Braindecode 1.5.0.dev176208946__tar.gz → 1.5.0.dev179040812__tar.gz

{braindecode-1.5.0.dev176208946/braindecode.egg-info → braindecode-1.5.0.dev179040812}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: braindecode
-Version: 1.5.0.dev176208946
+Version: 1.5.0.dev179040812
 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-1.5.0.dev176208946 → braindecode-1.5.0.dev179040812}/braindecode/models/__init__.py

@@ -5,10 +5,9 @@ from .attentionbasenet import AttentionBaseNet
 from .attn_sleep import AttnSleep
 from .base import EEGModuleMixin
 from .bendr import BENDR
-from .biot import BIOT, InterpolatedBIOT
+from .biot import BIOT
 from .brainmodule import BrainModule
 from .cbramod import CBraMod
-from .codebrain import CodeBrain
 from .contrawr import ContraWR
 from .ctnet import CTNet
 from .deep4 import Deep4Net
@@ -30,8 +29,7 @@ from .fblightconvnet import FBLightConvNet
 from .fbmsnet import FBMSNet
 from .hybrid import HybridNet
 from .ifnet import IFNet
-from .interpolated import InterpolatedModel
-from .labram import InterpolatedLaBraM, Labram
+from .labram import Labram
 from .luna import LUNA
 from .medformer import MEDFormer
 from .msvtnet import MSVTNet
@@ -40,7 +38,6 @@ from .reve import REVE
 from .sccnet import SCCNet
 from .shallow_fbcsp import ShallowFBCSPNet
 from .signal_jepa import (
-    InterpolatedSignalJEPA,
     SignalJEPA,
     SignalJEPA_Contextual,
     SignalJEPA_PostLocal,
@@ -75,7 +72,6 @@ __all__ = [
     "BIOT",
     "BENDR",
     "CBraMod",
-    "CodeBrain",
     "ContraWR",
     "CTNet",
     "Deep4Net",
@@ -99,10 +95,6 @@ __all__ = [
     "FBMSNet",
     "HybridNet",
     "IFNet",
-    "InterpolatedBIOT",
-    "InterpolatedLaBraM",
-    "InterpolatedModel",
-    "InterpolatedSignalJEPA",
     "Labram",
     "LUNA",
     "extract_channel_locations_from_chs_info",

{braindecode-1.5.0.dev176208946 → braindecode-1.5.0.dev179040812}/braindecode/models/attentionbasenet.py

@@ -1,8 +1,5 @@
 from __future__ import annotations
 
-# Authors: Sarthak Tayal <sarthaktayal2@gmail.com>
-#
-# License: BSD (3-clause)
 import math
 
 from einops.layers.torch import Rearrange
@@ -278,6 +275,8 @@ class AttentionBaseNet(EEGModuleMixin, nn.Module):
         activation: type[nn.Module] = nn.ELU,
         extra_params: bool = False,
     ):
+        super(AttentionBaseNet, self).__init__()
+
         super().__init__(
             n_outputs=n_outputs,
             n_chans=n_chans,

{braindecode-1.5.0.dev176208946 → braindecode-1.5.0.dev179040812}/braindecode/models/biot.py

@@ -1,57 +1,12 @@
 import math
 from warnings import warn
 
-import numpy as np
 import torch
 import torch.nn as nn
 from linear_attention_transformer import LinearAttentionTransformer
 
 from braindecode.models.base import EEGModuleMixin
 
-# -----------------------------------------------------------------------------
-# Canonical channel order for InterpolatedBIOT — the 18-channel TCP bipolar
-# montage used by BIOT's shhs-prest and six-datasets pretrained checkpoints.
-# Source: https://github.com/ycq091044/BIOT (README + datasets/TUAB/process.py
-# + datasets/SHHS/process.py). Indices 0-15 are the TCP 16-channel bipolar
-# derivations; indices 16-17 are SHHS differential channels.
-#
-# The `loc` values are only used to build an MNE interpolation matrix for
-# InterpolatedBIOT. All entries are bipolar / differential derivations.
-# TODO: positions are stored as the midpoint of the two constituent
-# electrodes. This is a simplification — a bipolar signal V(A)-V(B) cannot
-# be faithfully recovered by spatial interpolation at the midpoint. Revisit
-# in a follow-up PR (e.g. a dedicated BipolarDerivationLayer).
-# -----------------------------------------------------------------------------
-
-# fmt: off
-_BIOT_TARGET_CHS_TUPLES: list[tuple[str, tuple[float, float, float]]] = [
-    ("FP1-F7", (-0.04984980, 0.06319570, -0.00920500)),
-    ("F7-T7", (-0.07721200, 0.01322780, -0.01038300)),
-    ("T7-P7", (-0.07829770, -0.04473570, -0.00591650)),
-    ("P7-O1", (-0.05092385, -0.09295085, 0.00317600)),
-    ("FP2-F8", (0.05145770, 0.06465880, -0.00954000)),
-    ("F8-T8", (0.07906150, 0.01470070, -0.01074500)),
-    ("T8-P8", (0.07906780, -0.04404430, -0.00601500)),
-    ("P8-O2", (0.05144915, -0.09261215, 0.00313000)),
-    ("FP1-F3", (-0.03984025, 0.06851415, 0.01760100)),
-    ("F3-C3", (-0.05780095, 0.02073975, 0.05327500)),
-    ("C3-P3", (-0.05918270, -0.04520975, 0.06014900)),
-    ("P3-O1", (-0.04121035, -0.09561840, 0.03238950)),
-    ("FP2-F4", (0.04085425, 0.06960035, 0.01686700)),
-    ("F4-C4", (0.05947705, 0.02170225, 0.05219700)),
-    ("C4-P4", (0.06139230, -0.04473025, 0.06007050)),
-    ("P4-O2", (0.04275465, -0.09535810, 0.03268050)),
-    ("C3-A2", (0.01021790, -0.01832050, -0.00183650)),
-    ("C4-A1", (-0.00947910, -0.01794500, -0.00220300)),
-]
-# fmt: on
-
-_BIOT_TARGET_CHS_INFO = [
-    {"ch_name": ch, "kind": "eeg", "loc": np.asarray(loc, dtype=float)}
-    for ch, loc in _BIOT_TARGET_CHS_TUPLES
-]
-BIOT_CHANNEL_ORDER = [ch for ch, _ in _BIOT_TARGET_CHS_TUPLES]
-
 
 class BIOT(EEGModuleMixin, nn.Module):
     r"""BIOT from Yang et al (2023) [Yang2023]_
@@ -484,9 +439,7 @@ class _BIOTEncoder(nn.Module):
         self.channel_tokens = nn.Embedding(
             num_embeddings=n_chans, embedding_dim=emb_size
         )
-        self.register_buffer(
-            "index", torch.arange(n_chans, dtype=torch.long), persistent=False
-        )
+        self.index = nn.Parameter(torch.LongTensor(range(n_chans)), requires_grad=False)
 
     def stft(self, sample):
         """
@@ -600,16 +553,3 @@ class _BIOTEncoder(nn.Module):
         # (batch_size, emb)
         emb = self.transformer(emb).mean(dim=1)
         return emb
-
-
-# -----------------------------------------------------------------------------
-# InterpolatedBIOT — experimental channel-interpolation variant of BIOT
-# -----------------------------------------------------------------------------
-# Wraps :class:`BIOT` with an MNE-backed channel-interpolation layer that
-# projects arbitrary user ``chs_info`` to the canonical 18-channel BIOT
-# montage (:data:`_BIOT_TARGET_CHS_INFO`). Frozen by default; set
-# ``trainable=True`` to fine-tune the projection matrix.
-
-from braindecode.models.interpolated import InterpolatedModel  # noqa: E402
-
-InterpolatedBIOT = InterpolatedModel(BIOT, _BIOT_TARGET_CHS_INFO)

{braindecode-1.5.0.dev176208946 → braindecode-1.5.0.dev179040812}/braindecode/models/config.py

@@ -1,4 +1,3 @@
-# Authors: Sarthak Tayal <sarthaktayal2@gmail.com>
 from collections.abc import Callable
 from inspect import signature
 from types import UnionType
@@ -18,10 +17,10 @@ from braindecode.models.util import (
 
 try:
     from numpydantic import NDArray, Shape
-
-    _loc_type = NDArray[Shape["12"], np.float64]
 except ImportError:
-    _loc_type = np.ndarray  # type: ignore[misc]
+    # we can't use soft import for numpydantic because numpydantic does not define its version in __init__
+    NDArray = Any  # type: ignore
+    Shape = Any  # type: ignore
 
 
 class ChsInfoType(TypedDict, total=False, closed=True):  # type: ignore[call-arg]
@@ -30,7 +29,7 @@ class ChsInfoType(TypedDict, total=False, closed=True):  # type: ignore[call-arg
     coil_type: int
     coord_frame: int
     kind: str
-    loc: _loc_type  # type: ignore[valid-type,misc]
+    loc: NDArray[Shape["12"], np.float64]  # type: ignore[misc]
     logno: int
     range: float
     scanno: int