Within Session SSVEP

This Example show how to perform a within-session SSVEP analysis on the MAMEM dataset 3, using a CCA pipeline.

The within-session evaluation assesses the performance of a classification pipeline using a 5-fold cross-validation. The reported metric (here, accuracy) is the average of all fold.

# Authors: Sylvain Chevallier <sylvain.chevallier@uvsq.fr>
#
# License: BSD (3-clause)

import warnings

import matplotlib.pyplot as plt
import seaborn as sns
from sklearn.pipeline import make_pipeline

import moabb
from moabb.datasets import MAMEM3
from moabb.evaluations import WithinSessionEvaluation
from moabb.paradigms import SSVEP
from moabb.pipelines import SSVEP_CCA


warnings.simplefilter(action="ignore", category=FutureWarning)
warnings.simplefilter(action="ignore", category=RuntimeWarning)
moabb.set_log_level("info")

Out:

/home/runner/work/moabb/moabb/.venv/lib/python3.9/site-packages/seaborn/cm.py:1582: UserWarning: Trying to register the cmap 'rocket' which already exists.
  mpl_cm.register_cmap(_name, _cmap)
/home/runner/work/moabb/moabb/.venv/lib/python3.9/site-packages/seaborn/cm.py:1583: UserWarning: Trying to register the cmap 'rocket_r' which already exists.
  mpl_cm.register_cmap(_name + "_r", _cmap_r)
/home/runner/work/moabb/moabb/.venv/lib/python3.9/site-packages/seaborn/cm.py:1582: UserWarning: Trying to register the cmap 'mako' which already exists.
  mpl_cm.register_cmap(_name, _cmap)
/home/runner/work/moabb/moabb/.venv/lib/python3.9/site-packages/seaborn/cm.py:1583: UserWarning: Trying to register the cmap 'mako_r' which already exists.
  mpl_cm.register_cmap(_name + "_r", _cmap_r)
/home/runner/work/moabb/moabb/.venv/lib/python3.9/site-packages/seaborn/cm.py:1582: UserWarning: Trying to register the cmap 'icefire' which already exists.
  mpl_cm.register_cmap(_name, _cmap)
/home/runner/work/moabb/moabb/.venv/lib/python3.9/site-packages/seaborn/cm.py:1583: UserWarning: Trying to register the cmap 'icefire_r' which already exists.
  mpl_cm.register_cmap(_name + "_r", _cmap_r)
/home/runner/work/moabb/moabb/.venv/lib/python3.9/site-packages/seaborn/cm.py:1582: UserWarning: Trying to register the cmap 'vlag' which already exists.
  mpl_cm.register_cmap(_name, _cmap)
/home/runner/work/moabb/moabb/.venv/lib/python3.9/site-packages/seaborn/cm.py:1583: UserWarning: Trying to register the cmap 'vlag_r' which already exists.
  mpl_cm.register_cmap(_name + "_r", _cmap_r)
/home/runner/work/moabb/moabb/.venv/lib/python3.9/site-packages/seaborn/cm.py:1582: UserWarning: Trying to register the cmap 'flare' which already exists.
  mpl_cm.register_cmap(_name, _cmap)
/home/runner/work/moabb/moabb/.venv/lib/python3.9/site-packages/seaborn/cm.py:1583: UserWarning: Trying to register the cmap 'flare_r' which already exists.
  mpl_cm.register_cmap(_name + "_r", _cmap_r)
/home/runner/work/moabb/moabb/.venv/lib/python3.9/site-packages/seaborn/cm.py:1582: UserWarning: Trying to register the cmap 'crest' which already exists.
  mpl_cm.register_cmap(_name, _cmap)
/home/runner/work/moabb/moabb/.venv/lib/python3.9/site-packages/seaborn/cm.py:1583: UserWarning: Trying to register the cmap 'crest_r' which already exists.
  mpl_cm.register_cmap(_name + "_r", _cmap_r)

Loading Dataset

Load 2 subjects of MAMEM3 dataset

subj = [1, 3]
dataset = MAMEM3()
dataset.subject_list = subj

Choose Paradigm

We select the paradigm SSVEP, applying a bandpass filter (3-15 Hz) on the data and we keep only the first 3 classes, that is stimulation frequency of 6.66, 7.50 and 8.57 Hz.

paradigm = SSVEP(fmin=3, fmax=15, n_classes=3)

Create Pipelines

Use a Canonical Correlation Analysis classifier

interval = dataset.interval
freqs = paradigm.used_events(dataset)

pipeline = {}
pipeline["CCA"] = make_pipeline(SSVEP_CCA(interval=interval, freqs=freqs, n_harmonics=3))

Get Data (optional)

To get access to the EEG signals downloaded from the dataset, you could use dataset.get_data(subjects=[subject_id]) to obtain the EEG under MNE format, stored in a dictionary of sessions and runs. Otherwise, paradigm.get_data(dataset=dataset, subjects=[subject_id]) allows to obtain the EEG data in scikit format, the labels and the meta information. In paradigm.get_data, the EEG are preprocessed according to the paradigm requirement.

# sessions = dataset.get_data(subjects=[3])
# X, labels, meta = paradigm.get_data(dataset=dataset, subjects=[3])

Evaluation

The evaluation will return a DataFrame containing a single AUC score for each subject and pipeline.

overwrite = True  # set to True if we want to overwrite cached results

evaluation = WithinSessionEvaluation(
    paradigm=paradigm, datasets=dataset, suffix="examples", overwrite=overwrite
)
results = evaluation.process(pipeline)

print(results.head())

Out:

SSVEP MAMEM3-WithinSession:   0%|          | 0/2 [00:00<?, ?it/s]
SSVEP MAMEM3-WithinSession:  50%|#####     | 1/2 [00:18<00:18, 18.46s/it]
SSVEP MAMEM3-WithinSession: 100%|##########| 2/2 [00:37<00:00, 18.58s/it]
SSVEP MAMEM3-WithinSession: 100%|##########| 2/2 [00:37<00:00, 18.56s/it]
      score      time  samples  ... n_sessions       dataset  pipeline
0  0.688889  0.057410     45.0  ...          1  SSVEP MAMEM3       CCA
1  0.266667  0.056557     45.0  ...          1  SSVEP MAMEM3       CCA

[2 rows x 9 columns]

Plot Results

Here we plot the results, indicating the score for each subject

plt.figure()
sns.barplot(data=results, y="score", x="session", hue="subject", palette="viridis")
plot within session ssvep

Out:

<AxesSubplot:xlabel='session', ylabel='score'>

And the computation time in seconds

plt.figure()
ax = sns.barplot(data=results, y="time", x="session", hue="subject", palette="Reds")
ax.set_ylabel("Time (s)")
plt.show()
plot within session ssvep

Total running time of the script: ( 0 minutes 37.352 seconds)

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