braindecode 1.8.1.dev172484635__tar.gz → 1.8.1.dev172561613__tar.gz

{braindecode-1.8.1.dev172484635 → braindecode-1.8.1.dev172561613}/NOTICE.txt

@@ -13,9 +13,10 @@ The following components are licensed under the Creative Commons Attribution-Non
 
 - `braindecode/models/eegminer.py`
 - `braindecode/models/meta_neuromotor.py`
+- `braindecode/models/sleepfm.py`
 - `braindecode/models/brainmodule.py`
-
-As well as class later imported into the `braindecode.models.module` named as GeneralizedGaussianFilter.
+- `braindecode/models/neurorvq.py`
+- `braindecode/models/neurorvq_tokenizer.py`
 
 The `meta_neuromotor.py` file is a derivative of
 `facebookresearch/generic-neuromotor-interface`, released by Meta Platforms,
@@ -44,15 +45,32 @@ The following components are licensed under the MIT License:
 - `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`
+
+The `brainomni.py` file is a derivative of `OpenTSLab/BrainOmni` (MIT), whose
+SEANet codec derives from Meta's `facebookresearch/encodec` (MIT). The
+`quantization.py` module holds the residual vector quantization derived from
+`lucidrains/vector-quantize-pytorch` (MIT) and the BrainOmni port.
+The `linear_attention.py` module is the part of
+`lucidrains/linear-attention-transformer` (MIT) that BIOT and TFMTokenizer run.
 
 ### Apache-2.0 Licensed Files
 
 The following components are licensed under the Apache License 2.0:
 
+- `braindecode/models/axon.py`
 - `braindecode/models/mvpformer.py`
 - `braindecode/models/zuna.py`
 - `braindecode/models/luna.py`
+- `braindecode/models/mapa.py`
 - `braindecode/models/brant.py`
 - `braindecode/models/diver1.py`
 - `braindecode/models/mscformer.py`

{braindecode-1.8.1.dev172484635/braindecode.egg-info → braindecode-1.8.1.dev172561613}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: braindecode
-Version: 1.8.1.dev172484635
+Version: 1.8.1.dev172561613
 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>

{braindecode-1.8.1.dev172484635 → braindecode-1.8.1.dev172561613}/braindecode/augmentation/__init__.py

@@ -23,6 +23,7 @@ from .transforms import (
     SignFlip,
     SmoothTimeMask,
     TimeReverse,
+    TrivialAugment,
 )
 
 __all__ = [
@@ -30,6 +31,7 @@ __all__ = [
     "IdentityTransform",
     "Compose",
     "AugmentedDataLoader",
+    "TrivialAugment",
     "TimeReverse",
     "SignFlip",
     "FTSurrogate",

{braindecode-1.8.1.dev172484635 → braindecode-1.8.1.dev172561613}/braindecode/augmentation/functional.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)
 
@@ -931,7 +932,7 @@ 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(
@@ -1093,7 +1094,8 @@ def segmentation_reconstruction(
     y : torch.Tensor
         EEG labels for the example or batch.
     n_segments : int
-        Number of segments to use in the batch.
+        Number of segments to use in the batch. Any remaining samples are
+        included in the last segment.
     data_classes : list[tuple[int, torch.Tensor]]
         List of tuples. Each tuple contains the class index and the corresponding EEG data.
     rand_indices : array-like
@@ -1133,6 +1135,8 @@ def segmentation_reconstruction(
         for idx_segment in range(n_segments):
             start = idx_segment * segment_size
             end = (idx_segment + 1) * segment_size
+            if idx_segment == n_segments - 1:
+                end = window_size
 
             # Perform the data augmentation
             X_aug[np.arange(n_trials), :, start:end] = X_class[

{braindecode-1.8.1.dev172484635 → braindecode-1.8.1.dev172561613}/braindecode/augmentation/transforms.py

@@ -1457,3 +1457,188 @@ class BandRotation(Transform):
             "circular_jitter": self.circular_jitter,
             "random_state": self.rng,
         }
+
+
+class TrivialAugment(Transform):
+    """Apply one randomly sampled label-preserving augmentation per example.
+
+    For every example, independently samples one transform from the pool
+    below and one of ``num_bins`` strengths evenly spaced between that
+    transform's bounds, as in TrivialAugment [1]_. Examples that draw the
+    same transform and strength are transformed in one call; each pooled
+    transform still draws its own randomness per example.
+
+    Default pool (no assumption on the signal's unit, sampling frequency or
+    montage):
+
+    * :class:`TimeReverse` — no strength parameter.
+    * :class:`SignFlip` — no strength parameter.
+    * :class:`FTSurrogate` — phase noise magnitude, 0.2 to 1.
+    * :class:`ChannelsDropout` — channel drop probability, 0.05 to 0.4.
+    * :class:`ChannelsShuffle` — shuffle probability, 0.1 to 0.75.
+    * :class:`SmoothTimeMask` — mask length as a fraction of the window
+      length, 0.05 to 0.25.
+    * :class:`GaussianNoise` — noise standard deviation as a fraction of the
+      sub-batch standard deviation (volts or microvolts alike), 0.02 to 0.3.
+    * :class:`AmplitudeScale` — scale interval ``(1/s, s)``, ``s`` from 1.25
+      to 2.5.
+
+    ``sfreq`` adds :class:`BandstopFilter` (bandwidth 0.5 to 4 Hz, capped
+    2.5 Hz below Nyquist) and :class:`FrequencyShift` (maximum shift 0.5 to
+    2 Hz); ``sensors_positions_matrix`` adds :class:`SensorsRotation` around
+    the z axis (5 to 25 degrees).
+
+    Parameters
+    ----------
+    probability : float, optional
+        Probability of augmenting each example. Defaults to 1.0.
+    sfreq : float | None, optional
+        Sampling frequency of the signals, in Hz. Defaults to None.
+    sensors_positions_matrix : array-like | None, optional
+        Sensor positions of shape ``(3, n_channels)`` (see
+        :class:`SensorsRotation`). Defaults to None.
+    num_bins : int, optional
+        Number of strength levels per transform. Defaults to 10.
+    random_state : int | numpy.random.RandomState, optional
+        Seed shared by the per-example sampler and every pooled transform.
+        Defaults to None.
+
+    Attributes
+    ----------
+    op_names : list of str
+        Names of the transforms in the pool, in sampling order.
+
+    References
+    ----------
+    .. [1] Müller, S. G., & Hutter, F. (2021). TrivialAugment:
+       Tuning-free Yet State-of-the-Art Data Augmentation. Proceedings of
+       the IEEE/CVF International Conference on Computer Vision (ICCV),
+       pp. 774-782.
+    """
+
+    def __init__(
+        self,
+        probability=1.0,
+        sfreq=None,
+        sensors_positions_matrix=None,
+        num_bins=10,
+        random_state=None,
+    ):
+        super().__init__(probability=probability, random_state=random_state)
+        if not isinstance(num_bins, (int, np.integer)) or num_bins < 1:
+            raise ValueError(f"num_bins must be a positive integer, got {num_bins}")
+        self.num_bins = int(num_bins)
+        rng = self.rng
+        # (name, strength bounds or None, make(strength) or None: built per call)
+        specs = [
+            ("TimeReverse", None, lambda s: TimeReverse(1.0, random_state=rng)),
+            ("SignFlip", None, lambda s: SignFlip(1.0, random_state=rng)),
+            (
+                "FTSurrogate",
+                (0.2, 1.0),
+                lambda s: FTSurrogate(1.0, phase_noise_magnitude=s, random_state=rng),
+            ),
+            (
+                "ChannelsDropout",
+                (0.05, 0.4),
+                lambda s: ChannelsDropout(1.0, p_drop=s, random_state=rng),
+            ),
+            (
+                "ChannelsShuffle",
+                (0.1, 0.75),
+                lambda s: ChannelsShuffle(1.0, p_shuffle=s, random_state=rng),
+            ),
+            ("SmoothTimeMask", (0.05, 0.25), None),
+            ("GaussianNoise", (0.02, 0.3), None),
+            (
+                "AmplitudeScale",
+                (1.25, 2.5),
+                lambda s: AmplitudeScale(1.0, interval=(1.0 / s, s), random_state=rng),
+            ),
+        ]
+        if sfreq is not None:
+            nyquist = sfreq / 2.0
+            # BandstopFilter needs bandwidth < nyquist - 2; keep a margin
+            max_bandwidth = min(4.0, nyquist - 2.5)
+            if max_bandwidth <= 0.5:
+                raise ValueError(
+                    f"sfreq={sfreq} is too small to sample valid band-stop "
+                    "bandwidths (needs at least 6.0 Hz)."
+                )
+            specs += [
+                (
+                    "BandstopFilter",
+                    (0.5, max_bandwidth),
+                    lambda s: BandstopFilter(
+                        1.0,
+                        sfreq=sfreq,
+                        bandwidth=s,
+                        max_freq=nyquist,
+                        random_state=rng,
+                    ),
+                ),
+                (
+                    "FrequencyShift",
+                    (0.5, 2.0),
+                    lambda s: FrequencyShift(
+                        1.0, sfreq=sfreq, max_delta_freq=s, random_state=rng
+                    ),
+                ),
+            ]
+        if sensors_positions_matrix is not None:
+            specs.append(
+                (
+                    "SensorsRotation",
+                    (5.0, 25.0),
+                    lambda s: SensorsRotation(
+                        1.0,
+                        sensors_positions_matrix=sensors_positions_matrix,
+                        max_degrees=s,
+                        random_state=rng,
+                    ),
+                )
+            )
+
+        self._pool = []
+        for name, bounds, make in specs:
+            if bounds is None:
+                strengths = [None]
+            else:
+                strengths = np.linspace(*bounds, self.num_bins).tolist()
+            variants = None if make is None else [make(s) for s in strengths]
+            self._pool.append((name, strengths, variants))
+        # pre-built transforms as submodules (pickle, ``.to()``)
+        self._static_transforms = torch.nn.ModuleList(
+            v for _, _, variants in self._pool if variants for v in variants
+        )
+        self.op_names = [name for name, _, _ in self._pool]
+
+    def operation(self, X, y):
+        """Apply one sampled transform and strength to each example of X."""
+        n_strengths = np.array([len(strengths) for _, strengths, _ in self._pool])
+        op_ids = self.rng.randint(0, len(self._pool), size=X.shape[0])
+        bin_ids = self.rng.randint(0, self.num_bins, size=X.shape[0])
+        # magnitude-free transforms collapse all examples onto bin 0
+        bin_ids[n_strengths[op_ids] == 1] = 0
+        keys = op_ids * self.num_bins + bin_ids
+
+        out_X, out_y = X.clone(), y.clone()
+        for key in np.unique(keys):
+            group = torch.from_numpy(np.flatnonzero(keys == key)).to(X.device)
+            op_i, bin_j = divmod(int(key), self.num_bins)
+            name, strengths, variants = self._pool[op_i]
+            X_sub = X[group]
+            if variants is not None:
+                transform = variants[bin_j]
+            elif name == "SmoothTimeMask":
+                n_mask = max(1, int(round(strengths[bin_j] * X.shape[-1])))
+                transform = SmoothTimeMask(
+                    1.0, mask_len_samples=n_mask, random_state=self.rng
+                )
+            else:  # GaussianNoise, std relative to the sub-batch (unit-free)
+                std = strengths[bin_j] * X_sub.std().item()
+                transform = GaussianNoise(1.0, std=std, random_state=self.rng)
+            tr_X, tr_y = transform(X_sub, y[group])
+            out_X[group] = tr_X.to(out_X.dtype)
+            out_y[group] = tr_y
+        return out_X, out_y

{braindecode-1.8.1.dev172484635 → braindecode-1.8.1.dev172561613}/braindecode/classifier.py

@@ -212,11 +212,12 @@ class EEGClassifier(_EEGNeuralNet, NeuralNetClassifier):
             the number of predictions depend on the chosen window size and the
             receptive field of the network. If trials have different lengths,
             a list with one (n_classes x n_predictions) array per trial.
-        trial_targets : np.ndarray
-            Ground-truth targets from the dataset in a 2-dimensional array
-            (n_trials x n_targets). Only returned when ``return_targets=True``.
-            The number of targets depends on the decoding paradigm and can be
-            either a single value, multiple values, or a sequence.
+        trial_targets : np.ndarray | list of np.ndarray
+            Ground-truth targets from the dataset. Only returned when
+            ``return_targets=True``. An ``np.ndarray`` with a leading trial
+            dimension: ``(n_trials,)`` for scalar targets, with further
+            dimensions for multi-value or equal-length sequence targets. If
+            trial lengths differ, a list with one target array per trial.
         """
         if not self.cropped:
             warnings.warn(

{braindecode-1.8.1.dev172484635 → braindecode-1.8.1.dev172561613}/braindecode/datasets/base.py

@@ -1742,7 +1742,10 @@ class BaseConcatDataset(ConcatDataset, HubDatasetMixin, Generic[T]):
         # Create path if it doesn't exist
         os.makedirs(path, exist_ok=True)
 
-        path_contents = os.listdir(path)
+        # With an offset the caller fills one directory piece by piece (preprocess
+        # saves each recording at its index), so the other entries are expected:
+        # skip the scan that would stat them all on every call and list them in a warning.
+        path_contents = os.listdir(path) if offset == 0 else []
         n_sub_dirs = len(
             [e for e in path_contents if os.path.isdir(os.path.join(path, e))]
         )

{braindecode-1.8.1.dev172484635 → braindecode-1.8.1.dev172561613}/braindecode/datasets/tuh.py

@@ -11,10 +11,12 @@ TUH Abnormal EEG Corpus.
 from __future__ import annotations
 
 import glob
+import json
 import os
 import re
 import warnings
 from datetime import datetime, timezone
+from functools import cache
 from pathlib import Path
 from typing import Iterable, Literal
 from unittest import mock
@@ -183,11 +185,8 @@ class TUH(BaseConcatDataset):
         }
         raw.rename_channels(mapping_strip)
 
-        montage1005 = mne.channels.make_standard_montage(
-            resolve_montage_name("standard_1005")
-        )
         mapping_eeg_names = {
-            c.upper(): c for c in montage1005.ch_names if c.upper() in raw.ch_names
+            c.upper(): c for c in _standard_1005().ch_names if c.upper() in raw.ch_names
         }
 
         # Set channels whose type could not be inferred (defaulted to "eeg") to "misc":
@@ -210,10 +209,7 @@ class TUH(BaseConcatDataset):
 
     @staticmethod
     def _set_montage(raw):
-        montage = mne.channels.make_standard_montage(
-            resolve_montage_name("standard_1005")
-        )
-        raw.set_montage(montage, on_missing="ignore")
+        raw.set_montage(_standard_1005(), on_missing="ignore")
 
     @staticmethod
     def _create_dataset(
@@ -245,7 +241,11 @@ class TUH(BaseConcatDataset):
         # file paths, use this instead as before
         if "year" in description:
             meas_date = meas_date.replace(*description[["year", "month", "day"]])
-        raw.set_meas_date(meas_date)
+        # FIF (e.g. preprocess(..., save_dir=...)) stores dates from 1901-12-13 to
+        # 2038-01-19 only: undated recordings (year 1 above) and de-identified ones
+        # (TUAB has 1899-12-30) keep their date in the description only.
+        in_fif_range = -(2**31) <= meas_date.timestamp() < 2**31
+        raw.set_meas_date(meas_date if in_fif_range else None)
 
         d = {
             "age": int(age),
@@ -255,9 +255,9 @@ class TUH(BaseConcatDataset):
         # if not, get it from meas_date in raw.info and add to description
         # if meas_date is None, create fake one
         if "year" not in description:
-            d["year"] = raw.info["meas_date"].year
-            d["month"] = raw.info["meas_date"].month
-            d["day"] = raw.info["meas_date"].day
+            d["year"] = meas_date.year
+            d["month"] = meas_date.month
+            d["day"] = meas_date.day
 
         # read info relevant for preprocessing from raw without loading it
         if add_physician_reports:
@@ -269,6 +269,12 @@ class TUH(BaseConcatDataset):
         return base_dataset
 
 
+@cache
+def _standard_1005():
+    # Built once per process: set_montage copies the montage before using it.
+    return mne.channels.make_standard_montage(resolve_montage_name("standard_1005"))
+
+
 def _create_description(file_paths, version, ds_name):
     descriptions = [
         _parse_description_from_file_path(f, version, ds_name) for f in file_paths
@@ -289,7 +295,8 @@ def _read_date(file_path):
     date_path = file_path.replace(".edf", "_date.txt")
     # if date file exists, read it
     if os.path.exists(date_path):
-        description = pd.read_json(date_path, typ="series").to_dict()
+        with open(date_path) as f:
+            description = json.load(f)
     # otherwise read edf file, extract date and store to file
     else:
         raw = mne.io.read_raw_edf(file_path, preload=False, verbose="error")

{braindecode-1.8.1.dev172484635 → braindecode-1.8.1.dev172561613}/braindecode/eegneuralnet.py

@@ -144,7 +144,7 @@ class _EEGNeuralNet(NeuralNet, abc.ABC):
             i_window_in_trials.append(i[0].cpu().numpy())
             i_window_stops.append(i[2].cpu().numpy())
             with torch.no_grad():
-                preds.append(to_numpy(self.module_.forward(X.to(self.device))))
+                preds.append(to_numpy(self.module_(X.to(self.device))))
             window_ys.append(y.cpu().numpy())
         preds = np.concatenate(preds)
         i_window_in_trials = np.concatenate(i_window_in_trials)

{braindecode-1.8.1.dev172484635 → braindecode-1.8.1.dev172561613}/braindecode/functional/__init__.py

@@ -3,14 +3,17 @@ from .functions import (
     daubechies_filters,
     drop_path,
     dwt_max_level,
+    fft_conv1d,
     hilbert_freq,
     identity,
     iou_1d,
     pairwise_iou_1d,
     plv_time,
+    prefer_fft_conv,
     rotate_pairs,
     safe_log,
     sinusoidal_positional_encoding,
+    spectral_input,
     square,
     wavelet_decomposition,
 )
@@ -21,14 +24,17 @@ __all__ = [
     "daubechies_filters",
     "drop_path",
     "dwt_max_level",
+    "fft_conv1d",
     "hilbert_freq",
     "identity",
     "iou_1d",
     "pairwise_iou_1d",
     "plv_time",
+    "prefer_fft_conv",
     "rotate_pairs",
     "safe_log",
     "sinusoidal_positional_encoding",
+    "spectral_input",
     "square",
     "wavelet_decomposition",
     "glorot_weight_zero_bias",