#ifndef MEASURED_SED_H
#define MEASURED_SED_H

#include <map>

#include <aocommon/uvector.h>

#include <schaapcommon/fitters/nlplfitter.h>

#include "measurement.h"
#include "spectralenergydistribution.h"

class MeasuredSED : public SpectralEnergyDistribution {
 private:
  typedef std::map<long double, Measurement> FluxMap;

 public:
  typedef FluxMap::iterator iterator;
  typedef FluxMap::const_iterator const_iterator;
  typedef FluxMap::reverse_iterator reverse_iterator;
  typedef FluxMap::const_reverse_iterator const_reverse_iterator;
  typedef FluxMap::value_type value_type;

  MeasuredSED() {}

  MeasuredSED(long double fluxDensityJy, long double frequencyHz) {
    AddMeasurement(fluxDensityJy, frequencyHz);
  }

  template <typename T>
  MeasuredSED(const T* fluxDensityJy, long double frequencyHz) {
    AddMeasurement(fluxDensityJy, frequencyHz);
  }

  MeasuredSED(long double fluxDensityJy, long double frequencyHz,
              long double spectralIndex,
              aocommon::PolarizationEnum polarization =
                  aocommon::Polarization::StokesI) {
    AddMeasurement(fluxDensityJy, frequencyHz, spectralIndex, polarization);
  }

  MeasuredSED(long double fluxDensityAJy, long double frequencyAHz,
              long double fluxDensityBJy, long double frequencyBHz) {
    AddMeasurement(fluxDensityAJy, frequencyAHz);
    AddMeasurement(fluxDensityBJy, frequencyBHz);
  }

  MeasuredSED(const MeasuredSED& source)
      : _measurements(source._measurements) {}

  virtual MeasuredSED* Clone() const { return new MeasuredSED(*this); }

  void operator=(const MeasuredSED& source) {
    _measurements = source._measurements;
  }

  void operator+=(const SpectralEnergyDistribution& rhs) {
    for (iterator i = begin(); i != end(); ++i) {
      double freq = i->first;
      Measurement& m = i->second;
      for (size_t p = 0; p != 4; ++p) {
        m.SetFluxDensityFromIndex(p, m.FluxDensityFromIndex(p) +
                                         rhs.FluxAtFrequencyFromIndex(freq, p));
      }
    }
  }

  void operator*=(double factor) {
    for (iterator i = begin(); i != end(); ++i) {
      Measurement& m = i->second;
      for (size_t p = 0; p != 4; ++p) {
        m.SetFluxDensityFromIndex(p, m.FluxDensityFromIndex(p) * factor);
      }
    }
  }

  void CombineMeasurements(const MeasuredSED& other) {
    for (const_iterator i = other.begin(); i != other.end(); ++i) {
      double freq = i->first;
      if (_measurements.find(freq) != end())
        throw std::runtime_error(
            "Combining measurements for new frequencies, but frequencies "
            "overlap");
      const Measurement& m = i->second;
      AddMeasurement(m);
    }
  }

  void CombineMeasurementsWithAveraging(const MeasuredSED& other,
                                        double weight = 0.5) {
    for (const_iterator i = other.begin(); i != other.end(); ++i) {
      double freq = i->first;
      FluxMap::iterator pos = _measurements.find(freq);
      if (pos == end()) {
        const Measurement& m = i->second;
        AddMeasurement(m);
      } else {
        Measurement& m = pos->second;
        m.AverageWidth(i->second, weight);
      }
    }
  }

  void AddMeasurement(const Measurement& measurement) {
    _measurements.insert(std::pair<long double, Measurement>(
        measurement.FrequencyHz(), measurement));
  }

  void AddMeasurement(long double fluxDensityJy, long double frequencyHz) {
    Measurement measurement;
    measurement.SetFluxDensityFromIndex(0, fluxDensityJy);
    measurement.SetFluxDensityFromIndex(1, 0.0);
    measurement.SetFluxDensityFromIndex(2, 0.0);
    measurement.SetFluxDensityFromIndex(3, 0.0);
    measurement.SetFrequencyHz(frequencyHz);
    _measurements.insert(
        std::pair<long double, Measurement>(frequencyHz, measurement));
  }

  template <typename T>
  void AddMeasurement(const T* fluxDensityJyPerPol, long double frequencyHz) {
    Measurement measurement;
    for (size_t p = 0; p != 4; ++p)
      measurement.SetFluxDensityFromIndex(p, fluxDensityJyPerPol[p]);
    measurement.SetFrequencyHz(frequencyHz);
    _measurements.insert(
        std::pair<long double, Measurement>(frequencyHz, measurement));
  }

  void AddMeasurement(long double fluxDensityJy, long double frequencyHz,
                      long double spectralIndex,
                      aocommon::PolarizationEnum polarization =
                          aocommon::Polarization::StokesI) {
#ifdef EXTRA_ASSERTIONS
    if (!aocommon::Polarization::IsStokes(polarization))
      throw std::runtime_error("Cannot store specified polarization in model");
#endif
    Measurement measurementA, measurementB;
    measurementA.SetZeroExceptSinglePol(polarization, fluxDensityJy);
    measurementA.SetFrequencyHz(frequencyHz);
    _measurements.insert(
        std::pair<long double, Measurement>(frequencyHz, measurementA));
    if (spectralIndex != 0.0) {
      long double fluxB = /* Calculate the flux density for 1 Hz frequency */
          fluxDensityJy * std::pow(1.0 / frequencyHz, spectralIndex);
      long double refFreqB = frequencyHz + 15000000.0;
      if (refFreqB == frequencyHz) {
        refFreqB *= 2.0;
      }
      fluxB = fluxB * std::pow(refFreqB, spectralIndex);
      measurementB.SetZeroExceptSinglePol(polarization, fluxB);
      measurementB.SetFrequencyHz(refFreqB);
      _measurements.insert(
          std::pair<long double, Measurement>(refFreqB, measurementB));
    }
  }

  std::string ToString() const {
    std::ostringstream s;
    s.precision(15);
    for (FluxMap::const_iterator i = _measurements.begin();
         i != _measurements.end(); ++i) {
      i->second.ToStream(s);
    }
    return s.str();
  }

  long double FluxAtFrequencyFromIndex(long double frequencyHz,
                                       size_t pIndex) const {
    if (_measurements.size() <= 1) {
      if (_measurements.empty())
        return 0.0;
      else
        return _measurements.begin()->second.FluxDensityFromIndex(pIndex);
    }

    // 'right' will be first item which frequency >= frequencyHz
    FluxMap::const_iterator right = _measurements.lower_bound(frequencyHz);
    if (right != _measurements.end() && right->first == frequencyHz)
      return right->second.FluxDensityFromIndex(pIndex);

    FluxMap::const_iterator left;

    // If the requested frequency is outside the range, we extrapolate the SI of
    // the full range
    if (right == _measurements.begin() || right == _measurements.end()) {
      left = _measurements.begin();
      right = _measurements.end();
      --right;
    } else {
      // Requested frequency is within range (no extrapolation required)
      left = right;
      --left;
    }

    long double freqA = left->first,
                fluxA = left->second.FluxDensityFromIndex(pIndex),
                freqB = right->first,
                fluxB = right->second.FluxDensityFromIndex(pIndex);

    return SpectralEnergyDistribution::FluxAtFrequency(fluxA, freqA, fluxB,
                                                       freqB, frequencyHz);
  }

  long double IntegratedFlux(long double startFrequency,
                             long double endFrequency,
                             aocommon::PolarizationEnum polarization) const {
    if (startFrequency == endFrequency)
      return FluxAtFrequency(startFrequency, polarization);

    FluxMap::const_iterator iter = _measurements.lower_bound(startFrequency);

    /** Handle special cases */
    if (_measurements.size() <= 2) {
      if (_measurements.empty())
        return 0.0;
      else if (_measurements.size() == 1)
        return _measurements.begin()->second.FluxDensity(polarization);
      else {  // _measurements.size()==2
        long double freqA = _measurements.begin()->first,
                    fluxA =
                        _measurements.begin()->second.FluxDensity(polarization),
                    freqB = _measurements.rbegin()->first,
                    fluxB = _measurements.rbegin()->second.FluxDensity(
                        polarization);
        return SpectralEnergyDistribution::IntegratedFlux(
            fluxA, freqA, fluxB, freqB, startFrequency, endFrequency);
      }
    }
    if (iter ==
        _measurements.end()) {  // all keys are lower, so take entire range
      long double freqA = _measurements.begin()->first,
                  fluxA =
                      _measurements.begin()->second.FluxDensity(polarization),
                  freqB = _measurements.rbegin()->first,
                  fluxB =
                      _measurements.rbegin()->second.FluxDensity(polarization);
      return SpectralEnergyDistribution::IntegratedFlux(
          fluxA, freqA, fluxB, freqB, startFrequency, endFrequency);
    }

    if (iter != _measurements.begin()) --iter;

    if (iter->first >= endFrequency) {
      // all keys are outside range, higher than range
      long double freqA = _measurements.begin()->first,
                  fluxA =
                      _measurements.begin()->second.FluxDensity(polarization),
                  freqB = _measurements.rbegin()->first,
                  fluxB =
                      _measurements.rbegin()->second.FluxDensity(polarization);
      return SpectralEnergyDistribution::IntegratedFlux(
          fluxA, freqA, fluxB, freqB, startFrequency, endFrequency);
    }

    long double integratedSum = 0.0;
    long double leftFrequency = startFrequency;
    if (leftFrequency < iter->first) {
      // requested frequency is below first item; extrapolate
      long double freqA = _measurements.begin()->first,
                  fluxA =
                      _measurements.begin()->second.FluxDensity(polarization),
                  freqB = _measurements.rbegin()->first,
                  fluxB =
                      _measurements.rbegin()->second.FluxDensity(polarization);
      long double sumTerm = SpectralEnergyDistribution::IntegratedFlux(
          fluxA, freqA, fluxB, freqB, startFrequency, iter->first);
      integratedSum += sumTerm * (iter->first - startFrequency);
      leftFrequency = iter->first;
    }

    while (iter != _measurements.end() && iter->first < endFrequency) {
      FluxMap::const_iterator left = iter;
      FluxMap::const_iterator right = iter;
      ++right;

      long double rightFrequency;

      // If this is past the sampled frequencies, extrapolate full range
      if (right == _measurements.end()) {
        left = _measurements.begin();
        right = _measurements.end();
        --right;
        rightFrequency = endFrequency;
      } else {
        rightFrequency = right->first;
        if (rightFrequency > endFrequency) rightFrequency = endFrequency;
      }

      long double freqA = left->first,
                  fluxA = left->second.FluxDensity(polarization),
                  freqB = right->first,
                  fluxB = right->second.FluxDensity(polarization);

      if (leftFrequency < rightFrequency) {
        long double sumTerm = SpectralEnergyDistribution::IntegratedFlux(
            fluxA, freqA, fluxB, freqB, leftFrequency, rightFrequency);
        if (!std::isfinite(sumTerm)) {
          std::cerr << "Warning: integrating flux between " << leftFrequency
                    << " and " << rightFrequency << " with fluxes " << fluxA
                    << '@' << freqA << ',' << fluxB << '@' << freqB
                    << " gave non-finite result\n";
        }

        integratedSum += sumTerm * (rightFrequency - leftFrequency);
      }
      leftFrequency = rightFrequency;
      ++iter;
    }
    return integratedSum / (endFrequency - startFrequency);
  }

  long double AverageFlux(aocommon::PolarizationEnum polarization) const {
    long double sum = 0.0;
    size_t count = 0;
    for (FluxMap::const_iterator i = _measurements.begin();
         i != _measurements.end(); ++i) {
      const Measurement& m = i->second;
      long double flux = m.FluxDensity(polarization);
      if (std::isfinite(flux)) {
        ++count;
        sum += flux;
      }
    }
    return sum / (long double)count;
  }

  long double AverageFlux(long double startFrequency, long double endFrequency,
                          aocommon::PolarizationEnum polarization) const {
    if (startFrequency == endFrequency)
      return FluxAtFrequency(startFrequency, polarization);

    /** Handle special cases */
    if (_measurements.empty()) return 0.0;

    FluxMap::const_iterator iter = _measurements.lower_bound(startFrequency);
    if (iter == _measurements.end())  // all keys are lower
      return std::numeric_limits<long double>::quiet_NaN();

    size_t count = 0;
    long double fluxSum = 0.0;

    while (iter->first < endFrequency && iter != _measurements.end()) {
      long double flux = iter->second.FluxDensity(polarization);
      if (std::isfinite(flux)) {
        ++count;
        fluxSum += flux;
      }
      ++iter;
    }

    if (count == 0)
      return std::numeric_limits<long double>::quiet_NaN();
    else
      return fluxSum / count;
  }

  void FitPowerlaw(long double& factor, long double& exponent,
                   aocommon::PolarizationEnum polarization) const {
    long double sumxy = 0.0, sumx = 0.0, sumy = 0.0, sumxx = 0.0;
    size_t n = 0;
    bool requireNonLinear = false;
    for (FluxMap::const_iterator i = _measurements.begin();
         i != _measurements.end(); ++i) {
      const Measurement& m = i->second;
      long double flux = m.FluxDensity(polarization);
      if (flux <= 0) {
        requireNonLinear = true;
        break;
      }
      if (m.FrequencyHz() > 0 && flux > 0 && std::isfinite(flux)) {
        long double logx = std::log(m.FrequencyHz()), logy = std::log(flux);
        sumxy += logx * logy;
        sumx += logx;
        sumy += logy;
        sumxx += logx * logx;
        ++n;
      }
    }
    if (requireNonLinear) {
      schaapcommon::fitters::NonLinearPowerLawFitter fitter;
      n = 0;
      for (FluxMap::const_iterator i = _measurements.begin();
           i != _measurements.end(); ++i) {
        const Measurement& m = i->second;
        long double flux = m.FluxDensity(polarization);
        if (std::isfinite(m.FrequencyHz()) && std::isfinite(flux)) {
          fitter.AddDataPoint(m.FrequencyHz(), flux);
          ++n;
        }
      }
      float eTemp = 0.0, fTemp = 1.0;
      fitter.Fit(eTemp, fTemp);
      // if(n == 0)
      //	std::cout << "No valid data in power law fit\n";
      // else
      //	std::cout << "Non-linear fit yielded: " << fTemp << " * x^" <<
      // eTemp << "\n";
      exponent = eTemp;
      factor = fTemp;
    } else {
      if (n == 0) {
        exponent = std::numeric_limits<double>::quiet_NaN();
        factor = std::numeric_limits<double>::quiet_NaN();
      } else {
        exponent = (n * sumxy - sumx * sumy) / (n * sumxx - sumx * sumx);
        factor = std::exp((sumy - exponent * sumx) / n);
      }
    }
  }

  void FitPowerlaw2ndOrder(long double& a, long double& b, long double& c,
                           aocommon::PolarizationEnum polarization) const {
    schaapcommon::fitters::NonLinearPowerLawFitter fitter;
    size_t n = 0;
    for (FluxMap::const_iterator i = _measurements.begin();
         i != _measurements.end(); ++i) {
      const Measurement& m = i->second;
      long double flux = m.FluxDensity(polarization);
      if (std::isfinite(m.FrequencyHz()) && std::isfinite(flux)) {
        fitter.AddDataPoint(m.FrequencyHz(), flux);
        ++n;
      }
    }
    float aTemp = 0.0, bTemp = 1.0, cTemp = 0.0;
    fitter.Fit(aTemp, bTemp, cTemp);
    a = aTemp;
    b = bTemp;
    c = cTemp;
  }

  void FitLogPolynomial(std::vector<float>& terms, size_t nTerms,
                        aocommon::PolarizationEnum polarization,
                        double referenceFrequencyHz = 1.0) const {
    schaapcommon::fitters::NonLinearPowerLawFitter fitter;
    size_t n = 0;
    for (FluxMap::const_iterator i = _measurements.begin();
         i != _measurements.end(); ++i) {
      const Measurement& m = i->second;
      long double flux = m.FluxDensity(polarization);
      if (std::isfinite(m.FrequencyHz()) && std::isfinite(flux)) {
        fitter.AddDataPoint(m.FrequencyHz() / referenceFrequencyHz, flux);
        ++n;
      }
    }
    fitter.Fit(terms, nTerms);
  }

  virtual long double ReferenceFrequencyHz() const {
    return (_measurements.begin()->second.FrequencyHz() +
            _measurements.rbegin()->second.FrequencyHz()) *
           0.5;
  }

  long double FluxAtLowestFrequency() const {
    const Measurement& m = _measurements.begin()->second;
    return m.FluxDensityFromIndex(0);
  }

  bool HasValidMeasurement() const {
    for (FluxMap::const_iterator i = _measurements.begin();
         i != _measurements.end(); ++i) {
      if (std::isfinite(
              i->second.FluxDensity(aocommon::Polarization::StokesI)) ||
          std::isfinite(
              i->second.FluxDensity(aocommon::Polarization::StokesQ)) ||
          std::isfinite(
              i->second.FluxDensity(aocommon::Polarization::StokesU)) ||
          std::isfinite(i->second.FluxDensity(aocommon::Polarization::StokesV)))
        return true;
    }
    return false;
  }

  void RemoveInvalidMeasurements() {
    FluxMap::iterator i = _measurements.begin();
    while (i != _measurements.end()) {
      if (!std::isfinite(
              i->second.FluxDensity(aocommon::Polarization::StokesI)) ||
          !std::isfinite(
              i->second.FluxDensity(aocommon::Polarization::StokesQ)) ||
          !std::isfinite(
              i->second.FluxDensity(aocommon::Polarization::StokesU)) ||
          !std::isfinite(
              i->second.FluxDensity(aocommon::Polarization::StokesV))) {
        _measurements.erase(i);
        i = _measurements.begin();
      } else {
        ++i;
      }
    }
  }

  bool operator<(const SpectralEnergyDistribution& other) const {
    const MeasuredSED& msed = dynamic_cast<const MeasuredSED&>(other);
    double thisFrequency = _measurements.begin()->first;
    double otherFrequency = msed._measurements.begin()->first;
    double minFreq = std::min(thisFrequency, otherFrequency);
    return FluxAtFrequencyFromIndex(minFreq, 0) <
           msed.FluxAtFrequencyFromIndex(minFreq, 0);
  }

  size_t MeasurementCount() const { return _measurements.size(); }
  long double LowestFrequency() const { return _measurements.begin()->first; }
  long double HighestFrequency() const { return _measurements.rbegin()->first; }
  long double CentreFrequency() const {
    return 0.5 * (LowestFrequency() + HighestFrequency());
  }

  void GetMeasurements(std::vector<Measurement>& measurements) const {
    for (FluxMap::const_iterator i = _measurements.begin();
         i != _measurements.end(); ++i) {
      measurements.push_back(i->second);
    }
  }

  // iterator begin() { return boost::adaptors::values(_measurements).begin(); }
  iterator begin() { return _measurements.begin(); }
  const_iterator begin() const { return _measurements.begin(); }
  iterator end() { return _measurements.end(); }
  const_iterator end() const { return _measurements.end(); }

  reverse_iterator rbegin() { return _measurements.rbegin(); }
  const_reverse_iterator rbegin() const { return _measurements.rbegin(); }
  reverse_iterator rend() { return _measurements.rend(); }
  const_reverse_iterator rend() const { return _measurements.rend(); }

 private:
  FluxMap _measurements;
};

#endif
