def get_posterior_code_y_only(self,k,block,y):
N = 2**len(self.segments_at_position[block[k]])
if y == (0,1): slice = range(0,N)
else: slice = range(N,2*N)
return logsumexp(self.fwd_values[block[k]][slice] +
self.bwd_values[block[k]][slice]) - \
self.log_data_prob
def get_posterior_code_y_only(self, k, block, y):
N = 2**len(self.segments_at_position[block[k]])
if y == (0, 1): slice = range(0, N)
else: slice = range(N, 2 * N)
return logsumexp(self.fwd_values[block[k]][slice] +
self.bwd_values[block[k]][slice]) - \
self.log_data_prob
def run_forwards(self,block):
start, end = block[0], block[-1]
block_length = len(block)
fwd_values = dict()
fwd, fwd_prev = np.array([]), np.array([])
N, N_prev = 0, 0
with open(self.dir + "/c/forwards.c") as code_file:
forwards_code = code_file.read()
# compute probabilities and pointers:
for j, j_prev in ((block[k], block[(k-1) % block_length])
for k in xrange(len(block))):
N = len(self.segments_at_position[j])
N_prev = len(self.segments_at_position[j_prev])
np_free_indices = self.get_free_indices(j, j_prev)
N_free = len(np_free_indices)
fwd_prev = fwd
fwd = np.zeros(2**(N+1))
np_prob0, np_prob1 = self.get_prob_vectors(j)
np_current_to_prev_pos = self.get_position_map(j, j_prev)
np_clouds_at_position = self.get_clouds_at_position(j)
Nclouds = len(np_clouds_at_position)
start_position = int(j == start)
inline(forwards_code,
['j', 'fwd', 'fwd_prev',
'np_prob0', 'np_prob1',
'np_current_to_prev_pos', 'np_clouds_at_position',
'np_free_indices',
'N', 'N_prev', 'Nclouds', 'N_free', 'start_position'],
headers = ["<math.h>",
"\"" + self.dir + "/c/common.h\""],
type_converters = converters.blitz,
compiler = "gcc")
fwd_values[j] = fwd
self.fwd_values = fwd_values
self.log_data_prob = logsumexp(fwd)
def run_forwards(self, block):
start, end = block[0], block[-1]
block_length = len(block)
fwd_values = dict()
fwd, fwd_prev = np.array([]), np.array([])
N, N_prev = 0, 0
with open(self.dir + "/c/forwards.c") as code_file:
forwards_code = code_file.read()
# compute probabilities and pointers:
for j, j_prev in ((block[k], block[(k - 1) % block_length])
for k in xrange(len(block))):
N = len(self.segments_at_position[j])
N_prev = len(self.segments_at_position[j_prev])
np_free_indices = self.get_free_indices(j, j_prev)
N_free = len(np_free_indices)
fwd_prev = fwd
fwd = np.zeros(2**(N + 1))
np_prob0, np_prob1 = self.get_prob_vectors(j)
np_current_to_prev_pos = self.get_position_map(j, j_prev)
np_clouds_at_position = self.get_clouds_at_position(j)
Nclouds = len(np_clouds_at_position)
start_position = int(j == start)
inline(forwards_code, [
'j', 'fwd', 'fwd_prev', 'np_prob0', 'np_prob1',
'np_current_to_prev_pos', 'np_clouds_at_position',
'np_free_indices', 'N', 'N_prev', 'Nclouds', 'N_free',
'start_position'
],
headers=["<math.h>", "\"" + self.dir + "/c/common.h\""],
type_converters=converters.blitz,
compiler="gcc")
fwd_values[j] = fwd
self.fwd_values = fwd_values
self.log_data_prob = logsumexp(fwd)