Braindecode 1.3.0.dev168090315__tar.gz → 1.3.0.dev168496007__tar.gz

{braindecode-1.3.0.dev168090315/braindecode.egg-info → braindecode-1.3.0.dev168496007}/PKG-INFO

@@ -1,8 +1,8 @@
 Metadata-Version: 2.4
 Name: braindecode
-Version: 1.3.0.dev168090315
+Version: 1.3.0.dev168496007
 Summary: Deep learning software to decode EEG, ECG or MEG signals
-Author-email: Robin Tibor Schirrmeister <robintibor@gmail.com>, Bruno Aristimunha Pinto <b.aristimunha@gmail.com>, Alexandre Gramfort <agramfort@meta.com>
+Author-email: Robin Tibor Schirrmeister <robintibor@gmail.com>
 Maintainer-email: Alexandre Gramfort <agramfort@meta.com>, Bruno Aristimunha Pinto <b.aristimunha@gmail.com>, Robin Tibor Schirrmeister <robintibor@gmail.com>
 License: BSD-3-Clause
 Project-URL: homepage, https://braindecode.org
@@ -14,43 +14,42 @@ Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
 Classifier: Topic :: Software Development :: Build Tools
 Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
-Classifier: Programming Language :: Python :: 3.13
-Classifier: Programming Language :: Python :: 3.14
-Requires-Python: >=3.11
+Requires-Python: >=3.10
 Description-Content-Type: text/x-rst
 License-File: LICENSE.txt
 License-File: NOTICE.txt
-Requires-Dist: torch>=2.2
-Requires-Dist: torchaudio>=2.0
-Requires-Dist: mne>=1.11.0
+Requires-Dist: mne>=1.10.0
 Requires-Dist: mne_bids>=0.16
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: scipy
+Requires-Dist: matplotlib
 Requires-Dist: h5py
-Requires-Dist: skorch>=1.3.0
+Requires-Dist: skorch>=1.2.0
+Requires-Dist: torch<3.0,>=2.0
+Requires-Dist: torchaudio<3.0,>=2.0
+Requires-Dist: einops
 Requires-Dist: joblib
-Requires-Dist: torchinfo
+Requires-Dist: torchinfo~=1.8
 Requires-Dist: wfdb
+Requires-Dist: h5py
 Requires-Dist: linear_attention_transformer
 Requires-Dist: docstring_inheritance
-Requires-Dist: rotary_embedding_torch
 Provides-Extra: moabb
-Requires-Dist: moabb>=1.4.3; extra == "moabb"
+Requires-Dist: moabb>=1.2.0; extra == "moabb"
 Provides-Extra: eegprep
-Requires-Dist: eegprep[eeglabio]>=0.2.23; extra == "eegprep"
-Provides-Extra: hub
-Requires-Dist: huggingface_hub[torch]>=0.20.0; extra == "hub"
-Requires-Dist: zarr>=3.0; extra == "hub"
+Requires-Dist: eegprep[eeglabio]>=0.1.1; extra == "eegprep"
+Provides-Extra: hug
+Requires-Dist: huggingface_hub[torch]>=0.20.0; extra == "hug"
 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: mypy; extra == "tests"
-Requires-Dist: transformers>=4.57.0; extra == "tests"
-Provides-Extra: typing
-Requires-Dist: exca==0.4; extra == "typing"
-Requires-Dist: numpydantic>=1.7; extra == "typing"
 Provides-Extra: docs
 Requires-Dist: sphinx_gallery; extra == "docs"
 Requires-Dist: sphinx_rtd_theme; extra == "docs"
@@ -69,22 +68,10 @@ Requires-Dist: seaborn; extra == "docs"
 Requires-Dist: pre-commit; extra == "docs"
 Requires-Dist: openneuro-py; extra == "docs"
 Requires-Dist: plotly; extra == "docs"
-Requires-Dist: shap; extra == "docs"
-Requires-Dist: nbformat; extra == "docs"
-Requires-Dist: transformers; extra == "docs"
 Provides-Extra: all
-Requires-Dist: braindecode[moabb]; extra == "all"
-Requires-Dist: braindecode[tests]; extra == "all"
-Requires-Dist: braindecode[docs]; extra == "all"
-Requires-Dist: braindecode[hub]; extra == "all"
-Requires-Dist: braindecode[eegprep]; extra == "all"
-Requires-Dist: braindecode[typing]; extra == "all"
+Requires-Dist: braindecode[docs,eegprep,hug,moabb,tests]; extra == "all"
 Dynamic: license-file
 
-.. image:: https://zenodo.org/badge/232335424.svg
-   :target: https://doi.org/10.5281/zenodo.8214376
-   :alt: DOI
-
 .. image:: https://badges.gitter.im/braindecodechat/community.svg
    :alt: Join the chat at https://gitter.im/braindecodechat/community
    :target: https://gitter.im/braindecodechat/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge
@@ -100,7 +87,6 @@ Dynamic: license-file
    :target: https://codecov.io/gh/braindecode/braindecode
    :alt: Code Coverage
 
-
 .. |Braindecode| image:: https://user-images.githubusercontent.com/42702466/177958779-b00628aa-9155-4c51-96d1-d8c345aff575.svg
 .. _braindecode: braindecode.org/
 
@@ -157,15 +143,7 @@ https://gitter.im/braindecodechat/community
 Citing
 ======
 
-If you use Braindecode in scientific work, please cite the software using the Zenodo DOI shown in the badge below:
-
-.. image:: https://zenodo.org/badge/232335424.svg
-   :target: https://doi.org/10.5281/zenodo.8214376
-   :alt: DOI
-
-Additionally, we highly encourage you to cite the article that originally introduced
-the Braindecode library and has served as a foundational reference for many works
-on deep learning with EEG recordings. Please use the following reference:
+If you use this code in a scientific publication, please cite us as:
 
 .. code-block:: bibtex
 

{braindecode-1.3.0.dev168090315 → braindecode-1.3.0.dev168496007}/README.rst

@@ -1,7 +1,3 @@
-.. image:: https://zenodo.org/badge/232335424.svg
-   :target: https://doi.org/10.5281/zenodo.8214376
-   :alt: DOI
-
 .. image:: https://badges.gitter.im/braindecodechat/community.svg
    :alt: Join the chat at https://gitter.im/braindecodechat/community
    :target: https://gitter.im/braindecodechat/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge
@@ -17,7 +13,6 @@
    :target: https://codecov.io/gh/braindecode/braindecode
    :alt: Code Coverage
 
-
 .. |Braindecode| image:: https://user-images.githubusercontent.com/42702466/177958779-b00628aa-9155-4c51-96d1-d8c345aff575.svg
 .. _braindecode: braindecode.org/
 
@@ -74,15 +69,7 @@ https://gitter.im/braindecodechat/community
 Citing
 ======
 
-If you use Braindecode in scientific work, please cite the software using the Zenodo DOI shown in the badge below:
-
-.. image:: https://zenodo.org/badge/232335424.svg
-   :target: https://doi.org/10.5281/zenodo.8214376
-   :alt: DOI
-
-Additionally, we highly encourage you to cite the article that originally introduced
-the Braindecode library and has served as a foundational reference for many works
-on deep learning with EEG recordings. Please use the following reference:
+If you use this code in a scientific publication, please cite us as:
 
 .. code-block:: bibtex
 

{braindecode-1.3.0.dev168090315 → braindecode-1.3.0.dev168496007}/braindecode/augmentation/__init__.py

@@ -5,10 +5,8 @@ Utilities for data augmentation.
 from . import functional
 from .base import AugmentedDataLoader, Compose, IdentityTransform, Transform
 from .transforms import (
-    AmplitudeScale,
     BandstopFilter,
     ChannelsDropout,
-    ChannelsReref,
     ChannelsShuffle,
     ChannelsSymmetry,
     FrequencyShift,
@@ -48,7 +46,5 @@ __all__ = [
     "Mixup",
     "SegmentationReconstruction",
     "MaskEncoding",
-    "AmplitudeScale",
-    "ChannelsReref",
     "functional",
 ]

{braindecode-1.3.0.dev168090315 → braindecode-1.3.0.dev168496007}/braindecode/augmentation/functional.py

@@ -1,7 +1,6 @@
 # Authors: Cédric Rommel <cedric.rommel@inria.fr>
 #          Alexandre Gramfort <alexandre.gramfort@inria.fr>
 #          Gustavo Rodrigues <gustavenrique01@gmail.com>
-#          Bruna Lopes <brunajaflopes@gmail.com>
 #
 # License: BSD (3-clause)
 
@@ -1195,103 +1194,3 @@ def mask_encoding(
     X[mask] = 0
 
     return X, y  # Return the masked tensor and labels
-
-
-def channels_rereference(
-    X: torch.Tensor,
-    y: torch.Tensor,
-    random_state: int | np.random.RandomState | None = None,
-) -> tuple[torch.Tensor, torch.Tensor]:
-    """Randomly re-reference channels in EEG data matrix.
-
-    Part of the augmentations proposed in [1]_
-
-    Parameters
-    ----------
-    X : torch.Tensor
-        EEG input example or batch.
-    y : torch.Tensor
-        EEG labels for the example or batch.
-    random_state: int | numpy.random.Generator, optional
-        Seed to be used to instantiate numpy random number generator instance.
-        Defaults to None.
-
-    Returns
-    -------
-    torch.Tensor
-        Transformed inputs.
-    torch.Tensor
-        Transformed labels.
-
-    References
-    ----------
-    .. [1] Mohsenvand, M.N., Izadi, M.R. &amp; Maes, P.. (2020). Contrastive
-        Representation Learning for Electroencephalogram Classification. Proceedings
-        of the Machine Learning for Health NeurIPS Workshop, in Proceedings of Machine
-        Learning Research 136:238-253
-
-    """
-
-    rng = check_random_state(random_state)
-    batch_size, n_channels, _ = X.shape
-
-    ch = rng.randint(0, n_channels, size=batch_size)
-
-    X_ch = X[torch.arange(batch_size), ch, :]
-    X = X - X_ch.unsqueeze(1)
-    X[torch.arange(batch_size), ch, :] = -X_ch
-
-    return X, y
-
-
-def amplitude_scale(
-    X: torch.Tensor,
-    y: torch.Tensor,
-    scale: tuple,
-    random_state: int | np.random.RandomState | None = None,
-) -> tuple[torch.Tensor, torch.Tensor]:
-    """Rescale amplitude of each channel based on a random sampled scaling value.
-
-    Part of the augmentations proposed in [1]_
-
-    Parameters
-    ----------
-    X : torch.Tensor
-        EEG input example or batch.
-    y : torch.Tensor
-        EEG labels for the example or batch.
-    scale : tuple of floats
-        Interval from which ypu sample the scaling value
-    random_state: int | numpy.random.Generator, optional
-        Seed to be used to instantiate numpy random number generator instance.
-        Defaults to None.
-
-    Returns
-    -------
-    torch.Tensor
-        Transformed inputs.
-    torch.Tensor
-        Transformed labels.
-
-    References
-    ----------
-    .. [1] Mohsenvand, M.N., Izadi, M.R. &amp; Maes, P.. (2020). Contrastive
-        Representation Learning for Electroencephalogram Classification. Proceedings
-        of the Machine Learning for Health NeurIPS Workshop, in Proceedings of Machine
-        Learning Research 136:238-253
-
-    """
-
-    rng = torch.Generator()
-    rng.manual_seed(random_state)
-    batch_size, n_channels, _ = X.shape
-
-    # Parameter for scaling amplitude / channel / trial
-    l, h = scale
-    s = l + (h - l) * torch.rand(
-        batch_size, n_channels, 1, generator=rng, device=X.device, dtype=X.dtype
-    )
-
-    X = s * X
-
-    return X, y

{braindecode-1.3.0.dev168090315 → braindecode-1.3.0.dev168496007}/braindecode/augmentation/transforms.py

@@ -1,7 +1,6 @@
 # Authors: Cédric Rommel <cedric.rommel@inria.fr>
 #          Alexandre Gramfort <alexandre.gramfort@inria.fr>
 #          Gustavo Rodrigues <gustavenrique01@gmail.com>
-#          Bruna Lopes <brunajaflopes@gmail.com>
 #
 # License: BSD (3-clause)
 
@@ -14,11 +13,9 @@ from mne.channels import make_standard_montage
 
 from .base import Transform
 from .functional import (
-    amplitude_scale,
     bandstop_filter,
     channels_dropout,
     channels_permute,
-    channels_rereference,
     channels_shuffle,
     frequency_shift,
     ft_surrogate,
@@ -1274,74 +1271,3 @@ class MaskEncoding(Transform):
             "segment_length": segment_length,
             "n_segments": self.n_segments,
         }
-
-
-class ChannelsReref(Transform):
-    """Randomly re-reference channels in EEG data matrix.
-
-    Part of the augmentations proposed in [1]_
-
-    Parameters
-    ----------
-    probability: float
-        Float setting the probability of applying the operation.
-    random_state: int | numpy.random.Generator, optional
-        Seed to be used to instantiate numpy random number generator instance.
-        Used to decide whether or not to transform given the probability
-        argument, to sample which channels to shuffle and to carry the shuffle.
-        Defaults to None.
-
-    References
-    ----------
-    .. [1] Mohsenvand, M.N., Izadi, M.R. &amp; Maes, P.. (2020). Contrastive
-        Representation Learning for Electroencephalogram Classification. Proceedings
-        of the Machine Learning for Health NeurIPS Workshop, in Proceedings of Machine
-        Learning Research 136:238-253 Available from https://proceedings.mlr.press/v136/mohsenvand20a.html.
-
-    """
-
-    operation = staticmethod(channels_rereference)  # type: ignore[assignment]
-
-    def __init__(self, probability, random_state=None):
-        super().__init__(probability=probability, random_state=random_state)
-
-    def get_augmentation_params(self, *batch):
-        """Return transform parameters"""
-        return {
-            "random_state": self.rng,
-        }
-
-
-class AmplitudeScale(Transform):
-    """Rescale amplitude based on a random sampled scaling value.
-
-    Part of the augmentations proposed in [1]_
-
-    Parameters
-    ----------
-    probability: float
-        Float setting the probability of applying the operation.
-    random_state: int | numpy.random.Generator, optional
-        Seed to be used to instantiate numpy random number generator instance.
-        Used to decide whether or not to transform given the probability
-        argument, to sample which channels to shuffle and to carry the shuffle.
-        Defaults to None.
-
-    References
-    ----------
-    .. [1] Mohsenvand, M.N., Izadi, M.R. &amp; Maes, P.. (2020). Contrastive
-        Representation Learning for Electroencephalogram Classification. Proceedings
-        of the Machine Learning for Health NeurIPS Workshop, in Proceedings of Machine
-        Learning Research 136:238-253 Available from https://proceedings.mlr.press/v136/mohsenvand20a.html.
-
-    """
-
-    operation = staticmethod(amplitude_scale)  # type: ignore[assignment]
-
-    def __init__(self, probability, interval=(0.5, 2), random_state=None):
-        super().__init__(probability=probability, random_state=random_state)
-        self.scale = interval
-
-    def get_augmentation_params(self, *batch):
-        """Return transform parameters"""
-        return {"random_state": self.rng, "scale": self.scale}

{braindecode-1.3.0.dev168090315 → braindecode-1.3.0.dev168496007}/braindecode/classifier.py

@@ -8,6 +8,7 @@
 
 import warnings
 
+import numpy as np
 from skorch import NeuralNet
 from skorch.callbacks import EpochScoring
 from skorch.classifier import NeuralNetClassifier
@@ -236,9 +237,13 @@ class EEGClassifier(_EEGNeuralNet, NeuralNetClassifier):
             num_workers=self.get_iterator(X, training=False).loader.num_workers,
         )
 
-    @property
-    def mode(self):
-        return "classification"
+    def _get_n_outputs(self, y, classes):
+        classes_y = np.unique(y)
+        if classes is not None:
+            assert set(classes_y) <= set(classes)
+        else:
+            classes = classes_y
+        return len(classes)
 
     # Only add the 'accuracy' callback if we are not in cropped mode.
     @property

{braindecode-1.3.0.dev168090315 → braindecode-1.3.0.dev168496007}/braindecode/datasets/__init__.py

@@ -11,11 +11,9 @@ from .base import (
 )
 from .bcicomp import BCICompetitionIVDataset4
 from .bids import BIDSDataset, BIDSEpochsDataset
-from .chb_mit import CHBMIT
 from .mne import create_from_mne_epochs, create_from_mne_raw
-from .moabb import BNCI2014_001, HGD, MOABBDataset
+from .moabb import BNCI2014001, HGD, MOABBDataset
 from .nmt import NMT
-from .siena import SIENA
 from .sleep_physio_challe_18 import SleepPhysionetChallenge2018
 from .sleep_physionet import SleepPhysionet
 from .tuh import TUH, TUHAbnormal
@@ -31,14 +29,12 @@ __all__ = [
     "BIDSEpochsDataset",
     "MOABBDataset",
     "HGD",
-    "BNCI2014_001",
+    "BNCI2014001",
     "create_from_mne_raw",
     "create_from_mne_epochs",
     "TUH",
     "TUHAbnormal",
-    "SIENA",
     "NMT",
-    "CHBMIT",
     "SleepPhysionet",
     "SleepPhysionetChallenge2018",
     "create_from_X_y",

{braindecode-1.3.0.dev168090315 → braindecode-1.3.0.dev168496007}/braindecode/datasets/base.py

@@ -19,7 +19,7 @@ import warnings
 from abc import abstractmethod
 from collections.abc import Callable
 from glob import glob
-from typing import Any, Generic, Iterable, no_type_check
+from typing import Generic, Iterable, no_type_check
 
 import mne.io
 import numpy as np
@@ -28,9 +28,6 @@ from mne.utils.docs import deprecated
 from torch.utils.data import ConcatDataset, Dataset
 from typing_extensions import TypeVar
 
-from .hub import HubDatasetMixin
-from .registry import register_dataset
-
 
 def _create_description(description) -> pd.Series:
     if description is not None:
@@ -100,7 +97,6 @@ class RecordDataset(Dataset[tuple[np.ndarray, int | str, tuple[int, int, int]]])
 T = TypeVar("T", bound=RecordDataset)
 
 
-@register_dataset
 class RawDataset(RecordDataset):
     """Returns samples from an mne.io.Raw object along with a target.
 
@@ -133,7 +129,6 @@ class RawDataset(RecordDataset):
 
         # save target name for load/save later
         self.target_name = self._target_name(target_name)
-        self.raw_preproc_kwargs: list[dict[str, Any]] = []
 
     def __getitem__(self, index):
         X = self.raw[:, index][0]
@@ -181,12 +176,10 @@ class RawDataset(RecordDataset):
     "If you want to type a Braindecode dataset (i.e. RawDataset|EEGWindowsDataset|WindowsDataset), "
     "use the RecordDataset class instead."
 )
-@register_dataset
 class BaseDataset(RawDataset):
     pass
 
 
-@register_dataset
 class EEGWindowsDataset(RecordDataset):
     """Returns windows from an mne.Raw object, its window indices, along with a target.
 
@@ -242,7 +235,6 @@ class EEGWindowsDataset(RecordDataset):
         ].to_numpy()
         if self.targets_from == "metadata":
             self.y = metadata.loc[:, "target"].to_list()
-        self.raw_preproc_kwargs: list[dict[str, Any]] = []
 
     def __getitem__(self, index: int):
         """Get a window and its target.
@@ -293,7 +285,6 @@ class EEGWindowsDataset(RecordDataset):
         return len(self.crop_inds)
 
 
-@register_dataset
 class WindowsDataset(RecordDataset):
     """Returns windows from an mne.Epochs object along with a target.
 
@@ -343,8 +334,6 @@ class WindowsDataset(RecordDataset):
         ].to_numpy()
         if self.targets_from == "metadata":
             self.y = metadata.loc[:, "target"].to_list()
-        self.raw_preproc_kwargs: list[dict[str, Any]] = []
-        self.window_preproc_kwargs: list[dict[str, Any]] = []
 
     def __getitem__(self, index: int):
         """Get a window and its target.
@@ -385,16 +374,12 @@ class WindowsDataset(RecordDataset):
         return len(self.windows.events)
 
 
-@register_dataset
-class BaseConcatDataset(ConcatDataset, HubDatasetMixin, Generic[T]):
+class BaseConcatDataset(ConcatDataset, Generic[T]):
     """A base class for concatenated datasets.
 
     Holds either mne.Raw or mne.Epoch in self.datasets and has
     a pandas DataFrame with additional description.
 
-    Includes Hugging Face Hub integration via HubDatasetMixin for
-    uploading and downloading datasets.
-
     Parameters
     ----------
     list_of_ds : list
@@ -809,7 +794,7 @@ class BaseConcatDataset(ConcatDataset, HubDatasetMixin, Generic[T]):
                 kwargs = getattr(ds, kwargs_name)
                 if kwargs is not None:
                     with open(kwargs_file_path, "w") as f:
-                        json.dump(kwargs, f, indent=2)
+                        json.dump(kwargs, f)
 
     @staticmethod
     def _save_target_name(sub_dir, ds):

{braindecode-1.3.0.dev168090315 → braindecode-1.3.0.dev168496007}/braindecode/datasets/moabb.py

@@ -15,7 +15,6 @@ from typing import Any
 
 import mne
 import pandas as pd
-from mne.utils import deprecated
 
 from braindecode.util import _update_moabb_docstring
 
@@ -170,8 +169,8 @@ class MOABBDataset(BaseConcatDataset):
         super().__init__(all_base_ds)
 
 
-class BNCI2014_001(MOABBDataset):
-    doc = """See moabb.datasets.bnci.BNCI2014_001
+class BNCI2014001(MOABBDataset):
+    doc = """See moabb.datasets.bnci.BNCI2014001
 
     Parameters
     ----------
@@ -180,14 +179,14 @@ class BNCI2014_001(MOABBDataset):
         subjects is fetched.
     """
     try:
-        from moabb.datasets import BNCI2014_001
+        from moabb.datasets import BNCI2014001
 
-        __doc__ = _update_moabb_docstring(BNCI2014_001, doc)
+        __doc__ = _update_moabb_docstring(BNCI2014001, doc)
     except ModuleNotFoundError:
         pass  # keep moabb soft dependency, otherwise crash on loading of datasets.__init__.py
 
     def __init__(self, subject_ids):
-        super().__init__("BNCI2014_001", subject_ids=subject_ids)
+        super().__init__("BNCI2014001", subject_ids=subject_ids)
 
 
 class HGD(MOABBDataset):
@@ -208,12 +207,3 @@ class HGD(MOABBDataset):
 
     def __init__(self, subject_ids):
         super().__init__("Schirrmeister2017", subject_ids=subject_ids)
-
-
-@deprecated(
-    "`BNCI2014001` was renamed to `BNCI2014_001` in v1.13; this alias will be removed in v1.14."
-)
-class BNCI2014001(BNCI2014_001):
-    """Deprecated alias for BNCI2014001."""
-
-    pass