#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     Rips<PairDistances, 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, 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;

    std::string             infilename, boundary_name, cocycle_prefix, vertices_name, diagram_name;

    program_options(argc, argv, infilename, 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 << "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();

    PointContainer          points;

    read_points(infilename, points);

    PairDistances           distances(points);

    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());

    #ifdef COUNTERS

    Counter::CounterType    max_element_count = 0;

    unsigned                max_memory = 0;

    long                    max_rss = 0;

    long                    max_ixrss = 0;

    long                    max_idrss = 0;

    long                    max_isrss = 0;

    int                     max_uordblks = 0;

    int                     max_fordblks = 0;

    #endif

    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;

        #ifdef COUNTERS

        max_element_count = std::max(max_element_count, cCohomologyElementCount->count);

        #endif

    }

    // 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");

    #ifdef COUNTERS

    std::cout << "Max element count: " << max_element_count << std::endl;

    #endif

}

void        program_options(int argc, char* argv[], std::string& infilename, 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");

    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);

    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"))

    { 

        std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl;

        std::cout << visible << std::endl; 

        std::abort();

    }

}