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Extra filtering example #432

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merged 5 commits into from
Jan 24, 2022
Merged

Extra filtering example #432

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2a09c32
Extra filtering example
rob-luke Jan 24, 2022
10d11a3
Update environment.yml
rob-luke Jan 24, 2022
c89fb1a
Update github_actions_dependencies.sh
rob-luke Jan 24, 2022
07b0660
Update requirements_doc.txt
rob-luke Jan 24, 2022
d5e77ab
Update changelog.rst
rob-luke Jan 24, 2022
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2 changes: 1 addition & 1 deletion doc/changelog.rst
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Expand Up @@ -25,7 +25,7 @@ General

Enhancements

* Update SNIRF exporter to meet v1.0 validator requirements :meth:`mne_nirs.io.write_raw_snirf`. By `Robert Luke`_.
* Update SNIRF exporter to meet v1.0 validator requirements :meth:`mne_nirs.io.snirf.write_raw_snirf`. By `Robert Luke`_.
* Add ability to provide custom channel weighting in :meth:`mne_nirs.statistics.RegressionResults.to_dataframe_region_of_interest` computation. By `Robert Luke`_.


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2 changes: 1 addition & 1 deletion environment.yml
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Expand Up @@ -8,7 +8,7 @@ dependencies:
- scipy
- matplotlib
- numba
- pandas
- pandas==1.3.2
- xlrd
- scikit-learn
- h5py
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12 changes: 12 additions & 0 deletions examples/general/plot_30_frequency.py
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Expand Up @@ -199,6 +199,18 @@
fig.axes[0].set_title('')


# %%
# Filter Neural Signal
# ---------------------------------------------------------------------
#
# The effect of filtering on the neural signal is demonstrated below.
# The green line illustrates the signal before filtering, and the red line
# shows the signal after filtering.

fig = raw_haemo.plot_psd(average=True, fmax=2, xscale='log', color='r', show=False)
raw_haemo = raw_haemo.filter(l_freq=None, h_freq=0.4, h_trans_bandwidth=0.2)
raw_haemo.plot_psd(average=True, fmax=2, xscale='log', ax=fig.axes, color='g')


# %%
# Understanding the relation between stimulus presentation and response
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1 change: 0 additions & 1 deletion requirements_doc.txt
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Expand Up @@ -16,7 +16,6 @@ sphinx-multiversion
matplotlib
pillow
numpy
pandas
h5py
https://codeload.github.com/rob-luke/mne-bids/zip/nirs
lets-plot
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4 changes: 2 additions & 2 deletions tools/github_actions_dependencies.sh
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Expand Up @@ -14,8 +14,8 @@ else
pip install --progress-bar off --upgrade --pre --only-binary ":all:" python-dateutil pytz joblib threadpoolctl six
echo "PyQt5"
pip install --progress-bar off --upgrade --pre --only-binary ":all:" --no-deps --extra-index-url https://www.riverbankcomputing.com/pypi/simple PyQt5 PyQt5-sip PyQt5-Qt5
echo "NumPy/pandas etc."
pip install --progress-bar off --upgrade --pre --only-binary ":all:" --no-deps -i "https://pypi.anaconda.org/scipy-wheels-nightly/simple" numpy pandas "scikit-learn>=0.24.2" dipy
echo "NumPy etc."
pip install --progress-bar off --upgrade --pre --only-binary ":all:" --no-deps -i "https://pypi.anaconda.org/scipy-wheels-nightly/simple" numpy "scikit-learn>=0.24.2" dipy
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It's not great if you aren't testing --pre pandas, because it means the next time they cut a release user code will probably break. (You could require a specific version of pandas in setup.py, but then you could break someones' environment, which is worse than breaking one use case.)

Do you need help looking into the pandas issue here?

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Do you need help looking into the pandas issue here?

Yes please @larsoner I havent started digging yet, I was just focused on getting the CIs green first. but seems I may have made more issues than I solved. Thanks

echo "H5py, pillow, matplotlib"
pip install --progress-bar off --upgrade --pre --only-binary ":all:" --no-deps -f "https://7933911d6844c6c53a7d-47bd50c35cd79bd838daf386af554a83.ssl.cf2.rackcdn.com" h5py pillow matplotlib
echo "Numba, nilearn"
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