def update_analysis(limit=None):
s = db.session()
q = s.query(db.Pair,
FirstPulseFeatures).outerjoin(FirstPulseFeatures).filter(
FirstPulseFeatures.pair_id == None)
if limit is not None:
q = q.limit(limit)
print("Updating %d pairs.." % q.count())
records = q.all()
for i, record in enumerate(records):
pair = record[0]
pulse_responses, pulse_ids, pulse_response_amps = filter_pulse_responses(
pair)
if len(pulse_responses) > 0:
results = first_pulse_features(pair, pulse_responses,
pulse_response_amps)
fpf = FirstPulseFeatures(pair=pair,
n_sweeps=len(pulse_ids),
pulse_ids=pulse_ids,
**results)
s.add(fpf)
if i % 10 == 0:
s.commit()
print("%d pairs added to the DB of %d" % (i, len(records)))
s.commit()
s.close()
def build_detection_limits():
# silence warnings about fp issues
np.seterr(all='ignore')
# read all pair records from DB
classifier = strength_analysis.get_pair_classifier(seed=0,
use_vc_features=False)
conns = strength_analysis.query_all_pairs(classifier)
# filter
mask = np.isfinite(conns['ic_deconv_amp_mean'])
filtered = conns[mask]
# remove recordings with gain errors
mask = filtered['ic_deconv_amp_mean'] < 0.02
# remove recordings with high crosstalk
mask &= abs(filtered['ic_crosstalk_mean']) < 60e-6
# remove recordings with low sample count
mask &= filtered['ic_n_samples'] > 50
typs = filtered['pre_cre_type']
mask &= typs == filtered['post_cre_type']
typ_mask = ((typs == 'sim1') | (typs == 'tlx3') | (typs == 'unknown') |
(typs == 'rorb') | (typs == 'ntsr1'))
mask &= typ_mask
filtered = filtered[mask]
c_mask = filtered['synapse'] == True
u_mask = ~c_mask
signal = filtered['confidence']
background = filtered['ic_base_deconv_amp_mean']
session = db.session()
# do selected connections first
count = 0
for i, rec in enumerate(filtered):
print("================== %d/%d ===================== " %
(i, len(filtered)))
pair = session.query(
db.Pair).filter(db.Pair.id == rec['pair_id']).all()[0]
if pair.detection_limit is not None:
print(" skip!")
continue
try:
measure_limit(pair, session, classifier)
except Exception:
sys.excepthook(*sys.exc_info())
count += 1
if count > 100:
print("Bailing out before memory fills up.")
sys.exit(0)
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
brush=(120, 120, 120),
pen='k').setZValue(-10)
write_csv(csv_file, x,
"Figure 3E estimated PSP amplitude distribution bin edges (V)")
write_csv(
csv_file, y,
"Figure 3E estimated PSP amplitude distribution connections per bin")
print("Global connectivity correction factor:",
corrected_prof.sum() / amp_hist[0].sum())
trace_plots = []
deconv_plots = []
hist_plots = []
session = db.session()
def add_connection_plots(i, name, timestamp, pre_id, post_id):
global session, win, filtered
p = pg.debug.Profiler(disabled=True, delayed=False)
trace_plot = win.addPlot(i, 1)
trace_plots.append(trace_plot)
trace_plot.setYRange(-1.4e-3, 2.1e-3)
# deconv_plot = win.addPlot(i, 2)
# deconv_plots.append(deconv_plot)
# deconv_plot.hide()
hist_plot = win.addPlot(i, 2)
hist_plots.append(hist_plot)
limit_plot = win.addPlot(i, 3)
limit_plot.addLegend()
from __future__ import division
import time, datetime
import multipatch_analysis.database.database as db
from neuroanalysis.ui.plot_grid import PlotGrid
s = db.session()
q = """
select
pcrec.baseline_rms_noise,
substring(experiment.original_path from 36 for 1),
recording.device_key,
recording.start_time
from
patch_clamp_recording pcrec
join recording on pcrec.recording_id=recording.id
join sync_rec on recording.sync_rec_id=sync_rec.id
join experiment on sync_rec.experiment_id=experiment.id
where
pcrec.clamp_mode='ic'
and pcrec.baseline_rms_noise is not null
and recording.device_key is not null
and experiment.original_path is not null
"""
rec = s.execute(q)
rows = rec.fetchall()
import pyqtgraph as pg
import numpy as np
rms = np.array([row[0] for row in rows])