eegdash 0.4.0.dev132__py3-none-any.whl → 0.4.0.dev144__py3-none-any.whl

eegdash/__init__.py

@@ -1,3 +1,14 @@
+# Authors: The EEGDash contributors.
+# License: GNU General Public License
+# Copyright the EEGDash contributors.
+
+"""EEGDash: A comprehensive platform for EEG data management and analysis.
+
+EEGDash provides a unified interface for accessing, querying, and analyzing large-scale
+EEG datasets. It integrates with cloud storage, MongoDB databases, and machine learning
+frameworks to streamline EEG research workflows.
+"""
+
 from .api import EEGDash, EEGDashDataset
 from .dataset import EEGChallengeDataset
 from .hbn import preprocessing
@@ -7,4 +18,4 @@ _init_mongo_client()
 
 __all__ = ["EEGDash", "EEGDashDataset", "EEGChallengeDataset", "preprocessing"]
 
-__version__ = "0.4.0.dev132"
+__version__ = "0.4.0.dev144"

eegdash/api.py

@@ -1,3 +1,15 @@
+# Authors: The EEGDash contributors.
+# License: GNU General Public License
+# Copyright the EEGDash contributors.
+
+"""High-level interface to the EEGDash metadata database.
+
+This module provides the main EEGDash class which serves as the primary entry point for
+interacting with the EEGDash ecosystem. It offers methods to query, insert, and update
+metadata records stored in the EEGDash MongoDB database, and includes utilities to load
+EEG data from S3 for matched records.
+"""
+
 import os
 from pathlib import Path
 from typing import Any, Mapping
@@ -549,16 +561,54 @@ class EEGDashDataset(BaseConcatDataset, metaclass=NumpyDocstringInheritanceInitM
 
     Examples
     --------
-    # Find by single subject
-    >>> ds = EEGDashDataset(dataset="ds005505", subject="NDARCA153NKE")
-
-    # Find by a list of subjects and a specific task
-    >>> subjects = ["NDARCA153NKE", "NDARXT792GY8"]
-    >>> ds = EEGDashDataset(dataset="ds005505", subject=subjects, task="RestingState")
-
-    # Use a raw MongoDB query for advanced filtering
-    >>> raw_query = {"dataset": "ds005505", "subject": {"$in": subjects}}
-    >>> ds = EEGDashDataset(query=raw_query)
+    Basic usage with dataset and subject filtering:
+
+    >>> from eegdash import EEGDashDataset
+    >>> dataset = EEGDashDataset(
+    ...     cache_dir="./data",
+    ...     dataset="ds002718",
+    ...     subject="012"
+    ... )
+    >>> print(f"Number of recordings: {len(dataset)}")
+
+    Filter by multiple subjects and specific task:
+
+    >>> subjects = ["012", "013", "014"]
+    >>> dataset = EEGDashDataset(
+    ...     cache_dir="./data",
+    ...     dataset="ds002718",
+    ...     subject=subjects,
+    ...     task="RestingState"
+    ... )
+
+    Load and inspect EEG data from recordings:
+
+    >>> if len(dataset) > 0:
+    ...     recording = dataset[0]
+    ...     raw = recording.load()
+    ...     print(f"Sampling rate: {raw.info['sfreq']} Hz")
+    ...     print(f"Number of channels: {len(raw.ch_names)}")
+    ...     print(f"Duration: {raw.times[-1]:.1f} seconds")
+
+    Advanced filtering with raw MongoDB queries:
+
+    >>> from eegdash import EEGDashDataset
+    >>> query = {
+    ...     "dataset": "ds002718",
+    ...     "subject": {"$in": ["012", "013"]},
+    ...     "task": "RestingState"
+    ... }
+    >>> dataset = EEGDashDataset(cache_dir="./data", query=query)
+
+    Working with dataset collections and braindecode integration:
+
+    >>> # EEGDashDataset is a braindecode BaseConcatDataset
+    >>> for i, recording in enumerate(dataset):
+    ...     if i >= 2:  # limit output
+    ...         break
+    ...     print(f"Recording {i}: {recording.description}")
+    ...     raw = recording.load()
+    ...     print(f"  Channels: {len(raw.ch_names)}, Duration: {raw.times[-1]:.1f}s")
 
     Parameters
     ----------

eegdash/bids_eeg_metadata.py

@@ -1,3 +1,14 @@
+# Authors: The EEGDash contributors.
+# License: GNU General Public License
+# Copyright the EEGDash contributors.
+
+"""BIDS metadata processing and query building utilities.
+
+This module provides functions for processing BIDS-formatted EEG metadata, building database
+queries from user parameters, and enriching metadata records with participant information.
+It handles the translation between user-friendly query parameters and MongoDB query syntax.
+"""
+
 import re
 from pathlib import Path
 from typing import Any

eegdash/const.py

@@ -1,3 +1,21 @@
+# Authors: The EEGDash contributors.
+# License: GNU General Public License
+# Copyright the EEGDash contributors.
+
+"""Configuration constants and mappings for EEGDash.
+
+This module contains global configuration settings, allowed query fields, and mapping
+constants used throughout the EEGDash package. It defines the interface between EEGDash
+releases and OpenNeuro dataset identifiers, as well as validation rules for database queries.
+"""
+
+__all__ = [
+    "config",
+    "ALLOWED_QUERY_FIELDS",
+    "RELEASE_TO_OPENNEURO_DATASET_MAP",
+    "SUBJECT_MINI_RELEASE_MAP",
+]
+
 ALLOWED_QUERY_FIELDS = {
     "data_name",
     "dataset",

eegdash/data_utils.py

@@ -1,3 +1,14 @@
+# Authors: The EEGDash contributors.
+# License: GNU General Public License
+# Copyright the EEGDash contributors.
+
+"""Data utilities and dataset classes for EEG data handling.
+
+This module provides core dataset classes for working with EEG data in the EEGDash ecosystem,
+including classes for individual recordings and collections of datasets. It integrates with
+braindecode for machine learning workflows and handles data loading from both local and remote sources.
+"""
+
 import io
 import json
 import os

eegdash/dataset/__init__.py

@@ -1,4 +1,22 @@
+"""Public API for dataset helpers and dynamically generated datasets."""
+
+from . import dataset as _dataset_mod  # triggers dynamic class registration
 from .dataset import EEGChallengeDataset
 from .registry import register_openneuro_datasets
 
-__all__ = ["EEGChallengeDataset", "register_openneuro_datasets"]
+# Re-export dynamically generated dataset classes at the package level so that
+# ``eegdash.dataset`` shows them in the API docs and users can import as
+# ``from eegdash.dataset import DSXXXXX``.
+_dyn_names = []
+for _name in getattr(_dataset_mod, "__all__", []):
+    if _name == "EEGChallengeDataset":
+        # Already imported explicitly above
+        continue
+    _obj = getattr(_dataset_mod, _name, None)
+    if _obj is not None:
+        globals()[_name] = _obj
+        _dyn_names.append(_name)
+
+__all__ = ["EEGChallengeDataset", "register_openneuro_datasets"] + _dyn_names
+
+del _dataset_mod, _name, _obj, _dyn_names

eegdash/dataset/dataset_summary.csv

@@ -10,7 +10,6 @@
 8,ds005508,3342,324,10,129,500,269.281,229.81 GB,246753736933,0,,,,,
 9,ds005507,1812,184,10,129,500,168.649,139.37 GB,149646718160,0,,,,,
 10,ds005506,1405,150,10,129,500,127.896,111.88 GB,120126449650,0,,,,,
-11,test,2,1,1,64,500,20.556,0 B,0,0,,,,,
 12,ds004854,1,1,1,64,128,0.535,79.21 MB,83057080,0,,,,,
 13,ds004853,1,1,1,64,128,0.535,79.21 MB,83057080,0,,,,,
 14,ds004844,68,17,1,64,1024,21.252,22.33 GB,23976121966,0,ds004844,,,Multisensory,Decision-making

eegdash/dataset/registry.py

@@ -57,14 +57,8 @@ def register_openneuro_datasets(
 
         init = make_init(dataset_id)
 
-        doc = f"""OpenNeuro dataset ``{dataset_id}``.
-
-        {_markdown_table(row_series)}
-
-        This class is a thin convenience wrapper for the dataset ``{dataset_id}``.
-        Constructor arguments are forwarded to :class:`{base_class.__name__}`; see the
-        base class documentation for parameter details and examples.
-        """
+        # Generate rich docstring with dataset metadata
+        doc = _generate_rich_docstring(dataset_id, row_series, base_class)
 
         # init.__doc__ = doc
 
@@ -90,6 +84,94 @@ def register_openneuro_datasets(
     return registered
 
 
+def _generate_rich_docstring(dataset_id: str, row_series: pd.Series, base_class) -> str:
+    """Generate a comprehensive docstring for a dataset class."""
+    # Extract metadata with safe defaults
+    n_subjects = row_series.get("n_subjects", "Unknown")
+    n_records = row_series.get("n_records", "Unknown")
+    n_tasks = row_series.get("n_tasks", "Unknown")
+    modality = row_series.get("modality of exp", "")
+    exp_type = row_series.get("type of exp", "")
+    subject_type = row_series.get("Type Subject", "")
+    duration = row_series.get("duration_hours_total", "Unknown")
+    size = row_series.get("size", "Unknown")
+
+    # Create description based on available metadata
+    description_parts = []
+    if modality and str(modality).strip():
+        description_parts.append(f"**Modality**: {modality}")
+    if exp_type and str(exp_type).strip():
+        description_parts.append(f"**Type**: {exp_type}")
+    if subject_type and str(subject_type).strip():
+        description_parts.append(f"**Subjects**: {subject_type}")
+
+    description = (
+        " | ".join(description_parts)
+        if description_parts
+        else "EEG dataset from OpenNeuro"
+    )
+
+    # Generate the docstring
+    docstring = f"""OpenNeuro dataset ``{dataset_id}``.
+
+{description}
+
+This dataset contains {n_subjects} subjects with {n_records} recordings across {n_tasks} tasks.
+Total duration: {duration} hours. Dataset size: {size}.
+
+{_markdown_table(row_series)}
+
+This dataset class provides convenient access to the ``{dataset_id}`` dataset through the EEGDash interface.
+It inherits all functionality from :class:`~{base_class.__module__}.{base_class.__name__}` with the dataset filter pre-configured.
+
+Parameters
+----------
+cache_dir : str
+    Directory to cache downloaded data.
+query : dict, optional
+    Additional MongoDB-style filters to AND with the dataset selection.
+    Must not contain the key ``dataset``.
+s3_bucket : str, optional
+    Base S3 bucket used to locate the data.
+**kwargs
+    Additional arguments passed to the base dataset class.
+
+Examples
+--------
+Basic usage:
+
+>>> from eegdash.dataset import {dataset_id.upper()}
+>>> dataset = {dataset_id.upper()}(cache_dir="./data")
+>>> print(f"Number of recordings: {{len(dataset)}}")
+
+Load a specific recording:
+
+>>> if len(dataset) > 0:
+...     recording = dataset[0]
+...     raw = recording.load()
+...     print(f"Sampling rate: {{raw.info['sfreq']}} Hz")
+...     print(f"Number of channels: {{len(raw.ch_names)}}")
+
+Filter by additional criteria:
+
+>>> # Get subset with specific task or subject
+>>> filtered_dataset = {dataset_id.upper()}(
+...     cache_dir="./data",
+...     query={{"task": "RestingState"}}  # if applicable
+... )
+
+Notes
+-----
+More details available in the `NEMAR documentation <https://nemar.org/dataexplorer/detail?dataset_id={dataset_id}>`__.
+
+See Also
+--------
+{base_class.__name__} : Base dataset class with full API documentation
+"""
+
+    return docstring
+
+
 def _markdown_table(row_series: pd.Series) -> str:
     """Create a reStructuredText grid table from a pandas Series."""
     if row_series.empty:
@@ -128,7 +210,12 @@ def _markdown_table(row_series: pd.Series) -> str:
     table = tabulate(df, headers="keys", tablefmt="rst", showindex=False)
 
     # Add a caption for the table
-    caption = f"Short overview of dataset {dataset_id} more details in the `Nemar documentation <https://nemar.org/dataexplorer/detail?dataset_id={dataset_id}>`_."
+    # Use an anonymous external link (double underscore) to avoid duplicate
+    # target warnings when this docstring is repeated across many classes.
+    caption = (
+        f"Short overview of dataset {dataset_id} more details in the "
+        f"`NeMAR documentation <https://nemar.org/dataexplorer/detail?dataset_id={dataset_id}>`__."
+    )
     # adding caption below the table
     # Indent the table to fit within the admonition block
     indented_table = "\n".join("    " + line for line in table.split("\n"))

eegdash/downloader.py

@@ -1,3 +1,14 @@
+# Authors: The EEGDash contributors.
+# License: GNU General Public License
+# Copyright the EEGDash contributors.
+
+"""File downloading utilities for EEG data from cloud storage.
+
+This module provides functions for downloading EEG data files and BIDS dependencies from
+AWS S3 storage, with support for caching and progress tracking. It handles the communication
+between the EEGDash metadata database and the actual EEG data stored in the cloud.
+"""
+
 import re
 import tempfile
 from pathlib import Path

eegdash/features/serialization.py

@@ -1,6 +1,8 @@
-"""Convenience functions for storing and loading of features datasets.
+"""Convenience functions for storing and loading features datasets.
+
+See Also:
+    https://github.com/braindecode/braindecode//blob/master/braindecode/datautil/serialization.py#L165-L229
 
-see also: https://github.com/braindecode/braindecode//blob/master/braindecode/datautil/serialization.py#L165-L229
 """
 
 from pathlib import Path
@@ -15,7 +17,7 @@ from .datasets import FeaturesConcatDataset, FeaturesDataset
 
 
 def load_features_concat_dataset(path, ids_to_load=None, n_jobs=1):
-    """Load a stored FeaturesConcatDataset of FeaturesDatasets from files.
+    """Load a stored features dataset from files.
 
     Parameters
     ----------
@@ -28,7 +30,9 @@ def load_features_concat_dataset(path, ids_to_load=None, n_jobs=1):
 
     Returns
     -------
-    concat_dataset: FeaturesConcatDataset of FeaturesDatasets
+    concat_dataset: eegdash.features.datasets.FeaturesConcatDataset
+        A concatenation of multiple eegdash.features.datasets.FeaturesDataset
+        instances loaded from the given directory.
 
     """
     # Make sure we always work with a pathlib.Path

eegdash/hbn/__init__.py

@@ -1,3 +1,14 @@
+# Authors: The EEGDash contributors.
+# License: GNU General Public License
+# Copyright the EEGDash contributors.
+
+"""Healthy Brain Network (HBN) specific utilities and preprocessing.
+
+This module provides specialized functions for working with the Healthy Brain Network
+dataset, including preprocessing pipelines, annotation handling, and windowing utilities
+tailored for HBN EEG data analysis.
+"""
+
 from .preprocessing import hbn_ec_ec_reannotation
 from .windows import (
     add_aux_anchors,

eegdash/hbn/preprocessing.py

@@ -1,3 +1,14 @@
+# Authors: The EEGDash contributors.
+# License: GNU General Public License
+# Copyright the EEGDash contributors.
+
+"""Preprocessing utilities specific to the Healthy Brain Network dataset.
+
+This module contains preprocessing classes and functions designed specifically for
+HBN EEG data, including specialized annotation handling for eyes-open/eyes-closed
+paradigms and other HBN-specific preprocessing steps.
+"""
+
 import mne
 import numpy as np
 

eegdash/hbn/windows.py

@@ -1,3 +1,15 @@
+# Authors: The EEGDash contributors.
+# License: GNU General Public License
+# Copyright the EEGDash contributors.
+
+"""Windowing and trial processing utilities for HBN datasets.
+
+This module provides functions for building trial tables, adding auxiliary anchors,
+annotating trials with targets, and filtering recordings based on various criteria.
+These utilities are specifically designed for working with HBN EEG data structures
+and experimental paradigms.
+"""
+
 import logging
 
 import mne

eegdash/logging.py

@@ -1,3 +1,13 @@
+# Authors: The EEGDash contributors.
+# License: GNU General Public License
+# Copyright the EEGDash contributors.
+
+"""Logging configuration for EEGDash.
+
+This module sets up centralized logging for the EEGDash package using Rich for enhanced
+console output formatting. It provides a consistent logging interface across all modules.
+"""
+
 import logging
 
 from rich.logging import RichHandler

eegdash/mongodb.py

@@ -1,3 +1,14 @@
+# Authors: The EEGDash contributors.
+# License: GNU General Public License
+# Copyright the EEGDash contributors.
+
+"""MongoDB connection and operations management.
+
+This module provides thread-safe MongoDB connection management and high-level database
+operations for the EEGDash metadata database. It includes methods for finding, adding,
+and updating EEG data records with proper connection pooling and error handling.
+"""
+
 import threading
 
 from pymongo import MongoClient

eegdash/paths.py

@@ -1,3 +1,14 @@
+# Authors: The EEGDash contributors.
+# License: GNU General Public License
+# Copyright the EEGDash contributors.
+
+"""Path utilities and cache directory management.
+
+This module provides functions for resolving consistent cache directories and path
+management throughout the EEGDash package, with integration to MNE-Python's
+configuration system.
+"""
+
 from __future__ import annotations
 
 import os

eegdash/utils.py

@@ -1,3 +1,13 @@
+# Authors: The EEGDash contributors.
+# License: GNU General Public License
+# Copyright the EEGDash contributors.
+
+"""General utility functions for EEGDash.
+
+This module contains miscellaneous utility functions used across the EEGDash package,
+including MongoDB client initialization and configuration helpers.
+"""
+
 from mne.utils import get_config, set_config, use_log_level
 
 

{eegdash-0.4.0.dev132.dist-info → eegdash-0.4.0.dev144.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: eegdash
-Version: 0.4.0.dev132
+Version: 0.4.0.dev144
 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
@@ -65,6 +65,7 @@ Requires-Dist: ipython; extra == "docs"
 Requires-Dist: lightgbm; extra == "docs"
 Requires-Dist: plotly; extra == "docs"
 Requires-Dist: nbformat; extra == "docs"
+Requires-Dist: graphviz; extra == "docs"
 Provides-Extra: all
 Requires-Dist: eegdash[docs]; extra == "all"
 Requires-Dist: eegdash[dev]; extra == "all"

eegdash-0.4.0.dev144.dist-info/RECORD

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eegdash-0.4.0.dev132.dist-info/RECORD

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