NonStationaryMarkov.hpp

// Unfit: Data fitting and optimization software
//
// Copyright (C) 2012- Dr Martin Buist & Dr Alberto Corrias
// Contacts: martin.buist _at_ nus.edu.sg; alberto _at_ nus.edu.sg
//
// See the 'Contributors' file for a list of those who have contributed
// to this work.
//
// This program is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either version 3 of the License, or
// (at your option) any later version.
//
// This program is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with this program.  If not, see <http://www.gnu.org/licenses/>.
//
#ifndef UNFIT_EXAMPLES_NONSTATIONARYMARKOV_HPP_
#define UNFIT_EXAMPLES_NONSTATIONARYMARKOV_HPP_

#include <cmath>
#include <vector>
#include "GenericCostFunction.hpp"

namespace Unfit
{
namespace Examples
{
class NonStationaryMarkov : public GenericCostFunction
{
 public:
  NonStationaryMarkov(const std::vector<std::vector<double>> &markov_data)
    : markov_data_ {markov_data}
  {}

  std::vector<double> operator()(const std::vector<double> &param)
  {
    const std::size_t num_voltages = markov_data_.size();
    const std::size_t num_data_points = markov_data_[0].size();
    std::vector<double> residuals(num_voltages*num_data_points);
    double vm = -60.0;
    // Note that the zero index is time
    for (auto j = 1u; j < num_voltages; ++j) {
      for (unsigned i = 0u; i < num_data_points; ++i) {
        const auto t = markov_data_[0][i];  // time
        residuals[j*num_data_points + i] = markov_data_[j][i]      // experiment
            - param[0] * exp(vm / param[1]) * exp(-(t - param[2]) *
            (t - param[2]) / (2.0 * param[3] * param[3]));         // - model
       }
       vm += 10.0;
    }
    return residuals;
  }
 private:
  const std::vector<std::vector<double>> markov_data_;
};

}  // namespace Examples
}  // namespace Unfit

#endif