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# -*- coding: utf-8 -*-
# noqa: E501
"""
.. _tut-spectrum-class:
==============================================================
The Spectrum and EpochsSpectrum classes: frequency-domain data
==============================================================
This tutorial shows how to create and visualize frequency-domain
representations of your data, starting from continuous :class:`~mne.io.Raw`,
discontinuous :class:`~mne.Epochs`, or averaged :class:`~mne.Evoked` data.
As usual we'll start by importing the modules we need, and loading our
:ref:`sample dataset <sample-dataset>`:
"""
# %%
import numpy as np
import mne
sample_data_folder = mne.datasets.sample.data_path()
sample_data_raw_file = (sample_data_folder / 'MEG' / 'sample' /
'sample_audvis_raw.fif')
raw = mne.io.read_raw_fif(sample_data_raw_file, verbose=False).crop(tmax=60)
# %%
# All three sensor-space containers (:class:`~mne.io.Raw`,
# :class:`~mne.Epochs`, and :class:`~mne.Evoked`) have a
# :meth:`~mne.io.Raw.compute_psd` method with the same options.
raw.compute_psd()
# %%
# By default, the spectral estimation method will be the
# :footcite:t:`Welch1967` method for continuous data, and the multitaper
# method :footcite:`Slepian1978` for epoched or averaged data. This default can
# be overridden by passing ``method='welch'`` or ``method='multitaper'`` to the
# :meth:`~mne.io.Raw.compute_psd` method.
#
# There are many other options available as well; for example we can compute a
# spectrum from a given span of times, for a chosen frequency range, and for a
# subset of the available channels:
raw.compute_psd(method='multitaper', tmin=10, tmax=20, fmin=5, fmax=30,
picks='eeg')
# %%
# You can also pass some parameters to the underlying spectral estimation
# function, such as the FFT window length and overlap for the Welch method; see
# the docstrings of :class:`mne.time_frequency.Spectrum` (esp. its
# ``method_kw`` parameter) and the spectral estimation functions
# :func:`~mne.time_frequency.psd_array_welch` and
# :func:`~mne.time_frequency.psd_array_multitaper` for details.
#
# For epoched data, the class of the spectral estimate will be
# :class:`mne.time_frequency.EpochsSpectrum` instead of
# :class:`mne.time_frequency.Spectrum`, but most of the API is the same for the
# two classes. For example, both have a
# :meth:`~mne.time_frequency.EpochsSpectrum.get_data` method with an option to
# return the bin frequencies:
with mne.use_log_level('WARNING'): # hide some irrelevant info messages
events = mne.find_events(raw, stim_channel='STI 014')
event_dict = {'auditory/left': 1, 'auditory/right': 2, 'visual/left': 3,
'visual/right': 4}
epochs = mne.Epochs(raw, events, tmin=-0.3, tmax=0.7, event_id=event_dict,
preload=True)
epo_spectrum = epochs.compute_psd()
psds, freqs = epo_spectrum.get_data(return_freqs=True)
print(f'\nPSDs shape: {psds.shape}, freqs shape: {freqs.shape}')
epo_spectrum
# %%
# Additionally, both :class:`~mne.time_frequency.Spectrum` and
# :class:`~mne.time_frequency.EpochsSpectrum` have ``__getitem__`` methods,
# meaning their data can be accessed by square-bracket indexing. For
# :class:`~mne.time_frequency.Spectrum` objects (computed from
# :class:`~mne.io.Raw` or :class:`~mne.Evoked` data), the indexing works
# similar to a :class:`~mne.io.Raw` object or a
# :class:`NumPy array<numpy.ndarray>`:
evoked = epochs['auditory'].average()
evk_spectrum = evoked.compute_psd()
# the first 3 frequency bins for the first 4 channels:
print(evk_spectrum[:4, :3])
# %%
# .. hint::
# :class: sidebar
#
# If the original :class:`~mne.Epochs` object had a metadata dataframe
# attached, the derived :class:`~mne.time_frequency.EpochsSpectrum` will
# inherit that metadata and will hence also support subselecting epochs via
# :ref:`Pandas query strings <pandas:indexing.query>`.
#
# In contrast, the :class:`~mne.time_frequency.EpochsSpectrum` has indexing
# similar to :class:`~mne.Epochs` objects: you can use string values to select
# spectral estimates for specific epochs based on their condition names, and
# what you get back is a new instance of
# :class:`~mne.time_frequency.EpochsSpectrum` rather than a
# :class:`NumPy array<numpy.ndarray>` of the data values. Selection via
# :term:`hierarchical event descriptors` (HEDs) is also possible:
# get both "visual/left" and "visual/right" epochs:
epo_spectrum['visual']
# %%
# Visualizing Spectrum objects
# ----------------------------
#
# Both :class:`~mne.time_frequency.Spectrum` and
# :class:`~mne.time_frequency.EpochsSpectrum` objects have plotting methods
# :meth:`~mne.time_frequency.Spectrum.plot` (frequency × power),
# :meth:`~mne.time_frequency.Spectrum.plot_topo` (frequency × power separately
# for each sensor), and :meth:`~mne.time_frequency.Spectrum.plot_topomap`
# (interpolated scalp topography of power, in specific frequency bands). A few
# plot options are demonstrated below; see the docstrings for full details.
evk_spectrum.plot()
evk_spectrum.plot_topo(color='k', fig_facecolor='w', axis_facecolor='w')
# %%
evk_spectrum.plot_topomap(ch_type='eeg', agg_fun=np.median)
# %%
# Migrating legacy code
# ---------------------
#
# Below is a quick-reference table of equivalent code from before and after the
# introduction of the :class:`~mne.time_frequency.Spectrum` and
# :class:`~mne.time_frequency.EpochsSpectrum` classes.
#
# .. table:: Quick reference for common Spectral class actions
# :widths: auto
#
# +---------------------------------------------------+----------------------------------------------------------------------+
# | Old | New |
# +===================================================+======================================================================+
# | ``mne.time_frequency.psd_welch(raw)`` | ``raw.compute_psd().get_data(return_freqs=True)`` |
# +---------------------------------------------------+----------------------------------------------------------------------+
# | ``mne.time_frequency.psd_multitaper(raw)`` | ``raw.compute_psd(method='multitaper').get_data(return_freqs=True)`` |
# +---------------------------------------------------+----------------------------------------------------------------------+
# | ``raw.plot_psd(fmin, fmax, dB, area_mode='std')`` | ``raw.compute_psd(fmin, fmax).plot(dB, ci='std')`` |
# +---------------------------------------------------+----------------------------------------------------------------------+
# | ``raw.plot_psd_topo(n_fft, overlap, axes)`` | ``raw.compute_psd(n_fft, overlap).plot_topo(axes)`` |
# +---------------------------------------------------+----------------------------------------------------------------------+
# | ``epochs.plot_psd_topomap(tmax, bands)`` | ``epochs.compute_psd(tmax).plot_topomap(bands)`` |
# +---------------------------------------------------+----------------------------------------------------------------------+
#
#
# .. warning::
#
# The functions ``mne.time_frequency.psd_welch`` and
# ``mne.time_frequency.psd_multitaper`` have been removed; new code
# should use the :meth:`Raw.compute_psd()<mne.io.Raw.compute_psd>`,
# :meth:`Epochs.compute_psd()<mne.Epochs.compute_psd>`, and
# :meth:`Evoked.compute_psd()<mne.Evoked.compute_psd>` methods, and pass
# ``method='welch'`` or ``method='multitaper'`` as a parameter.
#
# The class methods :meth:`Raw.plot_psd()<mne.io.Raw.plot_psd>`,
# :meth:`Epochs.plot_psd()<mne.Epochs.plot_psd>`,
# :meth:`Raw.plot_psd_topo()<mne.io.Raw.plot_psd_topo>`, and
# :meth:`Epochs.plot_psd_topomap()<mne.Epochs.plot_psd_topomap>` have been
# kept in the API to support legacy code, but should be avoided when writing
# new code.
#
#
# References
# ----------
# .. footbibliography::
|
