/*******************************************************************************
*
* This file is part of the General Hidden Markov Model Library,
* GHMM version __VERSION__, see http://ghmm.org
*
* Filename: ghmm/ghmm/viterbi.c
* Authors: Wasinee Rungsarityotin, Benjamin Georgi
*
* Copyright (C) 1998-2004 Alexander Schliep
* Copyright (C) 1998-2001 ZAIK/ZPR, Universitaet zu Koeln
* Copyright (C) 2002-2004 Max-Planck-Institut fuer Molekulare Genetik,
* Berlin
*
* Contact: schliep@ghmm.org
*
* This library is free software; you can redistribute it and/or
* modify it under the terms of the GNU Library General Public
* License as published by the Free Software Foundation; either
* version 2 of the License, or (at your option) any later version.
*
* This library 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
* Library General Public License for more details.
*
* You should have received a copy of the GNU Library General Public
* License along with this library; if not, write to the Free
* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*
*
* This file is version $Revision$
* from $Date$
* last change by $Author$.
*
*******************************************************************************/
#ifdef HAVE_CONFIG_H
# include "../config.h"
#endif
#include <float.h>
#include <math.h>
#include <assert.h>
#include "ghmm.h"
#include "mes.h"
#include "mprintf.h"
#include "matrix.h"
#include "sdmodel.h"
#include "ghmm_internals.h"
typedef struct local_store_t {
double **log_in_a;
double **log_b;
double *phi;
double *phi_new;
int **psi;
int *path_len;
int *topo_order;
int topo_order_length;
} local_store_t;
/*----------------------------------------------------------------------------*/
static int viterbi_free(local_store_t **v, int n, int len)
{
#define CUR_PROC "viterbi_free"
int j;
mes_check_ptr(v, return -1);
if (!*v)
return 0;
for (j = 0; j < n; j++)
m_free((*v)->log_in_a[j]);
m_free((*v)->log_in_a);
ighmm_cmatrix_free(&((*v)->log_b), n);
m_free((*v)->phi);
m_free((*v)->phi_new);
/*ighmm_dmatrix_free( &((*v)->psi), len ); */
ighmm_dmatrix_stat_free(&((*v)->psi));
m_free((*v)->path_len);
m_free((*v)->topo_order);
m_free(*v);
return 0;
#undef CUR_PROC
} /* viterbi_free */
/*----------------------------------------------------------------------------*/
static local_store_t *viterbi_alloc(ghmm_dmodel *mo, int len)
{
#define CUR_PROC "sdviterbi_alloc"
local_store_t *v = NULL;
int j;
ARRAY_CALLOC(v, 1);
/* Allocate the log_in_a's -> individal lenghts */
ARRAY_CALLOC(v->log_in_a, mo->N);
for (j = 0; j < mo->N; j++) {
ARRAY_CALLOC(v->log_in_a[j], mo->s[j].in_states);
}
v->log_b = ighmm_cmatrix_alloc(mo->N, mo->M);
if (!(v->log_b)) {
GHMM_LOG_QUEUED(LCONVERTED);
goto STOP;
}
ARRAY_CALLOC(v->phi, mo->N);
ARRAY_CALLOC(v->phi_new, mo->N);
v->psi = ighmm_dmatrix_stat_alloc(len, mo->N);
if (!(v->psi)) {
GHMM_LOG_QUEUED(LCONVERTED);
goto STOP;
}
ARRAY_CALLOC(v->path_len, mo->N);
v->topo_order_length = 0;
ARRAY_CALLOC(v->topo_order, mo->N);
return v;
STOP: /* Label STOP from ARRAY_[CM]ALLOC */
viterbi_free(&v, mo->N, len);
return NULL;
#undef CUR_PROC
} /* viterbi_alloc */
/*----------------------------------------------------------------------------*/
static void Viterbi_precompute(ghmm_dmodel *mo, int *o, int len, local_store_t *v)
{
#define CUR_PROC "viterbi_precompute"
int i, j, t;
/* Precomputing the log(a_ij) */
for (j = 0; j < mo->N; j++) {
for (i = 0; i < mo->s[j].in_states; i++) {
if (mo->s[j].in_a[i] == 0.0) /* DBL_EPSILON ? */
v->log_in_a[j][i] = +1; /* Not used any further in the calculations */
else
v->log_in_a[j][i] = log(mo->s[j].in_a[i]);
}
}
/* Precomputing the log(bj(ot)) */
for (j = 0; j < mo->N; j++) {
for (t = 0; t < mo->M; t++) {
if (mo->s[j].b[t] == 0.0) /* DBL_EPSILON ? */
v->log_b[j][t] = +1;
else
v->log_b[j][t] = log(mo->s[j].b[t]);
}
}
#undef CUR_PROC
} /* viterbi_precompute */
/*----------------------------------------------------------------------------*/
static void viterbi_silent(ghmm_dmodel *mo, int t, local_store_t *v)
{
#define CUR_PROC "viterbi_silent"
int topocount;
int i, St, i_id, max_id;
double max_value, value;
for (topocount=0; topocount < mo->topo_order_length; topocount++) {
St = mo->topo_order[topocount];
if (mo->silent[St]) { /* Silent states */
/* Determine the maximum */
/* max_phi = phi[i] + log_in_a[j][i] ... */
max_value = -DBL_MAX;
max_id = -1;
for (i = 0; i < mo->s[St].in_states; i++) {
i_id = mo->s[St].in_id[i];
if (v->phi[i_id] != +1 && v->log_in_a[St][i] != +1) {
value = v->phi[i_id] + v->log_in_a[St][i];
if (value > max_value) {
max_value = value;
max_id = i_id;
}
}
}
/* No maximum found (that is, state never reached)
or the output O[t] = 0.0: */
if (max_id < 0) {
v->phi[St] = +1;
} else {
v->phi[St] = max_value;
v->psi[t][St] = max_id;
v->path_len[St] = v->path_len[max_id] + 1;
}
}
}
#undef CUR_PROC
}
/*============================================================================*/
/** Return the viterbi path of the sequence. */
int *ghmm_dmodel_viterbi(ghmm_dmodel * mo, int *o, int len, int *pathlen, double *log_p)
{
#define CUR_PROC "ghmm_dmodel_viterbi"
int *state_seq = NULL;
int t, j, i, i_id, St, max_id;
int end_state, next_state, prev_state;
int len_path, state_seq_index;
int *plen, *exchange;
double value, max_value, *temp;
local_store_t *v;
/* for silent states: initializing path length with a multiple
of the sequence length
and sort the silent states topological */
if (mo->model_type & GHMM_kSilentStates) {
ghmm_dmodel_order_topological(mo);
}
/* Allocate the matrices log_in_a, log_b,Vektor phi, phi_new, Matrix psi */
v = viterbi_alloc(mo, len);
if (!v) {
GHMM_LOG_QUEUED(LCONVERTED);
goto STOP;
}
ARRAY_CALLOC(plen, mo->N);
/* Precomputing the log(a_ij) and log(bj(ot)) */
Viterbi_precompute(mo, o, len, v);
/* Initialization, that is t = 0 */
for (j = 0; j < mo->N; j++) {
if (mo->s[j].pi == 0.0 || v->log_b[j][o[0]] == +1) /* instead of 0, DBL_EPS.? */
v->phi[j] = +1;
else {
v->phi[j] = log(mo->s[j].pi) + v->log_b[j][o[0]];
v->path_len[j] = 1;
}
}
if (mo->model_type & GHMM_kSilentStates) { /* could go into silent state at t=0 */
viterbi_silent(mo, t = 0, v);
}
/* t > 0 */
for (t = 1; t < len; t++) {
for (j = 0; j < mo->N; j++) {
/* initialization of phi, psi */
v->phi_new[j] = +1;
v->psi[t][j] = -1;
}
for (St=0; St < mo->N; St++) {
/* Determine the maximum */
/* max_phi = phi[i] + log_in_a[j][i] ... */
if (!(mo->model_type & GHMM_kSilentStates) || !mo->silent[St]) {
max_value = -DBL_MAX;
max_id = -1;
for (i = 0; i < mo->s[St].in_states; i++) {
i_id = mo->s[St].in_id[i];
if (v->phi[i_id] != +1 && v->log_in_a[St][i] != +1) {
value = v->phi[i_id] + v->log_in_a[St][i];
if (value > max_value) {
max_value = value;
max_id = i_id;
}
}
}
/* No maximum found (that is, state never reached)
or the output O[t] = 0.0: */
if (max_id >= 0 && v->log_b[St][o[t]] != +1) {
v->phi_new[St] = max_value + v->log_b[St][o[t]];
v->psi[t][St] = max_id;
plen[St] = v->path_len[max_id] + 1;
}
}
} /* complete time step for emitting states */
/* Exchange pointers */
temp = v->phi; v->phi = v->phi_new; v->phi_new = temp;
exchange = v->path_len; v->path_len = plen; plen = exchange;
/* complete time step for silent states */
if (mo->model_type & GHMM_kSilentStates) {
viterbi_silent(mo, t, v);
}
} /* Next observation , increment time-step */
/* Termination - find end state */
max_value = -DBL_MAX;
end_state = -1;
for (j=0; j < mo->N; j++) {
if (v->phi[j] != +1 && v->phi[j] > max_value) {
max_value = v->phi[j];
end_state = j;
}
}
if (end_state < 0) {
/* Sequence can't be generated from the model! */
*log_p = +1;
len_path = 1;
}
else {
*log_p = max_value;
len_path = v->path_len[end_state];
}
/* allocating state_seq array */
ARRAY_CALLOC(state_seq, len_path+1);
t = len-1;
state_seq_index = len_path-1;
state_seq[len_path] = -1;
state_seq[state_seq_index--] = end_state;
prev_state = end_state;
/* backtrace is simple if the path length is known */
for (; state_seq_index >= 0; state_seq_index--) {
next_state = v->psi[t][prev_state];
state_seq[state_seq_index] = prev_state = next_state;
if (!(mo->model_type & GHMM_kSilentStates) || !mo->silent[next_state])
t--;
}
*pathlen = len_path;
if (state_seq_index >= 0 || t > 0)
GHMM_LOG_PRINTF(LERROR, LOC, "state_seq_index = %d, t = %d", state_seq_index, t);
/* Free the memory space */
viterbi_free(&v, mo->N, len);
m_free(plen);
return state_seq;
STOP: /* Label STOP from ARRAY_[CM]ALLOC */
/* Free the memory space */
*pathlen = -1;
viterbi_free(&v, mo->N, len);
m_free(plen);
m_free(state_seq);
return NULL;
#undef CUR_PROC
} /* ghmm_dmodel_viterbi */
/*============================================================================*/
double ghmm_dmodel_viterbi_logp(ghmm_dmodel * mo, int *o, int len, int *state_seq)
{
#define CUR_PROC "ghmm_dmodel_viterbi_logp"
double log_p = 0.0;
int unused;
int *vpath = ghmm_dmodel_viterbi(mo, o, len, &unused, &log_p);
m_free(vpath);
return log_p;
#undef CUR_PROC
} /* ghmm_dmodel_viterbi_logp */