braindecode 1.3.0.dev173193230__tar.gz

braindecode-1.3.0.dev173193230/LICENSE.txt

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+BSD 3-Clause License
+
+Copyright (c) 2017-currently Braindecode Developers
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification,
+are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice,
+this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+this list of conditions and the following disclaimer in the documentation
+and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors
+may be used to endorse or promote products derived from this software
+without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A P
+ARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER
+OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT 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.

braindecode-1.3.0.dev173193230/MANIFEST.in

@@ -0,0 +1,8 @@
+include README.rst
+include LICENSE.txt
+include NOTICE.txt
+
+include braindecode/models/summary.csv
+
+recursive-include docs *.ipynb *.rst conf.py Makefile
+recursive-exclude docs *checkpoint.ipynb

braindecode-1.3.0.dev173193230/NOTICE.txt

@@ -0,0 +1,20 @@
+# BRAINDECODE Notice
+
+## Licensed Components
+
+### BSD-3-Clause Licensed Files
+
+All files within the `src/` directory are licensed under the BSD-3-Clause License.
+
+### CC BY-NC 4.0 Licensed Files
+
+The following components are licensed under the Creative Commons Attribution-NonCommercial 4.0 International License:
+
+- `braindecode/models/eegminer.py`
+
+As well as class later imported into the `braindecode.models.module` named as GeneralizedGaussianFilter.
+
+## License Links
+
+- [BSD-3-Clause License](https://opensource.org/licenses/BSD-3-Clause)
+- [CC BY-NC 4.0 License](https://creativecommons.org/licenses/by-nc/4.0/)

braindecode-1.3.0.dev173193230/PKG-INFO

@@ -0,0 +1,218 @@
+Metadata-Version: 2.4
+Name: braindecode
+Version: 1.3.0.dev173193230
+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"
+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/232335424.svg
+   :target: https://doi.org/10.5281/zenodo.8214376
+   :alt: DOI
+
+.. 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 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.dev173193230/README.rst

@@ -0,0 +1,135 @@
+.. image:: https://zenodo.org/badge/232335424.svg
+   :target: https://doi.org/10.5281/zenodo.8214376
+   :alt: DOI
+
+.. 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 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.dev173193230/braindecode/__init__.py

@@ -0,0 +1,9 @@
+from .classifier import EEGClassifier
+from .regressor import EEGRegressor
+from .version import __version__
+
+__all__ = [
+    "__version__",
+    "EEGClassifier",
+    "EEGRegressor",
+]

braindecode-1.3.0.dev173193230/braindecode/augmentation/__init__.py

@@ -0,0 +1,54 @@
+"""
+Utilities for data augmentation.
+"""
+
+from . import functional
+from .base import AugmentedDataLoader, Compose, IdentityTransform, Transform
+from .transforms import (
+    AmplitudeScale,
+    BandstopFilter,
+    ChannelsDropout,
+    ChannelsReref,
+    ChannelsShuffle,
+    ChannelsSymmetry,
+    FrequencyShift,
+    FTSurrogate,
+    GaussianNoise,
+    MaskEncoding,
+    Mixup,
+    SegmentationReconstruction,
+    SensorsRotation,
+    SensorsXRotation,
+    SensorsYRotation,
+    SensorsZRotation,
+    SignFlip,
+    SmoothTimeMask,
+    TimeReverse,
+)
+
+__all__ = [
+    "Transform",
+    "IdentityTransform",
+    "Compose",
+    "AugmentedDataLoader",
+    "TimeReverse",
+    "SignFlip",
+    "FTSurrogate",
+    "ChannelsShuffle",
+    "ChannelsDropout",
+    "GaussianNoise",
+    "ChannelsSymmetry",
+    "SmoothTimeMask",
+    "BandstopFilter",
+    "FrequencyShift",
+    "SensorsRotation",
+    "SensorsZRotation",
+    "SensorsYRotation",
+    "SensorsXRotation",
+    "Mixup",
+    "SegmentationReconstruction",
+    "MaskEncoding",
+    "AmplitudeScale",
+    "ChannelsReref",
+    "functional",
+]