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chkothechkothe
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added initial BIDS import/export/preproc support
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‎pyproject.toml‎

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@@ -26,13 +26,20 @@ dependencies = [
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"oct2py>=5.5.0",
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"torch>=1.10.0",
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"h5py>=3.3.0",
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"pybids>=0.4",
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"pyedflib>=0.1.42",
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"python-picard",
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"h5py"
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"neo",
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"pynvml",
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"psutil",
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"colorama",
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"threadpoolctl"
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]
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[tool.setuptools.package-data]
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"eegprep" = ["eeglab/*", "netICL.mat"]
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[project.urls]
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Homepage = "https://github.com/sccn/eegprep"
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Issues = "https://github.com/sccn/eegprep/issues"

‎requirements.txt‎

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@@ -6,4 +6,11 @@ oct2py>=5.5.0
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torch>=1.10.0
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numexpr>=2.0.0
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h5py>=3.3.0
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pybids>=0.4
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python-picard==0.8
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neo>=0.14.2
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pyedflib>=0.1.42
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psutil
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pynvml
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colorama
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threadpoolctl

‎src/eegprep/__init__.py‎

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from .clean_windows import clean_windows
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# from .eeg_compare import eeg_compare
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from .clean_artifacts import clean_artifacts
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from .pop_load_frombids import pop_load_frombids
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from .bids_list_eeg_files import bids_list_eeg_files
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from .bids_preproc import bids_preproc

‎src/eegprep/bids_list_eeg_files.py‎

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from typing import List
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# list of valid file extensions for raw EEG data files in BIDS format
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eeg_extensions = ('.vhdr', '.edf', '.bdf', '.set')
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def bids_list_eeg_files(root: str) -> List[str]:
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"""
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Return a list of all EEG raw-data files in a BIDS dataset.
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Parameters:
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-----------
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root : str
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The root directory containing BIDS data.
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Returns:
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--------
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List[str]
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A list of file paths to EEG files in the BIDS dataset.
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"""
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from bids import BIDSLayout
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layout = BIDSLayout(root)
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eeg_files = layout.get(suffix='eeg', return_type='filename')
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# have to filter by extension since the layout will also return the sidecar files
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# (e.g., .fdt and .vmrk) and other files that are not raw EEG data files
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filelist = [fn for fn in eeg_files if fn.endswith(eeg_extensions)]
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return filelist

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