def expt_tau(specimen_id):
#print(chr(27) + "[2J") # To clear terminal screen
#print "START EXPT_TAU" + str(specimen_id)
expt_taus = []
data_set = expt_data_set(specimen_id)
long_square_sweeps = lims_utils.get_sweeps_of_type("C1LSCOARSE",
specimen_id,
passed_only=True)
#print "expt specimen id= " + str(specimen_id)
for sweep in long_square_sweeps:
print str(specimen_id) + " expt_sweep_number: " + str(sweep)
if (data_set.get_sweep_metadata(sweep)["aibs_stimulus_amplitude_pa"] <
0):
v, i, t = lims_utils.get_sweep_v_i_t_from_set(data_set, sweep)
sweep_feat = EphysSweepFeatureExtractor(
t, v) # Get time and voltage of each hyperpolarizing sweep
try:
sweep_feat.estimate_time_constant(
) # Try statement included because estimate_time_constant errors on some sweeps ("could not find interval for time constant estimate")
except:
continue
else:
expt_taus.append(sweep_feat.estimate_time_constant(
)) # Append time constant of each sweep to list
mean_expt_tau = np.nanmean(expt_taus) # Mean time constant for this cell
#print "mean_expt_tau= " + str(mean_expt_tau)
return mean_expt_tau
def ve_tau(specimen_id, ve_path):
#print(chr(27) + "[2J") # To clear terminal screen
print "START VE_TAU " + str(specimen_id) + " " + str(ve_path)
expt_taus = []
data_set = NwbDataSet(ve_path)
long_square_sweeps = lims_utils.get_sweeps_of_type("C1LSCOARSE",
specimen_id,
passed_only=True)
print "ve specimen id= " + str(specimen_id)
for sweep in long_square_sweeps:
#print "ve_sweep_number: " + str(sweep)
#print(data_set.get_sweep_metadata(sweep))
try:
(data_set.get_sweep_metadata(sweep)["aibs_stimulus_amplitude_pa"])
except:
continue
else:
if (data_set.get_sweep_metadata(sweep)
["aibs_stimulus_amplitude_pa"] < 0):
v, i, t = lims_utils.get_sweep_v_i_t_from_set(data_set, sweep)
sweep_feat = EphysSweepFeatureExtractor(
t, v) # Get time and voltage of each hyperpolarizing sweep
if np.isnan(sweep_feat):
continue
else:
expt_taus.append(sweep_feat.estimate_time_constant(
)) # Append time constant of each sweep to list
mean_expt_tau = np.nanmean(expt_taus) # Mean time constant for this cell
print "mean_ve_tau= " + str(mean_expt_tau)
return mean_expt_tau