eegdash 0.4.0.dev171__py3-none-any.whl → 0.4.0.dev176__py3-none-any.whl

eegdash/__init__.py

@@ -18,4 +18,4 @@ _init_mongo_client()
 
 __all__ = ["EEGDash", "EEGDashDataset", "EEGChallengeDataset", "preprocessing"]
 
-__version__ = "0.4.0.dev171"
+__version__ = "0.4.0.dev176"

eegdash/data_utils.py

@@ -22,10 +22,10 @@ import mne
 import mne_bids
 import numpy as np
 import pandas as pd
-from bids import BIDSLayout
 from joblib import Parallel, delayed
 from mne._fiff.utils import _read_segments_file
 from mne.io import BaseRaw
+from mne.utils.check import _soft_import
 from mne_bids import BIDSPath
 
 from braindecode.datasets import BaseDataset
@@ -348,6 +348,14 @@ class EEGBIDSDataset:
         data_dir=None,  # location of bids dataset
         dataset="",  # dataset name
     ):
+        bids_lib = _soft_import("bids", purpose="digestion of datasets", strict=False)
+
+        if bids_lib is None:
+            raise ImportError(
+                "The 'pybids' package is required to use EEGBIDSDataset. "
+                "Please install it via 'pip install eegdash[digestion]'."
+            )
+
         if data_dir is None or not os.path.exists(data_dir):
             raise ValueError("data_dir must be specified and must exist")
         self.bidsdir = Path(data_dir)
@@ -359,7 +367,7 @@ class EEGBIDSDataset:
             raise AssertionError(
                 f"BIDS directory '{dir_name}' does not correspond to dataset '{self.dataset}'"
             )
-        self.layout = BIDSLayout(data_dir)
+        self.layout = bids_lib.BIDSLayout(data_dir)
 
         # get all recording files in the bids directory
         self.files = self._get_recordings(self.layout)
@@ -379,7 +387,7 @@ class EEGBIDSDataset:
         """
         return self.get_bids_file_attribute("modality", self.files[0]).lower() == "eeg"
 
-    def _get_recordings(self, layout: BIDSLayout) -> list[str]:
+    def _get_recordings(self, layout) -> list[str]:
         """Get a list of all EEG recording files in the BIDS layout."""
         files = []
         for ext, exts in self.RAW_EXTENSIONS.items():

eegdash/features/datasets.py

@@ -18,6 +18,11 @@ from braindecode.datasets.base import (
 
 from ..logging import logger
 
+__all__ = [
+    "FeaturesDataset",
+    "FeaturesConcatDataset",
+]
+
 
 class FeaturesDataset(EEGWindowsDataset):
     """A dataset of features extracted from EEG windows.

eegdash/features/decorators.py

@@ -10,6 +10,14 @@ from .extractors import (
     _get_underlying_func,
 )
 
+__all__ = [
+    "bivariate_feature",
+    "FeatureKind",
+    "FeaturePredecessor",
+    "multivariate_feature",
+    "univariate_feature",
+]
+
 
 class FeaturePredecessor:
     """A decorator to specify parent extractors for a feature function.

eegdash/features/extractors.py

@@ -8,6 +8,15 @@ from typing import Dict
 import numpy as np
 from numba.core.dispatcher import Dispatcher
 
+__all__ = [
+    "BivariateFeature",
+    "DirectedBivariateFeature",
+    "FeatureExtractor",
+    "MultivariateFeature",
+    "TrainableFeature",
+    "UnivariateFeature",
+]
+
 
 def _get_underlying_func(func: Callable) -> Callable:
     """Get the underlying function from a potential wrapper.

eegdash/features/feature_bank/signal.py

@@ -8,20 +8,21 @@ from ..extractors import FeatureExtractor
 
 __all__ = [
     "HilbertFeatureExtractor",
-    "signal_mean",
-    "signal_variance",
-    "signal_skewness",
+    "SIGNAL_PREDECESSORS",
+    "signal_decorrelation_time",
+    "signal_hjorth_activity",
+    "signal_hjorth_complexity",
+    "signal_hjorth_mobility",
     "signal_kurtosis",
-    "signal_std",
-    "signal_root_mean_square",
+    "signal_line_length",
+    "signal_mean",
     "signal_peak_to_peak",
     "signal_quantile",
+    "signal_root_mean_square",
+    "signal_skewness",
+    "signal_std",
+    "signal_variance",
     "signal_zero_crossings",
-    "signal_line_length",
-    "signal_hjorth_activity",
-    "signal_hjorth_mobility",
-    "signal_hjorth_complexity",
-    "signal_decorrelation_time",
 ]
 
 

eegdash/features/feature_bank/utils.py

@@ -1,5 +1,13 @@
 import numpy as np
 
+__all__ = [
+    "DEFAULT_FREQ_BANDS",
+    "get_valid_freq_band",
+    "reduce_freq_bands",
+    "slice_freq_band",
+]
+
+
 DEFAULT_FREQ_BANDS = {
     "delta": (1, 4.5),
     "theta": (4.5, 8),

eegdash/features/inspect.py

@@ -6,6 +6,14 @@ from collections.abc import Callable
 from . import extractors, feature_bank
 from .extractors import FeatureExtractor, MultivariateFeature, _get_underlying_func
 
+__all__ = [
+    "get_all_feature_extractors",
+    "get_all_feature_kinds",
+    "get_all_features",
+    "get_feature_kind",
+    "get_feature_predecessors",
+]
+
 
 def get_feature_predecessors(feature_or_extractor: Callable) -> list:
     """Get the dependency hierarchy for a feature or feature extractor.

eegdash/features/serialization.py

@@ -2,7 +2,7 @@
 
 See Also
 --------
-https://github.com/braindecode/braindecode//blob/master/braindecode/datautil/serialization.py#L165-L229
+https://github.com/braindecode/braindecode/blob/master/braindecode/datautil/serialization.py#L165-L229
 
 """
 
@@ -18,6 +18,10 @@ from braindecode.datautil.serialization import _load_kwargs_json
 
 from .datasets import FeaturesConcatDataset, FeaturesDataset
 
+__all__ = [
+    "load_features_concat_dataset",
+]
+
 
 def load_features_concat_dataset(
     path: str | Path, ids_to_load: list[int] | None = None, n_jobs: int = 1

eegdash/features/utils.py

@@ -17,6 +17,11 @@ from braindecode.datasets.base import (
 from .datasets import FeaturesConcatDataset, FeaturesDataset
 from .extractors import FeatureExtractor
 
+__all__ = [
+    "extract_features",
+    "fit_feature_extractors",
+]
+
 
 def _extract_features_from_windowsdataset(
     win_ds: EEGWindowsDataset | WindowsDataset,

{eegdash-0.4.0.dev171.dist-info → eegdash-0.4.0.dev176.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: eegdash
-Version: 0.4.0.dev171
+Version: 0.4.0.dev176
 Summary: EEG data for machine learning
 Author-email: Young Truong <dt.young112@gmail.com>, Arnaud Delorme <adelorme@gmail.com>, Aviv Dotan <avivd220@gmail.com>, Oren Shriki <oren70@gmail.com>, Bruno Aristimunha <b.aristimunha@gmail.com>
 License-Expression: GPL-3.0-only
@@ -29,11 +29,9 @@ Requires-Dist: mne_bids>=0.17.0
 Requires-Dist: numba
 Requires-Dist: numpy
 Requires-Dist: pandas
-Requires-Dist: pybids
 Requires-Dist: pymongo
 Requires-Dist: python-dotenv
 Requires-Dist: s3fs
-Requires-Dist: scipy
 Requires-Dist: tqdm
 Requires-Dist: h5io>=0.2.4
 Requires-Dist: pymatreader
@@ -44,6 +42,7 @@ Requires-Dist: rich
 Provides-Extra: tests
 Requires-Dist: pytest; extra == "tests"
 Requires-Dist: pytest-cov; extra == "tests"
+Requires-Dist: pytest-sugar; extra == "tests"
 Requires-Dist: codecov; extra == "tests"
 Requires-Dist: pytest_cases; extra == "tests"
 Requires-Dist: pytest-benchmark; extra == "tests"
@@ -66,10 +65,13 @@ Requires-Dist: lightgbm; extra == "docs"
 Requires-Dist: plotly; extra == "docs"
 Requires-Dist: nbformat; extra == "docs"
 Requires-Dist: graphviz; extra == "docs"
+Provides-Extra: digestion
+Requires-Dist: pybids; extra == "digestion"
 Provides-Extra: all
 Requires-Dist: eegdash[docs]; extra == "all"
 Requires-Dist: eegdash[dev]; extra == "all"
 Requires-Dist: eegdash[tests]; extra == "all"
+Requires-Dist: eegdash[digestion]; extra == "all"
 Dynamic: license-file
 
 # EEG-Dash

{eegdash-0.4.0.dev171.dist-info → eegdash-0.4.0.dev176.dist-info}/RECORD

@@ -1,8 +1,8 @@
-eegdash/__init__.py,sha256=WOL6nlqcp_GvfNydukEWbMYjRsGQOcUT1ODXQaWUAQc,704
+eegdash/__init__.py,sha256=A7Uh_kXQuDzVmoSuZyWHE7RRxwhA2_JzaAmLD7LZM4E,704
 eegdash/api.py,sha256=az7uUYrEvJfBtzvkzYKzXqEztDSCMsCmgIywpdzYqc8,38381
 eegdash/bids_eeg_metadata.py,sha256=kEmFUe07tivkuIoC5T-YwfO4QQYJBxuc769ZBV1UCKo,16682
 eegdash/const.py,sha256=9WMetN7YMQJbkN2PhzItxtVRZ4VBXLP82vFu9pY6xok,9066
-eegdash/data_utils.py,sha256=nCiGi1LGClTOUUnEPfykcCtza1o4BDW9kb0JBymwbs4,26206
+eegdash/data_utils.py,sha256=LOA-8ShugnIXlqmGmmSClTCBr3khQSconmYAcvT_9tY,26528
 eegdash/downloader.py,sha256=Z-9EEJildqJxIihwdtXc_h9kzCkuF9LWIwQEfyG9Huw,6030
 eegdash/logging.py,sha256=OQ4jMtwv1h-gzjxmr3PCpcsKi5-3Nhd3r9PJ4UN7oQI,1467
 eegdash/mongodb.py,sha256=9FJDeEebOD5RzNYfAf1lhr0R-pECAlnug6Sjhd9_oUw,3469
@@ -13,25 +13,25 @@ eegdash/dataset/dataset.py,sha256=DnR6LoirPNV45MECq42MNtIPyhL7DTFuwPWavVWZmmA,81
 eegdash/dataset/dataset_summary.csv,sha256=YJX-BitOyo-5nsHBd3ECIY1u7lFBjMQAFfCUPLYEgpo,25289
 eegdash/dataset/registry.py,sha256=5TOCWalA0RV7omRoYS0OzdcSaOTvXvqos74_Vj2jv0M,9127
 eegdash/features/__init__.py,sha256=BXNhjvL4_SSFAY1lcP9nyGpkbJNtoOMH4AHlF6OyABo,4078
-eegdash/features/datasets.py,sha256=5BQZMNwsUsugW05_qGSdKbCFVgI4KP8PGukLx5y8p2A,24569
-eegdash/features/decorators.py,sha256=xK6-HcusPRnKcUCot3DEzkoRjlazd9OLVvq6R8JO0Nw,3826
-eegdash/features/extractors.py,sha256=1srmgEsj0mFkkyQByFOsuL4r0ZpAQGdBPjiTpJWswQ8,11766
-eegdash/features/inspect.py,sha256=IF3kv1T-uLm2KKwaKhlBBDMrqNFnrnKqKpEvkOu8gJA,3911
-eegdash/features/serialization.py,sha256=ppRFvbd7qhrZBun61hJOY7e5X0HTTckcGh9dREMS2iI,3888
-eegdash/features/utils.py,sha256=lK-epGlkRm9_psqsbgiWzan_gFC8BuizCRu44PSTvco,6092
+eegdash/features/datasets.py,sha256=-Y-CxBypJu3dHyNDLFKFIo-zIi4qEInahZTgJslnrVQ,24636
+eegdash/features/decorators.py,sha256=VOCeL6rFa8wqkRJRnecWaTqdBW2B9MO724vGGk1AkGo,3965
+eegdash/features/extractors.py,sha256=R4csU3jj95xndtWI1VuMKoKi26xprzmuOp9wcy9iVzI,11937
+eegdash/features/inspect.py,sha256=XYuEDkiwNhEFYS0a0auyn8E96WvMaPrpNn4nMRk2foM,4069
+eegdash/features/serialization.py,sha256=Um5fseiyk7SXmXoSLaaVRl2-0a6iAiRLm5rAmqdYfpg,3938
+eegdash/features/utils.py,sha256=DiutW7SOVU0pnkRTKvWpdca0RW4UCJD6JvHGDNJPjXk,6161
 eegdash/features/feature_bank/__init__.py,sha256=YsMXLC1FEtHL3IEw9pYw1fc5IY0x_hr2qWQowI5gZj8,2991
 eegdash/features/feature_bank/complexity.py,sha256=eOLN0X_xaS15ZpLPDQcychuwjL459-FqZKYfOG51z-g,3366
 eegdash/features/feature_bank/connectivity.py,sha256=bQ6KlxWm5GNpCS9ypLqBUr2L171Yq7wpBQT2tRQKTZ4,2159
 eegdash/features/feature_bank/csp.py,sha256=jKPrmqBj7FliybNbg035cVZddvVSkhk9OazcscDpipU,3303
 eegdash/features/feature_bank/dimensionality.py,sha256=Pit3YNxv64-qHUyz_5c3nBo4sFD5AnCE5mTwgnzSndc,3980
-eegdash/features/feature_bank/signal.py,sha256=3Tb8z9gX7iZipxQJ9DSyy30JfdmW58kgvimSyZX74p8,3404
+eegdash/features/feature_bank/signal.py,sha256=iSMrgnZLKNn1qNdBPheEoE_UcJPPLAOv3qDTaRI1BcE,3431
 eegdash/features/feature_bank/spectral.py,sha256=bNB7skusePs1gX7NOU6yRlw_Gr4UOCkO_ylkCgybzug,3319
-eegdash/features/feature_bank/utils.py,sha256=DGh-Q7-XFIittP7iBBxvsJaZrlVvuY5mw-G7q6C-PCI,1237
+eegdash/features/feature_bank/utils.py,sha256=zCdkfDMLWJhPjBqb5Xz0jLKg8gm3qQDY1G1rZTLuCaM,1354
 eegdash/hbn/__init__.py,sha256=hsI5pmIuYDzr--aE5UiToO-P9XL5fVRKahZzdsAodro,794
 eegdash/hbn/preprocessing.py,sha256=xp0HBz8WGhLI5c2Zkk4QiVUzGoIZep8YypnHNZsUJ4o,3800
 eegdash/hbn/windows.py,sha256=Z_fhG3kaHd5MAPg60FwFnxMJay8EzacXytUaCsOENGc,14408
-eegdash-0.4.0.dev171.dist-info/licenses/LICENSE,sha256=asisR-xupy_NrQBFXnx6yqXeZcYWLvbAaiETl25iXT0,931
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