def parse_observable(self):
if 'file' in self.observable:
f = fn.FileNodeHelper(self.observable['file'], self.omt_root)
inform('Activation variable from file',
self.observable['file'],
indent=1,
verbosity=1)
return f.get_timeseries()
def before_running(self):
if 'file' in self.observable:
self.f = fn.FileNodeHelper(self.observable['file'], self.omt_root)
if self.f.tstamp:
inform('Attention! Preexistent datafile: ',
self.f.filename,
indent=2,
verbosity=1)
def parse_expected(self):
to_parse = self.expected
if isinstance(to_parse, list):
ts = to_parse
elif 'file' in to_parse:
f = fn.FileNodeHelper(to_parse['file'], self.mep_root)
ts = f.get_timeseries()
inform('Reading timeseries from: ', f, indent=1, verbosity=1)
return ts
def parse_spikes(self, to_parse):
if isinstance(to_parse, list):
spikes = to_parse
elif 'file' in to_parse:
f = fn.FileNodeHelper(to_parse['file'])
tv = f.get_timeseries()
inform('Reading timeseries from:', f, indent=1)
if 'spike detection' in to_parse:
sd = to_parse['spike detection']
method = sd.get('method', 'threshold')
threshold = float(sd.get('threshold', 0))
inform('Detecting spikes with method:', method, indent=2)
spikes = ts.spikes_from_timeseries(tv, method=method, threshold=threshold)
return spikes
def parseOMT(self, to_parse):
f = fn.FileNodeHelper(to_parse['file_Vm'], self.omt_root)
f_i = fn.FileNodeHelper(to_parse['file_VC_i'], self.omt_root)
inform('Calculating input resistance from files:',
(f.filename, f_i.filename),
indent=1,
verbosity=1)
h_voltage = to_parse.get('holding voltage', -70.)
cmd_voltage = to_parse.get('command voltage', -80.)
h_window = to_parse.get('holding window', [0., 0.])
cmd_window = to_parse.get('command window', [0., 0.])
# h_window = [float(t) for t in to_parse.get('holding window', [0., 0.])[0].split()]
# cmd_window = [float(t) for t in to_parse.get('command window', [0., 0.])[0].split()]
inform('Time wondow used for detection of current injections:',
(h_window, cmd_window),
indent=2,
verbosity=1)
input_resistance = ts.input_resistance(f.get_timeseries(),
f_i.get_timeseries(), h_window,
cmd_window,
(h_voltage, cmd_voltage))
return input_resistance
def parse_resting(self, to_parse):
if isinstance(to_parse, (int, float)):
resting = to_parse
inform('Explicit resting potential specified:', to_parse, indent=1)
elif 'file' in to_parse:
f = fn.FileNodeHelper(to_parse['file'])
inform('Calculating resting potential from file:',
f.filename,
indent=1)
window = to_parse.get('average last', 1)
if window > 1:
inform('Number of final points taken for averaging:',
window,
indent=2)
resting = ts.average_resting(f.get_timeseries(), window)
return resting