Initial commit

Author: v0lta

.flake8

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+#########################
+# Flake8 Configuration  #
+# (.flake8)             #
+#########################
+[flake8]
+ignore =
+    # asserts are ok when testing.
+    S101
+    # pickle
+    S301
+    # pickle
+    S403
+    S404
+    S603
+    # Line break before binary operator (flake8 is wrong)
+    W503
+    # Ignore the spaces black puts before columns.
+    E203
+    # allow path extensions for testing.
+    E402
+    DAR101
+    DAR201
+    # flake and pylance disagree on linebreaks in strings.
+    N400
+exclude =
+    .tox,
+    .git,
+    __pycache__,
+    docs/source/conf.py,
+    build,
+    dist,
+    tests/fixtures/*,
+    *.pyc,
+    *.bib,
+    *.egg-info,
+    .cache,
+    .eggs,
+    data.
+max-line-length = 120
+max-complexity = 20
+import-order-style = pycharm
+application-import-names =
+    seleqt
+    tests

.github/workflows/test.yml

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+name: Tests
+
+on: [ push, pull_request ]
+
+jobs:
+  lint:
+    name: Lint
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.10.8]
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: pip install nox
+      - name: Run flake8
+        run: nox -s lint
+      - name: Run mypy
+        run: nox -s typing

.gitignore

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+*.mat
+.vscode/
+.pytest_cache/
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/

README.md

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+# Exercise: Brain-Wave decoding with Convnets
+
+In this exercise we will apply CNN to decode Brain-Wave or EEG data.
+The data-set was recorded at the University of Freiburg and appeared in [Deep learning with convolutional neural networks for EEG decoding and visualization](https://onlinelibrary.wiley.com/doi/10.1002/hbm.23730).
+The authors describe it as follows:
+
+"Our “High-Gamma Dataset” is a 128-electrode dataset of which we later only use 44 sensors covering the
+motor cortex, (see Section 2.7.1), obtained from 14 healthy subjects (6 female, 2 left-handed, age $27.2\pm3.6$
+(mean $\pm$ std)) with roughly 1000 ($963.1\pm150.9$, mean $\pm$ std) four-second trials of executed movements divided
+into 13 runs per subject. The four classes of movements were movements of either the left hand, the right
+hand, both feet, and rest (no movement, but same type of visual cue as for the other classes)."
+
+
+### Setting up dependencies.
+Let's set up a conda environment for this exercise.
+Assuming conda is installed, please run:
+
+```bash
+conda create --name braindecode python=3.9
+```
+Activate the environment:
+``` bash
+conda activate braindecode
+```
+Install the exercise dependencies:
+``` bash
+pip install -r requirements.txt
+```
+
+
+
+### Getting the data
+
+The dataset is available [online](https://gin.g-node.org/robintibor/high-gamma-dataset). We have prepared a download script for you.
+To get the data run
+```bash
+cd data
+python download.py
+```
+Be patient. The script will take approximately an hour to complete.
+Run `nox -s test` to check if the data-loading works properly.
+The plot below shows the first four EEG sensors of a recording.
+
+![EEG-signal example](./figures/eeg-signal-example.png)
+
+Examine the data yourself.
+
+## Your task:
+Train a CNN to recognize the four actions given only the EEG data.
+Preprocessing code from the paper-authors is already ready for in `src/util.py`. To get started have a look at `src/train_brain_decoder.py` and load the data via:
+```python
+    from src.load_eeg import load_train_valid_test
+    low_cut_hz = 0
+    subject_id = 1
+
+    train_filename = os.path.join('./data', 'train/{:d}.mat'.format(subject_id))
+    test_filename = os.path.join('./data',
+                            'test/{:d}.mat'.format(subject_id))
+
+    # Create the dataset
+    train_set, valid_set, test_set = load_train_valid_test(
+        train_filename=train_filename, test_filename=test_filename,
+        low_cut_hz=low_cut_hz)
+
+```
+
+Use as much of your code from the last two days as possible. You can re-use your image-processing code treating the EEG signals as tensors with and 44 "color"-channels and a time dimension. Implement your solution in `src/train_brain_decoder.py`. Implement everything marked with a `TODO`.
+
+What happens if you train and test on two different study-participants?
+
+Solution for participant 1:
+
+![accuracy-plot](./figures/brain_decode_accuracy.png)

data/download.py

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+from tqdm import tqdm
+import urllib.request
+from pathlib import Path
+
+data_location = 'https://gin.g-node.org/robintibor/high-gamma-dataset/raw/master/data/'
+
+files = [str(i)+'.mat' for i in range(1,15)]
+train_files = [(data_location + 'train/' + file, 'train/' + file) for file in files]
+test_files = [(data_location + 'test/' + file, 'test/' + file) for file in files]
+
+
+
+def load_and_store(file_list):
+    for online_path, local_path in tqdm(file_list, desc='downloading'):
+        urllib.request.urlretrieve(online_path, local_path)
+
+print('dowloading... this will take a while. Please be patient.')
+Path("train/").mkdir(exist_ok=True)
+load_and_store(train_files)
+print('downloading test data.')
+Path("test/").mkdir(exist_ok=True)
+load_and_store(test_files)

figures/brain_decode_accuracy.png

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+"""This module implements our CI function calls."""
+
+import nox
+
+
+@nox.session(name="test")
+def run_test(session):
+    """Run pytest."""
+    session.install("-r", "requirements.txt")
+    session.run("pytest")
+    session.install("pytest")
+
+
+@nox.session(name="testgit")
+def run_test_git(session):
+    """Run pytest."""
+    session.install("-r", "requirements.txt")
+    session.install("pytest")
+    session.run("pytest", "./tests/test_brain_decoder.py", "./tests/test_function.py")
+
+
+@nox.session(name="lint")
+def lint(session):
+    """Check code conventions."""
+    session.install("flake8==4.0.1")
+    session.install(
+        "flake8-black",
+        "flake8-docstrings",
+        "flake8-bugbear",
+        "flake8-broken-line",
+        "pep8-naming",
+        "pydocstyle",
+        "darglint",
+    )
+    session.install("bandit==1.7.2")
+    session.run("flake8", "src/train_brain_decoder.py", "tests", "noxfile.py")
+
+
+@nox.session(name="typing")
+def mypy(session):
+    """Check type hints."""
+    session.install("-r", "requirements.txt")
+    session.install("mypy")
+    session.run(
+        "mypy",
+        "--install-types",
+        "--non-interactive",
+        "--ignore-missing-imports",
+        "--no-strict-optional",
+        "--no-warn-return-any",
+        "--implicit-reexport",
+        "--allow-untyped-calls",
+        "src/train_brain_decoder.py",
+    )
+
+
+@nox.session(name="format")
+def format(session):
+    """Fix common convention problems automatically."""
+    session.install("black")
+    session.install("isort")
+    session.run("isort", "src", "tests", "noxfile.py")
+    session.run("black", "src", "tests", "noxfile.py")