/**
 *  \file ClosePairContainer.cpp   \brief A list of ParticlePairs.
 *
 *  This file is generated by a script (core/tools/make-container).
 *  Do not edit directly.
 *
 *  Copyright 2007-2013 IMP Inventors. Close rights reserved.
 *
 */

#include "IMP/container/ClosePairContainer.h"
#include "IMP/core/internal/close_pairs_helpers.h"
#include <IMP/log.h>
#include <algorithm>
#include <boost/timer.hpp>
#include <IMP/algebra/internal/tnt_array2d.h>
#include <vector>


IMPCONTAINER_BEGIN_NAMESPACE


ClosePairContainer::ClosePairContainer(SingletonContainerAdaptor c,
                                       double distance,
                                       double slack):
  P(c, distance,
    core::internal::default_cpf(c->get_indexes().size()), slack){
}

ClosePairContainer::ClosePairContainer(SingletonContainerAdaptor c,
                                       double distance,
                                       core::ClosePairsFinder *cpf,
                                       double slack):
  P(c, distance, cpf, slack) {
}

void ClosePairContainer::do_show(std::ostream &) const {
}


namespace {
  struct Data {
    double slack;
    double lifetime;
    double rcost;
    double ccost;
  };
}

double
get_slack_estimate(const ParticlesTemp& ps,
                   double upper_bound,
                   double step,
                   const RestraintsTemp &restraints,
                   bool derivatives,
                   Optimizer *opt,
                   ClosePairContainer *cpc) {
  std::vector<Data> datas;
  for (double slack=0; slack< upper_bound; slack+= step) {
    IMP_LOG_VERBOSE( "Computing for " << slack << std::endl);
    datas.push_back(Data());
    datas.back().slack=slack;
    {
      boost::timer imp_timer;
      int count=0;
      base::SetLogState sl(opt->get_model(), SILENT);
      do {
        cpc->set_slack(slack);
        cpc->update();
        ++count;
      } while (imp_timer.elapsed()==0);
      datas.back().ccost= imp_timer.elapsed()/count;
      IMP_LOG_VERBOSE( "Close pair finding cost "
              << datas.back().ccost << std::endl);
    }
    {
      boost::timer imp_timer;
      double score=0;
      int count=0;
      int iters=1;
      base::SetLogState sl(opt->get_model(), SILENT);
      do {
        for ( int j=0; j< iters; ++j) {
          for (unsigned int i=0; i< restraints.size(); ++i) {
            score+=restraints[i]->evaluate(derivatives);
            // should restore
          }
        }
        count += iters;
        iters*=2;
      } while (imp_timer.elapsed()==0);
      datas.back().rcost= imp_timer.elapsed()/count;
      IMP_UNUSED(score);
      IMP_LOG_VERBOSE( "Restraint evaluation cost "
              << datas.back().rcost << std::endl);
    }
  }
  int ns=100;
  int last_ns=1;
  int opt_i=-1;
  std::vector<Floats > dists(1, Floats(1,0.0));
  std::vector< std::vector<algebra::Vector3D> >
    pos(1, std::vector<algebra::Vector3D>(ps.size()));
  for (unsigned int j=0; j< ps.size(); ++j) {
    pos[0][j]=core::XYZ(ps[j]).get_coordinates();
  }
  do {
    IMP_LOG_VERBOSE( "Stepping from " << last_ns << " to " << ns << std::endl);
    dists.resize(ns, Floats(ns, 0.0));
    for ( int i=0; i< last_ns; ++i) {
      dists[i].resize(ns, 0.0);
    }
    pos.resize(ns,  std::vector<algebra::Vector3D>(ps.size()));
    base::SetLogState sl(opt->get_model(), SILENT);
    for ( int i=last_ns; i< ns; ++i) {
      opt->optimize(1);
      for (unsigned int j=0; j< ps.size(); ++j) {
        pos[i][j]=core::XYZ(ps[j]).get_coordinates();
      }
    }
    for ( int i=last_ns; i< ns; ++i) {
      for ( int j=0; j< i; ++j) {
        double md=0;
        for (unsigned int k=0; k< ps.size(); ++k) {
          md= std::max(md, algebra::get_distance(pos[i][k], pos[j][k]));
        }
        dists[i][j]=md;
        dists[j][i]=md;
      }
    }
    // estimate lifetimes from slack
    for (unsigned int i=0; i< datas.size(); ++i) {
      Ints deaths;
      for ( int j=0; j< ns; ++j) {
        for ( int k=j+1; k < ns; ++k) {
          if (dists[j][k]> datas[i].slack) {
            deaths.push_back(k-j);
            break;
          }
        }
      }
      std::sort(deaths.begin(), deaths.end());
      // kaplan meier estimator
      double ml=0;
      if (deaths.empty()) {
        ml= ns;
      } else {
        //double l=1;
        IMP_INTERNAL_CHECK(deaths.size() < static_cast<unsigned int>(ns),
                           "Too much death");
        double S=1;
        for (unsigned int j=0; j< deaths.size(); ++j) {
          double n= ns-j;
          double t=(n-1.0)/n;
          ml+=(S-t*S)*deaths[j];
          S*=t;
        }
      }
      datas[i].lifetime=ml;
      IMP_LOG_VERBOSE( "Expected life of " << datas[i].slack
              << " is " << datas[i].lifetime << std::endl);
    }

    /**
       C(s) is cost to compute
       R(s) is const to eval restraints
       L(s) is lifetime of slack
       minimize C(s)/L(s)+R(s)
    */
    // smooth
    for (unsigned int i=1; i< datas.size()-1; ++i) {
      datas[i].rcost=(datas[i].rcost+ datas[i-1].rcost+datas[i+1].rcost)/3.0;
      datas[i].ccost=(datas[i].ccost+ datas[i-1].ccost+datas[i+1].ccost)/3.0;
      datas[i].lifetime=(datas[i].lifetime
                      + datas[i-1].lifetime+datas[i+1].lifetime)/3.0;
    }
    double min= std::numeric_limits<double>::max();
    for (unsigned int i=0; i< datas.size(); ++i) {
      double v= datas[i].rcost+ datas[i].ccost/datas[i].lifetime;
      IMP_LOG_VERBOSE( "Cost of " << datas[i].slack << " is " << v
              << " from " << datas[i].rcost
              << " " << datas[i].ccost << " " << datas[i].lifetime
              << std::endl);
      if (v < min) {
        min=v;
        opt_i=i;
      }
    }
    last_ns=ns;
    ns*=2;
    IMP_LOG_VERBOSE( "Opt is " << datas[opt_i].slack << std::endl);
    // 2 for the value, 2 for the doubling
    // if it more than 1000, just decide that is enough
  } while (datas[opt_i].lifetime > ns/4.0 && ns <1000);
  return datas[opt_i].slack;
}

IMPCONTAINER_END_NAMESPACE