plot_artifacts_correction_ica.py

"""

.. _tut_artifacts_correct_ica:

Artifact Correction with ICA
============================

ICA finds directions in the feature space
corresponding to projections with high non-Gaussianity. We thus obtain
a decomposition into independent components, and the artifact's contribution
is localized in only a small number of components.
These components have to be correctly identified and removed.

If EOG or ECG recordings are available, they can be used in ICA to
automatically select the corresponding artifact components from the
decomposition. To do so, you have to first build an Epoch object around
blink or heartbeat event.
"""

import numpy as np

import mne
from mne.datasets import sample

from mne.preprocessing import ICA
from mne.preprocessing import create_eog_epochs, create_ecg_epochs

# getting some data ready
data_path = sample.data_path()
raw_fname = data_path + '/MEG/sample/sample_audvis_filt-0-40_raw.fif'

raw = mne.io.read_raw_fif(raw_fname, preload=True)
# 1Hz high pass is often helpful for fitting ICA
raw.filter(1., 40., n_jobs=2, fir_design='firwin')

picks_meg = mne.pick_types(raw.info, meg=True, eeg=False, eog=False,
                           stim=False, exclude='bads')

###############################################################################
# Before applying artifact correction please learn about your actual artifacts
# by reading :ref:`tut_artifacts_detect`.

###############################################################################
# Fit ICA
# -------
#
# ICA parameters:

n_components = 25  # if float, select n_components by explained variance of PCA
method = 'fastica'  # for comparison with EEGLAB try "extended-infomax" here
decim = 3  # we need sufficient statistics, not all time points -> saves time

# we will also set state of the random number generator - ICA is a
# non-deterministic algorithm, but we want to have the same decomposition
# and the same order of components each time this tutorial is run
random_state = 23

###############################################################################
# Define the ICA object instance
ica = ICA(n_components=n_components, method=method, random_state=random_state)
print(ica)

###############################################################################
# we avoid fitting ICA on crazy environmental artifacts that would
# dominate the variance and decomposition
reject = dict(mag=5e-12, grad=4000e-13)
ica.fit(raw, picks=picks_meg, decim=decim, reject=reject)
print(ica)

###############################################################################
# Plot ICA components

ica.plot_components()  # can you spot some potential bad guys?


###############################################################################
# Component properties
# --------------------
#
# Let's take a closer look at properties of first three independent components.

# first, component 0:
ica.plot_properties(raw, picks=0)

###############################################################################
# we can see that the data were filtered so the spectrum plot is not
# very informative, let's change that:
ica.plot_properties(raw, picks=0, psd_args={'fmax': 35.})

###############################################################################
# we can also take a look at multiple different components at once:
ica.plot_properties(raw, picks=[1, 2], psd_args={'fmax': 35.})

###############################################################################
# Instead of opening individual figures with component properties, we can
# also pass an instance of Raw or Epochs in ``inst`` arument to
# ``ica.plot_components``. This would allow us to open component properties
# interactively by clicking on individual component topomaps. In the notebook
# this woks only when running matplotlib in interactive mode (``%matplotlib``).

# uncomment the code below to test the inteactive mode of plot_components:
# ica.plot_components(picks=range(10), inst=raw)

###############################################################################
# Advanced artifact detection
# ---------------------------
#
# Let's use a more efficient way to find artefacts

eog_average = create_eog_epochs(raw, reject=dict(mag=5e-12, grad=4000e-13),
                                picks=picks_meg).average()

# We simplify things by setting the maximum number of components to reject
n_max_eog = 1  # here we bet on finding the vertical EOG components
eog_epochs = create_eog_epochs(raw, reject=reject)  # get single EOG trials
eog_inds, scores = ica.find_bads_eog(eog_epochs)  # find via correlation

ica.plot_scores(scores, exclude=eog_inds)  # look at r scores of components
# we can see that only one component is highly correlated and that this
# component got detected by our correlation analysis (red).

ica.plot_sources(eog_average, exclude=eog_inds)  # look at source time course

###############################################################################
# We can take a look at the properties of that component, now using the
# data epoched with respect to EOG events.
# We will also use a little bit of smoothing along the trials axis in the
# epochs image:
ica.plot_properties(eog_epochs, picks=eog_inds, psd_args={'fmax': 35.},
                    image_args={'sigma': 1.})

###############################################################################
# That component is showing a prototypical average vertical EOG time course.
#
# Pay attention to the labels, a customized read-out of the
# ``mne.preprocessing.ICA.labels_``:
print(ica.labels_)

###############################################################################
# These labels were used by the plotters and are added automatically
# by artifact detection functions. You can also manually edit them to annotate
# components.
#
# Now let's see how we would modify our signals if we removed this component
# from the data
ica.plot_overlay(eog_average, exclude=eog_inds, show=False)
# red -> before, black -> after. Yes! We remove quite a lot!

# to definitely register this component as a bad one to be removed
# there is the ``ica.exclude`` attribute, a simple Python list
ica.exclude.extend(eog_inds)

# from now on the ICA will reject this component even if no exclude
# parameter is passed, and this information will be stored to disk
# on saving

# uncomment this for reading and writing
# ica.save('my-ica.fif')
# ica = read_ica('my-ica.fif')

###############################################################################
# Exercise: find and remove ECG artifacts using ICA!
ecg_epochs = create_ecg_epochs(raw, tmin=-.5, tmax=.5)
ecg_inds, scores = ica.find_bads_ecg(ecg_epochs, method='ctps')
ica.plot_properties(ecg_epochs, picks=ecg_inds, psd_args={'fmax': 35.})


###############################################################################
# What if we don't have an EOG channel?
# -------------------------------------
#
# We could either:
#
# 1. make a bipolar reference from frontal EEG sensors and use as virtual EOG
#    channel. This can be tricky though as you can only hope that the frontal
#    EEG channels only reflect EOG and not brain dynamics in the prefrontal
#    cortex.
# 2. go for a semi-automated approach, using template matching.
#
# In MNE-Python option 2 is easily achievable and it might give better results,
# so let's have a look at it.

from mne.preprocessing.ica import corrmap  # noqa

###############################################################################
# The idea behind corrmap is that artefact patterns are similar across subjects
# and can thus be identified by correlating the different patterns resulting
# from each solution with a template. The procedure is therefore
# semi-automatic. :func:`mne.preprocessing.corrmap` hence takes a list of
# ICA solutions and a template, that can be an index or an array.
#
# As we don't have different subjects or runs available today, here we will
# simulate ICA solutions from different subjects by fitting ICA models to
# different parts of the same recording. Then we will use one of the components
# from our original ICA as a template in order to detect sufficiently similar
# components in the simulated ICAs.
#
# The following block of code simulates having ICA solutions from different
# runs/subjects so it should not be used in real analysis - use independent
# data sets instead.

# We'll start by simulating a group of subjects or runs from a subject
start, stop = [0, len(raw.times) - 1]
intervals = np.linspace(start, stop, 4, dtype=int)
icas_from_other_data = list()
raw.pick_types(meg=True, eeg=False)  # take only MEG channels
for ii, start in enumerate(intervals):
    if ii + 1 < len(intervals):
        stop = intervals[ii + 1]
        print('fitting ICA from {0} to {1} seconds'.format(start, stop))
        this_ica = ICA(n_components=n_components, method=method).fit(
            raw, start=start, stop=stop, reject=reject)
        icas_from_other_data.append(this_ica)

###############################################################################
# Remember, don't do this at home! Start by reading in a collection of ICA
# solutions instead. Something like:
#
# ``icas = [mne.preprocessing.read_ica(fname) for fname in ica_fnames]``
print(icas_from_other_data)

###############################################################################
# We use our original ICA as reference.
reference_ica = ica

###############################################################################
# Investigate our reference ICA:
reference_ica.plot_components()

###############################################################################
# Which one is the bad EOG component?
# Here we rely on our previous detection algorithm. You would need to decide
# yourself if no automatic detection was available.
reference_ica.plot_sources(eog_average, exclude=eog_inds)

###############################################################################
# Indeed it looks like an EOG, also in the average time course.
#
# We construct a list where our reference run is the first element. Then we
# can detect similar components from the other runs (the other ICA objects)
# using :func:`mne.preprocessing.corrmap`. So our template must be a tuple like
# (reference_run_index, component_index):
icas = [reference_ica] + icas_from_other_data
template = (0, eog_inds[0])

###############################################################################
# Now we can run the CORRMAP algorithm.
fig_template, fig_detected = corrmap(icas, template=template, label="blinks",
                                     show=True, threshold=.8, ch_type='mag')

###############################################################################
# Nice, we have found similar ICs from the other (simulated) runs!
# In this way, you can detect a type of artifact semi-automatically for example
# for all subjects in a study.
# The detected template can also be retrieved as an array and stored; this
# array can be used as an alternative template to
# :func:`mne.preprocessing.corrmap`.
eog_component = reference_ica.get_components()[:, eog_inds[0]]

# If you calculate a new ICA solution, you can provide this array instead of
# specifying the template in reference to the list of ICA objects you want
# to run CORRMAP on. (Of course, the retrieved component map arrays can
# also be used for other purposes than artifact correction.)
#
# You can also use SSP to correct for artifacts. It is a bit simpler and
# faster but also less precise than ICA and requires that you know the event
# timing of your artifact.
# See :ref:`tut_artifacts_correct_ssp`.