eegdash 0.1.0__py3-none-any.whl → 0.2.1.dev178237806__py3-none-any.whl

eegdash/mongodb.py

@@ -0,0 +1,66 @@
+import threading
+
+from pymongo import MongoClient
+
+# MongoDB Operations
+# These methods provide a high-level interface to interact with the MongoDB
+# collection, allowing users to find, add, and update EEG data records.
+# - find:
+# - exist:
+# - add_request:
+# - add:
+# - update_request:
+# - remove_field:
+# - remove_field_from_db:
+# - close: Close the MongoDB connection.
+# - __del__: Destructor to close the MongoDB connection.
+
+
+class MongoConnectionManager:
+    """Singleton class to manage MongoDB client connections."""
+
+    _instances = {}
+    _lock = threading.Lock()
+
+    @classmethod
+    def get_client(cls, connection_string: str, is_staging: bool = False):
+        """Get or create a MongoDB client for the given connection string and staging flag.
+
+        Parameters
+        ----------
+        connection_string : str
+            The MongoDB connection string
+        is_staging : bool
+            Whether to use staging database
+
+        Returns
+        -------
+        tuple
+            A tuple of (client, database, collection)
+
+        """
+        # Create a unique key based on connection string and staging flag
+        key = (connection_string, is_staging)
+
+        if key not in cls._instances:
+            with cls._lock:
+                # Double-check pattern to avoid race conditions
+                if key not in cls._instances:
+                    client = MongoClient(connection_string)
+                    db_name = "eegdashstaging" if is_staging else "eegdash"
+                    db = client[db_name]
+                    collection = db["records"]
+                    cls._instances[key] = (client, db, collection)
+
+        return cls._instances[key]
+
+    @classmethod
+    def close_all(cls):
+        """Close all MongoDB client connections."""
+        with cls._lock:
+            for client, _, _ in cls._instances.values():
+                try:
+                    client.close()
+                except Exception:
+                    pass
+            cls._instances.clear()

eegdash/preprocessing.py

@@ -0,0 +1,65 @@
+import logging
+
+import mne
+import numpy as np
+
+from braindecode.preprocessing import (
+    Preprocessor,
+)
+
+logger = logging.getLogger("eegdash")
+
+
+class hbn_ec_ec_reannotation(Preprocessor):
+    """Preprocessor to reannotate the raw data for eyes open and eyes closed events.
+
+    This processor is designed for HBN datasets.
+
+    """
+
+    def __init__(self):
+        super().__init__(fn=self.transform, apply_on_array=False)
+
+    def transform(self, raw):
+        """Reannotate the raw data to create new events for eyes open and eyes closed
+
+        This function modifies the raw MNE object by creating new events based on
+        the existing annotations for "instructed_toCloseEyes" and "instructed_toOpenEyes".
+        It generates new events every 2 seconds within specified time ranges after
+        the original events, and replaces the existing annotations with these new events.
+
+        Parameters
+        ----------
+        raw : mne.io.Raw
+            The raw MNE object containing EEG data and annotations.
+
+        """
+        events, event_id = mne.events_from_annotations(raw)
+
+        logger.info("Original events found with ids: %s", event_id)
+
+        # Create new events array for 2-second segments
+        new_events = []
+        sfreq = raw.info["sfreq"]
+        for event in events[events[:, 2] == event_id["instructed_toCloseEyes"]]:
+            # For each original event, create events every 2 seconds from 15s to 29s after
+            start_times = event[0] + np.arange(15, 29, 2) * sfreq
+            new_events.extend([[int(t), 0, 1] for t in start_times])
+
+        for event in events[events[:, 2] == event_id["instructed_toOpenEyes"]]:
+            # For each original event, create events every 2 seconds from 5s to 19s after
+            start_times = event[0] + np.arange(5, 19, 2) * sfreq
+            new_events.extend([[int(t), 0, 2] for t in start_times])
+
+        # replace events in raw
+        new_events = np.array(new_events)
+
+        annot_from_events = mne.annotations_from_events(
+            events=new_events,
+            event_desc={1: "eyes_closed", 2: "eyes_open"},
+            sfreq=raw.info["sfreq"],
+        )
+
+        raw.set_annotations(annot_from_events)
+
+        return raw

eegdash/utils.py

@@ -0,0 +1,11 @@
+from mne.utils import get_config, set_config, use_log_level
+
+
+def __init__mongo_client():
+    with use_log_level("ERROR"):
+        if get_config("EEGDASH_DB_URI") is None:
+            set_config(
+                "EEGDASH_DB_URI",
+                "mongodb+srv://eegdash-user:mdzoMjQcHWTVnKDq@cluster0.vz35p.mongodb.net/?retryWrites=true&w=majority&appName=Cluster0",
+                set_env=True,
+            )

{eegdash-0.1.0.dist-info → eegdash-0.2.1.dev178237806.dist-info}/METADATA

@@ -1,14 +1,15 @@
 Metadata-Version: 2.4
 Name: eegdash
-Version: 0.1.0
+Version: 0.2.1.dev178237806
 Summary: EEG data for machine learning
-Author-email: Young Truong <dt.young112@gmail.com>, Arnaud Delorme <adelorme@gmail.com>
+Author-email: Young Truong <dt.young112@gmail.com>, Arnaud Delorme <adelorme@gmail.com>, Bruno Aristimunha <b.aristimunha@gmail.com>
 License: GNU General Public License
         
         Copyright (C) 2024-2025
         
         Young Truong, UCSD, dt.young112@gmail.com
         Arnaud Delorme, UCSD, adelorme@ucsd.edu
+        Bruno Aristimunha, b.aristimunha@gmail.com
         
         This program is free software; you can redistribute it and/or modify
         it under the terms of the GNU General Public License as published by
@@ -26,14 +27,27 @@ License: GNU General Public License
         
 Project-URL: Homepage, https://github.com/sccn/EEG-Dash-Data
 Project-URL: Issues, https://github.com/sccn/EEG-Dash-Data/issues
-Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
-Requires-Python: >3.10
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Developers
+Classifier: Programming Language :: Python
+Classifier: Topic :: Software Development
+Classifier: Topic :: Scientific/Engineering
+Classifier: Development Status :: 3 - Alpha
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Operating System :: POSIX
+Classifier: Operating System :: Unix
+Classifier: Operating System :: MacOS
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: braindecode
-Requires-Dist: mne_bids
+Requires-Dist: braindecode>=1.0
+Requires-Dist: mne_bids>=0.16.0
 Requires-Dist: numba
 Requires-Dist: numpy
 Requires-Dist: pandas
@@ -44,13 +58,37 @@ Requires-Dist: s3fs
 Requires-Dist: scipy
 Requires-Dist: tqdm
 Requires-Dist: xarray
-Requires-Dist: pre-commit
+Provides-Extra: tests
+Requires-Dist: pytest; extra == "tests"
+Requires-Dist: pytest-cov; extra == "tests"
+Requires-Dist: codecov; extra == "tests"
+Requires-Dist: pytest_cases; extra == "tests"
+Requires-Dist: pytest-benchmark; extra == "tests"
+Provides-Extra: dev
+Requires-Dist: pre-commit; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: sphinx; extra == "docs"
+Requires-Dist: sphinx_gallery; extra == "docs"
+Requires-Dist: sphinx_rtd_theme; extra == "docs"
+Requires-Dist: numpydoc; extra == "docs"
+Provides-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: sphinx; extra == "all"
+Requires-Dist: sphinx_gallery; extra == "all"
+Requires-Dist: sphinx_rtd_theme; extra == "all"
+Requires-Dist: numpydoc; extra == "all"
 Dynamic: license-file
 
 # EEG-Dash
+
 To leverage recent and ongoing advancements in large-scale computational methods and to ensure the preservation of scientific data generated from publicly funded research, the EEG-DaSh data archive will create a data-sharing resource for MEEG (EEG, MEG) data contributed by collaborators for machine learning (ML) and deep learning (DL) applications. 
 
 ## Data source
+
 The data in EEG-DaSh originates from a collaboration involving 25 laboratories, encompassing 27,053 participants. This extensive collection includes MEEG data, which is a combination of EEG and MEG signals. The data is sourced from various studies conducted by these labs, involving both healthy subjects and clinical populations with conditions such as ADHD, depression, schizophrenia, dementia, autism, and psychosis. Additionally, data spans different mental states like sleep, meditation, and cognitive tasks. In addition, EEG-DaSh will incorporate a subset of the data converted from NEMAR, which includes 330 MEEG BIDS-formatted datasets, further expanding the archive with well-curated, standardized neuroelectromagnetic data.
 
 ## Featured data
@@ -70,9 +108,11 @@ The following HBN datasets are currently featured on EEGDash. Documentation abou
 A total of [246 other datasets](datasets.md) are also available through EEGDash. 
 
 ## Data format
+
 EEGDash queries return a **Pytorch Dataset** formatted to facilitate machine learning (ML) and deep learning (DL) applications. PyTorch Datasets are the best format for EEGDash queries because they provide an efficient, scalable, and flexible structure for machine learning (ML) and deep learning (DL) applications. They allow seamless integration with PyTorch’s DataLoader, enabling efficient batching, shuffling, and parallel data loading, which is essential for training deep learning models on large EEG datasets.
 
 ## Data preprocessing
+
 EEGDash datasets are processed using the popular [BrainDecode](https://braindecode.org/stable/index.html) library. In fact, EEGDash datasets are BrainDecode datasets, which are themselves PyTorch datasets. This means that any preprocessing possible on BrainDecode datasets is also possible on EEGDash datasets. Refer to [BrainDecode](https://braindecode.org/stable/index.html) tutorials for guidance on preprocessing EEG data.
 
 ## EEG-Dash usage

eegdash-0.2.1.dev178237806.dist-info/RECORD

@@ -0,0 +1,28 @@
+eegdash/__init__.py,sha256=5WP-O-5EjRXkQ2BZAn_KKMPeMyWezCmWf5sYLb-dihE,245
+eegdash/api.py,sha256=IQ0c26g7TnqzXv6lqlvMB9EHlobiTrK0YpiDa7ShcrE,26786
+eegdash/data_config.py,sha256=OS6ERO-jHrnEOfMJUehY7ieABdsRw_qWzOKJ4pzSfqw,1323
+eegdash/data_utils.py,sha256=mR0TtERYIefakGQ98jwAeeRVKSNDU9eBlUoH1AY9tnc,23663
+eegdash/dataset.py,sha256=NK5CVGtHvGNlhdbZPaRUWtyLBDxUlyiSz-ot3BrxHQE,2443
+eegdash/mongodb.py,sha256=GD3WgA253oFgpzOHrYaj4P1mRjNtDMT5Oj4kVvHswjI,2006
+eegdash/preprocessing.py,sha256=wvqAO8UgDoQQz7xjVykrl4V8AawS4tpKR4Vrr_9BovY,2230
+eegdash/utils.py,sha256=wU9CBQZLW_LIQIBwhgQm5bU4X-rSsVNPdeF2iE4QGJ4,410
+eegdash/features/__init__.py,sha256=484CLxpPifc8ZQfeM8jWZLvtVKljCxn3qqlUCaq-Yxk,1284
+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/utils.py,sha256=eM6DdyOpdVfNh7dSPykJ0WaTDtaGvkCQWAmW0G8v60Y,3784
+eegdash/features/feature_bank/__init__.py,sha256=BKrM3aaggXrfey1yEjEBYaxOV5e3UK-o8oGeB30epOg,149
+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
+eegdash/features/feature_bank/dimensionality.py,sha256=j_Ds71Y1AbV2uLFQj8EuXQ4kzofLBlQtPV5snMkF7i4,3965
+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-0.1.0.dist-info → eegdash-0.2.1.dev178237806.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.8.0)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

{eegdash-0.1.0.dist-info → eegdash-0.2.1.dev178237806.dist-info}/licenses/LICENSE

@@ -4,6 +4,7 @@ Copyright (C) 2024-2025
 
 Young Truong, UCSD, dt.young112@gmail.com
 Arnaud Delorme, UCSD, adelorme@ucsd.edu
+Bruno Aristimunha, b.aristimunha@gmail.com
 
 This program is free software; you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by