indii/fmri/model/SingleSeedModel.hpp

#ifndef INDII_FMRI_MODEL_SINGLESEEDMODEL_HPP
#define INDII_FMRI_MODEL_SINGLESEEDMODEL_HPP

#include "../hemodynamic/LogNeuralBalloonModel.hpp"
#include "../hemodynamic/LogBOLDCalculator.hpp"

#include "indii/ml/ode/AdaptiveRungeKutta.hpp"
#include "indii/ml/filter/UnscentedKalmanFilterModel.hpp"
#include "indii/ml/aux/vector.hpp"
#include "indii/ml/aux/GaussianPdf.hpp"

namespace indii {
  namespace fmri {
    namespace model {

/**
 * Single seed time-series %model. May be used to filter a BOLD signal
 * to obtain an estimate of the underlying %neural activity.
 *
 *
 * @author Lawrence Murray <lawrence@indii.org>
 * @version $Rev: 309 $
 * @date $Date: 2007-10-03 14:16:40 +0100 (Wed, 03 Oct 2007) $
 *
 * Uses indii::fmri::hemodynamic::LogNeuralBalloonModel for state
 * transitions and indii::fmri::hemodynamic::LogBOLDCalculator for
 * predicted measurements. Works in log space to ensure that sigma
 * points sampled by the unscented Kalman filter are always positive
 * for \f$q\f$, \f$v\f$ and \f$f\f$.
 */
class SingleSeedModel :
    public indii::ml::filter::UnscentedKalmanFilterModel<double> {
public:
  /**
   * Indices for state variables in vectors.
   */
  enum SeedVariables {
    LN_Q,
    LN_V,
    LN_F,
    S,
    U,
    B,
    SEED_SIZE
  };

  /**
   * Constructor.
   *
   * @param M Number of sessions used for measurement.
   */
  SingleSeedModel(unsigned int M);

  /**
   * Destructor.
   */
  virtual ~SingleSeedModel();

  /**
   * @see indii::ml::model::UnscentedKalmanFilterModel
   */
  virtual indii::ml::aux::vector transition(const indii::ml::aux::vector &x,
      const indii::ml::aux::vector &w, double delta);

  /**
   * @see indii::ml::model::UnscentedKalmanFilterModel
   */
  virtual indii::ml::aux::vector measure(const indii::ml::aux::vector &x,
      const indii::ml::aux::vector &v);

  /**
   * Calculate a suggested prior over the initial state of the system.
   * 
   * @return Suggested prior over the initial state of the system.
   */
  indii::ml::aux::GaussianPdf suggestPrior();

  /**
   * Calculate a suggested system noise structure.
   * 
   * @return Suggested system noise.
   */
  indii::ml::aux::GaussianPdf suggestSystemNoise();

  /**
   * Calculate a suggested measurement noise structure.
   * 
   * @return Suggested measurement noise.
   */
  indii::ml::aux::GaussianPdf suggestMeasurementNoise();

private:
  /**
   * Number of sessions used for measurement.
   */
  unsigned int M;

  /**
   * Balloon model for transition function.
   */
  indii::fmri::hemodynamic::LogNeuralBalloonModel balloon;

  /**
   * Runge--Kutta for transition function.
   */
  indii::ml::ode::AdaptiveRungeKutta ode;

  /**
   * BOLD calculator for measurement function.
   */
  indii::fmri::hemodynamic::LogBOLDCalculator bold;

};

    }
  }
}

#endif

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