Braindecode 1.3.2.dev179935386__tar.gz → 1.3.2.dev179973481__tar.gz

{braindecode-1.3.2.dev179935386/braindecode.egg-info → braindecode-1.3.2.dev179973481}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: braindecode
-Version: 1.3.2.dev179935386
+Version: 1.3.2.dev179973481
 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>
@@ -25,6 +25,7 @@ License-File: NOTICE.txt
 Requires-Dist: torch>=2.2
 Requires-Dist: torchaudio>=2.0
 Requires-Dist: mne>=1.11.0
+Requires-Dist: pandas<3.0.0
 Requires-Dist: mne_bids>=0.18
 Requires-Dist: h5py
 Requires-Dist: skorch>=1.3.0
@@ -51,7 +52,7 @@ Requires-Dist: mypy; extra == "tests"
 Requires-Dist: transformers>=4.57.0; extra == "tests"
 Requires-Dist: bids_validator; extra == "tests"
 Provides-Extra: typing
-Requires-Dist: exca==0.4; extra == "typing"
+Requires-Dist: exca>=0.5.10; extra == "typing"
 Requires-Dist: numpydantic>=1.7; extra == "typing"
 Provides-Extra: docs
 Requires-Dist: sphinx_gallery; extra == "docs"

{braindecode-1.3.2.dev179935386 → braindecode-1.3.2.dev179973481}/braindecode/datasets/base.py

@@ -533,8 +533,12 @@ class BaseConcatDataset(ConcatDataset, HubDatasetMixin, Generic[T]):
             If a dict then each key will be used in the returned
             splits dict and each value should be a list of int.
         property : str
+            :bdg-warning:`Deprecated`
+
             Some property which is listed in the info DataFrame.
         split_ids : list | dict
+            :bdg-warning:`Deprecated`
+
             List of indices to be combined in a subset.
             It can be a list of int or a list of list of int.
 

{braindecode-1.3.2.dev179935386 → braindecode-1.3.2.dev179973481}/braindecode/datasets/tuh.py

@@ -515,7 +515,7 @@ class TUHAbnormal(TUH):
         rename_channels: bool = False,
         set_montage: bool = False,
         on_missing_files: Literal["warn", "raise"] = "raise",
-        version: Literal["v2.0.0", "v3.0.0"] = "v3.0.0",
+        version: Literal["v2.0.0", "v3.0.1"] = "v3.0.1",
         n_jobs: int = 1,
     ):
         super().__init__(
@@ -559,8 +559,14 @@ class TUHAbnormal(TUH):
 
     @property
     def _expected_files_count(self):
-        if self.version == "v3.0.0":
-            return 1521  # 150 (eval) + 1321 (train)
+        if self.version == "v3.0.1":
+            # dataset.description.groupby(["train", "pathological"]).path.count()
+            # train  pathological
+            # False  False            150
+            #        True             126
+            # True   False           1371
+            #        True            1346
+            return 2993
         return None
 
     @property
@@ -754,6 +760,9 @@ class TUHEvents(TUH):
             onsets = merged_onsets
             durations = merged_durations
             descriptions = merged_descriptions
+        # sort by onset time
+        sorted_events = sorted(zip(onsets, durations, descriptions))
+        onsets, durations, descriptions = zip(*sorted_events)  # type: ignore[assignment]
 
         annotations = mne.Annotations(
             onset=onsets,

{braindecode-1.3.2.dev179935386 → braindecode-1.3.2.dev179973481}/braindecode/preprocessing/windowers.py

@@ -18,7 +18,7 @@
 from __future__ import annotations
 
 import warnings
-from typing import Any, Callable
+from typing import Any, Callable, Literal
 
 import mne
 import numpy as np
@@ -210,6 +210,7 @@ def create_windows_from_events(
     on_missing: str = "error",
     accepted_bads_ratio: float = 0.0,
     use_mne_epochs: bool | None = None,
+    on_overlapping_events: Literal["raise", "warn", "ignore"] = "raise",
     n_jobs: int = 1,
     verbose: bool | str | int | None = "error",
 ) -> BaseConcatDataset[WindowsDataset | EEGWindowsDataset]:
@@ -285,6 +286,11 @@ def create_windows_from_events(
         If False, return EEGWindowsDataset objects.
         If True, return mne.Epochs objects encapsulated in WindowsDataset objects,
         which is substantially slower that EEGWindowsDataset.
+    on_overlapping_events: Literal['raise', 'warn', 'ignore']
+        Behavior when overlapping events are detected. Valid keys are
+        'raise' | 'warn' | 'ignore'. 'raise' (default) raises
+        NotImplementedError; 'warn' issues a warning and drops non-increasing
+        window starts; 'ignore' keeps overlapping starts.
     n_jobs: int
         Number of jobs to use to parallelize the windowing.
     verbose: bool | str | int | None
@@ -301,7 +307,10 @@ def create_windows_from_events(
         window_size_samples,
         window_stride_samples,
     )
-
+    if on_overlapping_events not in ["raise", "warn", "ignore"]:
+        raise ValueError(
+            f"Invalid value {on_overlapping_events} for on_overlapping_events."
+        )
     # If user did not specify mapping, we extract all events from all datasets
     # and map them to increasing integers starting from 0
     infer_mapping = mapping is None
@@ -340,6 +349,7 @@ def create_windows_from_events(
             accepted_bads_ratio,
             verbose,
             use_mne_epochs,
+            on_overlapping_events,
         )
         for ds in concat_ds.datasets
     )
@@ -478,6 +488,7 @@ def _create_windows_from_events(
     accepted_bads_ratio=0.0,
     verbose="error",
     use_mne_epochs=False,
+    on_overlapping_events: Literal["raise", "warn", "ignore"] = "raise",
 ):
     """Create WindowsDataset from RawDataset based on events.
 
@@ -587,8 +598,12 @@ def _create_windows_from_events(
         accepted_bads_ratio,
     )
 
-    if any(np.diff(starts) <= 0):
-        raise NotImplementedError("Trial overlap not implemented.")
+    if (on_overlapping_events != "ignore") and any(np.diff(starts) <= 0):
+        msg = "Overlapping trials detected. You can ignore, warn, or raise an error, using the on_overlapping_events argument."
+        if on_overlapping_events == "raise":
+            raise ValueError(msg)
+        if on_overlapping_events == "warn":
+            warnings.warn(msg)
 
     events = [
         [start, window_size_samples, description[i_trials[i_start]]]

braindecode-1.3.2.dev179973481/braindecode/version.py

@@ -0,0 +1 @@
+__version__ = "1.3.2.dev179973481"

{braindecode-1.3.2.dev179935386 → braindecode-1.3.2.dev179973481/braindecode.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: braindecode
-Version: 1.3.2.dev179935386
+Version: 1.3.2.dev179973481
 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>
@@ -25,6 +25,7 @@ License-File: NOTICE.txt
 Requires-Dist: torch>=2.2
 Requires-Dist: torchaudio>=2.0
 Requires-Dist: mne>=1.11.0
+Requires-Dist: pandas<3.0.0
 Requires-Dist: mne_bids>=0.18
 Requires-Dist: h5py
 Requires-Dist: skorch>=1.3.0
@@ -51,7 +52,7 @@ Requires-Dist: mypy; extra == "tests"
 Requires-Dist: transformers>=4.57.0; extra == "tests"
 Requires-Dist: bids_validator; extra == "tests"
 Provides-Extra: typing
-Requires-Dist: exca==0.4; extra == "typing"
+Requires-Dist: exca>=0.5.10; extra == "typing"
 Requires-Dist: numpydantic>=1.7; extra == "typing"
 Provides-Extra: docs
 Requires-Dist: sphinx_gallery; extra == "docs"

{braindecode-1.3.2.dev179935386 → braindecode-1.3.2.dev179973481}/braindecode.egg-info/requires.txt

@@ -1,6 +1,7 @@
 torch>=2.2
 torchaudio>=2.0
 mne>=1.11.0
+pandas<3.0.0
 mne_bids>=0.18
 h5py
 skorch>=1.3.0
@@ -62,5 +63,5 @@ transformers>=4.57.0
 bids_validator
 
 [typing]
-exca==0.4
+exca>=0.5.10
 numpydantic>=1.7

{braindecode-1.3.2.dev179935386 → braindecode-1.3.2.dev179973481}/docs/whats_new.rst

@@ -36,7 +36,8 @@ Enhancements
 - Add :class:`braindecode.models.CBraMod` model (:gh:`914` by `Pierre Guetschel`_)
 - Expose additional arguments of :func:`mne_bids.read_raw_bids` in :class:`braindecode.datasets.BIDSDataset` (:gh:`918` by `Pierre Guetschel`_)
 - Populate epochs metadata with the :class:`mne.Annotations`'s ``extras`` entries (:gh:`918` by `Pierre Guetschel`_)
-- Add :class:`braindecode.datasets.TUHEvents` dataset and improve other TUH datasets (:gh:`920` by `Pierre Guetschel`_)
+- Add :class:`braindecode.datasets.TUHEvents` dataset and improve other TUH datasets (:gh:`920` and :gh:`923` by `Pierre Guetschel`_)
+- Allow overlapping events in :func:`braindecode.preprocessing.create_windows_from_events` (:gh:`923` by `Pierre Guetschel`_)
 
 
 API changes

{braindecode-1.3.2.dev179935386 → braindecode-1.3.2.dev179973481}/pyproject.toml

@@ -47,8 +47,9 @@ requires-python = ">=3.11"
 dependencies = [
     "torch>=2.2",
     "torchaudio>=2.0",
-    'mne>=1.11.0',                  # we get matplotlib, numpy, pandas, scipy from here
-    'mne_bids>=0.18',               # in theory we get the mne here, but we prefer to have it explicit
+    'mne>=1.11.0',  # we get matplotlib, numpy, pandas, scipy from here
+    'pandas<3.0.0',  # to avoid issues with wfdb
+    'mne_bids>=0.18', # in theory we get the mne here, but we prefer to have it explicit
     'h5py',
     'skorch>=1.3.0',
     'joblib',
@@ -77,7 +78,10 @@ tests = [
     "transformers>=4.57.0",
     "bids_validator",
 ]
-typing = ['exca==0.4', 'numpydantic>=1.7']
+typing = [
+    'exca>=0.5.10',
+    'numpydantic>=1.7',
+]
 
 docs = [
     'sphinx_gallery',

braindecode-1.3.2.dev179935386/braindecode/version.py

@@ -1 +0,0 @@
-__version__ = "1.3.2.dev179935386"