[EDF to BIDS conversion] clean up obsolete commented lines of eyetrackingrun.py and make sure code snippets in edf_to_bids.md match eyetrackingrun.py

[celprov]

It seems originally the code wanted to support both eyes (that's the snippets that are referenced to in edf_to_bids.md), but the developers retracted (code implemented in eyetrackingrun.py). The changes were however not reflected in the notebook.

The code in eyetrackingrun.py moreover reflects changes in the BEP20, but those changes are not reflected in the code snippets in edf_to_bids.md.

Here are the concerned lines:

hcph-sops/code/eyetracking/eyetrackingrun.py

Lines 309 to 319 in c370b04

	thresholds_msg = messages.trialid.str.startswith("THRESHOLDS")
	if thresholds_msg.any():
	# self.metadata["PupilThreshold"] = [None] * len(self.eye)
	# self.metadata["CornealReflectionThreshold"] = [None] * len(self.eye)
	thresholds_chunks = (
	messages[thresholds_msg].trialid.iloc[-1].strip().split(" ")[1:]
	)
	# eye_index = self.eye.index(EYE_CODE_MAP[thresholds_chunks[0]])
	self.metadata["PupilThreshold"] = int(thresholds_chunks[-2])
	self.metadata["CornealReflectionThreshold"] = int(thresholds_chunks[-1])
	messages = messages.loc[~thresholds_msg]

hcph-sops/code/eyetracking/eyetrackingrun.py

Lines 367 to 395 in c370b04

	for eyenum, eyename in enumerate(self.eye):
	# Clean-up implausible values for pupil area (pa)
	self.recording.loc[
	self.recording[f"pa_{eyename}"] < 1, f"pa_{eyename}"
	] = np.nan
	self.recording = self.recording.rename(
	# columns={f"pa_{eyename}": f"eye{eyenum + 1}_pupil_size"},
	columns={f"pa_{eyename}": f"pupil_size"},
	)
	# Interpolate BIDS column names
	columns = list(
	set(self.recording.columns)
	- set(
	(
	"timestamp",
	"screen_ppdeg_x_coordinate",
	"screen_ppdeg_y_coordinate",
	"pupil_size",
	# "eye2_pupil_size",
	)
	)
	)
	bids_columns = []
	for eyenum, eyename in enumerate(self.eye):
	for name in columns:
	# colprefix = f"eye{eyenum + 1}" if name.endswith(f"_{eyename}") else ""
	colprefix = "" # Assume one eye only
	_newname = name.split("_")[0]

hcph-sops/code/eyetracking/eyetrackingrun.py

Lines 453 to 456 in c370b04

	# Process events: first generate empty columns
	self.recording["fixation"] = 0
	self.recording["saccade"] = 0
	self.recording["blink"] = 0

hcph-sops/code/eyetracking/eyetrackingrun.py

Lines 598 to 599 in c370b04

	# Replace suffix
	refname = refname.replace(f"_{suffix}", "_recording-eyetrack_physio")