def align_ethoscan_data(exp_start, eth_start, eth_obs, times):
'''Find the indices in the `times` vector at which the `eth_obs` occured.
Parameters
----------
exp_start : datetime.datetime
Start of the experiment; i.e. what datetime corresponds to the 0th
index of `times`.
eth_start : datetime.datetime
Start of the Ethoscan report. Ethoscan reports appear to start
behavioral classification 1 second after the report starts. Thus, this
datetime is 1 second before the first classified behavior.
eth_obs : np.array
A single observation (row) of parsed Ethoscan data.
times : np.array
Times since `exp_start` for raw observations.
Returns
-------
np.array
'''
eth_obs_start = add_seconds(eth_start, eth_obs[0])
eth_obs_end = add_seconds(eth_obs_start, eth_obs[2])
start = (eth_obs_start - exp_start).total_seconds()
end = (eth_obs_end - exp_start).total_seconds()
return np.searchsorted(times, [start, end], side='left')
def align_ethoscan_data(exp_start, eth_start, eth_obs, times):
'''Find the indices in the `times` vector at which the `eth_obs` occured.
Parameters
----------
exp_start : datetime.datetime
Start of the experiment; i.e. what datetime corresponds to the 0th
index of `times`.
eth_start : datetime.datetime
Start of the Ethoscan report. Ethoscan reports appear to start
behavioral classification 1 second after the report starts. Thus, this
datetime is 1 second before the first classified behavior.
eth_obs : np.array
A single observation (row) of parsed Ethoscan data.
times : np.array
Times since `exp_start` for raw observations.
Returns
-------
np.array
'''
eth_obs_start = add_seconds(eth_start, eth_obs[0])
eth_obs_end = add_seconds(eth_obs_start, eth_obs[2])
start = (eth_obs_start - exp_start).total_seconds()
end = (eth_obs_end - exp_start).total_seconds()
return np.searchsorted(times, [start, end], side='left')
def test_add_seconds(self):
dt = datetime.datetime(2016, 10, 6, 3, 45, 12)
seconds = 150
exp = datetime.datetime(2016, 10, 6, 3, 47, 42)
obs = add_seconds(dt, seconds)
self.assertEqual(obs, exp)
seconds = 1350232
exp = datetime.datetime(2016, 10, 21, 18, 49, 4)
obs = add_seconds(dt, seconds)
self.assertEqual(obs, exp)
dt = datetime.datetime(2016, 2, 24, 7, 45, 00)
seconds = 638859
exp = datetime.datetime(2016, 3, 2, 17, 12, 39)
obs = add_seconds(dt, seconds)
self.assertEqual(obs, exp)
def test_add_seconds(self):
dt = datetime.datetime(2016, 10, 6, 3, 45, 12)
seconds = 150
exp = datetime.datetime(2016, 10, 6, 3, 47, 42)
obs = add_seconds(dt, seconds)
self.assertEqual(obs, exp)
seconds = 1350232
exp = datetime.datetime(2016, 10, 21, 18, 49, 4)
obs = add_seconds(dt, seconds)
self.assertEqual(obs, exp)
dt = datetime.datetime(2016, 2, 24, 7, 45, 00)
seconds = 638859
exp = datetime.datetime(2016, 3, 2, 17, 12, 39)
obs = add_seconds(dt, seconds)
self.assertEqual(obs, exp)
# each obs is a row of data = a behavior quantified by ethoscan
for obs in eth_data:
obs_start = obs[0]
obs_duration = obs[2]
# Data parsed from the raw promethion files by our scripts
x1_data = x1[int(estart_idx + obs_start):int(estart_idx + obs_start +
obs_duration)]
y1_data = y1[int(estart_idx + obs_start):int(estart_idx + obs_start +
obs_duration)]
# Create the datetime at which the observation would be found in the raw
# file to reparse the data from the Promethion output. Basically a check of
# our parsing.
raw_data = []
dt_start = add_seconds(eth_start, int(obs_start))
dt_start_str = '%s/%s/%s %s' % (dt_start.month, dt_start.day,
dt_start.year, dt_start.strftime('%T'))
dt_end = add_seconds(eth_start, int(obs_start + obs_duration))
dt_end_str = '%s/%s/%s %s' % (dt_end.month, dt_end.day, dt_end.year,
dt_end.strftime('%T'))
start_line = subprocess.check_output("grep -m 1 -n '%s' %s" %
(dt_start_str, raw_data_fp),
shell=True)
end_line = subprocess.check_output("grep -m 1 -n '%s' %s" %
(dt_end_str, raw_data_fp),
shell=True)
start_line = int(start_line.strip().split(':')[0])
end_line = int(end_line.strip().split(':')[0])
# each obs is a row of data = a behavior quantified by ethoscan
for obs in eth_data:
obs_start = obs[0]
obs_duration = obs[2]
# Data parsed from the raw promethion files by our scripts
x1_data = x1[int(estart_idx + obs_start):
int(estart_idx + obs_start + obs_duration)]
y1_data = y1[int(estart_idx + obs_start):
int(estart_idx + obs_start + obs_duration)]
# Create the datetime at which the observation would be found in the raw
# file to reparse the data from the Promethion output. Basically a check of
# our parsing.
raw_data = []
dt_start = add_seconds(eth_start, int(obs_start))
dt_start_str = '%s/%s/%s %s' % (dt_start.month, dt_start.day,
dt_start.year, dt_start.strftime('%T'))
dt_end = add_seconds(eth_start, int(obs_start+obs_duration))
dt_end_str = '%s/%s/%s %s' % (dt_end.month, dt_end.day, dt_end.year,
dt_end.strftime('%T'))
start_line = subprocess.check_output("grep -m 1 -n '%s' %s" % (dt_start_str,
raw_data_fp),
shell=True)
end_line = subprocess.check_output("grep -m 1 -n '%s' %s" % (dt_end_str,
raw_data_fp),
shell=True)
start_line = int(start_line.strip().split(':')[0])
end_line = int(end_line.strip().split(':')[0])
