def validate_sweeps(data_set, sweep_numbers, extra_dur=0.2):
check_sweeps = data_set.sweep_set(sweep_numbers)
valid_sweep_stim = []
start = None
dur = None
for swp in check_sweeps.sweeps:
swp_start, swp_dur, _, _, _ = stf.get_stim_characteristics(
swp.i, swp.t, False)
if swp_start is None:
valid_sweep_stim.append(False)
else:
start = swp_start
dur = swp_dur
valid_sweep_stim.append(True)
if start is None:
# Could not find any sweeps to define stimulus interval
return [], None, None
end = start + dur
# Check that all sweeps are long enough and not ended early
good_sweep_numbers = [
n for n, s, v in zip(sweep_numbers, check_sweeps.sweeps,
valid_sweep_stim)
if s.t[-1] >= end + extra_dur and v is True and not np.all(
s.v[tsu.find_time_index(s.t, end) -
100:tsu.find_time_index(s.t, end)] == 0)
]
return good_sweep_numbers, start, end
def chirp_amp_phase(v,
i,
t,
start=0.78089,
end=49.21,
down_rate=20000.0,
min_freq=0.1,
max_freq=19.5):
""" Calculate amplitude and phase of chirp responses
Parameters
----------
sweep_set: SweepSet
Set of chirp sweeps
start: float (optional, default 0.6)
Start of chirp stimulus in seconds
end: float (optional, default 20.6)
End of chirp stimulus in seconds
down_rate: int (optional, default 2000)
Sampling rate for downsampling before FFT
min_freq: float (optional, default 0.2)
Minimum frequency for output to contain
max_freq: float (optional, default 40)
Maximum frequency for output to contain
Returns
-------
amplitude: array
Aka resistance
phase: array
Aka reactance
freq: array
Frequencies for amplitude and phase results
"""
ds_v, ds_i, ds_t = v, i, t
start_index = tsu.find_time_index(ds_t, start)
end_index = tsu.find_time_index(ds_t, end)
N = len(ds_v[start_index:end_index])
T = ds_t[1] - ds_t[0]
xf = np.linspace(0.0, 1.0 / (2.0 * T), N // 2)
v_fft = fftpack.fft(ds_v[start_index:end_index])
i_fft = fftpack.fft(ds_i[start_index:end_index])
Z = v_fft / i_fft
R = np.real(Z)
X = np.imag(Z)
resistance = np.abs(Z)[0:N // 2]
reactance = np.arctan(X / R)[0:N // 2]
low_ind = tsu.find_time_index(xf, min_freq)
high_ind = tsu.find_time_index(xf, max_freq)
return resistance[low_ind:high_ind], reactance[low_ind:high_ind], xf[
low_ind:high_ind]
def test_find_time_out_of_bounds():
t = np.array([0, 1, 2])
t_0 = 4
with pytest.raises(AssertionError):
tsu.find_time_index(t, t_0)
def chirp_amp_phase(v,
i,
t,
start=0.78089,
end=49.21,
down_rate=20000.0,
min_freq=0.1,
max_freq=19.5):
""" Calculate amplitude and phase of chirp responses
Parameters
----------
sweep_set: SweepSet
Set of chirp sweeps
start: float (optional, default 0.6)
Start of chirp stimulus in seconds
end: float (optional, default 20.6)
End of chirp stimulus in seconds
down_rate: int (optional, default 2000)
Sampling rate for downsampling before FFT
min_freq: float (optional, default 0.2)
Minimum frequency for output to contain
max_freq: float (optional, default 40)
Maximum frequency for output to contain
Returns
-------
amplitude: array
Aka resistance
phase: array
Aka reactance
freq: array
Frequencies for amplitude and phase results
"""
v_list = v
i_list = i
avg_v = np.vstack(v_list).mean(axis=0)
avg_i = np.vstack(i_list).mean(axis=0)
#plt.plot(t, avg_v)
#
#plt.plot(t, avg_i)
current_rate = np.rint(1 / (t[1] - t[0]))
if current_rate > down_rate:
width = int(current_rate / down_rate)
ds_v = ds_v = fv._subsample_average(avg_v, width)
ds_i = fv._subsample_average(avg_i, width)
ds_t = t[::width]
else:
ds_v = avg_v
ds_i = avg_i
ds_t = t
start_index = tsu.find_time_index(ds_t, start)
end_index = tsu.find_time_index(ds_t, end)
N = len(ds_v[start_index:end_index])
T = ds_t[1] - ds_t[0]
xf = np.linspace(0.0, 1.0 / (2.0 * T), N // 2)
v_fft = fftpack.fft(ds_v[start_index:end_index])
i_fft = fftpack.fft(ds_i[start_index:end_index])
Z = v_fft / i_fft
R = np.real(Z)
X = np.imag(Z)
resistance = np.abs(Z)[0:N // 2]
reactance = np.arctan(X / R)[0:N // 2]
low_ind = tsu.find_time_index(xf, min_freq)
high_ind = tsu.find_time_index(xf, max_freq)
v2 = R[0:N // 2]
return resistance[low_ind:high_ind], reactance[low_ind:high_ind], xf[
low_ind:high_ind], v2[low_ind:high_ind]
def extract_features(data_set, ramp_sweep_numbers, ssq_sweep_numbers, lsq_sweep_numbers,
amp_interval=20, max_above_rheo=100):
features = {}
# RAMP FEATURES -----------------
if len(ramp_sweep_numbers) > 0:
ramp_sweeps = data_set.sweep_set(ramp_sweep_numbers)
ramp_start, ramp_dur, _, _, _ = stf.get_stim_characteristics(ramp_sweeps.sweeps[0].i, ramp_sweeps.sweeps[0].t)
ramp_spx, ramp_spfx = dsf.extractors_for_sweeps(ramp_sweeps,
start = ramp_start,
**dsf.detection_parameters(data_set.RAMP))
ramp_an = spa.RampAnalysis(ramp_spx, ramp_spfx)
basic_ramp_features = ramp_an.analyze(ramp_sweeps)
first_spike_ramp_features = first_spike_ramp(ramp_an)
features.update(first_spike_ramp_features)
# SHORT SQUARE FEATURES -----------------
if len(ssq_sweep_numbers) > 0:
ssq_sweeps = data_set.sweep_set(ssq_sweep_numbers)
ssq_start, ssq_dur, _, _, _ = stf.get_stim_characteristics(ssq_sweeps.sweeps[0].i, ssq_sweeps.sweeps[0].t)
ssq_spx, ssq_spfx = dsf.extractors_for_sweeps(ssq_sweeps,
est_window = [ssq_start, ssq_start+0.001],
**dsf.detection_parameters(data_set.SHORT_SQUARE))
ssq_an = spa.ShortSquareAnalysis(ssq_spx, ssq_spfx)
basic_ssq_features = ssq_an.analyze(ssq_sweeps)
first_spike_ssq_features = first_spike_ssq(ssq_an)
first_spike_ssq_features["short_square_current"] = basic_ssq_features["stimulus_amplitude"]
features.update(first_spike_ssq_features)
# LONG SQUARE SUBTHRESHOLD FEATURES -----------------
if len(lsq_sweep_numbers) > 0:
check_lsq_sweeps = data_set.sweep_set(lsq_sweep_numbers)
lsq_start, lsq_dur, _, _, _ = stf.get_stim_characteristics(check_lsq_sweeps.sweeps[0].i, check_lsq_sweeps.sweeps[0].t)
# Check that all sweeps are long enough and not ended early
extra_dur = 0.2
good_lsq_sweep_numbers = [n for n, s in zip(lsq_sweep_numbers, check_lsq_sweeps.sweeps)
if s.t[-1] >= lsq_start + lsq_dur + extra_dur and not np.all(s.v[tsu.find_time_index(s.t, lsq_start + lsq_dur)-100:tsu.find_time_index(s.t, lsq_start + lsq_dur)] == 0)]
lsq_sweeps = data_set.sweep_set(good_lsq_sweep_numbers)
lsq_spx, lsq_spfx = dsf.extractors_for_sweeps(lsq_sweeps,
start = lsq_start,
end = lsq_start + lsq_dur,
**dsf.detection_parameters(data_set.LONG_SQUARE))
lsq_an = spa.LongSquareAnalysis(lsq_spx, lsq_spfx, subthresh_min_amp=-100.)
basic_lsq_features = lsq_an.analyze(lsq_sweeps)
features.update({
"input_resistance": basic_lsq_features["input_resistance"],
"tau": basic_lsq_features["tau"],
"v_baseline": basic_lsq_features["v_baseline"],
"sag_nearest_minus_100": basic_lsq_features["sag"],
"sag_measured_at": basic_lsq_features["vm_for_sag"],
"rheobase_i": int(basic_lsq_features["rheobase_i"]),
"fi_linear_fit_slope": basic_lsq_features["fi_fit_slope"],
})
# TODO (maybe): port sag_from_ri code over
# Identify suprathreshold set for analysis
sweep_table = basic_lsq_features["spiking_sweeps"]
mask_supra = sweep_table["stim_amp"] >= basic_lsq_features["rheobase_i"]
sweep_indexes = fv._consolidated_long_square_indexes(sweep_table.loc[mask_supra, :])
amps = np.rint(sweep_table.loc[sweep_indexes, "stim_amp"].values - basic_lsq_features["rheobase_i"])
spike_data = np.array(basic_lsq_features["spikes_set"])
for amp, swp_ind in zip(amps, sweep_indexes):
if (amp % amp_interval != 0) or (amp > max_above_rheo) or (amp < 0):
continue
amp_label = int(amp / amp_interval)
first_spike_lsq_sweep_features = first_spike_lsq(spike_data[swp_ind])
features.update({"ap_1_{:s}_{:d}_long_square".format(f, amp_label): v
for f, v in first_spike_lsq_sweep_features.items()})
mean_spike_lsq_sweep_features = mean_spike_lsq(spike_data[swp_ind])
features.update({"ap_mean_{:s}_{:d}_long_square".format(f, amp_label): v
for f, v in mean_spike_lsq_sweep_features.items()})
sweep_feature_list = [
"first_isi",
"avg_rate",
"isi_cv",
"latency",
"median_isi",
"adapt",
]
features.update({"{:s}_{:d}_long_square".format(f, amp_label): sweep_table.at[swp_ind, f]
for f in sweep_feature_list})
features["stimulus_amplitude_{:d}_long_square".format(amp_label)] = int(amp + basic_lsq_features["rheobase_i"])
rates = sweep_table.loc[sweep_indexes, "avg_rate"].values
features.update(fi_curve_fit(amps, rates))
return features