# -*- coding: utf-8 -*-
"""
.. _tut-projectors-background:
========================================
Background on projectors and projections
========================================
This tutorial provides background information on projectors and Signal Space
Projection (SSP), and covers loading and saving projectors, adding and removing
projectors from Raw objects, the difference between "applied" and "unapplied"
projectors, and at what stages MNE-Python applies projectors automatically.
We'll start by importing the Python modules we need; we'll also define a short
function to make it easier to make several plots that look similar:
"""
# %%
import os
import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D # noqa
from scipy.linalg import svd
import mne
def setup_3d_axes():
ax = plt.axes(projection='3d')
ax.view_init(azim=-105, elev=20)
ax.set_xlabel('x')
ax.set_ylabel('y')
ax.set_zlabel('z')
ax.set_xlim(-1, 5)
ax.set_ylim(-1, 5)
ax.set_zlim(0, 5)
return ax
# %%
# What is a projection?
# ^^^^^^^^^^^^^^^^^^^^^
#
# In the most basic terms, a *projection* is an operation that converts one set
# of points into another set of points, where repeating the projection
# operation on the resulting points has no effect. To give a simple geometric
# example, imagine the point :math:`(3, 2, 5)` in 3-dimensional space. A
# projection of that point onto the :math:`x, y` plane looks a lot like a
# shadow cast by that point if the sun were directly above it:
ax = setup_3d_axes()
# plot the vector (3, 2, 5)
origin = np.zeros((3, 1))
point = np.array([[3, 2, 5]]).T
vector = np.hstack([origin, point])
ax.plot(*vector, color='k')
ax.plot(*point, color='k', marker='o')
# project the vector onto the x,y plane and plot it
xy_projection_matrix = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 0]])
projected_point = xy_projection_matrix @ point
projected_vector = xy_projection_matrix @ vector
ax.plot(*projected_vector, color='C0')
ax.plot(*projected_point, color='C0', marker='o')
# add dashed arrow showing projection
arrow_coords = np.concatenate([point, projected_point - point]).flatten()
ax.quiver3D(*arrow_coords, length=0.96, arrow_length_ratio=0.1, color='C1',
linewidth=1, linestyle='dashed')
# %%
#
# .. note::
#
# The ``@`` symbol indicates matrix multiplication on NumPy arrays, and was
# introduced in Python 3.5 / NumPy 1.10. The notation ``plot(*point)`` uses
# Python `argument expansion`_ to "unpack" the elements of ``point`` into
# separate positional arguments to the function. In other words,
# ``plot(*point)`` expands to ``plot(3, 2, 5)``.
#
# Notice that we used matrix multiplication to compute the projection of our
# point :math:`(3, 2, 5)`onto the :math:`x, y` plane:
#
# .. math::
#
# \left[
# \begin{matrix} 1 & 0 & 0 \\ 0 & 1 & 0 \\ 0 & 0 & 0 \end{matrix}
# \right]
# \left[ \begin{matrix} 3 \\ 2 \\ 5 \end{matrix} \right] =
# \left[ \begin{matrix} 3 \\ 2 \\ 0 \end{matrix} \right]
#
# ...and that applying the projection again to the result just gives back the
# result again:
#
# .. math::
#
# \left[
# \begin{matrix} 1 & 0 & 0 \\ 0 & 1 & 0 \\ 0 & 0 & 0 \end{matrix}
# \right]
# \left[ \begin{matrix} 3 \\ 2 \\ 0 \end{matrix} \right] =
# \left[ \begin{matrix} 3 \\ 2 \\ 0 \end{matrix} \right]
#
# From an information perspective, this projection has taken the point
# :math:`x, y, z` and removed the information about how far in the :math:`z`
# direction our point was located; all we know now is its position in the
# :math:`x, y` plane. Moreover, applying our projection matrix to *any point*
# in :math:`x, y, z` space will reduce it to a corresponding point on the
# :math:`x, y` plane. The term for this is a *subspace*: the projection matrix
# projects points in the original space into a *subspace* of lower dimension
# than the original. The reason our subspace is the :math:`x,y` plane (instead
# of, say, the :math:`y,z` plane) is a direct result of the particular values
# in our projection matrix.
#
#
# Example: projection as noise reduction
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
# Another way to describe this "loss of information" or "projection into a
# subspace" is to say that projection reduces the rank (or "degrees of
# freedom") of the measurement — here, from 3 dimensions down to 2. On the
# other hand, if you know that measurement component in the :math:`z` direction
# is just noise due to your measurement method, and all you care about are the
# :math:`x` and :math:`y` components, then projecting your 3-dimensional
# measurement into the :math:`x, y` plane could be seen as a form of noise
# reduction.
#
# Of course, it would be very lucky indeed if all the measurement noise were
# concentrated in the :math:`z` direction; you could just discard the :math:`z`
# component without bothering to construct a projection matrix or do the matrix
# multiplication. Suppose instead that in order to take that measurement you
# had to pull a trigger on a measurement device, and the act of pulling the
# trigger causes the device to move a little. If you measure how
# trigger-pulling affects measurement device position, you could then "correct"
# your real measurements to "project out" the effect of the trigger pulling.
# Here we'll suppose that the average effect of the trigger is to move the
# measurement device by :math:`(3, -1, 1)`:
trigger_effect = np.array([[3, -1, 1]]).T
# %%
# Knowing that, we can compute a plane that is orthogonal to the effect of the
# trigger (using the fact that a plane through the origin has equation
# :math:`Ax + By + Cz = 0` given a normal vector :math:`(A, B, C)`), and
# project our real measurements onto that plane.
# compute the plane orthogonal to trigger_effect
x, y = np.meshgrid(np.linspace(-1, 5, 61), np.linspace(-1, 5, 61))
A, B, C = trigger_effect
z = (-A * x - B * y) / C
# cut off the plane below z=0 (just to make the plot nicer)
mask = np.where(z >= 0)
x = x[mask]
y = y[mask]
z = z[mask]
# %%
# Computing the projection matrix from the ``trigger_effect`` vector is done
# using `singular value decomposition `_ (SVD); interested readers may
# consult the internet or a linear algebra textbook for details on this method.
# With the projection matrix in place, we can project our original vector
# :math:`(3, 2, 5)` to remove the effect of the trigger, and then plot it:
# sphinx_gallery_thumbnail_number = 2
# compute the projection matrix
U, S, V = svd(trigger_effect, full_matrices=False)
trigger_projection_matrix = np.eye(3) - U @ U.T
# project the vector onto the orthogonal plane
projected_point = trigger_projection_matrix @ point
projected_vector = trigger_projection_matrix @ vector
# plot the trigger effect and its orthogonal plane
ax = setup_3d_axes()
ax.plot_trisurf(x, y, z, color='C2', shade=False, alpha=0.25)
ax.quiver3D(*np.concatenate([origin, trigger_effect]).flatten(),
arrow_length_ratio=0.1, color='C2', alpha=0.5)
# plot the original vector
ax.plot(*vector, color='k')
ax.plot(*point, color='k', marker='o')
offset = np.full((3, 1), 0.1)
ax.text(*(point + offset).flat, '({}, {}, {})'.format(*point.flat), color='k')
# plot the projected vector
ax.plot(*projected_vector, color='C0')
ax.plot(*projected_point, color='C0', marker='o')
offset = np.full((3, 1), -0.2)
ax.text(*(projected_point + offset).flat,
'({}, {}, {})'.format(*np.round(projected_point.flat, 2)),
color='C0', horizontalalignment='right')
# add dashed arrow showing projection
arrow_coords = np.concatenate([point, projected_point - point]).flatten()
ax.quiver3D(*arrow_coords, length=0.96, arrow_length_ratio=0.1,
color='C1', linewidth=1, linestyle='dashed')
# %%
# Just as before, the projection matrix will map *any point* in :math:`x, y, z`
# space onto that plane, and once a point has been projected onto that plane,
# applying the projection again will have no effect. For that reason, it should
# be clear that although the projected points vary in all three :math:`x`,
# :math:`y`, and :math:`z` directions, the set of projected points have only
# two *effective* dimensions (i.e., they are constrained to a plane).
#
# .. admonition:: Terminology
# :class: sidebar note
#
# In MNE-Python, the matrix used to project a raw signal into a subspace is
# usually called a :term:`projector` or a *projection
# operator* — these terms are interchangeable with the term *projection
# matrix* used above.
#
# Projections of EEG or MEG signals work in very much the same way: the point
# :math:`x, y, z` corresponds to the value of each sensor at a single time
# point, and the projection matrix varies depending on what aspects of the
# signal (i.e., what kind of noise) you are trying to project out. The only
# real difference is that instead of a single 3-dimensional point :math:`(x, y,
# z)` you're dealing with a time series of :math:`N`-dimensional "points" (one
# at each sampling time), where :math:`N` is usually in the tens or hundreds
# (depending on how many sensors your EEG/MEG system has). Fortunately, because
# projection is a matrix operation, it can be done very quickly even on signals
# with hundreds of dimensions and tens of thousands of time points.
#
#
# .. _ssp-tutorial:
#
# Signal-space projection (SSP)
# ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
#
# We mentioned above that the projection matrix will vary depending on what
# kind of noise you are trying to project away. Signal-space projection (SSP)
# :footcite:`UusitaloIlmoniemi1997` is a way of estimating what that projection
# matrix should be, by
# comparing measurements with and without the signal of interest. For example,
# you can take additional "empty room" measurements that record activity at the
# sensors when no subject is present. By looking at the spatial pattern of
# activity across MEG sensors in an empty room measurement, you can create one
# or more :math:`N`-dimensional vector(s) giving the "direction(s)" of
# environmental noise in sensor space (analogous to the vector for "effect of
# the trigger" in our example above). SSP is also often used for removing
# heartbeat and eye movement artifacts — in those cases, instead of empty room
# recordings the direction of the noise is estimated by detecting the
# artifacts, extracting epochs around them, and averaging. See
# :ref:`tut-artifact-ssp` for examples.
#
# Once you know the noise vectors, you can create a hyperplane that is
# orthogonal
# to them, and construct a projection matrix to project your experimental
# recordings onto that hyperplane. In that way, the component of your
# measurements associated with environmental noise can be removed. Again, it
# should be clear that the projection reduces the dimensionality of your data —
# you'll still have the same number of sensor signals, but they won't all be
# *linearly independent* — but typically there are tens or hundreds of sensors
# and the noise subspace that you are eliminating has only 3-5 dimensions, so
# the loss of degrees of freedom is usually not problematic.
#
#
# Projectors in MNE-Python
# ^^^^^^^^^^^^^^^^^^^^^^^^
#
# In our example data, :ref:`SSP ` has already been performed
# using empty room recordings, but the :term:`projectors ` are
# stored alongside the raw data and have not been *applied* yet (or,
# synonymously, the projectors are not *active* yet). Here we'll load
# the :ref:`sample data ` and crop it to 60 seconds; you can
# see the projectors in the output of :func:`~mne.io.read_raw_fif` below:
sample_data_folder = mne.datasets.sample.data_path()
sample_data_raw_file = os.path.join(sample_data_folder, 'MEG', 'sample',
'sample_audvis_raw.fif')
raw = mne.io.read_raw_fif(sample_data_raw_file)
raw.crop(tmax=60).load_data()
# %%
# In MNE-Python, the environmental noise vectors are computed using `principal
# component analysis `_, usually abbreviated "PCA", which is why the SSP
# projectors usually have names like "PCA-v1". (Incidentally, since the process
# of performing PCA uses `singular value decomposition `_ under the hood,
# it is also common to see phrases like "projectors were computed using SVD" in
# published papers.) The projectors are stored in the ``projs`` field of
# ``raw.info``:
print(raw.info['projs'])
# %%
# ``raw.info['projs']`` is an ordinary Python :class:`list` of
# :class:`~mne.Projection` objects, so you can access individual projectors by
# indexing into it. The :class:`~mne.Projection` object itself is similar to a
# Python :class:`dict`, so you can use its ``.keys()`` method to see what
# fields it contains (normally you don't need to access its properties
# directly, but you can if necessary):
first_projector = raw.info['projs'][0]
print(first_projector)
print(first_projector.keys())
# %%
# The :class:`~mne.io.Raw`, :class:`~mne.Epochs`, and :class:`~mne.Evoked`
# objects all have a boolean :attr:`~mne.io.Raw.proj` attribute that indicates
# whether there are any unapplied / inactive projectors stored in the object.
# In other words, the :attr:`~mne.io.Raw.proj` attribute is ``True`` if at
# least one :term:`projector` is present and all of them are active. In
# addition, each individual projector also has a boolean ``active`` field:
print(raw.proj)
print(first_projector['active'])
# %%
# Computing projectors
# ~~~~~~~~~~~~~~~~~~~~
#
# In MNE-Python, SSP vectors can be computed using general purpose functions
# :func:`mne.compute_proj_raw`, :func:`mne.compute_proj_epochs`, and
# :func:`mne.compute_proj_evoked`. The general assumption these functions make
# is that the data passed contains raw data, epochs or averages of the artifact
# you want to repair via projection. In practice this typically involves
# continuous raw data of empty room recordings or averaged ECG or EOG
# artifacts. A second set of high-level convenience functions is provided to
# compute projection vectors for typical use cases. This includes
# :func:`mne.preprocessing.compute_proj_ecg` and
# :func:`mne.preprocessing.compute_proj_eog` for computing the ECG and EOG
# related artifact components, respectively; see :ref:`tut-artifact-ssp` for
# examples of these uses. For computing the EEG reference signal as a
# projector, the function :func:`mne.set_eeg_reference` can be used; see
# :ref:`tut-set-eeg-ref` for more information.
#
# .. warning:: It is best to compute projectors only on channels that will be
# used (e.g., excluding bad channels). This ensures that
# projection vectors will remain ortho-normalized and that they
# properly capture the activity of interest.
#
#
# Visualizing the effect of projectors
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
# You can see the effect the projectors are having on the measured signal by
# comparing plots with and without the projectors applied. By default,
# ``raw.plot()`` will apply the projectors in the background before plotting
# (without modifying the :class:`~mne.io.Raw` object); you can control this
# with the boolean ``proj`` parameter as shown below, or you can turn them on
# and off interactively with the projectors interface, accessed via the
# :kbd:`Proj` button in the lower right corner of the plot window. Here we'll
# look at just the magnetometers, and a 2-second sample from the beginning of
# the file.
mags = raw.copy().crop(tmax=2).pick_types(meg='mag')
for proj in (False, True):
with mne.viz.use_browser_backend('matplotlib'):
fig = mags.plot(butterfly=True, proj=proj)
fig.subplots_adjust(top=0.9)
fig.suptitle('proj={}'.format(proj), size='xx-large', weight='bold')
# %%
# Additional ways of visualizing projectors are covered in the tutorial
# :ref:`tut-artifact-ssp`.
#
#
# Loading and saving projectors
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
# SSP can be used for other types of signal cleaning besides just reduction of
# environmental noise. You probably noticed two large deflections in the
# magnetometer signals in the previous plot that were not removed by the
# empty-room projectors — those are artifacts of the subject's heartbeat. SSP
# can be used to remove those artifacts as well. The sample data includes
# projectors for heartbeat noise reduction that were saved in a separate file
# from the raw data, which can be loaded with the :func:`mne.read_proj`
# function:
ecg_proj_file = os.path.join(sample_data_folder, 'MEG', 'sample',
'sample_audvis_ecg-proj.fif')
ecg_projs = mne.read_proj(ecg_proj_file)
print(ecg_projs)
# %%
# There is a corresponding :func:`mne.write_proj` function that can be used to
# save projectors to disk in ``.fif`` format:
#
# .. code-block:: python3
#
# mne.write_proj('heartbeat-proj.fif', ecg_projs)
#
# .. note::
#
# By convention, MNE-Python expects projectors to be saved with a filename
# ending in ``-proj.fif`` (or ``-proj.fif.gz``), and will issue a warning
# if you forgo this recommendation.
#
#
# Adding and removing projectors
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
# Above, when we printed the ``ecg_projs`` list that we loaded from a file, it
# showed two projectors for gradiometers (the first two, marked "planar"), two
# for magnetometers (the middle two, marked "axial"), and two for EEG sensors
# (the last two, marked "eeg"). We can add them to the :class:`~mne.io.Raw`
# object using the :meth:`~mne.io.Raw.add_proj` method:
raw.add_proj(ecg_projs)
# %%
# To remove projectors, there is a corresponding method
# :meth:`~mne.io.Raw.del_proj` that will remove projectors based on their index
# within the ``raw.info['projs']`` list. For the special case of replacing the
# existing projectors with new ones, use
# ``raw.add_proj(ecg_projs, remove_existing=True)``.
#
# To see how the ECG projectors affect the measured signal, we can once again
# plot the data with and without the projectors applied (though remember that
# the :meth:`~mne.io.Raw.plot` method only *temporarily* applies the projectors
# for visualization, and does not permanently change the underlying data).
# We'll compare the ``mags`` variable we created above, which had only the
# empty room SSP projectors, to the data with both empty room and ECG
# projectors:
mags_ecg = raw.copy().crop(tmax=2).pick_types(meg='mag')
for data, title in zip([mags, mags_ecg], ['Without', 'With']):
with mne.viz.use_browser_backend('matplotlib'):
fig = data.plot(butterfly=True, proj=True)
fig.subplots_adjust(top=0.9)
fig.suptitle('{} ECG projector'.format(title), size='xx-large',
weight='bold')
# %%
# When are projectors "applied"?
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
# By default, projectors are applied when creating :class:`epoched
# ` data from :class:`~mne.io.Raw` data, though application of the
# projectors can be *delayed* by passing ``proj=False`` to the
# :class:`~mne.Epochs` constructor. However, even when projectors have not been
# applied, the :meth:`mne.Epochs.get_data` method will return data *as if the
# projectors had been applied* (though the :class:`~mne.Epochs` object will be
# unchanged). Additionally, projectors cannot be applied if the data are not
# :ref:`preloaded `. If the data are `memory-mapped`_ (i.e., not
# preloaded), you can check the ``_projector`` attribute to see whether any
# projectors will be applied once the data is loaded in memory.
#
# Finally, when performing inverse imaging (i.e., with
# :func:`mne.minimum_norm.apply_inverse`), the projectors will be
# automatically applied. It is also possible to apply projectors manually when
# working with :class:`~mne.io.Raw`, :class:`~mne.Epochs` or
# :class:`~mne.Evoked` objects via the object's :meth:`~mne.io.Raw.apply_proj`
# method. For all instance types, you can always copy the contents of
# :samp:`{}.info['projs']` into a separate :class:`list` variable,
# use :samp:`{}.del_proj({})` to remove
# one or more projectors, and then add them back later with
# :samp:`{}.add_proj({})` if desired.
#
# .. warning::
#
# Remember that once a projector is applied, it can't be un-applied, so
# during interactive / exploratory analysis it's a good idea to use the
# object's :meth:`~mne.io.Raw.copy` method before applying projectors.
#
#
# Best practices
# ~~~~~~~~~~~~~~
#
# In general, it is recommended to apply projectors when creating
# :class:`~mne.Epochs` from :class:`~mne.io.Raw` data. There are two reasons
# for this recommendation:
#
# 1. It is computationally cheaper to apply projectors to data *after* the
# data have been reducted to just the segments of interest (the epochs)
#
# 2. If you are applying amplitude-based rejection criteria to epochs, it is
# preferable to reject based on the signal *after* projectors have been
# applied, because the projectors may reduce noise in some epochs to
# tolerable levels (thereby increasing the number of acceptable epochs and
# consequenty increasing statistical power in any later analyses).
#
#
# References
# ^^^^^^^^^^
#
# .. footbibliography::
#
#
# .. LINKS
#
# .. _`argument expansion`:
# https://docs.python.org/3/tutorial/controlflow.html#tut-unpacking-arguments
# .. _`pca`: https://en.wikipedia.org/wiki/Principal_component_analysis
# .. _`svd`: https://en.wikipedia.org/wiki/Singular_value_decomposition
# .. _`memory-mapped`: https://en.wikipedia.org/wiki/Memory-mapped_file