braindecode 1.8.1.dev168490289__tar.gz → 1.8.1.dev169087728__tar.gz

{braindecode-1.8.1.dev168490289 → braindecode-1.8.1.dev169087728}/NOTICE.txt

@@ -14,8 +14,7 @@ The following components are licensed under the Creative Commons Attribution-Non
 - `braindecode/models/eegminer.py`
 - `braindecode/models/meta_neuromotor.py`
 - `braindecode/models/brainmodule.py`
-
-As well as class later imported into the `braindecode.models.module` named as GeneralizedGaussianFilter.
+- `braindecode/models/neurorvq.py`
 
 The `meta_neuromotor.py` file is a derivative of
 `facebookresearch/generic-neuromotor-interface`, released by Meta Platforms,
@@ -43,6 +42,17 @@ The following components are licensed under the MIT License:
 - `braindecode/models/tcformer.py`
 - `braindecode/models/ifnet.py`
 - `braindecode/models/mirepnet.py`
+- `braindecode/models/popt.py`
+- `braindecode/modules/popt_modules.py`
+- `braindecode/models/brainomni.py`
+- `braindecode/modules/quantization.py`
+- `braindecode/models/seizure_transformer.py`
+- `docs/_static/model/seizure_transformer_arch.png`
+
+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.
 
 ### Apache-2.0 Licensed Files
 
@@ -51,6 +61,7 @@ The following components are licensed under the Apache License 2.0:
 - `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.dev168490289/braindecode.egg-info → braindecode-1.8.1.dev169087728}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: braindecode
-Version: 1.8.1.dev168490289
+Version: 1.8.1.dev169087728
 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>
@@ -60,6 +60,8 @@ Provides-Extra: typing
 Requires-Dist: exca>=0.5.10; extra == "typing"
 Requires-Dist: numpydantic>=1.7; extra == "typing"
 Provides-Extra: docs
+Requires-Dist: pytest<9.1; extra == "docs"
+Requires-Dist: sphinx-markdown-builder==0.6.11; extra == "docs"
 Requires-Dist: sphinx_gallery>=0.17; extra == "docs"
 Requires-Dist: sphinx_rtd_theme; extra == "docs"
 Requires-Dist: sphinx-autodoc-typehints; extra == "docs"

{braindecode-1.8.1.dev168490289 → braindecode-1.8.1.dev169087728}/braindecode/classifier.py

@@ -207,10 +207,11 @@ class EEGClassifier(_EEGNeuralNet, NeuralNetClassifier):
 
         Returns
         -------
-        trial_predictions : np.ndarray
+        trial_predictions : np.ndarray | list of np.ndarray
             3-dimensional array (n_trials x n_classes x n_predictions), where
             the number of predictions depend on the chosen window size and the
-            receptive field of the network.
+            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``.

{braindecode-1.8.1.dev168490289 → braindecode-1.8.1.dev169087728}/braindecode/datasets/tuh.py

@@ -815,7 +815,8 @@ def _get_header(*args, **kwargs):
     for paths_dict in [_TUH_EEG_PATHS, _TUH_EEG_ABNORMAL_PATHS, _TUH_EEG_EVENTS_PATHS]:
         for version_dict in paths_dict.values():
             all_paths.update(version_dict)
-    return all_paths[args[0]]
+    # Mock keys use POSIX separators; pathlib emits backslashes on Windows.
+    return all_paths[os.fspath(args[0]).replace("\\", "/")]
 
 
 _TUH_EEG_PATHS = {

{braindecode-1.8.1.dev168490289 → braindecode-1.8.1.dev169087728}/braindecode/models/__init__.py

@@ -9,6 +9,7 @@ from .bendr import BENDR, InterpolatedBENDR
 from .biot import BIOT, InterpolatedBIOT
 from .brainbert import BrainBERT
 from .brainmodule import BrainModule
+from .brainomni import BrainOmni, BrainTokenizer
 from .brant import Brant
 from .cbramod import CBraMod
 from .codebrain import CodeBrain
@@ -40,6 +41,7 @@ from .ifnet import IFNet
 from .interpolated import InterpolatedModel
 from .labram import InterpolatedLaBraM, Labram
 from .luna import LUNA
+from .mapa import MAPA
 from .medformer import MEDFormer
 from .meta_neuromotor import MetaNeuromotorHand
 from .mirepnet import MIRepNet
@@ -47,9 +49,12 @@ from .mscformer import MSCFormer
 from .msvtnet import MSVTNet
 from .mvpformer import MVPFormer
 from .neuropose import NeuroPose
+from .neurorvq import NeuroRVQ
 from .patchedtransformer import PBT
+from .popt import PopulationTransformer
 from .reve import REVE
 from .sccnet import SCCNet
+from .seizure_transformer import SeizureTransformer
 from .sensingdynamics import SensingDynamics
 from .shallow_fbcsp import ShallowFBCSPNet
 from .signal_jepa import (
@@ -95,6 +100,8 @@ __all__ = [
     "BIOT",
     "BENDR",
     "BrainBERT",
+    "BrainOmni",
+    "BrainTokenizer",
     "CBraMod",
     "CodeBrain",
     "ContraWR",
@@ -138,14 +145,18 @@ __all__ = [
     "LUNA",
     "extract_channel_locations_from_chs_info",
     "positions_from_chs_info",
+    "MAPA",
     "MEDFormer",
     "MIRepNet",
+    "NeuroRVQ",
     "MSCFormer",
     "MSVTNet",
     "MVPFormer",
     "PBT",
+    "PopulationTransformer",
     "REVE",
     "SCCNet",
+    "SeizureTransformer",
     "ShallowFBCSPNet",
     "SignalJEPA",
     "SignalJEPA_Contextual",

{braindecode-1.8.1.dev168490289 → braindecode-1.8.1.dev169087728}/braindecode/models/base.py

@@ -779,6 +779,22 @@ class EEGModuleMixin(_BaseHubMixin, metaclass=_BraindecodeDocstringMeta):
 
     if HAS_HF_HUB:
 
+        @classmethod
+        def from_pretrained(cls, *args, **kwargs):
+            # The Hub mixin fills omitted __init__ args from config.json; pin the
+            # derived geometry arg so it cannot clash with the caller's one
+            # (e.g. caller chs_info vs saved n_chans) in __init__'s checks.
+            if "chs_info" in kwargs and "n_chans" not in kwargs:
+                chs_info = kwargs["chs_info"]
+                kwargs["n_chans"] = None if chs_info is None else len(chs_info)
+            elif "n_chans" in kwargs and "chs_info" not in kwargs:
+                kwargs["chs_info"] = None
+            if ("n_times" in kwargs or "sfreq" in kwargs) and (
+                "input_window_seconds" not in kwargs
+            ):
+                kwargs["input_window_seconds"] = None
+            return super().from_pretrained(*args, **kwargs)
+
         @classmethod
         def _from_pretrained(
             cls,

{braindecode-1.8.1.dev168490289 → braindecode-1.8.1.dev169087728}/braindecode/models/bendr.py

@@ -11,6 +11,7 @@ from einops.layers.torch import Rearrange
 from torch import nn
 
 from braindecode.models.base import EEGModuleMixin
+from braindecode.modules.channel_tokenizer import ChannelTokenizer
 
 # The 20 channels used to pre-train BENDR, in the order expected by the
 # `braindecode/braindecode-bendr` checkpoint. The first 19 entries are the
@@ -288,26 +289,25 @@ class BENDR(EEGModuleMixin, nn.Module):
         # Keep these parameters if needed later, otherwise they are captured by the mixin
         del n_outputs, n_chans, chs_info, n_times, input_window_seconds, sfreq
 
-        # If the user supplies chs_info, require it to match BENDR_CHANNEL_ORDER
-        # exactly (case-insensitive). Arbitrary channel sets should go through
-        # InterpolatedBENDR — same pattern as Labram / InterpolatedLaBraM.
-        # When chs_info is absent (the usual n_chans=20 path, incl.
-        # from_pretrained), no check is performed.
+        # No chs_info (incl. from_pretrained) or the canonical order: no
+        # tokenizer, so released checkpoints stay bit-identical. Any other
+        # montage is projected onto the 20 canonical channels.
         try:
             _chs_info = self.chs_info
         except ValueError:
             _chs_info = None
+        self.channel_tokenizer = None
+        backbone_n_chans = self.n_chans
         if _chs_info is not None:
             user_names = [ch["ch_name"] for ch in _chs_info]  # type: ignore[index]
             canonical = BENDR_CHANNEL_ORDER
             if [n.lower() for n in user_names] != [n.lower() for n in canonical]:
-                raise ValueError(
-                    f"BENDR requires chs_info to match BENDR_CHANNEL_ORDER exactly "
-                    f"({len(canonical)} channels, specific order; last is 'SCALE'). "
-                    f"Got {len(user_names)} channel(s). For arbitrary channel sets, "
-                    f"use InterpolatedBENDR "
-                    f"(from braindecode.models import InterpolatedBENDR)."
+                self.channel_tokenizer = ChannelTokenizer(
+                    strategy="fixed_order",
+                    src_chs_info=_chs_info,
+                    target_chs_info=_BENDR_TARGET_CHS_INFO,
                 )
+                backbone_n_chans = len(_BENDR_TARGET_CHS_INFO)
 
         self.encoder_h = encoder_h
         self.contextualizer_hidden = contextualizer_hidden
@@ -315,7 +315,7 @@ class BENDR(EEGModuleMixin, nn.Module):
         self.encoder_only = encoder_only
 
         self.encoder = _ConvEncoderBENDR(
-            in_features=self.n_chans,
+            in_features=backbone_n_chans,
             encoder_h=encoder_h,
             dropout=drop_prob,
             projection_head=projection_head,
@@ -361,6 +361,8 @@ class BENDR(EEGModuleMixin, nn.Module):
         self._build_head(n_outputs)
 
     def forward(self, x, return_features=False):
+        if self.channel_tokenizer is not None:
+            x = self.channel_tokenizer(x)
         encoded = self.encoder(x)
         # encoded: [batch_size, encoder_h, n_encoded_times]