Example for using to_data_frame method on EpochsTFR by eioe · Pull Request #9275 · mne-tools/mne-python

eioe · 2021-04-09T15:25:09Z

Related to PR #9124

To demonstrate possible usage of the to_data_frame method, I adapted an example that uses an EpochsTFR instance.
@dengemann WDYT?
@cbrnr since I'm mutilating your (very nice) example - you should have a veto before this goes out. 🙂
Thx!

Also, in the original PR I forgot to do the housekeeping in terms of updating latest.inc and names.inc. So I'm sneaking this in here.

update to v23dev

cbrnr · 2021-04-09T16:46:44Z

Will take a look next week!

eioe · 2021-04-09T17:00:19Z

tbh, I do not understand why it crashes building the docs now and the CircleCI output is unclear to me. Can you maybe help @drammock ?

drammock · 2021-04-09T19:57:54Z

tbh, I do not understand why it crashes building the docs now and the CircleCI output is unclear to me. Can you maybe help @drammock ?

Looks like you're hit by the problem that @GuillaumeFavelier is trying to fix in #9274

eioe · 2021-04-10T13:00:26Z

ah yes, I see, thanks @drammock

eioe · 2021-04-15T10:44:29Z

@cbrnr fyi, building the docs now worked. If you want you can take a look at the rendered result here:
https://27276-1301584-gh.circle-artifacts.com/0/dev/auto_examples/time_frequency/plot_time_frequency_erds.html
I'm all open for any kind of suggestions.

examples/time_frequency/plot_time_frequency_erds.py

Co-authored-by: Daniel McCloy <dan@mccloy.info>

cbrnr · 2021-04-21T12:24:22Z

@eioe can you ping me once you've resolved @drammock's comments? Then I will take a look.

…into tfr_todf_example

eioe · 2021-04-22T14:06:56Z

@drammock I implemented all requested changes. Unfortunately, there's now a merging conflict that I don't understand. Can you point me into a direction how to fix it?

drammock · 2021-04-22T14:20:21Z

@drammock I implemented all requested changes. Unfortunately, there's now a merging conflict that I don't understand. Can you point me into a direction how to fix it?

probably related to #9292. All the examples/tutorials were renamed to no longer have filenames that start with plot_ (they originally did so because of a default setting in sphinx-gallery). You'll need to put your changes into the newly-renamed file and delete the old plot_* file.

examples/time_frequency/plot_time_frequency_erds.py

drammock

ok @eioe, I think this is my last round of comments! This is looking really good.

examples/time_frequency/time_frequency_erds.py

eioe · 2021-04-23T14:11:47Z

@drammock thanks again for the in-depth review and all the constructive suggestions. Learned a lot.
I implemented all of them.
Only, the original figures of the tutorial (the TFR plots) are now very small. I tried a lot to change their size (figsize=(...), fig.set_size_inches(...), fig.tight_layout(), fig.adjust_subplots(...), and various combinations) but without success. So I put it back in it's original state. Help is appreciated.
Running time of the script on CircleCI seems to be ~24s - if I interpret that correctly. Is that too long for an example? (Original version, before my changes, was at 7s. 😐 )

drammock · 2021-04-23T15:57:21Z

the original figures of the tutorial (the TFR plots) are now very small.

This was not caused by you; they are small in the current website too: https://mne.tools/dev/auto_examples/time_frequency/time_frequency_erds.html (they look bigger in the stable docs because that site has a wider width for the main content of the page).

This happens because if a code cell generates more than 1 figure, sphinx-gallery will always put them into two columns. If you want to force plots to be full width instead of side-by-side, you can do something like this:

fig1 = raw.plot()

###############################################################################

fig2 = raw.plot_psd()

That approach is harder with the code cell in this example because the 2 figures are generated by iterations of a for-loop, so you can't easily separate out the second plotting call from the first one.

@cbrnr I'm happy with this one, your turn to review/merge :)

cbrnr

Very nice addition and beautiful plots! I have a couple of (minor) comments that I think should be addressed before merging.

examples/time_frequency/time_frequency_erds.py

cbrnr · 2021-04-23T16:51:20Z

examples/time_frequency/time_frequency_erds.py

+df['channel'].cat.reorder_categories(['C3', 'Cz', 'C4'], ordered=True,
+                                     inplace=True)


Why does this need to be an ordered categorial variable? There isn't really any order imposed by the channels so I was wondering if we could drop ordered=True and it still works (I assume you want to change the alphabetical order). Can you try?

It is actually already a categorical variable (this happens automatically in our dataframe export code), here we're just changing the order. it determines what order the columns appear in the seaborn FacetGrid. To me it made sense to have Cz in the middle.

That was also my thinking - also for consistency with the time-freq plots above. I suggest keeping it in this order but can of course also take it out. Your call @cbrnr 🙂

examples/time_frequency/time_frequency_erds.py

cbrnr · 2021-04-23T16:56:45Z

examples/time_frequency/time_frequency_erds.py

+def map_bands(freq):
+    for band, (low_lim, high_lim) in freq_bands.items():
+        if low_lim <= freq <= high_lim:
+            return band
+
+
+df['band'] = pd.Categorical(
+    df['freq'].map(map_bands),
+    categories=['beta', 'alpha', 'theta', 'delta'],
+    ordered=True)


Could this binning be simplified with https://pandas.pydata.org/docs/reference/api/pandas.cut.html?

yes! I knew there was a function for that but I couldn't remember its name.

Ok, I'm doing this now:

freq_bounds = {'_': 0, 'delta': 3, 'theta': 7, 'alpha': 13, 'beta': 35, 'gamma': 140} df['band'] = pd.cut(df['freq'], list(freq_bounds.values()), labels=list(freq_bounds.keys())[1:])

wdyt?

list(freq_bounds.keys()) is the same as list(freq_bounds), FYI. Otherwise looks fine

actually looking at the rendering on CircleCI I wonder if you got the call to pd.cut correct? there's an empty row at the bottom of the plot and the top row looks really noisy.

argh, that's what you get when "quickly finishing something friday night" ... thanks for spotting.

there's an empty row at the bottom of the plot

Putting this fixed the empty row for gamma frequencies:
df['band'] = df['band'].cat.remove_unused_categories()

the top row looks really noisy

I think, that's because now only two freqs (2 & 3 Hz) go into this plot and the # of reps for the CI bootstrap is very low. It's a tiny bit better with 3 freqs (aka, having the boundary between delta and theta at 4 Hz instead) - but not so much.
I think that the actual call to to pd.cut is ok. I also tested it against the previous mapping method. Results were identical.

examples/time_frequency/time_frequency_erds.py

cbrnr · 2021-04-23T16:59:50Z

examples/time_frequency/time_frequency_erds.py

+g = sns.FacetGrid(df_mean, col='condition', col_order=['hands', 'feet'],
+                  margin_titles=True)
+g = (g.map(sns.violinplot, 'channel', 'value', 'band', n_boot=10,
+           palette='deep', order=['C3', 'Cz', 'C4'],
+           hue_order=['delta', 'theta', 'alpha', 'beta'])
+      .add_legend(ncol=4, loc='lower center'))
+
+g.map(plt.axhline, **axline_kw)
+g.set_axis_labels("", "ERDS (%)")
+g.set_titles(col_template="{col_name}", row_template="{row_name}")
+g.fig.subplots_adjust(left=0.1, right=0.9, top=0.9, bottom=0.3)


The violins are kind of hard to see - can you maybe disable their black outlines (and use no outline instead)?

I decreased the linewidth. Looks better to me than no outline at all. Agree? (Lates CircleCI rendering)

fix doc string layout Co-authored-by: Clemens Brunner <clemens.brunner@gmail.com>

Co-authored-by: Clemens Brunner <clemens.brunner@gmail.com>

…example

eioe · 2021-04-23T20:24:33Z

Thanks @cbrnr for the review. Fixes, comments and suggestions are commited.

drammock · 2021-04-23T21:44:10Z

CircleCI failure is real:

/home/circleci/project/doc/auto_examples/time_frequency/time_frequency_erds.rst:503: WARNING: py:obj reference target not found: time_format=None

probably you used single-backticks but needed 2 backticks on each side.

larsoner · 2021-04-26T12:37:19Z

All looks good, thanks @eioe !

eioe added 4 commits March 1, 2021 17:46

Merge pull request #1 from mne-tools/main

9cb1bba

update to v23dev

extend ERDS example with df method

898061a

housekeeping for PR #9124

811c6b7

rm space

0e79192

eioe changed the title ~~Tfr todf example~~ [WIP] example for using to_data_frame method on EpochsTFR Apr 9, 2021

Merge branch 'main' into tfr_todf_example

18389b0

eioe mentioned this pull request Apr 16, 2021

ENH: add to_data_frame method to EpochsTFR #9124

Merged

eioe changed the title ~~[WIP] example for using to_data_frame method on EpochsTFR~~ Example for using to_data_frame method on EpochsTFR Apr 16, 2021

eioe marked this pull request as ready for review April 16, 2021 09:05

Merge branch 'main' into tfr_todf_example

04135b0

cbrnr added this to the 0.23 milestone Apr 19, 2021

drammock requested changes Apr 19, 2021

View reviewed changes

eioe and others added 2 commits April 21, 2021 13:13

improve doc

aa7f9dd

Co-authored-by: Daniel McCloy <dan@mccloy.info>

improve code stringency

a8f6986

Co-authored-by: Daniel McCloy <dan@mccloy.info>

eioe added 3 commits April 22, 2021 13:18

refactor plotting to use FacetGrid

26fa0d5

Merge remote-tracking branch 'origin' into tfr_todf_example

40ea0aa

Merge branch 'tfr_todf_example' of https://github.com/eioe/mne-python …

3e0c6cf

…into tfr_todf_example

drammock reviewed Apr 22, 2021

View reviewed changes

examples/time_frequency/plot_time_frequency_erds.py Outdated Show resolved Hide resolved

eioe added 4 commits April 22, 2021 18:18

refactor using FacetGrid; rename file

4246f04

change filename

f7a84bc

Merge branch 'main' into tfr_todf_example

b831d83

test

f3683ca

drammock approved these changes Apr 22, 2021

View reviewed changes

eioe added 2 commits April 23, 2021 10:52

improve plotting

e8b4ea5

move legend

28fffb6

cbrnr requested changes Apr 23, 2021

View reviewed changes

eioe and others added 10 commits April 23, 2021 19:11

Update examples/time_frequency/time_frequency_erds.py

ae9a036

fix doc string layout Co-authored-by: Clemens Brunner <clemens.brunner@gmail.com>

rework text

2ba1665

Co-authored-by: Clemens Brunner <clemens.brunner@gmail.com>

rework text

db80779

Co-authored-by: Clemens Brunner <clemens.brunner@gmail.com>

fix spelling

b14a8b3

Co-authored-by: Clemens Brunner <clemens.brunner@gmail.com>

fix length block splitters

7fd38d8

add explanation for time_format=None

d373d2d

Merge branch 'main' into tfr_todf_example

7605768

change binning

d69bdf0

Merge remote-tracking branch 'origin/tfr_todf_example' into tfr_todf_…

9b68ecb

…example

thinner violin outlines

b5a3c46

eioe added 2 commits April 24, 2021 14:20

remove empty plots

778d60c

fix doc

d01e4da

larsoner merged commit dece679 into mne-tools:main Apr 26, 2021

		df['channel'].cat.reorder_categories(['C3', 'Cz', 'C4'], ordered=True,
		inplace=True)

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eioe commented Apr 9, 2021

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cbrnr commented Apr 9, 2021

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eioe commented Apr 9, 2021

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drammock commented Apr 9, 2021

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eioe commented Apr 10, 2021

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