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Open ephys RawIO back compatibility for events #1364

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merged 4 commits into from
Jan 26, 2024
Merged

Open ephys RawIO back compatibility for events #1364

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5f5cda9
Add support for event in OpenEphys<0.6
alejoe91 Dec 14, 2023
b2617de
Merge branch 'master' of https://github.com/NeuralEnsemble/python-neo…
alejoe91 Dec 14, 2023
dee258d
Convert timestamps to seconds
alejoe91 Dec 14, 2023
20d1e36
Update neo/rawio/openephysbinaryrawio.py
alejoe91 Dec 15, 2023
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60 changes: 32 additions & 28 deletions neo/rawio/openephysbinaryrawio.py
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Original file line number Diff line number Diff line change
Expand Up @@ -164,7 +164,7 @@ def _parse_header(self):
event_channels = []
for stream_ind, stream_name in enumerate(event_stream_names):
info = self._evt_streams[0][0][stream_ind]
if 'states' in info:
if 'states' in info or 'channel_states' in info:
evt_channel_type = "epoch"
else:
evt_channel_type = "event"
Expand Down Expand Up @@ -213,31 +213,35 @@ def _parse_header(self):
)

# # If available, use 'states' to compute event duration
if 'states' in info and info["states"].size:
states = info["states"]
timestamps = info["timestamps"]
labels = info["labels"]
rising = np.where(states > 0)[0]
falling = np.where(states < 0)[0]

# infer durations
durations = None
if len(states) > 0:
# make sure first event is rising and last is falling
if states[0] < 0:
falling = falling[1:]
if states[-1] > 0:
rising = rising[:-1]

if len(rising) == len(falling):
durations = timestamps[falling] - timestamps[rising]

info["rising"] = rising
info["timestamps"] = timestamps[rising]
info["labels"] = labels[rising]
info["durations"] = durations
else:
info["durations"] = None
info["durations"] = None
# 'states' was introduced in OpenEphys v0.6. For previous versions, events used 'channels_states'
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if 'states' in info or "channel_states" in info:
states = info["channel_states"] if "channel_states" in info else info["states"]
if states.size > 0:
timestamps = info["timestamps"]
labels = info["labels"]
rising = np.where(states > 0)[0]
falling = np.where(states < 0)[0]

# infer durations
durations = None
if len(states) > 0:
# make sure first event is rising and last is falling
if states[0] < 0:
falling = falling[1:]
if states[-1] > 0:
rising = rising[:-1]

if len(rising) == len(falling):
durations = timestamps[falling] - timestamps[rising]
if not self._use_direct_evt_timestamps:
timestamps = timestamps / info['sample_rate']
durations = durations / info['sample_rate']

info["rising"] = rising
info["timestamps"] = timestamps[rising]
info["labels"] = labels[rising]
info["durations"] = durations

# no spike read yet
# can be implemented on user demand
Expand Down Expand Up @@ -395,9 +399,9 @@ def _event_count(self, block_index, seg_index, event_channel_index):

def _get_event_timestamps(self, block_index, seg_index, event_channel_index, t_start, t_stop):
info = self._evt_streams[block_index][seg_index][event_channel_index]
timestamps = info['timestamps']
timestamps = info["timestamps"]
durations = info["durations"]
labels = info['labels']
labels = info["labels"]

# slice it if needed
if t_start is not None:
Expand Down