Retain HF noise channels during RANSAC when not bad by any other metr…

…ic (#64) * Retain HF noise channels during RANSAC * Updated whats_new.rst * Fix broken unit test
sappelhoff · Apr 12, 2021 · 032cad1 · 032cad1
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diff --git a/docs/whats_new.rst b/docs/whats_new.rst
@@ -38,6 +38,7 @@ Changelog
 - Added two keys to the :attr:`PrepPipeline.noisy_channels_original <prep_pipeline.PrepPipeline>` dictionary: ``bad_by_dropout`` and ``bad_by_SNR``, by `Yorguin Mantilla`_ (:gh:`45`)
 - Changed RANSAC chunking logic to reduce max memory use and prefer equal chunk sizes where possible, by `Austin Hurst`_ (:gh:`44`)
 - Changed RANSAC's random channel sampling code to produce the same results as MATLAB PREP for the same random seed, additionally changing the default RANSAC sample size from 25% of all *good* channels (e.g. 15 for a 64-channel dataset with 4 bad channels) to 25% of *all* channels (e.g. 16 for the same dataset), by `Austin Hurst`_ (:gh:`62`)
+- Changed RANSAC so that "bad by high-frequency noise" channels are retained when making channel predictions (provided they aren't flagged as bad by any other metric), matching MATLAB PREP behaviour, by `Austin Hurst`_ (:gh:`64`)
 
 Bug
 ~~~

diff --git a/pyprep/find_noisy_channels.py b/pyprep/find_noisy_channels.py
@@ -421,13 +421,18 @@ def find_bad_by_ransac(
             (2017). Autoreject: Automated Artifact Rejection for MEG and EEG
             Data. NeuroImage, 159, 417-429
         """
+        exclude_from_ransac = (
+            self.bad_by_correlation +
+            self.bad_by_deviation +
+            self.bad_by_dropout
+        )
         self.bad_by_ransac, _ = find_bad_by_ransac(
             self.EEGData,
             self.sample_rate,
             self.signal_len,
             self.ch_names_new,
             self.raw_mne._get_channel_positions(),
-            self.get_bads(),
+            exclude_from_ransac,
             n_samples,
             fraction_good,
             corr_thresh,

diff --git a/tests/test_find_noisy_channels.py b/tests/test_find_noisy_channels.py
@@ -153,7 +153,7 @@ def test_findnoisychannels(raw, montage):
     # Make 80% of channels bad
     num_bad_channels = int(raw._data.shape[0] * 0.8)
     bad_channels = raw.info["ch_names"][0:num_bad_channels]
-    nd.bad_by_hf_noise = bad_channels
+    nd.bad_by_deviation = bad_channels
     with pytest.raises(IOError):
         nd.find_bad_by_ransac()