/*============================================================================*/
static int pviterbi_propagate_free (plocal_propagate_store_t **v, int n,
int max_offset_x, int max_offset_y,
int len_y) {
#define CUR_PROC "pviterbi_propagate_free"
int j, i;
mes_check_ptr(v, return(-1));
if( !*v ) return(0);
for (j = 0; j < n; j++) {
for (i=0; i<(*v)->mo->s[j].in_states; i++)
m_free((*v)->log_in_a[j][i]);
m_free((*v)->log_in_a[j]);
}
m_free((*v)->log_in_a);
for (j=0; j<n; j++)
m_free((*v)->log_b[j]);
m_free((*v)->log_b);
ighmm_cmatrix_3d_free(&((*v)->phi), max_offset_x + 1, len_y + max_offset_y + 1);
m_free((*v)->phi_new);
if ((*v)->end_of_first) {
for (j=0; j<max_offset_x + 1; j++) {
if ((*v)->end_of_first[j]) {
for (i=0; i<len_y + max_offset_y + 1; i++)
if ((*v)->end_of_first[j][i])
m_free((*v)->end_of_first[j][i]);
m_free((*v)->end_of_first[j]);
}
}
m_free((*v)->end_of_first);
}
m_free((*v)->topo_order);
m_free(*v);
return(0);
#undef CUR_PROC
}
/*============================================================================*/
static int pviterbi_free(plocal_store_t **v, int n, int len_x, int len_y,
int max_offset_x, int max_offset_y) {
#define CUR_PROC "pviterbi_free"
int i, j;
mes_check_ptr(v, return(-1));
if( !*v ) return(0);
for (j = 0; j < n; j++) {
for (i=0; i < (*v)->mo->s[j].in_states; i++)
m_free((*v)->log_in_a[j][i]);
m_free((*v)->log_in_a[j]);
}
m_free((*v)->log_in_a);
for (j=0; j<n; j++)
m_free((*v)->log_b[j]);
m_free((*v)->log_b);
ighmm_cmatrix_3d_free( &((*v)->phi), max_offset_x + 1,
len_y + max_offset_y + 1);
m_free((*v)->phi_new);
ighmm_dmatrix_3d_free( &((*v)->psi), len_x + max_offset_x + 1, len_y + max_offset_y + 1);
m_free((*v)->topo_order);
(*v)->mo = NULL;
m_free(*v);
return(0);
#undef CUR_PROC
} /* viterbi_free */
//only uses first sequence
int* ghmm_bayes_hmm_fbgibbs(ghmm_bayes_hmm *bayes, ghmm_cmodel *mo, ghmm_cseq* seq,
int burnIn, int seed){
#define CUR_PROC "ghmm_cmodel_fbgibbs"
//XXX seed
GHMM_RNG_SET (RNG, seed);
int max_seq = ghmm_cseq_max_len(seq);
double **alpha = ighmm_cmatrix_alloc(max_seq,mo->N);
double ***pmats = ighmm_cmatrix_3d_alloc(max_seq, mo->N, mo->N);
int **Q;
ARRAY_CALLOC(Q, seq->seq_number);
int seq_iter;
for(seq_iter = 0; seq_iter < seq->seq_number; seq_iter++){
ARRAY_CALLOC(Q[seq_iter], seq->seq_len[seq_iter]);
}
ghmm_sample_data data;
ghmm_alloc_sample_data(bayes, &data);
ghmm_clear_sample_data(&data, bayes);//XXX swap parameter
for(; burnIn > 0; burnIn--){
for(seq_iter = 0; seq_iter < seq->seq_number; seq_iter++){
ghmm_cmodel_fbgibbstep(mo,seq->seq[seq_iter],seq->seq_len[seq_iter], Q[seq_iter],
alpha, pmats, NULL);
ghmm_get_sample_data(&data, bayes, Q[seq_iter], seq->seq[seq_iter],
seq->seq_len[seq_iter]);
ghmm_update_model(mo, bayes, &data);
ghmm_clear_sample_data(&data, bayes);
}
}
ighmm_cmatrix_free(&alpha, max_seq);
ighmm_cmatrix_3d_free(&pmats, max_seq,mo->N);
return Q;
STOP:
return NULL; //XXX error handle
#undef CUR_PROC
}
int* ghmm_bayes_hmm_fbgibbs_compressed(ghmm_bayes_hmm *bayes, ghmm_cmodel *mo, ghmm_cseq* seq,
int burnIn, int seed, double width, double delta, int max_len_permitted){
#define CUR_PROC "ghmm_cmodel_fbgibbs"
//XXX seed
GHMM_RNG_SET (RNG, seed);
block_stats *stats = compress_observations(seq, width*delta, delta);
stats = merge_observations(seq, width, max_len_permitted, stats);
print_stats(stats, seq->seq_len[0]);
//get max_block_len
int max_block_len = stats->length[0];
int i;
for(i = 1; i < stats->total; i++){
if(max_block_len < stats->length[i])
max_block_len = stats->length[i];
}
//printf("max b len %d\n", max_block_len);
double ***b = ighmm_cmatrix_3d_alloc(stats->total, mo->N, 2);
double **alpha = ighmm_cmatrix_alloc(seq->seq_len[0],mo->N);
double ***pmats = ighmm_cmatrix_3d_alloc(seq->seq_len[0], mo->N, mo->N);
int *Q;
ARRAY_CALLOC(Q, seq->seq_len[0]);//XXX extra length for compressed
ghmm_sample_data data;
ghmm_alloc_sample_data(bayes, &data);
ghmm_clear_sample_data(&data, bayes);//XXX swap parameter
for(; burnIn > 0; burnIn--){
//XXX only using seq 0
precompute_block_emission(mo, stats, max_block_len, b);//XXX maxlen
ghmm_cmodel_fbgibbstep(mo,seq->seq[0], stats->total, Q, alpha, pmats, b);
ghmm_get_sample_data_compressed(&data, bayes, Q, seq->seq[0],
stats->total, stats);
ghmm_update_model(mo, bayes, &data);
ghmm_clear_sample_data(&data, bayes);
}
ighmm_cmatrix_free(&alpha, seq->seq_len[0]);
ighmm_cmatrix_3d_free(&pmats, seq->seq_len[0],mo->N);
ighmm_cmatrix_3d_free(&b, stats->total, mo->N);
free_block_stats(&stats);
return Q;
STOP:
return NULL; //XXX error handle
#undef CUR_PROC
}
