Braindecode 1.5.0.dev174273210__tar.gz → 1.5.0.dev176208946__tar.gz

{braindecode-1.5.0.dev174273210/braindecode.egg-info → braindecode-1.5.0.dev176208946}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: braindecode
-Version: 1.5.0.dev174273210
+Version: 1.5.0.dev176208946
 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.dev174273210 → braindecode-1.5.0.dev176208946}/braindecode/models/__init__.py

@@ -5,7 +5,7 @@ from .attentionbasenet import AttentionBaseNet
 from .attn_sleep import AttnSleep
 from .base import EEGModuleMixin
 from .bendr import BENDR
-from .biot import BIOT
+from .biot import BIOT, InterpolatedBIOT
 from .brainmodule import BrainModule
 from .cbramod import CBraMod
 from .codebrain import CodeBrain
@@ -30,7 +30,8 @@ from .fblightconvnet import FBLightConvNet
 from .fbmsnet import FBMSNet
 from .hybrid import HybridNet
 from .ifnet import IFNet
-from .labram import Labram
+from .interpolated import InterpolatedModel
+from .labram import InterpolatedLaBraM, Labram
 from .luna import LUNA
 from .medformer import MEDFormer
 from .msvtnet import MSVTNet
@@ -39,6 +40,7 @@ from .reve import REVE
 from .sccnet import SCCNet
 from .shallow_fbcsp import ShallowFBCSPNet
 from .signal_jepa import (
+    InterpolatedSignalJEPA,
     SignalJEPA,
     SignalJEPA_Contextual,
     SignalJEPA_PostLocal,
@@ -97,6 +99,10 @@ __all__ = [
     "FBMSNet",
     "HybridNet",
     "IFNet",
+    "InterpolatedBIOT",
+    "InterpolatedLaBraM",
+    "InterpolatedModel",
+    "InterpolatedSignalJEPA",
     "Labram",
     "LUNA",
     "extract_channel_locations_from_chs_info",

{braindecode-1.5.0.dev174273210 → braindecode-1.5.0.dev176208946}/braindecode/models/biot.py

@@ -1,12 +1,57 @@
 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]_
@@ -439,7 +484,9 @@ 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))
+        self.register_buffer(
+            "index", torch.arange(n_chans, dtype=torch.long), persistent=False
+        )
 
     def stft(self, sample):
         """
@@ -553,3 +600,16 @@ 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/models/interpolated.py

@@ -0,0 +1,182 @@
+# Authors: Pierre Guetschel
+#
+# License: BSD (3-clause)
+from __future__ import annotations
+
+from typing import Literal, Optional, Type
+
+import numpy as np
+import torch.nn as nn
+
+from braindecode.modules.interpolation import ChannelInterpolationLayer
+
+
+def InterpolatedModel(
+    model_cls: Type,
+    target_chs_info: list[dict],
+    name: Optional[str] = None,
+) -> Type:
+    """Return a subclass of ``model_cls`` that interpolates channels to ``target_chs_info``.
+
+    .. warning:: Experimental. Public API may change without a deprecation cycle.
+
+    Parameters
+    ----------
+    model_cls : type
+        A braindecode model class (subclass of
+        :class:`~braindecode.models.base.EEGModuleMixin`).
+    target_chs_info : list of dict
+        The canonical channel set the backbone expects internally. Every
+        instance of the returned class projects its input channels to
+        this set via :class:`~braindecode.modules.ChannelInterpolationLayer`.
+    name : str, optional
+        ``__name__`` to assign to the returned class. Defaults to
+        ``f"Interpolated{model_cls.__name__}"``.
+
+    Returns
+    -------
+    type
+        A new subclass of ``model_cls`` whose ``__init__`` accepts
+        arbitrary user ``chs_info`` and automatically inserts a frozen
+        (by default) channel-interpolation layer before the backbone.
+    """
+    _is_sequential = issubclass(model_cls, nn.Sequential)
+
+    class _Interpolated(model_cls):
+        _TARGET_CHS_INFO = target_chs_info
+
+        def __init__(
+            self,
+            chs_info,
+            n_outputs=None,
+            n_times=None,
+            input_window_seconds=None,
+            sfreq=None,
+            n_chans=None,
+            interpolation_method: str = "spline",
+            interpolation_mode: Literal["always", "name_match"] = "name_match",
+            trainable: bool = False,
+            **kwargs,
+        ):
+            # Signal-related params are declared EXPLICITLY here so that
+            # skorch's ``EEGClassifier._set_signal_args`` (which inspects
+            # the ``__init__`` signature via ``inspect.signature``) can
+            # auto-forward them from the training dataset. They would not
+            # be discoverable if they were collapsed into ``**kwargs``.
+            # ``n_chans`` is declared for the same discoverability reason
+            # but intentionally ignored: the backbone must see
+            # ``len(target_chs_info)`` derived from ``chs_info``.
+            del n_chans
+            # Backbone init uses the target channels. During this call,
+            # some backbones run a dummy forward (e.g. to size the head);
+            # ``self.interpolation_layer`` does not exist yet — the
+            # ``forward`` override below falls back to pass-through when
+            # the attribute is absent. Assigning an ``nn.Identity()``
+            # before ``super()`` is impossible: ``nn.Module.__setattr__``
+            # requires ``nn.Module.__init__`` to have run, and the chain
+            # would wipe ``self._modules`` when it reaches it again.
+            super().__init__(
+                chs_info=target_chs_info,
+                n_outputs=n_outputs,
+                n_times=n_times,
+                input_window_seconds=input_window_seconds,
+                sfreq=sfreq,
+                **kwargs,
+            )
+
+            layer = ChannelInterpolationLayer(
+                src_chs_info=chs_info,
+                tgt_chs_info=target_chs_info,
+                mode=interpolation_mode,
+                method=interpolation_method,
+                trainable=trainable,
+            )
+            if _is_sequential:
+                # For nn.Sequential subclasses, prepend the interpolation
+                # layer so that nn.Sequential.forward runs it first.
+                # Registering via attribute assignment appends to _modules;
+                # instead we rebuild _modules with the layer first.
+                old_modules = list(self._modules.items())  # type: ignore[has-type]
+                self._modules.clear()  # type: ignore[has-type]
+                self._modules["interpolation_layer"] = layer  # type: ignore[index]
+                for k, v in old_modules:
+                    self._modules[k] = v  # type: ignore[index]
+            else:
+                self.interpolation_layer = layer
+
+            # Rebind private attrs so the user-facing view (.chs_info,
+            # .n_chans, .input_shape, build_model_config) reflects the
+            # user's channels. Properties are NOT overridden — we mutate
+            # the private attrs the base-class properties read from.
+            self._chs_info = chs_info
+            self._n_chans = len(chs_info)
+
+        if not _is_sequential:
+
+            def forward(self, x, *args, **kwargs):
+                # During super().__init__() the interpolation_layer attr
+                # does not exist yet; any dummy forward call (e.g. from
+                # get_output_shape) must pass through unchanged so the
+                # backbone sees its expected target-shape input.
+                # Forward *args / **kwargs so backbone-specific flags
+                # like ``return_features`` keep working through the
+                # wrapper.
+                interp = getattr(self, "interpolation_layer", None)
+                if interp is not None:
+                    x = interp(x)
+                return super().forward(x, *args, **kwargs)
+
+    _Interpolated.__name__ = name or f"Interpolated{model_cls.__name__}"
+    _Interpolated.__qualname__ = _Interpolated.__name__
+    # Propagate the backbone docstring so Sphinx and the categorization tests
+    # can read the class badges.  Prepend a short header so the class shows
+    # up clearly in documentation as distinct from the backbone.
+    backbone_doc = model_cls.__doc__ or ""
+    _Interpolated.__doc__ = (
+        f"Channel-interpolating wrapper around :class:`{model_cls.__name__}`.\n\n"
+        ":bdg-dark-line:`Channel`\n\n"
+        f"Accepts arbitrary user ``chs_info`` and projects them to the\n"
+        f"backbone's canonical channel set via\n"
+        f":class:`~braindecode.modules.ChannelInterpolationLayer`.\n\n"
+        f"For all other parameters and behavior see the backbone\n"
+        f"documentation reproduced below.\n\n" + backbone_doc
+    )
+    return _Interpolated
+
+
+def _build_chs_info_from_montage(names: list[str], montage: str) -> list[dict]:
+    """Build a ``list[dict]`` ``chs_info`` from channel names + an MNE montage.
+
+    Each returned dict has ``ch_name``, ``kind="eeg"``, and ``loc`` (shape
+    ``(3,)``). Used by braindecode's shipped ``Interpolated*`` variants to
+    turn a bare list of canonical channel names into the dict form
+    ``ChannelInterpolationLayer`` expects.
+
+    Parameters
+    ----------
+    names : list of str
+        Channel names in the desired order.
+    montage : str
+        Name of an MNE standard montage (e.g. ``"standard_1005"``).
+
+    Returns
+    -------
+    list of dict
+
+    Raises
+    ------
+    ValueError
+        If a name is not found in the montage.
+    """
+    import mne
+
+    mtg = mne.channels.make_standard_montage(montage)
+    ch_pos = mtg.get_positions()["ch_pos"]
+    out = []
+    for n in names:
+        if n not in ch_pos:
+            raise ValueError(f"Channel {n!r} not found in montage {montage!r}.")
+        out.append(
+            {"ch_name": n, "kind": "eeg", "loc": np.asarray(ch_pos[n], dtype=float)}
+        )
+    return out