braindecode 0.8__py3-none-any.whl → 1.0.0__py3-none-any.whl

braindecode/version.py

@@ -1 +1 @@
-__version__ = "0.8"
+__version__ = "1.0.0"

braindecode/visualization/__init__.py

@@ -0,0 +1,8 @@
+"""
+Functions for visualisations, especially of the ConvNets.
+"""
+
+from .confusion_matrices import plot_confusion_matrix
+from .gradients import compute_amplitude_gradients
+
+__all__ = ["compute_amplitude_gradients", "plot_confusion_matrix"]

braindecode/visualization/confusion_matrices.py

@@ -0,0 +1,289 @@
+# Authors: Robin Schirrmeister <robintibor@gmail.com>
+#
+# License: BSD (3-clause)
+
+import matplotlib.pyplot as plt
+import numpy as np
+from matplotlib import cm
+
+
+def plot_confusion_matrix(
+    confusion_mat,
+    class_names=None,
+    figsize=None,
+    colormap=cm.bwr,
+    textcolor="black",
+    vmin=None,
+    vmax=None,
+    fontweight="normal",
+    rotate_row_labels=90,
+    rotate_col_labels=0,
+    with_f1_score=False,
+    norm_axes=(0, 1),
+    rotate_precision=False,
+    class_names_fontsize=12,
+):
+    """
+
+    Generates a confusion matrix with additional precision and sensitivity metrics as in [1]_.
+
+    Parameters
+    ----------
+    confusion_mat: 2d numpy array
+        A confusion matrix, e.g. sklearn confusion matrix:
+        https://scikit-learn.org/stable/modules/generated/sklearn.metrics.confusion_matrix.html
+    class_names: array, optional
+        List of classes/targets.
+    figsize: tuple, optional
+        Size of the generated confusion matrix figure.
+    colormap: matplotlib cm colormap, optional
+    textcolor: str, optional
+        Color  of the text in the figure.
+    vmin, vmax: float, optional
+        The data range that the colormap covers.
+    fontweight: str, optional
+        Weight of the font in the figure:
+        [ 'normal' | 'bold' | 'heavy' | 'light' | 'ultrabold' | 'ultralight']
+    rotate_row_labels: int, optional
+        The rotation angle of the row labels
+    rotate_col_labels: int, optional
+        The rotation angle of the column labels
+    with_f1_score: bool, optional
+    norm_axes: tuple, optional
+    rotate_precision: bool, optional
+    class_names_fontsize: int, optional
+
+    Returns
+    -------
+    fig: matplotlib figure
+
+    References
+    ----------
+
+    .. [1] Schirrmeister, R. T., Springenberg, J. T., Fiederer, L. D. J.,
+       Glasstetter, M., Eggensperger, K., Tangermann, M., Hutter, F. & Ball, T. (2017).
+       Deep learning with convolutional neural networks for EEG decoding and
+       visualization.
+       Human Brain Mapping , Aug. 2017. Online: http://dx.doi.org/10.1002/hbm.23730
+    """
+    # transpose to get confusion matrix same way as matlab
+    confusion_mat = confusion_mat.T
+    n_classes = confusion_mat.shape[0]
+    if class_names is None:
+        class_names = [str(i_class + 1) for i_class in range(n_classes)]
+
+    # norm by all targets
+    normed_conf_mat = confusion_mat / np.float32(
+        np.sum(confusion_mat, axis=norm_axes, keepdims=True)
+    )
+
+    fig = plt.figure(figsize=figsize)
+    plt.clf()
+    ax = fig.add_subplot(111)
+    ax.set_aspect(1)
+    if vmin is None:
+        vmin = np.min(normed_conf_mat)
+    if vmax is None:
+        vmax = np.max(normed_conf_mat)
+
+    # see http://stackoverflow.com/a/31397438/1469195
+    # brighten so that black text remains readable
+    # used alpha=0.6 before
+    def _brighten(
+        x,
+    ):
+        brightened_x = 1 - ((1 - np.array(x)) * 0.4)
+        return brightened_x
+
+    brightened_cmap = _cmap_map(_brighten, colormap)  # colormap #
+    ax.imshow(
+        np.array(normed_conf_mat),
+        cmap=brightened_cmap,
+        interpolation="nearest",
+        vmin=vmin,
+        vmax=vmax,
+    )
+
+    # make space for precision and sensitivity
+    plt.xlim(-0.5, normed_conf_mat.shape[0] + 0.5)
+    plt.ylim(normed_conf_mat.shape[1] + 0.5, -0.5)
+    width = len(confusion_mat)
+    height = len(confusion_mat[0])
+    for x in range(width):
+        for y in range(height):
+            if x == y:
+                this_font_weight = "bold"
+            else:
+                this_font_weight = fontweight
+            annotate_str = "{:d}".format(confusion_mat[x][y])
+            annotate_str += "\n"
+            ax.annotate(
+                annotate_str.format(confusion_mat[x][y]),
+                xy=(y, x),
+                horizontalalignment="center",
+                verticalalignment="center",
+                fontsize=12,
+                color=textcolor,
+                fontweight=this_font_weight,
+            )
+            if x != y or (not with_f1_score):
+                ax.annotate(
+                    "\n\n{:4.1f}%".format(normed_conf_mat[x][y] * 100),
+                    xy=(y, x),
+                    horizontalalignment="center",
+                    verticalalignment="center",
+                    fontsize=10,
+                    color=textcolor,
+                    fontweight=this_font_weight,
+                )
+            else:
+                assert x == y
+                precision = confusion_mat[x][x] / float(np.sum(confusion_mat[x, :]))
+                sensitivity = confusion_mat[x][x] / float(np.sum(confusion_mat[:, y]))
+                f1_score = 2 * precision * sensitivity / (precision + sensitivity)
+
+                ax.annotate(
+                    "\n{:4.1f}%\n{:4.1f}% (F)".format(
+                        (confusion_mat[x][y] / float(np.sum(confusion_mat))) * 100,
+                        f1_score * 100,
+                    ),
+                    xy=(y, x + 0.1),
+                    horizontalalignment="center",
+                    verticalalignment="center",
+                    fontsize=10,
+                    color=textcolor,
+                    fontweight=this_font_weight,
+                )
+
+    # Add values for target correctness etc.
+    for x in range(width):
+        y = len(confusion_mat)
+        if float(np.sum(confusion_mat[x, :])) == 0:
+            annotate_str = "-"
+        else:
+            correctness = confusion_mat[x][x] / float(np.sum(confusion_mat[x, :]))
+            annotate_str = ""
+            annotate_str += "\n{:5.2f}%".format(correctness * 100)
+        ax.annotate(
+            annotate_str,
+            xy=(y, x),
+            horizontalalignment="center",
+            verticalalignment="center",
+            fontsize=12,
+        )
+
+    for y in range(height):
+        x = len(confusion_mat)
+        if float(np.sum(confusion_mat[:, y])) == 0:
+            annotate_str = "-"
+        else:
+            correctness = confusion_mat[y][y] / float(np.sum(confusion_mat[:, y]))
+            annotate_str = ""
+            annotate_str += "\n{:5.2f}%".format(correctness * 100)
+        ax.annotate(
+            annotate_str,
+            xy=(y, x),
+            horizontalalignment="center",
+            verticalalignment="center",
+            fontsize=12,
+        )
+
+    overall_correctness = np.sum(np.diag(confusion_mat)) / np.sum(confusion_mat).astype(
+        float
+    )
+    ax.annotate(
+        "{:5.2f}%".format(overall_correctness * 100),
+        xy=(len(confusion_mat), len(confusion_mat)),
+        horizontalalignment="center",
+        verticalalignment="center",
+        fontsize=12,
+        fontweight="bold",
+    )
+
+    plt.xticks(
+        range(width),
+        class_names,
+        fontsize=class_names_fontsize,
+        rotation=rotate_col_labels,
+    )
+    plt.yticks(
+        np.arange(0, height),
+        class_names,
+        va="center",
+        fontsize=class_names_fontsize,
+        rotation=rotate_row_labels,
+    )
+    plt.grid(False)
+    plt.ylabel("Predictions", fontsize=15)
+    plt.xlabel("Targets", fontsize=15)
+
+    # n classes is also shape of matrix/size
+    ax.text(-1.2, n_classes + 0.2, "Recall", ha="center", va="center", fontsize=13)
+    if rotate_precision:
+        rotation = 90
+        x_pos = -1.1
+        va = "center"
+    else:
+        rotation = 0
+        x_pos = -0.8
+        va = "top"
+    ax.text(
+        n_classes,
+        x_pos,
+        "Precision",
+        ha="center",
+        va=va,
+        rotation=rotation,  # 270,
+        fontsize=13,
+    )
+
+    return fig
+
+
+# see http://stackoverflow.com/a/31397438/1469195
+def _cmap_map(function, cmap, name="colormap_mod", N=None, gamma=None):
+    """
+    Modify a colormap using `function` which must operate on 3-element
+    arrays of [r, g, b] values.
+
+    You may specify the number of colors, `N`, and the opacity, `gamma`,
+    value of the returned colormap. These values default to the ones in
+    the input `cmap`.
+
+    You may also specify a `name` for the colormap, so that it can be
+    loaded using plt.get_cmap(name).
+    """
+    from matplotlib.colors import LinearSegmentedColormap as lsc
+
+    if N is None:
+        N = cmap.N
+    if gamma is None:
+        gamma = cmap._gamma
+    cdict = cmap._segmentdata
+    # Cast the steps into lists:
+    step_dict = {key: list(map(lambda x: x[0], cdict[key])) for key in cdict}
+    # Now get the unique steps (first column of the arrays):
+    step_dicts = np.array(list(step_dict.values()))
+    step_list = np.unique(step_dicts)
+    # 'y0', 'y1' are as defined in LinearSegmentedColormap docstring:
+    y0 = cmap(step_list)[:, :3]
+    y1 = y0.copy()[:, :3]
+    # Go back to catch the discontinuities, and place them into y0, y1
+    for iclr, key in enumerate(["red", "green", "blue"]):
+        for istp, step in enumerate(step_list):
+            try:
+                ind = step_dict[key].index(step)
+            except ValueError:
+                # This step is not in this color
+                continue
+            y0[istp, iclr] = cdict[key][ind][1]
+            y1[istp, iclr] = cdict[key][ind][2]
+    # Map the colors to their new values:
+    y0 = np.array(list(map(function, y0)))
+    y1 = np.array(list(map(function, y1)))
+    # Build the new colormap (overwriting step_dict):
+    for iclr, clr in enumerate(["red", "green", "blue"]):
+        step_dict[clr] = np.vstack((step_list, y0[:, iclr], y1[:, iclr])).T
+    # Remove alpha, otherwise crashes...
+    step_dict.pop("alpha", None)
+    return lsc(name, step_dict, N=N, gamma=gamma)

braindecode/visualization/gradients.py

@@ -0,0 +1,57 @@
+# Authors: Robin Schirrmeister <robintibor@gmail.com>
+#
+# License: BSD (3-clause)
+
+import numpy as np
+import torch
+from skorch.utils import to_numpy, to_tensor
+
+
+def compute_amplitude_gradients(model, dataset, batch_size):
+    loader = torch.utils.data.DataLoader(
+        dataset, batch_size=batch_size, drop_last=False, shuffle=False
+    )
+    all_amp_grads = []
+    for batch_X, _, _ in loader:
+        this_amp_grads = compute_amplitude_gradients_for_X(
+            model,
+            batch_X,
+        )
+        all_amp_grads.append(this_amp_grads)
+    all_amp_grads = np.concatenate(all_amp_grads, axis=1)
+    return all_amp_grads
+
+
+def compute_amplitude_gradients_for_X(model, X):
+    device = next(model.parameters()).device
+    ffted = np.fft.rfft(X, axis=2)
+    amps = np.abs(ffted)
+    phases = np.angle(ffted)
+    amps_th = to_tensor(amps.astype(np.float32), device=device).requires_grad_(True)
+    phases_th = to_tensor(phases.astype(np.float32), device=device).requires_grad_(True)
+
+    fft_coefs = amps_th.unsqueeze(-1) * torch.stack(
+        (torch.cos(phases_th), torch.sin(phases_th)), dim=-1
+    )
+    fft_coefs = fft_coefs.squeeze(3)
+
+    try:
+        complex_fft_coefs = torch.view_as_complex(fft_coefs)
+        iffted = torch.fft.irfft(complex_fft_coefs, n=X.shape[2], dim=2)
+    except AttributeError:
+        iffted = torch.irfft(  # Deprecated since 1.7
+            fft_coefs, signal_ndim=1, signal_sizes=(X.shape[2],)
+        )
+
+    outs = model(iffted)
+
+    n_filters = outs.shape[1]
+    amp_grads_per_filter = np.full((n_filters,) + ffted.shape, np.nan, dtype=np.float32)
+    for i_filter in range(n_filters):
+        mean_out = torch.mean(outs[:, i_filter])
+        mean_out.backward(retain_graph=True)
+        amp_grads = to_numpy(amps_th.grad.clone())
+        amp_grads_per_filter[i_filter] = amp_grads
+        amps_th.grad.zero_()
+    assert not np.any(np.isnan(amp_grads_per_filter))
+    return amp_grads_per_filter

{braindecode-0.8.dist-info → braindecode-1.0.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: braindecode
-Version: 0.8
+Version: 1.0.0
 Summary: Deep learning software to decode EEG, ECG or MEG signals
 Author-email: Robin Tibor Schirrmeister <robintibor@gmail.com>
 Maintainer-email: Alexandre Gramfort <agramfort@meta.com>, Bruno Aristimunha Pinto <b.aristimunha@gmail.com>, Robin Tibor Schirrmeister <robintibor@gmail.com>
@@ -15,14 +15,15 @@ Classifier: Intended Audience :: Science/Research
 Classifier: Topic :: Software Development :: Build Tools
 Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
 Classifier: License :: OSI Approved :: BSD License
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
-Requires-Python: >=3.8
+Classifier: Programming Language :: Python :: 3.12
+Requires-Python: >3.9
 Description-Content-Type: text/x-rst
 License-File: LICENSE.txt
-Requires-Dist: mne
+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
@@ -30,29 +31,36 @@ Requires-Dist: matplotlib
 Requires-Dist: h5py
 Requires-Dist: skorch
 Requires-Dist: torch
+Requires-Dist: torchaudio
 Requires-Dist: einops
 Requires-Dist: joblib
 Requires-Dist: torchinfo
-Requires-Dist: docstring-inheritance
-Provides-Extra: docs
-Requires-Dist: sphinx-gallery ; extra == 'docs'
-Requires-Dist: sphinx-rtd-theme ; 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: wfdb
+Requires-Dist: h5py
+Requires-Dist: linear_attention_transformer
+Requires-Dist: docstring_inheritance
 Provides-Extra: moabb
-Requires-Dist: moabb >=1.0.0 ; extra == 'moabb'
+Requires-Dist: moabb>=1.2.0; extra == "moabb"
 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: 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: 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"
+Dynamic: license-file
 
 .. image:: https://badges.gitter.im/braindecodechat/community.svg
    :alt: Join the chat at https://gitter.im/braindecodechat/community
@@ -166,37 +174,13 @@ as well as the `MNE-Python <https://mne.tools>`_ software that is used by braind
 Licensing
 ^^^^^^^^^
 
-Braindecode is **BSD-licenced** (BSD-3-Clause):
-
-    This software is OSI Certified Open Source Software.
-    OSI Certified is a certification mark of the Open Source Initiative.
-
-    Copyright (c) 2011-2022, authors of Braindecode.
-    All rights reserved.
-
-    Redistribution and use in source and binary forms, with or without
-    modification, are permitted provided that the following conditions are met:
-
-    * Redistributions of source code must retain the above copyright notice,
-      this list of conditions and the following disclaimer.
+This project is primarily licensed under the BSD-3-Clause License.
 
-    * 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.
+Additional Components
+~~~~~~~~~~~~~~~~~~~~~
 
-    * Neither the names of braindecode authors nor the names of any
-      contributors may be used to endorse or promote products derived from
-      this software without specific prior written permission.
+Some components within this repository are licensed under the Creative Commons Attribution-NonCommercial 4.0 International
+License.
 
-    **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 particular purpose are disclaimed. In no event shall the copyright
-    owner 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.**
+Please refer to the ``LICENSE`` and ``NOTICE`` files for more detailed
+information.

braindecode-1.0.0.dist-info/RECORD

@@ -0,0 +1,101 @@
+braindecode/__init__.py,sha256=Ac3LEEyIHWFY_fFh3eAY1GZUqXcUxVSJwOSUCwGEDvQ,182
+braindecode/classifier.py,sha256=k9vSCtfQbld0YVleDi5rrrmk6k_k5JYEPPBYcNxYjZ8,9807
+braindecode/eegneuralnet.py,sha256=dz8k_-2jV7WqkaX4bQG-dmr-vRT7ZtOwJqomXyC9PTw,15287
+braindecode/regressor.py,sha256=VLfrpiXklwI4onkwue3QmzlBWcvspu0tlrLo9RT1Oiw,9375
+braindecode/util.py,sha256=J-tBcDJNlMTIFW2mfOy6Ko0nsgdP4obRoEVDeg2rFH0,12686
+braindecode/version.py,sha256=J-j-u0itpEFT6irdmWmixQqYMadNl1X91TxUmoiLHMI,22
+braindecode/augmentation/__init__.py,sha256=LG7ONqCufYAF9NZt8POIp10lYXb8iSueYkF-CWGK2Ls,1001
+braindecode/augmentation/base.py,sha256=gg7wYsVfa9jfqBddtE03B5ZrPHFFmPl2sa3LOrRnGfo,7325
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+braindecode/datasets/__init__.py,sha256=CTl8ucbG948ZJqntEBELb-Pn8GsZLfFZLgVcB-fhw4k,891
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+braindecode/datasets/mne.py,sha256=Dg6RZAAwd8TVGrvLOPF5B_JrbyGUWg52vWmn6fLMOQM,6135
+braindecode/datasets/moabb.py,sha256=JmBcFV7QJT8GCgLNNKWgxJVnEVnO5wd9U_uiIqTIxDM,7091
+braindecode/datasets/nmt.py,sha256=E4T8OYBEwWRSjh7VFzmyxaZbf5ufFVEBYYmQEd1ghUU,10430
+braindecode/datasets/sleep_physio_challe_18.py,sha256=KTvUtuarOOYu6PHN6H1vcy4W9xilwtZE08n7JSrk8Cs,15414
+braindecode/datasets/sleep_physionet.py,sha256=jieRx6u-MQ4jn_5Zox_pVV8WjBwXKLv9uq4GXRAZ_58,4087
+braindecode/datasets/tuh.py,sha256=iG1hOtdevzKGEVpeuRFDBOnsW_rWa5zEmMFJfYR1hqg,22867
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+braindecode/datautil/__init__.py,sha256=53iVndXeqRYQ2k0S4qtjoMHYLqrrjIivYkUBgxT_wHw,1713
+braindecode/datautil/serialization.py,sha256=cqLn7H4NW_8O-Et-w7GoDMyCWuILZoV8LdqKGAGd13k,12574
+braindecode/datautil/util.py,sha256=ZfDoxLieKsgI8xcWQqebV-vJ5pJYRvRRHkEwhwpgoKU,674
+braindecode/functional/__init__.py,sha256=Jpp3A1OCdYoJ94y5VVDb9jjiimIcKk2RdrGnaOlh2cw,213
+braindecode/functional/functions.py,sha256=7HQHmGG-kk3VjPY5cE-XFK6_9Mlj0ZODbzYAlpcXW3U,8634
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{braindecode-0.8.dist-info → braindecode-1.0.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.41.3)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

{braindecode-0.8.dist-info → braindecode-1.0.0.dist-info/licenses}/LICENSE.txt

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2017-2020 Braindecode Developers
+Copyright (c) 2017-currently Braindecode Developers
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without modification,

braindecode-1.0.0.dist-info/licenses/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-0.8.dist-info/RECORD

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