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"""Functions to plot raw M/EEG data
"""
from __future__ import print_function
# Authors: Eric Larson <larson.eric.d@gmail.com>
#
# License: Simplified BSD
import copy
from functools import partial
import numpy as np
from ..externals.six import string_types
from ..io.pick import pick_types
from ..io.proj import setup_proj
from ..utils import set_config, get_config, verbose
from ..time_frequency import compute_raw_psd
from .utils import figure_nobar, _toggle_options
from .utils import _mutable_defaults, _toggle_proj, tight_layout
def _plot_update_raw_proj(params, bools):
"""Helper only needs to be called when proj is changed"""
inds = np.where(bools)[0]
params['info']['projs'] = [copy.deepcopy(params['projs'][ii])
for ii in inds]
params['proj_bools'] = bools
params['projector'], _ = setup_proj(params['info'], add_eeg_ref=False,
verbose=False)
_update_raw_data(params)
params['plot_fun']()
def _update_raw_data(params):
"""Helper only needs to be called when time or proj is changed"""
start = params['t_start']
stop = params['raw'].time_as_index(start + params['duration'])[0]
start = params['raw'].time_as_index(start)[0]
data, times = params['raw'][:, start:stop]
if params['projector'] is not None:
data = np.dot(params['projector'], data)
# remove DC
if params['remove_dc'] is True:
data -= np.mean(data, axis=1)[:, np.newaxis]
# scale
for di in range(data.shape[0]):
data[di] /= params['scalings'][params['types'][di]]
# stim channels should be hard limited
if params['types'][di] == 'stim':
data[di] = np.minimum(data[di], 1.0)
params['data'] = data
params['times'] = times
def _layout_raw(params):
"""Set raw figure layout"""
s = params['fig'].get_size_inches()
scroll_width = 0.33
hscroll_dist = 0.33
vscroll_dist = 0.1
l_border = 1.2
r_border = 0.1
t_border = 0.33
b_border = 0.5
# only bother trying to reset layout if it's reasonable to do so
if s[0] < 2 * scroll_width or s[1] < 2 * scroll_width + hscroll_dist:
return
# convert to relative units
scroll_width_x = scroll_width / s[0]
scroll_width_y = scroll_width / s[1]
vscroll_dist /= s[0]
hscroll_dist /= s[1]
l_border /= s[0]
r_border /= s[0]
t_border /= s[1]
b_border /= s[1]
# main axis (traces)
ax_width = 1.0 - scroll_width_x - l_border - r_border - vscroll_dist
ax_y = hscroll_dist + scroll_width_y + b_border
ax_height = 1.0 - ax_y - t_border
params['ax'].set_position([l_border, ax_y, ax_width, ax_height])
# vscroll (channels)
pos = [ax_width + l_border + vscroll_dist, ax_y,
scroll_width_x, ax_height]
params['ax_vscroll'].set_position(pos)
# hscroll (time)
pos = [l_border, b_border, ax_width, scroll_width_y]
params['ax_hscroll'].set_position(pos)
# options button
pos = [l_border + ax_width + vscroll_dist, b_border,
scroll_width_x, scroll_width_y]
params['ax_button'].set_position(pos)
params['fig'].canvas.draw()
def _helper_resize(event, params):
"""Helper for resizing"""
size = ','.join([str(s) for s in params['fig'].get_size_inches()])
set_config('MNE_BROWSE_RAW_SIZE', size)
_layout_raw(params)
def _pick_bad_channels(event, params):
"""Helper for selecting / dropping bad channels onpick"""
bads = params['raw'].info['bads']
# trade-off, avoid selecting more than one channel when drifts are present
# however for clean data don't click on peaks but on flat segments
f = lambda x, y: y(np.mean(x), x.std() * 2)
for l in event.inaxes.lines:
ydata = l.get_ydata()
if not isinstance(ydata, list) and not np.isnan(ydata).any():
ymin, ymax = f(ydata, np.subtract), f(ydata, np.add)
if ymin <= event.ydata <= ymax:
this_chan = vars(l)['ch_name']
if this_chan in params['raw'].ch_names:
if this_chan not in bads:
bads.append(this_chan)
l.set_color(params['bad_color'])
else:
bads.pop(bads.index(this_chan))
l.set_color(vars(l)['def-color'])
event.canvas.draw()
break
# update deep-copied info to persistently draw bads
params['info']['bads'] = bads
def _mouse_click(event, params):
"""Vertical select callback"""
if event.inaxes is None or event.button != 1:
return
plot_fun = params['plot_fun']
# vertical scrollbar changed
if event.inaxes == params['ax_vscroll']:
ch_start = max(int(event.ydata) - params['n_channels'] // 2, 0)
if params['ch_start'] != ch_start:
params['ch_start'] = ch_start
plot_fun()
# horizontal scrollbar changed
elif event.inaxes == params['ax_hscroll']:
_plot_raw_time(event.xdata - params['duration'] / 2, params)
elif event.inaxes == params['ax']:
_pick_bad_channels(event, params)
def _plot_raw_time(value, params):
"""Deal with changed time value"""
info = params['info']
max_times = params['n_times'] / float(info['sfreq']) - params['duration']
if value > max_times:
value = params['n_times'] / info['sfreq'] - params['duration']
if value < 0:
value = 0
if params['t_start'] != value:
params['t_start'] = value
params['hsel_patch'].set_x(value)
_update_raw_data(params)
params['plot_fun']()
def _plot_raw_onkey(event, params):
"""Interpret key presses"""
import matplotlib.pyplot as plt
# check for initial plot
plot_fun = params['plot_fun']
if event is None:
plot_fun()
return
# quit event
if event.key == 'escape':
plt.close(params['fig'])
return
# change plotting params
ch_changed = False
if event.key == 'down':
params['ch_start'] += params['n_channels']
ch_changed = True
elif event.key == 'up':
params['ch_start'] -= params['n_channels']
ch_changed = True
elif event.key == 'right':
_plot_raw_time(params['t_start'] + params['duration'], params)
return
elif event.key == 'left':
_plot_raw_time(params['t_start'] - params['duration'], params)
return
elif event.key in ['o', 'p']:
_toggle_options(None, params)
return
# deal with plotting changes
if ch_changed is True:
if params['ch_start'] >= len(params['info']['ch_names']):
params['ch_start'] = 0
elif params['ch_start'] < 0:
# wrap to end
rem = len(params['info']['ch_names']) % params['n_channels']
params['ch_start'] = len(params['info']['ch_names'])
params['ch_start'] -= rem if rem != 0 else params['n_channels']
if ch_changed:
plot_fun()
def _plot_traces(params, inds, color, bad_color, lines, event_line, offsets):
"""Helper for plotting raw"""
info = params['info']
n_channels = params['n_channels']
params['bad_color'] = bad_color
# do the plotting
tick_list = []
for ii in range(n_channels):
ch_ind = ii + params['ch_start']
# let's be generous here and allow users to pass
# n_channels per view >= the number of traces available
if ii >= len(lines):
break
elif ch_ind < len(info['ch_names']):
# scale to fit
ch_name = info['ch_names'][inds[ch_ind]]
tick_list += [ch_name]
offset = offsets[ii]
# do NOT operate in-place lest this get screwed up
this_data = params['data'][inds[ch_ind]]
this_color = bad_color if ch_name in info['bads'] else color
if isinstance(this_color, dict):
this_color = this_color[params['types'][inds[ch_ind]]]
# subtraction here gets corect orientation for flipped ylim
lines[ii].set_ydata(offset - this_data)
lines[ii].set_xdata(params['times'])
lines[ii].set_color(this_color)
vars(lines[ii])['ch_name'] = ch_name
vars(lines[ii])['def-color'] = color[params['types'][inds[ch_ind]]]
else:
# "remove" lines
lines[ii].set_xdata([])
lines[ii].set_ydata([])
# deal with event lines
if params['events'] is not None:
t = params['events']
t = t[np.where(np.logical_and(t >= params['times'][0],
t <= params['times'][-1]))[0]]
if len(t) > 0:
xs = list()
ys = list()
for tt in t:
xs += [tt, tt, np.nan]
ys += [0, 2 * n_channels + 1, np.nan]
event_line.set_xdata(xs)
event_line.set_ydata(ys)
else:
event_line.set_xdata([])
event_line.set_ydata([])
# finalize plot
params['ax'].set_xlim(params['times'][0],
params['times'][0] + params['duration'], False)
params['ax'].set_yticklabels(tick_list)
params['vsel_patch'].set_y(params['ch_start'])
params['fig'].canvas.draw()
def plot_raw(raw, events=None, duration=10.0, start=0.0, n_channels=None,
bgcolor='w', color=None, bad_color=(0.8, 0.8, 0.8),
event_color='cyan', scalings=None, remove_dc=True, order='type',
show_options=False, title=None, show=True, block=False):
"""Plot raw data
Parameters
----------
raw : instance of Raw
The raw data to plot.
events : array | None
Events to show with vertical bars.
duration : float
Time window (sec) to plot in a given time.
start : float
Initial time to show (can be changed dynamically once plotted).
n_channels : int
Number of channels to plot at once.
bgcolor : color object
Color of the background.
color : dict | color object | None
Color for the data traces. If None, defaults to:
`dict(mag='darkblue', grad='b', eeg='k', eog='k', ecg='r', emg='k',
ref_meg='steelblue', misc='k', stim='k', resp='k', chpi='k')`
bad_color : color object
Color to make bad channels.
event_color : color object
Color to use for events.
scalings : dict | None
Scale factors for the traces. If None, defaults to:
`dict(mag=1e-12, grad=4e-11, eeg=20e-6, eog=150e-6, ecg=5e-4, emg=1e-3,
ref_meg=1e-12, misc=1e-3, stim=1, resp=1, chpi=1e-4)`
remove_dc : bool
If True remove DC component when plotting data.
order : 'type' | 'original' | array
Order in which to plot data. 'type' groups by channel type,
'original' plots in the order of ch_names, array gives the
indices to use in plotting.
show_options : bool
If True, a dialog for options related to projecion is shown.
title : str | None
The title of the window. If None, and either the filename of the
raw object or '<unknown>' will be displayed as title.
show : bool
Show figure if True
block : bool
Whether to halt program execution until the figure is closed.
Useful for setting bad channels on the fly by clicking on a line.
Returns
-------
fig : Instance of matplotlib.figure.Figure
Raw traces.
Notes
-----
The arrow keys (up/down/left/right) can typically be used to navigate
between channels and time ranges, but this depends on the backend
matplotlib is configured to use (e.g., mpl.use('TkAgg') should work).
To mark or un-mark a channel as bad, click on the rather flat segments
of a channel's time series. The changes will be reflected immediately
in the raw object's ``raw.info['bads']`` entry.
"""
import matplotlib.pyplot as plt
import matplotlib as mpl
color, scalings = _mutable_defaults(('color', color),
('scalings_plot_raw', scalings))
# make a copy of info, remove projection (for now)
info = copy.deepcopy(raw.info)
projs = info['projs']
info['projs'] = []
n_times = raw.n_times
# allow for raw objects without filename, e.g., ICA
if title is None:
title = raw._filenames
if len(title) == 0: # empty list or absent key
title = '<unknown>'
elif len(title) == 1:
title = title[0]
else: # if len(title) > 1:
title = '%s ... (+ %d more) ' % (title[0], len(title) - 1)
if len(title) > 60:
title = '...' + title[-60:]
elif not isinstance(title, string_types):
raise TypeError('title must be None or a string')
if events is not None:
events = events[:, 0].astype(float) - raw.first_samp
events /= info['sfreq']
# reorganize the data in plotting order
inds = list()
types = list()
for t in ['grad', 'mag']:
inds += [pick_types(info, meg=t, ref_meg=False, exclude=[])]
types += [t] * len(inds[-1])
pick_kwargs = dict(meg=False, ref_meg=False, exclude=[])
for t in ['eeg', 'eog', 'ecg', 'emg', 'ref_meg', 'stim', 'resp',
'misc', 'chpi', 'syst', 'ias', 'exci']:
pick_kwargs[t] = True
inds += [pick_types(raw.info, **pick_kwargs)]
types += [t] * len(inds[-1])
pick_kwargs[t] = False
inds = np.concatenate(inds).astype(int)
if not len(inds) == len(info['ch_names']):
raise RuntimeError('Some channels not classified, please report '
'this problem')
# put them back to original or modified order for natral plotting
reord = np.argsort(inds)
types = [types[ri] for ri in reord]
if isinstance(order, str):
if order == 'original':
inds = inds[reord]
elif order != 'type':
raise ValueError('Unknown order type %s' % order)
elif isinstance(order, np.ndarray):
if not np.array_equal(np.sort(order),
np.arange(len(info['ch_names']))):
raise ValueError('order, if array, must have integers from '
'0 to n_channels - 1')
# put back to original order first, then use new order
inds = inds[reord][order]
# set up projection and data parameters
params = dict(raw=raw, ch_start=0, t_start=start, duration=duration,
info=info, projs=projs, remove_dc=remove_dc,
n_channels=n_channels, scalings=scalings, types=types,
n_times=n_times, events=events)
# set up plotting
size = get_config('MNE_BROWSE_RAW_SIZE')
if size is not None:
size = size.split(',')
size = tuple([float(s) for s in size])
# have to try/catch when there's no toolbar
fig = figure_nobar(facecolor=bgcolor, figsize=size)
fig.canvas.set_window_title('mne_browse_raw')
ax = plt.subplot2grid((10, 10), (0, 0), colspan=9, rowspan=9)
ax.set_title(title, fontsize=12)
ax_hscroll = plt.subplot2grid((10, 10), (9, 0), colspan=9)
ax_hscroll.get_yaxis().set_visible(False)
ax_hscroll.set_xlabel('Time (s)')
ax_vscroll = plt.subplot2grid((10, 10), (0, 9), rowspan=9)
ax_vscroll.set_axis_off()
ax_button = plt.subplot2grid((10, 10), (9, 9))
# store these so they can be fixed on resize
params['fig'] = fig
params['ax'] = ax
params['ax_hscroll'] = ax_hscroll
params['ax_vscroll'] = ax_vscroll
params['ax_button'] = ax_button
# populate vertical and horizontal scrollbars
for ci in range(len(info['ch_names'])):
this_color = (bad_color if info['ch_names'][inds[ci]] in info['bads']
else color)
if isinstance(this_color, dict):
this_color = this_color[types[inds[ci]]]
ax_vscroll.add_patch(mpl.patches.Rectangle((0, ci), 1, 1,
facecolor=this_color,
edgecolor=this_color))
vsel_patch = mpl.patches.Rectangle((0, 0), 1, n_channels, alpha=0.5,
facecolor='w', edgecolor='w')
ax_vscroll.add_patch(vsel_patch)
params['vsel_patch'] = vsel_patch
hsel_patch = mpl.patches.Rectangle((start, 0), duration, 1, color='k',
edgecolor=None, alpha=0.5)
ax_hscroll.add_patch(hsel_patch)
params['hsel_patch'] = hsel_patch
ax_hscroll.set_xlim(0, n_times / float(info['sfreq']))
n_ch = len(info['ch_names'])
ax_vscroll.set_ylim(n_ch, 0)
ax_vscroll.set_title('Ch.')
# make shells for plotting traces
offsets = np.arange(n_channels) * 2 + 1
ax.set_yticks(offsets)
ax.set_ylim([n_channels * 2 + 1, 0])
# plot event_line first so it's in the back
event_line = ax.plot([np.nan], color=event_color)[0]
lines = [ax.plot([np.nan])[0] for _ in range(n_ch)]
ax.set_yticklabels(['X' * max([len(ch) for ch in info['ch_names']])])
params['plot_fun'] = partial(_plot_traces, params=params, inds=inds,
color=color, bad_color=bad_color, lines=lines,
event_line=event_line, offsets=offsets)
# set up callbacks
opt_button = mpl.widgets.Button(ax_button, 'Opt')
callback_option = partial(_toggle_options, params=params)
opt_button.on_clicked(callback_option)
callback_key = partial(_plot_raw_onkey, params=params)
fig.canvas.mpl_connect('key_press_event', callback_key)
callback_pick = partial(_mouse_click, params=params)
fig.canvas.mpl_connect('button_press_event', callback_pick)
callback_resize = partial(_helper_resize, params=params)
fig.canvas.mpl_connect('resize_event', callback_resize)
# As here code is shared with plot_evoked, some extra steps:
# first the actual plot update function
params['plot_update_proj_callback'] = _plot_update_raw_proj
# then the toggle handler
callback_proj = partial(_toggle_proj, params=params)
# store these for use by callbacks in the options figure
params['callback_proj'] = callback_proj
params['callback_key'] = callback_key
# have to store this, or it could get garbage-collected
params['opt_button'] = opt_button
# do initial plots
callback_proj('none')
_layout_raw(params)
# deal with projectors
params['fig_opts'] = None
if show_options is True:
_toggle_options(None, params)
if show:
plt.show(block=block)
return fig
@verbose
def plot_raw_psds(raw, tmin=0.0, tmax=60.0, fmin=0, fmax=np.inf,
proj=False, n_fft=2048, picks=None, ax=None, color='black',
area_mode='std', area_alpha=0.33, n_jobs=1, verbose=None):
"""Plot the power spectral density across channels
Parameters
----------
raw : instance of io.Raw
The raw instance to use.
tmin : float
Start time for calculations.
tmax : float
End time for calculations.
fmin : float
Start frequency to consider.
fmax : float
End frequency to consider.
proj : bool
Apply projection.
n_fft : int
Number of points to use in Welch FFT calculations.
picks : array-like of int | None
List of channels to use. Cannot be None if `ax` is supplied. If both
`picks` and `ax` are None, separate subplots will be created for
each standard channel type (`mag`, `grad`, and `eeg`).
ax : instance of matplotlib Axes | None
Axes to plot into. If None, axes will be created.
color : str | tuple
A matplotlib-compatible color to use.
area_mode : str | None
Mode for plotting area. If 'std', the mean +/- 1 STD (across channels)
will be plotted. If 'range', the min and max (across channels) will be
plotted. Bad channels will be excluded from these calculations.
If None, no area will be plotted.
area_alpha : float
Alpha for the area.
n_jobs : int
Number of jobs to run in parallel.
verbose : bool, str, int, or None
If not None, override default verbose level (see mne.verbose).
"""
import matplotlib.pyplot as plt
if area_mode not in [None, 'std', 'range']:
raise ValueError('"area_mode" must be "std", "range", or None')
if picks is None:
if ax is not None:
raise ValueError('If "ax" is not supplied (None), then "picks" '
'must also be supplied')
megs = ['mag', 'grad', False]
eegs = [False, False, True]
names = ['Magnetometers', 'Gradiometers', 'EEG']
picks_list = list()
titles_list = list()
for meg, eeg, name in zip(megs, eegs, names):
picks = pick_types(raw.info, meg=meg, eeg=eeg, ref_meg=False)
if len(picks) > 0:
picks_list.append(picks)
titles_list.append(name)
if len(picks_list) == 0:
raise RuntimeError('No MEG or EEG channels found')
else:
picks_list = [picks]
titles_list = ['Selected channels']
ax_list = [ax]
make_label = False
fig = None
if ax is None:
fig = plt.figure()
ax_list = list()
for ii in range(len(picks_list)):
# Make x-axes change together
if ii > 0:
ax_list.append(plt.subplot(len(picks_list), 1, ii + 1,
sharex=ax_list[0]))
else:
ax_list.append(plt.subplot(len(picks_list), 1, ii + 1))
make_label = True
else:
fig = ax_list[0].get_figure()
for ii, (picks, title, ax) in enumerate(zip(picks_list, titles_list,
ax_list)):
psds, freqs = compute_raw_psd(raw, tmin=tmin, tmax=tmax, picks=picks,
fmin=fmin, fmax=fmax, n_fft=n_fft,
n_jobs=n_jobs, plot=False, proj=proj)
# Convert PSDs to dB
psds = 10 * np.log10(psds)
psd_mean = np.mean(psds, axis=0)
if area_mode == 'std':
psd_std = np.std(psds, axis=0)
hyp_limits = (psd_mean - psd_std, psd_mean + psd_std)
elif area_mode == 'range':
hyp_limits = (np.min(psds, axis=0), np.max(psds, axis=0))
else: # area_mode is None
hyp_limits = None
ax.plot(freqs, psd_mean, color=color)
if hyp_limits is not None:
ax.fill_between(freqs, hyp_limits[0], y2=hyp_limits[1],
color=color, alpha=area_alpha)
if make_label:
if ii == len(picks_list) - 1:
ax.set_xlabel('Freq (Hz)')
if ii == len(picks_list) / 2:
ax.set_ylabel('Power Spectral Density (dB/Hz)')
ax.set_title(title)
ax.set_xlim(freqs[0], freqs[-1])
if make_label:
tight_layout(pad=0.1, h_pad=0.1, w_pad=0.1, fig=fig)
plt.show()
return fig
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