Merge branch 'main' into complex_spectrum

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 repos:
   # Ruff mne
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.4
+    rev: v0.5.5
     hooks:
       - id: ruff
         name: ruff lint mne

doc/changes/devel/12759.bugfix.rst

@@ -0,0 +1 @@
+Assure that blink times are handled correctly :func:`mne.preprocessing.eyetracking.interpolate_blinks`, even when the raw object is cropped by `Scott Huberty`_ and :newcontrib:`Sammi Chekroud`.

doc/changes/devel/12760.bugfix.rst

@@ -0,0 +1 @@
+Fix bug in :func:`~mne.preprocessing.maxwell_filter_prepare_emptyroom` where a difference in sampling frequencies between data and emptyroom files was ignored, by `Daniel McCloy`_.

doc/changes/names.inc

@@ -627,3 +627,5 @@
 .. _Zvi Baratz: https://github.com/ZviBaratz
 
 .. _Seyed Yahya Shirazi: https://neuromechanist.github.io
+
+.. _Sammi Chekroud: https://github.com/schekroud

mne/preprocessing/eyetracking/_pupillometry.py

@@ -6,6 +6,7 @@
 import numpy as np
 
 from ..._fiff.constants import FIFF
+from ...annotations import _annotations_starts_stops
 from ...io import BaseRaw
 from ...utils import _check_preload, _validate_type, logger, warn
 
@@ -88,12 +89,15 @@ def _interpolate_blinks(raw, buffer, blink_annots, interpolate_gaze):
                 continue
         # Create an empty boolean mask
         mask = np.zeros_like(raw.times, dtype=bool)
-        for annot in blink_annots:
+        starts, ends = _annotations_starts_stops(raw, "BAD_blink")
+        starts = np.divide(starts, raw.info["sfreq"])
+        ends = np.divide(ends, raw.info["sfreq"])
+        for annot, start, end in zip(blink_annots, starts, ends):
             if "ch_names" not in annot or not annot["ch_names"]:
                 msg = f"Blink annotation missing values for 'ch_names' key: {annot}"
                 raise ValueError(msg)
-            start = annot["onset"] - pre_buffer
-            end = annot["onset"] + annot["duration"] + post_buffer
+            start -= pre_buffer
+            end += post_buffer
             if ch_info["ch_name"] not in annot["ch_names"]:
                 continue  # skip if the channel is not in the blink annotation
             # Update the mask for times within the current blink period

mne/preprocessing/eyetracking/tests/test_pupillometry.py

@@ -6,6 +6,7 @@
 import pytest
 
 from mne import create_info
+from mne.annotations import _annotations_starts_stops
 from mne.datasets.testing import data_path, requires_testing_data
 from mne.io import RawArray, read_raw_eyelink
 from mne.preprocessing.eyetracking import interpolate_blinks
@@ -16,17 +17,20 @@
 
 @requires_testing_data
 @pytest.mark.parametrize(
-    "buffer, match, cause_error, interpolate_gaze",
+    "buffer, match, cause_error, interpolate_gaze, crop",
     [
-        (0.025, "BAD_blink", False, False),
-        (0.025, "BAD_blink", False, True),
-        ((0.025, 0.025), ["random_annot"], False, False),
-        (0.025, "BAD_blink", True, False),
+        (0.025, "BAD_blink", False, False, False),
+        (0.025, "BAD_blink", False, True, True),
+        ((0.025, 0.025), ["random_annot"], False, False, False),
+        (0.025, "BAD_blink", True, False, False),
     ],
 )
-def test_interpolate_blinks(buffer, match, cause_error, interpolate_gaze):
+def test_interpolate_blinks(buffer, match, cause_error, interpolate_gaze, crop):
     """Test interpolating pupil data during blinks."""
     raw = read_raw_eyelink(fname, create_annotations=["blinks"], find_overlaps=True)
+    if crop:
+        raw.crop(tmin=2)
+        assert raw.first_time == 2.0
     # Create a dummy stim channel
     # this will hit a certain line in the interpolate_blinks function
     info = create_info(["STI"], raw.info["sfreq"], ["stim"])
@@ -35,8 +39,11 @@ def test_interpolate_blinks(buffer, match, cause_error, interpolate_gaze):
     raw.add_channels([stim_raw], force_update_info=True)
 
     # Get the indices of the first blink
-    first_blink_start = raw.annotations[0]["onset"]
-    first_blink_end = raw.annotations[0]["onset"] + raw.annotations[0]["duration"]
+    blink_starts, blink_ends = _annotations_starts_stops(raw, "BAD_blink")
+    blink_starts = np.divide(blink_starts, raw.info["sfreq"])
+    blink_ends = np.divide(blink_ends, raw.info["sfreq"])
+    first_blink_start = blink_starts[0]
+    first_blink_end = blink_ends[0]
     if match == ["random_annot"]:
         msg = "No annotations matching"
         with pytest.warns(RuntimeWarning, match=msg):

mne/preprocessing/maxwell.py

@@ -181,7 +181,8 @@ def maxwell_filter_prepare_emptyroom(
 
     # handle first_samp
     raw_er_prepared.annotations.onset += raw.first_time - raw_er_prepared.first_time
-    raw_er_prepared._cropped_samp = raw._cropped_samp
+    # don't copy _cropped_samp directly, as sfreqs may differ
+    raw_er_prepared._cropped_samp = raw_er_prepared.time_as_index(raw.first_time).item()
 
     # handle annotations
     if annotations != "keep":

mne/preprocessing/tests/test_maxwell.py

@@ -1820,8 +1820,9 @@ def test_prepare_emptyroom_bads(bads):
 @pytest.mark.parametrize("set_annot_when", ("before", "after"))
 @pytest.mark.parametrize("raw_meas_date", ("orig", None))
 @pytest.mark.parametrize("raw_er_meas_date", ("orig", None))
+@pytest.mark.parametrize("equal_sfreq", (False, True))
 def test_prepare_emptyroom_annot_first_samp(
-    set_annot_when, raw_meas_date, raw_er_meas_date
+    set_annot_when, raw_meas_date, raw_er_meas_date, equal_sfreq
 ):
     """Test prepare_emptyroom."""
     raw = read_raw_fif(raw_fname, allow_maxshield="yes", verbose=False)
@@ -1861,12 +1862,15 @@ def test_prepare_emptyroom_annot_first_samp(
         assert set_annot_when == "after"
         meas_date = "from_raw"
         want_date = raw.info["meas_date"]
+    if not equal_sfreq:
+        with raw_er.info._unlock():
+            raw_er.info["sfreq"] -= 100
     raw_er_prepared = maxwell_filter_prepare_emptyroom(
         raw_er=raw_er, raw=raw, meas_date=meas_date, emit_warning=True
     )
     assert raw_er.first_samp == raw_er_first_samp_orig
     assert raw_er_prepared.info["meas_date"] == want_date
-    assert raw_er_prepared.first_samp == raw.first_samp
+    assert raw_er_prepared.first_time == raw.first_time
 
     # Ensure (movement) annotations carry over regardless of whether they're
     # set before or after preparation
@@ -1878,7 +1882,8 @@ def test_prepare_emptyroom_annot_first_samp(
     prop_bad = np.isnan(raw.get_data([0], reject_by_annotation="nan")).mean()
     assert 0.3 < prop_bad < 0.4
     assert len(raw_er_prepared.annotations) == want_annot
-    prop_bad_er = np.isnan(
-        raw_er_prepared.get_data([0], reject_by_annotation="nan")
-    ).mean()
-    assert_allclose(prop_bad, prop_bad_er)
+    if equal_sfreq:
+        prop_bad_er = np.isnan(
+            raw_er_prepared.get_data([0], reject_by_annotation="nan")
+        ).mean()
+        assert_allclose(prop_bad, prop_bad_er)