eegdash 0.0.8__py3-none-any.whl → 0.1.0__py3-none-any.whl

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  1. eegdash/__init__.py +4 -1
  2. eegdash/data_config.py +28 -0
  3. eegdash/data_utils.py +193 -148
  4. eegdash/features/__init__.py +25 -0
  5. eegdash/features/datasets.py +456 -0
  6. eegdash/features/decorators.py +43 -0
  7. eegdash/features/extractors.py +210 -0
  8. eegdash/features/feature_bank/__init__.py +6 -0
  9. eegdash/features/feature_bank/complexity.py +96 -0
  10. eegdash/features/feature_bank/connectivity.py +59 -0
  11. eegdash/features/feature_bank/csp.py +101 -0
  12. eegdash/features/feature_bank/dimensionality.py +107 -0
  13. eegdash/features/feature_bank/signal.py +103 -0
  14. eegdash/features/feature_bank/spectral.py +116 -0
  15. eegdash/features/feature_bank/utils.py +48 -0
  16. eegdash/features/serialization.py +87 -0
  17. eegdash/features/utils.py +116 -0
  18. eegdash/main.py +250 -145
  19. {eegdash-0.0.8.dist-info → eegdash-0.1.0.dist-info}/METADATA +26 -56
  20. eegdash-0.1.0.dist-info/RECORD +23 -0
  21. {eegdash-0.0.8.dist-info → eegdash-0.1.0.dist-info}/WHEEL +1 -1
  22. eegdash-0.0.8.dist-info/RECORD +0 -8
  23. {eegdash-0.0.8.dist-info → eegdash-0.1.0.dist-info}/licenses/LICENSE +0 -0
  24. {eegdash-0.0.8.dist-info → eegdash-0.1.0.dist-info}/top_level.txt +0 -0
{eegdash-0.0.8.dist-info → eegdash-0.1.0.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: eegdash
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- Version: 0.0.8
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+ Version: 0.1.0
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  Summary: EEG data for machine learning
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  Author-email: Young Truong <dt.young112@gmail.com>, Arnaud Delorme <adelorme@gmail.com>
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  License: GNU General Public License
@@ -29,19 +29,22 @@ Project-URL: Issues, https://github.com/sccn/EEG-Dash-Data/issues
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  Classifier: Programming Language :: Python :: 3
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  Classifier: License :: OSI Approved :: MIT License
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  Classifier: Operating System :: OS Independent
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- Requires-Python: >=3.8
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+ Requires-Python: >3.10
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  Description-Content-Type: text/markdown
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  License-File: LICENSE
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- Requires-Dist: xarray
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+ Requires-Dist: braindecode
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+ Requires-Dist: mne_bids
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+ Requires-Dist: numba
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+ Requires-Dist: numpy
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+ Requires-Dist: pandas
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+ Requires-Dist: pybids
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+ Requires-Dist: pymongo
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  Requires-Dist: python-dotenv
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  Requires-Dist: s3fs
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- Requires-Dist: mne
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- Requires-Dist: pynwb
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- Requires-Dist: h5py
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- Requires-Dist: pymongo
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- Requires-Dist: joblib
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- Requires-Dist: braindecode
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- Requires-Dist: mne-bids
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+ Requires-Dist: scipy
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+ Requires-Dist: tqdm
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+ Requires-Dist: xarray
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+ Requires-Dist: pre-commit
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  Dynamic: license-file
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  # EEG-Dash
@@ -50,60 +53,21 @@ To leverage recent and ongoing advancements in large-scale computational methods
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  ## Data source
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  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.
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- ## Available data
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+ ## Featured data
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- The following datasets are currently available on EEGDash.
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+ The following HBN datasets are currently featured on EEGDash. Documentation about these datasets is available [here](https://neuromechanist.github.io/data/hbn/).
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  | DatasetID | Participants | Files | Sessions | Population | Channels | Is 10-20? | Modality | Size |
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  |---|---|---|---|---|---|---|---|---|
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- | [ds002181](https://nemar.org/dataexplorer/detail?dataset_id=ds002181) | 20 | 949 | 1 | Healthy | 63 | 10-20 | Visual | 0.163 GB |
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- | [ds002578](https://nemar.org/dataexplorer/detail?dataset_id=ds002578) | 2 | 22 | 1 | Healthy | 256 | 10-20 | Visual | 0.001 TB |
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- | [ds002680](https://nemar.org/dataexplorer/detail?dataset_id=ds002680) | 14 | 4977 | 2 | Healthy | 0 | 10-20 | Visual | 0.01 TB |
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- | [ds002691](https://nemar.org/dataexplorer/detail?dataset_id=ds002691) | 20 | 146 | 1 | Healthy | 32 | other | Visual | 0.001 TB |
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- | [ds002718](https://nemar.org/dataexplorer/detail?dataset_id=ds002718) | 18 | 582 | 1 | Healthy | 70 | other | Visual | 0.005 TB |
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- | [ds003061](https://nemar.org/dataexplorer/detail?dataset_id=ds003061) | 13 | 282 | 1 | Not specified | 64 | 10-20 | Auditory | 0.002 TB |
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- | [ds003690](https://nemar.org/dataexplorer/detail?dataset_id=ds003690) | 75 | 2630 | 1 | Healthy | 61 | 10-20 | Auditory | 0.023 TB |
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- | [ds003805](https://nemar.org/dataexplorer/detail?dataset_id=ds003805) | 1 | 10 | 1 | Healthy | 19 | 10-20 | Multisensory | 0 TB |
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- | [ds003838](https://nemar.org/dataexplorer/detail?dataset_id=ds003838) | 65 | 947 | 1 | Healthy | 63 | 10-20 | Auditory | 100.2 GB |
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- | [ds004010](https://nemar.org/dataexplorer/detail?dataset_id=ds004010) | 24 | 102 | 1 | Healthy | 64 | other | Multisensory | 0.025 TB |
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- | [ds004040](https://nemar.org/dataexplorer/detail?dataset_id=ds004040) | 13 | 160 | 2 | Healthy | 64 | 10-20 | Auditory | 0.012 TB |
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- | [ds004350](https://nemar.org/dataexplorer/detail?dataset_id=ds004350) | 24 | 960 | 2 | Healthy | 64 | other | Visual | 0.023 TB |
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- | [ds004362](https://nemar.org/dataexplorer/detail?dataset_id=ds004362) | 109 | 9162 | 1 | Healthy | 64 | 10-20 | Visual | 0.008 TB |
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- | [ds004504](https://nemar.org/dataexplorer/detail?dataset_id=ds004504) | 88 | 269 | 1 | Dementia | 19 | 10-20 | Resting State | 2.6 GB |
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- | [ds004554](https://nemar.org/dataexplorer/detail?dataset_id=ds004554) | 16 | 101 | 1 | Healthy | 99 | 10-20 | Visual | 0.009 TB |
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- | [ds004635](https://nemar.org/dataexplorer/detail?dataset_id=ds004635) | 48 | 292 | 1 | Healthy | 129 | other | Multisensory | 26.1 GB |
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- | [ds004657](https://nemar.org/dataexplorer/detail?dataset_id=ds004657) | 24 | 838 | 6 | Not specified | 64 | 10-20 | Motor | 43.1 GB |
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- | [ds004660](https://nemar.org/dataexplorer/detail?dataset_id=ds004660) | 21 | 299 | 1 | Healthy | 32 | 10-20 | Multisensory | 7.2 GB |
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- | [ds004661](https://nemar.org/dataexplorer/detail?dataset_id=ds004661) | 17 | 90 | 1 | Not specified | 64 | 10-20 | Multisensory | 1.4 GB |
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- | [ds004745](https://nemar.org/dataexplorer/detail?dataset_id=ds004745) | 52 | 762 | 1 | Healthy | 64 | ? | Auditory | 0 TB |
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- | [ds004785](https://nemar.org/dataexplorer/detail?dataset_id=ds004785) | 17 | 74 | 1 | Healthy | 32 | ? | Motor | 0 TB |
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- | [ds004841](https://nemar.org/dataexplorer/detail?dataset_id=ds004841) | 20 | 1034 | 2 | Not specified | 64 | 10-20 | Multisensory | 7.3 GB |
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- | [ds004842](https://nemar.org/dataexplorer/detail?dataset_id=ds004842) | 14 | 719 | 2 | Not specified | 64 | ? | Multisensory | 5.2 GB |
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- | [ds004843](https://nemar.org/dataexplorer/detail?dataset_id=ds004843) | 14 | 649 | 1 | Not specified | 64 | ? | Visual | 7.7 GB |
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- | [ds004844](https://nemar.org/dataexplorer/detail?dataset_id=ds004844) | 17 | 481 | 4 | Not specified | 64 | ? | Multisensory | 22.3 GB |
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- | [ds004849](https://nemar.org/dataexplorer/detail?dataset_id=ds004849) | 17 | 481 | 4 | Not specified | 64 | ? | Multisensory | 0.077 GB |
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- | [ds004850](https://nemar.org/dataexplorer/detail?dataset_id=ds004850) | 17 | 481 | 4 | Not specified | 64 | ? | Multisensory | 0.077 GB |
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- | [ds004851](https://nemar.org/dataexplorer/detail?dataset_id=ds004851) | 17 | 481 | 4 | Not specified | 64 | ? | Multisensory | 0.077 GB |
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- | [ds004852](https://nemar.org/dataexplorer/detail?dataset_id=ds004852) | 17 | 481 | 4 | Not specified | 64 | ? | Multisensory | 0.077 GB |
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- | [ds004853](https://nemar.org/dataexplorer/detail?dataset_id=ds004853) | 17 | 481 | 4 | Not specified | 64 | ? | Multisensory | 0.077 GB |
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- | [ds004854](https://nemar.org/dataexplorer/detail?dataset_id=ds004854) | 17 | 481 | 4 | Not specified | 64 | ? | Multisensory | 0.077 GB |
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- | [ds004855](https://nemar.org/dataexplorer/detail?dataset_id=ds004855) | 17 | 481 | 4 | Not specified | 64 | ? | Multisensory | 0.077 GB |
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- | [ds005034](https://nemar.org/dataexplorer/detail?dataset_id=ds005034) | 25 | 406 | 2 | Healthy | 129 | ? | Visual | 61.4 GB |
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- | [ds005079](https://nemar.org/dataexplorer/detail?dataset_id=ds005079) | 1 | 210 | 12 | Healthy | 64 | ? | Multisensory | 1.7 GB |
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- | [ds005342](https://nemar.org/dataexplorer/detail?dataset_id=ds005342) | 32 | 134 | 1 | Healthy | 17 | ? | Visual | 2 GB |
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- | [ds005410](https://nemar.org/dataexplorer/detail?dataset_id=ds005410) | 81 | 492 | 1 | Healthy | 63 | ? | ? | 19.8 GB |
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  | [ds005505](https://nemar.org/dataexplorer/detail?dataset_id=ds005505) | 136 | 5393 | 1 | Healthy | 129 | other | Visual | 103 GB |
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  | [ds005506](https://nemar.org/dataexplorer/detail?dataset_id=ds005506) | 150 | 5645 | 1 | Healthy | 129 | other | Visual | 112 GB |
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  | [ds005507](https://nemar.org/dataexplorer/detail?dataset_id=ds005507) | 184 | 7273 | 1 | Healthy | 129 | other | Visual | 140 GB |
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  | [ds005508](https://nemar.org/dataexplorer/detail?dataset_id=ds005508) | 324 | 13393 | 1 | Healthy | 129 | other | Visual | 230 GB |
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- | [ds005509](https://nemar.org/dataexplorer/detail?dataset_id=ds005509) | 330 | 19980 | 1 | Healthy | 129 | other | Visual | 224 GB |
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  | [ds005510](https://nemar.org/dataexplorer/detail?dataset_id=ds005510) | 135 | 4933 | 1 | Healthy | 129 | other | Visual | 91 GB |
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- | [ds005511](https://nemar.org/dataexplorer/detail?dataset_id=ds005511) | 381 | 18604 | 1 | Healthy | 129 | other | Visual | 245 GB |
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  | [ds005512](https://nemar.org/dataexplorer/detail?dataset_id=ds005512) | 257 | 9305 | 1 | Healthy | 129 | other | Visual | 157 GB |
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  | [ds005514](https://nemar.org/dataexplorer/detail?dataset_id=ds005514) | 295 | 11565 | 1 | Healthy | 129 | other | Visual | 185 GB |
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- | [ds005672](https://nemar.org/dataexplorer/detail?dataset_id=ds005672) | 3 | 18 | 1 | Healthy | 64 | 10-20 | Visual | 4.2 GB |
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- | [ds005697](https://nemar.org/dataexplorer/detail?dataset_id=ds005697) | 52 | 210 | 1 | Healthy | 64 | 10-20 | Visual | 67 GB |
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- | [ds005787](https://nemar.org/dataexplorer/detail?dataset_id=ds005787) | 30 | ? | 4 | Healthy | 64 | 10-20 | Visual | 185 GB |
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+ A total of [246 other datasets](datasets.md) are also available through EEGDash.
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  ## Data format
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  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.
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  ### Install
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  Use your preferred Python environment manager with Python > 3.9 to install the package.
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- * To install the eegdash package, use the following temporary command (a direct pip install eegdash option will be available soon): `pip install -i https://test.pypi.org/simple/eegdash`
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+ * To install the eegdash package, use the following command: `pip install eegdash`
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  * To verify the installation, start a Python session and type: `from eegdash import EEGDash`
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  ### Data access
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  ```python
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  from eegdash import EEGDashDataset
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- ds_NDARDB033FW5 = EEGDashDataset({'dataset': 'ds005514', 'task': 'RestingState', 'subject': 'NDARDB033FW5'})
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+ ds_NDARDB033FW5 = EEGDashDataset(
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+ {"dataset": "ds005514", "task": "RestingState", "subject": "NDARDB033FW5"}
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+ )
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  ```
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  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.
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  ```python
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+ {"dataset": "ds005505", "task": "RestingState"}, target_name="sex"
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+ )
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  ```
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  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.
eegdash-0.1.0.dist-info/RECORD ADDED
@@ -0,0 +1,23 @@
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+ eegdash/__init__.py,sha256=dyNvSv7ORVDYDz0P-XBNj_SApMlOqwt8LHQqfeuPKCg,105
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+ eegdash/data_config.py,sha256=sIwj7lnZ1hCjeFs-0CXeHn93btm9fX7mwgVTZVeVh-w,763
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+ eegdash/data_utils.py,sha256=LqAJygSpPpYEIerAnWHuHP0OMjd7jQtzXIodbvb0568,19436
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+ eegdash/main.py,sha256=CFI-Bro_oru5iRJdNQZ8IqeRPhrZKXj8wKoMdcrhFt8,14865
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+ eegdash/features/__init__.py,sha256=Ijhc-bLwysyF_HTmdJwbYoTHbxj2wxArs1xSUzhm7Hc,604
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+ eegdash/features/datasets.py,sha256=JB-VTfXTwfbxpgF9wq34gKK69YNCZPQwsnaKEXQisWk,17180
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+ eegdash/features/decorators.py,sha256=iVsbdQXGoLi-V6M9BgP6P8i_UzUtIAWQlf8Qq_LdRqY,1247
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+ eegdash/features/extractors.py,sha256=bITM4DXbW1Dq8Nm8hS3OrSGfRFV6-IwzkTzjiy_yg9k,6816
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+ eegdash/features/serialization.py,sha256=ceGcEvKCg4OsWyLpdAyJsvU1-6UXcvVx2q6nq58vt8Y,2873
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+ eegdash/features/utils.py,sha256=jjVNVLFSXFj3j7NWgEbUlt5faTrWKLLQY9ZYy0xLp_M,3782
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+ eegdash/features/feature_bank/__init__.py,sha256=BKrM3aaggXrfey1yEjEBYaxOV5e3UK-o8oGeB30epOg,149
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+ eegdash/features/feature_bank/complexity.py,sha256=WkLin-f1WTPUtcpkLDObY8nQYRsvpa08Xy9ly1k0hik,3017
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+ eegdash/features/feature_bank/connectivity.py,sha256=bQ6KlxWm5GNpCS9ypLqBUr2L171Yq7wpBQT2tRQKTZ4,2159
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+ eegdash/features/feature_bank/csp.py,sha256=O-kUijM47cOH7yfe7sYL9wT41w1dGaq6sOieh-h82pw,3300
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+ eegdash/features/feature_bank/dimensionality.py,sha256=e8rKpAT_xtZRsBDuVbznFx_daWdQj89Z3Zkt61Hs5qk,3734
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+ eegdash/features/feature_bank/signal.py,sha256=4jgIXRVS274puKfOnDNnqLoBP_yXRyP38iMnXRvobYo,2437
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+ eegdash/features/feature_bank/spectral.py,sha256=bNB7skusePs1gX7NOU6yRlw_Gr4UOCkO_ylkCgybzug,3319
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+ eegdash/features/feature_bank/utils.py,sha256=DGh-Q7-XFIittP7iBBxvsJaZrlVvuY5mw-G7q6C-PCI,1237
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+ eegdash-0.1.0.dist-info/licenses/LICENSE,sha256=Xafu48R-h_kyaNj2tuhfgdEv9_ovciktjUEgRRwMZ6w,812
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+ eegdash-0.1.0.dist-info/METADATA,sha256=RixWQ9dqP1IQzz_HCAZL2Sp-at190rx4ocpvy2DVaio,8551
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+ eegdash-0.1.0.dist-info/WHEEL,sha256=zaaOINJESkSfm_4HQVc5ssNzHCPXhJm0kEUakpsEHaU,91
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+ eegdash-0.1.0.dist-info/top_level.txt,sha256=zavO69HQ6MyZM0aQMR2zUS6TAFc7bnN5GEpDpOpFZzU,8
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+ eegdash-0.1.0.dist-info/RECORD,,
{eegdash-0.0.8.dist-info → eegdash-0.1.0.dist-info}/WHEEL RENAMED
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  Wheel-Version: 1.0
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- Generator: setuptools (78.0.2)
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  Root-Is-Purelib: true
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  Tag: py3-none-any
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eegdash-0.0.8.dist-info/RECORD DELETED
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- eegdash/__init__.py,sha256=DrliW5AazWcHJBznrmrS_YF8n8K48csOzfWWIvB6Esw,41
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- eegdash/data_utils.py,sha256=1ETB2rW-6HvXdli75pHW9yz3xjEZN7IqApKHn9XKHv4,19205
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- eegdash/main.py,sha256=QfFLzbs8iXmaJj4x_ylhFuEAuOCEKIKV6h_a__XPZ6Y,12048
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- eegdash-0.0.8.dist-info/licenses/LICENSE,sha256=Xafu48R-h_kyaNj2tuhfgdEv9_ovciktjUEgRRwMZ6w,812
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- eegdash-0.0.8.dist-info/METADATA,sha256=X3AsZ23uPQY71alITDp4cOHOvgD7QmlGVagiKHj4cjE,13881
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- eegdash-0.0.8.dist-info/WHEEL,sha256=DK49LOLCYiurdXXOXwGJm6U4DkHkg4lcxjhqwRa0CP4,91
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- eegdash-0.0.8.dist-info/top_level.txt,sha256=zavO69HQ6MyZM0aQMR2zUS6TAFc7bnN5GEpDpOpFZzU,8
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- eegdash-0.0.8.dist-info/RECORD,,