eegdash 0.2.1.dev178237806__tar.gz → 0.3.0__tar.gz

{eegdash-0.2.1.dev178237806 → eegdash-0.3.0}/PKG-INFO

@@ -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 → eegdash-0.3.0}/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-0.2.1.dev178237806 → eegdash-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-0.2.1.dev178237806 → eegdash-0.3.0}/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-0.3.0/eegdash/features/__init__.py

@@ -0,0 +1,148 @@
+from .datasets import FeaturesConcatDataset, FeaturesDataset
+from .decorators import (
+    FeatureKind,
+    FeaturePredecessor,
+    bivariate_feature,
+    multivariate_feature,
+    univariate_feature,
+)
+from .extractors import (
+    BivariateFeature,
+    DirectedBivariateFeature,
+    FeatureExtractor,
+    MultivariateFeature,
+    TrainableFeature,
+    UnivariateFeature,
+)
+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,
+    get_all_features,
+    get_feature_kind,
+    get_feature_predecessors,
+)
+from .serialization import load_features_concat_dataset
+from .utils import extract_features, fit_feature_extractors
+
+__all__ = [
+    "FeaturesConcatDataset",
+    "FeaturesDataset",
+    "FeatureKind",
+    "FeaturePredecessor",
+    "bivariate_feature",
+    "multivariate_feature",
+    "univariate_feature",
+    "BivariateFeature",
+    "DirectedBivariateFeature",
+    "FeatureExtractor",
+    "MultivariateFeature",
+    "TrainableFeature",
+    "UnivariateFeature",
+    "get_all_feature_extractors",
+    "get_all_feature_kinds",
+    "get_all_features",
+    "get_feature_kind",
+    "get_feature_predecessors",
+    "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-0.3.0/eegdash/features/feature_bank/__init__.py

@@ -0,0 +1,110 @@
+"""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-0.2.1.dev178237806 → eegdash-0.3.0}/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-0.2.1.dev178237806 → eegdash-0.3.0}/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 → eegdash-0.3.0}/eegdash.egg-info/PKG-INFO

@@ -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 → eegdash-0.3.0}/eegdash.egg-info/requires.txt

@@ -12,24 +12,35 @@ tqdm
 xarray
 
 [all]
+pre-commit
 pytest
 pytest-cov
 codecov
 pytest_cases
-pre-commit
+pytest-benchmark
 sphinx
+sphinx_design
 sphinx_gallery
 sphinx_rtd_theme
+pydata-sphinx-theme
 numpydoc
+memory_profiler
+ipython
+lightgbm
 
 [dev]
 pre-commit
 
 [docs]
 sphinx
+sphinx_design
 sphinx_gallery
 sphinx_rtd_theme
+pydata-sphinx-theme
 numpydoc
+memory_profiler
+ipython
+lightgbm
 
 [tests]
 pytest

{eegdash-0.2.1.dev178237806 → eegdash-0.3.0}/pyproject.toml

@@ -67,22 +67,34 @@ dev = [
 
 docs = [
   "sphinx",
+  "sphinx_design",
   "sphinx_gallery",
   "sphinx_rtd_theme",
-  "numpydoc"
+  "pydata-sphinx-theme",
+  "numpydoc",
+  "memory_profiler",
+  "ipython",
+  "lightgbm",
 ]
 
 all = [
+  "pre-commit",
   "pytest",
   "pytest-cov",
   "codecov",
   "pytest_cases",
-  "pre-commit",
+  "pytest-benchmark",
   "sphinx",
+  "sphinx_design",
   "sphinx_gallery",
   "sphinx_rtd_theme",
-  "numpydoc"
+  "pydata-sphinx-theme",
+  "numpydoc",
+  "memory_profiler",
+  "ipython",
+  "lightgbm",
 ]
+
 [tool.setuptools]
 py-modules = []
 

{eegdash-0.2.1.dev178237806 → eegdash-0.3.0}/tests/test_correctness.py

@@ -1,4 +1,5 @@
 import logging
+import shutil
 import warnings
 from pathlib import Path
 
@@ -91,6 +92,10 @@ def preprocess_instance(eeg_dash_dataset):
 
     except Exception as e:
         warnings.warn(f"Failed to load dataset creating a new instance: {e}. ")
+        if pre_processed_dir.exists():
+            # folder with issue, erasing and creating again
+            shutil.rmtree(pre_processed_dir)
+            pre_processed_dir.mkdir(parents=True, exist_ok=True)
 
         preprocessors = [
             hbn_ec_ec_reannotation(),

eegdash-0.2.1.dev178237806/eegdash/features/__init__.py

@@ -1,53 +0,0 @@
-from .datasets import FeaturesConcatDataset, FeaturesDataset
-from .decorators import (
-    FeatureKind,
-    FeaturePredecessor,
-    bivariate_feature,
-    multivariate_feature,
-    univariate_feature,
-)
-from .extractors import (
-    BivariateFeature,
-    DirectedBivariateFeature,
-    FeatureExtractor,
-    MultivariateFeature,
-    TrainableFeature,
-    UnivariateFeature,
-)
-from .feature_bank import *  # noqa: F401
-from .inspect import (
-    get_all_feature_extractors,
-    get_all_feature_kinds,
-    get_all_features,
-    get_feature_kind,
-    get_feature_predecessors,
-)
-from .serialization import load_features_concat_dataset
-from .utils import (
-    extract_features,
-    fit_feature_extractors,
-)
-
-__all__ = [
-    "FeaturesConcatDataset",
-    "FeaturesDataset",
-    "FeatureKind",
-    "FeaturePredecessor",
-    "bivariate_feature",
-    "multivariate_feature",
-    "univariate_feature",
-    "BivariateFeature",
-    "DirectedBivariateFeature",
-    "FeatureExtractor",
-    "MultivariateFeature",
-    "TrainableFeature",
-    "UnivariateFeature",
-    "get_all_feature_extractors",
-    "get_all_feature_kinds",
-    "get_all_features",
-    "get_feature_kind",
-    "get_feature_predecessors",
-    "load_features_concat_dataset",
-    "extract_features",
-    "fit_feature_extractors",
-]

eegdash-0.2.1.dev178237806/eegdash/features/feature_bank/__init__.py

@@ -1,6 +0,0 @@
-from .complexity import *
-from .connectivity import *
-from .csp import *
-from .dimensionality import *
-from .signal import *
-from .spectral import *