"""
.. _tut-eyetrack:

===========================================
Working with eye tracker data in MNE-Python
===========================================

In this tutorial we will explore simultaneously recorded eye-tracking and EEG data from
a pupillary light reflex task. We will combine the eye-tracking and EEG data, and plot
the ERP and pupil response to the light flashes (i.e. the pupillary light reflex).
"""

# Authors: Scott Huberty <seh33@uw.edu>
#          Dominik Welke <dominik.welke@web.de>
#
# License: BSD-3-Clause
# Copyright the MNE-Python contributors.

# %%
# Data loading
# ------------
#
# As usual we start by importing the modules we need and loading some
# :ref:`example data <eyelink-dataset>`: eye-tracking data recorded from SR research's
# ``'.asc'`` file format, and EEG data recorded from EGI's ``'.mff'`` file format. We'll
# pass ``create_annotations=["blinks"]`` to :func:`~mne.io.read_raw_eyelink` so that
# only blinks annotations are created (by default, annotations are created for blinks,
# saccades, fixations, and experiment messages).

import mne
from mne.datasets.eyelink import data_path
from mne.preprocessing.eyetracking import read_eyelink_calibration
from mne.viz.eyetracking import plot_gaze

et_fpath = data_path() / "eeg-et" / "sub-01_task-plr_eyetrack.asc"
eeg_fpath = data_path() / "eeg-et" / "sub-01_task-plr_eeg.mff"

raw_et = mne.io.read_raw_eyelink(et_fpath, create_annotations=["blinks"])
raw_eeg = mne.io.read_raw_egi(eeg_fpath, events_as_annotations=True).load_data()
raw_eeg.filter(1, 30)

# %%
# .. seealso:: :ref:`tut-importing-eyetracking-data`
#     :class: sidebar

# %%
# The info structure of the eye-tracking data tells us we loaded a monocular recording
# with 2 eyegaze channels (x- and y-coordinate positions), 1 pupil channel, 1 stim
# channel, and 3 channels for the head distance and position (since this data was
# collected using EyeLink's Remote mode).

raw_et.info

# %%
# Ocular annotations
# ------------------
# By default, EyeLink files will output ocular events (blinks, saccades, and
# fixations), and experiment messages. MNE will store these events
# as `mne.Annotations`. Ocular annotations contain channel information in the
# ``'ch_names'`` key. This means that we can see which eye an ocular event occurred in,
# which can be useful for binocular recordings:

print(raw_et.annotations[0]["ch_names"])  # a blink in the right eye

# %%
# Checking the calibration
# ------------------------
#
# EyeLink ``.asc`` files can also include calibration information.
# MNE-Python can load and visualize those eye-tracking calibrations, which
# is a useful first step in assessing the quality of the eye-tracking data.
# :func:`~mne.preprocessing.eyetracking.read_eyelink_calibration`
# will return a list of :class:`~mne.preprocessing.eyetracking.Calibration` instances,
# one for each calibration. We can index that list to access a specific calibration.

cals = read_eyelink_calibration(et_fpath, screen_resolution=(1920, 1080))
print(f"number of calibrations: {len(cals)}")
first_cal = cals[0]  # let's access the first (and only in this case) calibration
print(first_cal)

# %%
# Calibrations have dict-like attribute access; in addition to the attributes shown in
# the output above, additional attributes are ``'positions'`` (the x and y coordinates
# of each calibration point), ``'gaze'`` (the x and y coordinates of the actual gaze
# position to each calibration point), and ``'offsets'`` (the offset in visual degrees
# between the calibration position and the actual gaze position for each calibration
# point). Below is an example of how to access these data:

print(f"offset of the first calibration point: {first_cal['offsets'][0]}")
print(f"offset for each calibration point: {first_cal['offsets']}")
print(f"x-coordinate for each calibration point: {first_cal['positions'].T[0]}")

# %%
# Let's plot the calibration to get a better look. Below we see the location that each
# calibration point was displayed (gray dots), the positions of the actual gaze (red),
# and the offsets (in visual degrees) between the calibration position and the actual
# gaze position of each calibration point.

# %%
first_cal.plot()

# %%
# .. hint::
#   If you supply the eyetracker monitor’s screen resolution to
#   :class:`~mne.preprocessing.eyetracking.Calibration`,
#   :meth:`~mne.preprocessing.eyetracking.Calibration.plot` will automatically set the
#   canvas bounds accordingly.

# %%
# Standardizing eyetracking data to SI units
# ------------------------------------------
#
# EyeLink stores eyegaze positions in pixels, and pupil size in arbitrary units.
# MNE-Python expects eyegaze positions to be in radians of visual angle, and pupil
# size to be in meters. We can convert the eyegaze positions to radians using
# :func:`~mne.preprocessing.eyetracking.convert_units`. In addition to the
# screen resolution, we need to supply the eyetracker screen size and screen distance
# to our :class:`~mne.preprocessing.eyetracking.Calibration` object, before calling the
# convert units function.

first_cal["screen_size"] = (0.53, 0.3)
first_cal["screen_distance"] = 0.9
mne.preprocessing.eyetracking.convert_units(raw_et, calibration=first_cal, to="radians")

# %%
# Plot the raw eye-tracking data
# ------------------------------
#
# Let's plot the raw eye-tracking data. Since we did not convert the pupil size to
# meters, we'll pass a custom `dict` into the scalings argument to make the pupil size
# traces legible when plotting.

ps_scalings = dict(pupil=1e3)
raw_et.plot(scalings=ps_scalings)

# %%
# Handling blink artifacts
# ------------------------
#
# Naturally, there are blinks in our data, which occur within ``"BAD_blink"``
# annotations. During blink periods, eyegaze coordinates are not reported, and pupil
# size data are ``0``. We don't want these blink artifacts biasing our analysis, so we
# have two options: Drop the blink periods from our data during epoching, or interpolate
# the missing data during the blink periods. For this tutorial, let's interpolate the
# blink samples. We'll pass ``(0.05, 0.2)`` to
# :func:`~mne.preprocessing.eyetracking.interpolate_blinks`, expanding the interpolation
# window 50 ms before and 200 ms after the blink, so that the noisy data surrounding
# the blink is also interpolated.

mne.preprocessing.eyetracking.interpolate_blinks(
    raw_et, buffer=(0.05, 0.2), interpolate_gaze=True
)

# %%
# .. important:: By default, :func:`~mne.preprocessing.eyetracking.interpolate_blinks`,
#           will only interpolate blinks in pupil channels. Passing
#           ``interpolate_gaze=True`` will also interpolate the blink periods of the
#           eyegaze channels. Be aware, however, that eye movements can occur
#           during blinks which makes the gaze data less suitable for interpolation.

# %%
# Extract common stimulus events from the data
# --------------------------------------------
#
# In this experiment, a photodiode attached to the display screen was connected to both
# the EEG and eye-tracking systems. The photodiode was triggered by the the light flash
# stimuli, causing a signal to be sent to both systems simultaneously, signifying the
# onset of the flash. The photodiode signal was recorded as a digital input channel in
# the EEG and eye-tracking data. MNE loads these data as a :term:`stim channel`.
#
# We'll extract the flash event onsets from both the EEG and eye-tracking data, as they
# are necessary for aligning the data from the two recordings.

et_events = mne.find_events(raw_et, min_duration=0.01, shortest_event=1, uint_cast=True)
eeg_events = mne.find_events(raw_eeg, stim_channel="DIN3")

# %%
# The output above shows us that both the EEG and EyeLink data used event ID ``2`` for
# the flash events, so we'll create a dictionary to use later when plotting to label
# those events.

event_dict = dict(Flash=2)

# %%
# Align the eye-tracking data with EEG data
# -----------------------------------------
#
# In this dataset, eye-tracking and EEG data were recorded simultaneously, but on
# different systems, so we'll need to align the data before we can analyze them
# together. We can do this using the :func:`~mne.preprocessing.realign_raw` function,
# which will align the data based on the timing of the shared events that are present in
# both :class:`~mne.io.Raw` objects. We'll use the shared photodiode events we extracted
# above, but first we need to convert the event onsets from samples to seconds. Once the
# data have been aligned, we'll add the EEG channels to the eye-tracking raw object.

# Convert event onsets from samples to seconds
et_flash_times = et_events[:, 0] / raw_et.info["sfreq"]
eeg_flash_times = eeg_events[:, 0] / raw_eeg.info["sfreq"]
# Align the data
mne.preprocessing.realign_raw(
    raw_et, raw_eeg, et_flash_times, eeg_flash_times, verbose="error"
)
# Add EEG channels to the eye-tracking raw object
raw_et.add_channels([raw_eeg], force_update_info=True)
del raw_eeg  # free up some memory

# Define a few channel groups of interest and plot the data
frontal = ["E19", "E11", "E4", "E12", "E5"]
occipital = ["E61", "E62", "E78", "E67", "E72", "E77"]
pupil = ["pupil_right"]
# picks must be numeric (not string) when passed to `raw.plot(..., order=)`
picks_idx = mne.pick_channels(
    raw_et.ch_names, frontal + occipital + pupil, ordered=True
)
raw_et.plot(
    events=et_events,
    event_id=event_dict,
    event_color="g",
    order=picks_idx,
    scalings=ps_scalings,
)


# %%
# Showing the pupillary light reflex
# ----------------------------------
# Now let's extract epochs around our flash events. We should see a clear pupil
# constriction response to the flashes.

# Skip baseline correction for now. We will apply baseline correction later.
epochs = mne.Epochs(
    raw_et,
    events=et_events,
    event_id=event_dict,
    tmin=-0.3,
    tmax=3,
    baseline=None,
    picks="all",  # include eyetracking channels in the epochs
)
del raw_et  # free up some memory
epochs[:8].plot(
    events=et_events, event_id=event_dict, order=picks_idx, scalings=ps_scalings
)

# %%
# For this experiment, the participant was instructed to fixate on a crosshair in the
# center of the screen. Let's plot the gaze position data to confirm that the
# participant primarily kept their gaze fixated at the center of the screen.

plot_gaze(epochs, calibration=first_cal)

# %%
# .. seealso:: :ref:`tut-eyetrack-heatmap`

# %%
# Finally, let's plot the evoked responses to the light flashes to get a sense of the
# average pupillary light response, and the associated ERP in the EEG data.

epochs.apply_baseline().average(picks="all").plot(picks=occipital + pupil)
