From 2814e25cbc70160e57f426ec708f6d99180ef5fd Mon Sep 17 00:00:00 2001 From: glisse Date: Sun, 25 Oct 2015 21:41:01 +0000 Subject: Example to compute persistence of a Rips filtration "in parallel". On a machine with a gazillion cores, it gains a factor >2 at the expense of some memory. At this point, construction of the Rips graph and expansion are not negligible anymore and could use some parallelism. git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/tbb@875 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 53d6a74338f1346bd7d1ca018ec15dd1ee8287e8 --- src/Hasse_complex/include/gudhi/Hasse_complex.h | 14 +- .../example/parallel_rips_persistence.cpp | 180 +++++++++++++++++++++ 2 files changed, 187 insertions(+), 7 deletions(-) create mode 100644 src/Persistent_cohomology/example/parallel_rips_persistence.cpp diff --git a/src/Hasse_complex/include/gudhi/Hasse_complex.h b/src/Hasse_complex/include/gudhi/Hasse_complex.h index af9ae5e9..38887264 100644 --- a/src/Hasse_complex/include/gudhi/Hasse_complex.h +++ b/src/Hasse_complex/include/gudhi/Hasse_complex.h @@ -44,8 +44,7 @@ struct Hasse_simplex { template< class Complex_ds > Hasse_simplex(Complex_ds & cpx , typename Complex_ds::Simplex_handle sh) - : key_(cpx.key(sh)) - , filtration_(cpx.filtration(sh)) + : filtration_(cpx.filtration(sh)) , boundary_() { boundary_.reserve(cpx.dimension(sh) + 1); for (auto b_sh : cpx.boundary_simplex_range(sh)) { @@ -55,7 +54,7 @@ struct Hasse_simplex { Hasse_simplex(typename HasseCpx::Simplex_key key , typename HasseCpx::Filtration_value fil - , std::vector boundary) + , std::vector const& boundary) : key_(key) , filtration_(fil) , boundary_(boundary) { } @@ -197,11 +196,12 @@ class Hasse_complex { } void initialize_filtration() { + // Setting the keys is done by pcoh, Simplex_tree doesn't do it either. +#if 0 Simplex_key key = 0; - for (auto & h_simp : complex_) { - h_simp.key_ = key; - ++key; - } + for (auto & h_simp : complex_) + h_simp.key_ = key++; +#endif } std::vector< Hasse_simp, Gudhi::no_init_allocator > complex_; diff --git a/src/Persistent_cohomology/example/parallel_rips_persistence.cpp b/src/Persistent_cohomology/example/parallel_rips_persistence.cpp new file mode 100644 index 00000000..425a5b2c --- /dev/null +++ b/src/Persistent_cohomology/example/parallel_rips_persistence.cpp @@ -0,0 +1,180 @@ +/* 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, Marc Glisse + * + * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France), + * 2015 INRIA Saclay Île de 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 . + */ + +#include +#include +#include +#include +#include +#include "gudhi/Hasse_complex.h" + +#include + +#ifdef GUDHI_USE_TBB +#include +#endif + +#include +#include + +//////////////////////////////////////////////////////////////// +// // +// WARNING: persistence computation itself is not parallel, // +// and this uses more memory than rips_persistence. // +// // +//////////////////////////////////////////////////////////////// + +using namespace Gudhi; +using namespace Gudhi::persistent_cohomology; + +typedef int Vertex_handle; +typedef double Filtration_value; + +void program_options(int argc, char * argv[] + , std::string & filepoints + , std::string & filediag + , Filtration_value & threshold + , int & dim_max + , int & p + , Filtration_value & min_persistence); + +int main(int argc, char * argv[]) { + std::string filepoints; + std::string filediag; + Filtration_value threshold; + int dim_max; + int p; + Filtration_value min_persistence; + + program_options(argc, argv, filepoints, filediag, threshold, dim_max, p, min_persistence); + + // Extract the points from the file filepoints + typedef std::vector Point_t; + std::vector< Point_t > points; + read_points(filepoints, points); + + // Compute the proximity graph of the points + Graph_t prox_graph = compute_proximity_graph(points, threshold + , euclidean_distance); + + // Construct the Rips complex in a Simplex Tree + Simplex_tree<>& st = *new Simplex_tree<>; + // insert the proximity graph in the simplex tree + st.insert_graph(prox_graph); + // expand the graph until dimension dim_max + st.expansion(dim_max); + + std::cout << "The complex contains " << st.num_simplices() << " simplices \n"; + std::cout << " and has dimension " << st.dimension() << " \n"; + +#ifdef GUDHI_USE_TBB + // Unnecessary, but clarifies which operations are parallel. + tbb::task_scheduler_init ts; +#endif + + // Sort the simplices in the order of the filtration + st.initialize_filtration(); + int count = 0; + for (auto sh : st.filtration_simplex_range()) + st.assign_key(sh, count++); + + // Convert to a more convenient representation. + Hasse_complex<> hcpx(st); + +#ifdef GUDHI_USE_TBB + ts.terminate(); +#endif + + // Free some space. + delete &st; + + // Compute the persistence diagram of the complex + persistent_cohomology::Persistent_cohomology< Hasse_complex<>, Field_Zp > pcoh(hcpx); + // initializes the coefficient field for homology + pcoh.init_coefficients(p); + + pcoh.compute_persistent_cohomology(min_persistence); + + // Output the diagram in filediag + if (filediag.empty()) { + pcoh.output_diagram(); + } else { + std::ofstream out(filediag); + pcoh.output_diagram(out); + out.close(); + } +} + +void program_options(int argc, char * argv[] + , std::string & filepoints + , std::string & filediag + , Filtration_value & threshold + , int & dim_max + , int & p + , Filtration_value & min_persistence) { + namespace po = boost::program_options; + po::options_description hidden("Hidden options"); + hidden.add_options() + ("input-file", po::value(&filepoints), + "Name of file containing a point set. Format is one point per line: X1 ... Xd "); + + po::options_description visible("Allowed options", 100); + visible.add_options() + ("help,h", "produce help message") + ("output-file,o", po::value(&filediag)->default_value(std::string()), + "Name of file in which the persistence diagram is written. Default print in std::cout") + ("max-edge-length,r", po::value(&threshold)->default_value(0), + "Maximal length of an edge for the Rips complex construction.") + ("cpx-dimension,d", po::value(&dim_max)->default_value(1), + "Maximal dimension of the Rips complex we want to compute.") + ("field-charac,p", po::value(&p)->default_value(11), + "Characteristic p of the coefficient field Z/pZ for computing homology.") + ("min-persistence,m", po::value(&min_persistence), + "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals"); + + po::positional_options_description pos; + pos.add("input-file", 1); + + po::options_description all; + all.add(visible).add(hidden); + + po::variables_map vm; + po::store(po::command_line_parser(argc, argv). + options(all).positional(pos).run(), vm); + po::notify(vm); + + if (vm.count("help") || !vm.count("input-file")) { + std::cout << std::endl; + std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; + std::cout << "of a Rips complex defined on a set of input points.\n \n"; + std::cout << "The output diagram contains one bar per line, written with the convention: \n"; + std::cout << " p dim b d \n"; + std::cout << "where dim is the dimension of the homological feature,\n"; + std::cout << "b and d are respectively the birth and death of the feature and \n"; + std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; + + std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; + std::cout << visible << std::endl; + std::abort(); + } +} -- cgit v1.2.3