eegdash 0.2.1.dev178237806__py3-none-any.whl → 0.3.0__py3-none-any.whl

eegdash/__init__.py

@@ -5,4 +5,4 @@ from .utils import __init__mongo_client
 __init__mongo_client()
 
 __all__ = ["EEGDash", "EEGDashDataset", "EEGChallengeDataset"]
-__version__ = "0.2.1.dev178237806"
+__version__ = "0.3.0"

eegdash/api.py

@@ -34,8 +34,6 @@ class EEGDash:
 
     """
 
-    AWS_BUCKET = "s3://openneuro.org"
-
     def __init__(self, *, is_public: bool = True, is_staging: bool = False) -> None:
         """Create new instance of the EEGDash Database client.
 

eegdash/data_utils.py

@@ -14,9 +14,7 @@ from bids import BIDSLayout
 from joblib import Parallel, delayed
 from mne._fiff.utils import _read_segments_file
 from mne.io import BaseRaw
-from mne_bids import (
-    BIDSPath,
-)
+from mne_bids import BIDSPath
 
 from braindecode.datasets import BaseDataset
 
@@ -30,7 +28,7 @@ class EEGDashBaseDataset(BaseDataset):
     conjunction with the preprocessing and training pipelines of braindecode.
     """
 
-    AWS_BUCKET = "s3://openneuro.org"
+    _AWS_BUCKET = "s3://openneuro.org"
 
     def __init__(
         self,
@@ -64,7 +62,7 @@ class EEGDashBaseDataset(BaseDataset):
             suffix="eeg",
             **bids_kwargs,
         )
-        self.s3_bucket = s3_bucket if s3_bucket else self.AWS_BUCKET
+        self.s3_bucket = s3_bucket if s3_bucket else self._AWS_BUCKET
         self.s3file = self.get_s3path(record["bidspath"])
         self.filecache = self.cache_dir / record["bidspath"]
         self.bids_dependencies = record["bidsdependencies"]
@@ -176,7 +174,7 @@ class EEGDashBaseRaw(BaseRaw):
 
     """
 
-    AWS_BUCKET = "s3://openneuro.org"
+    _AWS_BUCKET = "s3://openneuro.org"
 
     def __init__(
         self,
@@ -218,7 +216,7 @@ class EEGDashBaseRaw(BaseRaw):
         )
 
     def get_s3path(self, filepath):
-        return f"{self.AWS_BUCKET}/{filepath}"
+        return f"{self._AWS_BUCKET}/{filepath}"
 
     def _download_s3(self):
         self.filecache.parent.mkdir(parents=True, exist_ok=True)

eegdash/features/__init__.py

@@ -14,7 +14,50 @@ from .extractors import (
     TrainableFeature,
     UnivariateFeature,
 )
-from .feature_bank import *  # noqa: F401
+from .feature_bank import (  # Complexity; Connectivity; CSP; Dimensionality; Signal; Spectral
+    CoherenceFeatureExtractor,
+    CommonSpatialPattern,
+    DBSpectralFeatureExtractor,
+    EntropyFeatureExtractor,
+    HilbertFeatureExtractor,
+    NormalizedSpectralFeatureExtractor,
+    SpectralFeatureExtractor,
+    complexity_approx_entropy,
+    complexity_lempel_ziv,
+    complexity_sample_entropy,
+    complexity_svd_entropy,
+    connectivity_imaginary_coherence,
+    connectivity_lagged_coherence,
+    connectivity_magnitude_square_coherence,
+    dimensionality_detrended_fluctuation_analysis,
+    dimensionality_higuchi_fractal_dim,
+    dimensionality_hurst_exp,
+    dimensionality_katz_fractal_dim,
+    dimensionality_petrosian_fractal_dim,
+    signal_decorrelation_time,
+    signal_hjorth_activity,
+    signal_hjorth_complexity,
+    signal_hjorth_mobility,
+    signal_kurtosis,
+    signal_line_length,
+    signal_mean,
+    signal_peak_to_peak,
+    signal_quantile,
+    signal_root_mean_square,
+    signal_skewness,
+    signal_std,
+    signal_variance,
+    signal_zero_crossings,
+    spectral_bands_power,
+    spectral_edge,
+    spectral_entropy,
+    spectral_hjorth_activity,
+    spectral_hjorth_complexity,
+    spectral_hjorth_mobility,
+    spectral_moment,
+    spectral_root_total_power,
+    spectral_slope,
+)
 from .inspect import (
     get_all_feature_extractors,
     get_all_feature_kinds,
@@ -23,10 +66,7 @@ from .inspect import (
     get_feature_predecessors,
 )
 from .serialization import load_features_concat_dataset
-from .utils import (
-    extract_features,
-    fit_feature_extractors,
-)
+from .utils import extract_features, fit_feature_extractors
 
 __all__ = [
     "FeaturesConcatDataset",
@@ -50,4 +90,59 @@ __all__ = [
     "load_features_concat_dataset",
     "extract_features",
     "fit_feature_extractors",
+    # Feature part
+    # Complexity
+    "EntropyFeatureExtractor",
+    "complexity_approx_entropy",
+    "complexity_sample_entropy",
+    "complexity_svd_entropy",
+    "complexity_lempel_ziv",
+    # Connectivity
+    "CoherenceFeatureExtractor",
+    "connectivity_magnitude_square_coherence",
+    "connectivity_imaginary_coherence",
+    "connectivity_lagged_coherence",
+    # CSP
+    "CommonSpatialPattern",
+    # Dimensionality
+    "dimensionality_higuchi_fractal_dim",
+    "dimensionality_petrosian_fractal_dim",
+    "dimensionality_katz_fractal_dim",
+    "dimensionality_hurst_exp",
+    "dimensionality_detrended_fluctuation_analysis",
+    # Signal
+    "HilbertFeatureExtractor",
+    "signal_mean",
+    "signal_variance",
+    "signal_skewness",
+    "signal_kurtosis",
+    "signal_std",
+    "signal_root_mean_square",
+    "signal_peak_to_peak",
+    "signal_quantile",
+    "signal_zero_crossings",
+    "signal_line_length",
+    "signal_hjorth_activity",
+    "signal_hjorth_mobility",
+    "signal_hjorth_complexity",
+    "signal_decorrelation_time",
+    # Spectral
+    "SpectralFeatureExtractor",
+    "NormalizedSpectralFeatureExtractor",
+    "DBSpectralFeatureExtractor",
+    "spectral_root_total_power",
+    "spectral_moment",
+    "spectral_entropy",
+    "spectral_edge",
+    "spectral_slope",
+    "spectral_bands_power",
+    "spectral_hjorth_activity",
+    "spectral_hjorth_mobility",
+    "spectral_hjorth_complexity",
 ]
+
+
+# This import is not working because of the indice
+# way of the numba, needs to be improve later.
+# TO DO
+#

eegdash/features/feature_bank/__init__.py

@@ -1,6 +1,110 @@
-from .complexity import *
-from .connectivity import *
-from .csp import *
-from .dimensionality import *
-from .signal import *
-from .spectral import *
+"""Feature bank public API exports.
+
+This module consolidates and re-exports the feature extractors and feature
+functions so users can import them directly from
+``eegdash.features.feature_bank``.
+"""
+
+from .complexity import (
+    EntropyFeatureExtractor,
+    complexity_approx_entropy,
+    complexity_lempel_ziv,
+    complexity_sample_entropy,
+    complexity_svd_entropy,
+)
+from .connectivity import (
+    CoherenceFeatureExtractor,
+    connectivity_imaginary_coherence,
+    connectivity_lagged_coherence,
+    connectivity_magnitude_square_coherence,
+)
+from .csp import CommonSpatialPattern
+from .dimensionality import (
+    dimensionality_detrended_fluctuation_analysis,
+    dimensionality_higuchi_fractal_dim,
+    dimensionality_hurst_exp,
+    dimensionality_katz_fractal_dim,
+    dimensionality_petrosian_fractal_dim,
+)
+from .signal import (
+    HilbertFeatureExtractor,
+    signal_decorrelation_time,
+    signal_hjorth_activity,
+    signal_hjorth_complexity,
+    signal_hjorth_mobility,
+    signal_kurtosis,
+    signal_line_length,
+    signal_mean,
+    signal_peak_to_peak,
+    signal_quantile,
+    signal_root_mean_square,
+    signal_skewness,
+    signal_std,
+    signal_variance,
+    signal_zero_crossings,
+)
+from .spectral import (
+    DBSpectralFeatureExtractor,
+    NormalizedSpectralFeatureExtractor,
+    SpectralFeatureExtractor,
+    spectral_bands_power,
+    spectral_edge,
+    spectral_entropy,
+    spectral_hjorth_activity,
+    spectral_hjorth_complexity,
+    spectral_hjorth_mobility,
+    spectral_moment,
+    spectral_root_total_power,
+    spectral_slope,
+)
+
+__all__ = [
+    # Complexity
+    "EntropyFeatureExtractor",
+    "complexity_approx_entropy",
+    "complexity_sample_entropy",
+    "complexity_svd_entropy",
+    "complexity_lempel_ziv",
+    # Connectivity
+    "CoherenceFeatureExtractor",
+    "connectivity_magnitude_square_coherence",
+    "connectivity_imaginary_coherence",
+    "connectivity_lagged_coherence",
+    # CSP
+    "CommonSpatialPattern",
+    # Dimensionality
+    "dimensionality_higuchi_fractal_dim",
+    "dimensionality_petrosian_fractal_dim",
+    "dimensionality_katz_fractal_dim",
+    "dimensionality_hurst_exp",
+    "dimensionality_detrended_fluctuation_analysis",
+    # Signal
+    "HilbertFeatureExtractor",
+    "signal_mean",
+    "signal_variance",
+    "signal_skewness",
+    "signal_kurtosis",
+    "signal_std",
+    "signal_root_mean_square",
+    "signal_peak_to_peak",
+    "signal_quantile",
+    "signal_zero_crossings",
+    "signal_line_length",
+    "signal_hjorth_activity",
+    "signal_hjorth_mobility",
+    "signal_hjorth_complexity",
+    "signal_decorrelation_time",
+    # Spectral
+    "SpectralFeatureExtractor",
+    "NormalizedSpectralFeatureExtractor",
+    "DBSpectralFeatureExtractor",
+    "spectral_root_total_power",
+    "spectral_moment",
+    "spectral_entropy",
+    "spectral_edge",
+    "spectral_slope",
+    "spectral_bands_power",
+    "spectral_hjorth_activity",
+    "spectral_hjorth_mobility",
+    "spectral_hjorth_complexity",
+]

eegdash/features/serialization.py

@@ -11,10 +11,7 @@ from mne.io import read_info
 
 from braindecode.datautil.serialization import _load_kwargs_json
 
-from .datasets import (
-    FeaturesConcatDataset,
-    FeaturesDataset,
-)
+from .datasets import FeaturesConcatDataset, FeaturesDataset
 
 
 def load_features_concat_dataset(path, ids_to_load=None, n_jobs=1):

eegdash/preprocessing.py

@@ -3,9 +3,7 @@ import logging
 import mne
 import numpy as np
 
-from braindecode.preprocessing import (
-    Preprocessor,
-)
+from braindecode.preprocessing import Preprocessor
 
 logger = logging.getLogger("eegdash")
 

{eegdash-0.2.1.dev178237806.dist-info → eegdash-0.3.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: eegdash
-Version: 0.2.1.dev178237806
+Version: 0.3.0
 Summary: EEG data for machine learning
 Author-email: Young Truong <dt.young112@gmail.com>, Arnaud Delorme <adelorme@gmail.com>, Bruno Aristimunha <b.aristimunha@gmail.com>
 License: GNU General Public License
@@ -68,19 +68,30 @@ Provides-Extra: dev
 Requires-Dist: pre-commit; extra == "dev"
 Provides-Extra: docs
 Requires-Dist: sphinx; extra == "docs"
+Requires-Dist: sphinx_design; extra == "docs"
 Requires-Dist: sphinx_gallery; extra == "docs"
 Requires-Dist: sphinx_rtd_theme; extra == "docs"
+Requires-Dist: pydata-sphinx-theme; extra == "docs"
 Requires-Dist: numpydoc; extra == "docs"
+Requires-Dist: memory_profiler; extra == "docs"
+Requires-Dist: ipython; extra == "docs"
+Requires-Dist: lightgbm; extra == "docs"
 Provides-Extra: all
+Requires-Dist: pre-commit; extra == "all"
 Requires-Dist: pytest; extra == "all"
 Requires-Dist: pytest-cov; extra == "all"
 Requires-Dist: codecov; extra == "all"
 Requires-Dist: pytest_cases; extra == "all"
-Requires-Dist: pre-commit; extra == "all"
+Requires-Dist: pytest-benchmark; extra == "all"
 Requires-Dist: sphinx; extra == "all"
+Requires-Dist: sphinx_design; extra == "all"
 Requires-Dist: sphinx_gallery; extra == "all"
 Requires-Dist: sphinx_rtd_theme; extra == "all"
+Requires-Dist: pydata-sphinx-theme; extra == "all"
 Requires-Dist: numpydoc; extra == "all"
+Requires-Dist: memory_profiler; extra == "all"
+Requires-Dist: ipython; extra == "all"
+Requires-Dist: lightgbm; extra == "all"
 Dynamic: license-file
 
 # EEG-Dash

{eegdash-0.2.1.dev178237806.dist-info → eegdash-0.3.0.dist-info}/RECORD

@@ -1,19 +1,19 @@
-eegdash/__init__.py,sha256=5WP-O-5EjRXkQ2BZAn_KKMPeMyWezCmWf5sYLb-dihE,245
-eegdash/api.py,sha256=IQ0c26g7TnqzXv6lqlvMB9EHlobiTrK0YpiDa7ShcrE,26786
+eegdash/__init__.py,sha256=MntTC7axANEZtRLMIzcWZGS6-WiuYqdtR5Ef6fTY28c,232
+eegdash/api.py,sha256=igpkLTCjH6NNQf8tEizA6SF8cYa1gE22-hNVxNRPszg,26747
 eegdash/data_config.py,sha256=OS6ERO-jHrnEOfMJUehY7ieABdsRw_qWzOKJ4pzSfqw,1323
-eegdash/data_utils.py,sha256=mR0TtERYIefakGQ98jwAeeRVKSNDU9eBlUoH1AY9tnc,23663
+eegdash/data_utils.py,sha256=Y8Kh52zcDKY5sXblMrYhbRrL4BkQ-QUghjs0RPeW0oo,23658
 eegdash/dataset.py,sha256=NK5CVGtHvGNlhdbZPaRUWtyLBDxUlyiSz-ot3BrxHQE,2443
 eegdash/mongodb.py,sha256=GD3WgA253oFgpzOHrYaj4P1mRjNtDMT5Oj4kVvHswjI,2006
-eegdash/preprocessing.py,sha256=wvqAO8UgDoQQz7xjVykrl4V8AawS4tpKR4Vrr_9BovY,2230
+eegdash/preprocessing.py,sha256=7S_TTRKPKEk47tTnh2D6WExBt4cctAMxUxGDjJqq5lU,2221
 eegdash/utils.py,sha256=wU9CBQZLW_LIQIBwhgQm5bU4X-rSsVNPdeF2iE4QGJ4,410
-eegdash/features/__init__.py,sha256=484CLxpPifc8ZQfeM8jWZLvtVKljCxn3qqlUCaq-Yxk,1284
+eegdash/features/__init__.py,sha256=BXNhjvL4_SSFAY1lcP9nyGpkbJNtoOMH4AHlF6OyABo,4078
 eegdash/features/datasets.py,sha256=kU1DO70ArSIy-LF1hHD2NN4iT-kJrI0mVpSkyV_OSeI,18301
 eegdash/features/decorators.py,sha256=v0qaJz_dcX703p1fvFYbAIXmwK3d8naYGlq7fRVKn_w,1313
 eegdash/features/extractors.py,sha256=H7h6tP3dKoRcjDJpWWAo0ppmokCq5QlhqMcehYwYV9s,6845
 eegdash/features/inspect.py,sha256=PmbWhx5H_WqpnorUpWONUSkUtaIHkZblRa_Xyk7Szyc,1569
-eegdash/features/serialization.py,sha256=pNsTz0EeRPPYE-A61XK7UoMShI9YBEHQqC5STbzUU6A,2861
+eegdash/features/serialization.py,sha256=snXuHVd0CoT2ese0iWi5RwZrVHCGc0oCZ8-SXqGY88I,2848
 eegdash/features/utils.py,sha256=eM6DdyOpdVfNh7dSPykJ0WaTDtaGvkCQWAmW0G8v60Y,3784
-eegdash/features/feature_bank/__init__.py,sha256=BKrM3aaggXrfey1yEjEBYaxOV5e3UK-o8oGeB30epOg,149
+eegdash/features/feature_bank/__init__.py,sha256=YsMXLC1FEtHL3IEw9pYw1fc5IY0x_hr2qWQowI5gZj8,2991
 eegdash/features/feature_bank/complexity.py,sha256=Ds1GAXZ0LGM32xB4EZC2jbMljUBv0yicf2SkuyLvN5I,3183
 eegdash/features/feature_bank/connectivity.py,sha256=bQ6KlxWm5GNpCS9ypLqBUr2L171Yq7wpBQT2tRQKTZ4,2159
 eegdash/features/feature_bank/csp.py,sha256=YOzieLnOcqjvfrcjvg8R3S4SWuC1BqK5J5WXVNCCTc0,3304
@@ -21,8 +21,8 @@ eegdash/features/feature_bank/dimensionality.py,sha256=j_Ds71Y1AbV2uLFQj8EuXQ4kz
 eegdash/features/feature_bank/signal.py,sha256=3Tb8z9gX7iZipxQJ9DSyy30JfdmW58kgvimSyZX74p8,3404
 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-0.2.1.dev178237806.dist-info/licenses/LICENSE,sha256=KykUD4H3kw3HLz5bZ0kxMWwZotnk8rhkfCCerGyX2sk,855
-eegdash-0.2.1.dev178237806.dist-info/METADATA,sha256=dn351VNZC1rthL5pYZejIE9ouYek-mp6ZbatrBlKm1k,10137
-eegdash-0.2.1.dev178237806.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-eegdash-0.2.1.dev178237806.dist-info/top_level.txt,sha256=zavO69HQ6MyZM0aQMR2zUS6TAFc7bnN5GEpDpOpFZzU,8
-eegdash-0.2.1.dev178237806.dist-info/RECORD,,
+eegdash-0.3.0.dist-info/licenses/LICENSE,sha256=KykUD4H3kw3HLz5bZ0kxMWwZotnk8rhkfCCerGyX2sk,855
+eegdash-0.3.0.dist-info/METADATA,sha256=N4w48rU1-1ESNg9ESdMG7HplEuOeIXvJX-h_anvWDN0,10621
+eegdash-0.3.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+eegdash-0.3.0.dist-info/top_level.txt,sha256=zavO69HQ6MyZM0aQMR2zUS6TAFc7bnN5GEpDpOpFZzU,8
+eegdash-0.3.0.dist-info/RECORD,,