#include <topology/rips.h>
#include <topology/filtration.h>
#include <topology/static-persistence.h>
#include <topology/dynamic-persistence.h>
#include <topology/persistence-diagram.h>
#include <utilities/containers.h>           // for BackInsertFunctor

#include <fstream>
#include <boost/archive/binary_oarchive.hpp>
#include <boost/serialization/map.hpp>

// Trivial example of size() points on a line with integer coordinates
struct Distances
{
    typedef         int             IndexType;
    typedef         double          DistanceType;

    DistanceType    operator()(IndexType a, IndexType b) const      { return std::abs(a - b); }

    size_t          size() const                                    { return 2000; }
    IndexType       begin() const                                   { return 0; }
    IndexType       end() const                                     { return size(); }
};

//typedef         Rips<ExplicitDistances<Distances> >                   Generator;
typedef         Rips<Distances>                                         Generator;
typedef         Generator::Simplex                                      Smplx;
typedef         Filtration<Smplx>                                       Fltr;
typedef         StaticPersistence<>                                     Persistence;
// typedef         DynamicPersistenceChains<>                              Persistence;
typedef         PersistenceDiagram<>                                    PDgm;


int main(int argc, char* argv[])
{
#ifdef LOGGING
	rlog::RLogInit(argc, argv);

	stdoutLog.subscribeTo( RLOG_CHANNEL("error") );
	stdoutLog.subscribeTo( RLOG_CHANNEL("info") );
	//stdoutLog.subscribeTo( RLOG_CHANNEL("rips/info") );
	//stdoutLog.subscribeTo( RLOG_CHANNEL("rips/debug") );
#endif

    Distances distances;
    
    // Storing ExplicitDistances speeds up the computation (at the price of memory)
    //ExplicitDistances<Distances> explicit_distances(distances);

    Generator               rips(distances);
    Generator::Evaluator    size(distances);
    Fltr                    f;
    
    // Generate 2-skeleton of the Rips complex for epsilon = 50
    rips.generate(2, 10, make_push_back_functor(f));
    rInfo("Generated complex of size: %d",  f.size());

    // Generate filtration with respect to distance and compute its persistence
    f.sort(Generator::Comparison(distances));
    Persistence p(f);
    p.pair_simplices();
    rInfo("Simplices paired");

    Persistence::SimplexMap<Fltr>   m = p.make_simplex_map(f);

    // Record the persistence intervals in the persistence diagrams
    std::map<Dimension, PDgm> dgms;
    init_diagrams(dgms, p.begin(), p.end(), 
                  evaluate_through_map(m, size), 
                  evaluate_through_map(m, Smplx::DimensionExtractor()));

    // Serialize the diagrams to a file
    std::ofstream ofs("rips-diagrams");
    boost::archive::binary_oarchive oa(ofs);
    oa << dgms;

    // Output cycles
    for (Persistence::iterator cur = p.begin(); cur != p.end(); ++cur)
    {
        const Persistence::Cycle& cycle = cur->cycle;

        if (!cur->sign())        // only negative simplices have non-empty cycles
        {
            Persistence::OrderIndex birth = cur->pair;      // the cycle that cur killed was born when we added birth (another simplex)

            const Smplx& b = m[birth];
            const Smplx& d = m[cur];
            
            if (b.dimension() != 1) continue;
            std::cout << "Pair: (" << size(b) << ", " << size(d) << ")" << std::endl;
        } else if (cur->unpaired())    // positive could be unpaired
        {
            const Smplx& b = m[cur];
            if (b.dimension() != 1) continue;
            
            std::cout << "Unpaired birth: " << size(b) << std::endl;
            // cycle = cur->chain;
        }

        // Iterate over the cycle
        for (Persistence::Cycle::const_iterator si =  cycle.begin(); si != cycle.end(); ++si)
        {
            const Smplx& s = m[*si];
            //std::cout << s.dimension() << std::endl;
            const Smplx::VertexContainer& vertices = s.vertices();          // std::vector<Vertex> where Vertex = Distances::IndexType
            AssertMsg(vertices.size() == s.dimension() + 1, "dimension of a simplex is one less than the number of its vertices");
            std::cout << vertices[0] << " " << vertices[1] << std::endl;
        }
    }
}