An easy-to-use platform for EEG experimentation in the classroom
patch pyodide
+79
-9
+7
-2
app/epics/pyodideEpics.ts
+7
-2
app/epics/pyodideEpics.ts
···
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plotTestPlot,
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saveEpochs,
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loadPyodide,
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loadPatches,
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applyPatches,
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loadUtils,
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} from '../utils/pyodide';
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import {
···
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tap(() => console.log('launching')),
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mergeMap(loadPyodide),
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tap((worker) => {
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console.log('loadPyodide completed, laoding utils');
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// loadUtils(worker);
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console.log('loadPyodide completed, loading patches');
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loadPatches(worker);
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applyPatches(worker);
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console.log('Now loading utils');
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loadUtils(worker);
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}),
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map(PyodideActions.SetPyodideWorker)
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);
+11
-1
app/utils/pyodide/index.ts
+11
-1
app/utils/pyodide/index.ts
···
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return freshWorker;
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};
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export const loadPatches = async (worker: Worker) =>
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worker.postMessage({
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data: readFileSync(path.join(__dirname, '/utils/pyodide/patches.py'), 'utf8'),
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});
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+
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export const applyPatches = async (worker: Worker) =>
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worker.postMessage({
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data: `apply_patches()`,
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});
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+
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export const loadUtils = async (worker: Worker) =>
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worker.postMessage({
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data: readFileSync(path.join(__dirname, '/utils/pyodide/utils.py'), 'utf8'),
···
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}
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// TODO: Figure out how to get image results from pyodide
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return worker.postMessage({
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data: `print('hello world')`,
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data: `import matplotlib.pyplot as plt; fig= plt.plot([1,2,3,4])`,
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});
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};
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+57
app/utils/pyodide/patches.py
+57
app/utils/pyodide/patches.py
···
1
+
# patch implemented in Pyolite
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# https://github.com/jupyterlite/jupyterlite/blob/0d563b9a4cca4b54411229128cb51ac4ba333c8f/packages/pyolite-kernel/py/pyolite/pyolite/patches.py
3
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def patch_matplotlib():
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import os
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from io import BytesIO
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+
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# before importing matplotlib
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# to avoid the wasm backend (which needs `js.document`, not available in worker)
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os.environ["MPLBACKEND"] = "AGG"
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+
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import matplotlib.pyplot
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from IPython.display import display
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+
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from .display import Image
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+
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_old_show = matplotlib.pyplot.show
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assert _old_show, "matplotlib.pyplot.show"
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+
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def show():
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buf = BytesIO()
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matplotlib.pyplot.savefig(buf, format="png")
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buf.seek(0)
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display(Image(buf.read()))
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matplotlib.pyplot.clf()
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+
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matplotlib.pyplot.show = show
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+
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+
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def patch_pillow():
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import base64
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from PIL import Image as PILImage
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_old_repr_png = PILImage.Image._repr_png_
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assert _old_repr_png
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+
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def _repr_png_(self):
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byte = _old_repr_png(self)
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return base64.b64encode(byte).decode("utf-8")
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PILImage.Image._repr_png_ = _repr_png_
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+
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+
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ALL_PATCHES = [
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patch_pillow,
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patch_matplotlib,
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]
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+
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+
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def apply_patches():
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import warnings
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+
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for patch in ALL_PATCHES:
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try:
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patch()
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except Exception as err:
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warnings.warn("faield to apply patch", patch, err)
+2
-4
app/utils/pyodide/utils.py
+2
-4
app/utils/pyodide/utils.py
···
12
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find_events, read_epochs, set_eeg_reference, viz)
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from mne.io import RawArray
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from io import StringIO
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-
from mne.channels import read_montage
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# plt.style.use(fivethirtyeight)
···
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# type of each channels
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ch_types = ['eeg'] * (len(ch_ind) - 1) + ['stim']
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montage = read_montage('standard_1005')
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# get data and exclude Aux channel
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data = data.values[:, ch_ind].T
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# create MNE object
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info = create_info(ch_names=ch_names, ch_types=ch_types,
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sfreq=sfreq, montage=montage)
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raw.append(RawArray(data=data, info=info))
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sfreq=sfreq)
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raw.append(RawArray(data=data, info=info).set_montage('standard_1005'))
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# concatenate all raw objects
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raws = concatenate_raws(raw)
+1
-1
app/utils/pyodide/webworker.js
+1
-1
app/utils/pyodide/webworker.js
···
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8
9
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async function loadPyodideAndPackages() {
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self.pyodide = await loadPyodide({ indexURL: './src/pyodide/' });
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await self.pyodide.loadPackage(['numpy']);
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await self.pyodide.loadPackage(['matplotlib', 'mne', 'pandas']);
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}
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let pyodideReadyPromise = loadPyodideAndPackages();
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14
+1
-1
internals/scripts/InstallPyodide.js
+1
-1
internals/scripts/InstallPyodide.js
···
6
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import url from 'url';
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import bz2 from 'unbzip2-stream';
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-
const PYODIDE_VERSION = '0.17.0';
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const PYODIDE_VERSION = '0.18.0';
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const TAR_NAME = `pyodide-build-${PYODIDE_VERSION}.tar.bz2`;
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const TAR_URL = `https://github.com/pyodide/pyodide/releases/download/${PYODIDE_VERSION}/pyodide-build-${PYODIDE_VERSION}.tar.bz2`;
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const PYODIDE_DIR = 'app/utils/pyodide/src/';