Braindecode 1.3.2.dev176759409__tar.gz → 1.3.2.dev178169072__tar.gz

{braindecode-1.3.2.dev176759409/braindecode.egg-info → braindecode-1.3.2.dev178169072}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: braindecode
-Version: 1.3.2.dev176759409
+Version: 1.3.2.dev178169072
 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>
@@ -22,7 +22,7 @@ Requires-Python: >=3.11
 Description-Content-Type: text/x-rst
 License-File: LICENSE.txt
 License-File: NOTICE.txt
-Requires-Dist: torch>=2.0
+Requires-Dist: torch>=2.2
 Requires-Dist: torchaudio>=2.0
 Requires-Dist: mne>=1.11.0
 Requires-Dist: pandas<3.0.0
@@ -84,8 +84,8 @@ Requires-Dist: braindecode[eegprep]; extra == "all"
 Requires-Dist: braindecode[typing]; extra == "all"
 Dynamic: license-file
 
-.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.17699192.svg
-    :target: https://doi.org/10.5281/zenodo.17699192
+.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.8214376.svg
+    :target: https://doi.org/10.5281/zenodo.8214376
     :alt: DOI
 
 .. image:: https://github.com/braindecode/braindecode/workflows/docs/badge.svg
@@ -173,43 +173,13 @@ https://github.com/braindecode/braindecode/blob/master/CONTRIBUTING.md
  Citing
 ########
 
-If you use Braindecode in scientific work, please cite the software using the global
-Zenodo DOI shown in the badge below:
+If you use Braindecode in scientific work, please cite the software using the Zenodo DOI
+shown in the badge below:
 
-.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.17699192.svg
-    :target: https://doi.org/10.5281/zenodo.17699192
+.. image:: https://zenodo.org/badge/232335424.svg
+    :target: https://doi.org/10.5281/zenodo.8214376
     :alt: DOI
 
-You can use the following BibTeX entry:
-
-.. code-block:: bibtex
-
-    @software{braindecode,
-      author = {Aristimunha, Bruno and
-                Guetschel, Pierre and
-                Wimpff, Martin and
-                Gemein, Lukas and
-                Rommel, Cedric and
-                Banville, Hubert and
-                Sliwowski, Maciej and
-                Wilson, Daniel and
-                Brandt, Simon and
-                Gnassounou, Théo and
-                Paillard, Joseph and
-                {Junqueira Lopes}, Bruna and
-                Sedlar, Sara and
-                Moreau, Thomas and
-                Chevallier, Sylvain and
-                Gramfort, Alexandre and
-                Schirrmeister, Robin Tibor},
-      title = {Braindecode: toolbox for decoding raw electrophysiological brain data
-               with deep learning models},
-      url = {https://github.com/braindecode/braindecode},
-      doi = {10.5281/zenodo.17699192},
-      publisher = {Zenodo},
-      license = {BSD-3-Clause},
-    }
-
 Additionally, we highly encourage you to cite the article that originally introduced the
 Braindecode library and has served as a foundational reference for many works on deep
 learning with EEG recordings. Please use the following reference:

{braindecode-1.3.2.dev176759409 → braindecode-1.3.2.dev178169072}/README.rst

@@ -1,5 +1,5 @@
-.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.17699192.svg
-    :target: https://doi.org/10.5281/zenodo.17699192
+.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.8214376.svg
+    :target: https://doi.org/10.5281/zenodo.8214376
     :alt: DOI
 
 .. image:: https://github.com/braindecode/braindecode/workflows/docs/badge.svg
@@ -87,43 +87,13 @@ https://github.com/braindecode/braindecode/blob/master/CONTRIBUTING.md
  Citing
 ########
 
-If you use Braindecode in scientific work, please cite the software using the global
-Zenodo DOI shown in the badge below:
+If you use Braindecode in scientific work, please cite the software using the Zenodo DOI
+shown in the badge below:
 
-.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.17699192.svg
-    :target: https://doi.org/10.5281/zenodo.17699192
+.. image:: https://zenodo.org/badge/232335424.svg
+    :target: https://doi.org/10.5281/zenodo.8214376
     :alt: DOI
 
-You can use the following BibTeX entry:
-
-.. code-block:: bibtex
-
-    @software{braindecode,
-      author = {Aristimunha, Bruno and
-                Guetschel, Pierre and
-                Wimpff, Martin and
-                Gemein, Lukas and
-                Rommel, Cedric and
-                Banville, Hubert and
-                Sliwowski, Maciej and
-                Wilson, Daniel and
-                Brandt, Simon and
-                Gnassounou, Théo and
-                Paillard, Joseph and
-                {Junqueira Lopes}, Bruna and
-                Sedlar, Sara and
-                Moreau, Thomas and
-                Chevallier, Sylvain and
-                Gramfort, Alexandre and
-                Schirrmeister, Robin Tibor},
-      title = {Braindecode: toolbox for decoding raw electrophysiological brain data
-               with deep learning models},
-      url = {https://github.com/braindecode/braindecode},
-      doi = {10.5281/zenodo.17699192},
-      publisher = {Zenodo},
-      license = {BSD-3-Clause},
-    }
-
 Additionally, we highly encourage you to cite the article that originally introduced the
 Braindecode library and has served as a foundational reference for many works on deep
 learning with EEG recordings. Please use the following reference:

{braindecode-1.3.2.dev176759409 → braindecode-1.3.2.dev178169072}/braindecode/datasets/base.py

@@ -579,89 +579,6 @@ class EEGWindowsDataset(RecordDataset):
             self.metadata,
         )
 
-    def to_epochs_dataset(self) -> WindowsDataset:
-        """Converts this :class:`EEGWindowsDataset` to :class:`WindowsDataset` with ``mne.Epochs``.
-
-        In Braindecode, the data can either be stored as ``mne.io.Raw`` (in :class:`EEGWindowsDataset`)
-        or as ``mne.Epochs`` (in :class:`WindowsDataset`). This function converts from the first type to the second,
-        which can be useful for reducing disk space when you want to save a dataset.
-
-        Returns
-        -------
-        WindowsDataset
-            A new :class:`WindowsDataset` with ``mne.Epochs``.
-
-        Raises
-        ------
-        ValueError
-            If the dataset is not compatible with conversion. This includes:
-            - If targets are not obtained from metadata
-            - If windows have inconsistent sizes or there are no windows to convert
-            - If raw.first_samp!=0 (not supported for simplicity)
-        """
-        # Check the targets:
-        if self.targets_from != "metadata":
-            raise ValueError(
-                "to_epochs_dataset only works if targets are obtained from metadata."
-            )
-
-        # Check and get window sizes:
-        i_start_in_trial = self.crop_inds[:, 1]
-        i_stop_in_trial = self.crop_inds[:, 2]
-        sizes = np.unique(i_stop_in_trial - i_start_in_trial)
-        if len(sizes) > 1:
-            raise ValueError("Windows have inconsistent sizes.")
-        if len(sizes) != 1:
-            raise ValueError("No windows to convert.")
-        input_window_seconds = (sizes[0] - 1) / self.raw.info["sfreq"]
-
-        # Check raw.first_samp:
-        if self.raw.first_samp != 0:
-            raise ValueError(
-                f"to_epochs_dataset only works if raw.first_samp is 0, found {self.raw.first_samp=}"
-            )
-
-        # Create events and epochs:
-        events = np.zeros((len(self), 3), dtype=int)
-        events[:, 0] = i_start_in_trial
-        events[:, 2] = 1
-        epochs = mne.Epochs(
-            raw=self.raw,
-            events=events,
-            event_id={"window": 1},
-            tmin=0,
-            tmax=input_window_seconds,
-            metadata=self.metadata.copy(),
-            baseline=None,
-        )
-        # we skip dropping bads to be consistent with EEGWindowsDataset:
-        epochs._bad_dropped = True
-
-        # Populate new WindowsDataset:
-        windows = WindowsDataset(
-            epochs,
-            description=self.description,
-            transform=self.transform,
-            targets_from=self.targets_from,
-            last_target_only=self.last_target_only,
-        )
-
-        window_kwargs = list(getattr(self, "window_kwargs", []))
-        window_kwargs.append((self.to_epochs_dataset.__name__, {}))
-        setattr(windows, "window_kwargs", window_kwargs)
-        if hasattr(self, "raw_preproc_kwargs"):
-            setattr(
-                windows, "raw_preproc_kwargs", list(getattr(self, "raw_preproc_kwargs"))
-            )
-        if hasattr(self, "window_preproc_kwargs"):
-            setattr(
-                windows,
-                "window_preproc_kwargs",
-                list(getattr(self, "window_preproc_kwargs")),
-            )
-
-        return windows
-
 
 @register_dataset
 class WindowsDataset(RecordDataset):
@@ -700,15 +617,6 @@ class WindowsDataset(RecordDataset):
         last_target_only: bool = True,
     ):
         super().__init__(description, transform)
-        self._fast_disk = self._can_use_fast_get_epoch_from_raw(windows)
-        if not (self._fast_disk or windows.preload):
-            warnings.warn(
-                "The provided mne.Epochs object does not meet the requirements for "
-                "fast epoch access. This may lead to slow data loading from disk. "
-                "Consider preloading the epochs or checking the conditions in "
-                "WindowsDataset._can_use_fast_get_epoch_from_raw.",
-                UserWarning,
-            )
         self.windows = windows
         self.last_target_only = last_target_only
         if targets_from not in ("metadata", "channels"):
@@ -725,20 +633,6 @@ class WindowsDataset(RecordDataset):
         self.raw_preproc_kwargs: list[dict[str, Any]] = []
         self.window_preproc_kwargs: list[dict[str, Any]] = []
 
-    @staticmethod
-    def _can_use_fast_get_epoch_from_raw(epochs: mne.BaseEpochs) -> bool:
-        """Check if we can use the fast _get_epoch_from_raw method,
-        or if we need to use the slow get_data method."""
-        return (
-            not epochs.preload
-            and epochs._bad_dropped
-            and epochs.detrend is None
-            and not epochs._do_baseline  # baseline is None
-            and (epochs._decim == 1)
-            and epochs._offset is None
-            and epochs._projector is None
-        )
-
     def __getitem__(self, index: int):
         """Get a window and its target.
 
@@ -756,10 +650,7 @@ class WindowsDataset(RecordDataset):
         np.ndarray
             Crop indices.
         """
-        if self._fast_disk:
-            X = self.windows._get_epoch_from_raw(index).astype("float32")
-        else:
-            X = self.windows.get_data(item=index)[0].astype("float32")
+        X = self.windows.get_data(item=index)[0].astype("float32")
         if self.transform is not None:
             X = self.transform(X)
         if self.targets_from == "metadata":
@@ -815,9 +706,7 @@ class BaseConcatDataset(ConcatDataset, HubDatasetMixin, Generic[T]):
 
     def __init__(
         self,
-        list_of_ds: (
-            list[T] | list[BaseConcatDataset[T]] | list[T | BaseConcatDataset[T]]
-        ),
+        list_of_ds: list[T | BaseConcatDataset[T]],
         target_transform: Callable | None = None,
         *,
         lazy: bool = False,
@@ -1394,40 +1283,3 @@ class BaseConcatDataset(ConcatDataset, HubDatasetMixin, Generic[T]):
 
     def _repr_html_(self):
         return self._build_repr().to_html()
-
-    def to_epochs_dataset(self) -> BaseConcatDataset[WindowsDataset]:
-        """Converts this :class:`BaseConcatDataset` such that all datasets are :class:`WindowsDataset` with ``mne.Epochs``.
-
-        In Braindecode, the data can either be stored as ``mne.io.Raw`` (in :class:`EEGWindowsDataset`)
-        or as ``mne.Epochs`` (in :class:`WindowsDataset`). This function converts all the underlying datasets to
-        :class:`WindowsDataset` with ``mne.Epochs``.
-        This can be useful for reducing disk space when you want to save a dataset.
-
-        Returns
-        -------
-        BaseConcatDataset[WindowsDataset]
-            A new :class:`BaseConcatDataset` where all datasets are :class:`WindowsDataset` with ``mne.Epochs``.
-
-        Raises
-        ------
-        ValueError
-            If any of the underlying datasets is a :class:`RawDataset` or any other type that is not
-            :class:`EEGWindowsDataset` or :class:`WindowsDataset`, as they cannot be converted to epochs.
-        """
-        datasets = self.datasets
-        if not all(
-            isinstance(ds, (EEGWindowsDataset, WindowsDataset)) for ds in datasets
-        ):
-            raise ValueError(
-                "All datasets must be EEGWindowsDataset or WindowsDataset to convert to WindowsDataset."
-            )
-        new_datasets: list[WindowsDataset] = []
-        for ds in datasets:
-            if isinstance(ds, EEGWindowsDataset):
-                new_ds = ds.to_epochs_dataset()
-                new_datasets.append(new_ds)
-            elif isinstance(ds, WindowsDataset):
-                new_datasets.append(ds)
-        return BaseConcatDataset(
-            new_datasets, target_transform=self.target_transform, lazy=self._lazy
-        )