eegdash 0.3.7.dev183881899__py3-none-any.whl → 0.3.9.dev114__py3-none-any.whl

eegdash/utils.py

@@ -1,7 +1,7 @@
 from mne.utils import get_config, set_config, use_log_level
 
 
-def __init__mongo_client():
+def _init_mongo_client():
     with use_log_level("ERROR"):
         if get_config("EEGDASH_DB_URI") is None:
             set_config(

{eegdash-0.3.7.dev183881899.dist-info → eegdash-0.3.9.dev114.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: eegdash
-Version: 0.3.7.dev183881899
+Version: 0.3.9.dev114
 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
@@ -40,6 +40,7 @@ Requires-Dist: h5io>=0.2.4
 Requires-Dist: pymatreader
 Requires-Dist: eeglabio
 Requires-Dist: tabulate
+Requires-Dist: docstring_inheritance
 Provides-Extra: tests
 Requires-Dist: pytest; extra == "tests"
 Requires-Dist: pytest-cov; extra == "tests"
@@ -62,6 +63,7 @@ Requires-Dist: memory_profiler; extra == "docs"
 Requires-Dist: ipython; extra == "docs"
 Requires-Dist: lightgbm; extra == "docs"
 Requires-Dist: plotly; extra == "docs"
+Requires-Dist: nbformat; extra == "docs"
 Provides-Extra: all
 Requires-Dist: eegdash[docs]; extra == "all"
 Requires-Dist: eegdash[dev]; extra == "all"
@@ -106,7 +108,7 @@ EEGDash queries return a **Pytorch Dataset** formatted to facilitate machine lea
 
 ## 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.
+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
 
@@ -129,7 +131,7 @@ ds_NDARDB033FW5 = EEGDashDataset(
 )
 ```
 
-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. 
+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:
 
@@ -145,7 +147,13 @@ This will search and download the metadata for the task 'RestingState' for all s
 
 ### Automatic caching
 
-EEGDash automatically caches the downloaded data in the .eegdash_cache folder of the current directory from which the script is called. 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.
+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.
 
 ## Education -- Coming soon...
 
@@ -159,4 +167,3 @@ EEG-DaSh is a collaborative initiative between the United States and Israel, sup
 
 
 
-

eegdash-0.3.9.dev114.dist-info/RECORD

@@ -0,0 +1,35 @@
+eegdash/__init__.py,sha256=GbvcGXcShlfNeEcbZkUCwStg_JfSpIiU5o9YEAVlGi0,284
+eegdash/api.py,sha256=xuNi5mP8zFmTETbRkYajSS7ba320HaDeX7XzcR_t3ZU,40216
+eegdash/bids_eeg_metadata.py,sha256=LZrGPGVdnGUbZlD4M_aAW4kEItzwTTeZFicH-jyqDyc,9712
+eegdash/const.py,sha256=qdFBEL9kIrsj9CdxbXhBkR61R3CrTGSaj5Iq0YOACIs,7313
+eegdash/data_utils.py,sha256=DZ-B03VleA9-mOUzGXcS4N18dVC2uFkFGXMFsKK8nUc,34166
+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
+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/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=snXuHVd0CoT2ese0iWi5RwZrVHCGc0oCZ8-SXqGY88I,2848
+eegdash/features/utils.py,sha256=eM6DdyOpdVfNh7dSPykJ0WaTDtaGvkCQWAmW0G8v60Y,3784
+eegdash/features/feature_bank/__init__.py,sha256=YsMXLC1FEtHL3IEw9pYw1fc5IY0x_hr2qWQowI5gZj8,2991
+eegdash/features/feature_bank/complexity.py,sha256=iy9uaLInsYdxKZlXHTWlgEpP9fVI-v9TqLGfnS15-Eg,3258
+eegdash/features/feature_bank/connectivity.py,sha256=bQ6KlxWm5GNpCS9ypLqBUr2L171Yq7wpBQT2tRQKTZ4,2159
+eegdash/features/feature_bank/csp.py,sha256=jKPrmqBj7FliybNbg035cVZddvVSkhk9OazcscDpipU,3303
+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/hbn/__init__.py,sha256=U8mK64napnKU746C5DOwkX7W7sg3iW5kb_cVv2pfFq0,394
+eegdash/hbn/preprocessing.py,sha256=7S_TTRKPKEk47tTnh2D6WExBt4cctAMxUxGDjJqq5lU,2221
+eegdash/hbn/windows.py,sha256=DU_QruLOHQOttZbXCgtO4mjKaG3E5STWjMQ0_s-g0gw,9929
+eegdash-0.3.9.dev114.dist-info/licenses/LICENSE,sha256=asisR-xupy_NrQBFXnx6yqXeZcYWLvbAaiETl25iXT0,931
+eegdash-0.3.9.dev114.dist-info/METADATA,sha256=HXQkpMeyev4hRj14J_H-ekM0Qz4fv0qP0g8C1iDe4Q4,10342
+eegdash-0.3.9.dev114.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+eegdash-0.3.9.dev114.dist-info/top_level.txt,sha256=zavO69HQ6MyZM0aQMR2zUS6TAFc7bnN5GEpDpOpFZzU,8
+eegdash-0.3.9.dev114.dist-info/RECORD,,

eegdash/data_config.py

@@ -1,34 +0,0 @@
-config = {
-    "required_fields": ["data_name"],
-    # Default set of user-facing primary record attributes expected in the database. Records
-    # where any of these are missing will be loaded with the respective attribute set to None.
-    # Additional fields may be returned if they are present in the database, notably bidsdependencies.
-    "attributes": {
-        "data_name": "str",
-        "dataset": "str",
-        "bidspath": "str",
-        "subject": "str",
-        "task": "str",
-        "session": "str",
-        "run": "str",
-        "sampling_frequency": "float",
-        "modality": "str",
-        "nchans": "int",
-        "ntimes": "int",  # note: this is really the number of seconds in the data, rounded down
-    },
-    # queryable descriptive fields for a given recording
-    "description_fields": ["subject", "session", "run", "task", "age", "gender", "sex"],
-    # list of filenames that may be present in the BIDS dataset directory that are used
-    # to load and interpret a given BIDS recording.
-    "bids_dependencies_files": [
-        "dataset_description.json",
-        "participants.tsv",
-        "events.tsv",
-        "events.json",
-        "eeg.json",
-        "electrodes.tsv",
-        "channels.tsv",
-        "coordsystem.json",
-    ],
-    "accepted_query_fields": ["data_name", "dataset"],
-}

eegdash/dataset.py

@@ -1,118 +0,0 @@
-import logging
-from pathlib import Path
-
-from mne.utils import warn
-
-from .api import EEGDashDataset
-from .const import RELEASE_TO_OPENNEURO_DATASET_MAP, SUBJECT_MINI_RELEASE_MAP
-from .registry import register_openneuro_datasets
-
-logger = logging.getLogger("eegdash")
-
-
-class EEGChallengeDataset(EEGDashDataset):
-    def __init__(
-        self,
-        release: str,
-        cache_dir: str,
-        mini: bool = True,
-        query: dict | None = None,
-        s3_bucket: str | None = "s3://nmdatasets/NeurIPS25",
-        **kwargs,
-    ):
-        """Create a new EEGDashDataset from a given query or local BIDS dataset directory
-        and dataset name. An EEGDashDataset is pooled collection of EEGDashBaseDataset
-        instances (individual recordings) and is a subclass of braindecode's BaseConcatDataset.
-
-        Parameters
-        ----------
-        release: str
-            Release name. Can be one of ["R1", ..., "R11"]
-        mini: bool, default True
-            Whether to use the mini-release version of the dataset. It is recommended
-            to use the mini version for faster training and evaluation.
-        query : dict | None
-            Optionally a dictionary that specifies a query to be executed,
-            in addition to the dataset (automatically inferred from the release argument).
-            See EEGDash.find() for details on the query format.
-        cache_dir : str
-            A directory where the dataset will be cached locally.
-        s3_bucket : str | None
-            An optional S3 bucket URI to use instead of the
-            default OpenNeuro bucket for loading data files.
-        kwargs : dict
-            Additional keyword arguments to be passed to the EEGDashDataset
-            constructor.
-
-        """
-        self.release = release
-        self.mini = mini
-
-        if release not in RELEASE_TO_OPENNEURO_DATASET_MAP:
-            raise ValueError(
-                f"Unknown release: {release}, expected one of {list(RELEASE_TO_OPENNEURO_DATASET_MAP.keys())}"
-            )
-
-        dataset_parameters = []
-        if isinstance(release, str):
-            dataset_parameters.append(RELEASE_TO_OPENNEURO_DATASET_MAP[release])
-        else:
-            raise ValueError(
-                f"Unknown release type: {type(release)}, the expected type is str."
-            )
-
-        if query and "dataset" in query:
-            raise ValueError(
-                "Query using the parameters `dataset` with the class EEGChallengeDataset is not possible."
-                "Please use the release argument instead, or the object EEGDashDataset instead."
-            )
-
-        if self.mini:
-            # Disallow mixing subject selection with mini=True since mini already
-            # applies a predefined subject subset.
-            if (query and "subject" in query) or ("subject" in kwargs):
-                raise ValueError(
-                    "Query using the parameters `subject` with the class EEGChallengeDataset and `mini==True` is not possible."
-                    "Please don't use the `subject` selection twice."
-                    "Set `mini=False` to use the `subject` selection."
-                )
-            kwargs["subject"] = SUBJECT_MINI_RELEASE_MAP[release]
-            s3_bucket = f"{s3_bucket}/{release}_mini_L100_bdf"
-        else:
-            s3_bucket = f"{s3_bucket}/{release}_L100_bdf"
-
-        warn(
-            "\n\n"
-            "[EEGChallengeDataset] EEG 2025 Competition Data Notice:\n"
-            "-------------------------------------------------------\n"
-            "This object loads the HBN dataset that has been preprocessed for the EEG Challenge:\n"
-            "  - Downsampled from 500Hz to 100Hz\n"
-            "  - Bandpass filtered (0.5–50 Hz)\n"
-            "\n"
-            "For full preprocessing details, see:\n"
-            "  https://github.com/eeg2025/downsample-datasets\n"
-            "\n"
-            "IMPORTANT: The data accessed via `EEGChallengeDataset` is NOT identical to what you get from `EEGDashDataset` directly.\n"
-            "If you are participating in the competition, always use `EEGChallengeDataset` to ensure consistency with the challenge data.\n"
-            "\n",
-            UserWarning,
-            module="eegdash",
-        )
-
-        super().__init__(
-            dataset=RELEASE_TO_OPENNEURO_DATASET_MAP[release],
-            query=query,
-            cache_dir=cache_dir,
-            s3_bucket=s3_bucket,
-            **kwargs,
-        )
-
-
-registered_classes = register_openneuro_datasets(
-    summary_file=Path(__file__).with_name("dataset_summary.csv"),
-    base_class=EEGDashDataset,
-    namespace=globals(),
-)
-
-
-__all__ = ["EEGChallengeDataset"] + list(registered_classes.keys())

eegdash/dataset_summary.csv

@@ -1,256 +0,0 @@
-dataset,n_records,n_subjects,n_tasks,nchans_set,sampling_freqs,duration_hours_total,size,size_bytes,s3_item_count
-ds002718,18,18,1,74,250,14.844,4.31 GB,4624315408,0
-ds005505,1342,136,10,129,500,125.366,103.11 GB,110708824369,0
-ds004745,6,6,1,,1000,0.0,242.08 MB,253839725,0
-ds005514,2885,295,10,129,500,213.008,185.03 GB,198677728665,0
-ds005512,2320,257,10,129,500,196.205,157.19 GB,168778507427,0
-ds005510,1227,135,10,129,500,112.464,90.80 GB,97492961757,0
-ds005511,3100,381,10,"6,129",500,285.629,244.83 GB,262883881898,0
-ds005509,3326,330,10,129,500,274.559,224.17 GB,240701124393,0
-ds005508,3342,324,10,129,500,269.281,229.81 GB,246753736933,0
-ds005507,1812,184,10,129,500,168.649,139.37 GB,149646718160,0
-ds005506,1405,150,10,129,500,127.896,111.88 GB,120126449650,0
-test,2,1,1,64,500,20.556,0 B,0,0
-ds004854,1,1,1,64,128,0.535,79.21 MB,83057080,0
-ds004853,1,1,1,64,128,0.535,79.21 MB,83057080,0
-ds004844,68,17,1,64,1024,21.252,22.33 GB,23976121966,0
-ds004843,92,14,1,64,256,29.834,7.66 GB,8229205795,0
-ds004842,102,14,1,64,256,20.102,5.21 GB,5589054270,0
-ds004852,1,1,1,64,128,0.535,79.21 MB,83057106,0
-ds004851,1,1,1,64,128,0.535,56.59 GB,60765064414,0
-ds004850,1,1,1,64,128,0.535,79.21 MB,83057078,0
-ds004855,1,1,1,64,128,0.535,79.21 MB,83057076,0
-ds004849,1,1,1,64,128,0.535,79.21 MB,83057084,0
-ds004841,147,20,1,64,256,29.054,7.31 GB,7846934401,0
-ds004661,17,17,1,64,128,10.137,1.40 GB,1505577392,0
-ds004660,42,21,1,32,"2048,512",23.962,7.25 GB,7782408710,0
-ds004657,119,24,1,64,"1024,8192",27.205,43.06 GB,46237302701,0
-ds004362,1526,109,1,64,"128,160",48.592,11.14 GB,11961862159,0
-ds004010,24,24,1,64,1000,26.457,23.14 GB,24844863976,0
-ds002181,226,226,1,125,500,7.676,150.89 MB,158222084,0
-ds004554,16,16,1,99,1000,0.024,8.79 GB,9432865762,0
-ds005697,50,50,1,"65,69",1000,77.689,66.58 GB,71486411402,0
-ds004350,240,24,5,64,256,41.265,26.83 GB,28810754598,0
-ds004785,17,17,1,32,500,0.019,351.17 MB,368224136,0
-ds004504,88,88,1,19,500,19.608,5.38 GB,5780997160,0
-ds004635,55,55,1,129,1000,20.068,30.56 GB,32817659781,0
-ds005787,448,19,1,"64,66","1000,500",23.733,27.09 GB,29087512003,0
-ds005079,60,1,15,65,500,3.25,1.68 GB,1809231997,0
-ds005342,32,32,1,17,250,33.017,2.03 GB,2181610593,0
-ds005034,100,25,2,129,1000,37.525,61.36 GB,65885315479,0
-ds002680,350,14,1,31,1000,21.244,9.22 GB,9902152149,0
-ds003805,1,1,1,19,500,0.033,16.96 MB,17781347,0
-ds003838,130,65,2,63,1000,136.757,253.29 GB,271965704312,0
-ds002691,20,20,1,32,250,6.721,776.76 MB,814491068,0
-ds003690,375,75,3,"64,66",500,46.771,21.46 GB,23043491552,0
-ds004040,4,2,1,64,512,4.229,11.59 GB,12440304224,0
-ds003061,39,13,1,79,256,8.196,2.26 GB,2421951821,0
-ds005672,3,3,1,"65,69",1000,4.585,4.23 GB,4545641306,0
-ds005410,81,81,1,63,1000,22.976,19.76 GB,21213481224,0
-ds003753,25,25,1,64,500,10.104,4.62 GB,4965253148,0
-ds005565,24,24,1,,500,11.436,2.62 GB,2816607296,0
-ds002893,52,49,1,33,"250,250.0293378038558",36.114,7.70 GB,8263047991,0
-ds002578,2,2,1,256,256,1.455,1.33 GB,1429254677,0
-ds005089,36,36,1,63,1000,68.82,68.01 GB,73021312961,0
-ds003822,25,25,1,64,500,12.877,5.82 GB,6248744522,0
-ds003670,62,25,1,32,2000,72.772,97.53 GB,104721234854,0
-ds005048,35,35,1,,250,5.203,355.91 MB,373200880,0
-ds004574,146,146,1,"63,64,66",500,31.043,13.48 GB,14470034208,0
-ds004519,40,40,1,62,250,0.067,12.56 GB,13486848019,0
-ds004602,546,182,3,128,"250,500",87.11,73.91 GB,79364456958,0
-ds004784,6,1,6,128,512,0.518,10.82 GB,11621460277,0
-ds004771,61,61,1,34,256,0.022,1.36 GB,1462195517,0
-ds003518,137,110,1,64,500,89.888,39.51 GB,42423490194,0
-ds005207,39,20,1,"6,10,12,14,15,16,17,18","128,250",422.881,69.12 GB,74214619739,0
-ds005866,60,60,1,,500,15.976,3.57 GB,3837211623,0
-ds003523,221,91,1,64,500,84.586,37.54 GB,40304852370,0
-ds004347,48,24,1,64,"128,512",6.389,2.69 GB,2890549319,0
-ds004588,42,42,1,24,300,4.957,601.76 MB,630994652,0
-ds005811,448,19,1,62,"1000,500",23.733,24.12 GB,25902600444,0
-ds003987,69,23,1,64,500.0930232558139,52.076,26.41 GB,28362707915,0
-ds004317,50,50,1,60,500,37.767,18.29 GB,19639199743,0
-ds004033,36,18,2,64,500,42.645,19.81 GB,21270391452,0
-ds004315,50,50,1,60,500,21.104,9.81 GB,10532856899,0
-ds003474,122,122,1,64,500,36.61,16.64 GB,17867805967,0
-ds003509,84,56,1,64,500,48.535,22.34 GB,23988721823,0
-ds005868,48,48,1,,500,13.094,2.93 GB,3146417813,0
-ds003516,25,25,1,47,500,22.57,13.46 GB,14451393616,0
-ds004942,62,62,1,65,1000,28.282,25.05 GB,26899933549,0
-ds004348,18,9,2,34,200,35.056,12.30 GB,13210476025,0
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