plot_visualize_raw.py

"""
.. _tut_viz_raw:

Visualize Raw data
==================

"""
import os.path as op
import numpy as np

import mne

data_path = op.join(mne.datasets.sample.data_path(), 'MEG', 'sample')
raw = mne.io.read_raw_fif(op.join(data_path, 'sample_audvis_raw.fif'),
                          preload=True)
raw.set_eeg_reference('average', projection=True)  # set EEG average reference
events = mne.read_events(op.join(data_path, 'sample_audvis_raw-eve.fif'))

###############################################################################
# The visualization module (:mod:`mne.viz`) contains all the plotting functions
# that work in combination with MNE data structures. Usually the easiest way to
# use them is to call a method of the data container. All of the plotting
# method names start with ``plot``. If you're using Ipython console, you can
# just write ``raw.plot`` and ask the interpreter for suggestions with a
# ``tab`` key.
#
# To visually inspect your raw data, you can use the python equivalent of
# ``mne_browse_raw``.
raw.plot(block=True, lowpass=40)

###############################################################################
# The channels are color coded by channel type. Generally MEG channels are
# colored in different shades of blue, whereas EEG channels are black. The
# scrollbar on right side of the browser window also tells us that two of the
# channels are marked as ``bad``. Bad channels are color coded gray. By
# clicking the lines or channel names on the left, you can mark or unmark a bad
# channel interactively. You can use +/- keys to adjust the scale (also = works
# for magnifying the data). Note that the initial scaling factors can be set
# with parameter ``scalings``. If you don't know the scaling factor for
# channels, you can automatically set them by passing scalings='auto'. With
# ``pageup/pagedown`` and ``home/end`` keys you can adjust the amount of data
# viewed at once.
#
# Drawing annotations
# -------------------
#
# You can enter annotation mode by pressing ``a`` key. In annotation mode you
# can mark segments of data (and modify existing annotations) with the left
# mouse button. You can use the description of any existing annotation or
# create a new description by typing when the annotation dialog is active.
# Notice that the description starting with the keyword ``'bad'`` means that
# the segment will be discarded when epoching the data. Existing annotations
# can be deleted with the right mouse button.  Annotation mode is exited by
# pressing ``a`` again or closing the annotation window. See also
# :class:`mne.Annotations` and :ref:`marking_bad_segments`. To see all the
# interactive features, hit ``?`` key or click ``help`` in the lower left
# corner of the browser window.
#
# .. warning:: Annotations are modified in-place immediately at run-time.
#              Deleted annotations cannot be retrieved after deletion.
#
# The channels are sorted by channel type by default. You can use the
# ``group_by`` parameter of :func:`raw.plot <mne.io.Raw.plot>` to group the
# channels in a different way. ``group_by='selection'`` uses the same channel
# groups as MNE-C's mne_browse_raw (see :ref:`CACCJEJD`). The selections are
# defined in ``mne-python/mne/data/mne_analyze.sel`` and by modifying the
# channels there, you can define your own selection groups. Notice that this
# also affects the selections returned by :func:`mne.read_selection`. By
# default the selections only work for Neuromag data, but
# ``group_by='position'`` tries to mimic this behavior for any data with sensor
# positions available. The channels are grouped by sensor positions to 8 evenly
# sized regions. Notice that for this to work effectively, all the data
# channels in the channel array must be present. The ``order`` parameter allows
# to customize the order and select a subset of channels for plotting (picks).
# Here we use the butterfly mode and group the channels by position. To toggle
# between regular and butterfly modes, press 'b' key when the plotter window is
# active. Notice that ``group_by`` also affects the channel groupings in
# butterfly mode.
raw.plot(butterfly=True, group_by='position')

###############################################################################
# We read the events from a file and passed it as a parameter when calling the
# method. The events are plotted as vertical lines so you can see how they
# align with the raw data.
#
# We can check where the channels reside with ``plot_sensors``. Notice that
# this method (along with many other MNE plotting functions) is callable using
# any MNE data container where the channel information is available.
raw.plot_sensors(kind='3d', ch_type='mag', ch_groups='position')

###############################################################################
# We used ``ch_groups='position'`` to color code the different regions. It uses
# the same algorithm for dividing the regions as ``order='position'`` of
# :func:`raw.plot <mne.io.Raw.plot>`. You can also pass a list of picks to
# color any channel group with different colors.
#
# Now let's add some ssp projectors to the raw data. Here we read them from a
# file and plot them.
projs = mne.read_proj(op.join(data_path, 'sample_audvis_eog-proj.fif'))
raw.add_proj(projs)
raw.plot_projs_topomap()

###############################################################################
# The first three projectors that we see are the SSP vectors from empty room
# measurements to compensate for the noise. The fourth one is the average EEG
# reference. These are already applied to the data and can no longer be
# removed. The next six are the EOG projections that we added. Every data
# channel type has two projection vectors each. Let's try the raw browser
# again.
raw.plot()

###############################################################################
# Now click the ``proj`` button at the lower right corner of the browser
# window. A selection dialog should appear, where you can toggle the projectors
# on and off. Notice that the first four are already applied to the data and
# toggling them does not change the data. However the newly added projectors
# modify the data to get rid of the EOG artifacts. Note that toggling the
# projectors here doesn't actually modify the data. This is purely for visually
# inspecting the effect. See :func:`mne.io.Raw.del_proj` to actually remove the
# projectors.
#
# Raw container also lets us easily plot the power spectra over the raw data.
# Here we plot the data using ``spatial_colors`` to map the line colors to
# channel locations (default in versions >= 0.15.0). Other option is to use the
# ``average`` (default in < 0.15.0). See the API documentation for more info.
raw.plot_psd(tmax=np.inf, average=False)

###############################################################################
# Plotting channel-wise power spectra is just as easy. The layout is inferred
# from the data by default when plotting topo plots. This works for most data,
# but it is also possible to define the layouts by hand. Here we select a
# layout with only magnetometer channels and plot it. Then we plot the channel
# wise spectra of first 30 seconds of the data.
layout = mne.channels.read_layout('Vectorview-mag')
layout.plot()
raw.plot_psd_topo(tmax=30., fmin=5., fmax=60., n_fft=1024, layout=layout)