Braindecode 1.2.0.dev182094932__tar.gz → 1.3.0__tar.gz

braindecode-1.3.0/PKG-INFO

@@ -0,0 +1,230 @@
+Metadata-Version: 2.4
+Name: braindecode
+Version: 1.3.0
+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 :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Requires-Python: >=3.11
+Description-Content-Type: text/x-rst
+License-File: LICENSE.txt
+License-File: NOTICE.txt
+Requires-Dist: torch>=2.2
+Requires-Dist: torchaudio>=2.0
+Requires-Dist: mne>=1.11.0
+Requires-Dist: mne_bids>=0.16
+Requires-Dist: h5py
+Requires-Dist: skorch>=1.3.0
+Requires-Dist: joblib
+Requires-Dist: torchinfo
+Requires-Dist: wfdb
+Requires-Dist: linear_attention_transformer
+Requires-Dist: docstring_inheritance
+Requires-Dist: rotary_embedding_torch
+Provides-Extra: moabb
+Requires-Dist: moabb>=1.4.3; extra == "moabb"
+Provides-Extra: eegprep
+Requires-Dist: eegprep[eeglabio]>=0.2.23; extra == "eegprep"
+Provides-Extra: hub
+Requires-Dist: huggingface_hub[torch]>=0.20.0; extra == "hub"
+Requires-Dist: zarr>=3.0; 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"
+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: numpydantic>=1.7; extra == "typing"
+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"
+Requires-Dist: shap; extra == "docs"
+Requires-Dist: nbformat; extra == "docs"
+Requires-Dist: transformers; extra == "docs"
+Provides-Extra: all
+Requires-Dist: braindecode[moabb]; extra == "all"
+Requires-Dist: braindecode[tests]; extra == "all"
+Requires-Dist: braindecode[docs]; extra == "all"
+Requires-Dist: braindecode[hub]; extra == "all"
+Requires-Dist: braindecode[eegprep]; extra == "all"
+Requires-Dist: braindecode[typing]; extra == "all"
+Dynamic: license-file
+
+.. 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
+    :target: https://github.com/braindecode/braindecode/actions
+    :alt: Docs Build Status
+
+.. image:: https://github.com/braindecode/braindecode/workflows/tests/badge.svg
+    :target: https://github.com/braindecode/braindecode/actions?query=branch%3Amaster
+    :alt: Test Build Status
+
+.. image:: https://codecov.io/gh/braindecode/braindecode/branch/master/graph/badge.svg
+    :target: https://codecov.io/gh/braindecode/braindecode
+    :alt: Code Coverage
+
+.. image:: https://img.shields.io/pypi/v/braindecode?color=blue&style=flat-square
+    :target: https://pypi.org/project/braindecode/
+    :alt: PyPI
+
+.. image:: https://img.shields.io/pypi/v/braindecode?label=version&color=orange&style=flat-square
+    :target: https://pypi.org/project/braindecode/
+    :alt: Version
+
+.. image:: https://img.shields.io/pypi/pyversions/braindecode?style=flat-square
+    :target: https://pypi.org/project/braindecode/
+    :alt: Python versions
+
+.. image:: https://pepy.tech/badge/braindecode
+    :target: https://pepy.tech/project/braindecode
+    :alt: Downloads
+
+.. |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
+
+########
+ Citing
+########
+
+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/232335424.svg
+    :target: https://doi.org/10.5281/zenodo.8214376
+    :alt: DOI
+
+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:
+
+.. 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/README.rst

@@ -0,0 +1,146 @@
+.. 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
+    :target: https://github.com/braindecode/braindecode/actions
+    :alt: Docs Build Status
+
+.. image:: https://github.com/braindecode/braindecode/workflows/tests/badge.svg
+    :target: https://github.com/braindecode/braindecode/actions?query=branch%3Amaster
+    :alt: Test Build Status
+
+.. image:: https://codecov.io/gh/braindecode/braindecode/branch/master/graph/badge.svg
+    :target: https://codecov.io/gh/braindecode/braindecode
+    :alt: Code Coverage
+
+.. image:: https://img.shields.io/pypi/v/braindecode?color=blue&style=flat-square
+    :target: https://pypi.org/project/braindecode/
+    :alt: PyPI
+
+.. image:: https://img.shields.io/pypi/v/braindecode?label=version&color=orange&style=flat-square
+    :target: https://pypi.org/project/braindecode/
+    :alt: Version
+
+.. image:: https://img.shields.io/pypi/pyversions/braindecode?style=flat-square
+    :target: https://pypi.org/project/braindecode/
+    :alt: Python versions
+
+.. image:: https://pepy.tech/badge/braindecode
+    :target: https://pepy.tech/project/braindecode
+    :alt: Downloads
+
+.. |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
+
+########
+ Citing
+########
+
+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/232335424.svg
+    :target: https://doi.org/10.5281/zenodo.8214376
+    :alt: DOI
+
+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:
+
+.. 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-1.2.0.dev182094932 → braindecode-1.3.0}/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,
@@ -46,5 +46,7 @@ __all__ = [
     "Mixup",
     "SegmentationReconstruction",
     "MaskEncoding",
+    "AmplitudeScale",
+    "ChannelsReref",
     "functional",
 ]

{braindecode-1.2.0.dev182094932 → braindecode-1.3.0}/braindecode/augmentation/base.py

@@ -31,7 +31,8 @@ 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
@@ -42,7 +43,7 @@ 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.
@@ -125,7 +126,7 @@ 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
         )
@@ -153,7 +154,7 @@ class Compose(Transform):
 
     Parameters
     ----------
-    transforms: list
+    transforms : list
         Sequence of Transforms to be composed.
     """
 
@@ -169,7 +170,9 @@ 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)
@@ -189,7 +192,7 @@ class AugmentedDataLoader(DataLoader):
 
     Parameters
     ----------
-    dataset : BaseDataset
+    dataset : RecordDataset
         The dataset containing the signals.
     transforms : list | Transform, optional
         Transform or sequence of Transform to be applied to each batch.