"""
.. _tut-artifact-ssp:

============================
Repairing artifacts with SSP
============================

This tutorial covers the basics of signal-space projection (SSP) and shows
how SSP can be used for artifact repair; extended examples illustrate use
of SSP for environmental noise reduction, and for repair of ocular and
heartbeat artifacts.

We begin as always by importing the necessary Python modules. To save ourselves
from repeatedly typing ``mne.preprocessing`` we'll directly import a handful of
functions from that submodule:
"""

# Authors: The MNE-Python contributors.
# License: BSD-3-Clause
# Copyright the MNE-Python contributors.

# %%

import os

import matplotlib.pyplot as plt
import numpy as np

import mne
from mne.preprocessing import (
    compute_proj_ecg,
    compute_proj_eog,
    create_ecg_epochs,
    create_eog_epochs,
)

# %%
# .. note::
#     Before applying SSP (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 SSP?
# ^^^^^^^^^^^^
#
# Signal-space projection (SSP) :footcite:`UusitaloIlmoniemi1997` is a
# technique for removing noise from EEG
# and MEG signals by :term:`projecting <projector>` the signal onto a
# lower-dimensional subspace. The subspace is chosen by calculating the average
# pattern across sensors when the noise is present, treating that pattern as
# a "direction" in the sensor space, and constructing the subspace to be
# orthogonal to the noise direction (for a detailed walk-through of projection
# see :ref:`tut-projectors-background`).
#
# The most common use of SSP is to remove noise from MEG signals when the noise
# comes from environmental sources (sources outside the subject's body and the
# MEG system, such as the electromagnetic fields from nearby electrical
# equipment) and when that noise is *stationary* (doesn't change much over the
# duration of the recording). However, SSP can also be used to remove
# biological artifacts such as heartbeat (ECG) and eye movement (EOG)
# artifacts. Examples of each of these are given below.
#
#
# Example: Environmental noise reduction from empty-room recordings
# ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
#
# The :ref:`example data <sample-dataset>` was recorded on a Neuromag system,
# which stores SSP projectors for environmental noise removal in the system
# configuration (so that reasonably clean raw data can be viewed in real-time
# during acquisition). For this reason, all the `~mne.io.Raw` data in
# the example dataset already includes SSP projectors, which are noted in the
# output when loading the data:

sample_data_folder = mne.datasets.sample.data_path()
sample_data_raw_file = os.path.join(
    sample_data_folder, "MEG", "sample", "sample_audvis_raw.fif"
)
# here we crop and resample just for speed
raw = mne.io.read_raw_fif(sample_data_raw_file).crop(0, 60)
raw.load_data().resample(100)

# %%
# The :ref:`example data <sample-dataset>` also includes an "empty room"
# recording taken the same day as the recording of the subject. This will
# provide a more accurate estimate of environmental noise than the projectors
# stored with the system (which are typically generated during annual
# maintenance and tuning). Since we have this subject-specific empty-room
# recording, we'll create our own projectors from it and discard the
# system-provided SSP projectors (saving them first, for later comparison with
# the custom ones):

system_projs = raw.info["projs"]
raw.del_proj()
empty_room_file = os.path.join(sample_data_folder, "MEG", "sample", "ernoise_raw.fif")
# cropped to 60 s just for speed
empty_room_raw = mne.io.read_raw_fif(empty_room_file).crop(0, 30)

# %%
# Notice that the empty room recording itself has the system-provided SSP
# projectors in it — we'll remove those from the empty room file too.

empty_room_raw.del_proj()

# %%
#
# Visualizing the empty-room noise
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
# Let's take a look at the spectrum of the empty room noise. We can view an
# individual spectrum for each sensor, or an average (with confidence band)
# across sensors:

raw.info["bads"] = ["MEG 2443"]
spectrum = empty_room_raw.compute_psd()
for average in (False, True):
    spectrum.plot(
        average=average,
        dB=False,
        amplitude=True,
        xscale="log",
        picks="data",
        exclude="bads",
    )

# %%
# Creating the empty-room projectors
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
# We create the SSP vectors using `~mne.compute_proj_raw`, and control
# the number of projectors with parameters ``n_grad`` and ``n_mag``. Once
# created, the field pattern of the projectors can be easily visualized with
# `~mne.viz.plot_projs_topomap`. We include the parameter
# ``vlim='joint'`` so that the colormap is computed jointly for all projectors
# of a given channel type; this makes it easier to compare their relative
# smoothness. Note that for the function to know the types of channels in a
# projector, you must also provide the corresponding `~mne.Info` object:

empty_room_projs = mne.compute_proj_raw(empty_room_raw, n_grad=3, n_mag=3)
mne.viz.plot_projs_topomap(
    empty_room_projs, colorbar=True, vlim="joint", info=empty_room_raw.info
)

# %%
# Notice that the gradiometer-based projectors seem to reflect problems with
# individual sensor units rather than a global noise source (indeed, planar
# gradiometers are much less sensitive to distant sources). This is the reason
# that the system-provided noise projectors are computed only for
# magnetometers. Comparing the system-provided projectors to the
# subject-specific ones, we can see they are reasonably similar (though in a
# different order) and the left-right component seems to have changed
# polarity.

fig, axs = plt.subplots(2, 3)
for idx, _projs in enumerate([system_projs, empty_room_projs[3:]]):
    mne.viz.plot_projs_topomap(
        _projs, axes=axs[idx], colorbar=True, vlim="joint", info=empty_room_raw.info
    )

# %%
# Visualizing how projectors affect the signal
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
# We could visualize the different effects these have on the data by applying
# each set of projectors to different copies of the `~mne.io.Raw` object
# using `~mne.io.Raw.apply_proj`. However, the `~mne.io.Raw.plot`
# method has a ``proj`` parameter that allows us to *temporarily* apply
# projectors while plotting, so we can use this to visualize the difference
# without needing to copy the data. Because the projectors are so similar, we
# need to zoom in pretty close on the data to see any differences:

mags = mne.pick_types(raw.info, meg="mag")
for title, projs in [
    ("system", system_projs),
    ("subject-specific", empty_room_projs[3:]),
]:
    raw.add_proj(projs, remove_existing=True)
    with mne.viz.use_browser_backend("matplotlib"):
        fig = raw.plot(proj=True, order=mags, duration=1, n_channels=2)
    fig.subplots_adjust(top=0.9)  # make room for title
    fig.suptitle(f"{title} projectors", size="xx-large", weight="bold")

# %%
# The effect is sometimes easier to see on averaged data. Here we use an
# interactive feature of `mne.Evoked.plot_topomap` to turn projectors on
# and off to see the effect on the data. Of course, the interactivity won't
# work on the tutorial website, but you can download the tutorial and try it
# locally:

events = mne.find_events(raw, stim_channel="STI 014")
event_id = {"auditory/left": 1}

# NOTE: appropriate rejection criteria are highly data-dependent
reject = dict(
    mag=4000e-15,  # 4000 fT
    grad=4000e-13,  # 4000 fT/cm
    eeg=150e-6,  # 150 µV
    eog=250e-6,
)  # 250 µV

# time range where we expect to see the auditory N100: 50-150 ms post-stimulus
times = np.linspace(0.05, 0.15, 5)

epochs = mne.Epochs(raw, events, event_id, proj="delayed", reject=reject)
fig = epochs.average().plot_topomap(times, proj="interactive")

# %%
# Plotting the ERP/F using ``evoked.plot()`` or ``evoked.plot_joint()`` with
# and without projectors applied can also be informative, as can plotting with
# ``proj='reconstruct'``, which can reduce the signal bias introduced by
# projections (see :ref:`tut-artifact-ssp-reconstruction` below).
#
# Example: EOG and ECG artifact repair
# ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
#
# Visualizing the artifacts
# ~~~~~~~~~~~~~~~~~~~~~~~~~
#
# As mentioned in :ref:`the ICA tutorial <tut-artifact-ica>`, an important
# first step is visualizing the artifacts you want to repair. Here they are 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))

# %%
# Repairing ECG artifacts with SSP
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
# MNE-Python provides several functions for detecting and removing heartbeats
# from EEG and MEG data. As we saw in :ref:`tut-artifact-overview`,
# `~mne.preprocessing.create_ecg_epochs` can be used to both detect and
# extract heartbeat artifacts into an `~mne.Epochs` object, which can
# be used to visualize how the heartbeat artifacts manifest across the sensors:

ecg_evoked = create_ecg_epochs(raw).average()
ecg_evoked.plot_joint()

# %%
# Looks like the EEG channels are pretty spread out; let's baseline-correct and
# plot again:

ecg_evoked.apply_baseline((None, None))
ecg_evoked.plot_joint()

# %%
# To compute SSP projectors for the heartbeat artifact, you can use
# `~mne.preprocessing.compute_proj_ecg`, which takes a
# `~mne.io.Raw` object as input and returns the requested number of
# projectors for magnetometers, gradiometers, and EEG channels (default is two
# projectors for each channel type).
# `~mne.preprocessing.compute_proj_ecg` also returns an :term:`events`
# array containing the sample numbers corresponding to the peak of the
# `R wave <https://en.wikipedia.org/wiki/QRS_complex>`__ of each detected
# heartbeat.

projs, events = compute_proj_ecg(raw, n_grad=1, n_mag=1, n_eeg=1, reject=None)

# %%
# The first line of output tells us that
# `~mne.preprocessing.compute_proj_ecg` found three existing projectors
# already in the `~mne.io.Raw` object, and will include those in the
# list of projectors that it returns (appending the new ECG projectors to the
# end of the list). If you don't want that, you can change that behavior with
# the boolean ``no_proj`` parameter. Since we've already run the computation,
# we can just as easily separate out the ECG projectors by indexing the list of
# projectors:

ecg_projs = projs[3:]
print(ecg_projs)

# %%
# Just like with the empty-room projectors, we can visualize the scalp
# distribution:

mne.viz.plot_projs_topomap(ecg_projs, info=raw.info)

# %%
# Moreover, because these projectors were created using epochs chosen
# specifically because they contain time-locked artifacts, we can do a
# joint plot of the projectors and their effect on the time-averaged epochs.
# This figure has three columns:
#
# 1. The left shows the data traces before (black) and after (green)
#    projection. We can see that the ECG artifact is well suppressed by one
#    projector per channel type.
# 2. The center shows the topomaps associated with the projectors, in this case
#    just a single topography for our one projector per channel type.
# 3. The right again shows the data traces (black), but this time with those
#    traces also projected onto the first projector for each channel type (red)
#    plus one surrogate ground truth for an ECG channel (MEG 0111).

# sphinx_gallery_thumbnail_number = 17

# ideally here we would just do `picks_trace='ecg'`, but this dataset did not
# have a dedicated ECG channel recorded, so we just pick a channel that was
# very sensitive to the artifact
fig = mne.viz.plot_projs_joint(ecg_projs, ecg_evoked, picks_trace="MEG 0111")
fig.suptitle("ECG projectors")

# %%
# Since no dedicated ECG sensor channel was detected in the
# `~mne.io.Raw` object, by default
# `~mne.preprocessing.compute_proj_ecg` used the magnetometers to
# estimate the ECG signal (as stated on the third line of output, above). You
# can also supply the ``ch_name`` parameter to restrict which channel to use
# for ECG artifact detection; this is most useful when you had an ECG sensor
# but it is not labeled as such in the `~mne.io.Raw` file.
#
# The next few lines of the output describe the filter used to isolate ECG
# events. The default settings are usually adequate, but the filter can be
# customized via the parameters ``ecg_l_freq``, ``ecg_h_freq``, and
# ``filter_length`` (see the documentation of
# `~mne.preprocessing.compute_proj_ecg` for details).
#
# .. TODO what are the cases where you might need to customize the ECG filter?
#    infants? Heart murmur?
#
# Once the ECG events have been identified,
# `~mne.preprocessing.compute_proj_ecg` will also filter the data
# channels before extracting epochs around each heartbeat, using the parameter
# values given in ``l_freq``, ``h_freq``, ``filter_length``, ``filter_method``,
# and ``iir_params``. Here again, the default parameter values are usually
# adequate.
#
# .. TODO should advice for filtering here be the same as advice for filtering
#    raw data generally? (e.g., keep high-pass very low to avoid peak shifts?
#    what if your raw data is already filtered?)
#
# By default, the filtered epochs will be averaged together
# before the projection is computed; this can be controlled with the boolean
# ``average`` parameter. In general this improves the signal-to-noise (where
# "signal" here is our artifact!) ratio because the artifact temporal waveform
# is fairly similar across epochs and well time locked to the detected events.
#
# To get a sense of how the heartbeat affects the signal at each sensor, you
# can plot the data with and without the ECG projectors:


raw.del_proj()
for title, proj in [("Without", empty_room_projs), ("With", ecg_projs)]:
    raw.add_proj(proj, remove_existing=False)
    with mne.viz.use_browser_backend("matplotlib"):
        fig = raw.plot(order=artifact_picks, n_channels=len(artifact_picks))
    fig.subplots_adjust(top=0.9)  # make room for title
    fig.suptitle(f"{title} ECG projectors", size="xx-large", weight="bold")

# %%
# Finally, note that above we passed ``reject=None`` to the
# `~mne.preprocessing.compute_proj_ecg` function, meaning that all
# detected ECG epochs would be used when computing the projectors (regardless
# of signal quality in the data sensors during those epochs). The default
# behavior is to reject epochs based on signal amplitude: epochs with
# peak-to-peak amplitudes exceeding 50 µV in EEG channels, 250 µV in EOG
# channels, 2000 fT/cm in gradiometer channels, or 3000 fT in magnetometer
# channels. You can change these thresholds by passing a dictionary with keys
# ``eeg``, ``eog``, ``mag``, and ``grad`` (though be sure to pass the threshold
# values in volts, teslas, or teslas/meter). Generally, it is a good idea to
# reject such epochs when computing the ECG projectors (since presumably the
# high-amplitude fluctuations in the channels are noise, not reflective of
# brain activity); passing ``reject=None`` above was done simply to avoid the
# dozens of extra lines of output (enumerating which sensor(s) were responsible
# for each rejected epoch) from cluttering up the tutorial.
#
# .. note::
#
#     `~mne.preprocessing.compute_proj_ecg` has a similar parameter
#     ``flat`` for specifying the *minimum* acceptable peak-to-peak amplitude
#     for each channel type.
#
# While `~mne.preprocessing.compute_proj_ecg` conveniently combines
# several operations into a single function, MNE-Python also provides functions
# for performing each part of the process. Specifically:
#
# - `mne.preprocessing.find_ecg_events` for detecting heartbeats in a
#   `~mne.io.Raw` object and returning a corresponding :term:`events`
#   array
#
# - `mne.preprocessing.create_ecg_epochs` for detecting heartbeats in a
#   `~mne.io.Raw` object and returning an `~mne.Epochs` object
#
# - `mne.compute_proj_epochs` for creating projector(s) from any
#   `~mne.Epochs` object
#
# See the documentation of each function for further details.
#
# .. note::
#     In situations only limited electrodes are available for analysis, removing the
#     cardiac artefact using techniques which rely on the availability of spatial
#     information (such as SSP) may not be possible. In these instances, it may be of
#     use to consider algorithms which require information only regarding heartbeat
#     instances in the time domain, such as :func:`mne.preprocessing.apply_pca_obs`.
#
#
# Repairing EOG artifacts with SSP
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
# Once again let's visualize our artifact before trying to repair it. We've
# seen above the large deflections in frontal EEG channels in the raw data;
# here is how the ocular artifacts manifests across all the sensors:

eog_evoked = create_eog_epochs(raw).average(picks="all")
eog_evoked.apply_baseline((None, None))
eog_evoked.plot_joint()

# %%
# Just like we did with the heartbeat artifact, we can compute SSP projectors
# for the ocular artifact using `~mne.preprocessing.compute_proj_eog`,
# which again takes a `~mne.io.Raw` object as input and returns the
# requested number of projectors for magnetometers, gradiometers, and EEG
# channels (default is two projectors for each channel type). This time, we'll
# pass ``no_proj`` parameter (so we get back only the new EOG projectors, not
# also the existing projectors in the `~mne.io.Raw` object), and we'll
# ignore the events array by assigning it to ``_`` (the conventional way of
# handling unwanted return elements in Python).

eog_projs, _ = compute_proj_eog(
    raw, n_grad=1, n_mag=1, n_eeg=1, reject=None, no_proj=True
)

# %%
# Just like with the empty-room and ECG projectors, we can visualize the scalp
# distribution:

mne.viz.plot_projs_topomap(eog_projs, info=raw.info)

# %%
# And we can do a joint image:

fig = mne.viz.plot_projs_joint(eog_projs, eog_evoked, "eog")
fig.suptitle("EOG projectors")

# %%
# And finally, we can make a joint visualization with our EOG evoked. We will
# also make a bad choice here and select *two* EOG projectors for EEG and
# magnetometers, and we will see them show up as noise in the plot. Even though
# the projected time course (left column) looks perhaps okay, problems show
# up in the center (topomaps) and right plots (projection of channel data
# onto the projection vector):
#
# 1. The second magnetometer topomap has a bilateral auditory field pattern.
# 2. The uniformly-scaled projected temporal time course (solid lines) show
#    that, while the first projector trace (red) has a large EOG-like
#    amplitude, the second projector trace (blue-green) is much smaller.
# 3. The re-normalized projected temporal time courses show that the
#    second PCA trace is very noisy relative to the EOG channel data (yellow).

eog_projs_bad, _ = compute_proj_eog(
    raw, n_grad=1, n_mag=2, n_eeg=2, reject=None, no_proj=True
)
fig = mne.viz.plot_projs_joint(eog_projs_bad, eog_evoked, picks_trace="eog")
fig.suptitle("Too many EOG projectors")

# %%
# Now we repeat the plot from above (with empty room and ECG projectors) and
# compare it to a plot with empty room, ECG, and EOG projectors, to see how
# well the ocular artifacts have been repaired:

for title in ("Without", "With"):
    if title == "With":
        raw.add_proj(eog_projs)
    with mne.viz.use_browser_backend("matplotlib"):
        fig = raw.plot(order=artifact_picks, n_channels=len(artifact_picks))
    fig.subplots_adjust(top=0.9)  # make room for title
    fig.suptitle(f"{title} EOG projectors", size="xx-large", weight="bold")

# %%
# Notice that the small peaks in the first to magnetometer channels (``MEG
# 1411`` and ``MEG 1421``) that occur at the same time as the large EEG
# deflections have also been removed.
#
#
# Choosing the number of projectors
# ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
#
# In the examples above, we used 3 projectors (all magnetometer) to capture
# empty room noise, and saw how projectors computed for the gradiometers failed
# to capture *global* patterns (and thus we discarded the gradiometer
# projectors). Then we computed 3 projectors (1 for each channel type) to
# capture the heartbeat artifact, and 3 more to capture the ocular artifact.
# How did we choose these numbers? The short answer is "based on experience" —
# knowing how heartbeat artifacts typically manifest across the sensor array
# allows us to recognize them when we see them, and recognize when additional
# projectors are capturing something else other than a heartbeat artifact (and
# thus may be removing brain signal and should be discarded).
#
# .. _tut-artifact-ssp-reconstruction:
#
# Visualizing SSP sensor-space bias via signal reconstruction
# ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
# .. admonition:: SSP reconstruction
#     :class: sidebar note
#
#     Internally, the reconstruction is performed by effectively using a
#     minimum-norm source localization to a spherical source space with the
#     projections accounted for, and then projecting the source-space data
#     back out to sensor space.
#
# Because SSP performs an orthogonal projection, any spatial component in the
# data that is not perfectly orthogonal to the SSP spatial direction(s) will
# have its overall amplitude reduced by the projection operation. In other
# words, SSP typically introduces some amount of amplitude reduction bias in
# the sensor space data.
#
# When performing source localization of M/EEG data, these projections are
# properly taken into account by being applied not just to the M/EEG data
# but also to the forward solution, and hence SSP should not bias the estimated
# source amplitudes. However, for sensor space analyses, it can be useful to
# visualize the extent to which SSP projection has biased the data. This can be
# explored by using ``proj='reconstruct'`` in evoked plotting functions, for
# example via `evoked.plot() <mne.Evoked.plot>`, here restricted to just
# EEG channels for speed:

evoked_eeg = epochs.average().pick("eeg")
evoked_eeg.del_proj().add_proj(ecg_projs).add_proj(eog_projs)
fig, axes = plt.subplots(
    1, 3, figsize=(8, 3), sharex=True, sharey=True, layout="constrained"
)
for pi, proj in enumerate((False, True, "reconstruct")):
    ax = axes[pi]
    evoked_eeg.plot(proj=proj, axes=ax, spatial_colors=True)
    parts = ax.get_title().split("(")
    ylabel = (
        f"{parts[0]} ({ax.get_ylabel()})\n{parts[1].replace(')', '')}"
        if pi == 0
        else ""
    )
    ax.set(ylabel=ylabel, title=f"proj={proj}")
    ax.yaxis.set_tick_params(labelbottom=True)
    for text in list(ax.texts):
        text.remove()

# %%
# Note that here the bias in the EEG and magnetometer channels is reduced by
# the reconstruction. This suggests that the application of SSP has slightly
# reduced the amplitude of our signals in sensor space, but that it should not
# bias the amplitudes in source space.
#
#
# References
# ^^^^^^^^^^
#
# .. footbibliography::
