#include <string>
#include <iostream>
#include <iomanip>
#include <limits>
#include <map>
#include <vector>

#include "TROOT.h"
#include "TFile.h"
#include "TH1D.h"
#include "TF1.h"
#include "TMath.h"

#include "km3net-dataformat/online/JDAQ.hh"
#include "JDAQ/JDAQEventIO.hh"
#include "JDAQ/JDAQTimesliceIO.hh"
#include "JDAQ/JDAQEvaluator.hh"
#include "JDetector/JDetector.hh"
#include "JDetector/JDetectorToolkit.hh"
#include "JDetector/JDAQHitRouter.hh"
#include "JDetector/JPMTParametersMap.hh"
#include "JTrigger/JBuildL0.hh"
#include "JTrigger/JBuildL1.hh"
#include "JLang/JSinglePointer.hh"
#include "JROOT/JManager.hh"
#include "JTools/JWeight.hh"
#include "JROOT/JROOTClassSelector.hh"
#include "JSupport/JSingleFileScanner.hh"
#include "JSupport/JTreeScannerInterface.hh"
#include "JSupport/JTreeScanner.hh"
#include "JSupport/JAutoTreeScanner.hh"
#include "JSupport/JSupport.hh"
#include "JSupport/JMeta.hh"

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

namespace {

  // status of module
  enum JStatus_t {
    DEFAULT       =  0,      //!< module exists in detector
    NODATA        = -2,      //!< module not present in data or no entries
    OUT_SYNC      = -3,      //!< module is out-of-sync
    ERROR         = -4,      //!< module is out-of-sync, possibly multiple time offsets
    IN_SYNC       = +1       //!< module is in-sync
  };
}


/**
 * \file
 *
 * Example program to search for correlations between triggered events and timeslice data.
 * \author mdejong
 */
int main(int argc, char **argv)
{
  using namespace std;
  using namespace JPP;
  using namespace KM3NETDAQ;

  JSingleFileScanner<> inputFile;
  JLimit_t&          numberOfEvents = inputFile.getLimit();
  string             outputFile;
  string             detectorFile;
  double             TMaxLocal_ns;
  string             pmtFile;
  int                numberOfTimeslices;
  double             binWidth_ns;
  double             Pmin;
  JROOTClassSelector selector;
  int                qaqc;
  int                debug;
  
  string             peaks;

  try { 

    JParser<> zap("Example program to search for correlations between triggered events and timeslice data.");
    
    zap['f'] = make_field(inputFile);
    zap['o'] = make_field(outputFile)          = "";
    zap['a'] = make_field(detectorFile);
    zap['n'] = make_field(numberOfEvents)      = JLimit::max();
    zap['T'] = make_field(TMaxLocal_ns)        = 20.0;
    zap['P'] = make_field(pmtFile)             = "";
    zap['N'] = make_field(numberOfTimeslices)  = 100;
    zap['W'] = make_field(binWidth_ns)         = 10e3;
    zap['p'] = make_field(Pmin)                = 1.0e-6;
    zap['C'] = make_field(selector)            = "", getROOTClassSelection<JDAQTimesliceTypes_t>();
    zap['Q'] = make_field(qaqc)                =  0;
    zap['d'] = make_field(debug)               =  2;
    
    zap['O'] = make_field(peaks)               = ""; //Make a small summary file, with the list of the peaks

    zap.read(argc, argv);
  }
  catch(const exception& error) {
    FATAL(error.what() << endl);
  }

  
  JDetector detector;

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

  const double TMax_ns = max(binWidth_ns, getMaximalTime(detector));

  typedef  double    hit_type;
  
  JBuildL0<hit_type> buildL0;
  JBuildL1<hit_type> buildL1(JBuildL1Parameters(TMaxLocal_ns, true));
  vector  <hit_type> data;  
  
  typedef JManager<int, TH1D>  JManager_t;

  const Double_t xmin = -(numberOfTimeslices + 1) * getFrameTime() - 0.5*binWidth_ns;
  const Double_t xmax = +(numberOfTimeslices + 1) * getFrameTime() + 0.5*binWidth_ns;
  const Int_t    nx   = (Int_t) ((xmax - xmin) / binWidth_ns);
  
  JManager_t manager(new TH1D("M_%", NULL, nx, xmin, xmax));

  JTreeScanner<>::debug = debug;
  
  JSinglePointer< JTreeScannerInterface<JDAQTimeslice> > ps;

  JAutoTreeScanner<JDAQTimeslice> zmap = JType<JDAQTimesliceTypes_t>();
  
  if (selector == "") {

    if ((ps = new JTreeScanner< JAssertConversion<JDAQTimesliceSN, JDAQTimeslice> >(inputFile))->getEntries() != 0 ||
	(ps = new JTreeScanner< JAssertConversion<JDAQTimesliceL2, JDAQTimeslice> >(inputFile))->getEntries() != 0 ||
	(ps = new JTreeScanner< JAssertConversion<JDAQTimesliceL1, JDAQTimeslice> >(inputFile))->getEntries() != 0 ||
	(ps = new JTreeScanner< JAssertConversion<JDAQTimesliceL0, JDAQTimeslice> >(inputFile))->getEntries() != 0 ||
	(ps = new JTreeScanner< JAssertConversion<JDAQTimeslice,   JDAQTimeslice> >(inputFile))->getEntries() != 0) {
    } else {
      FATAL("No timeslice data." << endl);
    }

    NOTICE("Selected class " << ps->getClassName() << endl);

  } else {

    ps = zmap[selector];
    
    ps->configure(inputFile);
  }

  /*   Updated method  :
   *   OOS DOMs can have an impact on the histogram of other DOMs   
   *   especialy OOS DOMs on adjacent In Sync or OOS DOMs (presence of ghost peaks)
   *   To remove these ghost peaks, the idea is to iterate the method, removing 
   *   at each loop the most OOS DOM, and recomputing the histograms without 
   *   them (removing events where they are involved)
   *   Once there is no more OOS DOMs in the remaining DOMs, end of precedure.   
   *   Steps of procedure (from J. Hofestaedt, code updated by R. Le Breton)    
   *   1) Check if any DOM shows a peak away from 0 (OOS)   
   *      If no OOS -> finish procedure                                         
   *   2) If at least one OOS, then identify the DOM that is most OOS,          
   *      ie. highest peak (other than delta time = 0)                       	  
   *   3) Remove the most OOS DOM and calculate the histograms again but do not
   *      consider the OOS DOM (in later iterations more than one DOM is OOS and not   
   *      considered for histogram filling).
   *   4) start with 1) again
   */

  ps->setLimit(inputFile.getLimit());

  typedef map<int, vector<double> > map_type;    // frame index -> event times

  bool OOS = true; //Boolean: to continue or not the procedure
  map_type buffer;
    
  map_type peaksPerDoms;
  
  map<int, JStatus_t> status2;

  //OOS DOMs IDs : if at least one OOS DOM, one ID is added into oosDomsId at each iteration 
  map<int, bool> oosDomsId; 
  
  //Default value for all modules : false
  for (JDetector::const_iterator module = detector.begin(); module != detector.end(); ++module) {
    oosDomsId[module->getID()] = false;
  }

  do{    
    for (JTreeScanner<JDAQEvent> in(inputFile.getFilename()); in.hasNext(); ) {
      
      STATUS("event: " << setw(10) << in.getCounter() << '\r'); DEBUG(endl);
      
      JDAQEvent* event = in.next();
      
      // Average time of triggered hits
      
      double t0 = 0.0;
      bool test_OOS = false; //If an OOS DOM is involved in an event, remove this event
      
      for (JDAQEvent::const_iterator<JDAQTriggeredHit> hit = event->begin<JDAQTriggeredHit>(); hit != event->end<JDAQTriggeredHit>(); ++hit) {
	t0 += getTime(*hit, router.getPMT(*hit));

	if(oosDomsId[hit->getModuleID()]) {
	  test_OOS = true;
	  break;
	}
      }

      if(test_OOS) continue; //If true, event not taken into account

      t0 /= event->size<JDAQTriggeredHit>();
      t0 += event->getFrameIndex() * getFrameTime();
      
      buffer[event->getFrameIndex()].push_back(t0);
    }    
    STATUS(endl);
    
    //Events : start from the beginning
    ps->rewind();
    
    while (ps->hasNext()) {
      
      STATUS("event: " << setw(10) << ps->getCounter() << '\r'); DEBUG(endl);
      
      JDAQTimeslice* timeslice = ps->next();
      
      map_type::const_iterator p = buffer.lower_bound(timeslice->getFrameIndex() - numberOfTimeslices);
      map_type::const_iterator q = buffer.upper_bound(timeslice->getFrameIndex() + numberOfTimeslices);
      
      int number_of_events = 0;
      
      for (map_type::const_iterator i = p; i != q; ++i) {
	number_of_events += i->second.size();
      }
      
      if (number_of_events == 0) {
	continue;
      }
      
      for (JDAQTimeslice::const_iterator frame = timeslice->begin(); frame != timeslice->end(); ++frame) {
	  
	data.clear();
	
	buildL1(*frame, router.getModule(frame->getModuleID()), back_inserter(data));
	
	TH1D* h1 = manager[frame->getModuleID()];
	
	for (vector<hit_type>::const_iterator hit = data.begin(); hit != data.end(); ++hit) {
	  
	  const double t1 = *hit + frame->getFrameIndex() * getFrameTime();
	  
	  for (map_type::const_iterator i = p; i != q; ++i) {
	    for (map_type::mapped_type::const_iterator j = i->second.begin(); j != i->second.end(); ++j) {
	      
	      const double t0 = *j;
	      
	      h1->Fill(t1 - t0);
	    }
	  }
	}
      }
    }

    buffer.clear(); //Clear the buffer for the next loop, if any

    STATUS(endl);
      
    Double_t most_OOS_peak = 0;
    Int_t most_OOS_ID = 0;
    
    TF1 f1("f1", "[0]*exp(-0.5*(x-[1])*(x-[1])/([2]*[2])) + [3]");
    
    string option = "L";
    
    if (debug < debug_t) {
      option += "Q";
    }
    
    for (JDetector::const_iterator module = detector.begin(); module != detector.end(); ++module) {
      
      bool status = false;

      status2[module->getID()] = DEFAULT;
      
      JManager_t::iterator p = manager.find(module->getID());
      
      if (p == manager.end() || p->second->GetEntries() == 0) {

	status2[module->getID()] = NODATA;

	continue;
      }
	
      TH1D* h1       = p->second;
	  
      // start values
      
      Double_t ymax  =   0.0;
      Double_t x0    =   0.0;    // [ns]
      Double_t sigma = 250.0;    // [ns]
      Double_t ymin  =   0.0;
      
      for (int i = 1; i != h1->GetNbinsX(); ++i) {
	
	const Double_t x = h1->GetBinCenter (i);
	const Double_t y = h1->GetBinContent(i);
	
	if (y > ymax) {
	  ymax = y;
	  x0   = x;
	}
	
	ymin += y;
      }
      
      ymin /= h1->GetNbinsX();
      
      f1.SetParameter(0, ymax);
      f1.SetParameter(1, x0);
      if (binWidth_ns < sigma) 
	f1.SetParameter(2, sigma);
      else
	f1.FixParameter(2, binWidth_ns/sqrt(12.0));
      f1.SetParameter(3, ymin);
      
      // fit
      
      h1->Fit(&f1, option.c_str(), "same", x0 - 5 * sigma, x0 + 5 * sigma);
      
      status = (fabs(f1.GetParameter(1)) <= 0.5*getFrameTime() && // position
		f1.GetParameter(0)       >= f1.GetParameter(3)); // S/N

      if (status) status2[module->getID()] = IN_SYNC;

	
      // look for peaks at offsets equal to a multiple of frame time
      JWeight           bg;    // background 
      map<int, JWeight> sn;    // signal(s)
      
      for (Int_t i = 1, ns = -(numberOfTimeslices + 1); i <= h1->GetNbinsX(); ++i) {
	  
	const Double_t x = h1->GetBinCenter (i);
	const Double_t y = h1->GetBinContent(i);
	
	while (x > (ns + 1) * getFrameTime() - TMax_ns) { ++ns; }
	
	if (fabs(x - ns * getFrameTime()) < TMax_ns)
	  sn[ns].put(y);
	else
	  bg    .put(y);
      }

      DEBUG("Module " << setw(8) << module->getID() << endl);
      
      for (map<int, JWeight>::iterator i = sn.begin(); i != sn.end(); ) {
	
	const Double_t y = bg.getTotal() * i->second.getCount() / bg.getCount();
	const Double_t P = TMath::PoissonI(i->second.getTotal(), y);

	DEBUG("Peak at " << setw(4) << i->first << " [frame time] "
	      << "S/N = "
	      << FIXED(7,1) << i->second.getTotal() << " / "
	      << FIXED(7,1) << y                    << ' '
	      << SCIENTIFIC(12,3) << P              << endl);
	
	if (P < Pmin && i->second.getTotal() > y) //Avoid edge effect (second bolean)
	  ++i;               // keep 
	else
	  sn.erase(i++);     // remove
      }
      
      if (!(sn.size()         == 1 &&
	    sn.begin()->first == 0)) {
	
	WARNING("Module " << setw(8) << module->getID() << " number of peaks " << sn.size() << endl);
	
	for (map<int, JWeight>::const_iterator i = sn.begin(); i != sn.end(); ++i) {
	  
	  const Double_t noise = bg.getTotal() * i->second.getCount() / bg.getCount();
       
	  WARNING("Peak at " << setw(4) << i->first << " [frame time] "
		  << "S/N = "
		  << FIXED(7,1) << i->second.getTotal()                                 << " / "
		  << FIXED(7,1) << noise << endl);
	  
	  peaksPerDoms[module->getID()].push_back(sn.size());
	  peaksPerDoms[module->getID()].push_back(i->first);
	  peaksPerDoms[module->getID()].push_back(i->second.getTotal());
	  peaksPerDoms[module->getID()].push_back(noise);
	}

	status2[module->getID()] = (sn.size() == 1 ? OUT_SYNC : ERROR);
      }
      

      //if DOM is OOS 
      if (!status) {
	//if OOS peak greater than the last and not in OOS DOMs vector
	if ((f1.GetParameter(0) > most_OOS_peak) && !(oosDomsId[module->getID()])){
	  
	  most_OOS_peak = f1.GetParameter(0);
	  most_OOS_ID = module->getID();
	}
      }
    }
    
    if (most_OOS_ID != 0) {
      oosDomsId[most_OOS_ID] = true;//exclude the DOM to compute the histograms
   
      //Reseting all histograms
      for (JDetector::const_iterator module = detector.begin(); module != detector.end(); ++module) {
	manager[module->getID()]->Reset("ICESM");
      }
      peaksPerDoms.clear();
    }
    else{
      OOS = false;
    }
  }while(OOS);
    
  //To manage non working and OOS DOMs 
  NOTICE("Managing non-working and OOS DOMs." << endl);
  if (pmtFile != "") {

    JPMTParametersMap parameters;

    try {
      parameters.load(pmtFile.c_str());
    }
    catch(const JException& error) {}

    for (map<int, JStatus_t>::const_iterator i = status2.begin(); i != status2.end(); ++i) {

      if (i->second != IN_SYNC) {

        NOTICE("Module " << setw(8) << i->first << " set QEs of all PMTs to zero." << endl);

        for (int pmt = 0; pmt != NUMBER_OF_PMTS; ++pmt) {
          parameters[JPMTIdentifier(i->first, pmt)].QE = 0.0;
        }
      }
    }

    ofstream out(pmtFile.c_str());

    parameters.comment.add(JMeta(argc, argv));

    out << parameters << endl;

    out.close();
  }
  
  if (outputFile != "") {
    manager.Write(outputFile.c_str()); 
  }

  //print small summary file of the peaks
  if (peaks != ""){
    ofstream stream(peaks);

    stream << "#DOM NB_PEAKS TIMESLICE_SHIFT SIGNAL NOISE\n";
    
    for (map_type::const_iterator dom = peaksPerDoms.begin(); dom != peaksPerDoms.end(); ++dom) {
      stream << dom->first << "  ";
      int i = 1;
      for (map_type::mapped_type::const_iterator data = dom->second.begin(); data != dom->second.end(); ++data) {
	stream << *data;
	((i%4 == 0) ? stream << "\n" : stream <<  "  ");
	i++;
      }
    }
    stream.close();
  }

  //QAQC
  int nin  = 0;
  int nout = 0;

  for (map<int, JStatus_t>::const_iterator i = status2.begin(); i != status2.end(); ++i) {
    if (i->second == IN_SYNC) {
      ++nin;
    }
    if (i->second != IN_SYNC &&
        i->second != NODATA) {
      ++nout;
    }
  }

  NOTICE("Number of modules out/in sync " << nout << '/' << nin << endl);

  QAQC(nin << ' ' << nout << endl);

  return 0;

}