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Calib fix #6

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Merged
merged 2 commits into from
Jul 21, 2025
Merged

Calib fix #6

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a3385b4
make mark_calibration_bad robust to duplicated calibration triggers, …
jshanna100 Jul 18, 2025
7323b97
more informative message for duplicate calibration events. calibratio…
jshanna100 Jul 21, 2025
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5 changes: 5 additions & 0 deletions mne_bids_pipeline/_config.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1216,6 +1216,11 @@
```
"""

sync_calibration_string: str | None = ".* Recalibration (start|end) \\| (.*)"
"""
Regular expression used for searching for calibration events
"""

# ### SSP, ICA, and artifact regression

regress_artifact: dict[str, Any] | None = None
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15 changes: 10 additions & 5 deletions mne_bids_pipeline/steps/preprocessing/_05b_sync_eyelink.py
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Expand Up @@ -35,14 +35,14 @@ def _check_HEOG_ET_vars(cfg):

return heog_ch, et_ch, bipolar

def _mark_calibration_as_bad(raw):
def _mark_calibration_as_bad(raw, cfg):
# marks recalibration beginnings and ends as one bad segment
cur_idx = None
cur_start_time = 0.
last_status = None
for annot in raw.annotations:
calib_match = re.match(".* Recalibration (start|end) \\| (\\d*)", annot["description"])
calib_match = re.match(cfg.sync_calibration_string, annot["description"])
if not calib_match: continue

calib_status, calib_idx = calib_match.group(1), calib_match.group(2)
if calib_idx == cur_idx and calib_status == "end":
duration = annot["onset"] - cur_start_time
Expand All @@ -51,8 +51,12 @@ def _mark_calibration_as_bad(raw):
elif calib_status == "start" and cur_idx is None:
cur_idx = calib_idx
cur_start_time = annot["onset"]
elif calib_status == last_status:
logger.info(**gen_log_kwargs(message=f"Encountered apparent duplicate calibration event ({calib_status}, {calib_idx}) - skipping"))
elif calib_status == "start" and cur_idx is not None:
raise ValueError(f"Annotation {annot["description"]} could not be assigned membership")
raise ValueError(f"Annotation {annot["description"]} could not be assigned membership"
f"")
last_status = calib_status

return raw

Expand Down Expand Up @@ -246,7 +250,7 @@ def sync_eyelink(
# create bipolar HEOG
raw = mne.set_bipolar_reference(raw, *cfg.sync_heog_ch, ch_name=heog_ch, drop_refs=False)
raw.filter(l_freq=cfg.sync_heog_highpass, h_freq=cfg.sync_heog_lowpass, picks=heog_ch) # get rid of drift and high freq noise
_mark_calibration_as_bad(raw)
_mark_calibration_as_bad(raw, cfg)
# extract HEOG and ET as arrays
heog_array = raw.get_data(picks=[heog_ch], reject_by_annotation="omit")
et_array = raw.get_data(picks=et_ch, reject_by_annotation="omit")
Expand Down Expand Up @@ -344,6 +348,7 @@ def get_config(
sync_heog_highpass = config.sync_heog_highpass,
sync_heog_lowpass = config.sync_heog_lowpass,
sync_plot_samps = config.sync_plot_samps,
sync_calibration_string = config.sync_calibration_string,
processing= "filt" if config.regress_artifact is None else "regress",
_raw_split_size=config._raw_split_size,

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