def load(vidname):
import reader, trace, traj
vname, wname, mname = fnames(vidname)
v = reader.Reader(vname, adjuststipple=0)
w = trace.Load_Whiskers(wname)
try:
m = traj.MeasurementsTable(mname)
except:
traceback.print_exc(file=sys.stdout)
sys.stdout.flush()
m = None
return v, w, m
dst)[0]
if not all(map(os.path.exists, args)):
raise IOError, "Could not find one or more input source files."
if all(
map(
lambda f: os.path.splitext(f)[-1] in
['.trajectories', '.whiskers'], args)):
if len(args) == 1:
src = args[0]
tfile = None
else:
src = args[
1] #know the order b.c. already sorted by file extenstion
tfile = args[0]
w = trace.Load_Whiskers(src)
data = numpy.array(list(summary.features(w, options.face)))
if tfile:
t, tid = load_trajectories(tfile)
summary.commit_traj_to_data_table(t, data)
elif all(
map(
lambda f: os.path.splitext(f)[-1] in
['.trajectories', '.measurements'], args)):
sources = dict(map(lambda f: (os.path.splitext(f)[-1], f), args))
try:
data = traj.MeasurementsTable(sources['.measurements']).asarray()
except KeyError:
raise UserException, "A .measurements file must be provided as one of the source files."
wrowcmp = lambda a, b: wcmp(a[1], b[1])
for fid, wv in wvd.iteritems():
#print fid
seq = wid_sequence_from_frame(wv) #ordered wid's
labels, p, vp = model.viterbi_by_lookup(fid, seq)
tids = map(statemap.get, labels)
logp[fid] = p
vlogp[fid] = vp
for tid, wid in zip(tids, seq):
if not tid is None:
traj.setdefault(tid, {})[fid] = wid
return traj, logp, vlogp
if __name__ == '__main__':
import sys, traj, trace
name, whisker_src, measurements_src, dest = sys.argv
wvd = trace.Load_Whiskers(whisker_src)
table = traj.MeasurementsTable(measurements_src)
data = table.asarray()
traj = table.get_trajectories()
model = LeftRightModel()
model.train(wvd, traj, data=data)
traj_hmm, logp, vlogp = apply_model(wvd, model)
table.commit_trajectories(traj)
table.save(dest)
import trace
# Other imports
import matplotlib.pyplot as plt
import numpy as np, os.path, pandas
# Data location
session = '0509A_cropped_truncated_4'
side = 'top'
#~ session = '0527_cropped_truncated_5'; side = 'left'
whisk_rootdir = os.path.expanduser('~/mnt/bruno-nix/whisker_video/processed')
whisk_file = os.path.join(whisk_rootdir, session, session + '.whiskers')
measure_file = os.path.join(whisk_rootdir, session, session + '.measurements')
# Load the traces
frame2segment_id2whisker_seg = trace.Load_Whiskers(whisk_file)
# Load the correspondence between traces and identified whiskers
tmt = traj.MeasurementsTable(measure_file)
whisker_id2frame2segment_id = tmt.get_trajectories()
# Identify any missing frames
frames_l = frame2segment_id2whisker_seg.keys()
sorted_frames = np.sort(frames_l)
# Iterate over frames
rec_l = []
# Iterate over whiskers
# It looks like it numbers them from Bottom to Top for side == 'left'
# whiski colors them R, G, B