Braindecode 1.3.0.dev173767962__tar.gz → 1.3.0.dev174201910__tar.gz

{braindecode-1.3.0.dev173767962/braindecode.egg-info → braindecode-1.3.0.dev174201910}/PKG-INFO

@@ -1,8 +1,8 @@
 Metadata-Version: 2.4
 Name: braindecode
-Version: 1.3.0.dev173767962
+Version: 1.3.0.dev174201910
 Summary: Deep learning software to decode EEG, ECG or MEG signals
-Author-email: Robin Tibor Schirrmeister <robintibor@gmail.com>
+Author-email: Robin Tibor Schirrmeister <robintibor@gmail.com>, Bruno Aristimunha Pinto <b.aristimunha@gmail.com>, Alexandre Gramfort <agramfort@meta.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
@@ -14,40 +14,43 @@ 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
-Requires-Python: >=3.10
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Requires-Python: >=3.11
 Description-Content-Type: text/x-rst
 License-File: LICENSE.txt
 License-File: NOTICE.txt
-Requires-Dist: mne>=1.10.0
+Requires-Dist: torch>=2.2
+Requires-Dist: torchaudio>=2.0
+Requires-Dist: mne>=1.11.0
 Requires-Dist: mne_bids>=0.16
-Requires-Dist: numpy
-Requires-Dist: pandas
-Requires-Dist: scipy
-Requires-Dist: matplotlib
 Requires-Dist: h5py
-Requires-Dist: skorch>=1.2.0
-Requires-Dist: torch<3.0,>=2.0
-Requires-Dist: torchaudio<3.0,>=2.0
-Requires-Dist: einops
+Requires-Dist: skorch>=1.3.0
 Requires-Dist: joblib
-Requires-Dist: torchinfo~=1.8
+Requires-Dist: torchinfo
 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>=1.2.0; extra == "moabb"
-Provides-Extra: hug
-Requires-Dist: huggingface_hub[torch]>=0.20.0; extra == "hug"
+Requires-Dist: moabb>=1.4.3; 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"
 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"
@@ -66,10 +69,22 @@ 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[docs,hug,moabb,tests]; 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"
 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
@@ -85,6 +100,7 @@ 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/
 
@@ -141,7 +157,15 @@ https://gitter.im/braindecodechat/community
 Citing
 ======
 
-If you use this code in a scientific publication, please cite us as:
+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:
 
 .. code-block:: bibtex
 

{braindecode-1.3.0.dev173767962 → braindecode-1.3.0.dev174201910}/README.rst

@@ -1,3 +1,7 @@
+.. 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
@@ -13,6 +17,7 @@
    :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/
 
@@ -69,7 +74,15 @@ https://gitter.im/braindecodechat/community
 Citing
 ======
 
-If you use this code in a scientific publication, please cite us as:
+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:
 
 .. code-block:: bibtex
 

{braindecode-1.3.0.dev173767962 → braindecode-1.3.0.dev174201910}/braindecode/augmentation/__init__.py

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

{braindecode-1.3.0.dev173767962 → braindecode-1.3.0.dev174201910}/braindecode/augmentation/functional.py

@@ -1,6 +1,7 @@
 # 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)
 
@@ -1194,3 +1195,103 @@ 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.dev173767962 → braindecode-1.3.0.dev174201910}/braindecode/augmentation/transforms.py

@@ -1,6 +1,7 @@
 # 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)
 
@@ -13,9 +14,11 @@ 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,
@@ -1271,3 +1274,74 @@ 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.dev173767962 → braindecode-1.3.0.dev174201910}/braindecode/classifier.py

@@ -8,7 +8,6 @@
 
 import warnings
 
-import numpy as np
 from skorch import NeuralNet
 from skorch.callbacks import EpochScoring
 from skorch.classifier import NeuralNetClassifier
@@ -237,13 +236,9 @@ class EEGClassifier(_EEGNeuralNet, NeuralNetClassifier):
             num_workers=self.get_iterator(X, training=False).loader.num_workers,
         )
 
-    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)
+    @property
+    def mode(self):
+        return "classification"
 
     # Only add the 'accuracy' callback if we are not in cropped mode.
     @property

{braindecode-1.3.0.dev173767962 → braindecode-1.3.0.dev174201910}/braindecode/datasets/__init__.py

@@ -11,9 +11,20 @@ from .base import (
 )
 from .bcicomp import BCICompetitionIVDataset4
 from .bids import BIDSDataset, BIDSEpochsDataset
+from .bids_format import (
+    BIDSDerivativesLayout,
+    create_channels_tsv,
+    create_eeg_json_sidecar,
+    create_events_tsv,
+    create_participants_tsv,
+    description_to_bids_path,
+    make_dataset_description,
+)
+from .chb_mit import CHBMIT
 from .mne import create_from_mne_epochs, create_from_mne_raw
-from .moabb import BNCI2014001, HGD, MOABBDataset
+from .moabb import BNCI2014_001, 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
@@ -27,14 +38,23 @@ __all__ = [
     "BaseConcatDataset",
     "BIDSDataset",
     "BIDSEpochsDataset",
+    "BIDSDerivativesLayout",
+    "create_events_tsv",
+    "create_participants_tsv",
+    "create_channels_tsv",
+    "create_eeg_json_sidecar",
+    "make_dataset_description",
+    "description_to_bids_path",
     "MOABBDataset",
     "HGD",
-    "BNCI2014001",
+    "BNCI2014_001",
     "create_from_mne_raw",
     "create_from_mne_epochs",
     "TUH",
     "TUHAbnormal",
+    "SIENA",
     "NMT",
+    "CHBMIT",
     "SleepPhysionet",
     "SleepPhysionetChallenge2018",
     "create_from_X_y",

{braindecode-1.3.0.dev173767962 → braindecode-1.3.0.dev174201910}/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 Generic, Iterable, no_type_check
+from typing import Any, Generic, Iterable, no_type_check
 
 import mne.io
 import numpy as np
@@ -28,6 +28,9 @@ 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:
@@ -97,6 +100,7 @@ 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.
 
@@ -129,6 +133,7 @@ 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]
@@ -176,10 +181,12 @@ 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.
 
@@ -235,6 +242,7 @@ 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.
@@ -285,6 +293,7 @@ class EEGWindowsDataset(RecordDataset):
         return len(self.crop_inds)
 
 
+@register_dataset
 class WindowsDataset(RecordDataset):
     """Returns windows from an mne.Epochs object along with a target.
 
@@ -334,6 +343,8 @@ 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.
@@ -374,12 +385,16 @@ class WindowsDataset(RecordDataset):
         return len(self.windows.events)
 
 
-class BaseConcatDataset(ConcatDataset, Generic[T]):
+@register_dataset
+class BaseConcatDataset(ConcatDataset, HubDatasetMixin, 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
@@ -794,7 +809,7 @@ class BaseConcatDataset(ConcatDataset, Generic[T]):
                 kwargs = getattr(ds, kwargs_name)
                 if kwargs is not None:
                     with open(kwargs_file_path, "w") as f:
-                        json.dump(kwargs, f)
+                        json.dump(kwargs, f, indent=2)
 
     @staticmethod
     def _save_target_name(sub_dir, ds):