def viterbi(self, sequence):
S = self._S
E = self.make_emmissions_matrix(sequence)
T = self._T
seq = array(range(len(sequence)), dtype=int32)
p, vp, s = trace.viterbi_log2(seq, S, T, E)
return map(lambda i: self.states[i], s), p, vp
def viterbi_by_lookup(self, fid, widseq): S = self._S E = self.make_emmissions_matrix_by_lookup([(fid,wid) for wid in widseq]) T = self._T seq = array( range(len(widseq)), dtype=int32) p,vp,s = trace.viterbi_log2( seq, S, T, E ) return map( lambda i: self.states[i], s ), p, vp
def viterbi(self, sequence): S = self._S E = self.make_emmissions_matrix(sequence) T = self._T seq = array( range(len(sequence)), dtype=int32) p,vp,s = trace.viterbi_log2( seq, S, T, E ) return map( lambda i: self.states[i], s ), p, vp
def viterbi_by_lookup(self, fid, widseq):
S = self._S
E = self.make_emmissions_matrix_by_lookup([(fid, wid)
for wid in widseq])
T = self._T
seq = array(range(len(widseq)), dtype=int32)
p, vp, s = trace.viterbi_log2(seq, S, T, E)
return map(lambda i: self.states[i], s), p, vp
DRY = 0
DRYISH = 1
DAMP = 2
SOGGY = 3
NOBS = 4
sprob = array([0.63, 0.17, 0.20])
tprob = array([
[0.5, 0.25, 0.25], ## src = rows, dest = cols
[0.375, 0.125, 0.375],
[0.125, 0.675, 0.375]
])
eprob = array([
[0.60, 0.20, 0.15, 0.05], ## state = rows, obs = cols
[0.25, 0.25, 0.25, 0.25],
[0.05, 0.10, 0.35, 0.50]
])
sequence = [DRY, DAMP, SOGGY, DRY, DAMP, SOGGY]
## should give sunny -> rainy -> rainy -> cloudy -> rainy -> rainy with vprob 2.5754047e-5
expected = 2.5754047e-5
from trace import viterbi_log2
t, p, labels = viterbi_log2(sequence,
log2(sprob),
log2(tprob),
log2(eprob),
do_checks=True)
print 2**t, 2**p
for e in labels:
print states[e]
"dryish",
"damp",
"soggy"]
DRY =0
DRYISH=1
DAMP =2
SOGGY =3
NOBS =4
sprob = array( [ 0.63, 0.17, 0.20])
tprob = array( [[0.5 , 0.25 , 0.25 ],## src = rows, dest = cols
[0.375, 0.125, 0.375],
[0.125, 0.675, 0.375]])
eprob = array( [[0.60, 0.20, 0.15, 0.05],## state = rows, obs = cols
[0.25, 0.25, 0.25, 0.25],
[0.05, 0.10, 0.35, 0.50]])
sequence = [ DRY,
DAMP,
SOGGY,
DRY,
DAMP,
SOGGY ]; ## should give sunny -> rainy -> rainy -> cloudy -> rainy -> rainy with vprob 2.5754047e-5
expected = 2.5754047e-5;
from trace import viterbi_log2
t,p,labels = viterbi_log2( sequence, log2(sprob), log2(tprob), log2(eprob), do_checks = True )
print 2**t,2**p
for e in labels:
print states[e]
