Ctrl+K

Note

Go to the end to download the full example code.

Plotting eye-tracking heatmaps in MNE-Python#

This tutorial covers plotting eye-tracking position data as a heatmap.

See also

Importing Data from Eyetracking devices Working with eye tracker data in MNE-Python

# License: BSD-3-Clause
# Copyright the MNE-Python contributors.

Data loading#

As usual we start by importing the modules we need and loading some example data: eye-tracking data recorded from SR research’s '.asc' file format.

import matplotlib.pyplot as plt

import mne
from mne.viz.eyetracking import plot_gaze

task_fpath = mne.datasets.eyelink.data_path() / "freeviewing"
et_fpath = task_fpath / "sub-01_task-freeview_eyetrack.asc"
stim_fpath = task_fpath / "stim" / "naturalistic.png"

raw = mne.io.read_raw_eyelink(et_fpath)
calibration = mne.preprocessing.eyetracking.read_eyelink_calibration(
    et_fpath,
    screen_resolution=(1920, 1080),
    screen_size=(0.53, 0.3),
    screen_distance=0.9,
)[0]

Loading /home/circleci/mne_data/MNE-eyelink-data/freeviewing/sub-01_task-freeview_eyetrack.asc
Pixel coordinate data detected.Pass `scalings=dict(eyegaze=1e3)` when using plot method to make traces more legible.
Pupil-size area detected.
There are 10 recording blocks in this file. Times between blocks will be annotated with BAD_ACQ_SKIP.
Reading calibration data from /home/circleci/mne_data/MNE-eyelink-data/freeviewing/sub-01_task-freeview_eyetrack.asc

Process and epoch the data#

First we will interpolate missing data during blinks and epoch the data.

mne.preprocessing.eyetracking.interpolate_blinks(raw, interpolate_gaze=True)
raw.annotations.rename({"dvns": "natural"})  # more intuitive

epochs = mne.Epochs(raw, event_id=["natural"], tmin=0, tmax=20, baseline=None)

Interpolating missing data during blinks...
Interpolated 3 channels: ['xpos_left', 'ypos_left', 'pupil_left']
Removing 'BAD_' from BAD_blink.
Used Annotations descriptions: ['-1 SYNC FRAME No.114', '-1 SYNC FRAME No.139', '-1 SYNC FRAME No.14', '-1 SYNC FRAME No.194', '-1 SYNC FRAME No.339', '-1 SYNC FRAME No.349', '-1 SYNC FRAME No.39', '-1 SYNC FRAME No.429', '-1 SYNC FRAME No.499', '-1 SYNC FRAME No.504', '-10 CALIB_ANIMATION_ONSET', '-10 SYNC FRAME No.103', '-10 SYNC FRAME No.108', '-10 SYNC FRAME No.113', '-10 SYNC FRAME No.118', '-10 SYNC FRAME No.123', '-10 SYNC FRAME No.128', '-10 SYNC FRAME No.13', '-10 SYNC FRAME No.133', '-10 SYNC FRAME No.138', '-10 SYNC FRAME No.143', '-10 SYNC FRAME No.148', '-10 SYNC FRAME No.153', '-10 SYNC FRAME No.158', '-10 SYNC FRAME No.163', '-10 SYNC FRAME No.168', '-10 SYNC FRAME No.173', '-10 SYNC FRAME No.178', '-10 SYNC FRAME No.18', '-10 SYNC FRAME No.183', '-10 SYNC FRAME No.188', '-10 SYNC FRAME No.193', '-10 SYNC FRAME No.198', '-10 SYNC FRAME No.203', '-10 SYNC FRAME No.208', '-10 SYNC FRAME No.213', '-10 SYNC FRAME No.218', '-10 SYNC FRAME No.223', '-10 SYNC FRAME No.228', '-10 SYNC FRAME No.23', '-10 SYNC FRAME No.233', '-10 SYNC FRAME No.238', '-10 SYNC FRAME No.243', '-10 SYNC FRAME No.248', '-10 SYNC FRAME No.253', '-10 SYNC FRAME No.258', '-10 SYNC FRAME No.263', '-10 SYNC FRAME No.268', '-10 SYNC FRAME No.273', '-10 SYNC FRAME No.278', '-10 SYNC FRAME No.28', '-10 SYNC FRAME No.283', '-10 SYNC FRAME No.288', '-10 SYNC FRAME No.293', '-10 SYNC FRAME No.298', '-10 SYNC FRAME No.303', '-10 SYNC FRAME No.308', '-10 SYNC FRAME No.313', '-10 SYNC FRAME No.318', '-10 SYNC FRAME No.323', '-10 SYNC FRAME No.328', '-10 SYNC FRAME No.33', '-10 SYNC FRAME No.333', '-10 SYNC FRAME No.338', '-10 SYNC FRAME No.343', '-10 SYNC FRAME No.348', '-10 SYNC FRAME No.353', '-10 SYNC FRAME No.358', '-10 SYNC FRAME No.363', '-10 SYNC FRAME No.368', '-10 SYNC FRAME No.373', '-10 SYNC FRAME No.378', '-10 SYNC FRAME No.38', '-10 SYNC FRAME No.383', '-10 SYNC FRAME No.388', '-10 SYNC FRAME No.393', '-10 SYNC FRAME No.398', '-10 SYNC FRAME No.403', '-10 SYNC FRAME No.408', '-10 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No.38', '-11 SYNC FRAME No.380', '-11 SYNC FRAME No.383', '-11 SYNC FRAME No.385', '-11 SYNC FRAME No.388', '-11 SYNC FRAME No.393', '-11 SYNC FRAME No.395', '-11 SYNC FRAME No.398', '-11 SYNC FRAME No.40', '-11 SYNC FRAME No.400', '-11 SYNC FRAME No.403', '-11 SYNC FRAME No.405', '-11 SYNC FRAME No.408', '-11 SYNC FRAME No.413', '-11 SYNC FRAME No.418', '-11 SYNC FRAME No.420', '-11 SYNC FRAME No.423', '-11 SYNC FRAME No.425', '-11 SYNC FRAME No.428', '-11 SYNC FRAME No.43', '-11 SYNC FRAME No.430', '-11 SYNC FRAME No.433', '-11 SYNC FRAME No.438', '-11 SYNC FRAME No.443', '-11 SYNC FRAME No.445', '-11 SYNC FRAME No.448', '-11 SYNC FRAME No.45', '-11 SYNC FRAME No.450', '-11 SYNC FRAME No.453', '-11 SYNC FRAME No.458', '-11 SYNC FRAME No.460', '-11 SYNC FRAME No.463', '-11 SYNC FRAME No.468', '-11 SYNC FRAME No.470', '-11 SYNC FRAME No.473', '-11 SYNC FRAME No.475', '-11 SYNC FRAME No.478', '-11 SYNC FRAME No.48', '-11 SYNC FRAME No.483', '-11 SYNC FRAME No.488', '-11 SYNC FRAME 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FRAME No.365', '-13 SYNC FRAME No.370', '-13 SYNC FRAME No.375', '-13 SYNC FRAME No.380', '-13 SYNC FRAME No.385', '-13 SYNC FRAME No.390', '-13 SYNC FRAME No.395', '-13 SYNC FRAME No.40', '-13 SYNC FRAME No.400', '-13 SYNC FRAME No.405', '-13 SYNC FRAME No.410', '-13 SYNC FRAME No.415', '-13 SYNC FRAME No.420', '-13 SYNC FRAME No.425', '-13 SYNC FRAME No.430', '-13 SYNC FRAME No.435', '-13 SYNC FRAME No.440', '-13 SYNC FRAME No.445', '-13 SYNC FRAME No.45', '-13 SYNC FRAME No.450', '-13 SYNC FRAME No.455', '-13 SYNC FRAME No.460', '-13 SYNC FRAME No.465', '-13 SYNC FRAME No.470', '-13 SYNC FRAME No.475', '-13 SYNC FRAME No.480', '-13 SYNC FRAME No.485', '-13 SYNC FRAME No.490', '-13 SYNC FRAME No.495', '-13 SYNC FRAME No.50', '-13 SYNC FRAME No.500', '-13 SYNC FRAME No.505', '-13 SYNC FRAME No.510', '-13 SYNC FRAME No.515', '-13 SYNC FRAME No.520', '-13 SYNC FRAME No.55', '-13 SYNC FRAME No.60', '-13 SYNC FRAME No.65', '-13 SYNC FRAME No.70', '-13 SYNC FRAME No.75', '-13 SYNC FRAME 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'-9 SYNC FRAME No.38', '-9 SYNC FRAME No.388', '-9 SYNC FRAME No.393', '-9 SYNC FRAME No.398', '-9 SYNC FRAME No.4', '-9 SYNC FRAME No.408', '-9 SYNC FRAME No.428', '-9 SYNC FRAME No.43', '-9 SYNC FRAME No.438', '-9 SYNC FRAME No.453', '-9 SYNC FRAME No.468', '-9 SYNC FRAME No.478', '-9 SYNC FRAME No.483', '-9 SYNC FRAME No.488', '-9 SYNC FRAME No.498', '-9 SYNC FRAME No.5', '-9 SYNC FRAME No.503', '-9 SYNC FRAME No.523', '-9 SYNC FRAME No.68', '-9 SYNC FRAME No.73', '-9 SYNC FRAME No.8', '-9 SYNC FRAME No.83', '-9 SYNC FRAME No.88', '-9 SYNC FRAME No.93', '0 GAZE_TO_CALIB', 'TRACKER_TIME 2 934630.350', 'TRACKER_TIME 3 994633.368', 'TRACKER_TIME 4 1054655.986', 'blink', 'dvss', 'fixation', 'natural', 'saccade']
Ignoring annotation durations and creating fixed-duration epochs around annotation onsets.
Not setting metadata
5 matching events found
No baseline correction applied
0 projection items activated

Plot a heatmap of the eye-tracking data#

To make a heatmap of the eye-tracking data, we can use the function plot_gaze(). We will need to define the dimensions of our canvas; for this file, the eye position data are reported in pixels, so we’ll use the screen resolution of the participant screen (1920x1080) as the width and height. We can also use the sigma parameter to smooth the plot.

cmap = plt.get_cmap("viridis")
plot_gaze(epochs["natural"], calibration=calibration, cmap=cmap, sigma=50)
Gaze heatmap
Using data from preloaded Raw for 5 events and 10001 original time points ...
0 bad epochs dropped

Overlaying plots with images#

We can use matplotlib to plot gaze heatmaps on top of stimuli images. We’ll customize a Colormap to make some values of the heatmap completely transparent. We’ll then use the vlim parameter to force the heatmap to start at a value greater than the darkest value in our previous heatmap, which will make the darkest colors of the heatmap transparent.

cmap.set_under("k", alpha=0)  # make the lowest values transparent
ax = plt.subplot()
ax.imshow(plt.imread(stim_fpath))
plot_gaze(
    epochs["natural"],
    calibration=calibration,
    vlim=(0.0003, None),
    sigma=50,
    cmap=cmap,
    axes=ax,
)
Gaze heatmap
Using data from preloaded Raw for 5 events and 10001 original time points ...
0 bad epochs dropped

Displaying the heatmap in units of visual angle#

In scientific publications it is common to report gaze data as the visual angle from the participants eye to the screen. We can convert the units of our gaze data to radians of visual angle before plotting the heatmap:

epochs.load_data()
mne.preprocessing.eyetracking.convert_units(epochs, calibration, to="radians")
plot_gaze(
    epochs["natural"],
    calibration=calibration,
    sigma=50,
)
Gaze heatmap
Using data from preloaded Raw for 5 events and 10001 original time points ...
0 bad epochs dropped
Converted ['xpos_left', 'ypos_left'] to radians.

Total running time of the script: (0 minutes 10.214 seconds)

Estimated memory usage: 106 MB

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