#ifndef __RUNANALYZER__
#define __RUNANALYZER__

#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 "TFile.h"
#include "TH1D.h"
#include "JRunHistograms.hh"

using namespace std ;
using namespace KM3NETDAQ ;
using namespace JPP ;

/**
 * \author rgruiz, adomi
 */

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

  string          inputFile;
  JDetector       detector;
  JModuleRouter*  router;
  JRA_Histograms  histograms;
  int             modulesPerString;
  JLimit_t        numberOfTimeslices;
  JLimit_t        numberOfSummaryslices;
  JLimit_t        numberOfEvents;
  bool            pmt_analysis;
  
public :

  /**
   * Default constructor.
   */
  RunAnalyzer(){}

  /**
   * Constructor.
   *
   * \param file Path to the file to be analyzed
   * \param detectorFile path to a detector file
   * \param nTimeslices Number of timeslices to be read
   * \param nSummaryslices Number of summary slices to be read
   * \param nEvents Number of frames to be read
   * \param pmtanalysis PMT analysis option
   */
  RunAnalyzer (string file , string detectorFile , JLimit_t nTimeslices , JLimit_t nSummaryslices , JLimit_t nEvents, bool pmtanalysis):
    inputFile                       (file),
    router                          (NULL),
    numberOfTimeslices       (nTimeslices),
    numberOfSummaryslices (nSummaryslices),
    numberOfEvents               (nEvents),
    pmt_analysis             (pmtanalysis)
  {
    try {
      load (detectorFile, detector);
    }
    catch(const JException & error) {
      cerr << "FATAL ERROR. Could not open detector file '" << detectorFile << "'." << endl;
      exit(1);
    }
    
    histograms       = JRA_Histograms(detector);
    router           = new JModuleRouter(detector);
    modulesPerString = JDETECTOR::getNumberOfModules (detector) / getNumberOfStrings (detector);
  } 

  /**
   * Destructor.
   */
  ~RunAnalyzer(){}

  /*
   * Function template used to read time ordered 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_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);
	}
      }

      for (JDAQEvent::const_iterator<JDAQTriggeredHit> hit = event.begin<JDAQTriggeredHit>(); hit != event.end<JDAQTriggeredHit>(); ++hit) {

	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);
	
	  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());
	}
      }
      
      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(pmt_analysis == true){
	    
	    (*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 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) {
    
    std::map <int,vector<vector <JQuantile>>> PMT_rate_quantiles;
    std::map <int,vector<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 ();
	
	  PMT_rate_quantiles[string].resize(modulesPerString , vector <JQuantile>(NUMBER_OF_PMTS)); 

	  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);
	  }
	
	  if (status.testDAQStatus() == false) {
	    histograms.h_summary.h_daq_status_per_dom->Fill(string , floor);	  
	  }
	
	  histograms.h_summary.h_fifo_per_dom->Fill(string , floor , nFIFOcount); 

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

	    double rate = 0;	

	    for (int i = 0 ; i < NUMBER_OF_PMTS ; i++){

	      rate += frame->getRate(i);

              h2->Fill(i , frame->getRate(i) * 1e-3);

	      PMT_rate_quantiles[string][floor-1][i].put(frame->getRate(i)*1e-3); 

	    }

	    DOM_rate_quantiles[string].resize(modulesPerString);
	  
	    DOM_rate_quantiles[string][floor-1].put(rate * 1e-3);
	    
	  } else {

	    double rate = 0;	
		  
	    for (int i = 0 ; i < NUMBER_OF_PMTS ; i++){
	      rate += frame->getRate(i);
	      histograms.h_summary.h_pmt_rate_distribution->Fill(frame->getRate(i)*1e-3);
	    }
	    
	    histograms.h_summary.h_dom_rate_distribution->Fill(rate*1e-3);

	    DOM_rate_quantiles[string].resize(modulesPerString);
	  
	    DOM_rate_quantiles[string][floor-1].put(rate * 1e-3);
	    
	  }
	  
	}else{
	  FATAL("JModuleRouter trying to access non existing identifier: "<< frame->getModuleID());
	}      
      }
    }
    
  
    for (std::map<int , vector<JQuantile> >::const_iterator i = DOM_rate_quantiles.begin() ; i!= DOM_rate_quantiles.end() ; ++i) {
      
      for (int j=1 ; j < modulesPerString + 1 ; j++) {
      
	if (i->second[j-1].getCount() > 0) histograms.h_summary.h_rate_summary->Fill(i->first, j, i->second[j-1].getMean());
      }
    }

    
    if(pmt_analysis == true){
    
      for (std::map<int , vector < vector<JQuantile> > >::const_iterator i = PMT_rate_quantiles.begin() ; i!= PMT_rate_quantiles.end() ; ++i) {
    
	for (int j=0 ; j < modulesPerString ; 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+1, 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. 
   * \param frame_index_range the range of the indices of the frames to be 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(pmt_analysis == true){
	  
	    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);
    }
  }

  /*
   * Returns the histograms produced from the data in the file.
   */
  JRA_Histograms getHistograms(){

    return histograms ;
  }
};

#endif