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Replaced deprecated pick_types with raw.pick #154

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Replaced deprecated pick_types with raw.pick #154

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f4911b7
Replaced deprecated `pick_types` with `raw.pick`
Ayush-Devs Aug 20, 2024
a9d7c59
all tests passed
Ayush-Devs Aug 21, 2024
b7a3aff
added tests for utils.py
Ayush-Devs Aug 21, 2024
b412d3c
added new tests
Ayush-Devs Aug 21, 2024
e16f246
tests passed
Ayush-Devs Aug 22, 2024
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2 changes: 1 addition & 1 deletion pyprep/find_noisy_channels.py
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Original file line number Diff line number Diff line change
Expand Up @@ -54,7 +54,7 @@ def __init__(self, raw, do_detrend=True, random_state=None, matlab_strict=False)

raw.load_data()
self.raw_mne = raw.copy()
self.raw_mne.pick_types(eeg=True)
self.raw_mne.pick(picks="eeg")
self.sample_rate = raw.info["sfreq"]
if do_detrend:
self.raw_mne._data = removeTrend(
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2 changes: 1 addition & 1 deletion pyprep/reference.py
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Expand Up @@ -79,7 +79,7 @@ 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(picks="eeg")
self.ch_names_eeg = self.raw.ch_names
self.EEG = self.raw.get_data()
self.reference_channels = params["ref_chs"]
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5 changes: 2 additions & 3 deletions pyprep/tests/test_prep_pipeline.py
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@@ -1,6 +1,5 @@
"""Test the full PREP pipeline."""
import matplotlib.pyplot as plt
import mne
import numpy as np
import pytest
import scipy.io as sio
Expand All @@ -13,7 +12,7 @@
@pytest.mark.usefixtures("raw", "montage")
def test_prep_pipeline(raw, montage):
"""Test prep pipeline."""
eeg_index = mne.pick_types(raw.info, eeg=True, eog=False, meg=False)
eeg_index = raw.pick(picks="eeg")
raw_copy = raw.copy()
ch_names = raw_copy.info["ch_names"]
ch_names_eeg = list(np.asarray(ch_names)[eeg_index])
Expand Down Expand Up @@ -254,7 +253,7 @@ def test_prep_pipeline_non_eeg(raw, montage):
@pytest.mark.usefixtures("raw", "montage")
def test_prep_pipeline_filter_kwargs(raw, montage):
"""Test prep pipeline with filter kwargs."""
eeg_index = mne.pick_types(raw.info, eeg=True, eog=False, meg=False)
eeg_index = raw.pick(picks="eeg")
raw_copy = raw.copy()
ch_names = raw_copy.info["ch_names"]
ch_names_eeg = list(np.asarray(ch_names)[eeg_index])
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6 changes: 3 additions & 3 deletions pyprep/utils.py
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Expand Up @@ -2,7 +2,7 @@
import math
from cmath import sqrt

import mne
# import mne
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please just remove this line instead of commenting it out

import numpy as np
import scipy.interpolate
from mne.surface import _normalize_vectors
Expand Down Expand Up @@ -355,8 +355,8 @@ def _eeglab_interpolate_bads(raw):

"""
# Get the indices of good and bad EEG channels
eeg_chans = mne.pick_types(raw.info, eeg=True, exclude=[])
good_idx = mne.pick_types(raw.info, eeg=True, exclude="bads")
eeg_chans = raw.pick(picks="eeg", exclude=[])
good_idx = raw.pick(picks="eeg", exclude="bads")
bad_idx = sorted(_set_diff(eeg_chans, good_idx))

# Get the spatial coordinates of the good and bad electrodes
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