eegdash 0.3.9.dev170082126__py3-none-any.whl → 0.4.0.dev132__py3-none-any.whl

eegdash/features/datasets.py

@@ -3,7 +3,6 @@ from __future__ import annotations
 import json
 import os
 import shutil
-import warnings
 from collections.abc import Callable
 from typing import Dict, List
 
@@ -17,6 +16,8 @@ from braindecode.datasets.base import (
     _create_description,
 )
 
+from ..logging import logger
+
 
 class FeaturesDataset(EEGWindowsDataset):
     """Returns samples from a pandas DataFrame object along with a target.
@@ -283,7 +284,7 @@ class FeaturesConcatDataset(BaseConcatDataset):
             # the following will be True for all datasets preprocessed and
             # stored in parallel with braindecode.preprocessing.preprocess
             if i_ds + 1 + offset < n_sub_dirs:
-                warnings.warn(
+                logger.warning(
                     f"The number of saved datasets ({i_ds + 1 + offset}) "
                     f"does not match the number of existing "
                     f"subdirectories ({n_sub_dirs}). You may now "
@@ -294,7 +295,7 @@ class FeaturesConcatDataset(BaseConcatDataset):
         # if path contains files or directories that were not touched, raise
         # warning
         if path_contents:
-            warnings.warn(
+            logger.warning(
                 f"Chosen directory {path} contains other "
                 f"subdirectories or files {path_contents}."
             )

eegdash/hbn/preprocessing.py

@@ -1,11 +1,9 @@
-import logging
-
 import mne
 import numpy as np
 
 from braindecode.preprocessing import Preprocessor
 
-logger = logging.getLogger("eegdash")
+from ..logging import logger
 
 
 class hbn_ec_ec_reannotation(Preprocessor):

eegdash/hbn/windows.py

@@ -7,8 +7,6 @@ from mne_bids import get_bids_path_from_fname
 
 from braindecode.datasets.base import BaseConcatDataset
 
-logger = logging.getLogger("eegdash")
-
 
 def build_trial_table(events_df: pd.DataFrame) -> pd.DataFrame:
     """One row per contrast trial with stimulus/response metrics."""

eegdash/logging.py

@@ -0,0 +1,23 @@
+import logging
+
+from rich.logging import RichHandler
+
+# Get the root logger
+root_logger = logging.getLogger()
+
+# --- This is the key part ---
+# 1. Remove any handlers that may have been added by default
+root_logger.handlers = []
+
+# 2. Add your RichHandler
+root_logger.addHandler(RichHandler(rich_tracebacks=True, markup=True))
+# ---------------------------
+
+# 3. Set the level for the root logger
+root_logger.setLevel(logging.INFO)
+
+# Now, get your package-specific logger. It will inherit the
+# configuration from the root logger we just set up.
+logger = logging.getLogger("eegdash")
+
+logger.setLevel(logging.INFO)

{eegdash-0.3.9.dev170082126.dist-info → eegdash-0.4.0.dev132.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: eegdash
-Version: 0.3.9.dev170082126
+Version: 0.4.0.dev132
 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
@@ -25,7 +25,7 @@ Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: braindecode>=1.0
-Requires-Dist: mne_bids>=0.16.0
+Requires-Dist: mne_bids>=0.17.0
 Requires-Dist: numba
 Requires-Dist: numpy
 Requires-Dist: pandas
@@ -41,6 +41,7 @@ Requires-Dist: pymatreader
 Requires-Dist: eeglabio
 Requires-Dist: tabulate
 Requires-Dist: docstring_inheritance
+Requires-Dist: rich
 Provides-Extra: tests
 Requires-Dist: pytest; extra == "tests"
 Requires-Dist: pytest-cov; extra == "tests"
@@ -86,22 +87,6 @@ To leverage recent and ongoing advancements in large-scale computational methods
 
 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
-
-The following HBN datasets are currently featured on EEGDash. Documentation about these datasets is available [here](https://neuromechanist.github.io/data/hbn/).
-
-| DatasetID | Participants | Files | Sessions | Population | Channels | Is 10-20? | Modality | Size |
-|---|---|---|---|---|---|---|---|---|
-| [ds005505](https://nemar.org/dataexplorer/detail?dataset_id=ds005505) | 136 | 5393 | 1 | Healthy | 129 | other | Visual | 103 GB |
-| [ds005506](https://nemar.org/dataexplorer/detail?dataset_id=ds005506) | 150 | 5645 | 1 | Healthy | 129 | other | Visual | 112 GB |
-| [ds005507](https://nemar.org/dataexplorer/detail?dataset_id=ds005507) | 184 | 7273 | 1 | Healthy | 129 | other | Visual | 140 GB |
-| [ds005508](https://nemar.org/dataexplorer/detail?dataset_id=ds005508) | 324 | 13393 | 1 | Healthy | 129 | other | Visual | 230 GB |
-| [ds005510](https://nemar.org/dataexplorer/detail?dataset_id=ds005510) | 135 | 4933 | 1 | Healthy | 129 | other | Visual | 91 GB |
-| [ds005512](https://nemar.org/dataexplorer/detail?dataset_id=ds005512) | 257 | 9305 | 1 | Healthy | 129 | other | Visual | 157 GB |
-| [ds005514](https://nemar.org/dataexplorer/detail?dataset_id=ds005514) | 295 | 11565 | 1 | Healthy | 129 | other | Visual | 185 GB |
-
-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.
@@ -113,47 +98,11 @@ EEGDash datasets are processed using the popular [braindecode](https://braindeco
 ## EEG-Dash usage
 
 ### Install
-Use your preferred Python environment manager with Python > 3.9 to install the package.
+Use your preferred Python environment manager with Python > 3.10 to install the package.
 * To install the eegdash package, use the following command: `pip install eegdash`
 * To verify the installation, start a Python session and type: `from eegdash import EEGDash`
 
-### Data access
-
-To use the data from a single subject, enter:
-
-```python
-from eegdash import EEGDashDataset
-
-ds_NDARDB033FW5 = EEGDashDataset(
-    {"dataset": "ds005514", "task":
-     "RestingState", "subject": "NDARDB033FW5"}, 
-     cache_dir="."
-)
-```
-
-This will search and download the metadata for the task **RestingState** for subject **NDARDB033FW5** in BIDS dataset **ds005514**. The actual data will not be downloaded at this stage. Following standard practice, data is only downloaded once it is processed. The **ds_NDARDB033FW5** object is a fully functional braindecode dataset, which is itself a PyTorch dataset. This [tutorial](https://github.com/sccn/EEGDash/blob/develop/notebooks/tutorial_eoec.ipynb) shows how to preprocess the EEG data, extracting portions of the data containing eyes-open and eyes-closed segments, then perform eyes-open vs. eyes-closed classification using a (shallow) deep-learning model. 
-
-To use the data from multiple subjects, enter:
-
-```python
-from eegdash import EEGDashDataset
-
-ds_ds005505rest = EEGDashDataset(
-    {"dataset": "ds005505", "task": "RestingState"}, target_name="sex", cache_dir=".
-)
-```
-
-This will search and download the metadata for the task 'RestingState' for all subjects in BIDS dataset 'ds005505' (a total of 136). As above, the actual data will not be downloaded at this stage so this command is quick to execute. Also, the target class for each subject is assigned using the target_name parameter. This means that this object is ready to be directly fed to a deep learning model, although the [tutorial script](https://github.com/sccn/EEGDash/blob/develop/notebooks/tutorial_sex_classification.ipynb) performs minimal processing on it, prior to training a deep-learning model. Because 14 gigabytes of data are downloaded, this tutorial takes about 10 minutes to execute.
-
-### Automatic caching
-
-By default, EEGDash caches downloaded data under a single, consistent folder:
-
-- If ``EEGDASH_CACHE_DIR`` is set in your environment, that path is used.
-- Else, if MNE’s ``MNE_DATA`` config is set, that path is used to align with other EEG tooling.
-- Otherwise, ``.eegdash_cache`` in the current working directory is used.
-
-This means that if you run the tutorial [scripts](https://github.com/sccn/EEGDash/tree/develop/notebooks), the data will only be downloaded the first time the script is executed and reused thereafter.
+Please check our tutorial webpages to explore what you can do with [eegdash](https://eegdash.org/)! 
 
 ## Education -- Coming soon...
 

{eegdash-0.3.9.dev170082126.dist-info → eegdash-0.4.0.dev132.dist-info}/RECORD

@@ -1,17 +1,19 @@
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 eegdash/const.py,sha256=qdFBEL9kIrsj9CdxbXhBkR61R3CrTGSaj5Iq0YOACIs,7313
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 eegdash/mongodb.py,sha256=GD3WgA253oFgpzOHrYaj4P1mRjNtDMT5Oj4kVvHswjI,2006
 eegdash/paths.py,sha256=246xkectTxDAYcREs1Qma_F1Y-oSmLlb0hn0F2Za5Ss,866
 eegdash/utils.py,sha256=7TfQ9D0LrAJ7FgnSXEvWgeHWK2QqaqS-_WcWXD86ObQ,408
 eegdash/dataset/__init__.py,sha256=Qmzki5G8GaFlzTb10e4SmC3WkKuJyo1Ckii15tCEHAo,157
-eegdash/dataset/dataset.py,sha256=YuyzmqN5M0itimzUD1NF1hcDwkb6fg91dRZtK6HbYOc,6521
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 eegdash/dataset/dataset_summary.csv,sha256=XF0vdHz77DFyVLTaET8lL5gQQ4r-q1xAfSDWH5GTPLA,23655
 eegdash/dataset/registry.py,sha256=genOqAuf9cQBnHhPqRwfLP7S1XsnkLot6sLyJozPtf4,4150
 eegdash/features/__init__.py,sha256=BXNhjvL4_SSFAY1lcP9nyGpkbJNtoOMH4AHlF6OyABo,4078
-eegdash/features/datasets.py,sha256=kU1DO70ArSIy-LF1hHD2NN4iT-kJrI0mVpSkyV_OSeI,18301
+eegdash/features/datasets.py,sha256=eV4d86EU4fu1yoIMdPQnot6YZDRGG4qE9h77lk7iVhU,18317
 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
@@ -26,10 +28,10 @@ eegdash/features/feature_bank/signal.py,sha256=3Tb8z9gX7iZipxQJ9DSyy30JfdmW58kgv
 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/hbn/__init__.py,sha256=U8mK64napnKU746C5DOwkX7W7sg3iW5kb_cVv2pfFq0,394
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