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

#include <type_traits>
#include <functional>
#include <future>
#include <mutex>
#include <thread>
#include <vector>
#include <queue>

#include "TROOT.h"
#include "TFile.h"

#include "JLang/JPredicate.hh"
#include "JLang/JComparator.hh"
#include "JLang/JComparison.hh"
#include "JLang/JFileStream.hh"

#include "JDetector/JDetector.hh"
#include "JDetector/JDetectorToolkit.hh"
#include "JDetector/JTripod.hh"
#include "JDetector/JTransmitter.hh"
#include "JDetector/JModule.hh"
#include "JDetector/JHydrophone.hh"

#include "JTools/JHashMap.hh"
#include "JTools/JRange.hh"
#include "JTools/JQuantile.hh"

#include "JSupport/JMultipleFileScanner.hh"
#include "JSupport/JSingleFileScanner.hh"
#include "JSupport/JFileRecorder.hh"
#include "JSupport/JMeta.hh"

#include "JAcoustics/JSoundVelocity.hh"
#include "JAcoustics/JEmitter.hh"
#include "JAcoustics/JAcousticsToolkit.hh"
#include "JAcoustics/JHit.hh"
#include "JAcoustics/JFitParameters.hh"
#include "JAcoustics/JGlobalfit.hh"
#include "JAcoustics/JEvent.hh"
#include "JAcoustics/JSuperEvt.hh"
#include "JAcoustics/JSuperEvtToolkit.hh"
#include "JAcoustics/JSupport.hh"
#include "JAcoustics/JTransmission_t.hh"
#include "JAcoustics/JFremantle_t.hh"

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


/**
 * \file
 *
 * Application to make a global fit of the detector geometry to acoustic data.\n
 * \author mdejong
 */
int main(int argc, char **argv)
{
  using namespace std;
  using namespace JPP;

  typedef JContainer< vector<JTripod> >      tripods_container;
  typedef JContainer< vector<JTransmitter> > transmitters_container;
  typedef JContainer< vector<JHydrophone> >  hydrophones_container;
  typedef JContainer< set<JTransmission_t> > disable_container;

  JMultipleFileScanner<JEvent>  inputFile;
  JFileRecorder<JTYPELIST<JSuperEvt, JFitParameters, JMeta>::typelist>  outputFile;
  string                  detectorFile;
  JLimit_t&               numberOfEvents = inputFile.getLimit();
  JSoundVelocity          V              = getSoundVelocity;    // default sound velocity
  tripods_container       tripods;                              // tripods
  transmitters_container  transmitters;                         // transmitters
  hydrophones_container   hydrophones;                          // hydrophones
  JFitParameters          parameters;                           // fit parameters
  disable_container       disable;                              // disable tansmissions
  size_t                  threads;                              // number of parallel threads
  bool&                   squash  =  JFremantle::squash;
  int                     debug;

  try {

    JParser<> zap("Application to fit position calibration model to acoustic data.");

    zap['f'] = make_field(inputFile,       "output of JAcousticEventBuilder[.sh]");
    zap['o'] = make_field(outputFile)                                        = "";
    zap['n'] = make_field(numberOfEvents)                                    = JLimit::max();
    zap['a'] = make_field(detectorFile);
    zap['@'] = make_field(parameters)                                        = JPARSER::initialised();
    zap['V'] = make_field(V,               "sound velocity")                 = JPARSER::initialised();
    zap['T'] = make_field(tripods,         "tripod data");
    zap['Y'] = make_field(transmitters,    "transmitter data")               = JPARSER::initialised();
    zap['H'] = make_field(hydrophones,     "hydrophone data")                = JPARSER::initialised();
    zap['M'] = make_field(getMechanics,    "mechanics data")                 = JPARSER::initialised();
    zap['!'] = make_field(disable,         "disable transmission")           = JPARSER::initialised();
    zap['N'] = make_field(threads,         "number of threads")              = 1;
    zap['s'] = make_field(squash,          "squash transmissions in output");
    zap['d'] = make_field(debug)                                             = 1;

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

  ROOT::EnableThreadSafety();

  JDetector detector;

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

  JHashMap<int, JLocation>   receivers;
  JHashMap<int, JEmitter>    emitters;

  for (JDetector::const_iterator i = detector.begin(); i != detector.end(); ++i) {
    receivers[i->getID()] = i->getLocation();
  }

  for (tripods_container::const_iterator i = tripods.begin(); i != tripods.end(); ++i) {
    emitters[i->getID()]  = JEmitter(i->getID(), i->getUTMPosition() - detector.getUTMPosition());
  }

  for (transmitters_container::const_iterator i = transmitters.begin(); i != transmitters.end(); ++i) {
    try {
      emitters[i->getID()]  = JEmitter(i->getID(), i->getPosition() + detector.getModule(i->getLocation()).getPosition());
    }
    catch(const exception&) {}                         // if no module available, discard transmitter
  }

  V.set(detector.getUTMZ());                           // sound velocity at detector depth

  JGeometry   geometry(detector, hydrophones);
  JGlobalfit  katoomba(geometry, V, parameters);

  JKatoomba<JEstimator>::MATRIX_INVERSION = LDU_t;
  
  JKatoomba<JGandalf>::debug              = debug;
  JKatoomba<JGandalf>::MAXIMUM_ITERATIONS = 10000;

  if (inputFile.size() > 1u) {                         // sort input files

    map<double, string> zmap;

    for (const string& file_name : inputFile) {

      STATUS(file_name << '\r'); DEBUG(endl);

      for (JSingleFileScanner<JEvent> in(file_name, 1); in.hasNext(); ) {

	const JEvent* evt = in.next();

	if (JFremantle::detid != evt->getDetectorID()) {
	  FATAL("Invalid detector identifier " << evt->getDetectorID() << " != " << JFremantle::detid << endl);
	}

	if (!evt->empty()) {
	  zmap[evt->begin()->getToE()] = file_name;
	}
      }
    }
    STATUS(endl);

    inputFile.clear();

    for (map<double, string>::const_iterator i = zmap.begin(); i != zmap.end(); ++i) {
      inputFile.push_back(i->second);
    }
  }

  if (outputFile.getFilename() != "" &&
      outputFile.getFilename() != "--") {

    outputFile.open();

    JFremantle::output = &outputFile;
  }
  /*
  outputFile.put(JMeta(argc, argv));
  outputFile.put(parameters);
  */
  
  try {
    
    JFremantle fremantle(geometry, V, parameters, threads, 2 * threads);

    typedef deque<JEvent> buffer_type;

    for (buffer_type zbuf; inputFile.hasNext(); ) {

      STATUS(inputFile.getFilename() << '\r'); DEBUG(endl);

      // read one file at a time
    
      for (const string file_name = inputFile.getFilename(); inputFile.hasNext() && file_name == inputFile.getFilename(); ) {

	const JEvent* evt = inputFile.next();

	if (!evt->empty() && emitters.has(evt->getID())) {
	  zbuf.push_back(*evt);
	}
      }

      sort(zbuf.begin(), zbuf.end());                  // sort according first time-of-emission

      for (buffer_type::iterator p = zbuf.begin(), q; p != zbuf.end(); p = q) {
  
	for (q = p; ++q != zbuf.end() && q->begin()->getToE() <= p->rbegin()->getToE() + parameters.Tmax_s; ) {}

	if (q == zbuf.end()) {
	
	  if (inputFile.hasNext()) {
    	  
	    zbuf.erase(zbuf.begin(), p);               // remove processed data and continue reading

	    break;
	  }
	}

	JEvent::overlap(p, q, parameters.deadTime_s);  // empty overlapping events
      
	if (getNumberOfEmitters(p,q) >= parameters.Nmin) {

	  const JWeight getWeight(p, q);

	  JFremantle::input_type data;

	  for (buffer_type::iterator evt = p; evt != q; ++evt) {

	    sort(evt->begin(), evt->end(), JKatoomba<>::compare);

	    JEvent::iterator __end  = unique(evt->begin(), evt->end(), make_comparator(&JTransmission::getID, JComparison::eq()));

	    const JEmitter& emitter = emitters [evt->getID()];
	    const double    weight  = getWeight(evt->getID());

	    for (JEvent::const_iterator i = evt->begin(); i != __end; ++i) {

	      if (disable.count(JTransmission_t(evt->getID(), i->getID())) == 0 &&
		  disable.count(JTransmission_t(-1,           i->getID())) == 0) {

		if (receivers.has(i->getID()) && geometry.hasLocation(receivers[i->getID()]) && i->getQ() >= parameters.Qmin * (parameters.Qmin <= 1.0 ? i->getW() : 1.0)) {

		  data.push_back(JHit(emitter,
				      distance(p,evt),
				      receivers[i->getID()],
				      i->getToA(),
				      parameters.sigma_s,
				      weight));
		}
	      }
	    }
	  }

	  if (getMinimumNumberOfEmitters(data.begin(), data.end()) >= parameters.Nmin) {
	    fremantle.enqueue(data);
	  }
	}
      }
    }
    STATUS(endl);
  }
  catch(const exception& error) {
    FATAL("main " << error.what());
  }
  /*
  JMultipleFileScanner<JMeta> io(inputFile);

  io >> outputFile;
  */
  outputFile.close();

  JFileOutputStream(3) << SCIENTIFIC(1,10) << JFremantle::Q.getMean(numeric_limits<float>::max()) << endl;
}