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Diffstat (limited to 'src/Persistent_cohomology/benchmark/performance_rips_persistence.cpp')
-rw-r--r-- | src/Persistent_cohomology/benchmark/performance_rips_persistence.cpp | 217 |
1 files changed, 217 insertions, 0 deletions
diff --git a/src/Persistent_cohomology/benchmark/performance_rips_persistence.cpp b/src/Persistent_cohomology/benchmark/performance_rips_persistence.cpp new file mode 100644 index 00000000..a9eab5dd --- /dev/null +++ b/src/Persistent_cohomology/benchmark/performance_rips_persistence.cpp @@ -0,0 +1,217 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Clément Maria + * + * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * + * This program 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. + * + * This program 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 this program. If not, see <http://www.gnu.org/licenses/>. + */ + +#include <gudhi/Rips_complex.h> +#include <gudhi/distance_functions.h> +#include <gudhi/Simplex_tree.h> +#include <gudhi/Persistent_cohomology.h> +#include <gudhi/Persistent_cohomology/Multi_field.h> +#include <gudhi/Hasse_complex.h> +#include <gudhi/Points_off_io.h> + +#include <chrono> +#include <string> +#include <vector> + +// Types definition +using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>; +using Filtration_value = Simplex_tree::Filtration_value; +using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>; +using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; +using Multi_field = Gudhi::persistent_cohomology::Multi_field; +using Point = std::vector<double>; +using Points_off_reader = Gudhi::Points_off_reader<Point>; + +/* Compute the persistent homology of the complex cpx with coefficients in Z/pZ. */ +template< typename FilteredComplex> +void timing_persistence(FilteredComplex & cpx + , int p); + +/* Compute multi-field persistent homology of the complex cpx with coefficients in + * Z/rZ for all prime number r in [p;q].*/ +template< typename FilteredComplex> +void timing_persistence(FilteredComplex & cpx + , int p + , int q); + +/* Timings for the computation of persistent homology with different + * representations of a Rips complex and different coefficient fields. The + * Rips complex is built on a set of 10000 points sampling a Klein bottle embedded + * in dimension 5. + * We represent complexes with a simplex tree and + * with a Hasse diagram. The Hasse diagram represents explicitly all + * codimension 1 incidence relations in the complex, and hence leads to + * a faster computation of persistence because boundaries are precomputed. + * Hovewer, the simplex tree may be constructed directly from a point cloud and + * is more compact. + * We compute persistent homology with coefficient fields Z/2Z and Z/1223Z. + * We present also timings for the computation of multi-field persistent + * homology in all fields Z/rZ for r prime between 2 and 1223. + */ +int main(int argc, char * argv[]) { + std::chrono::time_point<std::chrono::system_clock> start, end; + int elapsed_sec; + { + + std::string off_file_points = "Kl.off"; + Filtration_value threshold = 0.27; + int dim_max = 3; + int p = 2; + int q = 1223; + + // Extract the points from the file off_file_points + Points_off_reader off_reader(off_file_points); + + // Compute the proximity graph of the points + start = std::chrono::system_clock::now(); + Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold, + euclidean_distance<Filtration_value, Point>); + end = std::chrono::system_clock::now(); + elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count(); + std::cout << "Compute Rips graph in " << elapsed_sec << " ms.\n"; + + // Construct the Rips complex in a Simplex Tree + Simplex_tree st; + start = std::chrono::system_clock::now(); + + // insert the proximity graph in the simplex tree + // expand the graph until dimension dim_max + rips_complex_from_file.create_complex(st, dim_max); + + end = std::chrono::system_clock::now(); + elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count(); + std::cout << "Compute Rips complex in " << elapsed_sec << " ms.\n"; + std::cout << " - dimension = " << st.dimension() << std::endl; + std::cout << " - number of simplices = " << st.num_simplices() << std::endl; + + // Sort the simplices in the order of the filtration + start = std::chrono::system_clock::now(); + st.initialize_filtration(); + end = std::chrono::system_clock::now(); + elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count(); + std::cout << "Order the simplices of the filtration in " << elapsed_sec << " ms.\n"; + + // Copy the keys inside the simplices + start = std::chrono::system_clock::now(); + { + int count = 0; + for (auto sh : st.filtration_simplex_range()) + st.assign_key(sh, count++); + } + end = std::chrono::system_clock::now(); + elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count(); + std::cout << "Copied the keys inside the simplices in " << elapsed_sec << " ms.\n"; + + // Convert the simplex tree into a hasse diagram + start = std::chrono::system_clock::now(); + Gudhi::Hasse_complex<> hcpx(st); + end = std::chrono::system_clock::now(); + elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count(); + std::cout << "Convert the simplex tree into a Hasse diagram in " << elapsed_sec << " ms.\n"; + + + std::cout << "Timings when using a simplex tree: \n"; + timing_persistence(st, p); + timing_persistence(st, q); + timing_persistence(st, p, q); + + std::cout << "Timings when using a Hasse complex: \n"; + timing_persistence(hcpx, p); + timing_persistence(hcpx, q); + timing_persistence(hcpx, p, q); + + start = std::chrono::system_clock::now(); + } + end = std::chrono::system_clock::now(); + elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count(); + std::cout << "Running the complex destructors in " << elapsed_sec << " ms.\n"; + return 0; +} + +template< typename FilteredComplex> +void +timing_persistence(FilteredComplex & cpx + , int p) { + std::chrono::time_point<std::chrono::system_clock> start, end; + int elapsed_sec; + { + start = std::chrono::system_clock::now(); + Gudhi::persistent_cohomology::Persistent_cohomology< FilteredComplex, Field_Zp > pcoh(cpx); + end = std::chrono::system_clock::now(); + elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count(); + std::cout << " Initialize pcoh in " << elapsed_sec << " ms.\n"; + // initializes the coefficient field for homology + start = std::chrono::system_clock::now(); + pcoh.init_coefficients(p); + end = std::chrono::system_clock::now(); + elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count(); + std::cout << " Initialize the coefficient field in " << elapsed_sec << " ms.\n"; + + start = std::chrono::system_clock::now(); + + pcoh.compute_persistent_cohomology(INFINITY); + + end = std::chrono::system_clock::now(); + elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count(); + std::cout << " Compute persistent homology in Z/" << p << "Z in " << elapsed_sec << " ms.\n"; + start = std::chrono::system_clock::now(); + } + end = std::chrono::system_clock::now(); + elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count(); + std::cout << " Run the persistence destructors in " << elapsed_sec << " ms.\n"; +} + +template< typename FilteredComplex> +void +timing_persistence(FilteredComplex & cpx + , int p + , int q) { + std::chrono::time_point<std::chrono::system_clock> start, end; + int elapsed_sec; + { + start = std::chrono::system_clock::now(); + Gudhi::persistent_cohomology::Persistent_cohomology< FilteredComplex, Multi_field > pcoh(cpx); + end = std::chrono::system_clock::now(); + elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count(); + std::cout << " Initialize pcoh in " << elapsed_sec << " ms.\n"; + // initializes the coefficient field for homology + start = std::chrono::system_clock::now(); + pcoh.init_coefficients(p, q); + end = std::chrono::system_clock::now(); + elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count(); + std::cout << " Initialize the coefficient field in " << elapsed_sec << " ms.\n"; + // compute persistent homology, disgarding persistent features of life shorter than min_persistence + + start = std::chrono::system_clock::now(); + + pcoh.compute_persistent_cohomology(INFINITY); + + end = std::chrono::system_clock::now(); + elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count(); + std::cout << " Compute multi-field persistent homology in all coefficient fields Z/pZ " + << "with p in [" << p << ";" << q << "] in " << elapsed_sec << " ms.\n"; + start = std::chrono::system_clock::now(); + } + end = std::chrono::system_clock::now(); + elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count(); + std::cout << " Run the persistence destructors in " << elapsed_sec << " ms.\n"; +} |