indii/fmri/neural/MultiSeedNeuralModelMk2.hpp

#ifndef INDII_ML_ODE_MULTISEEDNEURALMODELMK2_HPP
#define INDII_ML_ODE_MULTISEEDNEURALMODELMK2_HPP

#include "indii/ml/aux/vector.hpp"
#include "indii/ml/aux/matrix.hpp"
#include "indii/ml/ode/DifferentialModel.hpp"
#include "indii/ml/ode/FunctionModel.hpp"

namespace indii {
  namespace fmri {
    namespace neural {

/**
 * Multi-seed differential %model with %experimental input.
 *
 * @author Lawrence Murray <lawrence@indii.org>
 * @version $Rev: 285 $
 * @date $Date: 2007-07-20 17:25:40 +0100 (Fri, 20 Jul 2007) $
 *
 * Neural activities of \f$N\f$ seeds \f$\mathbf{x}\f$ and the effects
 * of an %experimental input \f$u(t)\f$ are related according to the
 * differential system:
 *
 * \f[
 *   \frac{d\mathbf{x}}{dt} = A\mathbf{x} + \mathbf{c}u
 * \f]
 *
 * where \f$A\f$ is an \f$N \times N\f$ matrix of efficacies between
 * seeds and \f$\mathbf{c}\f$ a vector of \f$N\f$ efficacies of the
 * input on the seeds.
 */
class MultiSeedNeuralModelMk2 : public indii::ml::ode::DifferentialModel {
public:
  /**
   * Construct new %model with given number of seeds. The efficacies
   * remain uninitialised.
   *
   * @param N \f$N\f$; the number of seeds.
   * @param u \f$u(t)\f$; the %experimental input, e.g. an
   * instantiation of indii::fmri::experimental::BlockDesignModel.
   */
  MultiSeedNeuralModelMk2(const unsigned int N,
      indii::ml::ode::FunctionModel* u);

  /**
   * Construct new %model with given efficacies.
   *
   * @param A \f$A\f$; efficacies between seeds, assumed to be \f$N
   * \times N\f$ in size.
   * @param c \f$\mathbf{c}\f$; efficacies of input on seeds, must be
   * of size \f$N\f$.
   * @param u \f$u(t)\f$; the %experimental input, e.g. an
   * instantiation of indii::fmri::experimental::BlockDesignModel.
   */
  MultiSeedNeuralModelMk2(const indii::ml::aux::matrix& A,
      const indii::ml::aux::vector& c, indii::ml::ode::FunctionModel* u);

  /**
   * Destructor.
   */
  virtual ~MultiSeedNeuralModelMk2();

  /**
   * Set all efficacies between all seeds.
   *
   * @param A \f$A\f$; efficacies between seeds, must be \f$N \times
   * N\f$ in size.
   */
  void setEfficacies(const indii::ml::aux::matrix& A);

  /**
   * Set all efficacies of input on seeds.
   *
   * @param c \f$c\f$; efficacies of input on seeds, must be of size
   * \f$N\f$.
   */
  void setInputEfficacies(const indii::ml::aux::vector& c);

  /**
   * Set the efficacy between two seeds.
   *
   * @param i \f$i\f$; index of the affected seed.
   * @param j \f$j\f$; index of the affecting seed.
   * @param A_ij \f$A_{ij}\f$; efficacy of seed \f$j\f$ on seed
   * \f$i\f$.
   */
  void setEfficacy(const unsigned int i, const unsigned int j,
      const double A_ij);

  /**
   * Set the efficacy of the input on a seed.
   *
   * @param i \f$i\f$; index of the affected seed.
   * @param c_i \f$c_i\f$; efficacy of the input on seed \f$i\f$.
   */
  void setInputEfficacy(const unsigned int i, const double c_i);

  /**
   * @see indii::ml::ode::DifferentialModel
   */
  virtual void calculateDerivatives(double t, const double y[], double dydt[]);

private:
  /**
   * \f$N\f$n; the number of seeds in the model.
   */
  const unsigned int N;

  /**
   * \f$A\f$; the efficacy matrix.
   */
  indii::ml::aux::matrix A;

  /**
   * \f$\mathbf{c}\f$; the input efficacy vector.
   */
  indii::ml::aux::vector c;

  /**
   * \f$u(t)\f$; the input.
   */
  indii::ml::ode::FunctionModel* u;

};

    }
  }
}

#endif

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