braindecode 1.3.0.dev177069446__py3-none-any.whl → 1.3.0.dev177628147__py3-none-any.whl

braindecode/regressor.py

@@ -89,8 +89,7 @@ class EEGRegressor(_EEGNeuralNet, NeuralNetRegressor):
             return iterator
 
     def predict_proba(self, X):
-        """Return the output of the module's forward method as a numpy.
-
+        """Return the output of the module's forward method as a numpy
         array. In case of cropped decoding returns averaged values for
         each trial.
 
@@ -117,15 +116,16 @@ class EEGRegressor(_EEGNeuralNet, NeuralNetRegressor):
           If this doesn't work with your data, you have to pass a
           ``Dataset`` that can deal with the data.
 
-        Returns
-        -------
-        y_proba : numpy ndarray
-
         Warnings
         --------
         Regressors predict regression targets, so output of this method
         can't be interpreted as probabilities. We advise you to use
         `predict` method instead of `predict_proba`.
+
+        Returns
+        -------
+        y_proba : numpy ndarray
+
         """
         y_pred = super().predict_proba(X)
         # Normally, we have to average the predictions across crops/timesteps
@@ -139,24 +139,23 @@ class EEGRegressor(_EEGNeuralNet, NeuralNetRegressor):
             return y_pred
 
     def predict_trials(self, X, return_targets=True):
-        """Create trialwise predictions and optionally also return trialwise.
-
+        """Create trialwise predictions and optionally also return trialwise
         labels from cropped dataset.
 
         Parameters
         ----------
-        X : braindecode.datasets.BaseConcatDataset
+        X: braindecode.datasets.BaseConcatDataset
             A braindecode dataset to be predicted.
-        return_targets : bool
+        return_targets: bool
             If True, additionally returns the trial targets.
 
         Returns
         -------
-        trial_predictions : np.ndarray
+        trial_predictions: np.ndarray
             3-dimensional array (n_trials x n_classes x n_predictions), where
             the number of predictions depend on the chosen window size and the
             receptive field of the network.
-        trial_labels : np.ndarray
+        trial_labels: np.ndarray
             2-dimensional array (n_trials x n_targets) where the number of
             targets depends on the decoding paradigm and can be either a single
             value, multiple values, or a sequence.
@@ -229,6 +228,10 @@ class EEGRegressor(_EEGNeuralNet, NeuralNetRegressor):
                 y = np.array(y).reshape(-1, 1)
         super().fit(X=X, y=y, **kwargs)
 
-    @property
-    def mode(self):
-        return "regression"
+    def _get_n_outputs(self, y, classes):
+        if y is None:
+            return None
+        if y.ndim == 1:
+            return 1
+        else:
+            return y.shape[-1]

braindecode/samplers/ssl.py

@@ -190,7 +190,7 @@ class DistributedRelativePositioningSampler(DistributedRecordingSampler):
         self.tau_max = np.inf if tau_max is None else tau_max
         self.same_rec_neg = same_rec_neg
 
-        self.n_examples = n_examples * self.n_recordings // self.info.shape[0]
+        self.n_examples = n_examples // self.info.shape[0] * self.n_recordings
         warnings.warn(
             f"Rank {dist.get_rank()} - Number of datasets: {self.n_recordings}"
         )

braindecode/util.py

@@ -1,10 +1,10 @@
 # Authors: Robin Schirrmeister <robintibor@gmail.com>
 #
 # License: BSD (3-clause)
+
 import glob
 import os
 import random
-import re
 from warnings import warn
 
 import h5py
@@ -23,11 +23,11 @@ def set_random_seeds(seed, cuda, cudnn_benchmark=None):
 
     Parameters
     ----------
-    seed : int
+    seed: int
         Random seed.
-    cuda : bool
+    cuda: bool
         Whether to set cuda seed with torch.
-    cudnn_benchmark : bool (default=None)
+    cudnn_benchmark: bool (default=None)
         Whether pytorch will use cudnn benchmark. When set to `None` it will not modify
         torch.backends.cudnn.benchmark (displays warning in the case of possible lack of
         reproducibility). When set to True, results may not be reproducible (no warning displayed).
@@ -71,17 +71,17 @@ def np_to_th(X, requires_grad=False, dtype=None, pin_memory=False, **tensor_kwar
 
     Parameters
     ----------
-    X : ndarray or list or number
+    X: ndarray or list or number
         Input arrays
-    requires_grad : bool
+    requires_grad: bool
         passed on to Variable constructor
-    dtype : numpy dtype, optional
+    dtype: numpy dtype, optional
     var_kwargs:
         passed on to Variable constructor
 
     Returns
     -------
-    var : `torch.Tensor`
+    var: `torch.Tensor`
     """
     if not hasattr(X, "__len__"):
         X = [X]
@@ -95,23 +95,21 @@ def np_to_th(X, requires_grad=False, dtype=None, pin_memory=False, **tensor_kwar
 
 
 def th_to_np(var: Tensor):
-    """Convenience function to transform `torch.Tensor` to numpy.
-
+    """Convenience function to transform `torch.Tensor` to numpy
     array.
-    Should work both for CPU and GPU.
-    """
+
+    Should work both for CPU and GPU."""
     return var.cpu().data.numpy()
 
 
 def corr(a, b):
     """
-    Computes correlation only between terms of a and terms of b, not within.
-
+    Computes correlation only between terms of a and terms of b, not within
     a and b.
 
     Parameters
     ----------
-    a, b : 2darray, features x samples
+    a, b: 2darray, features x samples
 
     Returns
     -------
@@ -126,13 +124,12 @@ def corr(a, b):
 
 def cov(a, b):
     """
-    Computes covariance only between terms of a and terms of b, not within.
-
+    Computes covariance only between terms of a and terms of b, not within
     a and b.
 
     Parameters
     ----------
-    a, b : 2darray, features x samples
+    a, b: 2darray, features x samples
 
     Returns
     -------
@@ -159,24 +156,23 @@ def _cov_and_var_to_corr(this_cov, var_a, var_b):
 
 def wrap_reshape_apply_fn(stat_fn, a, b, axis_a, axis_b):
     """
-    Reshape two nd-arrays into 2d-arrays, apply function and reshape.
-
+    Reshape two nd-arrays into 2d-arrays, apply function and reshape
     result back.
 
     Parameters
     ----------
-    stat_fn : function
+    stat_fn: function
         Function to apply to 2d-arrays
-    a : nd-array: nd-array
-    b : nd-array
-    axis_a : int or list of int
+    a: nd-array: nd-array
+    b: nd-array
+    axis_a: int or list of int
         sample axis
-    axis_b : int or list of int
+    axis_b: int or list of int
         sample axis
 
     Returns
     -------
-    result : nd-array
+    result: nd-array
         The result reshaped to remaining_dims_a + remaining_dims_b
     """
     if not hasattr(axis_a, "__len__"):
@@ -204,8 +200,7 @@ def wrap_reshape_apply_fn(stat_fn, a, b, axis_a, axis_b):
 
 
 def get_balanced_batches(n_trials, rng, shuffle, n_batches=None, batch_size=None):
-    """Create indices for batches balanced in size.
-
+    """Create indices for batches balanced in size
     (batches will have maximum size difference of 1).
     Supply either batch size or number of batches. Resulting batches
     will not have the given batch size but rather the next largest batch size
@@ -223,7 +218,7 @@ def get_balanced_batches(n_trials, rng, shuffle, n_batches=None, batch_size=None
 
     Returns
     -------
-    batches : list of list of int
+    batches: list of list of int
         Indices for each batch.
     """
     assert batch_size is not None or n_batches is not None
@@ -386,29 +381,24 @@ def update_estimator_docstring(base_class, docstring):
 
 def _update_moabb_docstring(base_class, docstring):
     base_doc = base_class.__doc__
-    # Clean up malformed rubrics from moabb docstrings
-    # Remove lines that have ".. rubric::" followed by content on same line or improper formatting
-
-    base_doc = re.sub(r"\.\. rubric:: (.+?)\n\s+\.\. note::", r".. note::", base_doc)
     out_docstring = base_doc + f"\n\n{docstring}"
     return out_docstring
 
 
 def read_all_file_names(directory, extension):
-    """Read all files with specified extension from given path and sorts them.
-
+    """Read all files with specified extension from given path and sorts them
     based on a given sorting key.
 
     Parameters
     ----------
-    directory : str
+    directory: str
         Parent directory to be searched for files of the specified type.
-    extension : str
+    extension: str
         File extension, i.e. ".edf" or ".txt".
 
     Returns
     -------
-    file_paths : list(str)
+    file_paths: list(str)
         List of all files found in (sub)directories of path.
     """
     assert extension.startswith(".")

braindecode/version.py

@@ -1 +1 @@
-__version__ = "1.3.0.dev177069446"
+__version__ = "1.3.0.dev177628147"

braindecode-1.3.0.dev177628147.dist-info/METADATA

@@ -0,0 +1,202 @@
+Metadata-Version: 2.4
+Name: braindecode
+Version: 1.3.0.dev177628147
+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.dev177628147.dist-info/RECORD

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braindecode/datasets/bids/__init__.py

@@ -1,54 +0,0 @@
-# mypy: ignore-errors
-"""
-BIDS (Brain Imaging Data Structure) integration for braindecode.
-
-This subpackage provides:
-- BIDS dataset loading (BIDSDataset, BIDSEpochsDataset)
-- BIDS-like format utilities for Hub integration
-- Hugging Face Hub push/pull functionality
-- Validation utilities for Hub operations
-
-More information on BIDS can be found at https://bids.neuroimaging.io
-"""
-
-# Authors: Bruno Aristimunha <b.aristimunha@gmail.com>
-#          Pierre Guetschel <pierre.guetschel@gmail.com>
-#          Kuntal Kokate
-#
-# License: BSD (3-clause)
-
-from typing import TYPE_CHECKING
-
-# Only import hub at init level (needed by base.py)
-# Other imports are deferred to avoid circular imports
-from .hub import HubDatasetMixin
-
-# For static type checkers (mypy), provide explicit imports
-if TYPE_CHECKING:
-    from .datasets import BIDSDataset, BIDSEpochsDataset
-    from .iterable import BIDSIterableDataset
-
-
-def __getattr__(name: str):
-    """Lazy imports to avoid circular dependencies."""
-    if name in ("BIDSDataset", "BIDSEpochsDataset"):
-        from .datasets import BIDSDataset, BIDSEpochsDataset
-
-        return {"BIDSDataset": BIDSDataset, "BIDSEpochsDataset": BIDSEpochsDataset}[
-            name
-        ]
-    elif name == "BIDSIterableDataset":
-        from .iterable import BIDSIterableDataset
-
-        return BIDSIterableDataset
-    raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
-
-
-__all__ = [
-    # Dataset classes
-    "BIDSDataset",
-    "BIDSEpochsDataset",
-    "BIDSIterableDataset",
-    # Hub integration
-    "HubDatasetMixin",
-]