Braindecode 1.3.0.dev176481332__tar.gz → 1.3.0.dev176529508__tar.gz

{braindecode-1.3.0.dev176481332/braindecode.egg-info → braindecode-1.3.0.dev176529508}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: braindecode
-Version: 1.3.0.dev176481332
+Version: 1.3.0.dev176529508
 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>
@@ -38,6 +38,7 @@ Requires-Dist: wfdb
 Requires-Dist: h5py
 Requires-Dist: linear_attention_transformer
 Requires-Dist: docstring_inheritance
+Requires-Dist: rotary_embedding_torch
 Provides-Extra: moabb
 Requires-Dist: moabb>=1.2.0; extra == "moabb"
 Provides-Extra: eegprep

{braindecode-1.3.0.dev176481332 → braindecode-1.3.0.dev176529508}/braindecode/datasets/__init__.py

@@ -12,7 +12,7 @@ from .base import (
 from .bcicomp import BCICompetitionIVDataset4
 from .bids import BIDSDataset, BIDSEpochsDataset
 from .mne import create_from_mne_epochs, create_from_mne_raw
-from .moabb import BNCI2014001, HGD, MOABBDataset
+from .moabb import BNCI2014_001, HGD, MOABBDataset
 from .nmt import NMT
 from .sleep_physio_challe_18 import SleepPhysionetChallenge2018
 from .sleep_physionet import SleepPhysionet
@@ -29,7 +29,7 @@ __all__ = [
     "BIDSEpochsDataset",
     "MOABBDataset",
     "HGD",
-    "BNCI2014001",
+    "BNCI2014_001",
     "create_from_mne_raw",
     "create_from_mne_epochs",
     "TUH",

{braindecode-1.3.0.dev176481332 → braindecode-1.3.0.dev176529508}/braindecode/datasets/base.py

@@ -19,7 +19,7 @@ import warnings
 from abc import abstractmethod
 from collections.abc import Callable
 from glob import glob
-from typing import Generic, Iterable, no_type_check
+from typing import Any, Generic, Iterable, no_type_check
 
 import mne.io
 import numpy as np
@@ -129,6 +129,7 @@ class RawDataset(RecordDataset):
 
         # save target name for load/save later
         self.target_name = self._target_name(target_name)
+        self.raw_preproc_kwargs: list[dict[str, Any]] = []
 
     def __getitem__(self, index):
         X = self.raw[:, index][0]
@@ -235,6 +236,7 @@ class EEGWindowsDataset(RecordDataset):
         ].to_numpy()
         if self.targets_from == "metadata":
             self.y = metadata.loc[:, "target"].to_list()
+        self.raw_preproc_kwargs: list[dict[str, Any]] = []
 
     def __getitem__(self, index: int):
         """Get a window and its target.
@@ -334,6 +336,8 @@ class WindowsDataset(RecordDataset):
         ].to_numpy()
         if self.targets_from == "metadata":
             self.y = metadata.loc[:, "target"].to_list()
+        self.raw_preproc_kwargs: list[dict[str, Any]] = []
+        self.window_preproc_kwargs: list[dict[str, Any]] = []
 
     def __getitem__(self, index: int):
         """Get a window and its target.
@@ -794,7 +798,7 @@ class BaseConcatDataset(ConcatDataset, Generic[T]):
                 kwargs = getattr(ds, kwargs_name)
                 if kwargs is not None:
                     with open(kwargs_file_path, "w") as f:
-                        json.dump(kwargs, f)
+                        json.dump(kwargs, f, indent=2)
 
     @staticmethod
     def _save_target_name(sub_dir, ds):

{braindecode-1.3.0.dev176481332 → braindecode-1.3.0.dev176529508}/braindecode/datasets/moabb.py

@@ -15,6 +15,7 @@ from typing import Any
 
 import mne
 import pandas as pd
+from mne.utils import deprecated
 
 from braindecode.util import _update_moabb_docstring
 
@@ -169,8 +170,8 @@ class MOABBDataset(BaseConcatDataset):
         super().__init__(all_base_ds)
 
 
-class BNCI2014001(MOABBDataset):
-    doc = """See moabb.datasets.bnci.BNCI2014001
+class BNCI2014_001(MOABBDataset):
+    doc = """See moabb.datasets.bnci.BNCI2014_001
 
     Parameters
     ----------
@@ -179,14 +180,14 @@ class BNCI2014001(MOABBDataset):
         subjects is fetched.
     """
     try:
-        from moabb.datasets import BNCI2014001
+        from moabb.datasets import BNCI2014_001
 
-        __doc__ = _update_moabb_docstring(BNCI2014001, doc)
+        __doc__ = _update_moabb_docstring(BNCI2014_001, doc)
     except ModuleNotFoundError:
         pass  # keep moabb soft dependency, otherwise crash on loading of datasets.__init__.py
 
     def __init__(self, subject_ids):
-        super().__init__("BNCI2014001", subject_ids=subject_ids)
+        super().__init__("BNCI2014_001", subject_ids=subject_ids)
 
 
 class HGD(MOABBDataset):
@@ -207,3 +208,12 @@ class HGD(MOABBDataset):
 
     def __init__(self, subject_ids):
         super().__init__("Schirrmeister2017", subject_ids=subject_ids)
+
+
+@deprecated(
+    "`BNCI2014001` was renamed to `BNCI2014_001` in v1.13; this alias will be removed in v1.14."
+)
+class BNCI2014001(BNCI2014_001):
+    """Deprecated alias for BNCI2014001."""
+
+    pass

{braindecode-1.3.0.dev176481332 → braindecode-1.3.0.dev176529508}/braindecode/datautil/__init__.py

@@ -2,6 +2,10 @@
 Utilities for data manipulation.
 """
 
+from .channel_utils import (
+    division_channels_idx,
+    match_hemisphere_chans,
+)
 from .serialization import (
     _check_save_dir_empty,
     load_concat_dataset,
@@ -49,4 +53,10 @@ def __getattr__(name):
     raise AttributeError("No possible import named " + name)
 
 
-__all__ = ["load_concat_dataset", "save_concat_dataset", "_check_save_dir_empty"]
+__all__ = [
+    "load_concat_dataset",
+    "save_concat_dataset",
+    "_check_save_dir_empty",
+    "match_hemisphere_chans",
+    "division_channels_idx",
+]

braindecode-1.3.0.dev176529508/braindecode/datautil/channel_utils.py

@@ -0,0 +1,114 @@
+"""
+Utilities for EEG channel manipulation and selection.
+
+This module provides functions for dividing and matching EEG channels,
+particularly for hemisphere-aware processing.
+"""
+
+import re
+from re import search
+
+
+def match_hemisphere_chans(left_chs, right_chs):
+    """
+    Match channels of the left and right hemispheres based on their names.
+
+    This function pairs channels from the left and right hemispheres by matching
+    their numeric identifiers. For a left channel with number N, it finds the
+    corresponding right channel with number N+1.
+
+    Parameters
+    ----------
+    left_chs : list of str
+        A list of channel names from the left hemisphere.
+    right_chs : list of str
+        A list of channel names from the right hemisphere.
+
+    Returns
+    -------
+    list of tuples
+        List of tuples with matched channel names from the left and right hemispheres.
+        Each tuple contains (left_channel, right_channel).
+
+    Raises
+    ------
+    ValueError
+        If the left and right channels do not match in length.
+    ValueError
+        If a channel name does not contain a number.
+    ValueError
+        If no matching right hemisphere channel is found for a left channel.
+
+    Examples
+    --------
+    >>> left = ['C3', 'F3']
+    >>> right = ['C4', 'F4']
+    >>> match_hemisphere_chans(left, right)
+    [('C3', 'C4'), ('F3', 'F4')]
+    """
+    if len(left_chs) != len(right_chs):
+        raise ValueError("Left and right channels do not match.")
+    right_chs = list(right_chs)
+    regexp = r"\d+"
+    out = []
+    for left in left_chs:
+        match = re.search(regexp, left)
+        if match is None:
+            raise ValueError(f"Channel '{left}' does not contain a number.")
+        chan_idx = 1 + int(match.group())
+        target_r = re.sub(regexp, str(chan_idx), left)
+        for right in right_chs:
+            if right == target_r:
+                out.append((left, right))
+                right_chs.remove(right)
+                break
+        else:
+            raise ValueError(
+                f"Found no right hemisphere matching channel for '{left}'."
+            )
+    return out
+
+
+def division_channels_idx(ch_names):
+    """
+    Divide EEG channel names into left, right, and middle based on numbering.
+
+    This function categorizes channels by their numeric suffix:
+    - Odd-numbered channels → left hemisphere
+    - Even-numbered channels → right hemisphere
+    - Channels without numbers → middle/midline
+
+    Parameters
+    ----------
+    ch_names : list of str
+        A list of EEG channel names to be divided based on their numbering.
+
+    Returns
+    -------
+    tuple of lists
+        Three lists containing the channel names:
+        - left: Odd-numbered channels (e.g., C3, F3, P3)
+        - right: Even-numbered channels (e.g., C4, F4, P4)
+        - middle: Channels without numbers (e.g., Cz, Fz, Pz)
+
+    Notes
+    -----
+    The function identifies channel numbers by searching for numeric characters
+    in the channel names. Standard 10-20 system EEG channel naming conventions
+    use odd numbers for left hemisphere and even numbers for right hemisphere.
+
+    Examples
+    --------
+    >>> channels = ['FP1', 'FP2', 'O1', 'O2', 'FZ']
+    >>> division_channels_idx(channels)
+    (['FP1', 'O1'], ['FP2', 'O2'], ['FZ'])
+    """
+    left, right, middle = [], [], []
+    for ch in ch_names:
+        number = search(r"\d+", ch)
+        if number is not None:
+            (left if int(number[0]) % 2 else right).append(ch)
+        else:
+            middle.append(ch)
+
+    return left, right, middle

{braindecode-1.3.0.dev176481332 → braindecode-1.3.0.dev176529508}/braindecode/datautil/serialization.py

@@ -302,7 +302,6 @@ def _load_kwargs_json(kwargs_name, sub_dir):
     kwargs_file_path = os.path.join(sub_dir, kwargs_file_name)
     if os.path.exists(kwargs_file_path):
         kwargs = json.load(open(kwargs_file_path, "r"))
-        kwargs = [tuple(kwarg) for kwarg in kwargs]
         return kwargs
 
 

{braindecode-1.3.0.dev176481332 → braindecode-1.3.0.dev176529508}/braindecode/models/__init__.py

@@ -20,6 +20,7 @@ from .eegminer import EEGMiner
 from .eegnet import EEGNet, EEGNetv4
 from .eegnex import EEGNeX
 from .eegsimpleconv import EEGSimpleConv
+from .eegsym import EEGSym
 from .eegtcnet import EEGTCNet
 from .fbcnet import FBCNet
 from .fblightconvnet import FBLightConvNet
@@ -27,6 +28,8 @@ from .fbmsnet import FBMSNet
 from .hybrid import HybridNet
 from .ifnet import IFNet
 from .labram import Labram
+from .luna import LUNA
+from .medformer import MEDFormer
 from .msvtnet import MSVTNet
 from .patchedtransformer import PBT
 from .sccnet import SCCNet
@@ -47,7 +50,11 @@ from .tcn import BDTCN, TCN
 from .tidnet import TIDNet
 from .tsinception import TSception
 from .usleep import USleep
-from .util import _init_models_dict, models_mandatory_parameters
+from .util import (
+    _init_models_dict,
+    extract_channel_locations_from_chs_info,
+    models_mandatory_parameters,
+)
 
 # Call this last in order to make sure the dataset list is populated with
 # the models imported in this file.
@@ -72,6 +79,7 @@ __all__ = [
     "EEGNet",
     "EEGNetv4",
     "EEGNeX",
+    "EEGSym",
     "EEGSimpleConv",
     "EEGTCNet",
     "FBCNet",
@@ -80,6 +88,9 @@ __all__ = [
     "HybridNet",
     "IFNet",
     "Labram",
+    "LUNA",
+    "extract_channel_locations_from_chs_info",
+    "MEDFormer",
     "MSVTNet",
     "PBT",
     "SCCNet",