def format_trace(trace, baseline_win, x_offset=1e-3, align='spike'):
# align can be to the pre-synaptic spike (default) or the onset of the PSP ('psp')
baseline = float_mode(trace.time_slice(baseline_win[0],baseline_win[1]).data)
trace = TSeries(data=(trace.data-baseline), sample_rate=db.default_sample_rate)
if align == 'psp':
trace.t0 = x_offset
return trace
def create_test_pulse(start=5 * ms,
pdur=10 * ms,
pamp=-10 * pA,
mode='ic',
dt=10 * us,
r_access=10 * MOhm,
c_soma=5 * pF,
noise=5 * pA):
# update patch pipette access resistance
model_cell.clamp.ra = r_access
# update noise amplitude
model_cell.mechs['noise'].stdev = noise
# make pulse array
duration = start + pdur * 3
pulse = np.zeros(int(duration / dt))
pstart = int(start / dt)
pstop = pstart + int(pdur / dt)
pulse[pstart:pstop] = pamp
# simulate response
result = model_cell.test(TSeries(pulse, dt), mode)
# generate a PatchClampTestPulse to test against
tp = PatchClampTestPulse(result)
return tp
def baseline_tseries(self):
bl = self.baseline
if bl is None:
return None
return TSeries(bl.data,
sample_rate=default_sample_rate,
t0=bl.data_start_time)
def simulate_response(fg_recs, bg_results, amp, rtime, seed=None):
if seed is not None:
np.random.seed(seed)
dt = 1.0 / db.default_sample_rate
t = np.arange(0, 15e-3, dt)
template = Psp.psp_func(t, xoffset=0, yoffset=0, rise_time=rtime, decay_tau=15e-3, amp=1, rise_power=2)
r_amps = scipy.stats.binom.rvs(p=0.2, n=24, size=len(fg_recs)) * scipy.stats.norm.rvs(scale=0.3, loc=1, size=len(fg_recs))
r_amps *= amp / r_amps.mean()
r_latency = np.random.normal(size=len(fg_recs), scale=200e-6, loc=13e-3)
fg_results = []
traces = []
fg_recs = [RecordWrapper(rec) for rec in fg_recs] # can't modify fg_recs, so we wrap records with a mutable shell
for k,rec in enumerate(fg_recs):
rec.data = rec.data.copy()
start = int(r_latency[k] * db.default_sample_rate)
length = len(rec.data) - start
rec.data[start:] += template[:length] * r_amps[k]
fg_result = analyze_response_strength(rec, 'baseline')
fg_results.append(fg_result)
traces.append(TSeries(rec.data, sample_rate=db.default_sample_rate))
traces[-1].amp = r_amps[k]
fg_results = str_analysis_result_table(fg_results, fg_recs)
conn_result = analyze_pair_connectivity({('ic', 'fg'): fg_results, ('ic', 'bg'): bg_results, ('vc', 'fg'): [], ('vc', 'bg'): []}, sign=1)
return conn_result, traces
def plot_all(self):
self.plots.clear()
self.plots.set_shape(len(self.sorted_recs), 1)
psp = StackedPsp()
stim_keys = sorted(list(self.sorted_recs.keys()))
for i, stim_key in enumerate(stim_keys):
prs = self.sorted_recs[stim_key]
plt = self.plots[i, 0]
plt.setTitle("%s %0.0f Hz %0.2f s" % stim_key)
for recording in prs:
pulses = sorted(list(prs[recording].keys()))
for pulse_n in pulses:
rec = prs[recording][pulse_n]
# spike-align pulse + offset for pulse number
spike_t = rec.stim_pulse.first_spike_time
if spike_t is None:
spike_t = rec.stim_pulse.onset_time + 1e-3
qc_pass = rec.pulse_response.in_qc_pass if rec.synapse.synapse_type == 'in' else rec.pulse_response.ex_qc_pass
pen = (255, 255, 255, 100) if qc_pass else (100, 0, 0, 100)
t0 = rec.pulse_response.data_start_time - spike_t
ts = TSeries(data=rec.data,
t0=t0,
sample_rate=db.default_sample_rate)
c = plt.plot(ts.time_values, ts.data, pen=pen)
# arrange plots nicely
shift = (pulse_n * 35e-3 + (30e-3 if pulse_n > 8 else 0),
0)
c.setPos(*shift)
if not qc_pass:
c.setZValue(-10)
continue
# evaluate recorded fit for this response
fit_par = rec.pulse_response_fit
if fit_par.fit_amp is None:
continue
fit = psp.eval(
x=ts.time_values,
exp_amp=fit_par.fit_exp_amp,
exp_tau=fit_par.fit_decay_tau,
amp=fit_par.fit_amp,
rise_time=fit_par.fit_rise_time,
decay_tau=fit_par.fit_decay_tau,
xoffset=fit_par.fit_latency,
yoffset=fit_par.fit_yoffset,
rise_power=2,
)
c = plt.plot(ts.time_values, fit, pen=(0, 255, 0, 100))
c.setZValue(10)
c.setPos(*shift)
def format_responses(responses):
n_trials = len(responses['data'])
response = {}
if n_trials != 0:
for trial in range(n_trials):
stim_params = responses['stim_param'][trial]
if stim_params not in response:
response[stim_params] = []
response[stim_params].append(
TSeries(data=responses['data'][trial],
dt=responses['dt'][trial],
stim_param=[responses['stim_param'][trial]]))
return response
def test_threshold_events():
empty_result = np.array([], dtype=dtype)
d = TSeries(np.zeros(10), dt=0.1)
check_events(threshold_events(d, 1), empty_result)
check_events(threshold_events(d, 0), empty_result)
d.data[5:7] = 6
ev = threshold_events(d, 1)
expected = np.array([(5, 2, 12., 6., 5, 0.5, 0.2, 0.6, 0.5)], dtype=dtype)
check_events(threshold_events(d, 1), expected)
d.data[2:4] = -6
expected = np.array([
(2, 2, -12., -6., 2, 0.2, 0.2, -0.6, 0.2),
(5, 2, 12., 6., 5, 0.5, 0.2, 0.6, 0.5)],
dtype=dtype
)
check_events(threshold_events(d, 1), expected)
# data ends above threshold
d.data[:] = 0
d.data[5:] = 6
check_events(threshold_events(d, 1), empty_result)
expected = np.array([(5, 5, 30., 6., 5, 0.5, 0.5, 2.4, 0.5)], dtype=dtype)
check_events(threshold_events(d, 1, omit_ends=False), expected)
# data begins above threshold
d.data[:] = 6
d.data[5:] = 0
check_events(threshold_events(d, 1), empty_result)
expected = np.array([(0, 5, 30., 6., 0, 0., 0.5, 2.4, 0.)], dtype=dtype)
check_events(threshold_events(d, 1, omit_ends=False), expected)
# all points above threshold
d.data[:] = 6
check_events(threshold_events(d, 1), empty_result)
expected = np.array([(0, 10, 60., 6., 0, 0., 1., 5.4, 0.)], dtype=dtype)
check_events(threshold_events(d, 1, omit_ends=False), expected)
def test_exp_deconv_psp_params():
from neuroanalysis.event_detection import exp_deconvolve, exp_deconv_psp_params
from neuroanalysis.data import TSeries
from neuroanalysis.fitting import Psp
x = np.linspace(0, 0.02, 10000)
amp = 1
rise_time = 4e-3
decay_tau = 10e-3
rise_power = 2
# Make a PSP waveform
psp = Psp()
y = psp.eval(x=x,
xoffset=0,
yoffset=0,
amp=amp,
rise_time=rise_time,
decay_tau=decay_tau,
rise_power=rise_power)
# exponential deconvolution
y_ts = TSeries(y, time_values=x)
y_deconv = exp_deconvolve(y_ts, decay_tau).data
# show that we can get approximately the same result using exp_deconv_psp_params
d_amp, d_rise_time, d_rise_power, d_decay_tau = exp_deconv_psp_params(
amp, rise_time, rise_power, decay_tau)
y2 = psp.eval(x=x,
xoffset=0,
yoffset=0,
amp=d_amp,
rise_time=d_rise_time,
decay_tau=d_decay_tau,
rise_power=d_rise_power)
assert np.allclose(y_deconv, y2[1:], atol=0.02)
def load_next():
global all_pulses, ui, last_result
try:
(expt_id, cell_id, sweep, channel, chunk) = next(all_pulses)
except StopIteration:
ui.widget.hide()
return
# run spike detection on each chunk
pulse_edges = chunk.meta['pulse_edges']
spikes = detect_evoked_spikes(chunk, pulse_edges, ui=ui)
ui.show_result(spikes)
# copy just the necessary parts of recording data for export to file
export_chunk = PatchClampRecording(
channels={
k: TSeries(chunk[k].data,
t0=chunk[k].t0,
sample_rate=chunk[k].sample_rate)
for k in chunk.channels
})
export_chunk.meta.update(chunk.meta)
# construct test case
tc = SpikeDetectTestCase()
tc._meta = {
'expt_id': expt_id,
'cell_id': cell_id,
'device_id': channel,
'sweep_id': sweep.key,
}
tc._input_args = {
'data': export_chunk,
'pulse_edges': chunk.meta['pulse_edges'],
}
last_result = tc
def recorded_tseries(self):
if self._rec_tseries is None:
self._rec_tseries = TSeries(self.data,
sample_rate=default_sample_rate,
t0=self.data_start_time)
return self._rec_tseries
on_times = np.argwhere(diff > 0)[:, 0]
off_times = np.argwhere(diff < 0)[:, 0]
# decide on the region of the trace to focus on
start = on_times[1] - 1000
stop = off_times[8] + 1000
chunk = trace[start:stop]
# plot the selected chunk
t = np.arange(chunk.shape[0]) * dt
plot.plot(t[:-1], np.diff(ndi.gaussian_filter(chunk, sigma)), pen=0.5)
plot.plot(t, chunk)
# detect spike times
peak_inds = []
rise_inds = []
for j in range(8): # loop over pulses
pstart = on_times[j + 1] - start
pstop = off_times[j + 1] - start
spike_info = detect_vc_evoked_spike(TSeries(chunk, dt=dt),
pulse_edges=(pstart, pstop))
if spike_info is not None:
peak_inds.append(spike_info['peak_index'])
rise_inds.append(spike_info['rise_index'])
# display spike rise and peak times as ticks
pticks = pg.VTickGroup(np.array(peak_inds) * dt, yrange=[0, 0.3], pen='r')
rticks = pg.VTickGroup(np.array(rise_inds) * dt, yrange=[0, 0.3], pen='y')
plot.addItem(pticks)
plot.addItem(rticks)
def analyze_pair_connectivity(amps, sign=None):
"""Given response strength records for a single pair, generate summary
statistics characterizing strength, latency, and connectivity.
Parameters
----------
amps : dict
Contains foreground and background strength analysis records
(see input format below)
sign : None, -1, or +1
If None, then automatically determine whether to treat this connection as
inhibitory or excitatory.
Input must have the following structure::
amps = {
('ic'): recs,
('vc'): recs,
}
Where each *recs* must be a structured array containing fields as returned
by get_amps().
The overall strategy here is:
1. Make an initial decision on whether to treat this pair as excitatory or
inhibitory, based on differences between foreground and background amplitude
measurements
2. Generate mean and stdev for amplitudes, deconvolved amplitudes, and deconvolved
latencies
3. Generate KS test p values describing the differences between foreground
and background distributions for amplitude, deconvolved amplitude, and
deconvolved latency
"""
# Filter by QC
for k, v in amps.items():
mask = v['qc_pass'].astype(bool)
amps[k] = v[mask]
# See if any data remains
if all([len(a) == 0 for a in amps]):
return None
requested_sign = sign
fields = {} # used to fill the new DB record
# Use KS p value to check for differences between foreground and background
qc_amps = {}
ks_pvals = {}
amp_means = {}
amp_diffs = {}
for clamp_mode in ('ic', 'vc'):
clamp_mode_amps = amps[clamp_mode]
if len(clamp_mode_amps) == 0:
continue
for sign in ('pos', 'neg'):
# Separate into positive/negative tests and filter out responses that failed qc
qc_field = {
'vc': {
'pos': 'in_qc_pass',
'neg': 'ex_qc_pass'
},
'ic': {
'pos': 'ex_qc_pass',
'neg': 'in_qc_pass'
}
}[clamp_mode][sign]
fg = clamp_mode_amps[clamp_mode_amps[qc_field]]
qc_amps[sign, clamp_mode] = fg
if len(fg) == 0:
continue
# Measure some statistics from these records
bg = fg['baseline_' + sign + '_dec_amp']
fg = fg[sign + '_dec_amp']
pval = scipy.stats.ks_2samp(fg, bg).pvalue
ks_pvals[(sign, clamp_mode)] = pval
# we could ensure that the average amplitude is in the right direction:
fg_mean = np.mean(fg)
bg_mean = np.mean(bg)
amp_means[sign, clamp_mode] = {'fg': fg_mean, 'bg': bg_mean}
amp_diffs[sign, clamp_mode] = fg_mean - bg_mean
if requested_sign is None:
# Decide whether to treat this connection as excitatory or inhibitory.
# strategy: accumulate evidence for either possibility by checking
# the ks p-values for each sign/clamp mode and the direction of the deflection
is_exc = 0
# print(expt.acq_timestamp, pair.pre_cell.ext_id, pair.post_cell.ext_id)
for sign in ('pos', 'neg'):
for mode in ('ic', 'vc'):
ks = ks_pvals.get((sign, mode), None)
if ks is None:
continue
# turn p value into a reasonable scale factor
ks = norm_pvalue(ks)
dif_sign = 1 if amp_diffs[sign, mode] > 0 else -1
if mode == 'vc':
dif_sign *= -1
is_exc += dif_sign * ks
# print(" ", sign, mode, is_exc, dif_sign * ks)
else:
is_exc = requested_sign
if is_exc > 0:
fields['synapse_type'] = 'ex'
signs = {'ic': 'pos', 'vc': 'neg'}
else:
fields['synapse_type'] = 'in'
signs = {'ic': 'neg', 'vc': 'pos'}
# compute the rest of statistics for only positive or negative deflections
for clamp_mode in ('ic', 'vc'):
sign = signs[clamp_mode]
fg = qc_amps.get((sign, clamp_mode))
if fg is None or len(fg) == 0:
fields[clamp_mode + '_n_samples'] = 0
continue
fields[clamp_mode + '_n_samples'] = len(fg)
fields[clamp_mode + '_crosstalk_mean'] = np.mean(fg['crosstalk'])
fields[clamp_mode + '_base_crosstalk_mean'] = np.mean(
fg['baseline_crosstalk'])
# measure mean, stdev, and statistical differences between
# fg and bg for each measurement
for val, field in [('amp', 'amp'), ('deconv_amp', 'dec_amp'),
('latency', 'dec_latency')]:
f = fg[sign + '_' + field]
b = fg['baseline_' + sign + '_' + field]
fields[clamp_mode + '_' + val + '_mean'] = np.mean(f)
fields[clamp_mode + '_' + val + '_stdev'] = np.std(f)
fields[clamp_mode + '_base_' + val + '_mean'] = np.mean(b)
fields[clamp_mode + '_base_' + val + '_stdev'] = np.std(b)
# statistical tests comparing fg vs bg
# Note: we use log(1-log(pval)) because it's nicer to plot and easier to
# use as a classifier input
tt_pval = scipy.stats.ttest_ind(f, b, equal_var=False).pvalue
ks_pval = scipy.stats.ks_2samp(f, b).pvalue
fields[clamp_mode + '_' + val + '_ttest'] = norm_pvalue(tt_pval)
fields[clamp_mode + '_' + val + '_ks2samp'] = norm_pvalue(ks_pval)
### generate the average response and psp fit
# collect all bg and fg traces
fg_traces = TSeriesList()
for rec in fg:
if not np.isfinite(
rec['max_slope_time']) or rec['max_slope_time'] is None:
continue
t0 = rec['response_start_time'] - rec[
'max_slope_time'] # time-align to presynaptic spike
trace = TSeries(rec['data'],
sample_rate=db.default_sample_rate,
t0=t0)
fg_traces.append(trace)
# get averages
if len(fg_traces) == 0:
continue
# bg_avg = bg_traces.mean()
fg_avg = fg_traces.mean()
base_rgn = fg_avg.time_slice(-6e-3, 0)
base = float_mode(base_rgn.data)
fields[clamp_mode + '_average_response'] = fg_avg.data
fields[clamp_mode + '_average_response_t0'] = fg_avg.t0
fields[clamp_mode + '_average_base_stdev'] = base_rgn.std()
sign = {'pos': 1, 'neg': -1}[signs[clamp_mode]]
fg_bsub = fg_avg.copy(data=fg_avg.data -
base) # remove base to help fitting
try:
fit = fit_psp(fg_bsub,
clamp_mode=clamp_mode,
sign=sign,
search_window=[0, 6e-3])
for param, val in fit.best_values.items():
fields['%s_fit_%s' % (clamp_mode, param)] = val
fields[clamp_mode +
'_fit_yoffset'] = fit.best_values['yoffset'] + base
fields[clamp_mode + '_fit_nrmse'] = fit.nrmse()
except:
print("Error in PSP fit:")
sys.excepthook(*sys.exc_info())
continue
#global fit_plot
#if fit_plot is None:
#fit_plot = FitExplorer(fit)
#fit_plot.show()
#else:
#fit_plot.set_fit(fit)
#raw_input("Waiting to continue..")
return fields
def test_trace_timing():
# Make sure sample timing is handled exactly--need to avoid fp error here
a = np.random.normal(size=300)
sr = 50000
dt = 2e-5
t = np.arange(len(a)) * dt
# trace with no timing information
tr = TSeries(a)
assert not tr.has_timing
assert not tr.has_time_values
with raises(TypeError):
tr.dt
with raises(TypeError):
tr.sample_rate
with raises(TypeError):
tr.time_values
with raises(TypeError):
tr.time_at(0)
with raises(TypeError):
tr.index_at(0.1)
with raises(TypeError):
tr.value_at(0.1)
view = tr[100:200]
assert not tr.has_timing
assert not tr.has_time_values
# invalid data
with raises(ValueError):
TSeries(data=np.zeros((10, 10)))
# invalid timing information
with raises(TypeError):
TSeries(data=a, dt=dt, time_values=t)
with raises(TypeError):
TSeries(data=a, sample_rate=sr, time_values=t)
with raises(TypeError):
TSeries(data=a, dt=dt, t0=0, time_values=t)
with raises(TypeError):
TSeries(data=a, dt=dt, t0=0, sample_rate=sr)
with raises(ValueError):
TSeries(data=a, time_values=t[:-1])
# trace with only dt
tr = TSeries(a, dt=dt)
assert tr.dt == dt
assert np.allclose(tr.sample_rate, sr)
check_trace(tr, data=a, time_values=t, has_timing=True, has_time_values=False, regularly_sampled=True)
# trace with only sample_rate
tr = TSeries(a, sample_rate=sr)
assert tr.dt == dt
assert tr.sample_rate == sr
assert np.all(tr.time_values == t)
check_trace(tr, data=a, time_values=t, has_timing=True, has_time_values=False, regularly_sampled=True)
# trace with only regularly-sampled time_values
tr = TSeries(a, time_values=t)
assert tr.dt == dt
assert np.allclose(tr.sample_rate, sr)
assert np.all(tr.time_values == t)
check_trace(tr, data=a, time_values=t, has_timing=True, has_time_values=True, regularly_sampled=True)
# trace with irregularly-sampled time values
t1 = np.cumsum(np.random.normal(loc=1, scale=0.02, size=a.shape))
tr = TSeries(a, time_values=t1)
assert tr.dt == t1[1] - t1[0]
assert np.all(tr.time_values == t1)
check_trace(tr, data=a, time_values=t1, has_timing=True, has_time_values=True, regularly_sampled=False)
def extract_first_pulse_info_from_Pair_object(pair, desired_clamp='ic'):
"""Extract first pulse responses and relevant information
from entry in the pair database. Screen out pulses that are
not current clamp or do not pass the corresponding
inhibitory or excitatory qc.
Input
-----
pair: aisynphys.database.database.Pair object
desired_clamp: string
Specifies whether current or voltage clamp sweeps are desired.
Options are:
'ic': current clamp
'vc': voltage clamp
Return
------
pulse_responses: TSeriesList
traces where the start of each trace is 10 ms before the spike
pulse_ids: list of ints
pulse ids of *pulse_responses*
psp_amps_measured: list of floats
amplitude of *pulse_responses* from the *pulse_response* table
stim_freq: list of floats
the stimulation frequency corresponding to the *pulse_responses*
"""
if pair.synapse_prediction is None:
# print ("\t\tSKIPPING: pair_id %s, is not yielding pair.synapse_prediction" % pair.id)
return [], [], [], []
if pair.synapse_prediction.synapse_type is None:
# print ("\t\tSKIPPING: pair_id %s, is not yielding pair.synapse_prediction.synapse_type" % pair.id)
return [], [], [], []
synapse_type = pair.synapse_prediction.synapse_type
pulse_responses = []
psp_amps_measured = []
pulse_ids = []
stim_freqs = []
if len(pair.pulse_responses) == 0:
# print ("\t\tSKIPPING: pair_id %s, no pulse responses in pair table" % (pair.id))
return [], [], [], []
for pr in pair.pulse_responses:
stim_pulse = pr.stim_pulse
n_spikes = stim_pulse.n_spikes
pulse_number = stim_pulse.pulse_number
pulse_id = pr.stim_pulse_id
ex_qc_pass = pr.ex_qc_pass
in_qc_pass = pr.in_qc_pass
pcr = stim_pulse.recording.patch_clamp_recording
stim_freq = pcr.multi_patch_probe.induction_frequency
clamp_mode = pcr.clamp_mode
# current clamp
if clamp_mode != desired_clamp:
continue
# ensure that there was only 1 presynaptic spike
if n_spikes != 1:
continue
# we only want the first pulse of the train
if pulse_number != 1:
continue
data = pr.data
start_time = pr.data_start_time
spike_time = stim_pulse.spikes[0].max_slope_time
if spike_time is None:
continue
data_trace = TSeries(
data=data,
t0=start_time - spike_time + time_before_spike,
sample_rate=db.default_sample_rate).time_slice(
start=0, stop=None) #start of the data is the spike time
# append to output lists if neurons pass qc
if (synapse_type == 'ex'
and ex_qc_pass is True) or (synapse_type == 'in'
and in_qc_pass is True):
pulse_responses.append(data_trace)
pulse_ids.append(pulse_id)
stim_freqs.append(stim_freq)
if synapse_type == 'in' and in_qc_pass is True:
psp_amps_measured.append(pr.pulse_response_strength.neg_amp)
if synapse_type == 'ex' and ex_qc_pass is True:
psp_amps_measured.append(pr.pulse_response_strength.pos_amp)
return pulse_responses, pulse_ids, psp_amps_measured, stim_freq
def fit_single_first_pulse(pr, pair):
#TODO: HAS THE APPROPRIATE QC HAPPENED?
message = None #initialize error message for downstream processing
# excitatory or inhibitory?
excitation = pair.synapse_prediction.synapse_type
if not excitation:
raise Exception('there is no synapse_type in synapse_prediction')
if excitation == 'in':
if not pr.in_qc_pass:
return {'error': 'this pulse does not pass inhibitory qc'}
if excitation == 'ex':
if not pr.ex_qc_pass:
return {'error': 'this pulse does not pass excitatory qc'}
# get response latency from average first pulse table
if not pair.avg_first_pulse_fit:
return {'error': 'no entry in avg_first_pulse_fit table for this pair'}
if pr.clamp_mode == 'vc':
weight_i = np.array([0])
latency_i = None
amp_i = None
rise_time_i = None
decay_tau_i = None
data_waveform_i = np.array([0])
fit_waveform_i = np.array([0])
dt_i = None
nrmse_i = None
if pair.avg_first_pulse_fit.vc_latency:
data_trace = TSeries(
data=pr.data,
t0=pr.response_start_time - pr.spike_time + time_before_spike,
sample_rate=db.default_sample_rate).time_slice(start=0,
stop=None)
xoffset = pair.avg_first_pulse_fit.vc_latency
# weight and fit the trace
weight_v = np.ones(len(
data_trace.data)) * 10. #set everything to ten initially
weight_v[int((time_before_spike + .0001 + xoffset) /
data_trace.dt):int(
(time_before_spike + .0001 + xoffset + 4e-3) /
data_trace.dt)] = 30. #area around steep PSP rise
fit_v = fit_trace(data_trace,
excitation=excitation,
clamp_mode='vc',
weight=weight_v,
latency=xoffset,
latency_jitter=.5e-3)
latency_v = fit_v.best_values['xoffset'] - time_before_spike
amp_v = fit_v.best_values['amp']
rise_time_v = fit_v.best_values['rise_time']
decay_tau_v = fit_v.best_values['decay_tau']
data_waveform_v = data_trace.data
fit_waveform_v = fit_v.best_fit
dt_v = data_trace.dt
nrmse_v = fit_v.nrmse()
else:
return {
'error':
'no vc_latency available from avg_first_pulse_fit table'
} #no row will be made in the table because the error message is not none
elif pr.clamp_mode == 'ic':
# set voltage to none since this is current clamp
weight_v = np.array([0])
latency_v = None
amp_v = None
rise_time_v = None
decay_tau_v = None
data_waveform_v = np.array([0])
fit_waveform_v = np.array([0])
dt_v = None
nrmse_v = None
if pair.avg_first_pulse_fit.ic_latency:
data_trace = TSeries(
data=pr.data,
t0=pr.response_start_time - pr.spike_time + time_before_spike,
sample_rate=db.default_sample_rate).time_slice(
start=0, stop=None
) #TODO: annoys me that this is repetitive in vc code above.
xoffset = pair.avg_first_pulse_fit.ic_latency
# weight and fit the trace
weight_i = np.ones(len(
data_trace.data)) * 10. #set everything to ten initially
weight_i[int((time_before_spike - 3e-3) / data_trace.dt):int(
time_before_spike / data_trace.dt
)] = 0. #area around stim artifact note that since this is spike aligned there will be some blur in where the cross talk is
weight_i[int((time_before_spike + .0001 + xoffset) /
data_trace.dt):int(
(time_before_spike + .0001 + xoffset + 4e-3) /
data_trace.dt)] = 30. #area around steep PSP rise
fit_i = fit_trace(data_trace,
excitation=excitation,
weight=weight_i,
latency=xoffset,
latency_jitter=.5e-3)
latency_i = fit_i.best_values['xoffset'] - time_before_spike
amp_i = fit_i.best_values['amp']
rise_time_i = fit_i.best_values['rise_time']
decay_tau_i = fit_i.best_values['decay_tau']
data_waveform_i = data_trace.data
fit_waveform_i = fit_i.best_fit
dt_i = data_trace.dt
nrmse_i = fit_i.nrmse()
else:
return {
'error':
'no ic_latency available from avg_first_pulse_fit table'
} #no row will be made in the table because the error message is not none
else:
raise Exception('There is no clamp mode associated with this pulse')
#------------ done with fitting section ------------------------------
# dictionary for ease of translation into the output table
out_dict = {
'ic_amp': amp_i,
'ic_latency': latency_i,
'ic_rise_time': rise_time_i,
'ic_decay_tau': decay_tau_i,
'ic_psp_data': data_waveform_i,
'ic_psp_fit': fit_waveform_i,
'ic_dt': dt_i,
'ic_nrmse': nrmse_i,
'vc_amp': amp_v,
'vc_latency': latency_v,
'vc_rise_time': rise_time_v,
'vc_decay_tau': decay_tau_v,
'vc_psp_data': data_waveform_v,
'vc_psp_fit': fit_waveform_v,
'vc_dt': dt_v,
'vc_nrmse': nrmse_v,
'error': message
}
return out_dict
def filter_pulse_responses(pair):
### get first pulse response if it passes qc for excitatory or inhibitory analysis
# TODO: learn how to do what's below in one query
# s = db.session()
# q = s.query(db.PulseResponse.data, db.StimSpike, db.PatchClampRecording)
# q = q.join(db.StimPulse).join(db.StimSpike).join(db.PatchClampRecording)
# filters = [
# (db.Pair == pair)
# (db.StimPulse.pulse_number == 1),
# (db.StimPulse.n_spikes == 1),
# (db.StimSpike.max_dvdt_time != None),
# (db.PulseResponse.ex_qc_pass == True)
# (db.PatchClampRecording.clamp_mode == 'ic')
# ]
#
# for filter_arg in filters:
# q = q.filter(*filter_arg)
synapse_type = pair.synapse_prediction.synapse_type
pulse_responses = []
pulse_response_amps = []
pulse_ids = []
for pr in pair.pulse_responses:
stim_pulse = pr.stim_pulse
n_spikes = stim_pulse.n_spikes
pulse_number = stim_pulse.pulse_number
pulse_id = pr.stim_pulse_id
ex_qc_pass = pr.ex_qc_pass
in_qc_pass = pr.in_qc_pass
pcr = stim_pulse.recording.patch_clamp_recording
stim_freq = pcr.multi_patch_probe[0].induction_frequency
clamp_mode = pcr.clamp_mode
# current clamp
if clamp_mode != 'ic':
continue
# ensure that there was only 1 presynaptic spike
if n_spikes != 1:
continue
# we only want the first pulse of the train
if pulse_number != 1:
continue
# only include frequencies up to 50Hz
if stim_freq > 50:
continue
data = pr.data
start_time = pr.start_time
spike_time = stim_pulse.spikes[0].max_dvdt_time
data_trace = TSeries(data=data,
t0=start_time - spike_time,
sample_rate=db.default_sample_rate)
if synapse_type == 'ex' and ex_qc_pass is True:
pulse_responses.append(data_trace)
pulse_ids.append(pulse_id)
pulse_response_amps.append(pr.pulse_response_strength.pos_amp)
if synapse_type == 'in' and in_qc_pass is True:
pulse_responses.append(data_trace)
pulse_ids.append(pulse_id)
pulse_response_amps.append(pr.pulse_response_strength.neg_amp)
return pulse_responses, pulse_ids, pulse_response_amps
def plot_element_data(self, pre_class, post_class, element, field_name, color='g', trace_plt=None):
val = element[field_name].mean()
line = pg.InfiniteLine(val, pen={'color': color, 'width': 2}, movable=False)
scatter = None
baseline_window = int(db.default_sample_rate * 5e-3)
values = []
tracesA = []
tracesB = []
point_data = []
for pair, value in element[field_name].iteritems():
latency = self.results.loc[pair]['Latency']
trace_itemA = None
trace_itemB = None
if pair.has_synapse is not True:
continue
if np.isnan(value):
continue
syn_typ = pair.synapse.synapse_type
rsf = pair.resting_state_fit
if rsf is not None:
nrmse = rsf.vc_nrmse if field_name.startswith('PSC') else rsf.ic_nrmse
# if nrmse is None or nrmse > 0.8:
# continue
data = rsf.vc_avg_data if field_name.startswith('PSC') else rsf.ic_avg_data
traceA = TSeries(data=data, sample_rate=db.default_sample_rate)
if field_name.startswith('PSC'):
traceA = bessel_filter(traceA, 5000, btype='low', bidir=True)
bessel_filter(traceA, 5000, btype='low', bidir=True)
start_time = rsf.vc_avg_data_start_time if field_name.startswith('PSC') else rsf.ic_avg_data_start_time
if latency is not None and start_time is not None:
if field_name == 'Latency':
xoffset = start_time + latency
else:
xoffset = start_time - latency
baseline_window = [abs(xoffset)-1e-3, abs(xoffset)]
traceA = format_trace(traceA, baseline_window, x_offset=xoffset, align='psp')
trace_itemA = trace_plt[1].plot(traceA.time_values, traceA.data)
trace_itemA.pair = pair
trace_itemA.curve.setClickable(True)
trace_itemA.sigClicked.connect(self.trace_plot_clicked)
tracesA.append(traceA)
if field_name == 'Latency' and rsf.vc_nrmse is not None: #and rsf.vc_nrmse < 0.8:
traceB = TSeries(data=rsf.vc_avg_data, sample_rate=db.default_sample_rate)
traceB = bessel_filter(traceB, 5000, btype='low', bidir=True)
start_time = rsf.vc_avg_data_start_time
if latency is not None and start_time is not None:
xoffset = start_time + latency
baseline_window = [abs(xoffset)-1e-3, abs(xoffset)]
traceB = format_trace(traceB, baseline_window, x_offset=xoffset, align='psp')
trace_itemB = trace_plt[0].plot(traceB.time_values, traceB.data)
trace_itemB.pair = pair
trace_itemB.curve.setClickable(True)
trace_itemB.sigClicked.connect(self.trace_plot_clicked)
tracesB.append(traceB)
self.pair_items[pair.id] = [trace_itemA, trace_itemB]
if trace_itemA is not None:
values.append(value)
point_data.append(pair)
y_values = pg.pseudoScatter(np.asarray(values, dtype=float), spacing=1)
scatter = pg.ScatterPlotItem(symbol='o', brush=(color + (150,)), pen='w', size=12)
scatter.setData(values, y_values + 10., data=point_data)
for point in scatter.points():
pair_id = point.data().id
self.pair_items[pair_id].extend([point, color])
scatter.sigClicked.connect(self.scatter_plot_clicked)
if len(tracesA) > 0:
if field_name == 'Latency':
spike_line = pg.InfiniteLine(0, pen={'color': 'w', 'width': 1, 'style': pg.QtCore.Qt.DotLine}, movable=False)
trace_plt[0].addItem(spike_line)
x_label = 'Time from presynaptic spike'
else:
x_label = 'Response Onset'
grand_trace = TSeriesList(tracesA).mean()
name = ('%s->%s, n=%d' % (pre_class, post_class, len(tracesA)))
trace_plt[1].plot(grand_trace.time_values, grand_trace.data, pen={'color': color, 'width': 3}, name=name)
units = 'A' if field_name.startswith('PSC') else 'V'
title = 'Voltage Clamp' if field_name.startswith('PSC') else 'Current Clamp'
trace_plt[1].setXRange(-5e-3, 20e-3)
trace_plt[1].setLabels(left=('', units), bottom=(x_label, 's'))
trace_plt[1].setTitle(title)
if len(tracesB) > 0:
trace_plt[1].setLabels(right=('', units))
trace_plt[1].hideAxis('left')
spike_line = pg.InfiniteLine(0, pen={'color': 'w', 'width': 1, 'style': pg.QtCore.Qt.DotLine}, movable=False)
trace_plt[0].addItem(spike_line)
grand_trace = TSeriesList(tracesB).mean()
trace_plt[0].plot(grand_trace.time_values, grand_trace.data, pen={'color': color, 'width': 3})
trace_plt[0].setXRange(-5e-3, 20e-3)
trace_plt[0].setLabels(left=('', 'A'), bottom=('Time from presynaptic spike', 's'))
trace_plt[0].setTitle('Voltage Clamp')
return line, scatter
import pyqtgraph as pg
from pyqtgraph.Qt import QtGui, QtCore
import numpy as np
from neuroanalysis.data import TSeries
from neuroanalysis.ui.event_detection import EventDetector
from neuroanalysis.ui.plot_grid import PlotGrid
pg.mkQApp()
data = np.load("test_data/synaptic_events/events1.npz")
trace_names = sorted([x for x in data.keys() if x.startswith('trace')])
traces = {
n: TSeries(data[n], dt=1.0 / data['sample_rates'][i])
for i, n in enumerate(trace_names)
}
evd = EventDetector()
evd.params['threshold'] = 5e-10
hs = QtGui.QSplitter(QtCore.Qt.Horizontal)
pt = pg.parametertree.ParameterTree(showHeader=False)
params = pg.parametertree.Parameter.create(name='params',
type='group',
children=[
dict(name='data',
type='list',
values=trace_names),
evd.params,
])
def set_data(self, data, show_spikes=False, subtract_baseline=True):
self.spike_plot.setVisible(show_spikes)
self.spike_plot.enableAutoRange(False, False)
self.data_plot.enableAutoRange(False, False)
psp = StackedPsp()
for recording in data:
pulses = sorted(list(data[recording].keys()))
for pulse_n in pulses:
rec = data[recording][pulse_n]
# spike-align pulse + offset for pulse number
spike_t = rec.StimPulse.first_spike_time
if spike_t is None:
spike_t = rec.StimPulse.onset_time + 1e-3
qc_pass = rec.PulseResponse.in_qc_pass if rec.Synapse.synapse_type == 'in' else rec.PulseResponse.ex_qc_pass
pen = (255, 255, 255, 100) if qc_pass else (200, 50, 0, 100)
t0 = rec.PulseResponse.data_start_time - spike_t
ts = TSeries(data=rec.data,
t0=t0,
sample_rate=db.default_sample_rate)
c = self.data_plot.plot(ts.time_values, ts.data, pen=pen)
# arrange plots nicely
y0 = 0 if not subtract_baseline else ts.time_slice(None,
0).median()
shift = (pulse_n * 35e-3 + (30e-3 if pulse_n > 8 else 0), -y0)
zval = 0 if qc_pass else -10
c.setPos(*shift)
c.setZValue(zval)
if show_spikes:
t0 = rec.spike_data_start_time - spike_t
spike_ts = TSeries(data=rec.spike_data,
t0=t0,
sample_rate=db.default_sample_rate)
c = self.spike_plot.plot(spike_ts.time_values,
spike_ts.data,
pen=pen)
c.setPos(*shift)
c.setZValue(zval)
# evaluate recorded fit for this response
fit_par = rec.PulseResponseFit
if fit_par.fit_amp is None:
continue
fit = psp.eval(
x=ts.time_values,
exp_amp=fit_par.fit_exp_amp,
exp_tau=fit_par.fit_decay_tau,
amp=fit_par.fit_amp,
rise_time=fit_par.fit_rise_time,
decay_tau=fit_par.fit_decay_tau,
xoffset=fit_par.fit_latency,
yoffset=fit_par.fit_yoffset,
rise_power=2,
)
pen = (0, 255, 0, 100) if qc_pass else (50, 150, 0, 100)
c = self.data_plot.plot(ts.time_values, fit, pen=pen)
c.setZValue(10)
c.setPos(*shift)
if not qc_pass:
print(
"qc fail: ",
rec.PulseResponse.meta.get('qc_failures',
'no qc failures recorded'))
self.spike_plot.enableAutoRange(True, True)
self.data_plot.enableAutoRange(True, True)
def analyze_response_strength(rec,
source,
remove_artifacts=False,
deconvolve=True,
lpf=True,
bsub=True,
lowpass=1000):
"""Perform a standardized strength analysis on a record selected by response_query or baseline_query.
1. Determine timing of presynaptic stimulus pulse edges and spike
2. Measure peak deflection on raw trace
3. Apply deconvolution / artifact removal / lpf
4. Measure peak deflection on deconvolved trace
"""
data = TSeries(rec.data, sample_rate=db.default_sample_rate)
if source == 'pulse_response':
# Find stimulus pulse edges for artifact removal
start = rec.pulse_start - rec.rec_start
pulse_times = [start, start + rec.pulse_dur]
if rec.spike_time is None:
# these pulses failed QC, but we analyze them anyway to make all data visible
spike_time = 11e-3
else:
spike_time = rec.spike_time - rec.rec_start
elif source == 'baseline':
# Fake stimulus information to ensure that background data receives
# the same filtering / windowing treatment
pulse_times = [10e-3, 12e-3]
spike_time = 11e-3
else:
raise ValueError("Invalid source %s" % source)
results = {}
results['raw_trace'] = data
results['pulse_times'] = pulse_times
results['spike_time'] = spike_time
# Measure crosstalk from pulse onset
p1 = data.time_slice(pulse_times[0] - 200e-6, pulse_times[0]).median()
p2 = data.time_slice(pulse_times[0], pulse_times[0] + 200e-6).median()
results['crosstalk'] = p2 - p1
# crosstalk artifacts in VC are removed before deconvolution
if rec.clamp_mode == 'vc' and remove_artifacts is True:
data = remove_crosstalk_artifacts(data, pulse_times)
remove_artifacts = False
# Measure deflection on raw data
results['pos_amp'], _ = measure_peak(data, '+', spike_time, pulse_times)
results['neg_amp'], _ = measure_peak(data, '-', spike_time, pulse_times)
# Deconvolution / artifact removal / filtering
if deconvolve:
tau = 15e-3 if rec.clamp_mode == 'ic' else 5e-3
else:
tau = None
dec_data = deconv_filter(data,
pulse_times,
tau=tau,
lpf=lpf,
remove_artifacts=remove_artifacts,
bsub=bsub,
lowpass=lowpass)
results['dec_trace'] = dec_data
# Measure deflection on deconvolved data
results['pos_dec_amp'], results['pos_dec_latency'] = measure_peak(
dec_data, '+', spike_time, pulse_times)
results['neg_dec_amp'], results['neg_dec_latency'] = measure_peak(
dec_data, '-', spike_time, pulse_times)
return results
def measure_response(rec, baseline_rec):
"""Curve fit a single pulse response to measure its amplitude / kinetics.
Uses the known latency and kinetics of the synapse to seed the fit.
Optionally fit a baseline at the same time for noise measurement.
"""
if rec.clamp_mode == 'ic':
rise_time = rec.psp_rise_time
decay_tau = rec.psp_decay_tau
else:
rise_time = rec.psc_rise_time
decay_tau = rec.psc_decay_tau
# make sure all parameters are available
for v in [rec.spike_time, rec.latency, rise_time, decay_tau]:
if v is None or rec.latency is None or not np.isfinite(v):
return None, None
data = TSeries(rec.data,
t0=rec.rec_start - rec.spike_time,
sample_rate=db.default_sample_rate)
# decide whether/how to constrain the sign of the fit
if rec.synapse_type == 'ex':
sign = 1
elif rec.synapse_type == 'in':
if rec.baseline_potential > -60e-3:
sign = -1
else:
sign = 0
else:
sign = 0
if rec.clamp_mode == 'vc':
sign = -sign
# fit response region
response_fit = fit_psp(
data,
search_window=rec.latency + np.array([-100e-6, 100e-6]),
clamp_mode=rec.clamp_mode,
sign=sign,
baseline_like_psp=True,
init_params={
'rise_time': rise_time,
'decay_tau': decay_tau
},
refine=False,
)
# fit baseline region
if baseline_rec is None:
baseline_fit = None
else:
baseline = TSeries(baseline_rec.data,
t0=data.t0,
sample_rate=db.default_sample_rate)
baseline_fit = fit_psp(
baseline,
search_window=rec.latency + np.array([-100e-6, 100e-6]),
clamp_mode=rec.clamp_mode,
sign=sign,
baseline_like_psp=True,
init_params={
'rise_time': rise_time,
'decay_tau': decay_tau
},
refine=False,
)
return response_fit, baseline_fit
def save_fit_psp_test_set():
"""NOTE THIS CODE DOES NOT WORK BUT IS HERE FOR DOCUMENTATION PURPOSES SO
THAT WE CAN TRACE BACK HOW THE TEST DATA WAS CREATED IF NEEDED.
Create a test set of data for testing the fit_psp function. Uses Steph's
original first_puls_feature.py code to filter out error causing data.
Example run statement
python save save_fit_psp_test_set.py --organism mouse --connection ee
Comment in the code that does the saving at the bottom
"""
import pyqtgraph as pg
import numpy as np
import csv
import sys
import argparse
from multipatch_analysis.experiment_list import cached_experiments
from manuscript_figures import get_response, get_amplitude, response_filter, feature_anova, write_cache, trace_plot, \
colors_human, colors_mouse, fail_rate, pulse_qc, feature_kw
from synapse_comparison import load_cache, summary_plot_pulse
from neuroanalysis.data import TSeriesList, TSeries
from neuroanalysis.ui.plot_grid import PlotGrid
from multipatch_analysis.connection_detection import fit_psp
from rep_connections import ee_connections, human_connections, no_include, all_connections, ie_connections, ii_connections, ei_connections
from multipatch_analysis.synaptic_dynamics import DynamicsAnalyzer
from scipy import stats
import time
import pandas as pd
import json
import os
app = pg.mkQApp()
pg.dbg()
pg.setConfigOption('background', 'w')
pg.setConfigOption('foreground', 'k')
parser = argparse.ArgumentParser(
description=
'Enter organism and type of connection you"d like to analyze ex: mouse ee (all mouse excitatory-'
'excitatory). Alternatively enter a cre-type connection ex: sim1-sim1')
parser.add_argument('--organism',
dest='organism',
help='Select mouse or human')
parser.add_argument('--connection',
dest='connection',
help='Specify connections to analyze')
args = vars(parser.parse_args(sys.argv[1:]))
all_expts = cached_experiments()
manifest = {
'Type': [],
'Connection': [],
'amp': [],
'latency': [],
'rise': [],
'rise2080': [],
'rise1090': [],
'rise1080': [],
'decay': [],
'nrmse': [],
'CV': []
}
fit_qc = {'nrmse': 8, 'decay': 499e-3}
if args['organism'] == 'mouse':
color_palette = colors_mouse
calcium = 'high'
age = '40-60'
sweep_threshold = 3
threshold = 0.03e-3
connection = args['connection']
if connection == 'ee':
connection_types = ee_connections.keys()
elif connection == 'ii':
connection_types = ii_connections.keys()
elif connection == 'ei':
connection_types = ei_connections.keys()
elif connection == 'ie':
connection_types == ie_connections.keys()
elif connection == 'all':
connection_types = all_connections.keys()
elif len(connection.split('-')) == 2:
c_type = connection.split('-')
if c_type[0] == '2/3':
pre_type = ('2/3', 'unknown')
else:
pre_type = (None, c_type[0])
if c_type[1] == '2/3':
post_type = ('2/3', 'unknown')
else:
post_type = (None, c_type[0])
connection_types = [(pre_type, post_type)]
elif args['organism'] == 'human':
color_palette = colors_human
calcium = None
age = None
sweep_threshold = 5
threshold = None
connection = args['connection']
if connection == 'ee':
connection_types = human_connections.keys()
else:
c_type = connection.split('-')
connection_types = [((c_type[0], 'unknown'), (c_type[1],
'unknown'))]
plt = pg.plot()
scale_offset = (-20, -20)
scale_anchor = (0.4, 1)
holding = [-65, -75]
qc_plot = pg.plot()
grand_response = {}
expt_ids = {}
feature_plot = None
feature2_plot = PlotGrid()
feature2_plot.set_shape(5, 1)
feature2_plot.show()
feature3_plot = PlotGrid()
feature3_plot.set_shape(1, 3)
feature3_plot.show()
amp_plot = pg.plot()
synapse_plot = PlotGrid()
synapse_plot.set_shape(len(connection_types), 1)
synapse_plot.show()
for c in range(len(connection_types)):
cre_type = (connection_types[c][0][1], connection_types[c][1][1])
target_layer = (connection_types[c][0][0], connection_types[c][1][0])
conn_type = connection_types[c]
expt_list = all_expts.select(cre_type=cre_type,
target_layer=target_layer,
calcium=calcium,
age=age)
color = color_palette[c]
grand_response[conn_type[0]] = {
'trace': [],
'amp': [],
'latency': [],
'rise': [],
'dist': [],
'decay': [],
'CV': [],
'amp_measured': []
}
expt_ids[conn_type[0]] = []
synapse_plot[c, 0].addLegend()
for expt in expt_list:
for pre, post in expt.connections:
if [expt.uid, pre, post] in no_include:
continue
cre_check = expt.cells[pre].cre_type == cre_type[
0] and expt.cells[post].cre_type == cre_type[1]
layer_check = expt.cells[pre].target_layer == target_layer[
0] and expt.cells[post].target_layer == target_layer[1]
if cre_check is True and layer_check is True:
pulse_response, artifact = get_response(
expt, pre, post, analysis_type='pulse')
if threshold is not None and artifact > threshold:
continue
response_subset, hold = response_filter(
pulse_response,
freq_range=[0, 50],
holding_range=holding,
pulse=True)
if len(response_subset) >= sweep_threshold:
qc_plot.clear()
qc_list = pulse_qc(response_subset,
baseline=1.5,
pulse=None,
plot=qc_plot)
if len(qc_list) >= sweep_threshold:
avg_trace, avg_amp, amp_sign, peak_t = get_amplitude(
qc_list)
# if amp_sign is '-':
# continue
# #print ('%s, %0.0f' %((expt.uid, pre, post), hold, ))
# all_amps = fail_rate(response_subset, '+', peak_t)
# cv = np.std(all_amps)/np.mean(all_amps)
#
# # weight parts of the trace during fitting
dt = avg_trace.dt
weight = np.ones(
len(avg_trace.data
)) * 10. #set everything to ten initially
weight[int(10e-3 / dt):int(
12e-3 / dt)] = 0. #area around stim artifact
weight[int(12e-3 / dt):int(
19e-3 / dt)] = 30. #area around steep PSP rise
# check if the test data dir is there and if not create it
test_data_dir = 'test_psp_fit'
if not os.path.isdir(test_data_dir):
os.mkdir(test_data_dir)
save_dict = {}
save_dict['input'] = {
'data': avg_trace.data.tolist(),
'dtype': str(avg_trace.data.dtype),
'dt': float(avg_trace.dt),
'amp_sign': amp_sign,
'yoffset': 0,
'xoffset': 14e-3,
'avg_amp': float(avg_amp),
'method': 'leastsq',
'stacked': False,
'rise_time_mult_factor': 10.,
'weight': weight.tolist()
}
# need to remake trace because different output is created
avg_trace_simple = TSeries(
data=np.array(save_dict['input']['data']),
dt=save_dict['input']
['dt']) # create TSeries object
psp_fits_original = fit_psp(
avg_trace,
sign=save_dict['input']['amp_sign'],
yoffset=save_dict['input']['yoffset'],
xoffset=save_dict['input']['xoffset'],
amp=save_dict['input']['avg_amp'],
method=save_dict['input']['method'],
stacked=save_dict['input']['stacked'],
rise_time_mult_factor=save_dict['input']
['rise_time_mult_factor'],
fit_kws={
'weights': save_dict['input']['weight']
})
psp_fits_simple = fit_psp(
avg_trace_simple,
sign=save_dict['input']['amp_sign'],
yoffset=save_dict['input']['yoffset'],
xoffset=save_dict['input']['xoffset'],
amp=save_dict['input']['avg_amp'],
method=save_dict['input']['method'],
stacked=save_dict['input']['stacked'],
rise_time_mult_factor=save_dict['input']
['rise_time_mult_factor'],
fit_kws={
'weights': save_dict['input']['weight']
})
print expt.uid, pre, post
if psp_fits_original.nrmse(
) != psp_fits_simple.nrmse():
print ' the nrmse values dont match'
print '\toriginal', psp_fits_original.nrmse()
print '\tsimple', psp_fits_simple.nrmse()
def plot_features(organism=None,
conn_type=None,
calcium=None,
age=None,
sweep_thresh=None,
fit_thresh=None):
s = db.session()
filters = {
'organism': organism,
'conn_type': conn_type,
'calcium': calcium,
'age': age
}
selection = [{}]
for key, value in filters.iteritems():
if value is not None:
temp_list = []
value_list = value.split(',')
for v in value_list:
temp = [s1.copy() for s1 in selection]
for t in temp:
t[key] = v
temp_list = temp_list + temp
selection = list(temp_list)
if len(selection) > 0:
response_grid = PlotGrid()
response_grid.set_shape(len(selection), 1)
response_grid.show()
feature_grid = PlotGrid()
feature_grid.set_shape(6, 1)
feature_grid.show()
for i, select in enumerate(selection):
pre_cell = aliased(db.Cell)
post_cell = aliased(db.Cell)
q_filter = []
if sweep_thresh is not None:
q_filter.append(FirstPulseFeatures.n_sweeps >= sweep_thresh)
species = select.get('organism')
if species is not None:
q_filter.append(db.Slice.species == species)
c_type = select.get('conn_type')
if c_type is not None:
pre_type, post_type = c_type.split('-')
pre_layer, pre_cre = pre_type.split(';')
if pre_layer == 'None':
pre_layer = None
post_layer, post_cre = post_type.split(';')
if post_layer == 'None':
post_layer = None
q_filter.extend([
pre_cell.cre_type == pre_cre,
pre_cell.target_layer == pre_layer,
post_cell.cre_type == post_cre,
post_cell.target_layer == post_layer
])
calc_conc = select.get('calcium')
if calc_conc is not None:
q_filter.append(db.Experiment.acsf.like(calc_conc + '%'))
age_range = select.get('age')
if age_range is not None:
age_lower, age_upper = age_range.split('-')
q_filter.append(
db.Slice.age.between(int(age_lower), int(age_upper)))
q = s.query(FirstPulseFeatures).join(db.Pair, FirstPulseFeatures.pair_id==db.Pair.id)\
.join(pre_cell, db.Pair.pre_cell_id==pre_cell.id)\
.join(post_cell, db.Pair.post_cell_id==post_cell.id)\
.join(db.Experiment, db.Experiment.id==db.Pair.expt_id)\
.join(db.Slice, db.Slice.id==db.Experiment.slice_id)
for filter_arg in q_filter:
q = q.filter(filter_arg)
results = q.all()
trace_list = []
for pair in results:
#TODO set t0 to latency to align to foot of PSP
trace = TSeries(data=pair.avg_psp,
sample_rate=db.default_sample_rate)
trace_list.append(trace)
response_grid[i, 0].plot(trace.time_values, trace.data)
if len(trace_list) > 0:
grand_trace = TSeriesList(trace_list).mean()
response_grid[i, 0].plot(grand_trace.time_values,
grand_trace.data,
pen='b')
response_grid[i, 0].setTitle(
'layer %s, %s-> layer %s, %s; n_synapses = %d' %
(pre_layer, pre_cre, post_layer, post_cre,
len(trace_list)))
else:
print('No synapses for layer %s, %s-> layer %s, %s' %
(pre_layer, pre_cre, post_layer, post_cre))
return response_grid, feature_grid
def plot_element_data(self, pre_class, post_class, element, field_name, color='g', trace_plt=None):
summary = element.agg(self.summary_stat)
val = summary[field_name]['metric_summary']
line = pg.InfiniteLine(val, pen={'color': color, 'width': 2}, movable=False)
scatter = None
tracesA = []
tracesB = []
connections = element[element['Connected'] == True].index.tolist()
for pair in connections:
# rsf = pair.resting_state_fit
synapse = pair.synapse
if synapse is None:
continue
arfs = pair.avg_response_fits
latency = pair.synapse.latency
syn_typ = pair.synapse.synapse_type
self.pair_items[pair.id] = []
trace_itemA = None
trace_itemB = None
# if rsf is not None:
# traceA = TSeries(data=rsf.ic_avg_data, sample_rate=db.default_sample_rate)
# start_time = rsf.ic_avg_data_start_time
# if latency is not None and start_time is not None:
# xoffset = start_time - latency
# baseline_window = [abs(xoffset)-1e-3, abs(xoffset)]
# traceA = format_trace(traceA, baseline_window, x_offset=xoffset, align='psp')
# trace_itemA = trace_plt[0].plot(traceA.time_values, traceA.data)
# trace_itemA.pair = pair
# trace_itemA.curve.setClickable(True)
# trace_itemA.sigClicked.connect(self.trace_plot_clicked)
# self.pair_items[pair.id].append(trace_itemA)
# tracesA.append(traceA)
if arfs is not None:
for arf in arfs:
if arf.holding in syn_typ_holding[syn_typ] and arf.manual_qc_pass is True and latency is not None:
if arf.clamp_mode == 'vc' and trace_itemA is None:
traceA = TSeries(data=arf.avg_data, sample_rate=db.default_sample_rate)
traceA = bessel_filter(traceA, 5000, btype='low', bidir=True)
start_time = arf.avg_data_start_time
if start_time is not None:
xoffset = start_time - latency
baseline_window = [abs(xoffset)-1e-3, abs(xoffset)]
traceA = format_trace(traceA, baseline_window, x_offset=xoffset, align='psp')
trace_itemA = trace_plt[0].plot(traceA.time_values, traceA.data)
trace_itemA.pair = pair
trace_itemA.curve.setClickable(True)
trace_itemA.sigClicked.connect(self.trace_plot_clicked)
self.pair_items[pair.id].append(trace_itemA)
tracesA.append(traceA)
if arf.clamp_mode == 'ic' and trace_itemB is None:
traceB = TSeries(data=arf.avg_data, sample_rate=db.default_sample_rate)
start_time = arf.avg_data_start_time
if latency is not None and start_time is not None:
xoffset = start_time - latency
baseline_window = [abs(xoffset)-1e-3, abs(xoffset)]
traceB = format_trace(traceB, baseline_window, x_offset=xoffset, align='psp')
trace_itemB = trace_plt[1].plot(traceB.time_values, traceB.data)
trace_itemB.pair = pair
trace_itemB.curve.setClickable(True)
trace_itemB.sigClicked.connect(self.trace_plot_clicked)
tracesB.append(traceB)
self.pair_items[pair.id] = [trace_itemA, trace_itemB]
if len(tracesA) > 0:
grand_trace = TSeriesList(tracesA).mean()
name = ('%s->%s' % (pre_class, post_class))
# trace_plt[0].addLegend()
trace_plt[0].plot(grand_trace.time_values, grand_trace.data, pen={'color': color, 'width': 3}, name=name)
trace_plt[0].setXRange(-5e-3, 20e-3)
trace_plt[0].setLabels(left=('', 'A'), bottom=('Response Onset', 's'))
trace_plt[0].setTitle('Voltage Clamp')
if len(tracesB) > 0:
grand_trace = TSeriesList(tracesB).mean()
trace_plt[1].plot(grand_trace.time_values, grand_trace.data, pen={'color': color, 'width': 3})
trace_plt[1].setLabels(right=('', 'V'), bottom=('Response Onset', 's'))
trace_plt[1].setTitle('Current Clamp')
return line, scatter