser::compute_barcodes() { for (index_t i = 0; i < n; ++i) if (dset.find(i) == i) { #ifdef PRINT_PERSISTENCE_PAIRS - std::cout << " [0, )" << std::endl << std::flush; + std::cout << "dim 0: [0, )" << std::endl << std::flush; #endif #ifdef __native_client__ pp::VarDictionary var_dict;