#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/JSingleFileScanner.hh"

#include "JAcoustics/JSoundVelocity.hh"
#include "JAcoustics/JEmitter.hh"
#include "JAcoustics/JAcousticsToolkit.hh"
#include "JAcoustics/JHit.hh"
#include "JAcoustics/JFitParameters.hh"
#include "JAcoustics/JKatoomba_t.hh"
#include "JAcoustics/JSuperEvt.hh"
#include "JAcoustics/JSuperEvtToolkit.hh"
#include "JAcoustics/JSupport.hh"
#include "JAcoustics/JPlatypus_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;

  JSingleFileScanner<JSuperEvt>  inputFile;
  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
  size_t                  threads;                              // number of parallel threads
  int                     debug;

  try {

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

    zap['f'] = make_field(inputFile,       "output of JAcousticEventBuilder[.sh]");
    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['N'] = make_field(threads,         "number of threads")              = 1;
    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, JEmitter>    emitters;

  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);

  JKatoomba<JGandalf>::debug              = debug;
  JKatoomba<JGandalf>::MAXIMUM_ITERATIONS = 10000;

  try {
    JPlatypus platypus(geometry, emitters, V, parameters, inputFile, threads);
  }
  catch(const exception& error) {
    FATAL("main " << error.what());
  }

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