src/hmm.h

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/***************************************************************************
 *   Copyright (C) 2008/2009 by Matthias Ihrke                                  *
 *   mihrke@uni-goettingen.de                                              *
 *                                                                         *
 *   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 2 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, write to the                         *
 *   Free Software Foundation, Inc.,                                       *
 *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
 ***************************************************************************/

#ifndef HMM_H
# define HMM_H

#include "mathadd.h"
#include "definitions.h"
#include "eeg.h"
#include <gsl/gsl_rng.h>
#include <gsl/gsl_randist.h>

#ifdef __cplusplus
extern "C" {
#endif


  typedef struct{
     int K; 
     int n; 
     int M; 
     int Q; 
     double *q; 
     double *u; 
     int J; 
     double *d; 
     double s[2]; 
     double **tau; 
     int    **phi; 
     double *z; 
     double sigma; 
     gsl_rng_type *random_number_type; 
     gsl_rng *rng; 
     long seed;   
  } CPHiddenMarkovModel;

  double cphmm_get_transition_prob( CPHiddenMarkovModel *m, int k, int i, int j );


  CPHiddenMarkovModel* cphmm_alloc( int K, int n, int M, int Q, int J );
  CPHiddenMarkovModel* eeg_cphmm_init( EEG *eeg, int channel, double **X );
  void cphmm_init( CPHiddenMarkovModel *m, double **X );
  void cphmm_free( CPHiddenMarkovModel *m );

#ifdef __cplusplus
}
#endif


#endif