ENH: Create a Calibrations class for eyetracking data (#11719)

Co-authored-by: Eric Larson <[email protected]> Co-authored-by: Mathieu Scheltienne <[email protected]> Co-authored-by: Richard Höchenberger <[email protected]>
mne-tools · Jun 20, 2023 · 35d3797 · 35d3797
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diff --git a/doc/changes/latest.inc b/doc/changes/latest.inc
@@ -25,6 +25,7 @@ Enhancements
 ~~~~~~~~~~~~
 - Add ``cmap`` argument for the :func:`mne.viz.plot_sensors` (:gh:`11720` by :newcontrib:`Gennadiy Belonosov`)
 - When failing to locate a file, we now print the full path in quotation marks to help spot accidentally added trailing spaces (:gh:`11718` by `Richard Höchenberger`_)
+- Added :class:`mne.preprocessing.eyetracking.Calibration` to store eye-tracking calibration info, and :func:`mne.preprocessing.eyetracking.read_eyelink_calibration` to read calibration data from EyeLink systems (:gh:`11719` by `Scott Huberty`_)
 
 Bugs
 ~~~~
@@ -35,7 +36,9 @@ Bugs
 - Fix bug with PySide6 compatibility (:gh:`11721` by `Eric Larson`_)
 - Fix hanging interpreter with matplotlib figures using ``mne/viz/_mpl_figure.py`` in spyder console and jupyter notebooks (:gh:`11696` by `Mathieu Scheltienne`_)
 - Fix bug with overlapping text for :meth:`mne.Evoked.plot` (:gh:`11698` by `Alex Rockhill`_)
+- For :func:`mne.io.read_raw_eyelink`, the default value of the ``gap_description`` parameter is now ``'BAD_ACQ_SKIP'``, following MNE convention (:gh:`11719` by `Scott Huberty`_)
 
 API changes
 ~~~~~~~~~~~
 - The ``baseline`` argument can now be array-like (e.g. ``list``, ``tuple``, ``np.ndarray``, ...) instead of only a ``tuple`` (:gh:`11713` by `Clemens Brunner`_)
+- Deprecated ``gap_description`` keyword argument of :func:`mne.io.read_raw_eyelink`, which will be removed in mne version 1.6, in favor of using :meth:`mne.Annotations.rename` (:gh:`11719` by `Scott Huberty`_)
diff --git a/doc/conf.py b/doc/conf.py
@@ -398,6 +398,7 @@
     r"\.fromkeys",
     r"\.items",
     r"\.keys",
+    r"\.move_to_end",
     r"\.pop",
     r"\.popitem",
     r"\.setdefault",
@@ -735,6 +736,7 @@ def append_attr_meth_examples(app, what, name, obj, options, lines):
     ("py:class", "(k, v), remove and return some (key, value) pair as a"),
     ("py:class", "_FuncT"),  # type hint used in @verbose decorator
     ("py:class", "mne.utils._logging._FuncT"),
+    ("py:class", "None.  Remove all items from od."),
 ]
 nitpick_ignore_regex = [
     ("py:.*", r"mne\.io\.BaseRaw.*"),

diff --git a/doc/file_io.rst b/doc/file_io.rst
@@ -61,4 +61,4 @@ Base class:
    :toctree: generated
    :template: autosummary/class_no_members.rst
 
-   BaseEpochs
+   BaseEpochs
diff --git a/doc/preprocessing.rst b/doc/preprocessing.rst
@@ -153,6 +153,8 @@ Projections:
 .. autosummary::
    :toctree: generated/
 
+   Calibration
+   read_eyelink_calibration
    set_channel_types_eyetrack
 
 EEG referencing:

diff --git a/mne/io/eyelink/__init__.py b/mne/io/eyelink/__init__.py
@@ -1,6 +1,7 @@
 """Module for loading Eye-Tracker data."""
 
-# Author: Dominik Welke <[email protected]>
+# Authors: Dominik Welke <[email protected]>
+#          Scott Huberty <[email protected]>
 #
 # License: BSD-3-Clause
 

diff --git a/mne/io/eyelink/_utils.py b/mne/io/eyelink/_utils.py
@@ -0,0 +1,113 @@
+"""Helper functions for reading eyelink ASCII files."""
+# Authors: Scott Huberty <[email protected]>
+# License: BSD-3-Clause
+
+import re
+import numpy as np
+
+
+def _find_recording_start(lines):
+    """Return the first START line in an SR Research EyeLink ASCII file.
+
+    Parameters
+    ----------
+        lines: A list of strings, which are The lines in an eyelink ASCII file.
+
+    Returns
+    -------
+        The line that contains the info on the start of the recording.
+    """
+    for line in lines:
+        if line.startswith("START"):
+            return line
+    raise ValueError("Could not find the start of the recording.")
+
+
+def _parse_validation_line(line):
+    """Parse a single line of eyelink validation data.
+
+    Parameters
+    ----------
+        line: A string containing a line of validation data from an eyelink
+        ASCII file.
+
+    Returns
+    -------
+        A list of tuples containing the validation data.
+    """
+    tokens = line.split()
+    xy = tokens[-6].strip("[]").split(",")  # e.g. '960, 540'
+    xy_diff = tokens[-2].strip("[]").split(",")  # e.g. '-1.5, -2.8'
+    vals = [float(v) for v in [*xy, tokens[-4], *xy_diff]]
+    vals[3] += vals[0]  # pos_x + eye_x i.e. 960 + -1.5
+    vals[4] += vals[1]  # pos_y + eye_y
+
+    return tuple(vals)
+
+
+def _parse_calibration(
+    lines, screen_size=None, screen_distance=None, screen_resolution=None
+):
+    """Parse the lines in the given list and returns a list of Calibration instances.
+
+    Parameters
+    ----------
+        lines: A list of strings, which are The lines in an eyelink ASCII file.
+
+    Returns
+    -------
+        A list containing one or more Calibration instances,
+        one for each calibration that was recorded in the eyelink ASCII file
+        data.
+    """
+    from ...preprocessing.eyetracking.calibration import Calibration
+
+    regex = re.compile(r"\d+")  # for finding numeric characters
+    calibrations = list()
+    rec_start = float(_find_recording_start(lines).split()[1])
+
+    for line_number, line in enumerate(lines):
+        if (
+            "!CAL VALIDATION " in line and "ABORTED" not in line
+        ):  # Start of a calibration
+            tokens = line.split()
+            model = tokens[4]  # e.g. 'HV13'
+            this_eye = tokens[6].lower()  # e.g. 'left'
+            timestamp = float(tokens[1])
+            onset = (timestamp - rec_start) / 1000.0  # in seconds
+            avg_error = float(line.split("avg.")[0].split()[-1])  # e.g. 0.3
+            max_error = float(line.split("max")[0].split()[-1])  # e.g. 0.9
+
+            n_points = int(regex.search(model).group())  # e.g. 13
+            n_points *= 2 if "LR" in line else 1  # one point per eye if "LR"
+            # The next n_point lines contain the validation data
+            points = []
+            for validation_index in range(n_points):
+                subline = lines[line_number + validation_index + 1]
+                if "!CAL VALIDATION" in subline:
+                    continue  # for bino mode, skip the second eye's validation summary
+                subline_eye = subline.split("at")[0].split()[-1].lower()  # e.g. 'left'
+                if subline_eye != this_eye:
+                    continue  # skip the validation lines for the other eye
+                point_info = _parse_validation_line(subline)
+                points.append(point_info)
+            # Convert the list of validation data into a numpy array
+            positions = np.array([point[:2] for point in points])
+            offsets = np.array([point[2] for point in points])
+            gaze = np.array([point[3:] for point in points])
+            # create the Calibration instance
+            calibration = Calibration(
+                onset=max(0.0, onset),  # 0 if calibrated before recording
+                model=model,
+                eye=this_eye,
+                avg_error=avg_error,
+                max_error=max_error,
+                positions=positions,
+                offsets=offsets,
+                gaze=gaze,
+                screen_size=screen_size,
+                screen_distance=screen_distance,
+                screen_resolution=screen_resolution,
+            )
+            calibrations.append(calibration)
+    return calibrations
diff --git a/mne/io/eyelink/eyelink.py b/mne/io/eyelink/eyelink.py
@@ -1,3 +1,5 @@
+"""SR Research Eyelink Load Function."""
+
 # Authors: Dominik Welke <[email protected]>
 #          Scott Huberty <[email protected]>
 #          Christian O'Reilly <[email protected]>
@@ -12,7 +14,7 @@
 from ..base import BaseRaw
 from ..meas_info import create_info
 from ...annotations import Annotations
-from ...utils import logger, verbose, fill_doc, _check_pandas_installed
+from ...utils import _check_fname, _check_pandas_installed, fill_doc, logger, verbose
 
 EYELINK_COLS = {
     "timestamp": ("time",),
@@ -293,13 +295,13 @@ def read_raw_eyelink(
     apply_offsets=False,
     find_overlaps=False,
     overlap_threshold=0.05,
-    gap_description="bad_rec_gap",
+    gap_description=None,
 ):
     """Reader for an Eyelink .asc file.
 
     Parameters
     ----------
-    fname : str
+    fname : path-like
         Path to the eyelink file (.asc).
     %(preload)s
     %(verbose)s
@@ -318,15 +320,20 @@ def read_raw_eyelink(
         saccades) if their start times and their stop times are both not
         separated by more than overlap_threshold.
     overlap_threshold : float (default 0.05)
-        Time in seconds. Threshold of allowable time-gap between the start and
-        stop times of the left and right eyes. If gap is larger than threshold,
-        the :class:`mne.Annotations` will be kept separate (i.e. "blink_L",
-        "blink_R"). If the gap is smaller than the threshold, the
-        :class:`mne.Annotations` will be merged (i.e. "blink_both").
-    gap_description : str (default 'bad_rec_gap')
-        If there are multiple recording blocks in the file, the description of
+        Time in seconds. Threshold of allowable time-gap between both the start and
+        stop times of the left and right eyes. If the gap is larger than the threshold,
+        the :class:`mne.Annotations` will be kept separate (i.e. ``"blink_L"``,
+        ``"blink_R"``). If the gap is smaller than the threshold, the
+        :class:`mne.Annotations` will be merged and labeled as ``"blink_both"``.
+        Defaults to ``0.05`` seconds (50 ms), meaning that if the blink start times of
+        the left and right eyes are separated by less than 50 ms, and the blink stop
+        times of the left and right eyes are separated by less than 50 ms, then the
+        blink will be merged into a single :class:`mne.Annotations`.
+    gap_description : str (default 'BAD_ACQ_SKIP')
+        This parameter is deprecated and will be removed in 1.6.
+        Use :meth:`mne.Annotations.rename` instead.
         the annotation that will span across the gap period between the
-        blocks. Uses 'bad_rec_gap' by default so that these time periods will
+        blocks. Uses ``'BAD_ACQ_SKIP'`` by default so that these time periods will
         be considered bad by MNE and excluded from operations like epoching.
 
     Returns
@@ -337,17 +344,26 @@ def read_raw_eyelink(
     See Also
     --------
     mne.io.Raw : Documentation of attribute and methods.
+
+    Notes
+    -----
+    It is common for SR Research Eyelink eye trackers to only record data during trials.
+    To avoid frequent data discontinuities and to ensure that the data is continuous
+    so that it can be aligned with EEG and MEG data (if applicable), this reader will
+    preserve the times between recording trials and annotate them with
+    ``'BAD_ACQ_SKIP'``.
     """
-    extension = Path(fname).suffix
+    fname = _check_fname(fname, overwrite="read", must_exist=True, name="fname")
+    extension = fname.suffix
     if extension not in ".asc":
         raise ValueError(
             "This reader can only read eyelink .asc files."
-            f" Got extension {extension} instead. consult eyelink"
-            " manual for converting eyelink data format (.edf)"
+            f" Got extension {extension} instead. consult EyeLink"
+            " manual for converting EyeLink data format (.edf)"
             " files to .asc format."
         )
 
-    return RawEyelink(
+    raw_eyelink = RawEyelink(
         fname,
         preload=preload,
         verbose=verbose,
@@ -357,6 +373,7 @@ def read_raw_eyelink(
         overlap_threshold=overlap_threshold,
         gap_desc=gap_description,
     )
+    return raw_eyelink
 
 
 @fill_doc
@@ -365,7 +382,7 @@ class RawEyelink(BaseRaw):
 
     Parameters
     ----------
-    fname : str
+    fname : path-like
         Path to the data file (.XXX).
     create_annotations : bool | list (default True)
         Whether to create mne.Annotations from occular events
@@ -387,11 +404,15 @@ class RawEyelink(BaseRaw):
         the :class:`mne.Annotations` will be kept separate (i.e. "blink_L",
         "blink_R"). If the gap is smaller than the threshold, the
         :class:`mne.Annotations` will be merged (i.e. "blink_both").
-    gap_desc : str (default 'bad_rec_gap')
+    gap_desc : str
         If there are multiple recording blocks in the file, the description of
         the annotation that will span across the gap period between the
-        blocks. Uses 'bad_rec_gap' by default so that these time periods will
-        be considered bad by MNE and excluded from operations like epoching.
+        blocks. Default is ``None``, which uses 'BAD_ACQ_SKIP' by default so that these
+        timeperiods will be considered bad by MNE and excluded from operations like
+        epoching. Note that this parameter is deprecated and will be removed in 1.6.
+        Use ``mne.annotations.rename`` instead.
+
+
     %(preload)s
     %(verbose)s
 
@@ -402,23 +423,6 @@ class RawEyelink(BaseRaw):
     dataframes : dict
         Dictionary of pandas DataFrames. One for eyetracking samples,
         and one for each type of eyelink event (blinks, messages, etc)
-    _sample_lines : list
-        List of lists, each list is one sample containing eyetracking
-        X/Y and pupil channel data (+ other channels, if they exist)
-    _event_lines : dict
-        Each key contains a list of lists, for an event-type that occurred
-        during the recording period. Events can vary, from occular events
-        (blinks, saccades, fixations), to messages from the stimulus
-        presentation software, or info from a response controller.
-    _system_lines : list
-        List of tab delimited strings. Each string is a system message,
-        that in most cases aren't needed. System messages occur for
-        Eyelinks DataViewer application.
-    _tracking_mode : str
-        Whether whether a single eye was tracked ('monocular'), or both
-        ('binocular').
-    _gap_desc : str
-        The description to be used for annotations returned by _make_gap_annots
 
     See Also
     --------
@@ -435,17 +439,26 @@ def __init__(
         apply_offsets=False,
         find_overlaps=False,
         overlap_threshold=0.05,
-        gap_desc="bad_rec_gap",
+        gap_desc=None,
     ):
         logger.info("Loading {}".format(fname))
 
         self.fname = Path(fname)
-        self._sample_lines = None
-        self._event_lines = None
-        self._system_lines = None
+        self._sample_lines = None  # sample lines from file
+        self._event_lines = None  # event messages from file
+        self._system_lines = None  # unparsed lines of system messages from file
         self._tracking_mode = None  # assigned in self._infer_col_names
         self._meas_date = None
         self._rec_info = None
+        if gap_desc is None:
+            gap_desc = "BAD_ACQ_SKIP"
+        else:
+            logger.warn(
+                "gap_description is deprecated in 1.5 and will be removed in 1.6, "
+                "use raw.annotations.rename to use a description other than "
+                "'BAD_ACQ_SKIP'",
+                FutureWarning,
+            )
         self._gap_desc = gap_desc
         self.dataframes = {}
 

diff --git a/mne/io/eyelink/tests/test_eyelink.py b/mne/io/eyelink/tests/test_eyelink.py
@@ -28,6 +28,7 @@ def test_eyetrack_not_data_ch():
 @pytest.mark.parametrize(
     "fname, create_annotations, find_overlaps",
     [
+        (fname, False, False),
         (fname, False, False),
         (fname, True, False),
         (fname, True, True),
@@ -37,7 +38,9 @@ def test_eyetrack_not_data_ch():
 def test_eyelink(fname, create_annotations, find_overlaps):
     """Test reading eyelink asc files."""
     raw = read_raw_eyelink(
-        fname, create_annotations=create_annotations, find_overlaps=find_overlaps
+        fname,
+        create_annotations=create_annotations,
+        find_overlaps=find_overlaps,
     )
 
     # First, tests that shouldn't change based on function arguments

diff --git a/mne/preprocessing/eyetracking/__init__.py b/mne/preprocessing/eyetracking/__init__.py
@@ -5,3 +5,4 @@
 # License: BSD-3-Clause
 
 from .eyetracking import set_channel_types_eyetrack
+from .calibration import Calibration, read_eyelink_calibration
Original file line number	Diff line number	Diff line change
Expand Up		@@ -5,3 +5,4 @@
		# License: BSD-3-Clause

		from .eyetracking import set_channel_types_eyetrack
		from .calibration import Calibration, read_eyelink_calibration