indii/fmri/hemodynamic/LogBOLDCalculator.hpp

#ifndef INDII_FMRI_HEMODYNAMIC_LOGBOLDCALCULATOR_HPP
#define INDII_FMRI_HEMODYNAMIC_LOGBOLDCALCULATOR_HPP

#include "indii/ml/aux/vector.hpp"
#include "indii/ml/ode/ParameterCollection.hpp"

namespace indii {
  namespace fmri {
    namespace hemodynamic {

      class BalloonModel;

/**
 * Calculates Blood Oxygenation Level Dependent (BOLD) signal from a
 * LogFlowBalloonModel or LogNeuralBalloonModel.
 *
 * @author Lawrence Murray <lawrence@indii.org>
 * @version $Rev: 285 $
 * @date $Date: 2007-07-20 17:25:40 +0100 (Fri, 20 Jul 2007) $
 *
 * Calculates the BOLD signal as for BOLDCalculator, but from a
 * BalloonModel working in log space.
 */
class LogBOLDCalculator : public indii::ml::ode::ParameterCollection {
public:
  /**
   * Biophysical parameters. These are initialised according to the
   * values in BOLDCalculatorDefaults, but may be overridden using
   * setParameter().
   */
  enum BiophysicalParameter {
    /**
     * \f$k_1\f$
     */
    K_1,

    /**
     * \f$k_2\f$
     */
    K_2,

    /**
     * \f$k_3\f$
     */
    K_3
  };

  /**
   * Create new log BOLD calculator with default biophysical
   * parameters, coupled with the given balloon %model.
   *
   * @param m LogFlowBalloonModel or LogNeuralBalloonModel from which
   * to calculate BOLD signal.
   */
  LogBOLDCalculator(const BalloonModel* m);

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

  /**
   * Calculate BOLD signal from coupled balloon %model and given
   * state.
   *
   * @param y State of the balloon %model, usually provided by the
   * ordinary differential equation solver being used on the balloon
   * %model, such as indii::ml::ode::AdaptiveRungeKutta.
   *
   * @return The BOLD signal produced by the coupled balloon %model in
   * the given state.
   */
  double calculate(const indii::ml::aux::vector& y);

private:
  /**
   * Balloon %model for which to calculate BOLD response.
   */
  const BalloonModel* m;

  /**
   * Number of biophysical parameters.
   */
  static const unsigned int NUM_PARAMETERS = 3;

};

    }
  }
}

#endif

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