JMuonEnergy.cc

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#include <string>
#include <iostream>
#include <iomanip>
#include <vector>
#include <set>
#include <algorithm>
#include <limits>
#include <map>
#include <memory>

#include "TMath.h"

#include "km3net-dataformat/offline/Head.hh"
#include "km3net-dataformat/offline/Evt.hh"
#include "km3net-dataformat/definitions/fitparameters.hh"
#include "JDAQ/JDAQEventIO.hh"
#include "JDAQ/JDAQTimesliceIO.hh"
#include "JDAQ/JDAQSummarysliceIO.hh"

#include "JDetector/JDetector.hh"
#include "JDetector/JDetectorSubset.hh"
#include "JDetector/JDetectorToolkit.hh"
#include "JDetector/JModuleRouter.hh"

#include "JDynamics/JDynamics.hh"

#include "JTrigger/JHit.hh"
#include "JTrigger/JFrame.hh"
#include "JTrigger/JTimeslice.hh"
#include "JTrigger/JHitL0.hh"
#include "JTrigger/JHitR1.hh"
#include "JTrigger/JBuildL0.hh"
#include "JTrigger/JTriggerParameters.hh"

#include "JSupport/JSingleFileScanner.hh"
#include "JSupport/JParallelFileScanner.hh"
#include "JSupport/JFileRecorder.hh"
#include "JSupport/JSupport.hh"
#include "JSupport/JMeta.hh"
#include "JSupport/JSummaryFileRouter.hh"

#include "JFit/JLine1Z.hh"
#include "JFit/JEnergy.hh"
#include "JFit/JEnergyRegressor.hh"
#include "JFit/JFitToolkit.hh"
#include "JFit/JNPEHit.hh"
#include "JFit/JMEstimator.hh"
#include "JFit/JTimeRange.hh"
#include "JFit/JModel.hh"

#include "JReconstruction/JEvt.hh"
#include "JReconstruction/JEvtToolkit.hh"
#include "JReconstruction/JMuonEnergyParameters_t.hh"
#include "JReconstruction/JEnergyCorrection.hh"

#include "JPhysics/JConstants.hh"
#include "JTools/JRange.hh"
#include "JTools/JFunction1D_t.hh"
#include "JTools/JFunctionalMap_t.hh"

#include "JPhysics/JPDFTable.hh"
#include "JPhysics/JPDFToolkit.hh"
#include "JPhysics/JNPETable.hh"

#include "JLang/JComparator.hh"

#include "Jeep/JParser.hh"
#include "Jeep/JMessage.hh"


namespace {

  using namespace JPP;
  
  
  /**
   * Auxiliary class for energy estimation.
   */
  struct JResult {
    /**
     * Constructor.
     *
     * \param  x               Energy [log(E/GeV)]
     * \param  chi2            chi2  
     */
    JResult(const JEnergy& x    = 0.0,
            const double   chi2 = std::numeric_limits<double>::max())
    {
      this->x    = x;
      this->chi2 = chi2;
    }

    
    /**
     * Type conversion.
     *
     * \return                 true if valid chi2; else false
     */
    operator bool() const
    {
      return chi2 != std::numeric_limits<double>::max();
    }
    
    JEnergy x;      //!< Energy
    double  chi2;   //!< chi2
  };

  
  /**
   * Type definition of energy range.
   */
  typedef JTOOLS::JRange<JEnergy>     JEnergyRange;
}


/**
 * \file
 *
 * Program to perform JFIT::JRegressor<JEnergy, JGandalf> fit using I/O of JFIT::JEvt data.
 * \author mdejong
 */
int main(int argc, char **argv)
{
  using namespace std;
  using namespace JPP;
  using namespace KM3NETDAQ;

  typedef JTYPELIST<JAllTypes_t, JFIT::JEvt>::typelist             typelist;
  typedef JParallelFileScanner< JTypeList<JDAQEvent, JFIT::JEvt> > JParallelFileScanner_t;
  typedef JParallelFileScanner_t::multi_pointer_type               multi_pointer_type;
  typedef JTYPELIST<JCOMPASS::JOrientation,
                    JACOUSTICS::JEvt>::typelist                    calibration_types;
  typedef JMultipleFileScanner<calibration_types>                  JCalibration_t;

  JParallelFileScanner_t   inputFile;
  JFileRecorder<typelist>  outputFile;
  JLimit_t&                numberOfEvents = inputFile.getLimit();
  string                   detectorFile;
  JCalibration_t           calibrationFile;
  double                   Tmax_s;
  string                   pdfFile;
  JEnergyCorrection        correct;
  JMuonEnergyParameters_t  parameters;
  int                      debug;

  try { 

    JParser<> zap("Program to perform fit of muon energy to data.");
    
    zap['f'] = make_field(inputFile);
    zap['o'] = make_field(outputFile)          = "energy.root";
    zap['a'] = make_field(detectorFile);
    zap['+'] = make_field(calibrationFile)     = JPARSER::initialised();
    zap['T'] = make_field(Tmax_s)              = 100.0;
    zap['n'] = make_field(numberOfEvents)      = JLimit::max();
    zap['P'] = make_field(pdfFile);
    zap['E'] = make_field(correct)             = JEnergyCorrection();            // off
    zap['@'] = make_field(parameters)          = JPARSER::initialised();
    zap['d'] = make_field(debug)               = 1;
    
    zap(argc, argv);
  }
  catch(const exception& error) {
    FATAL(error.what() << endl);
  }


  cout.tie(&cerr);


  JDetector detector;

  try {
    load(detectorFile, detector);
  }
  catch(const JException& error) {
    FATAL(error);
  }

  getMechanics.load(detector.getID());

  unique_ptr<JDynamics> dynamics;

  try {

    dynamics.reset(new JDynamics(detector, Tmax_s));

    dynamics->load(calibrationFile);
  }
  catch(const exception& error) {
    if (!calibrationFile.empty()) {
      FATAL(error.what());
    }
  }

  const JModuleRouter router(dynamics ? dynamics->getDetector() : detector);

  JSummaryFileRouter  summary(inputFile, parameters.R_Hz);


  typedef vector<JHitL0>  JDataL0_t;
  const JBuildL0<JHitL0>  buildL0;
  
  typedef JRegressor<JEnergy>      JRegressor_t;

  JRegressor_t::debug = debug;
  JRegressor_t::T_ns.setRange(parameters.TMin_ns, parameters.TMax_ns);

  JRegressor_t fit(pdfFile);

  fit.estimator.reset(getMEstimator(parameters.mestimator));

  if (!fit.estimator.is_valid()) {
    FATAL("Invalid M-Estimator." << endl);
  }

  if (fit.getRmax() < parameters.roadWidth_m) {
    parameters.roadWidth_m = fit.getRmax();
  }


  outputFile.open();

  outputFile.put(JMeta(argc, argv));

  while (inputFile.hasNext()) {

    STATUS("event: " << setw(10) << inputFile.getCounter() << '\r'); DEBUG(endl);

    multi_pointer_type ps  = inputFile.next();

    const JDAQEvent*   tev = ps;
    const JFIT::JEvt*  in  = ps;

    summary.update(*tev);

    if (dynamics) {
      dynamics->update(*tev);
    }

    // select start values

    JFIT::JEvt cp  = *in;
    JFIT::JEvt out;

    if (parameters.reprocess) {
      cp.select(JHistory::is_not_event(JMUONENERGY));
    }

    cp.select(parameters.numberOfPrefits, qualitySorter);

    if (!cp.empty()) {
      cp.select(JHistory::is_event(cp.begin()->getHistory()));
    }


    JDataL0_t dataL0;

    buildL0(*tev, router, true, back_inserter(dataL0));

      
    for (JFIT::JEvt::const_iterator track = cp.begin(); track != cp.end(); ++track) {

      const JRotation3D           R (getDirection(*track));
      const JLine1Z               tz(getPosition (*track).rotate(R), track->getT());
      const JFIT::JModel<JLine1Z> match(tz, parameters.roadWidth_m, JRegressor_t::T_ns);
        

      multiset<JDAQPMTIdentifier> top;
        
      for (JDataL0_t::const_iterator i = dataL0.begin(); i != dataL0.end(); ++i) {
            
        JHitR1 hit(*i);

        hit.rotate(R);

        if (match(hit)) {
          top.insert(i->getPMTIdentifier());
        }
      }


      double         EMin_log = parameters.EMin_log;
      double         EMax_log = parameters.EMax_log;
      JRange<double> Z_m;

      if (track->hasW(JSTART_LENGTH_METRES) && track->getW(JSTART_LENGTH_METRES) > 0.0) {

        Z_m.setLowerLimit(parameters.ZMin_m);

        //EMin_log = log10(track->getW(JSTART_LENGTH_METRES) * gWater.getA());
      }


      vector<JNPEHit> data;

      const JDetectorSubset_t subdetector(detector, getAxis(*track), parameters.roadWidth_m, Z_m);

      for (JDetector::const_iterator module = subdetector.begin(); module != subdetector.end(); ++module) {

        if (summary.hasSummaryFrame(module->getID())) {

          const JDAQSummaryFrame& frame = summary.getSummaryFrame(module->getID());

          for (size_t i = 0; i != module->size(); ++i) {

            if (getDAQStatus(frame, *module, i)            &&
                getPMTStatus(frame, *module, i)            &&
                !module->getPMT(i).has(PMT_DISABLE)) {

              const double rate_Hz = frame.getRate(i);
              const size_t count   = top.count(JDAQPMTIdentifier(module->getID(), i));

              data.push_back(JNPEHit(fit.getNPE(module->getPMT(i), rate_Hz), count));
            }
          }
        }
      }

      const int NDF = distance(data.begin(), data.end()) - 1;

      if (NDF >= 0) {


        // 5-point search between given limits

        const int      N  =  5;

        JResult result[N];

        for (int i = 0; i != N; ++i) {
          result[i].x = EMin_log + i * (EMax_log - EMin_log) / (N-1);
        }

        map<double, double> buffer;
          
        do {

          int j = 0;

          for (int i = 0; i != N; ++i) {

            if (!result[i]) {

              const JEnergy x    = result[i].x;
              const double  chi2 = fit(x, data.begin(), data.end());

              result[i].chi2 = chi2;
              buffer[chi2]   = x.getE();
            }

            if (result[i].chi2 < result[j].chi2) {
              j = i;
            }
          }

          for (int i = 0; i != N; ++i) {
            DEBUG(' ' << FIXED(5,2) << result[i].x << ' ' << FIXED(9,3) << result[i].chi2);
          }
          DEBUG(endl);
          
          
          // squeeze range

          switch (j) {

          case 0:
            result[4] = result[1];
            result[2] = result[0];
            result[0] = JResult(2*result[2].x - result[4].x);
            break;

          case 1:
            result[4] = result[2];
            result[2] = result[1];
            break;

          case 2:
            result[0] = result[1];
            result[4] = result[3];
            break;

          case 3:
            result[0] = result[2];
            result[2] = result[3];
            break;

          case 4:
            result[0] = result[3];
            result[2] = result[4];
            result[4] = JResult(2*result[2].x - result[0].x);
            break;
          }

          result[1] = JResult(0.5 * (result[0].x + result[2].x));
          result[3] = JResult(0.5 * (result[2].x + result[4].x));

        } while (result[4].x - result[0].x > parameters.resolution);


        if (result[1].chi2 != result[3].chi2) {

          result[2].x    += 0.25 * (result[3].x - result[1].x) * (result[1].chi2 - result[3].chi2) / (result[1].chi2 + result[3].chi2 - 2*result[2].chi2);
          result[2].chi2  = fit(result[2].x, data.begin(), data.end());
        }
          
        const double chi2 = result[2].chi2;
        const double E    = result[2].x.getE();

        // calculate additional variables

        double Emin = numeric_limits<double>::max();
        double Emax = numeric_limits<double>::lowest();

        for (map<double, double>::const_iterator i = buffer.begin(); i != buffer.end() && i->first <= chi2 + 1.0; ++i) {
          if (i->second < Emin) { Emin = i->second; }
          if (i->second > Emax) { Emax = i->second; }
        }

        const double mu_range   = gWater(E);           // range of a muon with the reconstructed energy

        double noise_likelihood = 0.0;                 // log-likelihood of every hit being from K40
        int    number_of_hits   = 0;                   // number of hits selected for JEnergy

        for (vector<JNPEHit>::const_iterator i = data.begin(); i != data.end(); ++i) {
          noise_likelihood += log10(i->getP());        // probability of getting the observed multiplicity with K40
          number_of_hits   += i->getN();               // hit multiplicity
        }


        out.push_back(JFIT::JFit(*track).add(JMUONENERGY));

        // set corrected energy

        out.rbegin()->setE(correct(E));

        // set additional values            

        out.rbegin()->setW(track->getW());
        out.rbegin()->setW(JENERGY_ENERGY,            E);
        out.rbegin()->setW(JENERGY_CHI2,              chi2);
        out.rbegin()->setW(JENERGY_MUON_RANGE_METRES, mu_range);
        out.rbegin()->setW(JENERGY_NOISE_LIKELIHOOD,  noise_likelihood);
        out.rbegin()->setW(JENERGY_NDF,               NDF);
        out.rbegin()->setW(JENERGY_NUMBER_OF_HITS,    number_of_hits);
        out.rbegin()->setW(JENERGY_MINIMAL_ENERGY,    Emin);
        out.rbegin()->setW(JENERGY_MAXIMAL_ENERGY,    Emax);
      }
    }

    if (dynamics) {

      const JDynamics::coverage_type coverage = dynamics->getCoverage();

      for (JFIT::JEvt::iterator i = out.begin(); i != out.end(); ++i) {
        i->setW(JPP_COVERAGE_ORIENTATION, coverage.orientation);
        i->setW(JPP_COVERAGE_POSITION,    coverage.position);
      }
    }

    // apply default sorter

    sort(out.begin(), out.end(), qualitySorter);    

    copy(in->begin(), in->end(), back_inserter(out));

    outputFile.put(out);
  }
  STATUS(endl);

  JSingleFileScanner<JRemove<typelist, JFIT::JEvt>::typelist> io(inputFile);

  io >> outputFile;

  outputFile.close();
}