Reference interpolates instead of deletes channels manually marked as…

… bad, closes #146 (#156)

* allows manually marked bad channels to be excluded from reference / interpolated, without being removed (which had been causing an error)

* adds new contributor to CITATION.cff

* adds new contributor ORCID

* Update authors.rst

* Update changelog.rst

* fixes some formatting issues flagged by CI

* adds manual bad channels to find_noisy_channels

* changes name of manual bads to match find_noisy_channels (which requires a specific format to work properly)

* adds test coverage

* fixes bug and formatting in test

* format

CITATION.cff

@@ -51,6 +51,10 @@ authors:
     - given-names: Ayush
       family-names: Agarwal
       affiliation: 'Techno India University, India'
+    - given-names: John
+      family-names: Veillette
+      affiliation: 'Department of Psychology, University of Chicago, Chicago, IL, USA'
+      orcid: 'https://orcid.org/0000-0002-0332-4372'
 type: software
 repository-code: 'https://github.com/sappelhoff/pyprep'
 license: MIT

docs/authors.rst

@@ -10,3 +10,4 @@
 .. _Stefan Appelhoff: https://stefanappelhoff.com/
 .. _Victor Xiang: https://github.com/Nick3151
 .. _Yorguin Mantilla: https://github.com/yjmantilla
+.. _John Veillette: https://github.com/john-veillette

docs/changelog.rst

@@ -31,7 +31,7 @@ Changelog
 
 Bug
 ~~~
-- nothing yet
+- :class:`~pyprep.Reference` now keeps and interpolates channels channels manually marked as bad before PREP, by `John Veillette`_ (:gh:`146`)
 
 Code health
 ~~~~~~~~~~~

pyprep/find_noisy_channels.py

@@ -59,6 +59,7 @@ def __init__(self, raw, do_detrend=True, random_state=None, matlab_strict=False)
 
         raw.load_data()
         self.raw_mne = raw.copy()
+        self.bad_by_manual = raw.info["bads"]
         self.raw_mne.pick_types(eeg=True)
         self.sample_rate = raw.info["sfreq"]
         if do_detrend:
@@ -162,6 +163,7 @@ def get_bads(self, verbose=False, as_dict=False):
             "bad_by_SNR": self.bad_by_SNR,
             "bad_by_dropout": self.bad_by_dropout,
             "bad_by_ransac": self.bad_by_ransac,
+            "bad_by_manual": self.bad_by_manual,
         }
 
         all_bads = set()

pyprep/reference.py

@@ -83,7 +83,7 @@ def __init__(
         raw.load_data()
         self.raw = raw.copy()
         self.ch_names = self.raw.ch_names
-        self.raw.pick_types(eeg=True, eog=False, meg=False)
+        self.raw.pick_types(eeg=True, eog=False, meg=False, exclude=[])
         self.ch_names_eeg = self.raw.ch_names
         self.EEG = self.raw.get_data()
         self.reference_channels = params["ref_chs"]
@@ -97,6 +97,7 @@ def __init__(
         self.random_state = check_random_state(random_state)
         self._extra_info = {}
         self.matlab_strict = matlab_strict
+        self.bads_manual = raw.info["bads"]
 
     def perform_reference(self, max_iterations=4):
         """Estimate the true signal mean and interpolate bad channels.
@@ -149,6 +150,7 @@ def perform_reference(self, max_iterations=4):
         self.bad_before_interpolation = noisy_detector.get_bads(verbose=True)
         self.EEG_before_interpolation = self.EEG.copy()
         self.noisy_channels_before_interpolation = noisy_detector.get_bads(as_dict=True)
+        self.noisy_channels_before_interpolation["bad_by_manual"] = self.bads_manual
         self._extra_info["interpolated"] = noisy_detector._extra_info
 
         bad_channels = _union(self.bad_before_interpolation, self.unusable_channels)
@@ -223,7 +225,7 @@ def robust_reference(self, max_iterations=4):
         # Determine channels to use/exclude from initial reference estimation
         self.unusable_channels = _union(
             noisy_detector.bad_by_nan + noisy_detector.bad_by_flat,
-            noisy_detector.bad_by_SNR,
+            noisy_detector.bad_by_SNR + self.bads_manual,
         )
         reference_channels = _set_diff(self.reference_channels, self.unusable_channels)
 
@@ -237,6 +239,7 @@ def robust_reference(self, max_iterations=4):
             "bad_by_SNR": [],
             "bad_by_dropout": [],
             "bad_by_ransac": [],
+            "bad_by_manual": self.bads_manual,
             "bad_all": [],
         }
 
@@ -282,7 +285,8 @@ def robust_reference(self, max_iterations=4):
                 noisy[bad_type] = _union(noisy[bad_type], noisy_new[bad_type])
                 if bad_type not in ignore:
                     bad_chans.update(noisy[bad_type])
-            noisy["bad_all"] = list(bad_chans)
+            noisy["bad_by_manual"] = self.bads_manual
+            noisy["bad_all"] = list(bad_chans) + self.bads_manual
             logger.info(f"Bad channels: {noisy}")
 
             if (

tests/test_find_noisy_channels.py

@@ -74,6 +74,20 @@ def test_bad_by_nan(raw_tmp):
     assert nd.bad_by_nan == [raw_tmp.ch_names[nan_idx]]
 
 
+def test_bad_by_manual(raw_tmp):
+    """Test the detection of channels marked bad a priori."""
+    n_chans = raw_tmp.get_data().shape[0]
+    nan_idx = int(rng.integers(0, n_chans, 1)[0])
+    raw_tmp._data[nan_idx, 3] = np.nan
+    raw_tmp.info["bads"] = [raw_tmp.ch_names[0]]
+
+    # Test record of a priori bad channels on NoisyChannels init
+    nd = NoisyChannels(raw_tmp, do_detrend=False)
+    assert nd.bad_by_manual == [raw_tmp.ch_names[0]]
+    assert raw_tmp.ch_names[0] in nd.get_bads(as_dict=False)
+    raw_tmp.info["bads"] = []
+
+
 def test_bad_by_flat(raw_tmp):
     """Test the detection of channels with flat or very weak signals."""
     # Make the signal for a random channel extremely weak

tests/test_reference.py

@@ -23,6 +23,7 @@ def test_basic_input(raw, montage):
     reference = Reference(raw_tmp, params, ransac=False)
     reference.perform_reference()
     assert isinstance(reference.noisy_channels, dict)
+    assert isinstance(reference.noisy_channels["bad_by_manual"], list)
     assert isinstance(reference.noisy_channels_original, dict)
     assert isinstance(reference.bad_before_interpolation, list)
     assert isinstance(reference.reference_signal, np.ndarray)