Reading files with neo.rawio

compare with read_files_neo_io.py

import urllib
from neo.rawio import PlexonRawIO

url_repo = "https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/"

# Get Plexon files
distantfile = url_repo + "plexon/File_plexon_3.plx"
localfile = "File_plexon_3.plx"
urllib.request.urlretrieve(distantfile, localfile)

# create a reader
reader = PlexonRawIO(filename="File_plexon_3.plx")
reader.parse_header()
print(reader)
print(reader.header)

# Read signal chunks
channel_indexes = None  # could be channel_indexes = [0]
raw_sigs = reader.get_analogsignal_chunk(
    block_index=0, seg_index=0, i_start=1024, i_stop=2048, channel_indexes=channel_indexes
)
float_sigs = reader.rescale_signal_raw_to_float(raw_sigs, dtype="float64")
sampling_rate = reader.get_signal_sampling_rate()
t_start = reader.get_signal_t_start(block_index=0, seg_index=0)
units = reader.header["signal_channels"][0]["units"]
print(raw_sigs.shape, raw_sigs.dtype)
print(float_sigs.shape, float_sigs.dtype)
print(sampling_rate, t_start, units)

# Count units and spikes per unit
nb_unit = reader.spike_channels_count()
print("nb_unit", nb_unit)
for spike_channel_index in range(nb_unit):
    nb_spike = reader.spike_count(block_index=0, seg_index=0, spike_channel_index=spike_channel_index)
    print("spike_channel_index", spike_channel_index, "nb_spike", nb_spike)

# Read spike times
spike_timestamps = reader.get_spike_timestamps(
    block_index=0, seg_index=0, spike_channel_index=0, t_start=0.0, t_stop=10.0
)
print(spike_timestamps.shape, spike_timestamps.dtype, spike_timestamps[:5])
spike_times = reader.rescale_spike_timestamp(spike_timestamps, dtype="float64")
print(spike_times.shape, spike_times.dtype, spike_times[:5])

# Read spike waveforms
raw_waveforms = reader.get_spike_raw_waveforms(
    block_index=0, seg_index=0, spike_channel_index=0, t_start=0.0, t_stop=10.0
)
print(raw_waveforms.shape, raw_waveforms.dtype, raw_waveforms[0, 0, :4])
float_waveforms = reader.rescale_waveforms_to_float(raw_waveforms, dtype="float32", spike_channel_index=0)
print(float_waveforms.shape, float_waveforms.dtype, float_waveforms[0, 0, :4])

# Read event timestamps and times (take another file)
distantfile = url_repo + "plexon/File_plexon_2.plx"
localfile = "File_plexon_2.plx"
urllib.request.urlretrieve(distantfile, localfile)

# Count events per channel
reader = PlexonRawIO(filename="File_plexon_2.plx")
reader.parse_header()
nb_event_channel = reader.event_channels_count()
print("nb_event_channel", nb_event_channel)
for chan_index in range(nb_event_channel):
    nb_event = reader.event_count(block_index=0, seg_index=0, event_channel_index=chan_index)
    print("chan_index", chan_index, "nb_event", nb_event)

ev_timestamps, ev_durations, ev_labels = reader.get_event_timestamps(
    block_index=0, seg_index=0, event_channel_index=0, t_start=None, t_stop=None
)
print(ev_timestamps, ev_durations, ev_labels)
ev_times = reader.rescale_event_timestamp(ev_timestamps, dtype="float64")
print(ev_times)