def extract_out_cos(transmat, cos, state):
""" Helper function for building HMMs from matrices: Used for
transition matrices with 'cos' transition classes.
Extract outgoing transitions for 'state' from the complete list
of transition matrices
Allocates: .out_id vector and .out_a array (of size cos x N)
"""
lis = []
# parsing indixes belonging to postive probabilites
for j in range(cos):
for i in range(len(transmat[j][state])):
if transmat[j][state][i] != 0.0 and i not in lis:
lis.append(i)
#lis.sort()
#print "lis: ", lis
trans_id = ghmmwrapper.int_array_alloc(len(lis))
probsarray = ghmmwrapper.double_matrix_alloc(cos, len(lis)) # C-function
# creating list with positive probabilities
for k in range(cos):
for j in range(len(lis)):
ghmmwrapper.double_matrix_setitem(probsarray, k, j, transmat[k][state][lis[j]])
# initializing C state index array
for i in range(len(lis)):
ghmmwrapper.int_array_setitem(trans_id, i, lis[i])
return [len(lis),trans_id,probsarray]
def extract_in_cos(transmat, cos, state):
""" Helper function for building HMMs from matrices: Used for
transition matrices with 'cos' transition classes.
Extract ingoing transitions for 'state' from the complete list
of transition matrices
Allocates: .in_id vector and .in_a array (of size cos x N)
"""
lis = []
# parsing indixes belonging to postive probabilites
for j in range(cos):
transmat_col_state = map(lambda x: x[state], transmat[j])
for i in range(len(transmat_col_state)):
if transmat_col_state[i] != 0.0 and i not in lis:
lis.append(i)
#lis.sort()
#print "lis: ", lis
trans_id = ghmmwrapper.int_array_alloc(len(lis))
probsarray = ghmmwrapper.double_matrix_alloc(cos, len(lis)) # C-function
# creating list with positive probabilities
for k in range(cos):
for j in range(len(lis)):
ghmmwrapper.double_matrix_setitem(probsarray, k, j,
transmat[k][lis[j]][state])
# initializing C state index array
for i in range(len(lis)):
ghmmwrapper.int_array_setitem(trans_id, i, lis[i])
return [len(lis), trans_id, probsarray]
def extract_out(lisprobs):
""" Helper function for building HMMs from matrices: Used for
transition matrices without transition classes.
Extract out-/ingoing transitions from the row-vector resp. the
column vector (corresponding to incoming transitions) of the
transition matrix
Allocates: .[out|in]_id and .[out|in]_a vectors
"""
lis = []
for i in range(len(lisprobs)):
if lisprobs[i]!=0:
lis.append(i)
trans_id = ghmmwrapper.int_array_alloc(len(lis))
trans_prob = ghmmwrapper.double_array_alloc(len(lis))
for i in range(len(lis)):
ghmmwrapper.int_array_setitem(trans_id, i, lis[i])
ghmmwrapper.double_array_setitem(trans_prob, i, lisprobs[lis[i]])
return [len(lis),trans_id,trans_prob]
def extract_out(lisprobs):
""" Helper function for building HMMs from matrices: Used for
transition matrices without transition classes.
Extract out-/ingoing transitions from the row-vector resp. the
column vector (corresponding to incoming transitions) of the
transition matrix
Allocates: .[out|in]_id and .[out|in]_a vectors
"""
lis = []
for i in range(len(lisprobs)):
if lisprobs[i] != 0:
lis.append(i)
trans_id = ghmmwrapper.int_array_alloc(len(lis))
trans_prob = ghmmwrapper.double_array_alloc(len(lis))
for i in range(len(lis)):
ghmmwrapper.int_array_setitem(trans_id, i, lis[i])
ghmmwrapper.double_array_setitem(trans_prob, i, lisprobs[lis[i]])
return [len(lis), trans_id, trans_prob]