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fixes to get docs building by github action #210

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Oct 27, 2022
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fixes to get docs building by github action #210

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0ce831c
fixes to get docs building by github action
pellet Oct 23, 2022
a0aa01e
reverted some changes
pellet Oct 25, 2022
bd4aaf4
Update 01r__ssvep_viz.py
JohnGriffiths Oct 27, 2022
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15 changes: 8 additions & 7 deletions .github/workflows/docs.yml
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Expand Up @@ -2,26 +2,27 @@ name: Docs

on:
push:
branches: [ master, develop, 'dev/*' ]
branches: [ '**' ]
pull_request:
branches: [ master, develop ]
branches: [ '**' ]

jobs:
build:
runs-on: ubuntu-18.04
runs-on: ubuntu-20.04
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3
- name: Set up Python
uses: actions/setup-python@v1
uses: actions/setup-python@v4
with:
python-version: 3.7
python-version: 3.8
- name: Install dependencies
run: |
python -m pip install --upgrade pip wheel
python -m pip install attrdict

# Install wxPython wheels since they are distribution-specific and therefore not on PyPI
# See: https://wxpython.org/pages/downloads/index.html
pip install -U -f https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-18.04 wxPython
pip install -f https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-20.04 wxPython

pip install .
- name: Build docs
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3 changes: 3 additions & 0 deletions .gitignore
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Expand Up @@ -14,3 +14,6 @@ examples/visual_cueing/*.csv
.coverage
coverage.xml
htmlcov

# PyCharm
.idea/
4 changes: 2 additions & 2 deletions examples/visual_cueing/01r__cueing_singlesub_analysis.py
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Expand Up @@ -132,7 +132,7 @@
# Left Cue
tfr, itc = tfr_morlet(epochs['LeftCue'], freqs=frequencies,
n_cycles=wave_cycles, return_itc=True)
tfr = tfr.apply_baseline([-1,-.5],mode='mean')
tfr = tfr.apply_baseline((-1,-.5),mode='mean')
tfr.plot(picks=[0], mode='logratio',
title='TP9 - Ipsi');
tfr.plot(picks=[1], mode='logratio',
Expand All @@ -143,7 +143,7 @@
# Right Cue
tfr, itc = tfr_morlet(epochs['RightCue'], freqs=frequencies,
n_cycles=wave_cycles, return_itc=True)
tfr = tfr.apply_baseline([-1,-.5],mode='mean')
tfr = tfr.apply_baseline((-1,-.5),mode='mean')
tfr.plot(picks=[0], mode='logratio',
title='TP9 - Contra');
tfr.plot(picks=[1], mode='logratio',
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4 changes: 2 additions & 2 deletions examples/visual_cueing/02r__cueing_group_analysis.py
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Expand Up @@ -123,7 +123,7 @@
# Left Cue
tfr, itc = tfr_morlet(epochs['LeftCue'], freqs=frequencies,
n_cycles=wave_cycles, return_itc=True)
tfr = tfr.apply_baseline([-1,-.5],mode='mean')
tfr = tfr.apply_baseline((-1,-.5),mode='mean')
#tfr.plot(picks=[0], mode='logratio',
# title='TP9 - Ipsi');
#tfr.plot(picks=[3], mode='logratio',
Expand All @@ -134,7 +134,7 @@
# Right Cue
tfr, itc = tfr_morlet(epochs['RightCue'], freqs=frequencies,
n_cycles=wave_cycles, return_itc=True)
tfr = tfr.apply_baseline([-1,-.5],mode='mean')
tfr = tfr.apply_baseline((-1,-.5),mode='mean')
#tfr.plot(picks=[0], mode='logratio',
# title='TP9 - Contra');
#tfr.plot(picks=[3], mode='logratio',
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4 changes: 2 additions & 2 deletions examples/visual_cueing/04r__cueing_group_analysis_winter2019.py
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Expand Up @@ -136,14 +136,14 @@
# Left Cue
tfr, itc = tfr_morlet(epochs['LeftCue'], freqs=frequencies,
n_cycles=wave_cycles, return_itc=True)
tfr = tfr.apply_baseline([-1,-.5],mode='mean')
tfr = tfr.apply_baseline((-1,-.5),mode='mean')
power_Ipsi_TP9 = tfr.data[0,:,:]
power_Contra_TP10 = tfr.data[1,:,:]

# Right Cue
tfr, itc = tfr_morlet(epochs['RightCue'], freqs=frequencies,
n_cycles=wave_cycles, return_itc=True)
tfr = tfr.apply_baseline([-1,-.5],mode='mean')
tfr = tfr.apply_baseline((-1,-.5),mode='mean')
power_Contra_TP9 = tfr.data[0,:,:]
power_Ipsi_TP10 = tfr.data[1,:,:]

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4 changes: 2 additions & 2 deletions examples/visual_cueing/CueingAnalysis_Colab.ipynb
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Expand Up @@ -434,7 +434,7 @@
"# Left Cue\n",
"tfr, itc = tfr_morlet(epochs['LeftCue'], freqs=frequencies, \n",
" n_cycles=wave_cycles, return_itc=True)\n",
"tfr = tfr.apply_baseline([-1,-.5],mode='mean')\n",
"tfr = tfr.apply_baseline((-1,-.5),mode='mean')\n",
"tfr.plot(picks=[0], mode='logratio', \n",
" title='TP9 - Ipsi');\n",
"tfr.plot(picks=[1], mode='logratio', \n",
Expand All @@ -445,7 +445,7 @@
"# Right Cue\n",
"tfr, itc = tfr_morlet(epochs['RightCue'], freqs=frequencies, \n",
" n_cycles=wave_cycles, return_itc=True)\n",
"tfr = tfr.apply_baseline([-1,-.5],mode='mean')\n",
"tfr = tfr.apply_baseline((-1,-.5),mode='mean')\n",
"tfr.plot(picks=[0], mode='logratio', \n",
" title='TP9 - Contra');\n",
"tfr.plot(picks=[1], mode='logratio', \n",
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4 changes: 2 additions & 2 deletions examples/visual_cueing/CueingGroupAnalysis_Colab.ipynb
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Expand Up @@ -215,7 +215,7 @@
" # Left Cue\n",
" tfr, itc = tfr_morlet(epochs['LeftCue'], freqs=frequencies, \n",
" n_cycles=wave_cycles, return_itc=True)\n",
" tfr = tfr.apply_baseline([-1,-.5],mode='mean')\n",
" tfr = tfr.apply_baseline((-1,-.5),mode='mean')\n",
" #tfr.plot(picks=[0], mode='logratio', \n",
" # title='TP9 - Ipsi');\n",
" #tfr.plot(picks=[3], mode='logratio', \n",
Expand All @@ -226,7 +226,7 @@
" # Right Cue\n",
" tfr, itc = tfr_morlet(epochs['RightCue'], freqs=frequencies, \n",
" n_cycles=wave_cycles, return_itc=True)\n",
" tfr = tfr.apply_baseline([-1,-.5],mode='mean')\n",
" tfr = tfr.apply_baseline((-1,-.5),mode='mean')\n",
" #tfr.plot(picks=[0], mode='logratio', \n",
" # title='TP9 - Contra');\n",
" #tfr.plot(picks=[3], mode='logratio', \n",
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4 changes: 2 additions & 2 deletions examples/visual_cueing/CueingGroupAnalysis_Colab_Winter2019.ipynb
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Expand Up @@ -215,14 +215,14 @@
" # Left Cue\n",
" tfr, itc = tfr_morlet(epochs['LeftCue'], freqs=frequencies, \n",
" n_cycles=wave_cycles, return_itc=True)\n",
" tfr = tfr.apply_baseline([-1,-.5],mode='mean')\n",
" tfr = tfr.apply_baseline((-1,-.5),mode='mean')\n",
" power_Ipsi_TP9 = tfr.data[0,:,:]\n",
" power_Contra_TP10 = tfr.data[1,:,:]\n",
"\n",
" # Right Cue\n",
" tfr, itc = tfr_morlet(epochs['RightCue'], freqs=frequencies, \n",
" n_cycles=wave_cycles, return_itc=True)\n",
" tfr = tfr.apply_baseline([-1,-.5],mode='mean')\n",
" tfr = tfr.apply_baseline((-1,-.5),mode='mean')\n",
" power_Contra_TP9 = tfr.data[0,:,:]\n",
" power_Ipsi_TP10 = tfr.data[1,:,:]\n",
"\n",
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4 changes: 2 additions & 2 deletions examples/visual_cueing/cueing.ipynb
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Expand Up @@ -529,7 +529,7 @@
"# Left Cue\n",
"tfr, itc = tfr_morlet(epochs['LeftCue'], freqs=frequencies, \n",
" n_cycles=wave_cycles, return_itc=True)\n",
"tfr = tfr.apply_baseline([-1,-.5],mode='mean')\n",
"tfr = tfr.apply_baseline((-1,-.5),mode='mean')\n",
"tfr.plot(picks=[0], mode='logratio', \n",
" title='TP9 - Ipsi');\n",
"tfr.plot(picks=[1], mode='logratio', \n",
Expand All @@ -540,7 +540,7 @@
"# Right Cue\n",
"tfr, itc = tfr_morlet(epochs['RightCue'], freqs=frequencies, \n",
" n_cycles=wave_cycles, return_itc=True)\n",
"tfr = tfr.apply_baseline([-1,-.5],mode='mean')\n",
"tfr = tfr.apply_baseline((-1,-.5),mode='mean')\n",
"tfr.plot(picks=[0], mode='logratio', \n",
" title='TP9 - Contra');\n",
"tfr.plot(picks=[1], mode='logratio', \n",
Expand Down
4 changes: 2 additions & 2 deletions examples/visual_cueing/cueing_group_analysis.ipynb
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Expand Up @@ -225,7 +225,7 @@
" # Left Cue\n",
" tfr, itc = tfr_morlet(epochs['LeftCue'], freqs=frequencies, \n",
" n_cycles=wave_cycles, return_itc=True)\n",
" tfr = tfr.apply_baseline([-1,-.5],mode='mean')\n",
" tfr = tfr.apply_baseline((-1,-.5),mode='mean')\n",
" #tfr.plot(picks=[0], mode='logratio', \n",
" # title='TP9 - Ipsi');\n",
" #tfr.plot(picks=[3], mode='logratio', \n",
Expand All @@ -236,7 +236,7 @@
" # Right Cue\n",
" tfr, itc = tfr_morlet(epochs['RightCue'], freqs=frequencies, \n",
" n_cycles=wave_cycles, return_itc=True)\n",
" tfr = tfr.apply_baseline([-1,-.5],mode='mean')\n",
" tfr = tfr.apply_baseline((-1,-.5),mode='mean')\n",
" #tfr.plot(picks=[0], mode='logratio', \n",
" # title='TP9 - Contra');\n",
" #tfr.plot(picks=[3], mode='logratio', \n",
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4 changes: 2 additions & 2 deletions examples/visual_cueing/cueing_loop.ipynb
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Expand Up @@ -601,7 +601,7 @@
" # Left Cue\n",
" tfr, itc = tfr_morlet(epochs['LeftCue'], freqs=frequencies, \n",
" n_cycles=wave_cycles, return_itc=True)\n",
" tfr = tfr.apply_baseline([-1,-.5],mode='mean')\n",
" tfr = tfr.apply_baseline((-1,-.5),mode='mean')\n",
" #tfr.plot(picks=[0], mode='logratio', \n",
" # title='TP9 - Ipsi');\n",
" #tfr.plot(picks=[3], mode='logratio', \n",
Expand All @@ -612,7 +612,7 @@
" # Right Cue\n",
" tfr, itc = tfr_morlet(epochs['RightCue'], freqs=frequencies, \n",
" n_cycles=wave_cycles, return_itc=True)\n",
" tfr = tfr.apply_baseline([-1,-.5],mode='mean')\n",
" tfr = tfr.apply_baseline((-1,-.5),mode='mean')\n",
" #tfr.plot(picks=[0], mode='logratio', \n",
" # title='TP9 - Contra');\n",
" #tfr.plot(picks=[3], mode='logratio', \n",
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5 changes: 3 additions & 2 deletions examples/visual_ssvep/01r__ssvep_viz.py
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Expand Up @@ -101,8 +101,9 @@
axs[0].plot(freq1, psd1_mean[[0, 3], :].mean(0), color='b', label='30 Hz')
axs[0].plot(freq2, psd2_mean[[0, 3], :].mean(0), color='r', label='20 Hz')

axs[1].plot(freq1, psd1_mean[4, :], color='b', label='30 Hz')
axs[1].plot(freq2, psd2_mean[4, :], color='r', label='20 Hz')
# TODO fix: IndexError: index 4 is out of bounds for axis 0 with size 4
# axs[1].plot(freq1, psd1_mean[4, :], color='b', label='30 Hz')
# axs[1].plot(freq2, psd2_mean[4, :], color='r', label='20 Hz')
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Commenting out these lines of code is out of the scope of "Fixing the Docs" and messes with a visualization for SSVEP. This should be reverted and changed in another PR.

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Unfortunately the docs won't build without the change, I think I noticed the same issue a long time ago when trying to run the example locally. Would you be able to help me figure out why it is giving the out of bounds error?

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The problem seems to be that this line

>> psd1, freq1 = psd_welch(epochs['30 Hz'], n_fft=1028, n_per_seg=256 * 3, picks='all')

Is returning only 4 chans in its output object, whereas in this example there are 5 chans used (i.e. a muse 2016 with one extra auxiliary electrode over occipital cortex).

>> psd1.shape
>> (105, 4, 129)

Trying to determine why this is happening...

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Ok got it: the channel type for the Aux electrode is not 'eeg'

In [83]: raw.ch_names
Out[83]: ['TP9', 'AF7', 'AF8', 'TP10', 'POz', 'stim']
In [82]: raw.get_channel_types()
Out[82]: ['eeg', 'eeg', 'eeg', 'eeg', 'misc', 'stim']

Easily fixed with

raw.set_channel_types({'POz': 'eeg'})

or something similar


axs[0].set_title('TP9 and TP10')
axs[1].set_title('POz')
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