#ifndef __JRUNANALYZER__
#define __JRUNANALYZER__

#include "JSupport/JSupport.hh"
#include "JSupport/JSupportToolkit.hh"
#include "JSupport/JMultipleFileScanner.hh"
#include "JDetector/JModuleRouter.hh"
#include "JDetector/JDetectorToolkit.hh"
#include "JROOT/JManager.hh"
#include "JTools/JQuantile.hh"
#include "JTools/JRange.hh"
#include "JSupport/JTreeScanner.hh"
#include "JSupport/JParallelFileScanner.hh"
#include "JSupport/JTriggerParametersSupportkit.hh"
#include "JMath/JConstants.hh"
#include "JTrigger/JHitL0.hh"
#include "JTrigger/JBuildL0.hh"
#include "TFile.h"
#include "TH1D.h"
#include "JRunHistograms.hh"

/**
 * \author rgruiz, adomi
 */

using JSUPPORT::JSingleFileScanner;

/**
 * Class dedicated to the analysis of %KM3NeT runs. 
 *
 */
class JRunAnalyzer {

  JSingleFileScanner<>  inputFile;
  JModuleRouter         router;
  TFile                 *outputFile;
  JRA_Histograms        histograms;
  int                   highest_floor;
  JLimit_t              numberOfTimeslices;
  JLimit_t              numberOfSummaryslices;
  JLimit_t              numberOfEvents;
  int                   analysis_level;
  
public :

  /**
   * Constructor.
   *
   * \param file            file name
   * \param detector        detector
   * \param out             pointer to output file
   * \param nTimeslices     number of timeslices to be read
   * \param nSummaryslices  number of summary slices to be read
   * \param nEvents         number of events to be read
   * \param analysislevel   option for analysis of PMT or reco data
   */
  JRunAnalyzer (const JSingleFileScanner<>& file, const JDetector& detector, TFile *out, 
		JLimit_t nTimeslices, JLimit_t nSummaryslices, JLimit_t nEvents, int analysislevel):
    inputFile                       (file),
    router                      (detector),
    outputFile                       (out),
    numberOfTimeslices       (nTimeslices),
    numberOfSummaryslices (nSummaryslices),
    numberOfEvents               (nEvents),
    analysis_level         (analysislevel)
  {
    using namespace JPP;
    using namespace std;
    
    histograms     = JRA_Histograms(detector);
    highest_floor  = getRangeOfFloors(detector).getUpperLimit();
  } 

  /**
   * Destructor.
   */
  ~JRunAnalyzer(){}
  
  /*
   * Function template used to read events from a tree.
   *
   * \param scanner A JTreeScanner
   * \param 
   */
  void iterateEventTree (JTreeScanner < JDAQEvent > & scanner) {

    while (scanner.hasNext()) {

      JDAQEvent event = *(scanner.next());

      histograms.h_trigger.h_Snapshot_hits      -> Fill((Double_t) event.size<JDAQSnapshotHit> ());
      histograms.h_trigger.h_Triggered_hits     -> Fill((Double_t) event.size<JDAQTriggeredHit> ());
      histograms.h_trigger.h_Triggered_over_Snapshot_hits -> Fill((Double_t) event.size<JDAQTriggeredHit> () / event.size<JDAQSnapshotHit > ());
      histograms.h_trigger.h_Number_of_overlays -> Fill(event.getOverlays());

      for (unsigned int i = 0; i != NUMBER_OF_TRIGGER_BITS; ++i) {

	if (event.hasTriggerBit(i)) {

	  histograms.h_trigger.h_Trigger_bit_event -> Fill((Double_t) i);
	}
      }

      int counter_3dmuon = 0;
      typedef JRange<double>  JRange_t;
      JRange_t range(JRange_t::DEFAULT_RANGE());
      
      for (JDAQEvent::const_iterator<JDAQTriggeredHit> hit = event.begin<JDAQTriggeredHit>(); hit != event.end<JDAQTriggeredHit>(); ++hit) {

	const JModule& module = router.getModule(hit->getModuleID());
	const double   t1     = getTime(hit->getT(), module.getPMT(hit->getPMT()));
	
	range.include(t1);
	
	JDAQTriggerMask trigger_mask(event.getTriggerMask(*hit));

	if(trigger_mask.hasTriggerBit(getTriggerBit<JTrigger3DMuon>()))	counter_3dmuon++; 
	 
	if (router.hasModule(hit->getModuleID())) {

	  const JModule& module = router.getModule (hit->getModuleID());
	
	  histograms.h_trigger.h_pmt_distribution_triggered_hits->Fill(hit->getPMT());
	  histograms.h_trigger.h_tot_distribution_triggered_hits->Fill(hit->getToT());

	  int String = module.getString();
	  int Floor  = module.getFloor();

	  histograms.h_trigger.h_Triggered_hits_per_module        -> Fill(String , Floor);

	  if(trigger_mask.hasTriggerBit(getTriggerBit<JTrigger3DMuon>())){
	    histograms.h_trigger.h_Triggered_hits_3dmuon_per_module -> Fill(String , Floor);
	  }
	  
	  for (unsigned int i = 0; i != NUMBER_OF_TRIGGER_BITS; ++i) {
	  
	    if (hit -> hasTriggerBit(i)) {

	      histograms.h_trigger.h_Trigger_bit_hit->Fill((Double_t) i);
	    }
	  }
	}else{
	  FATAL("JModuleRouter trying to access non existing identifier: "<< hit->getModuleID());
	}
      }

      histograms.h_trigger.h_event_duration->Fill(range.getLength());

      histograms.h_trigger.h_pmt_distribution_triggered_hits->Scale(1. / (Double_t) event.size<JDAQTriggeredHit> ());
     
      if(counter_3dmuon != 0) histograms.h_trigger.h_Triggered_hits_3dmuon->Fill(counter_3dmuon);
	  
      for (JDAQEvent::const_iterator<JDAQSnapshotHit> hit = event.begin<JDAQSnapshotHit>() ; hit != event.end<JDAQSnapshotHit>() ; ++hit){

	if (router.hasModule(hit->getModuleID())) {

	  const JModule& module = router.getModule (hit->getModuleID());
	
	  int String = module.getString();
	  int Floor  = module.getFloor();
	  int pmt    = hit->  getPMT();

	  if(analysis_level == 1){
	    
	    (*histograms.h_trigger.m_Snapshot_hits_per_pmt)[MAKE_STRING("Detector/DU" + to_string(String))] -> Fill(pmt, Floor);

	  }

	  histograms.h_trigger.h_pmt_distribution_snapshot_hits -> Fill(hit->getPMT());	
	  histograms.h_trigger.h_tot_distribution_snapshot_hits -> Fill(hit->getToT());
	  histograms.h_trigger.h_Snapshot_hits_per_module       -> Fill(String, Floor);
	  
	  }else{
	    FATAL("JModuleRouter trying to access non existing identifier: "<< hit->getModuleID());
	}
      }
    }
  }

  /*
   * Function template used to read reconstructed events from a tree.
   *
   * \param scanner A ParallelFileScanner for JDAQEvent and JEvt
   * \param 
   */
  void iterateRecoEventTree (JParallelFileScanner< JTypeList<JDAQEvent, JFIT::JEvt> > & scanner, TFile & f) {

    TH1D* h_tres = new TH1D("h_tres", ";Time residuals [ns]; Entries", 100, -50, 150);
    TH1D* h_likelihood = new TH1D ("h_likelihood", " ; Likelihood; Reconstructed Events ", 100, -1000, 1000);
    TH1D* h_beta0 = new TH1D("h_beta0", "; beta0; Reconstructed Events", 20, 0, 1);
    TH1D* h_energy = new TH1D ("h_energy", " ; Energy [GeV]; Reconstructed Events ", 65, 0, 9);
    setLogarithmicX(h_energy);
    TH1D* h_zenith = new TH1D("h_zenith", "; cosZenith; Reconstructed Events", 20, -1, 1);
    TH1D* h_azimuth = new TH1D("h_azimuth", "; cosAzimuth; Reconstructed Events", 20, -1, 1);
    TH1D* h_radial_position = new TH1D ("h_radial_position", "; Radial Position [m]; Reconstructed Events", 60, 0, 4.2);
    setLogarithmicX(h_radial_position);
    TH1D* h_z_position = new TH1D ("h_z_position", "; Z Position [m] ; Reconstructed Events", 50, 0, 3.2);
    setLogarithmicX(h_z_position);

    while (scanner.hasNext()) {

      JParallelFileScanner< JTypeList<JDAQEvent, JFIT::JEvt> >::multi_pointer_type  ps  = scanner.next();

      JEvt* evt = ps;
      JDAQEvent* event = ps;
      
      if (!evt->empty()) {

	JEvt::iterator best = evt->begin();  
	h_energy -> Fill(best->getE());
	h_likelihood -> Fill(best->getQ());
	h_z_position -> Fill(best->getZ());
	h_radial_position -> Fill(sqrt(best->getX()*best->getX() + best->getY()*best->getY()));
	
	JTrack3D track = getTrack(*best); 
	h_zenith -> Fill(cos(track.getDirection().getTheta()));
	h_azimuth -> Fill(cos(track.getDirection().getPhi()));
	h_beta0 -> Fill(best->getW(JGANDALF_BETA0_RAD));

	std::vector<JHitL0> dataL0;
	const JBuildL0<JHitL0> buildL0;
	buildL0(JDAQTimeslice(*event, false),  router, back_inserter(dataL0));

	for (std::vector<JHitL0>::const_iterator hit = dataL0.begin(); hit != dataL0.end(); ++hit) {

	  h_tres -> Fill(hit->getT() - track.getT(hit->getPosition()));
	}
      }
    }

    f.mkdir("Reco");                                                                                                          
    f.cd("Reco");                                                                                                            

    h_energy->Write();
    h_likelihood -> Write();
    h_z_position -> Write();
    h_radial_position -> Write();
    h_zenith -> Write();
    h_azimuth -> Write();
    h_beta0 -> Write();
    h_tres -> Write();
  }

  struct dom_type :
    public std::vector< JQuantile>
  {
    dom_type() :
      std::vector<JQuantile>(NUMBER_OF_PMTS)
    {}
  };

  /*
   * Function template to read and process time ordered summary slices.
   * 
   * \param scanner A JTreeScanner from which time ordered summary slices are accessed. 
   */
  void iterateSummarysliceTree (JTreeScanner < JDAQSummaryslice > & scanner) {

    using namespace std;
    using namespace JPP;

    map<int, map<int, dom_type> >      PMT_rate_quantiles;
    map<int, map<int, JQuantile> >      DOM_rate_quantiles;

    while (scanner.hasNext()){

      JDAQSummaryslice slice = *(scanner.next());

      for (JDAQSummaryslice::const_iterator frame = slice.begin() ; frame != slice.end() ; ++ frame) {

	if (router.hasModule(frame->getModuleID())) {

	  const JModule& module = router.getModule (frame->getModuleID());

	  int string = module.getString();
	  int floor  = module.getFloor ();

	  JDAQFrameStatus status = frame -> getDAQFrameStatus();
	  int nFIFOcount         = status.countFIFOStatus();
	  int nHRVcount          = status.countHighRateVeto();

	  if (nHRVcount > 0) {
	    histograms.h_summary.h_hrv_per_dom->Fill(string , floor, nHRVcount);
	  }
	
	  if (status.testDAQStatus() == false) {
	    histograms.h_summary.h_daq_status_per_dom->Fill(string , floor, (1./distance(scanner.begin(), scanner.end()))*100);	  
	  }
	
	  histograms.h_summary.h_fifo_per_dom->Fill(string , floor , nFIFOcount); 

	  if(analysis_level == 1){
	  
	    TH2D*  h2   = (*histograms.h_summary.m_summary_rate_distribution)[MAKE_STRING("Detector/DU" + to_string(string) + "/F" + to_string(floor))];

	    double rate = 0;	
	    const double factor = 1.0e-3;   // [kHz]
	      
	    for (int i = 0 ; i < NUMBER_OF_PMTS ; i++){

	      rate += frame->getRate(i, factor);

              h2->Fill(i , frame->getRate(i, factor));

	      PMT_rate_quantiles[string][floor][i].put(frame->getRate(i, factor)); 
	      
	      histograms.h_summary.h_pmt_rate_distribution->Fill(frame->getRate(i, factor), frame->getWeight(i, factor));

	    }

	    histograms.h_summary.h_dom_rate_distribution->Fill(rate);
	    
	    DOM_rate_quantiles[string][floor].put(rate);
	    
	  } else {

	    double rate = 0;	
	    const double factor = 1.0e-3;   // [kHz]
		  
	    for (int i = 0 ; i < NUMBER_OF_PMTS ; i++){

	      rate += frame->getRate(i, factor);

	      histograms.h_summary.h_pmt_rate_distribution->Fill(frame->getRate(i, factor), frame->getWeight(i, factor));
	    }

	    histograms.h_summary.h_dom_rate_distribution->Fill(rate);

	    DOM_rate_quantiles[string][floor].put(rate);
	    
	  }
	  
	}else{
	  FATAL("JModuleRouter trying to access non existing identifier: "<< frame->getModuleID());
	}      
      }      
    }

    for(auto& i : DOM_rate_quantiles){
      
      for (int j=1; j <= highest_floor; j++) {
      
	if (i.second[j].getCount() > 0) histograms.h_summary.h_rate_summary->Fill(i.first, j, i.second[j].getMean());
      }
    }

    if(analysis_level == 1){

      for(auto& i : PMT_rate_quantiles){

	for (int j = 1; j <= highest_floor; j++){
      
	  for (int k=0 ; k < NUMBER_OF_PMTS ; k++){

	    if (i.second[j][k].getCount() > 0){

	      (*histograms.h_summary.m_mean_summary_rate)             [MAKE_STRING("Detector/DU" + to_string(i.first))]->Fill(k, j, i.second[j][k].getMean());
	      (*histograms.h_summary.m_mean_summary_rate_distribution)[MAKE_STRING("Detector/DU" + to_string(i.first))]->Fill( i.second[j][k].getMean());
	    }
	  }
	}
      }
    }
  }
  
  /*
   * Function template to read and process time ordered timeslices.
   * 
   * \param scanner A JTreeScanner from which time ordered timeslices are accessed. 
   */
  template <class T>
  void iterateTimesliceTree (JTreeScanner < T > & scanner) {
    
    int ts_type = JIndexOf<JDAQTimesliceTypes_t , T>::value;

    std::map < int , std::map <int , JQuantile> > DOM_rate_quantiles;

    double inverseFrameTimeSec = 1. / (1.0e-9 * getFrameTime());

    while (scanner.hasNext()){
      
      T slice = *(scanner.next());

      for(auto & frame : slice) {
	if (router.hasModule(frame.getModuleID())) {

	  const JModule& module = router.getModule (frame.getModuleID());
	  double  rate   = frame.numberOfHits * inverseFrameTimeSec;
	  int     string = module.getString();
	  int     floor  = module.getFloor ();

	  DOM_rate_quantiles[string][floor].put(rate);

	  vector <int>  pmt_hit_count (NUMBER_OF_PMTS , 0) ;

	  if(analysis_level == 1){
	  
	    TH2D* h2 = (*histograms.h_timeslice.m_pmt_tot_distributions[ts_type])[MAKE_STRING("Detector/DU" + to_string(string) + "/F" + to_string(floor) + "/" + to_string(frame.getModuleID()))];
	    
	    for (JDAQSuperFrame::const_iterator hit = frame.begin() ; hit != frame.end() ; ++hit){
	  
	    h2 -> Fill(hit->getPMT() , hit->getToT()) ;
	    
	    pmt_hit_count[hit->getPMT()]++;
	    
	    }
	    
	    for (int pmt = 0 ; pmt != NUMBER_OF_PMTS ; ++pmt) {
	    
	      (*histograms.h_timeslice.m_pmt_rate_distributions[ts_type])[MAKE_STRING("Detector/DU" + to_string(string) + "/F" + to_string(floor))] -> Fill(pmt , 1e-3 * pmt_hit_count[pmt] * inverseFrameTimeSec);
	    	  
	    }

	  }
	    
	  }else{
	    FATAL("JModuleRouter trying to access non existing identifier: "<< frame.getModuleID());
	  }      
	}      
    }
          
    for (std::map< int , std::map<int,JQuantile>>::const_iterator i = DOM_rate_quantiles.begin() ; i != DOM_rate_quantiles.end() ; i++){

      for (std::map<int , JQuantile>::const_iterator j = i->second.begin() ; j != i->second.end() ; j++){

	if (j->second.getCount() > 0) histograms.h_timeslice.h_dom_mean_rates[ts_type] -> Fill (i->first , j->first , j->second.getMean() ) ;
      }
    }
  }

  /*
   * Checks through the use of a JTreeScanner, if summary slices are present in the run file.
   * In case they are, the corresponding tree is iterated. 
   *
   */
  void readSummaryData() {

    JTreeScanner <JDAQSummaryslice> scanner(inputFile, numberOfSummaryslices);
    if (scanner.hasNext()) {
      histograms.initialize_summary_histograms();
      scanner.rewind();
      iterateSummarysliceTree(scanner);
    }
  }

  /*
   * Function template that checks through the use of a JTreeScanner, if objects of different timeslice classes are present in the run file.
   * In case they are, the corresponding tree is iterated. 
   *
   */
  template <class T>
  void readTimesliceData() {

    JTreeScanner <T> scanner(inputFile, numberOfTimeslices);
    if(scanner.hasNext()) {
      
      histograms.initialize_timeslice_histograms <T>();
      scanner.rewind();
      iterateTimesliceTree(scanner);
    }
  }

  /*
   * Function template that checks through the use of a JTreeScanner, if JDAQEvent objects are present in the run file.
   * In case they are, the corresponding tree is read. 
   *
   */
  void readEvents() {

    JTreeScanner <JDAQEvent> scanner(inputFile, numberOfEvents);
        
    if(scanner.hasNext()) {

      histograms.initialize_trigger_histograms();
      scanner.rewind();
      iterateEventTree(scanner);
    }
  }

  /*
   * Function template that checks through the use of a JTreeScanner, if JEvt objects are present in the run file.
   * In case they are, the corresponding tree is read. 
   */
  void readRecoEvents() {

    JParallelFileScanner< JTypeList<JDAQEvent, JFIT::JEvt> >  scanner(inputFile, numberOfEvents);
        
    if(scanner.hasNext()) {

      scanner.rewind();
      iterateRecoEventTree(scanner, *outputFile);
    }
  }

   /*                                                                   
   * Writes the histograms to a root file.                                 
   * \param f The root file.                                    
   */
  void writeToFile(TFile *f,int analysis_level){

    f->mkdir("Detector");
    f->cd("Detector");

    if (histograms.h_summary.h_fifo_per_dom)          histograms.h_summary.h_fifo_per_dom          -> Write();
    if (histograms.h_summary.h_daq_status_per_dom)    histograms.h_summary.h_daq_status_per_dom    -> Write();
    if (histograms.h_summary.h_hrv_per_dom)           histograms.h_summary.h_hrv_per_dom           -> Write();
    if (histograms.h_summary.h_rate_summary)          histograms.h_summary.h_rate_summary          -> Write();
    if (histograms.h_summary.h_pmt_rate_distribution) histograms.h_summary.h_pmt_rate_distribution -> Write();
    if (histograms.h_summary.h_dom_rate_distribution) histograms.h_summary.h_dom_rate_distribution -> Write();

    histograms.Write_histogram_table_to_file(*f , MAKE_STRING("Detector"), histograms.h_timeslice.h_dom_mean_rates);

    for (typename vector < JManager < string , TH2D >* >::const_iterator i = histograms.h_timeslice.m_pmt_tot_distributions.begin();
	 i != histograms.h_timeslice.m_pmt_tot_distributions.end() ; ++i){

      if ((*i)){

        for (typename JManager < string , TH2D >::const_iterator j = (*i) -> begin() ; j != (*i) -> end() ; ++j){

	  j->second->Scale(1., "width");
        }
      }
    }

    histograms.Write_manager_table_in_key_dir (*f , histograms.h_timeslice.m_pmt_tot_distributions);
    histograms.Write_manager_table_in_key_dir (*f , histograms.h_timeslice.m_pmt_rate_distributions);

    if (histograms.h_summary.m_summary_rate_distribution) histograms.Write_manager_in_key_dir (*f , histograms.h_summary.m_summary_rate_distribution);

    if (histograms.h_summary.m_mean_summary_rate)              histograms.Write_manager_in_key_dir(*f , histograms.h_summary.m_mean_summary_rate);
    if (histograms.h_summary.m_mean_summary_rate_distribution) histograms.Write_manager_in_key_dir(*f , histograms.h_summary.m_mean_summary_rate_distribution);

    histograms.h_timeslice.Fill_mean_ToT_histograms();

    histograms.Write_manager_table_in_key_dir (*f , histograms.h_timeslice.m_mean_ToT);
    histograms.Write_manager_table_in_key_dir (*f , histograms.h_timeslice.m_mean_ToT_distribution);

    f->mkdir ( MAKE_STRING ("JDAQEvent").c_str());
    f->cd    ("JDAQEvent");

    if (histograms.h_trigger.h_Trigger_bit_event) histograms.h_trigger.h_Trigger_bit_event -> Write();
    if (histograms.h_trigger.h_Trigger_bit_hit)   histograms.h_trigger.h_Trigger_bit_hit   -> Write();
    if (histograms.h_trigger.h_Triggered_hits)        histograms.h_trigger.h_Triggered_hits        -> Write();
    if (histograms.h_trigger.h_Triggered_hits_3dmuon) histograms.h_trigger.h_Triggered_hits_3dmuon -> Write();
    if (histograms.h_trigger.h_Triggered_hits_3dmuon_per_module) histograms.h_trigger.h_Triggered_hits_3dmuon_per_module -> Write();
    if (histograms.h_trigger.h_Snapshot_hits)         histograms.h_trigger.h_Snapshot_hits         -> Write();
    if (histograms.h_trigger.h_Triggered_over_Snapshot_hits)       histograms.h_trigger.h_Triggered_over_Snapshot_hits  -> Write();
    if (histograms.h_trigger.h_event_duration)  histograms.h_trigger.h_event_duration -> Write();
    if (histograms.h_trigger.h_Number_of_overlays)  histograms.h_trigger.h_Number_of_overlays -> Write();
    if (histograms.h_trigger.h_pmt_distribution_triggered_hits) {histograms.h_trigger.h_pmt_distribution_triggered_hits -> Write();}
    if (histograms.h_trigger.h_pmt_distribution_snapshot_hits)  {histograms.h_trigger.h_pmt_distribution_snapshot_hits  -> Write();}
    if (histograms.h_trigger.h_tot_distribution_triggered_hits) { histograms.h_trigger.h_tot_distribution_triggered_hits->Scale(1, "width") ; histograms.h_trigger.h_tot_distribution_triggered_hits-> Write();}
    if (histograms.h_trigger.h_tot_distribution_snapshot_hits)  {histograms.h_trigger.h_tot_distribution_snapshot_hits->Scale(1, "width") ; histograms.h_trigger.h_tot_distribution_snapshot_hits -> Write();}
    if (histograms.h_trigger.h_Triggered_hits_per_module) { histograms.h_trigger.h_Triggered_hits_per_module-> Write();}
    if (histograms.h_trigger.h_Snapshot_hits_per_module)  { histograms.h_trigger.h_Snapshot_hits_per_module -> Write();}
    if (histograms.h_trigger.m_Snapshot_hits_per_pmt) histograms.Write_manager_in_key_dir(*f , histograms.h_trigger.m_Snapshot_hits_per_pmt);
  
  }
};

#endif