def _read_signal_file(
filepaths: List[str],
signal_unit: Quantity = None) -> IrregularlySampledSignal:
# things are a bit complicated here as the signal is not necessarily covering the whole experiment!
try:
# get the continous signal file
signal_file = [
file for file in filepaths
if "continuous" in os.path.basename(file).lower()
][0]
times = []
signal = []
# open the file for reading
with open(signal_file, "r") as file:
# and create a reader
reader = csv.reader(file, delimiter=",")
# this try/catch handles the exception that is raised by "next" if the reader reached the file ending
try:
while True:
# read time and signal rows
time_row = np.array([float(val) for val in next(reader)])
signal_row = np.array([float(val) for val in next(reader)])
assert len(time_row) == len(signal_row)
times.append(time_row)
signal.append(signal_row)
except StopIteration:
pass
# concatenate our list of arrays
times = np.concatenate(times) * second
signal = np.concatenate(signal)
assert len(times) == len(signal)
if not signal_unit is None:
signal = Quantity(signal, signal_unit)
else:
signal = Quantity(signal, "dimensionless")
result = IrregularlySampledSignal(times=times,
signal=signal,
name="Irregularly Sampled Signal",
file_origin=signal_file)
channel_id = f"{TypeID.RAW_DATA.value}.0"
result.annotate(id=channel_id, type_id=TypeID.RAW_DATA.value)
return result
# something might go wrong as we perform some IO operations here
except Exception as ex:
traceback.print_exc()
def create_all_annotated(cls):
times = cls.rquant(1, pq.s)
signal = cls.rquant(1, pq.V)
blk = Block()
blk.annotate(**cls.rdict(3))
cls.populate_dates(blk)
seg = Segment()
seg.annotate(**cls.rdict(4))
cls.populate_dates(seg)
blk.segments.append(seg)
asig = AnalogSignal(signal=signal, sampling_rate=pq.Hz)
asig.annotate(**cls.rdict(2))
seg.analogsignals.append(asig)
isig = IrregularlySampledSignal(times=times,
signal=signal,
time_units=pq.s)
isig.annotate(**cls.rdict(2))
seg.irregularlysampledsignals.append(isig)
epoch = Epoch(times=times, durations=times)
epoch.annotate(**cls.rdict(4))
seg.epochs.append(epoch)
event = Event(times=times)
event.annotate(**cls.rdict(4))
seg.events.append(event)
spiketrain = SpikeTrain(times=times, t_stop=pq.s, units=pq.s)
d = cls.rdict(6)
d["quantity"] = pq.Quantity(10, "mV")
d["qarray"] = pq.Quantity(range(10), "mA")
spiketrain.annotate(**d)
seg.spiketrains.append(spiketrain)
chx = ChannelIndex(name="achx", index=[1, 2], channel_ids=[0, 10])
chx.annotate(**cls.rdict(5))
blk.channel_indexes.append(chx)
unit = Unit()
unit.annotate(**cls.rdict(2))
chx.units.append(unit)
return blk
def create_all_annotated(cls):
times = cls.rquant(1, pq.s)
signal = cls.rquant(1, pq.V)
blk = Block()
blk.annotate(**cls.rdict(3))
seg = Segment()
seg.annotate(**cls.rdict(4))
blk.segments.append(seg)
asig = AnalogSignal(signal=signal, sampling_rate=pq.Hz)
asig.annotate(**cls.rdict(2))
seg.analogsignals.append(asig)
isig = IrregularlySampledSignal(times=times, signal=signal,
time_units=pq.s)
isig.annotate(**cls.rdict(2))
seg.irregularlysampledsignals.append(isig)
epoch = Epoch(times=times, durations=times)
epoch.annotate(**cls.rdict(4))
seg.epochs.append(epoch)
event = Event(times=times)
event.annotate(**cls.rdict(4))
seg.events.append(event)
spiketrain = SpikeTrain(times=times, t_stop=pq.s, units=pq.s)
d = cls.rdict(6)
d["quantity"] = pq.Quantity(10, "mV")
d["qarray"] = pq.Quantity(range(10), "mA")
spiketrain.annotate(**d)
seg.spiketrains.append(spiketrain)
chx = ChannelIndex(name="achx", index=[1, 2], channel_ids=[0, 10])
chx.annotate(**cls.rdict(5))
blk.channel_indexes.append(chx)
unit = Unit()
unit.annotate(**cls.rdict(2))
chx.units.append(unit)
return blk
