braindecode 1.2.0.dev182094932__tar.gz → 1.3.0.dev176728557__tar.gz

{braindecode-1.2.0.dev182094932/braindecode.egg-info → braindecode-1.3.0.dev176728557}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: braindecode
-Version: 1.2.0.dev182094932
+Version: 1.3.0.dev176728557
 Summary: Deep learning software to decode EEG, ECG or MEG signals
 Author-email: Robin Tibor Schirrmeister <robintibor@gmail.com>
 Maintainer-email: Alexandre Gramfort <agramfort@meta.com>, Bruno Aristimunha Pinto <b.aristimunha@gmail.com>, Robin Tibor Schirrmeister <robintibor@gmail.com>
@@ -17,7 +17,7 @@ Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
-Requires-Python: >3.10
+Requires-Python: >=3.10
 Description-Content-Type: text/x-rst
 License-File: LICENSE.txt
 License-File: NOTICE.txt
@@ -49,6 +49,10 @@ Requires-Dist: mypy; extra == "tests"
 Provides-Extra: docs
 Requires-Dist: sphinx_gallery; extra == "docs"
 Requires-Dist: sphinx_rtd_theme; extra == "docs"
+Requires-Dist: sphinx-autodoc-typehints; extra == "docs"
+Requires-Dist: sphinx-autobuild; extra == "docs"
+Requires-Dist: sphinxcontrib-bibtex; extra == "docs"
+Requires-Dist: sphinx_sitemap; extra == "docs"
 Requires-Dist: pydata_sphinx_theme; extra == "docs"
 Requires-Dist: numpydoc; extra == "docs"
 Requires-Dist: memory_profiler; extra == "docs"
@@ -59,6 +63,7 @@ Requires-Dist: lightning; extra == "docs"
 Requires-Dist: seaborn; extra == "docs"
 Requires-Dist: pre-commit; extra == "docs"
 Requires-Dist: openneuro-py; extra == "docs"
+Requires-Dist: plotly; extra == "docs"
 Provides-Extra: all
 Requires-Dist: braindecode[docs,moabb,tests]; extra == "all"
 Dynamic: license-file

braindecode-1.3.0.dev176728557/braindecode/datasets/experimental.py

@@ -0,0 +1,218 @@
+from __future__ import annotations
+
+import random
+from pathlib import Path
+from typing import Callable, Sequence
+
+import mne_bids
+from torch.utils.data import IterableDataset, get_worker_info
+
+
+class BIDSIterableDataset(IterableDataset):
+    """Dataset for loading BIDS.
+
+    .. warning::
+        This class is experimental and may change in the future.
+
+    .. warning::
+        This dataset is not consistent with the Braindecode API.
+
+    This class has the same parameters as the :func:`mne_bids.find_matching_paths` function
+    as it will be used to find the files to load. The default ``extensions`` parameter was changed.
+
+    More information on BIDS (Brain Imaging Data Structure)
+    can be found at https://bids.neuroimaging.io
+
+    Examples
+    --------
+    >>> from braindecode.datasets import BaseDataset, BaseConcatDataset
+    >>> from braindecode.datasets.bids import BIDSIterableDataset, _description_from_bids_path
+    >>> from braindecode.preprocessing import create_fixed_length_windows
+    >>>
+    >>> def my_reader_fn(path):
+    ...     raw = mne_bids.read_raw_bids(path)
+    ...     desc = _description_from_bids_path(path)
+    ...     ds = BaseDataset(raw, description=desc)
+    ...     windows_ds = create_fixed_length_windows(
+    ...         BaseConcatDataset([ds]),
+    ...         window_size_samples=400,
+    ...         window_stride_samples=200,
+    ...     )
+    ...     return windows_ds
+    >>>
+    >>> dataset = BIDSIterableDataset(
+    ...     reader_fn=my_reader_fn,
+    ...     root="root/of/my/bids/dataset/",
+    ... )
+
+    Parameters
+    ----------
+    reader_fn : Callable[[mne_bids.BIDSPath], Sequence]
+        A function that takes a BIDSPath and returns a dataset.
+    pool_size : int
+        The number of recordings to read and sample from.
+    bids_paths : list[mne_bids.BIDSPath] | None
+        A list of BIDSPaths to load. If None, will use the paths found by
+        :func:`mne_bids.find_matching_paths` and the arguments below.
+    root : pathlib.Path | str
+        The root of the BIDS path.
+    subjects : str | array-like of str | None
+        The subject ID. Corresponds to "sub".
+    sessions : str | array-like of str | None
+        The acquisition session. Corresponds to "ses".
+    tasks : str | array-like of str | None
+        The experimental task. Corresponds to "task".
+    acquisitions: str | array-like of str | None
+        The acquisition parameters. Corresponds to "acq".
+    runs : str | array-like of str | None
+        The run number. Corresponds to "run".
+    processings : str | array-like of str | None
+        The processing label. Corresponds to "proc".
+    recordings : str | array-like of str | None
+        The recording name. Corresponds to "rec".
+    spaces : str | array-like of str | None
+        The coordinate space for anatomical and sensor location
+        files (e.g., ``*_electrodes.tsv``, ``*_markers.mrk``).
+        Corresponds to "space".
+        Note that valid values for ``space`` must come from a list
+        of BIDS keywords as described in the BIDS specification.
+    splits : str | array-like of str | None
+        The split of the continuous recording file for ``.fif`` data.
+        Corresponds to "split".
+    descriptions : str | array-like of str | None
+        This corresponds to the BIDS entity ``desc``. It is used to provide
+        additional information for derivative data, e.g., preprocessed data
+        may be assigned ``description='cleaned'``.
+    suffixes : str | array-like of str | None
+        The filename suffix. This is the entity after the
+        last ``_`` before the extension. E.g., ``'channels'``.
+        The following filename suffix's are accepted:
+        'meg', 'markers', 'eeg', 'ieeg', 'T1w',
+        'participants', 'scans', 'electrodes', 'coordsystem',
+        'channels', 'events', 'headshape', 'digitizer',
+        'beh', 'physio', 'stim'
+    extensions : str | array-like of str | None
+        The extension of the filename. E.g., ``'.json'``.
+        By default, uses the ones accepted by :func:`mne_bids.read_raw_bids`.
+    datatypes : str | array-like of str | None
+        The BIDS data type, e.g., ``'anat'``, ``'func'``, ``'eeg'``, ``'meg'``,
+        ``'ieeg'``.
+    check : bool
+        If ``True``, only returns paths that conform to BIDS. If ``False``
+        (default), the ``.check`` attribute of the returned
+        :class:`mne_bids.BIDSPath` object will be set to ``True`` for paths that
+        do conform to BIDS, and to ``False`` for those that don't.
+    preload : bool
+        If True, preload the data. Defaults to False.
+    n_jobs : int
+        Number of jobs to run in parallel. Defaults to 1.
+    """
+
+    def __init__(
+        self,
+        reader_fn: Callable[[mne_bids.BIDSPath], Sequence],
+        pool_size: int = 4,
+        bids_paths: list[mne_bids.BIDSPath] | None = None,
+        root: Path | str | None = None,
+        subjects: str | list[str] | None = None,
+        sessions: str | list[str] | None = None,
+        tasks: str | list[str] | None = None,
+        acquisitions: str | list[str] | None = None,
+        runs: str | list[str] | None = None,
+        processings: str | list[str] | None = None,
+        recordings: str | list[str] | None = None,
+        spaces: str | list[str] | None = None,
+        splits: str | list[str] | None = None,
+        descriptions: str | list[str] | None = None,
+        suffixes: str | list[str] | None = None,
+        extensions: str | list[str] | None = [
+            ".con",
+            ".sqd",
+            ".pdf",
+            ".fif",
+            ".ds",
+            ".vhdr",
+            ".set",
+            ".edf",
+            ".bdf",
+            ".EDF",
+            ".snirf",
+            ".cdt",
+            ".mef",
+            ".nwb",
+        ],
+        datatypes: str | list[str] | None = None,
+        check: bool = False,
+    ):
+        if bids_paths is None:
+            bids_paths = mne_bids.find_matching_paths(
+                root=root,
+                subjects=subjects,
+                sessions=sessions,
+                tasks=tasks,
+                acquisitions=acquisitions,
+                runs=runs,
+                processings=processings,
+                recordings=recordings,
+                spaces=spaces,
+                splits=splits,
+                descriptions=descriptions,
+                suffixes=suffixes,
+                extensions=extensions,
+                datatypes=datatypes,
+                check=check,
+                ignore_json=True,
+            )
+            # Filter out _epo.fif files:
+            bids_paths = [
+                bids_path
+                for bids_path in bids_paths
+                if not (bids_path.suffix == "epo" and bids_path.extension == ".fif")
+            ]
+        self.bids_paths = bids_paths
+        self.reader_fn = reader_fn
+        self.pool_size = pool_size
+
+    def __add__(self, other):
+        assert isinstance(other, BIDSIterableDataset)
+        return BIDSIterableDataset(
+            reader_fn=self.reader_fn,
+            bids_paths=self.bids_paths + other.bids_paths,
+            pool_size=self.pool_size,
+        )
+
+    def __iadd__(self, other):
+        assert isinstance(other, BIDSIterableDataset)
+        self.bids_paths += other.bids_paths
+        return self
+
+    def __iter__(self):
+        worker_info = get_worker_info()
+        if worker_info is None:  # single-process data loading, return the full iterator
+            bids_paths = self.bids_paths
+        else:  # in a worker process
+            # split workload
+            bids_paths = self.bids_paths[worker_info.id :: worker_info.num_workers]
+
+        pool = []
+        end = False
+        paths_it = iter(random.sample(bids_paths, k=len(bids_paths)))
+        while not (end and len(pool) == 0):
+            while not end and len(pool) < self.pool_size:
+                try:
+                    bids_path = next(paths_it)
+                    ds = self.reader_fn(bids_path)
+                    if ds is None:
+                        print(f"Skipping {bids_path} as it is too short.")
+                        continue
+                    idx = iter(random.sample(range(len(ds)), k=len(ds)))
+                    pool.append((ds, idx))
+                except StopIteration:
+                    end = True
+            i_pool = random.randint(0, len(pool) - 1)
+            ds, idx = pool[i_pool]
+            try:
+                i_ds = next(idx)
+                yield ds[i_ds]
+            except StopIteration:
+                pool.pop(i_pool)

{braindecode-1.2.0.dev182094932 → braindecode-1.3.0.dev176728557}/braindecode/models/__init__.py

@@ -4,6 +4,7 @@ Some predefined network architectures for EEG decoding.
 
 from .atcnet import ATCNet
 from .attentionbasenet import AttentionBaseNet
+from .attn_sleep import AttnSleep
 from .base import EEGModuleMixin
 from .biot import BIOT
 from .contrawr import ContraWR
@@ -15,9 +16,8 @@ from .eeginception_erp import EEGInceptionERP
 from .eeginception_mi import EEGInceptionMI
 from .eegitnet import EEGITNet
 from .eegminer import EEGMiner
-from .eegnet import EEGNetv1, EEGNetv4
+from .eegnet import EEGNet, EEGNetv4
 from .eegnex import EEGNeX
-from .eegresnet import EEGResNet
 from .eegsimpleconv import EEGSimpleConv
 from .eegtcnet import EEGTCNet
 from .fbcnet import FBCNet
@@ -38,12 +38,11 @@ from .signal_jepa import (
 from .sinc_shallow import SincShallowNet
 from .sleep_stager_blanco_2020 import SleepStagerBlanco2020
 from .sleep_stager_chambon_2018 import SleepStagerChambon2018
-from .sleep_stager_eldele_2021 import SleepStagerEldele2021
 from .sparcnet import SPARCNet
 from .syncnet import SyncNet
 from .tcn import BDTCN, TCN
 from .tidnet import TIDNet
-from .tsinception import TSceptionV1
+from .tsinception import TSception
 from .usleep import USleep
 from .util import _init_models_dict, models_mandatory_parameters
 
@@ -53,6 +52,7 @@ _init_models_dict()
 
 __all__ = [
     "ATCNet",
+    "AttnSleep",
     "AttentionBaseNet",
     "EEGModuleMixin",
     "BIOT",
@@ -65,10 +65,9 @@ __all__ = [
     "EEGInceptionMI",
     "EEGITNet",
     "EEGMiner",
-    "EEGNetv1",
+    "EEGNet",
     "EEGNetv4",
     "EEGNeX",
-    "EEGResNet",
     "EEGSimpleConv",
     "EEGTCNet",
     "FBCNet",
@@ -87,13 +86,12 @@ __all__ = [
     "SincShallowNet",
     "SleepStagerBlanco2020",
     "SleepStagerChambon2018",
-    "SleepStagerEldele2021",
     "SPARCNet",
     "SyncNet",
     "BDTCN",
     "TCN",
     "TIDNet",
-    "TSceptionV1",
+    "TSception",
     "USleep",
     "_init_models_dict",
     "models_mandatory_parameters",

{braindecode-1.2.0.dev182094932 → braindecode-1.3.0.dev176728557}/braindecode/models/atcnet.py

@@ -13,13 +13,154 @@ from braindecode.modules import CausalConv1d, Ensure4d, MaxNormLinear
 
 
 class ATCNet(EEGModuleMixin, nn.Module):
-    """ATCNet model from Altaheri et al. (2022) [1]_
+    """ATCNet from Altaheri et al. (2022) [1]_.
 
-    Pytorch implementation based on official tensorflow code [2]_.
+    :bdg-success:`Convolution` :bdg-info:`Small Attention`
 
     .. figure:: https://user-images.githubusercontent.com/25565236/185449791-e8539453-d4fa-41e1-865a-2cf7e91f60ef.png
-       :align: center
-       :alt: ATCNet Architecture
+        :align: center
+        :alt: ATCNet Architecture
+        :width: 650px
+
+    .. rubric:: Architectural Overview
+
+    ATCNet is a *convolution-first* architecture augmented with a *lightweight attention–TCN*
+    sequence module. The end-to-end flow is:
+
+    - (i) :class:`_ConvBlock` learns temporal filter-banks and spatial projections (EEGNet-style),
+      downsampling time to a compact feature map;
+
+    - (ii) Sliding Windows carve overlapping temporal windows from this map;
+
+    - (iii) for each window, :class:`_AttentionBlock` applies small multi-head self-attention
+      over time, followed by a :class:`_TCNResidualBlock` stack (causal, dilated);
+
+    - (iv) window-level features are aggregated (mean of window logits or concatenation)
+      and mapped via a max-norm–constrained linear layer.
+
+    Relative to ViT, ATCNet replaces linear patch projection with learned *temporal–spatial*
+    convolutions; it processes *parallel* window encoders (attention→TCN) instead of a deep
+    stack; and swaps the MLP head for a TCN suited to 1-D EEG sequences.
+
+    .. rubric:: Macro Components
+
+    - :class:`_ConvBlock` **(Shallow conv stem → feature map)**
+
+        - *Operations.*
+        - **Temporal conv** (:class:`torch.nn.Conv2d`) with kernel ``(L_t, 1)`` builds a
+            FIR-like filter bank (``F1`` maps).
+        - **Depthwise spatial conv** (:class:`torch.nn.Conv2d`, ``groups=F1``) with kernel
+          ``(1, n_chans)`` learns per-filter spatial projections (akin to EEGNet’s CSP-like step).
+        - **BN → ELU → AvgPool → Dropout** to stabilize and condense activations.
+        - **Refining temporal conv** (:class:`torch.nn.Conv2d`) with kernel ``(L_r, 1)`` +
+          **BN → ELU → AvgPool → Dropout**.
+
+    The output shape is ``(B, F2, T_c, 1)`` with ``F2 = F1·D`` and ``T_c = T/(P1·P2)``.
+    Temporal kernels behave as FIR filters; the depthwise-spatial conv yields frequency-specific
+    topographies. Pooling acts as a local integrator, reducing variance and imposing a
+    useful inductive bias on short EEG windows.
+
+    - **Sliding-Window Sequencer**
+
+      From the condensed time axis (length ``T_c``), ATCNet forms ``n`` overlapping windows
+      of width ``T_w = T_c - n + 1`` (one start per index). Each window produces a sequence
+      ``(B, F2, T_w)`` forwarded to its own attention–TCN branch. This creates *parallel*
+      encoders over shifted contexts and is key to robustness on nonstationary EEG.
+
+    - :class:`_AttentionBlock` **(small MHA on temporal positions)**
+
+        - *Operations.*
+        - Rearrange to ``(B, T_w, F2)``,
+        - Normalization :class:`torch.nn.LayerNorm`
+        - Custom MultiHeadAttention :class:`_MHA` (``num_heads=H``, per-head dim ``d_h``) + residual add,
+        - Dropout :class:`torch.nn.Dropout`
+        - Rearrange back to ``(B, F2, T_w)``.
+
+
+    **Note**: Attention is *local to a window* and purely temporal.
+
+    *Role.* Re-weights evidence across the window, letting the model emphasize informative
+    segments (onsets, bursts) before causal convolutions aggregate history.
+
+    - :class:`_TCNResidualBlock` **(causal dilated temporal CNN)**
+
+        - *Operations.*
+        - Two :class:`braindecode.modules.CausalConv1d` layers per block with dilation  ``1, 2, 4, …``
+        - Across blocks of `torch.nn.ELU` + `torch.nn.BatchNorm1d` + `torch.nn.Dropout`) +
+          a residual (identity or 1x1 mapping).
+        - The final feature used per window is the *last* causal step ``[..., -1]`` (forecast-style).
+
+    *Role.* Efficient long-range temporal integration with stable gradients; the dilated
+    receptive field complements attention’s soft selection.
+
+    - **Aggregation & Classifier**
+
+        - *Operations.*
+        - Either (a) map each window feature ``(B, F2)`` to logits via :class:`braindecode.modules.MaxNormLinear`
+        and **average** across windows (default, matching official code), or
+        - (b) **concatenate** all window features ``(B, n·F2)`` and apply a single :class:`MaxNormLinear`.
+        The max-norm constraint regularizes the readout.
+
+    .. rubric:: Convolutional Details
+
+    - **Temporal.** Temporal structure is learned in three places:
+        - (1) the stem’s wide ``(L_t, 1)`` conv (learned filter bank),
+        - (2) the refining ``(L_r, 1)`` conv after pooling (short-term dynamics), and
+        - (3) the TCN’s causal 1-D convolutions with exponentially increasing dilation
+          (long-range dependencies). The minimum sequence length required by the TCN stack is
+          ``(K_t - 1)·2^{L-1} + 1``; the implementation *auto-scales* kernels/pools/windows
+          when inputs are shorter to preserve feasibility.
+
+    - **Spatial.** A depthwise spatial conv spans the **full montage** (kernel ``(1, n_chans)``),
+        producing *per-temporal-filter* spatial projections (no cross-filter mixing at this step).
+        This mirrors EEGNet’s interpretability: each temporal filter has its own spatial pattern.
+
+
+    .. rubric:: Attention / Sequential Modules
+
+    - **Type.** Multi-head self-attention with ``H`` heads and per-head dim ``d_h`` implemented
+      in :class:`_MHA`, allowing ``embed_dim = H·d_h`` independent of input and output dims.
+    - **Shapes.** ``(B, F2, T_w) → (B, T_w, F2) → (B, F2, T_w)``. Attention operates along
+      the **temporal** axis within a window; channels/features stay in the embedding dim ``F2``.
+    - **Role.** Highlights salient temporal positions prior to causal convolution; small attention
+      keeps compute modest while improving context modeling over pooled features.
+
+    .. rubric:: Additional Mechanisms
+
+    - **Parallel encoders over shifted windows.** Improves montage/phase robustness by
+      ensembling nearby contexts rather than committing to a single segmentation.
+    - **Max-norm classifier.** Enforces weight norm constraints at the readout, a common
+      stabilization trick in EEG decoding.
+    - **ViT vs. ATCNet (design choices).** Convolutional *nonlinear* projection rather than
+      linear patchification; attention followed by **TCN** (not MLP); *parallel* window
+      encoders rather than stacked encoders.
+
+    .. rubric:: Usage and Configuration
+
+        - ``conv_block_n_filters (F1)``, ``conv_block_depth_mult (D)`` → capacity of the stem
+        (with ``F2 = F1·D`` feeding attention/TCN), dimensions aligned to ``F2``, like :class:`EEGNet`.
+        - Pool sizes ``P1,P2`` trade temporal resolution for stability/compute; they set
+        ``T_c = T/(P1·P2)`` and thus window width ``T_w``.
+        - ``n_windows`` controls the ensemble over shifts (compute ∝ windows).
+        - ``att_num_heads``, ``att_head_dim`` set attention capacity; keep ``H·d_h ≈ F2``.
+        - ``tcn_depth``, ``tcn_kernel_size`` govern receptive field; larger values demand
+        longer inputs (see minimum length above). The implementation warns and *rescales*
+        kernels/pools/windows if inputs are too short.
+        - **Aggregation choice.** ``concat=False`` (default, average of per-window logits) matches
+        the official code; ``concat=True`` mirrors the paper’s concatenation variant.
+
+
+    Notes
+    -----
+    - Inputs substantially shorter than the implied minimum length trigger **automatic
+      downscaling** of kernels, pools, windows, and TCN kernel size to maintain validity.
+    - The attention–TCN sequence operates **per window**; the last causal step is used as the
+      window feature, aligning the temporal semantics across windows.
+
+    .. versionadded:: 1.1
+
+        - More detailed documentation of the model.
+
 
     Parameters
     ----------
@@ -85,15 +226,13 @@ class ATCNet(EEGModuleMixin, nn.Module):
         Maximum L2-norm constraint imposed on weights of the last
         fully-connected layer. Defaults to 0.25.
 
-
     References
     ----------
-    .. [1] H. Altaheri, G. Muhammad and M. Alsulaiman,
-        Physics-informed attention temporal convolutional network for EEG-based
-        motor imagery classification in IEEE Transactions on Industrial Informatics,
-        2022, doi: 10.1109/TII.2022.3197419.
-    .. [2] EEE-ATCNet implementation.
-       https://github.com/Altaheri/EEG-ATCNet/blob/main/models.py
+    .. [1] H. Altaheri, G. Muhammad, M. Alsulaiman (2022).
+        *Physics-informed attention temporal convolutional network for EEG-based motor imagery classification.*
+        IEEE Transactions on Industrial Informatics. doi:10.1109/TII.2022.3197419.
+    .. [2] Official EEG-ATCNet implementation (TensorFlow):
+        https://github.com/Altaheri/EEG-ATCNet/blob/main/models.py
     """
 
     def __init__(
@@ -556,7 +695,8 @@ class _TCNResidualBlock(nn.Module):
         # Reshape the input for the residual connection when necessary
         if in_channels != n_filters:
             self.reshaping_conv = nn.Conv1d(
-                n_filters,
+                in_channels=in_channels,
+                out_channels=n_filters,
                 kernel_size=1,
                 padding="same",
             )