Braindecode 1.8.1.dev177939635__tar.gz → 1.8.1.dev178149397__tar.gz

{braindecode-1.8.1.dev177939635 → braindecode-1.8.1.dev178149397}/NOTICE.txt

@@ -40,19 +40,22 @@ The following components are licensed under the MIT License:
 
 - `braindecode/models/ctnet.py`
 - `braindecode/models/dance.py`
+- `braindecode/models/duin.py`
 - `braindecode/models/medformer.py`
 - `braindecode/models/tcformer.py`
 - `braindecode/models/ifnet.py`
 - `braindecode/models/mirepnet.py`
 - `braindecode/models/popt.py`
 - `braindecode/models/tfm_tokenizer.py`
-- `braindecode/modules/popt_modules.py`
 - `braindecode/models/brainomni.py`
 - `braindecode/modules/quantization.py`
 - `braindecode/modules/linear_attention.py`
 - `braindecode/models/seizure_transformer.py`
 - `docs/_static/model/seizure_transformer_arch.png`
+- `braindecode/models/guetschel2026.py`
 - `braindecode/models/tmsanet.py`
+- `braindecode/models/epint.py`
+- `braindecode/models/gcnsnet.py`
 
 The `brainomni.py` file is a derivative of `OpenTSLab/BrainOmni` (MIT), whose
 SEANet codec derives from Meta's `facebookresearch/encodec` (MIT). The

{braindecode-1.8.1.dev177939635/braindecode.egg-info → braindecode-1.8.1.dev178149397}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: braindecode
-Version: 1.8.1.dev177939635
+Version: 1.8.1.dev178149397
 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>
 Maintainer-email: Alexandre Gramfort <agramfort@meta.com>, Bruno Aristimunha Pinto <b.aristimunha@gmail.com>, Robin Tibor Schirrmeister <robintibor@gmail.com>
@@ -32,8 +32,8 @@ Requires-Dist: joblib
 Requires-Dist: torchinfo
 Requires-Dist: pandas
 Requires-Dist: wfdb>=4.3.1
-Requires-Dist: linear_attention_transformer
 Requires-Dist: docstring_inheritance
+Requires-Dist: einops
 Requires-Dist: pydantic>=2.0
 Provides-Extra: moabb
 Requires-Dist: moabb>=1.4.3; extra == "moabb"
@@ -50,6 +50,7 @@ Provides-Extra: tests
 Requires-Dist: pytest<9.1; extra == "tests"
 Requires-Dist: pytest-cov; extra == "tests"
 Requires-Dist: pytest-xdist>=3.8.0; extra == "tests"
+Requires-Dist: pytest-timeout; extra == "tests"
 Requires-Dist: codecov; extra == "tests"
 Requires-Dist: pytest_cases; extra == "tests"
 Requires-Dist: mypy; extra == "tests"

{braindecode-1.8.1.dev177939635 → braindecode-1.8.1.dev178149397}/braindecode/augmentation/__init__.py

@@ -10,9 +10,11 @@ from .transforms import (
     ChannelsReref,
     ChannelsShuffle,
     ChannelsSymmetry,
+    CutMix,
     FrequencyShift,
     FTSurrogate,
     GaussianNoise,
+    LabelSmoothing,
     MaskEncoding,
     Mixup,
     SegmentationReconstruction,
@@ -36,8 +38,10 @@ __all__ = [
     "SignFlip",
     "FTSurrogate",
     "ChannelsShuffle",
+    "CutMix",
     "ChannelsDropout",
     "GaussianNoise",
+    "LabelSmoothing",
     "ChannelsSymmetry",
     "SmoothTimeMask",
     "BandstopFilter",

{braindecode-1.8.1.dev177939635 → braindecode-1.8.1.dev178149397}/braindecode/augmentation/base.py

@@ -171,7 +171,13 @@ class Compose(Transform):
         self.transforms = transforms
         super().__init__()
 
-    def forward(self, X, y):
+    def forward(self, X, y=None):
+        # like Transform.forward, return only X when no target is given (each
+        # transform then returns a single tensor, not an (X, y) pair)
+        if y is None:
+            for transform in self.transforms:
+                X = transform(X)
+            return X
         for transform in self.transforms:
             X, y = transform(X, y)
         return X, y

{braindecode-1.8.1.dev177939635 → braindecode-1.8.1.dev178149397}/braindecode/augmentation/functional.py

@@ -19,7 +19,22 @@ from mne.filter import notch_filter
 from scipy.interpolate import Rbf
 from sklearn.utils import check_random_state
 from torch.fft import fft, ifft
-from torch.nn.functional import pad
+from torch.nn.functional import one_hot, pad
+
+
+def _max_float_dtype(device: torch.device | str) -> torch.dtype:
+    """float64, or float32 on Apple MPS, which has no float64."""
+    return torch.float32 if torch.device(device).type == "mps" else torch.float64
+
+
+def _to_device(t: torch.Tensor, device: torch.device | str) -> torch.Tensor:
+    """Move ``t`` to ``device``, in single precision on MPS (no float64 there)."""
+    if torch.device(device).type == "mps":
+        if t.dtype == torch.float64:
+            return t.float().to(device)
+        if t.dtype == torch.complex128:
+            return t.to(torch.complex64).to(device)
+    return t.to(device)
 
 
 def identity(X: torch.Tensor, y: torch.Tensor) -> tuple[torch.Tensor, torch.Tensor]:
@@ -92,10 +107,11 @@ def _new_random_fft_phase_odd(
     rng = check_random_state(random_state)
     random_phase = torch.from_numpy(
         2j * np.pi * rng.random((batch_size, c, (n - 1) // 2))
-    ).to(device)
+    )
+    random_phase = _to_device(random_phase, device)
     return torch.cat(
         [
-            torch.zeros((batch_size, c, 1), device=device),
+            torch.zeros((batch_size, c, 1), device=device, dtype=random_phase.dtype),
             random_phase,
             -torch.flip(random_phase, [-1]),
         ],
@@ -113,12 +129,13 @@ def _new_random_fft_phase_even(
     rng = check_random_state(random_state)
     random_phase = torch.from_numpy(
         2j * np.pi * rng.random((batch_size, c, n // 2 - 1))
-    ).to(device)
+    )
+    random_phase = _to_device(random_phase, device)
     return torch.cat(
         [
-            torch.zeros((batch_size, c, 1), device=device),
+            torch.zeros((batch_size, c, 1), device=device, dtype=random_phase.dtype),
             random_phase,
-            torch.zeros((batch_size, c, 1), device=device),
+            torch.zeros((batch_size, c, 1), device=device, dtype=random_phase.dtype),
             -torch.flip(random_phase, [-1]),
         ],
         dim=-1,
@@ -178,7 +195,7 @@ def ft_surrogate(
         and 0 <= phase_noise_magnitude <= 1
     ), f"eps must be a float between 0 and 1. Got {phase_noise_magnitude}."
 
-    f = fft(X.double(), dim=-1)
+    f = fft(X.to(_max_float_dtype(X.device)), dim=-1)
     device = X.device
 
     n = f.shape[-1]
@@ -580,6 +597,7 @@ def _frequency_shift(X: torch.Tensor, fs: float, f_shift: float) -> torch.Tensor
         _f_shift = torch.as_tensor(f_shift).float()
     else:
         raise ValueError(f"Invalid f_shift type: {type(f_shift)}")
+    _f_shift = _f_shift.to(X.device)
     f_shift_stack = _f_shift.repeat(N_padded, n_channels, 1)
     reshaped_f_shift = f_shift_stack.permute(
         *torch.arange(f_shift_stack.ndim - 1, -1, -1)
@@ -911,7 +929,15 @@ def _rotate_signals(
     sensors_positions_matrix: torch.Tensor,
     spherical: bool = True,
 ) -> torch.Tensor:
-    sensors_positions_matrix = sensors_positions_matrix.to(X.device)
+    if X.device.type == "mps":
+        # MPS has no float64: compute the small (n_chans x n_chans) spherical
+        # spline matrices on CPU in double precision, only move the result
+        # (two separate steps: a combined device + dtype .to() from MPS
+        # returns zeros with some torch versions)
+        sensors_positions_matrix = sensors_positions_matrix.cpu().double()
+        rotations = [rotation.cpu().double() for rotation in rotations]
+    else:
+        sensors_positions_matrix = sensors_positions_matrix.to(X.device)
     rot_sensors_matrices = [
         rotation.matmul(sensors_positions_matrix) for rotation in rotations
     ]
@@ -921,9 +947,10 @@ def _rotate_signals(
                 torch.as_tensor(
                     _torch_make_interpolation_matrix(
                         sensors_positions_matrix.T, rot_sensors_matrix.T
-                    ),
-                    device=X.device,
-                ).float()
+                    )
+                )
+                .float()
+                .to(X.device)
                 for rot_sensors_matrix in rot_sensors_matrices
             ]
         )
@@ -932,7 +959,7 @@ def _rotate_signals(
         transformed_X = X.clone()
         sensors_positions = list(sensors_positions_matrix)
         for s, rot_sensors_matrix in enumerate(rot_sensors_matrices):
-            rot_sensors_positions = list(rot_sensors_matrix.T)
+            rot_sensors_positions = list(rot_sensors_matrix)
             for time in range(X.shape[-1]):
                 interpolator_t = Rbf(*sensors_positions, X[s, :, time])
                 transformed_X[s, :, time] = torch.from_numpy(
@@ -1062,10 +1089,12 @@ def mixup(
         Online: https://arxiv.org/abs/1710.09412
     .. [2] https://github.com/facebookresearch/mixup-cifar10/blob/master/train.py
     """
-    device = X.device
     batch_size, n_channels, n_times = X.shape
 
-    X_mix = torch.zeros((batch_size, n_channels, n_times)).to(device)
+    X_mix = X.new_zeros(
+        (batch_size, n_channels, n_times),
+        dtype=X.dtype if X.is_floating_point() else torch.get_default_dtype(),
+    )
     y_a = y.clone()
     y_b = y[idx_perm].clone()
 
@@ -1075,6 +1104,145 @@ def mixup(
     return X_mix, (y_a, y_b, lam)
 
 
+def cutmix(
+    X: torch.Tensor,
+    y: torch.Tensor,
+    idx_perm: torch.Tensor,
+    cut_t_start: torch.Tensor,
+    cut_t_len: torch.Tensor,
+) -> tuple[torch.Tensor, torch.Tensor]:
+    """Paste a time region of shuffled examples into the original examples.
+
+    See [1]_ for details.
+
+    Parameters
+    ----------
+    X : torch.Tensor
+        EEG data in form ``batch_size, n_channels, n_times``
+    y : torch.Tensor
+        Target of length ``batch_size``
+    idx_perm : torch.Tensor
+        Permuted indices of example that are mixed into original examples.
+    cut_t_start : torch.Tensor
+        Start index of the pasted time region for each example.
+    cut_t_len : torch.Tensor
+        Length of the pasted time region for each example.
+
+    Returns
+    -------
+    tuple
+        ``X``, ``y``. Where ``X`` is augmented and ``y`` is a tuple of length
+        3 containing the labels of the two mixed examples and the fraction of
+        each example kept from the original, ``1 - cut_t_len / n_times``.
+
+    References
+    ----------
+    .. [1] Sangdoo Yun, Dongyoon Han, Seong Joon Oh, Sanghyuk Chun,
+        Junsuk Choe, Youngjoon Yoo (2019). CutMix: Regularization Strategy
+        to Train Strong Classifiers with Localizable Features. In 2019
+        IEEE/CVF International Conference on Computer Vision (ICCV)
+        Online: https://arxiv.org/abs/1905.04899
+    """
+    n_times = X.shape[-1]
+    t = torch.arange(n_times, device=X.device)
+    start = cut_t_start[:, None]
+    in_cut = (t >= start) & (t < start + cut_t_len[:, None])
+    X_mix = torch.where(in_cut[:, None], X[idx_perm], X)
+    lam = (n_times - cut_t_len).to(X.dtype) / n_times
+    return X_mix, (y.clone(), y[idx_perm].clone(), lam)
+
+
+def label_smoothing(
+    X: torch.Tensor,
+    y: torch.Tensor,
+    epsilon: float,
+    num_classes: int | None = None,
+) -> tuple[torch.Tensor, torch.Tensor]:
+    """Smooth targets toward the uniform distribution over the classes.
+
+    See [1]_ for details.
+
+    Parameters
+    ----------
+    X : torch.Tensor
+        EEG data in form ``batch_size, n_channels, n_times``. Returned
+        unchanged.
+    y : torch.Tensor
+        Target of length ``batch_size`` holding class indices (float values
+        are accepted when they are integral), or a floating-point tensor of
+        shape ``batch_size, num_classes`` holding target distributions.
+    epsilon : float
+        Smoothing parameter between 0 and 1: the weight of the uniform
+        distribution mixed into the targets. ``0`` returns the unsmoothed
+        targets.
+    num_classes : int | None, optional
+        Number of classes. Required when ``y`` holds class indices; when
+        ``y`` already holds distributions, it must match the size of the
+        last dimension of ``y``. Defaults to None.
+
+    Returns
+    -------
+    tuple
+        ``X``, ``y``. Where ``X`` is unchanged and ``y`` is a
+        floating-point tensor of shape ``batch_size, num_classes`` whose
+        rows sum to one.
+
+    References
+    ----------
+    .. [1] Christian Szegedy, Vincent Vanhoucke, Jonathon Shlens and
+        Zbigniew Wojna (2016). Rethinking the Inception Architecture for
+        Computer Vision. In 2016 IEEE Conference on Computer Vision and
+        Pattern Recognition (CVPR), pp. 2818-2826.
+        Online: https://arxiv.org/abs/1512.00567
+    """
+    if not isinstance(epsilon, Real) or not 0.0 <= float(epsilon) <= 1.0:
+        raise ValueError(
+            f"epsilon should be a real number between 0 and 1. Got {epsilon!r}."
+        )
+    if num_classes is not None and (
+        not isinstance(num_classes, int)
+        or isinstance(num_classes, bool)
+        or num_classes < 2
+    ):
+        raise ValueError(
+            f"num_classes should be an integer of at least 2. Got {num_classes!r}."
+        )
+
+    if y.dim() == 1:
+        # class-index targets: smooth their one-hot encoding
+        if num_classes is None:
+            raise ValueError("num_classes is required when y holds class indices.")
+        if not torch.all(y == y.floor()):
+            raise ValueError(
+                "y holds non-integral values; class-index targets should be "
+                "integers or integral floats."
+            )
+        if y.numel() > 0 and (y.min() < 0 or y.max() >= num_classes):
+            raise ValueError(f"y holds class indices outside [0, {num_classes}).")
+        one_hot_y = one_hot(y.long(), num_classes).to(dtype=X.dtype)
+        return X, one_hot_y * (1.0 - epsilon) + epsilon / num_classes
+
+    if y.is_floating_point() and y.dim() >= 2:
+        # target distributions: interpolate them toward the uniform one
+        n_classes = y.shape[-1]
+        if num_classes is not None and num_classes != n_classes:
+            raise ValueError(
+                f"num_classes ({num_classes}) does not match the size of the "
+                f"last dimension of y ({n_classes})."
+            )
+        if n_classes < 2:
+            raise ValueError(
+                f"y should hold distributions over at least 2 classes. Got {n_classes}."
+            )
+        return X, y * (1.0 - epsilon) + epsilon / n_classes
+
+    raise ValueError(
+        "y should hold class indices or floating-point target distributions "
+        f"with a class dimension; got dtype {y.dtype} and shape "
+        f"{tuple(y.shape)}."
+    )
+
+
 def segmentation_reconstruction(
     X: torch.Tensor,
     y: torch.Tensor,

{braindecode-1.8.1.dev177939635 → braindecode-1.8.1.dev178149397}/braindecode/augmentation/transforms.py

@@ -3,6 +3,7 @@
 #          Gustavo Rodrigues <gustavenrique01@gmail.com>
 #          Bruna Lopes <brunajaflopes@gmail.com>
 #          Sarthak Tayal <sarthaktayal2@gmail.com>
+#          Anton Soloviev <anton@praviel.com>
 #
 # License: BSD (3-clause)
 
@@ -17,6 +18,7 @@ from braindecode.util import resolve_montage_name
 
 from .base import Transform
 from .functional import (
+    _max_float_dtype,
     amplitude_scale,
     band_rotation,
     bandstop_filter,
@@ -24,9 +26,11 @@ from .functional import (
     channels_permute,
     channels_rereference,
     channels_shuffle,
+    cutmix,
     frequency_shift,
     ft_surrogate,
     gaussian_noise,
+    label_smoothing,
     mask_encoding,
     mixup,
     segmentation_reconstruction,
@@ -492,6 +496,7 @@ class SmoothTimeMask(Transform):
                 size=X.shape[0],
             ),
             device=X.device,
+            dtype=_max_float_dtype(X.device),
         ) * (seq_length - mask_len_samples)
         return {
             "mask_start_per_sample": mask_start,
@@ -673,7 +678,11 @@ class FrequencyShift(Transform):
             return super().get_augmentation_params(*batch)
         X = batch[0]
 
-        u = torch.as_tensor(self.rng.uniform(size=X.shape[0]), device=X.device)
+        u = torch.as_tensor(
+            self.rng.uniform(size=X.shape[0]),
+            device=X.device,
+            dtype=_max_float_dtype(X.device),
+        )
         max_delta_freq = self.max_delta_freq
         if isinstance(max_delta_freq, torch.Tensor):
             max_delta_freq = max_delta_freq.to(X.device)
@@ -831,7 +840,10 @@ class SensorsRotation(Transform):
         if isinstance(max_degrees, torch.Tensor):
             max_degrees = max_degrees.to(X.device)
         random_angles = (
-            torch.as_tensor(u, device=X.device) * 2 * max_degrees - max_degrees
+            torch.as_tensor(u, device=X.device, dtype=_max_float_dtype(X.device))
+            * 2
+            * max_degrees
+            - max_degrees
         )
         return {
             "sensors_positions_matrix": self.sensors_positions_matrix,
@@ -1095,6 +1107,147 @@ class Mixup(Transform):
         }
 
 
+class CutMix(Mixup):
+    """Implements CutMix for EEG data.
+
+    A random time region of each example is replaced by the same region of
+    a shuffled example of the batch, see [1]_. As in the reference code [2]_,
+    a coefficient ``lam`` is drawn from a Beta distribution, the region is
+    ``(1 - lam) * n_times`` long (the 1-D analogue of the cut area ratio
+    ``1 - lam``) around a uniformly drawn center, it is clipped at the trial
+    boundaries, and ``lam`` is then recomputed from the pasted length.
+
+    Like :class:`Mixup`, it applies to whole batches and returns targets
+    ``(y_a, y_b, lam)`` for :func:`braindecode.training.mixup_criterion`.
+
+    Parameters
+    ----------
+    alpha : float
+        Parameter of the Beta distribution of ``lam``. ``alpha <= 0`` cuts
+        nothing.
+    beta_per_sample : bool (default=False)
+        By default, one ``lam`` per batch is drawn. If True, one per sample.
+    random_state : int | numpy.random.Generator, optional
+        Seed to be used to instantiate numpy random number generator instance.
+        Defaults to None.
+
+    References
+    ----------
+    .. [1] Sangdoo Yun, Dongyoon Han, Seong Joon Oh, Sanghyuk Chun,
+       Junsuk Choe, Youngjoon Yoo (2019). CutMix: Regularization Strategy
+       to Train Strong Classifiers with Localizable Features. In 2019
+       IEEE/CVF International Conference on Computer Vision (ICCV)
+       Online: https://arxiv.org/abs/1905.04899
+    .. [2] https://github.com/clovaai/CutMix-PyTorch/blob/master/train.py
+    """
+
+    operation = staticmethod(cutmix)  # type: ignore[assignment]
+
+    def get_augmentation_params(self, *batch):
+        """Return idx_perm and the cut_t_start, cut_t_len of each region."""
+        params = super().get_augmentation_params(*batch)
+        lam = params.pop("lam")
+        n_times = batch[0].shape[-1]
+        half = ((1 - lam) * n_times).long() // 2
+        center = torch.as_tensor(self.rng.randint(n_times, size=len(lam)))
+        center = center.to(lam.device)
+        start = (center - half).clamp(min=0)
+        end = (center + half).clamp(max=n_times)
+        return dict(params, cut_t_start=start, cut_t_len=end - start)
+
+
+class LabelSmoothing(Transform):
+    """Label smoothing from Szegedy et al. (2016) [1]_.
+
+    Replaces each target with its convex combination with the uniform
+    distribution over the classes, penalizing over-confident predictions.
+    The signals are returned unchanged; only the targets change.
+
+    The smoothed targets are floating-point distributions of shape
+    ``batch_size, num_classes`` (each row sums to one), so the training
+    loss must accept target distributions, e.g. soft cross-entropy
+    ``-(y * torch.log_softmax(logits, dim=-1)).sum(-1).mean()`` or
+    ``torch.nn.KLDivLoss``. The transform composes before target-mixing
+    transforms such as :class:`braindecode.augmentation.Mixup`, whose
+    fractional-target path then mixes the smoothed distributions. The
+    fixed-expansion mode (``n_augmentation > 0``) of
+    :class:`braindecode.augmentation.AugmentedDataLoader` is not supported:
+    it cannot concatenate the unsmoothed original targets with the reshaped
+    smoothed copies.
+
+    Parameters
+    ----------
+    epsilon : float
+        Smoothing parameter between 0 and 1: the weight of the uniform
+        distribution mixed into the targets. ``0`` disables smoothing.
+    num_classes : int | None, optional
+        Number of classes. Required when the targets are class indices;
+        when the targets are already distributions of shape
+        ``batch_size, num_classes``, it must match their last dimension.
+        Defaults to None.
+    random_state : int | numpy.random.Generator, optional
+        Seed to be used to instantiate numpy random number generator
+        instance. The transform is deterministic, so the seed only feeds
+        the application-probability machinery, which is inactive here.
+        Defaults to None.
+
+    References
+    ----------
+    .. [1] Christian Szegedy, Vincent Vanhoucke, Jonathon Shlens and
+       Zbigniew Wojna (2016). Rethinking the Inception Architecture for
+       Computer Vision. In 2016 IEEE Conference on Computer Vision and
+       Pattern Recognition (CVPR), pp. 2818-2826.
+       Online: https://arxiv.org/abs/1512.00567
+    """
+
+    operation = staticmethod(label_smoothing)  # type: ignore[assignment]
+
+    def __init__(self, epsilon, num_classes=None, random_state=None):
+        super().__init__(
+            probability=1.0,  # LabelSmoothing has to be applied to whole batches
+            random_state=random_state,
+        )
+        if not isinstance(epsilon, Real) or not 0.0 <= float(epsilon) <= 1.0:
+            raise ValueError(
+                f"epsilon should be a real number between 0 and 1. Got {epsilon!r}."
+            )
+        if num_classes is not None and (
+            not isinstance(num_classes, int)
+            or isinstance(num_classes, bool)
+            or num_classes < 2
+        ):
+            raise ValueError(
+                f"num_classes should be an integer of at least 2. Got {num_classes!r}."
+            )
+        self.epsilon = epsilon
+        self.num_classes = num_classes
+
+    def get_augmentation_params(self, *batch):
+        """Return transform parameters.
+
+        Parameters
+        ----------
+        X : tensor.Tensor
+            The data.
+        y : tensor.Tensor
+            The labels.
+
+        Returns
+        -------
+        params : dict
+            Contains
+
+            * epsilon : float
+                Smoothing parameter between 0 and 1.
+            * num_classes : int | None
+                The number of classes.
+        """
+        return {
+            "epsilon": self.epsilon,
+            "num_classes": self.num_classes,
+        }
+
+
 class SegmentationReconstruction(Transform):
     """Segmentation Reconstruction from Lotte (2015) [Lotte2015]_.
 
@@ -1283,7 +1436,7 @@ class MaskEncoding(Transform):
         )
 
         time_start = self.rng.randint(
-            0, n_times - segment_length, (batch_size, self.n_segments)
+            0, n_times - segment_length + 1, (batch_size, self.n_segments)
         )
         time_start = torch.from_numpy(time_start)