#include <topology/cohomology-persistence.h>
#include <topology/rips.h>
#include <geometry/l2distance.h>
#include <geometry/distances.h>
#include <utilities/containers.h> // for BackInsertFunctor
#include <utilities/property-maps.h>
#include <utilities/timer.h>
#include <utilities/log.h>
#include <utilities/counter.h>
#include <utilities/memory.h>
#include <string>
#include <boost/tuple/tuple.hpp>
#include <boost/program_options.hpp>
#include <boost/progress.hpp>
#include "wrappers.h"
typedef PairwiseDistances<PointContainer, L2Distance> PairDistances;
typedef PairDistances::DistanceType DistanceType;
typedef PairDistances::IndexType Vertex;
typedef boost::tuple<Dimension, DistanceType> BirthInfo;
typedef CohomologyPersistence<BirthInfo, Wrapper<unsigned> > Persistence;
typedef Persistence::SimplexIndex Index;
typedef Persistence::Death Death;
typedef Persistence::CocyclePtr CocyclePtr;
typedef ExplicitDistances< PairDistances > Distances;
typedef Rips<Distances, Simplex<Vertex, Index> > Generator;
typedef Generator::Simplex Smplx;
typedef std::vector<Smplx> SimplexVector;
typedef SimplexVector::const_iterator SV_const_iterator;
typedef std::map<Smplx, Index, Smplx::VertexComparison> Complex;
#include "output.h" // for output_*()
void program_options(int argc, char* argv[], std::string& infilename, unsigned& pt_size, Dimension& skeleton, DistanceType& max_distance, ZpField::Element& prime, std::string& boundary_name, std::string& cocycle_prefix, std::string& vertices_name, std::string& diagram_name);
int main(int argc, char* argv[])
{
#ifdef LOGGING
rlog::RLogInit(argc, argv);
stderrLog.subscribeTo( RLOG_CHANNEL("error") );
#endif
Dimension skeleton;
DistanceType max_distance;
ZpField::Element prime;
unsigned pt_size;
std::string infilename, boundary_name, cocycle_prefix, vertices_name, diagram_name;
program_options(argc, argv, infilename, pt_size, skeleton, max_distance, prime, boundary_name, cocycle_prefix, vertices_name, diagram_name);
std::ofstream bdry_out(boundary_name.c_str());
std::ofstream vertices_out(vertices_name.c_str());
std::ofstream diagram_out(diagram_name.c_str());
std::cout << "# of points: " << pt_size << std::endl;
std::cout << "Boundary matrix: " << boundary_name << std::endl;
std::cout << "Cocycles: " << cocycle_prefix << "*.ccl" << std::endl;
std::cout << "Vertices: " << vertices_name << std::endl;
std::cout << "Diagram: " << diagram_name << std::endl;
Timer total_timer; total_timer.start();
// Read the pairwise distances
std::ifstream in(infilename.c_str());
Distances distances(pt_size);
for (unsigned i = 0; i < pt_size; ++i)
for (unsigned j = 0; j < pt_size; ++j)
in >> distances(i,j);
Generator rips(distances);
Generator::Evaluator size(distances);
Generator::Comparison cmp(distances);
SimplexVector v;
Timer rips_timer; rips_timer.start();
rips.generate(skeleton, max_distance, make_push_back_functor(v));
std::sort(v.begin(), v.end(), Smplx::VertexComparison());
std::vector<unsigned> index_in_v(v.size());
for (unsigned idx = 0; idx < v.size(); ++idx)
index_in_v[idx] = idx;
std::sort(index_in_v.begin(), index_in_v.end(), IndirectIndexComparison<SimplexVector, Generator::Comparison>(v, cmp));
BinarySearchMap<Smplx, SimplexVector::iterator, Smplx::VertexComparison> map_of_v(v.begin(), v.end());
rips_timer.stop();
std::cout << "Simplex vector generated, size: " << v.size() << std::endl;
output_boundary_matrix(bdry_out, v, Smplx::VertexComparison());
output_vertex_indices(vertices_out, v);
Timer persistence_timer; persistence_timer.start();
ZpField zp(prime);
Persistence p(zp);
boost::progress_display show_progress(v.size());
for (unsigned j = 0; j < index_in_v.size(); ++j)
{
SimplexVector::const_iterator cur = v.begin() + index_in_v[j];
std::vector<Index> boundary;
for (Smplx::BoundaryIterator bcur = cur->boundary_begin(); bcur != cur->boundary_end(); ++bcur)
boundary.push_back(map_of_v[*bcur]->data());
Index idx; Death d; CocyclePtr ccl;
bool store = cur->dimension() < skeleton;
boost::tie(idx, d, ccl) = p.add(boundary.begin(), boundary.end(), boost::make_tuple(cur->dimension(), size(*cur)), store, index_in_v[j]);
// c[*cur] = idx;
if (store)
map_of_v[*cur]->data() = idx;
if (d && (size(*cur) - d->get<1>()) > 0)
{
AssertMsg(d->get<0>() == cur->dimension() - 1, "Dimensions must match");
diagram_out << (cur->dimension() - 1) << " " << d->get<1>() << " " << size(*cur) << std::endl;
}
++show_progress;
}
// output infinte persistence pairs
for (Persistence::CocycleIndex cur = p.begin(); cur != p.end(); ++cur)
diagram_out << cur->birth.get<0>() << " " << cur->birth.get<1>() << " inf" << std::endl;
persistence_timer.stop();
// p.show_cocycles();
// Output alive cocycles of dimension 1
if (!cocycle_prefix.empty())
{
unsigned i = 0;
for (Persistence::Cocycles::const_iterator cur = p.begin(); cur != p.end(); ++cur)
{
if (cur->birth.get<0>() != 1) continue;
output_cocycle(cocycle_prefix, i, v, cur->birth, cur->zcolumn, prime);
// std::cout << "Cocycle of dimension: " << cur->birth.get<0>() << " born at " << cur->birth.get<1>() << std::endl;
++i;
}
}
total_timer.stop();
rips_timer.check("Rips timer");
persistence_timer.check("Persistence timer");
total_timer.check("Total timer");
}
void program_options(int argc, char* argv[], std::string& infilename, unsigned& pt_size, Dimension& skeleton, DistanceType& max_distance, ZpField::Element& prime, std::string& boundary_name, std::string& cocycle_prefix, std::string& vertices_name, std::string& diagram_name)
{
namespace po = boost::program_options;
po::options_description hidden("Hidden options");
hidden.add_options()
("input-file", po::value<std::string>(&infilename), "Point set whose Rips zigzag we want to compute")
("num-pts", po::value<unsigned>(&pt_size), "Number of points in the input");
po::options_description visible("Allowed options", 100);
visible.add_options()
("help,h", "produce help message")
("skeleton-dimsnion,s", po::value<Dimension>(&skeleton)->default_value(2), "Dimension of the Rips complex we want to compute")
("prime,p", po::value<ZpField::Element>(&prime)->default_value(11), "Prime p for the field F_p")
("max-distance,m", po::value<DistanceType>(&max_distance)->default_value(Infinity), "Maximum value for the Rips complex construction")
("boundary,b", po::value<std::string>(&boundary_name), "Filename where to output the boundary matrix")
("cocycle,c", po::value<std::string>(&cocycle_prefix), "Prefix of the filename where to output the 1-dimensional cocycles")
("vertices,v", po::value<std::string>(&vertices_name), "Filename where to output the simplex-vertex mapping")
("diagram,d", po::value<std::string>(&diagram_name), "Filename where to output the persistence diagram");
#if LOGGING
std::vector<std::string> log_channels;
visible.add_options()
("log,l", po::value< std::vector<std::string> >(&log_channels), "log channels to turn on (info, debug, etc)");
#endif
po::positional_options_description pos;
pos.add("input-file", 1);
pos.add("num-pts", 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 LOGGING
for (std::vector<std::string>::const_iterator cur = log_channels.begin(); cur != log_channels.end(); ++cur)
stderrLog.subscribeTo( RLOG_CHANNEL(cur->c_str()) );
#endif
if (vm.count("help") || !vm.count("input-file")|| !vm.count("num-pts"))
{
std::cout << "Usage: " << argv[0] << " [options] input-file num-pts" << std::endl;
std::cout << visible << std::endl;
std::abort();
}
}