def pulses(self):
"""Return a list of (start, stop, amp) tuples describing square pulses
in the stimulus.
"""
if self._pulses is None:
trace = self.rec['command']
pulses = find_square_pulses(trace)
self._pulses = []
for p in pulses:
start = trace.index_at(p.global_start_time)
stop = trace.index_at(p.global_start_time + p.duration)
self._pulses.append((start, stop, p.amplitude))
return self._pulses
def pulses(self, channel='command'):
"""Return a list of (start_time, stop_time, amp) tuples describing square pulses
in the stimulus.
"""
if self._pulses.get(channel) is None:
trace = self.rec[channel]
pulses = find_square_pulses(trace)
self._pulses[channel] = []
for p in pulses:
start = p.global_start_time
stop = p.global_start_time + p.duration
self._pulses[channel].append((start, stop, p.amplitude))
return self._pulses[channel]
def pulses(self):
"""Return a list of (start, stop, amp) tuples describing square pulses
in the stimulus.
"""
if self._pulses is None:
trace = self.rec['command']
pulses = find_square_pulses(trace)
self._pulses = []
for p in pulses:
start = trace.index_at(p.global_start_time)
stop = trace.index_at(p.global_start_time + p.duration)
self._pulses.append((start, stop, p.amplitude))
return self._pulses
def pulses(self, channel=None):
"""Return a list of (start_time, stop_time, amp) tuples describing square pulses
in the specified channel.
"""
self._check_channel(channel)
if self._pulses.get(channel) is None:
trace = self.rec[channel]
if trace.data[:10].std() > 0:
pulses = find_noisy_square_pulses(trace, std_threshold=10)
else:
pulses = find_square_pulses(trace)
self._pulses[channel] = []
for p in pulses:
start = p.global_start_time
stop = p.global_start_time + p.duration
self._pulses[channel].append((start, stop, p.amplitude))
return self._pulses[channel]
def pulses(self, channel=None):
"""Return a list of SquarePulses found in the given channel of the recording.
If there is pulse-width modulation (higher than %s Hz), it will be grouped
into a single SquarePulse with lower amplitude.
Example:
_____|||||_______________|||||_____________|||||____________
<---> <---> <--->
The trace shown above has pulse width modulation would return a
list of 3 SquarePulses with an amplitude equal to the mean of the
trace during the periods indicated by the arrows.
The trace shown below (no pulse width modulation) would also
return a list of 3 SquarePulses, but with an amplitude of 1.
_____ _____ _____
____| |_____________| |___________| |___________
Parameters:
-----------
channel : str | None
The channel to analyze pulses from.
""" % str(self.pwm_min_frequency)
self._check_channel(channel)
if self._pulses.get(channel) is None:
trace = self.rec[channel]
if trace.data[:10].std() > 0:
all_pulses = find_noisy_square_pulses(trace)
else:
all_pulses = find_square_pulses(trace)
## figure out if there is pwm happening
pwm = False
if len(all_pulses) > 1:
for i in range(len(all_pulses) - 1):
if all_pulses[i + 1].global_start_time - all_pulses[
i].global_start_time <= self.pwm_min_delay: ## dealing with pwm
pwm = True
break
## convert pwm pulses into single stimulation pulses
if pwm:
pulses = []
self._pwm_params[channel] = []
### make an array of start times
starts = np.array([p.global_start_time for p in all_pulses])
### do a diff on the array - look for points larger than 1/min_frequency
breaks = np.argwhere(
np.diff(starts) > self.pwm_min_delay
) ## gives indices of the last pulse in a pwm pulse
if len(breaks) == 0: ## only one pulse
pulse, params = self._create_pulse_from_pwm(all_pulses)
pulses.append(pulse)
self._pwm_params[channel].append(params)
### take the pulses between large diffs and turn them into one pulse with appropriate duration and amplitude
else:
start_i = 0
for i, b in enumerate(breaks):
pulse, params = self._create_pulse_from_pwm(
all_pulses[start_i:b + 1])
pulses.append(pulse)
self._pwm_params[channel].append(params)
start_i = b + 1
pulse, params = self._create_pulse_from_pwm(
all_pulses[start_i:])
pulses.append(pulse)
self._pwm_params[channel].append(params)
else:
self._pwm_params[channel] = None
pulses = [
SquarePulse(start_time=p.global_start_time,
duration=p.duration,
amplitude=1,
units='percent') for p in all_pulses
]
### convert from SquarePulse to (start, stop, amplitude)
self._pulses[channel] = pulses
return self._pulses[channel]