# -*- coding: utf-8 -*-
"""
.. _tut-artifact-ica:

============================
Repairing artifacts with ICA
============================

This tutorial covers the basics of independent components analysis (ICA) and
shows how ICA can be used for artifact repair; an extended example illustrates
repair of ocular and heartbeat artifacts. For conceptual background on ICA, see
:ref:`this scikit-learn tutorial
<sphx_glr_auto_examples_decomposition_plot_ica_blind_source_separation.py>`.

We begin as always by importing the necessary Python modules and loading some
:ref:`example data <sample-dataset>`. Because ICA can be computationally
intense, we'll also crop the data to 60 seconds; and to save ourselves from
repeatedly typing ``mne.preprocessing`` we'll directly import a few functions
and classes from that submodule:
"""

# %%

import os
import mne
from mne.preprocessing import (ICA, create_eog_epochs, create_ecg_epochs,
                               corrmap)

sample_data_folder = mne.datasets.sample.data_path()
sample_data_raw_file = os.path.join(sample_data_folder, 'MEG', 'sample',
                                    'sample_audvis_filt-0-40_raw.fif')
raw = mne.io.read_raw_fif(sample_data_raw_file)
# Here we'll crop to 60 seconds and drop gradiometer channels for speed
raw.crop(tmax=60.).pick_types(meg='mag', eeg=True, stim=True, eog=True)
raw.load_data()

# %%
# .. note::
#     Before applying ICA (or any artifact repair strategy), be sure to observe
#     the artifacts in your data to make sure you choose the right repair tool.
#     Sometimes the right tool is no tool at all — if the artifacts are small
#     enough you may not even need to repair them to get good analysis results.
#     See :ref:`tut-artifact-overview` for guidance on detecting and
#     visualizing various types of artifact.
#
# What is ICA?
# ^^^^^^^^^^^^
#
# Independent components analysis (ICA) is a technique for estimating
# independent source signals from a set of recordings in which the source
# signals were mixed together in unknown ratios. A common example of this is
# the problem of `blind source separation`_: with 3 musical instruments playing
# in the same room, and 3 microphones recording the performance (each picking
# up all 3 instruments, but at varying levels), can you somehow "unmix" the
# signals recorded by the 3 microphones so that you end up with a separate
# "recording" isolating the sound of each instrument?
#
# It is not hard to see how this analogy applies to EEG/MEG analysis: there are
# many "microphones" (sensor channels) simultaneously recording many
# "instruments" (blinks, heartbeats, activity in different areas of the brain,
# muscular activity from jaw clenching or swallowing, etc). As long as these
# various source signals are `statistically independent`_ and non-gaussian, it
# is usually possible to separate the sources using ICA, and then re-construct
# the sensor signals after excluding the sources that are unwanted.
#
#
# ICA in MNE-Python
# ~~~~~~~~~~~~~~~~~
#
# .. admonition:: ICA and dimensionality reduction
#     :class: sidebar hint
#
#     If you want to perform ICA with *no* dimensionality reduction (other than
#     the number of Independent Components (ICs) given in ``n_components``, and
#     any subsequent exclusion of ICs you specify in ``ICA.exclude``), simply
#     pass ``n_components``.
#
#     However, if you *do* want to reduce dimensionality, consider this
#     example: if you have 300 sensor channels and you set ``n_components=50``
#     during instantiation and pass ``n_pca_components=None`` to
#     `~mne.preprocessing.ICA.apply`, then the the first 50
#     PCs are sent to the ICA algorithm (yielding 50 ICs), and during
#     reconstruction `~mne.preprocessing.ICA.apply` will use the 50 ICs
#     plus PCs number 51-300 (the full PCA residual). If instead you specify
#     ``n_pca_components=120`` in `~mne.preprocessing.ICA.apply`, it will
#     reconstruct using the 50 ICs plus the first 70 PCs in the PCA residual
#     (numbers 51-120), thus discarding the smallest 180 components.
#
#     **If you have previously been using EEGLAB**'s ``runica()`` and are
#     looking for the equivalent of its ``'pca', n`` option to reduce
#     dimensionality, set ``n_components=n`` during initialization and pass
#     ``n_pca_components=n`` to `~mne.preprocessing.ICA.apply`.
#
# MNE-Python implements three different ICA algorithms: ``fastica`` (the
# default), ``picard``, and ``infomax``. FastICA and Infomax are both in fairly
# widespread use; Picard is a newer (2017) algorithm that is expected to
# converge faster than FastICA and Infomax, and is more robust than other
# algorithms in cases where the sources are not completely independent, which
# typically happens with real EEG/MEG data. See
# :footcite:`AblinEtAl2018` for more information.
#
# The ICA interface in MNE-Python is similar to the interface in
# `scikit-learn`_: some general parameters are specified when creating an
# `~mne.preprocessing.ICA` object, then the `~mne.preprocessing.ICA` object is
# fit to the data using its `~mne.preprocessing.ICA.fit` method. The results of
# the fitting are added to the `~mne.preprocessing.ICA` object as attributes
# that end in an underscore (``_``), such as ``ica.mixing_matrix_`` and
# ``ica.unmixing_matrix_``. After fitting, the ICA component(s) that you want
# to remove must be chosen, and the ICA fit must then be applied to the
# `~mne.io.Raw` or `~mne.Epochs` object using the `~mne.preprocessing.ICA`
# object's `~mne.preprocessing.ICA.apply` method.
#
# As is typically done with ICA, the data are first scaled to unit variance and
# whitened using principal components analysis (PCA) before performing the ICA
# decomposition. This is a two-stage process:
#
# 1. To deal with different channel types having different units
#    (e.g., Volts for EEG and Tesla for MEG), data must be pre-whitened.
#    If ``noise_cov=None`` (default), all data of a given channel type is
#    scaled by the standard deviation across all channels. If ``noise_cov`` is
#    a `~mne.Covariance`, the channels are pre-whitened using the covariance.
# 2. The pre-whitened data are then decomposed using PCA.
#
# From the resulting principal components (PCs), the first ``n_components`` are
# then passed to the ICA algorithm if ``n_components`` is an integer number.
# It can also be a float between 0 and 1, specifying the **fraction** of
# explained variance that the PCs should capture; the appropriate number of
# PCs (i.e., just as many PCs as are required to explain the given fraction
# of total variance) is then passed to the ICA.
#
# After visualizing the Independent Components (ICs) and excluding any that
# capture artifacts you want to repair, the sensor signal can be reconstructed
# using the `~mne.preprocessing.ICA` object's
# `~mne.preprocessing.ICA.apply` method. By default, signal
# reconstruction uses all of the ICs (less any ICs listed in ``ICA.exclude``)
# plus all of the PCs that were not included in the ICA decomposition (i.e.,
# the "PCA residual"). If you want to reduce the number of components used at
# the reconstruction stage, it is controlled by the ``n_pca_components``
# parameter (which will in turn reduce the rank of your data; by default
# ``n_pca_components=None`` resulting in no additional dimensionality
# reduction). The fitting and reconstruction procedures and the
# parameters that control dimensionality at various stages are summarized in
# the diagram below:
#
#
# .. raw:: html
#
#    <a href=
#     "../../_images/graphviz-7483cb1cf41f06e2a4ef451b17f073dbe584ba30.png">
#
# .. graphviz:: ../../_static/diagrams/ica.dot
#    :alt: Diagram of ICA procedure in MNE-Python
#    :align: left
#
# .. raw:: html
#
#    </a>
#
# See the Notes section of the `~mne.preprocessing.ICA` documentation
# for further details. Next we'll walk through an extended example that
# illustrates each of these steps in greater detail.
#
# Example: EOG and ECG artifact repair
# ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
#
# Visualizing the artifacts
# ~~~~~~~~~~~~~~~~~~~~~~~~~
#
# Let's begin by visualizing the artifacts that we want to repair. In this
# dataset they are big enough to see easily in the raw data:

# pick some channels that clearly show heartbeats and blinks
regexp = r'(MEG [12][45][123]1|EEG 00.)'
artifact_picks = mne.pick_channels_regexp(raw.ch_names, regexp=regexp)
raw.plot(order=artifact_picks, n_channels=len(artifact_picks),
         show_scrollbars=False)

# %%
# We can get a summary of how the ocular artifact manifests across each channel
# type using `~mne.preprocessing.create_eog_epochs` like we did in the
# :ref:`tut-artifact-overview` tutorial:

eog_evoked = create_eog_epochs(raw).average()
eog_evoked.apply_baseline(baseline=(None, -0.2))
eog_evoked.plot_joint()

# %%
# Now we'll do the same for the heartbeat artifacts, using
# `~mne.preprocessing.create_ecg_epochs`:

ecg_evoked = create_ecg_epochs(raw).average()
ecg_evoked.apply_baseline(baseline=(None, -0.2))
ecg_evoked.plot_joint()

# %%
# Filtering to remove slow drifts
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
# Before we run the ICA, an important step is filtering the data to remove
# low-frequency drifts, which can negatively affect the quality of the ICA fit.
# The slow drifts are problematic because they reduce the independence of the
# assumed-to-be-independent sources (e.g., during a slow upward drift, the
# neural, heartbeat, blink, and other muscular sources will all tend to have
# higher values), making it harder for the algorithm to find an accurate
# solution. A high-pass filter with 1 Hz cutoff frequency is recommended.
# However, because filtering is a linear operation, the ICA solution found from
# the filtered signal can be applied to the unfiltered signal (see
# :footcite:`WinklerEtAl2015` for
# more information), so we'll keep a copy of the unfiltered
# `~mne.io.Raw` object around so we can apply the ICA solution to it
# later.

filt_raw = raw.copy().filter(l_freq=1., h_freq=None)

# %%
# Fitting ICA
# ~~~~~~~~~~~
#
# .. admonition:: Ignoring the time domain
#     :class: sidebar hint
#
#     The ICA algorithms implemented in MNE-Python find patterns across
#     channels, but ignore the time domain. This means you can compute ICA on
#     discontinuous `~mne.Epochs` or `~mne.Evoked` objects (not
#     just continuous `~mne.io.Raw` objects), or only use every Nth
#     sample by passing the ``decim`` parameter to ``ICA.fit()``.
#
# Now we're ready to set up and fit the ICA. Since we know (from observing our
# raw data) that the EOG and ECG artifacts are fairly strong, we would expect
# those artifacts to be captured in the first few dimensions of the PCA
# decomposition that happens before the ICA. Therefore, we probably don't need
# a huge number of components to do a good job of isolating our artifacts
# (though it is usually preferable to include more components for a more
# accurate solution). As a first guess, we'll run ICA with ``n_components=15``
# (use only the first 15 PCA components to compute the ICA decomposition) — a
# very small number given that our data has over 300 channels, but with the
# advantage that it will run quickly and we will able to tell easily whether it
# worked or not (because we already know what the EOG / ECG artifacts should
# look like).
#
# ICA fitting is not deterministic (e.g., the components may get a sign
# flip on different runs, or may not always be returned in the same order), so
# we'll also specify a `random seed`_ so that we get identical results each
# time this tutorial is built by our web servers.
#
# .. warning::
#
#     `~mne.Epochs` used for fitting ICA should not be
#     baseline-corrected. Because cleaning the data via ICA may
#     introduce DC offsets, we suggest to baseline correct your data
#     **after** cleaning (and not before), should you require
#     baseline correction.

ica = ICA(n_components=15, max_iter='auto', random_state=97)
ica.fit(filt_raw)
ica

# %%
# Some optional parameters that we could have passed to the
# `~mne.preprocessing.ICA.fit` method include ``decim`` (to use only
# every Nth sample in computing the ICs, which can yield a considerable
# speed-up) and ``reject`` (for providing a rejection dictionary for maximum
# acceptable peak-to-peak amplitudes for each channel type, just like we used
# when creating epoched data in the :ref:`tut-overview` tutorial).

# %%
# Looking at the ICA solution
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Now we can examine the ICs to see what they captured.
#
# Using :meth:`~mne.preprocessing.ICA.get_explained_variance_ratio`, we can
# retrieve the fraction of variance in the original data that is explained by
# our ICA components in the form of a dictionary:

explained_var_ratio = ica.get_explained_variance_ratio(filt_raw)
for channel_type, ratio in explained_var_ratio.items():
    print(
        f'Fraction of {channel_type} variance explained by all components: '
        f'{ratio}'
    )

# %%
# The values were calculated for all ICA components jointly, but separately for
# each channel type (here: magnetometers and EEG).
#
# We can also explicitly request for which component(s) and channel type(s) to
# perform the computation:
explained_var_ratio = ica.get_explained_variance_ratio(
    filt_raw,
    components=[0],
    ch_type='eeg'
)
# This time, print as percentage.
ratio_percent = round(100 * explained_var_ratio['eeg'])
print(
    f'Fraction of variance in EEG signal explained by first component: '
    f'{ratio_percent}%'
)

# %%
# `~mne.preprocessing.ICA.plot_sources` will show the time series of the
# ICs. Note that in our call to `~mne.preprocessing.ICA.plot_sources` we
# can use the original, unfiltered `~mne.io.Raw` object. A helpful tip is that
# right clicking (or control + click with a trackpad) on the name of the
# component will bring up a plot of its properties. In this plot, you can
# also toggle the channel type in the topoplot (if you have multiple channel
# types) with 't' and whether the spectrum is log-scaled or not with 'l'.

raw.load_data()
ica.plot_sources(raw, show_scrollbars=False)

# %%
# Here we can pretty clearly see that the first component (``ICA000``) captures
# the EOG signal quite well, and the second component (``ICA001``) looks a lot
# like `a heartbeat <qrs_>`_ (for more info on visually identifying Independent
# Components, `this EEGLAB tutorial`_ is a good resource). We can also
# visualize the scalp field distribution of each component using
# `~mne.preprocessing.ICA.plot_components`. These are interpolated based
# on the values in the ICA mixing matrix:

# sphinx_gallery_thumbnail_number = 9
ica.plot_components()

# %%
# .. note::
#
#     `~mne.preprocessing.ICA.plot_components` (which plots the scalp
#     field topographies for each component) has an optional ``inst`` parameter
#     that takes an instance of `~mne.io.Raw` or `~mne.Epochs`.
#     Passing ``inst`` makes the scalp topographies interactive: clicking one
#     will bring up a diagnostic `~mne.preprocessing.ICA.plot_properties`
#     window (see below) for that component.
#
# In the plots above it's fairly obvious which ICs are capturing our EOG and
# ECG artifacts, but there are additional ways visualize them anyway just to
# be sure. First, we can plot an overlay of the original signal against the
# reconstructed signal with the artifactual ICs excluded, using
# `~mne.preprocessing.ICA.plot_overlay`:

# blinks
ica.plot_overlay(raw, exclude=[0], picks='eeg')
# heartbeats
ica.plot_overlay(raw, exclude=[1], picks='mag')

# %%
# We can also plot some diagnostics of each IC using
# `~mne.preprocessing.ICA.plot_properties`:

ica.plot_properties(raw, picks=[0, 1])

# %%
# In the remaining sections, we'll look at different ways of choosing which ICs
# to exclude prior to reconstructing the sensor signals.
#
#
# Selecting ICA components manually
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
# Once we're certain which components we want to exclude, we can specify that
# manually by setting the ``ica.exclude`` attribute. Similar to marking bad
# channels, merely setting ``ica.exclude`` doesn't do anything immediately (it
# just adds the excluded ICs to a list that will get used later when it's
# needed). Once the exclusions have been set, ICA methods like
# `~mne.preprocessing.ICA.plot_overlay` will exclude those component(s)
# even if no ``exclude`` parameter is passed, and the list of excluded
# components will be preserved when using `mne.preprocessing.ICA.save`
# and `mne.preprocessing.read_ica`.

ica.exclude = [0, 1]  # indices chosen based on various plots above

# %%
# Now that the exclusions have been set, we can reconstruct the sensor signals
# with artifacts removed using the `~mne.preprocessing.ICA.apply` method
# (remember, we're applying the ICA solution from the *filtered* data to the
# original *unfiltered* signal). Plotting the original raw data alongside the
# reconstructed data shows that the heartbeat and blink artifacts are repaired.

# ica.apply() changes the Raw object in-place, so let's make a copy first:
reconst_raw = raw.copy()
ica.apply(reconst_raw)

raw.plot(order=artifact_picks, n_channels=len(artifact_picks),
         show_scrollbars=False)
reconst_raw.plot(order=artifact_picks, n_channels=len(artifact_picks),
                 show_scrollbars=False)
del reconst_raw

# %%
# Using an EOG channel to select ICA components
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
# It may have seemed easy to review the plots and manually select which ICs to
# exclude, but when processing dozens or hundreds of subjects this can become
# a tedious, rate-limiting step in the analysis pipeline. One alternative is to
# use dedicated EOG or ECG sensors as a "pattern" to check the ICs against, and
# automatically mark for exclusion any ICs that match the EOG/ECG pattern. Here
# we'll use `~mne.preprocessing.ICA.find_bads_eog` to automatically find
# the ICs that best match the EOG signal, then use
# `~mne.preprocessing.ICA.plot_scores` along with our other plotting
# functions to see which ICs it picked. We'll start by resetting
# ``ica.exclude`` back to an empty list:

ica.exclude = []
# find which ICs match the EOG pattern
eog_indices, eog_scores = ica.find_bads_eog(raw)
ica.exclude = eog_indices

# barplot of ICA component "EOG match" scores
ica.plot_scores(eog_scores)

# plot diagnostics
ica.plot_properties(raw, picks=eog_indices)

# plot ICs applied to raw data, with EOG matches highlighted
ica.plot_sources(raw, show_scrollbars=False)

# plot ICs applied to the averaged EOG epochs, with EOG matches highlighted
ica.plot_sources(eog_evoked)

# %%
# Note that above we used `~mne.preprocessing.ICA.plot_sources` on both
# the original `~mne.io.Raw` instance and also on an
# `~mne.Evoked` instance of the extracted EOG artifacts. This can be
# another way to confirm that `~mne.preprocessing.ICA.find_bads_eog` has
# identified the correct components.
#
#
# Using a simulated channel to select ICA components
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
# If you don't have an EOG channel,
# `~mne.preprocessing.ICA.find_bads_eog` has a ``ch_name`` parameter that
# you can use as a proxy for EOG. You can use a single channel, or create a
# bipolar reference from frontal EEG sensors and use that as virtual EOG
# channel. This carries a risk however: you must hope that the frontal EEG
# channels only reflect EOG and not brain dynamics in the prefrontal cortex (or
# you must not care about those prefrontal signals).
#
# For ECG, it is easier: `~mne.preprocessing.ICA.find_bads_ecg` can use
# cross-channel averaging of magnetometer or gradiometer channels to construct
# a virtual ECG channel, so if you have MEG channels it is usually not
# necessary to pass a specific channel name.
# `~mne.preprocessing.ICA.find_bads_ecg` also has two options for its
# ``method`` parameter: ``'ctps'`` (cross-trial phase statistics
# :footcite:`DammersEtAl2008`) and
# ``'correlation'`` (Pearson correlation between data and ECG channel).

ica.exclude = []
# find which ICs match the ECG pattern
ecg_indices, ecg_scores = ica.find_bads_ecg(raw, method='correlation',
                                            threshold='auto')
ica.exclude = ecg_indices

# barplot of ICA component "ECG match" scores
ica.plot_scores(ecg_scores)

# plot diagnostics
ica.plot_properties(raw, picks=ecg_indices)

# plot ICs applied to raw data, with ECG matches highlighted
ica.plot_sources(raw, show_scrollbars=False)

# plot ICs applied to the averaged ECG epochs, with ECG matches highlighted
ica.plot_sources(ecg_evoked)

# %%
# The last of these plots is especially useful: it shows us that the heartbeat
# artifact is coming through on *two* ICs, and we've only caught one of them.
# In fact, if we look closely at the output of
# `~mne.preprocessing.ICA.plot_sources` (online, you can right-click →
# "view image" to zoom in), it looks like ``ICA014`` has a weak periodic
# component that is in-phase with ``ICA001``. It might be worthwhile to re-run
# the ICA with more components to see if that second heartbeat artifact
# resolves out a little better:

# refit the ICA with 30 components this time
new_ica = ICA(n_components=30, max_iter='auto', random_state=97)
new_ica.fit(filt_raw)

# find which ICs match the ECG pattern
ecg_indices, ecg_scores = new_ica.find_bads_ecg(raw, method='correlation',
                                                threshold='auto')
new_ica.exclude = ecg_indices

# barplot of ICA component "ECG match" scores
new_ica.plot_scores(ecg_scores)

# plot diagnostics
new_ica.plot_properties(raw, picks=ecg_indices)

# plot ICs applied to raw data, with ECG matches highlighted
new_ica.plot_sources(raw, show_scrollbars=False)

# plot ICs applied to the averaged ECG epochs, with ECG matches highlighted
new_ica.plot_sources(ecg_evoked)

# %%
# Much better! Now we've captured both ICs that are reflecting the heartbeat
# artifact (and as a result, we got two diagnostic plots: one for each IC that
# reflects the heartbeat). This demonstrates the value of checking the results
# of automated approaches like `~mne.preprocessing.ICA.find_bads_ecg`
# before accepting them.

# %%
# For EEG, activation of muscles for postural control of the head and neck
# contaminate the signal as well. This is usually not detected by MEG. For
# an example showing how to remove these components, see :ref:`ex-muscle-ica`.

# clean up memory before moving on
del raw, ica, new_ica

# %%
# Selecting ICA components using template matching
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
# When dealing with multiple subjects, it is also possible to manually select
# an IC for exclusion on one subject, and then use that component as a
# *template* for selecting which ICs to exclude from other subjects' data,
# using `mne.preprocessing.corrmap` :footcite:`CamposViolaEtAl2009`.
# The idea behind `~mne.preprocessing.corrmap` is that the artifact patterns
# are similar
# enough across subjects that corresponding ICs can be identified by
# correlating the ICs from each ICA solution with a common template, and
# picking the ICs with the highest correlation strength.
# `~mne.preprocessing.corrmap` takes a list of ICA solutions, and a
# ``template`` parameter that specifies which ICA object and which component
# within it to use as a template.
#
# Since our sample dataset only contains data from one subject, we'll use a
# different dataset with multiple subjects: the EEGBCI dataset
# :footcite:`SchalkEtAl2004,GoldbergerEtAl2000`. The
# dataset has 109 subjects, we'll just download one run (a left/right hand
# movement task) from each of the first 4 subjects:

raws = list()
icas = list()

for subj in range(4):
    # EEGBCI subjects are 1-indexed; run 3 is a left/right hand movement task
    fname = mne.datasets.eegbci.load_data(subj + 1, runs=[3])[0]
    raw = mne.io.read_raw_edf(fname).load_data().resample(50)
    # remove trailing `.` from channel names so we can set montage
    mne.datasets.eegbci.standardize(raw)
    raw.set_montage('standard_1005')
    # high-pass filter
    raw_filt = raw.copy().load_data().filter(l_freq=1., h_freq=None)
    # fit ICA, using low max_iter for speed
    ica = ICA(n_components=30, max_iter=100, random_state=97)
    ica.fit(raw_filt, verbose='error')
    raws.append(raw)
    icas.append(ica)

# %%
# Now let's run `~mne.preprocessing.corrmap`:

# use the first subject as template; use Fpz as proxy for EOG
raw = raws[0]
ica = icas[0]
eog_inds, eog_scores = ica.find_bads_eog(raw, ch_name='Fpz')
corrmap(icas, template=(0, eog_inds[0]))

# %%
# The first figure shows the template map, while the second figure shows all
# the maps that were considered a "match" for the template (including the
# template itself). There is one match for each subject, but it's a good idea
# to also double-check the ICA sources for each subject:

for index, (ica, raw) in enumerate(zip(icas, raws)):
    with mne.viz.use_browser_backend('matplotlib'):
        fig = ica.plot_sources(raw, show_scrollbars=False)
    fig.subplots_adjust(top=0.9)  # make space for title
    fig.suptitle('Subject {}'.format(index))

# %%
# Notice that subjects 2 and 3 each seem to have *two* ICs that reflect ocular
# activity (components ``ICA000`` and ``ICA002``), but only one was caught by
# `~mne.preprocessing.corrmap`. Let's try setting the threshold manually:

corrmap(icas, template=(0, eog_inds[0]), threshold=0.9)

# %%
# This time it found 2 ICs for each of subjects 2 and 3 (which is good).
# At this point we'll re-run `~mne.preprocessing.corrmap` with
# parameters ``label='blink', plot=False`` to *label* the ICs from each subject
# that capture the blink artifacts (without plotting them again).

corrmap(icas, template=(0, eog_inds[0]), threshold=0.9, label='blink',
        plot=False)
print([ica.labels_ for ica in icas])

# %%
# Notice that the first subject has 3 different labels for the IC at index 0:
# "eog/0/Fpz", "eog", and "blink". The first two were added by
# `~mne.preprocessing.ICA.find_bads_eog`; the "blink" label was added by the
# last call to `~mne.preprocessing.corrmap`. Notice also that each subject has
# at least one IC index labelled "blink", and subjects 2 and 3 each have two
# components (0 and 2) labelled "blink" (consistent with the plot of IC sources
# above). The ``labels_`` attribute of `~mne.preprocessing.ICA` objects can
# also be manually edited to annotate the ICs with custom labels. They also
# come in handy when plotting:

icas[3].plot_components(picks=icas[3].labels_['blink'])
icas[3].exclude = icas[3].labels_['blink']
icas[3].plot_sources(raws[3], show_scrollbars=False)

# %%
# As a final note, it is possible to extract ICs numerically using the
# `~mne.preprocessing.ICA.get_components` method of
# `~mne.preprocessing.ICA` objects. This will return a :class:`NumPy
# array <numpy.ndarray>` that can be passed to
# `~mne.preprocessing.corrmap` instead of the :class:`tuple` of
# ``(subject_index, component_index)`` we passed before, and will yield the
# same result:

template_eog_component = icas[0].get_components()[:, eog_inds[0]]
corrmap(icas, template=template_eog_component, threshold=0.9)
print(template_eog_component)

# %%
# An advantage of using this numerical representation of an IC to capture a
# particular artifact pattern is that it can be saved and used as a template
# for future template-matching tasks using `~mne.preprocessing.corrmap`
# without having to load or recompute the ICA solution that yielded the
# template originally. Put another way, when the template is a NumPy array, the
# `~mne.preprocessing.ICA` object containing the template does not need
# to be in the list of ICAs provided to `~mne.preprocessing.corrmap`.
#
# .. LINKS
#
# .. _`blind source separation`:
#    https://en.wikipedia.org/wiki/Signal_separation
# .. _`statistically independent`:
#    https://en.wikipedia.org/wiki/Independence_(probability_theory)
# .. _`scikit-learn`: https://scikit-learn.org
# .. _`random seed`: https://en.wikipedia.org/wiki/Random_seed
# .. _`regular expression`: https://www.regular-expressions.info/
# .. _`qrs`: https://en.wikipedia.org/wiki/QRS_complex
# .. _`this EEGLAB tutorial`: https://labeling.ucsd.edu/tutorial/labels


# %%
# Compute ICA components on Epochs
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
# ICA is now fit to epoched MEG data instead of the raw data.
# We assume that the non-stationary EOG artifacts have already been removed.
# The sources matching the ECG are automatically found and displayed.
#
# .. note::
#     This example is computationally intensive, so it might take a few minutes
#     to complete.
#
# After reading the data, preprocessing consists of:
#
# - MEG channel selection
# - 1-30 Hz band-pass filter
# - epoching -0.2 to 0.5 seconds with respect to events
# - rejection based on peak-to-peak amplitude
#
# Note that we don't baseline correct the epochs here – we'll do this after
# cleaning with ICA is completed. Baseline correction before ICA is not
# recommended by the MNE-Python developers, as it doesn't guarantee optimal
# results.

filt_raw.pick_types(meg=True, eeg=False, exclude='bads', stim=True).load_data()
filt_raw.filter(1, 30, fir_design='firwin')

# peak-to-peak amplitude rejection parameters
reject = dict(mag=4e-12)
# create longer and more epochs for more artifact exposure
events = mne.find_events(filt_raw, stim_channel='STI 014')
# don't baseline correct epochs
epochs = mne.Epochs(filt_raw, events, event_id=None, tmin=-0.2, tmax=0.5,
                    reject=reject, baseline=None)

# %%
# Fit ICA model using the FastICA algorithm, detect and plot components
# explaining ECG artifacts.

ica = ICA(n_components=15, method='fastica', max_iter="auto").fit(epochs)

ecg_epochs = create_ecg_epochs(filt_raw, tmin=-.5, tmax=.5)
ecg_inds, scores = ica.find_bads_ecg(ecg_epochs, threshold='auto')

ica.plot_components(ecg_inds)

# %%
# Plot the properties of the ECG components:
ica.plot_properties(epochs, picks=ecg_inds)

# %%
# Plot the estimated sources of detected ECG related components:
ica.plot_sources(filt_raw, picks=ecg_inds)

# %%
# References
# ^^^^^^^^^^
# .. footbibliography::
