Braindecode 1.3.0.dev168639307__tar.gz → 1.3.0.dev169126795__tar.gz

braindecode-1.3.0.dev169126795/PKG-INFO

@@ -0,0 +1,202 @@
+Metadata-Version: 2.4
+Name: braindecode
+Version: 1.3.0.dev169126795
+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>
+License: BSD-3-Clause
+Project-URL: homepage, https://braindecode.org
+Project-URL: repository, https://github.com/braindecode/braindecode
+Project-URL: documentation, https://braindecode.org/stable/index.html
+Keywords: python,deep-learning,neuroscience,pytorch,meg,eeg,neuroimaging,electroencephalography,magnetoencephalography,electrocorticography,ecog,electroencephalogram
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Software Development :: Build Tools
+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
+Description-Content-Type: text/x-rst
+License-File: LICENSE.txt
+License-File: NOTICE.txt
+Requires-Dist: mne>=1.10.0
+Requires-Dist: mne_bids>=0.16
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: scipy
+Requires-Dist: matplotlib
+Requires-Dist: h5py
+Requires-Dist: skorch>=1.2.0
+Requires-Dist: torch<3.0,>=2.0
+Requires-Dist: torchaudio<3.0,>=2.0
+Requires-Dist: einops
+Requires-Dist: joblib
+Requires-Dist: torchinfo~=1.8
+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
+Requires-Dist: eegprep[eeglabio]>=0.1.1; extra == "eegprep"
+Provides-Extra: hub
+Requires-Dist: huggingface_hub[torch]>=0.20.0; extra == "hub"
+Requires-Dist: zarr<3.0,>=2.18; extra == "hub"
+Provides-Extra: tests
+Requires-Dist: pytest; extra == "tests"
+Requires-Dist: pytest-cov; extra == "tests"
+Requires-Dist: codecov; extra == "tests"
+Requires-Dist: pytest_cases; extra == "tests"
+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"
+Requires-Dist: pillow; extra == "docs"
+Requires-Dist: ipython; extra == "docs"
+Requires-Dist: sphinx_design; extra == "docs"
+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[moabb]; extra == "all"
+Requires-Dist: braindecode[hub]; extra == "all"
+Requires-Dist: braindecode[tests]; extra == "all"
+Requires-Dist: braindecode[docs]; extra == "all"
+Requires-Dist: braindecode[eegprep]; extra == "all"
+Dynamic: license-file
+
+.. image:: https://badges.gitter.im/braindecodechat/community.svg
+   :alt: Join the chat at https://gitter.im/braindecodechat/community
+   :target: https://gitter.im/braindecodechat/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge
+
+.. image:: https://github.com/braindecode/braindecode/workflows/docs/badge.svg
+   :target: https://github.com/braindecode/braindecode/actions
+
+.. image:: https://circleci.com/gh/braindecode/braindecode.svg?style=svg
+   :target: https://circleci.com/gh/braindecode/braindecode
+   :alt: Doc build on CircleCI
+
+.. image:: https://codecov.io/gh/braindecode/braindecode/branch/master/graph/badge.svg
+   :target: https://codecov.io/gh/braindecode/braindecode
+   :alt: Code Coverage
+
+.. |Braindecode| image:: https://user-images.githubusercontent.com/42702466/177958779-b00628aa-9155-4c51-96d1-d8c345aff575.svg
+.. _braindecode: braindecode.org/
+
+Braindecode
+===========
+
+Braindecode is an open-source Python toolbox for decoding raw electrophysiological brain
+data with deep learning models. It includes dataset fetchers, data preprocessing and
+visualization tools, as well as implementations of several deep learning
+architectures and data augmentations for analysis of EEG, ECoG and MEG.
+
+For neuroscientists who want to work with deep learning and
+deep learning researchers who want to work with neurophysiological data.
+
+
+Installation Braindecode
+========================
+
+1. Install pytorch from http://pytorch.org/ (you don't need to install torchvision).
+
+2. If you want to download EEG datasets from `MOABB <https://github.com/NeuroTechX/moabb>`_, install it:
+
+.. code-block:: bash
+
+  pip install moabb
+
+3. Install latest release of braindecode via pip:
+
+.. code-block:: bash
+
+  pip install braindecode
+
+If you want to install the latest development version of braindecode, please refer to `contributing page <https://github.com/braindecode/braindecode/blob/master/CONTRIBUTING.md>`__
+
+
+Documentation
+=============
+
+Documentation is online under https://braindecode.org, both in the stable and dev versions.
+
+
+Contributing to Braindecode
+===========================
+
+Guidelines for contributing to the library can be found on the braindecode github:
+
+https://github.com/braindecode/braindecode/blob/master/CONTRIBUTING.md
+
+Braindecode chat
+================
+
+https://gitter.im/braindecodechat/community
+
+Citing
+======
+
+If you use this code in a scientific publication, please cite us as:
+
+.. code-block:: bibtex
+
+  @article {HBM:HBM23730,
+  author = {Schirrmeister, Robin Tibor and Springenberg, Jost Tobias and Fiederer,
+    Lukas Dominique Josef and Glasstetter, Martin and Eggensperger, Katharina and Tangermann, Michael and
+    Hutter, Frank and Burgard, Wolfram and Ball, Tonio},
+  title = {Deep learning with convolutional neural networks for EEG decoding and visualization},
+  journal = {Human Brain Mapping},
+  issn = {1097-0193},
+  url = {http://dx.doi.org/10.1002/hbm.23730},
+  doi = {10.1002/hbm.23730},
+  month = {aug},
+  year = {2017},
+  keywords = {electroencephalography, EEG analysis, machine learning, end-to-end learning, brain–machine interface,
+    brain–computer interface, model interpretability, brain mapping},
+  }
+
+as well as the `MNE-Python <https://mne.tools>`_ software that is used by braindecode:
+
+.. code-block:: bibtex
+
+  @article{10.3389/fnins.2013.00267,
+  author={Gramfort, Alexandre and Luessi, Martin and Larson, Eric and Engemann, Denis and Strohmeier, Daniel and Brodbeck, Christian and Goj, Roman and Jas, Mainak and Brooks, Teon and Parkkonen, Lauri and Hämäläinen, Matti},
+  title={{MEG and EEG data analysis with MNE-Python}},
+  journal={Frontiers in Neuroscience},
+  volume={7},
+  pages={267},
+  year={2013},
+  url={https://www.frontiersin.org/article/10.3389/fnins.2013.00267},
+  doi={10.3389/fnins.2013.00267},
+  issn={1662-453X},
+  }
+
+
+
+
+Licensing
+^^^^^^^^^
+
+This project is primarily licensed under the BSD-3-Clause License.
+
+Additional Components
+~~~~~~~~~~~~~~~~~~~~~
+
+Some components within this repository are licensed under the Creative Commons Attribution-NonCommercial 4.0 International
+License.
+
+Please refer to the ``LICENSE`` and ``NOTICE`` files for more detailed
+information.

braindecode-1.3.0.dev169126795/README.rst

@@ -0,0 +1,122 @@
+.. image:: https://badges.gitter.im/braindecodechat/community.svg
+   :alt: Join the chat at https://gitter.im/braindecodechat/community
+   :target: https://gitter.im/braindecodechat/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge
+
+.. image:: https://github.com/braindecode/braindecode/workflows/docs/badge.svg
+   :target: https://github.com/braindecode/braindecode/actions
+
+.. image:: https://circleci.com/gh/braindecode/braindecode.svg?style=svg
+   :target: https://circleci.com/gh/braindecode/braindecode
+   :alt: Doc build on CircleCI
+
+.. image:: https://codecov.io/gh/braindecode/braindecode/branch/master/graph/badge.svg
+   :target: https://codecov.io/gh/braindecode/braindecode
+   :alt: Code Coverage
+
+.. |Braindecode| image:: https://user-images.githubusercontent.com/42702466/177958779-b00628aa-9155-4c51-96d1-d8c345aff575.svg
+.. _braindecode: braindecode.org/
+
+Braindecode
+===========
+
+Braindecode is an open-source Python toolbox for decoding raw electrophysiological brain
+data with deep learning models. It includes dataset fetchers, data preprocessing and
+visualization tools, as well as implementations of several deep learning
+architectures and data augmentations for analysis of EEG, ECoG and MEG.
+
+For neuroscientists who want to work with deep learning and
+deep learning researchers who want to work with neurophysiological data.
+
+
+Installation Braindecode
+========================
+
+1. Install pytorch from http://pytorch.org/ (you don't need to install torchvision).
+
+2. If you want to download EEG datasets from `MOABB <https://github.com/NeuroTechX/moabb>`_, install it:
+
+.. code-block:: bash
+
+  pip install moabb
+
+3. Install latest release of braindecode via pip:
+
+.. code-block:: bash
+
+  pip install braindecode
+
+If you want to install the latest development version of braindecode, please refer to `contributing page <https://github.com/braindecode/braindecode/blob/master/CONTRIBUTING.md>`__
+
+
+Documentation
+=============
+
+Documentation is online under https://braindecode.org, both in the stable and dev versions.
+
+
+Contributing to Braindecode
+===========================
+
+Guidelines for contributing to the library can be found on the braindecode github:
+
+https://github.com/braindecode/braindecode/blob/master/CONTRIBUTING.md
+
+Braindecode chat
+================
+
+https://gitter.im/braindecodechat/community
+
+Citing
+======
+
+If you use this code in a scientific publication, please cite us as:
+
+.. code-block:: bibtex
+
+  @article {HBM:HBM23730,
+  author = {Schirrmeister, Robin Tibor and Springenberg, Jost Tobias and Fiederer,
+    Lukas Dominique Josef and Glasstetter, Martin and Eggensperger, Katharina and Tangermann, Michael and
+    Hutter, Frank and Burgard, Wolfram and Ball, Tonio},
+  title = {Deep learning with convolutional neural networks for EEG decoding and visualization},
+  journal = {Human Brain Mapping},
+  issn = {1097-0193},
+  url = {http://dx.doi.org/10.1002/hbm.23730},
+  doi = {10.1002/hbm.23730},
+  month = {aug},
+  year = {2017},
+  keywords = {electroencephalography, EEG analysis, machine learning, end-to-end learning, brain–machine interface,
+    brain–computer interface, model interpretability, brain mapping},
+  }
+
+as well as the `MNE-Python <https://mne.tools>`_ software that is used by braindecode:
+
+.. code-block:: bibtex
+
+  @article{10.3389/fnins.2013.00267,
+  author={Gramfort, Alexandre and Luessi, Martin and Larson, Eric and Engemann, Denis and Strohmeier, Daniel and Brodbeck, Christian and Goj, Roman and Jas, Mainak and Brooks, Teon and Parkkonen, Lauri and Hämäläinen, Matti},
+  title={{MEG and EEG data analysis with MNE-Python}},
+  journal={Frontiers in Neuroscience},
+  volume={7},
+  pages={267},
+  year={2013},
+  url={https://www.frontiersin.org/article/10.3389/fnins.2013.00267},
+  doi={10.3389/fnins.2013.00267},
+  issn={1662-453X},
+  }
+
+
+
+
+Licensing
+^^^^^^^^^
+
+This project is primarily licensed under the BSD-3-Clause License.
+
+Additional Components
+~~~~~~~~~~~~~~~~~~~~~
+
+Some components within this repository are licensed under the Creative Commons Attribution-NonCommercial 4.0 International
+License.
+
+Please refer to the ``LICENSE`` and ``NOTICE`` files for more detailed
+information.

{braindecode-1.3.0.dev168639307 → braindecode-1.3.0.dev169126795}/braindecode/augmentation/__init__.py

@@ -1,12 +1,12 @@
-"""Utilities for data augmentation."""
+"""
+Utilities for data augmentation.
+"""
 
 from . import functional
 from .base import AugmentedDataLoader, Compose, IdentityTransform, Transform
 from .transforms import (
-    AmplitudeScale,
     BandstopFilter,
     ChannelsDropout,
-    ChannelsReref,
     ChannelsShuffle,
     ChannelsSymmetry,
     FrequencyShift,
@@ -46,7 +46,5 @@ __all__ = [
     "Mixup",
     "SegmentationReconstruction",
     "MaskEncoding",
-    "AmplitudeScale",
-    "ChannelsReref",
     "functional",
 ]

{braindecode-1.3.0.dev168639307 → braindecode-1.3.0.dev169126795}/braindecode/augmentation/base.py

@@ -31,8 +31,7 @@ Operation = Callable[
 
 
 class Transform(torch.nn.Module):
-    """Basic transform class used for implementing data augmentation.
-
+    """Basic transform class used for implementing data augmentation
     operations.
 
     Parameters
@@ -43,7 +42,7 @@ class Transform(torch.nn.Module):
     probability : float, optional
         Float between 0 and 1 defining the uniform probability of applying the
         operation. Set to 1.0 by default (e.g always apply the operation).
-    random_state : int, optional
+    random_state: int, optional
         Seed to be used to instantiate numpy random number generator instance.
         Used to decide whether or not to transform given the probability
         argument. Defaults to None.
@@ -126,7 +125,7 @@ class Transform(torch.nn.Module):
             return out_X
 
     def _get_mask(self, batch_size, device) -> torch.Tensor:
-        """Samples whether to apply operation or not over the whole batch."""
+        """Samples whether to apply operation or not over the whole batch"""
         return torch.as_tensor(self.probability > self.rng.uniform(size=batch_size)).to(
             device
         )
@@ -154,7 +153,7 @@ class Compose(Transform):
 
     Parameters
     ----------
-    transforms : list
+    transforms: list
         Sequence of Transforms to be composed.
     """
 
@@ -170,9 +169,7 @@ class Compose(Transform):
 
 def _make_collateable(transform, device=None):
     """Wraps a transform to make it collateable.
-
-    with device control.
-    """
+    with device control."""
 
     def _collate_fn(batch):
         collated_batch = default_collate(batch)

{braindecode-1.3.0.dev168639307 → braindecode-1.3.0.dev169126795}/braindecode/augmentation/functional.py

@@ -144,7 +144,7 @@ def ft_surrogate(
         EEG input example or batch.
     y : torch.Tensor
         EEG labels for the example or batch.
-    phase_noise_magnitude : float
+    phase_noise_magnitude: float
         Float between 0 and 1 setting the range over which the phase
         perturbation is uniformly sampled:
         [0, `phase_noise_magnitude` * 2 * `pi`].
@@ -152,7 +152,7 @@ def ft_surrogate(
         Whether to sample phase perturbations independently for each channel or
         not. It is advised to set it to False when spatial information is
         important for the task, like in BCI.
-    random_state : int | numpy.random.Generator, optional
+    random_state: int | numpy.random.Generator, optional
         Used to draw the phase perturbation. Defaults to None.
 
     Returns
@@ -289,10 +289,10 @@ def channels_shuffle(
         EEG input example or batch.
     y : torch.Tensor
         EEG labels for the example or batch.
-    p_shuffle : float | None
+    p_shuffle: float | None
         Float between 0 and 1 setting the probability of including the channel
         in the set of permutted channels.
-    random_state : int | numpy.random.Generator, optional
+    random_state: int | numpy.random.Generator, optional
         Seed to be used to instantiate numpy random number generator instance.
         Used to sample which channels to shuffle and to carry the shuffle.
         Defaults to None.
@@ -335,7 +335,7 @@ def gaussian_noise(
         EEG labels for the example or batch.
     std : float
         Standard deviation to use for the additive noise.
-    random_state : int | numpy.random.Generator, optional
+    random_state: int | numpy.random.Generator, optional
         Seed to be used to instantiate numpy random number generator instance.
         Defaults to None.
 
@@ -468,8 +468,7 @@ def bandstop_filter(
     bandwidth: float,
     freqs_to_notch: npt.ArrayLike | None,
 ) -> tuple[torch.Tensor, torch.Tensor]:
-    """Apply a band-stop filter with desired bandwidth at the desired frequency.
-
+    """Apply a band-stop filter with desired bandwidth at the desired frequency
     position.
 
     Suggested e.g. in [1]_ and [2]_
@@ -621,7 +620,6 @@ def _torch_legval(
 ) -> torch.Tensor:
     """
     Evaluate a Legendre series at points x.
-
     If `c` is of length `n + 1`, this function returns the value:
     .. math:: p(x) = c_0 * L_0(x) + c_1 * L_1(x) + ... + c_n * L_n(x)
     The parameter `x` is converted to an array only if it is a tuple or a
@@ -807,6 +805,12 @@ def _torch_make_interpolation_matrix(
         The interpolation matrix that maps good signals to the location
         of bad signals.
 
+    References
+    ----------
+    [1] Perrin, F., Pernier, J., Bertrand, O. and Echallier, JF. (1989).
+        Spherical splines for scalp potential and current density mapping.
+        Electroencephalography Clinical Neurophysiology, Feb; 72(2):184-7.
+
     Notes
     -----
     Code copied and modified from MNE-Python:
@@ -837,12 +841,6 @@ def _torch_make_interpolation_matrix(
     LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
     OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
     DAMAGE.
-
-    References
-    ----------
-    [1] Perrin, F., Pernier, J., Bertrand, O. and Echallier, JF. (1989).
-        Spherical splines for scalp potential and current density mapping.
-        Electroencephalography Clinical Neurophysiology, Feb; 72(2):184-7.
     """
     pos_from = pos_from.clone()
     pos_to = pos_to.clone()
@@ -970,8 +968,7 @@ def sensors_rotation(
     angles: npt.ArrayLike,
     spherical_splines: bool,
 ) -> tuple[torch.Tensor, torch.Tensor]:
-    """Interpolates EEG signals over sensors rotated around the desired axis.
-
+    """Interpolates EEG signals over sensors rotated around the desired axis
     with the desired angle.
 
     Suggested in [1]_
@@ -1030,7 +1027,7 @@ def mixup(
     lam : torch.Tensor
         Values between 0 and 1 setting the linear interpolation between
         examples.
-    idx_perm : torch.Tensor
+    idx_perm: torch.Tensor
         Permuted indices of example that are mixed into original examples.
 
     Returns
@@ -1083,20 +1080,18 @@ def segmentation_reconstruction(
         EEG labels for the example or batch.
     n_segments : int
         Number of segments to use in the batch.
-    data_classes : list[tuple[int, torch.Tensor]]
+    data_classes: list[tuple[int, torch.Tensor]]
         List of tuples. Each tuple contains the class index and the corresponding EEG data.
-    rand_indices : array-like
+    rand_indices: array-like
         Array of indices that indicates which trial to use in each segment.
-    idx_shuffle : array-like
+    idx_shuffle: array-like
         Array of indices to shuffle the new generated trials.
-
     Returns
     -------
     torch.Tensor
         Transformed inputs.
     torch.Tensor
         Transformed labels.
-
     References
     ----------
     .. [1] Lotte, F. (2015). Signal processing approaches to minimize or
@@ -1150,7 +1145,7 @@ def mask_encoding(
     segment_length: int,
     n_segments: int,
 ) -> tuple[torch.Tensor, torch.Tensor]:
-    """Mark encoding from Ding et al (2024) from [ding2024]_.
+    """Mark encoding from Ding et al. (2024) from [ding2024]_.
 
     Replaces a contiguous part (or parts) of all channels by zeros
     (if more than one segment, it may overlap).
@@ -1217,7 +1212,7 @@ def channels_rereference(
         EEG input example or batch.
     y : torch.Tensor
         EEG labels for the example or batch.
-    random_state : int | numpy.random.Generator, optional
+    random_state: int | numpy.random.Generator, optional
         Seed to be used to instantiate numpy random number generator instance.
         Defaults to None.
 
@@ -1234,6 +1229,7 @@ def channels_rereference(
         Representation Learning for Electroencephalogram Classification. Proceedings
         of the Machine Learning for Health NeurIPS Workshop, in Proceedings of Machine
         Learning Research 136:238-253
+
     """
 
     rng = check_random_state(random_state)
@@ -1266,7 +1262,7 @@ def amplitude_scale(
         EEG labels for the example or batch.
     scale : tuple of floats
         Interval from which ypu sample the scaling value
-    random_state : int | numpy.random.Generator, optional
+    random_state: int | numpy.random.Generator, optional
         Seed to be used to instantiate numpy random number generator instance.
         Defaults to None.
 
@@ -1283,6 +1279,7 @@ def amplitude_scale(
         Representation Learning for Electroencephalogram Classification. Proceedings
         of the Machine Learning for Health NeurIPS Workshop, in Proceedings of Machine
         Learning Research 136:238-253
+
     """
 
     rng = torch.Generator()