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# -*- coding: utf-8 -*-
"""Functions to plot evoked M/EEG data (besides topographies)."""
from __future__ import print_function
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Denis Engemann <denis.engemann@gmail.com>
# Martin Luessi <mluessi@nmr.mgh.harvard.edu>
# Eric Larson <larson.eric.d@gmail.com>
# Cathy Nangini <cnangini@gmail.com>
# Mainak Jas <mainak@neuro.hut.fi>
#
# License: Simplified BSD
from functools import partial
from copy import deepcopy
from numbers import Integral
import numpy as np
from ..io.pick import (channel_type, _pick_data_channels,
_VALID_CHANNEL_TYPES, channel_indices_by_type,
_DATA_CH_TYPES_SPLIT, _pick_inst, _get_channel_types,
_PICK_TYPES_DATA_DICT)
from ..externals.six import string_types
from ..defaults import _handle_default
from .utils import (_draw_proj_checkbox, tight_layout, _check_delayed_ssp,
plt_show, _process_times, DraggableColorbar, _setup_cmap,
_setup_vmin_vmax, _grad_pair_pick_and_name, _check_cov,
_validate_if_list_of_axes, _triage_rank_sss,
_connection_line, _get_color_list, _setup_ax_spines,
_setup_plot_projector, _prepare_joint_axes,
_set_title_multiple_electrodes, _check_time_unit,
_plot_masked_image)
from ..utils import (logger, _clean_names, warn, _pl, verbose, _validate_type,
_check_if_nan, _check_ch_locs)
from .topo import _plot_evoked_topo
from .topomap import (_prepare_topo_plot, plot_topomap, _check_outlines,
_draw_outlines, _prepare_topomap, _set_contour_locator)
from ..channels.layout import _pair_grad_sensors, _auto_topomap_coords
def _butterfly_onpick(event, params):
"""Add a channel name on click."""
params['need_draw'] = True
ax = event.artist.axes
ax_idx = np.where([ax is a for a in params['axes']])[0]
if len(ax_idx) == 0: # this can happen if ax param is used
return # let the other axes handle it
else:
ax_idx = ax_idx[0]
lidx = np.where([l is event.artist for l in params['lines'][ax_idx]])[0][0]
ch_name = params['ch_names'][params['idxs'][ax_idx][lidx]]
text = params['texts'][ax_idx]
x = event.artist.get_xdata()[event.ind[0]]
y = event.artist.get_ydata()[event.ind[0]]
text.set_x(x)
text.set_y(y)
text.set_text(ch_name)
text.set_color(event.artist.get_color())
text.set_alpha(1.)
text.set_zorder(len(ax.lines)) # to make sure it goes on top of the lines
text.set_path_effects(params['path_effects'])
# do NOT redraw here, since for butterfly plots hundreds of lines could
# potentially be picked -- use on_button_press (happens once per click)
# to do the drawing
def _butterfly_on_button_press(event, params):
"""Only draw once for picking."""
if params['need_draw']:
event.canvas.draw()
else:
idx = np.where([event.inaxes is ax for ax in params['axes']])[0]
if len(idx) == 1:
text = params['texts'][idx[0]]
text.set_alpha(0.)
text.set_path_effects([])
event.canvas.draw()
params['need_draw'] = False
def _line_plot_onselect(xmin, xmax, ch_types, info, data, times, text=None,
psd=False, time_unit='s'):
"""Draw topomaps from the selected area."""
import matplotlib.pyplot as plt
ch_types = [type_ for type_ in ch_types if type_ in ('eeg', 'grad', 'mag')]
if len(ch_types) == 0:
raise ValueError('Interactive topomaps only allowed for EEG '
'and MEG channels.')
if ('grad' in ch_types and
len(_pair_grad_sensors(info, topomap_coords=False,
raise_error=False)) < 2):
ch_types.remove('grad')
if len(ch_types) == 0:
return
vert_lines = list()
if text is not None:
text.set_visible(True)
ax = text.axes
vert_lines.append(ax.axvline(xmin, zorder=0, color='red'))
vert_lines.append(ax.axvline(xmax, zorder=0, color='red'))
fill = ax.axvspan(xmin, xmax, alpha=0.2, color='green')
evoked_fig = plt.gcf()
evoked_fig.canvas.draw()
evoked_fig.canvas.flush_events()
minidx = np.abs(times - xmin).argmin()
maxidx = np.abs(times - xmax).argmin()
fig, axarr = plt.subplots(1, len(ch_types), squeeze=False,
figsize=(3 * len(ch_types), 3))
for idx, ch_type in enumerate(ch_types):
if ch_type not in ('eeg', 'grad', 'mag'):
continue
picks, pos, merge_grads, _, ch_type = _prepare_topo_plot(
info, ch_type, layout=None)
if len(pos) < 2:
fig.delaxes(axarr[0][idx])
continue
this_data = data[picks, minidx:maxidx]
if merge_grads:
from ..channels.layout import _merge_grad_data
method = 'mean' if psd else 'rms'
this_data = _merge_grad_data(this_data, method=method)
title = '%s %s' % (ch_type, method.upper())
else:
title = ch_type
this_data = np.average(this_data, axis=1)
axarr[0][idx].set_title(title)
vmin = min(this_data) if psd else None
vmax = max(this_data) if psd else None # All negative for dB psd.
cmap = 'Reds' if psd else None
plot_topomap(this_data, pos, cmap=cmap, vmin=vmin, vmax=vmax,
axes=axarr[0][idx], show=False)
unit = 'Hz' if psd else time_unit
fig.suptitle('Average over %.2f%s - %.2f%s' % (xmin, unit, xmax, unit),
y=0.1)
tight_layout(pad=2.0, fig=fig)
plt_show()
if text is not None:
text.set_visible(False)
close_callback = partial(_topo_closed, ax=ax, lines=vert_lines,
fill=fill)
fig.canvas.mpl_connect('close_event', close_callback)
evoked_fig.canvas.draw()
evoked_fig.canvas.flush_events()
def _topo_closed(events, ax, lines, fill):
"""Remove lines from evoked plot as topomap is closed."""
for line in lines:
ax.lines.remove(line)
ax.patches.remove(fill)
ax.get_figure().canvas.draw()
def _rgb(x, y, z):
"""Transform x, y, z values into RGB colors."""
rgb = np.array([x, y, z]).T
rgb -= rgb.min(0)
rgb /= np.maximum(rgb.max(0), 1e-16) # avoid div by zero
return rgb
def _plot_legend(pos, colors, axis, bads, outlines, loc, size=30):
"""Plot (possibly colorized) channel legends for evoked plots."""
from mpl_toolkits.axes_grid1.inset_locator import inset_axes
axis.get_figure().canvas.draw()
bbox = axis.get_window_extent() # Determine the correct size.
ratio = bbox.width / bbox.height
ax = inset_axes(axis, width=str(size / ratio) + '%',
height=str(size) + '%', loc=loc)
ax.set_adjustable("box")
pos_x, pos_y = _prepare_topomap(pos, ax, check_nonzero=False)
ax.scatter(pos_x, pos_y, color=colors, s=size * .8, marker='.', zorder=1)
if bads:
bads = np.array(bads)
ax.scatter(pos_x[bads], pos_y[bads], s=size / 6, marker='.',
color='w', zorder=1)
_draw_outlines(ax, outlines)
def _plot_evoked(evoked, picks, exclude, unit, show, ylim, proj, xlim, hline,
units, scalings, titles, axes, plot_type, cmap=None,
gfp=False, window_title=None, spatial_colors=False,
set_tight_layout=True, selectable=True, zorder='unsorted',
noise_cov=None, colorbar=True, mask=None, mask_style=None,
mask_cmap=None, mask_alpha=.25, time_unit='s',
show_names=False, group_by=None):
"""Aux function for plot_evoked and plot_evoked_image (cf. docstrings).
Extra param is:
plot_type : str, value ('butterfly' | 'image')
The type of graph to plot: 'butterfly' plots each channel as a line
(x axis: time, y axis: amplitude). 'image' plots a 2D image where
color depicts the amplitude of each channel at a given time point
(x axis: time, y axis: channel). In 'image' mode, the plot is not
interactive.
"""
import matplotlib.pyplot as plt
# For evoked.plot_image ...
# First input checks for group_by and axes if any of them is not None.
# Either both must be dicts, or neither.
# If the former, the two dicts provide picks and axes to plot them to.
# Then, we call this function recursively for each entry in `group_by`.
if plot_type == "image" and isinstance(group_by, dict):
if axes is None:
axes = dict()
for sel in group_by:
plt.figure()
axes[sel] = plt.axes()
if not isinstance(axes, dict):
raise ValueError("If `group_by` is a dict, `axes` must be "
"a dict of axes or None.")
_validate_if_list_of_axes(list(axes.values()))
remove_xlabels = any([ax.is_last_row() for ax in axes.values()])
for sel in group_by: # ... we loop over selections
if sel not in axes:
raise ValueError(sel + " present in `group_by`, but not "
"found in `axes`")
ax = axes[sel]
# the unwieldy dict comp below defaults the title to the sel
_plot_evoked(evoked, group_by[sel], exclude, unit, show, ylim,
proj, xlim, hline, units, scalings,
(titles if titles is not None else
{channel_type(evoked.info, idx): sel
for idx in group_by[sel]}),
ax, plot_type, cmap=cmap, gfp=gfp,
window_title=window_title,
set_tight_layout=set_tight_layout,
selectable=selectable, noise_cov=noise_cov,
colorbar=colorbar, mask=mask,
mask_style=mask_style, mask_cmap=mask_cmap,
mask_alpha=mask_alpha, time_unit=time_unit,
show_names=show_names)
if remove_xlabels and not ax.is_last_row():
ax.set_xticklabels([])
ax.set_xlabel("")
ims = [ax.images[0] for ax in axes.values()]
clims = np.array([im.get_clim() for im in ims])
min, max = clims.min(), clims.max()
for im in ims:
im.set_clim(min, max)
figs = [ax.get_figure() for ax in axes.values()]
if len(set(figs)) is 1:
return figs[0]
else:
return figs
elif isinstance(axes, dict):
raise ValueError("If `group_by` is not a dict, "
"`axes` must not be a dict either.")
time_unit, times = _check_time_unit(time_unit, evoked.times)
info = evoked.info
if axes is not None and proj == 'interactive':
raise RuntimeError('Currently only single axis figures are supported'
' for interactive SSP selection.')
if isinstance(gfp, string_types) and gfp != 'only':
raise ValueError('gfp must be boolean or "only". Got %s' % gfp)
scalings = _handle_default('scalings', scalings)
titles = _handle_default('titles', titles)
units = _handle_default('units', units)
if picks is None:
picks = list(range(info['nchan']))
if len(picks) != len(set(picks)):
raise ValueError("`picks` are not unique. Please remove duplicates.")
bad_ch_idx = [info['ch_names'].index(ch) for ch in info['bads']
if ch in info['ch_names']]
if len(exclude) > 0:
if isinstance(exclude, string_types) and exclude == 'bads':
exclude = bad_ch_idx
elif (isinstance(exclude, list) and
all(isinstance(ch, string_types) for ch in exclude)):
exclude = [info['ch_names'].index(ch) for ch in exclude]
else:
raise ValueError(
'exclude has to be a list of channel names or "bads"')
picks = [pick for pick in picks if pick not in exclude]
picks = np.array(picks)
types = np.array([channel_type(info, idx) for idx in picks], np.unicode)
ch_types_used = list()
for this_type in _VALID_CHANNEL_TYPES:
if this_type in types:
ch_types_used.append(this_type)
fig = None
if axes is None:
fig, axes = plt.subplots(len(ch_types_used), 1)
plt.subplots_adjust(0.175, 0.08, 0.94, 0.94, 0.2, 0.63)
if isinstance(axes, plt.Axes):
axes = [axes]
fig.set_size_inches(6.4, 2 + len(axes))
if isinstance(axes, plt.Axes):
axes = [axes]
elif isinstance(axes, np.ndarray):
axes = list(axes)
if fig is None:
fig = axes[0].get_figure()
if window_title is not None:
fig.canvas.set_window_title(window_title)
if len(axes) != len(ch_types_used):
raise ValueError('Number of axes (%g) must match number of channel '
'types (%d: %s)' % (len(axes), len(ch_types_used),
sorted(ch_types_used)))
noise_cov = _check_cov(noise_cov, info)
projector, whitened_ch_names = _setup_plot_projector(
info, noise_cov, proj=proj is True, nave=evoked.nave)
evoked = evoked.copy()
if len(whitened_ch_names) > 0:
unit = False
if projector is not None:
evoked.data[:] = np.dot(projector, evoked.data)
if plot_type == 'butterfly':
_plot_lines(evoked.data, info, picks, fig, axes, spatial_colors, unit,
units, scalings, hline, gfp, types, zorder, xlim, ylim,
times, bad_ch_idx, titles, ch_types_used, selectable,
False, line_alpha=1., nave=evoked.nave,
time_unit=time_unit)
plt.setp(axes, xlabel='Time (%s)' % time_unit)
elif plot_type == 'image':
for ai, (ax, this_type) in enumerate(zip(axes, ch_types_used)):
use_nave = evoked.nave if ai == 0 else None
this_picks = list(picks[types == this_type])
_plot_image(evoked.data, ax, this_type, this_picks, cmap, unit,
units, scalings, times, xlim, ylim, titles,
colorbar=colorbar, mask=mask, mask_style=mask_style,
mask_cmap=mask_cmap, mask_alpha=mask_alpha,
nave=use_nave, time_unit=time_unit,
show_names=show_names, ch_names=evoked.ch_names)
if proj == 'interactive':
_check_delayed_ssp(evoked)
params = dict(evoked=evoked, fig=fig, projs=info['projs'], axes=axes,
types=types, units=units, scalings=scalings, unit=unit,
ch_types_used=ch_types_used, picks=picks,
plot_update_proj_callback=_plot_update_evoked,
plot_type=plot_type)
_draw_proj_checkbox(None, params)
plt.setp(fig.axes[:len(ch_types_used) - 1], xlabel='')
fig.canvas.draw() # for axes plots update axes.
if set_tight_layout:
tight_layout(fig=fig)
plt_show(show)
return fig
def _plot_lines(data, info, picks, fig, axes, spatial_colors, unit, units,
scalings, hline, gfp, types, zorder, xlim, ylim, times,
bad_ch_idx, titles, ch_types_used, selectable, psd,
line_alpha, nave, time_unit='ms'):
"""Plot data as butterfly plot."""
from matplotlib import patheffects, pyplot as plt
from matplotlib.widgets import SpanSelector
assert len(axes) == len(ch_types_used)
texts = list()
idxs = list()
lines = list()
path_effects = [patheffects.withStroke(linewidth=2, foreground="w",
alpha=0.75)]
gfp_path_effects = [patheffects.withStroke(linewidth=5, foreground="w",
alpha=0.75)]
if selectable:
selectables = np.ones(len(ch_types_used), dtype=bool)
for type_idx, this_type in enumerate(ch_types_used):
idx = picks[types == this_type]
if len(idx) < 2 or (this_type == 'grad' and len(idx) < 4):
# prevent unnecessary warnings for e.g. EOG
if this_type in _DATA_CH_TYPES_SPLIT:
logger.info('Need more than one channel to make '
'topography for %s. Disabling interactivity.'
% (this_type,))
selectables[type_idx] = False
if selectable:
# Parameters for butterfly interactive plots
params = dict(axes=axes, texts=texts, lines=lines,
ch_names=info['ch_names'], idxs=idxs, need_draw=False,
path_effects=path_effects)
fig.canvas.mpl_connect('pick_event',
partial(_butterfly_onpick, params=params))
fig.canvas.mpl_connect('button_press_event',
partial(_butterfly_on_button_press,
params=params))
for ai, (ax, this_type) in enumerate(zip(axes, ch_types_used)):
line_list = list() # 'line_list' contains the lines for this axes
if unit is False:
this_scaling = 1.0
ch_unit = 'NA' # no unit
else:
this_scaling = 1. if scalings is None else scalings[this_type]
ch_unit = units[this_type]
idx = list(picks[types == this_type])
idxs.append(idx)
if len(idx) > 0:
# Set amplitude scaling
D = this_scaling * data[idx, :]
_check_if_nan(D)
gfp_only = (isinstance(gfp, string_types) and gfp == 'only')
if not gfp_only:
chs = [info['chs'][i] for i in idx]
locs3d = np.array([ch['loc'][:3] for ch in chs])
if spatial_colors is True and not _check_ch_locs(chs):
warn('Channel locations not available. Disabling spatial '
'colors.')
spatial_colors = selectable = False
if spatial_colors is True and len(idx) != 1:
x, y, z = locs3d.T
colors = _rgb(x, y, z)
_handle_spatial_colors(colors, info, idx, this_type, psd,
ax)
else:
if isinstance(spatial_colors, (tuple, string_types)):
col = [spatial_colors]
else:
col = ['k']
colors = col * len(idx)
for i in bad_ch_idx:
if i in idx:
colors[idx.index(i)] = 'r'
if zorder == 'std':
# find the channels with the least activity
# to map them in front of the more active ones
z_ord = D.std(axis=1).argsort()
elif zorder == 'unsorted':
z_ord = list(range(D.shape[0]))
elif not callable(zorder):
error = ('`zorder` must be a function, "std" '
'or "unsorted", not {0}.')
raise TypeError(error.format(type(zorder)))
else:
z_ord = zorder(D)
# plot channels
for ch_idx, z in enumerate(z_ord):
line_list.append(
ax.plot(times, D[ch_idx], picker=3.,
zorder=z + 1 if spatial_colors is True else 1,
color=colors[ch_idx], alpha=line_alpha,
linewidth=0.5)[0])
if gfp: # 'only' or boolean True
gfp_color = 3 * (0.,) if spatial_colors is True else (0., 1.,
0.)
this_gfp = np.sqrt((D * D).mean(axis=0))
this_ylim = ax.get_ylim() if (ylim is None or this_type not in
ylim.keys()) else ylim[this_type]
if gfp_only:
y_offset = 0.
else:
y_offset = this_ylim[0]
this_gfp += y_offset
ax.fill_between(times, y_offset, this_gfp, color='none',
facecolor=gfp_color, zorder=1, alpha=0.2)
line_list.append(ax.plot(times, this_gfp, color=gfp_color,
zorder=3, alpha=line_alpha)[0])
ax.text(times[0] + 0.01 * (times[-1] - times[0]),
this_gfp[0] + 0.05 * np.diff(ax.get_ylim())[0],
'GFP', zorder=4, color=gfp_color,
path_effects=gfp_path_effects)
for ii, line in zip(idx, line_list):
if ii in bad_ch_idx:
line.set_zorder(2)
if spatial_colors is True:
line.set_linestyle("--")
ax.set_ylabel(ch_unit)
# for old matplotlib, we actually need this to have a bounding
# box (!), so we have to put some valid text here, change
# alpha and path effects later
texts.append(ax.text(0, 0, 'blank', zorder=3,
verticalalignment='baseline',
horizontalalignment='left',
fontweight='bold', alpha=0))
if xlim is not None:
if xlim == 'tight':
xlim = (times[0], times[-1])
ax.set_xlim(xlim)
if ylim is not None and this_type in ylim:
ax.set_ylim(ylim[this_type])
ax.set(title=r'%s (%d channel%s)'
% (titles[this_type], len(D), _pl(len(D))))
if ai == 0:
_add_nave(ax, nave)
if hline is not None:
for h in hline:
c = ('grey' if spatial_colors is True else 'r')
ax.axhline(h, linestyle='--', linewidth=2, color=c)
lines.append(line_list)
if selectable:
for ax in np.array(axes)[selectables]:
if len(ax.lines) == 1:
continue
text = ax.annotate('Loading...', xy=(0.01, 0.1),
xycoords='axes fraction', fontsize=20,
color='green', zorder=3)
text.set_visible(False)
callback_onselect = partial(_line_plot_onselect,
ch_types=ch_types_used, info=info,
data=data, times=times, text=text,
psd=psd, time_unit=time_unit)
blit = False if plt.get_backend() == 'MacOSX' else True
minspan = 0 if len(times) < 2 else times[1] - times[0]
ax._span_selector = SpanSelector(
ax, callback_onselect, 'horizontal', minspan=minspan,
useblit=blit, rectprops=dict(alpha=0.5, facecolor='red'))
def _add_nave(ax, nave):
"""Add nave to axes."""
if nave is not None:
ax.annotate(
r'N$_{\mathrm{ave}}$=%d' % nave, ha='left', va='bottom',
xy=(0, 1), xycoords='axes fraction',
xytext=(0, 5), textcoords='offset pixels')
def _handle_spatial_colors(colors, info, idx, ch_type, psd, ax):
"""Set up spatial colors."""
used_nm = np.array(_clean_names(info['ch_names']))[idx]
# find indices for bads
bads = [np.where(used_nm == bad)[0][0] for bad in info['bads'] if bad in
used_nm]
pos = _auto_topomap_coords(info, idx, ignore_overlap=True, to_sphere=True)
pos, outlines = _check_outlines(pos, np.array([1, 1]),
{'center': (0, 0), 'scale': (0.5, 0.5)})
loc = 1 if psd else 2 # Legend in top right for psd plot.
_plot_legend(pos, colors, ax, bads, outlines, loc)
def _plot_image(data, ax, this_type, picks, cmap, unit, units, scalings, times,
xlim, ylim, titles, colorbar=True, mask=None, mask_cmap=None,
mask_style=None, mask_alpha=.25, nave=None,
time_unit='s', show_names=False, ch_names=None):
"""Plot images."""
import matplotlib.pyplot as plt
assert time_unit is not None
if show_names == "auto":
if picks is not None:
show_names = "all" if len(picks) < 25 else True
else:
show_names = False
cmap = _setup_cmap(cmap)
ch_unit = units[this_type]
this_scaling = scalings[this_type]
if unit is False:
this_scaling = 1.0
ch_unit = 'NA' # no unit
if picks is not None:
data = data[picks]
if mask is not None:
mask = mask[picks]
# Show the image
# Set amplitude scaling
data = this_scaling * data
if ylim is None or this_type not in ylim:
vmax = np.abs(data).max()
vmin = -vmax
else:
vmin, vmax = ylim[this_type]
_check_if_nan(data)
im, t_end = _plot_masked_image(
ax, data, times, mask, picks=None, yvals=None, cmap=cmap[0],
vmin=vmin, vmax=vmax, mask_style=mask_style, mask_alpha=mask_alpha,
mask_cmap=mask_cmap)
if xlim is not None:
if xlim == 'tight':
xlim = (times[0], times[-1])
ax.set_xlim(xlim)
if colorbar:
cbar = plt.colorbar(im, ax=ax)
cbar.ax.set_title(ch_unit)
if cmap[1]:
ax.CB = DraggableColorbar(cbar, im)
ylabel = "Channels" if show_names else 'Channel (index)'
t = titles[this_type] + ' (%d channel%s' % (len(data), _pl(data)) + t_end
ax.set(ylabel=ylabel, xlabel='Time (%s)' % (time_unit,), title=t)
_add_nave(ax, nave)
if show_names is not False:
if show_names == "all":
yticks = np.arange(len(picks)).astype(int)
yticklabels = np.array(ch_names)[picks]
else:
max_tick = len(picks)
yticks = [tick for tick in ax.get_yticks() if tick < max_tick]
yticks = np.array(yticks).astype(int)
# these should only ever be ints right?
yticklabels = np.array(ch_names)[picks][yticks]
ax.set(yticks=yticks + .5, yticklabels=yticklabels)
@verbose
def plot_evoked(evoked, picks=None, exclude='bads', unit=True, show=True,
ylim=None, xlim='tight', proj=False, hline=None, units=None,
scalings=None, titles=None, axes=None, gfp=False,
window_title=None, spatial_colors=False, zorder='unsorted',
selectable=True, noise_cov=None, time_unit='s', verbose=None):
"""Plot evoked data using butterfly plots.
Left click to a line shows the channel name. Selecting an area by clicking
and holding left mouse button plots a topographic map of the painted area.
.. note:: If bad channels are not excluded they are shown in red.
Parameters
----------
evoked : instance of Evoked
The evoked data
picks : array-like of int | None
The indices of channels to plot. If None show all.
exclude : list of str | 'bads'
Channels names to exclude from being shown. If 'bads', the
bad channels are excluded.
unit : bool
Scale plot with channel (SI) unit.
show : bool
Show figure if True.
ylim : dict | None
ylim for plots (after scaling has been applied). e.g.
ylim = dict(eeg=[-20, 20])
Valid keys are eeg, mag, grad, misc. If None, the ylim parameter
for each channel equals the pyplot default.
xlim : 'tight' | tuple | None
xlim for plots.
proj : bool | 'interactive'
If true SSP projections are applied before display. If 'interactive',
a check box for reversible selection of SSP projection vectors will
be shown.
hline : list of floats | None
The values at which to show an horizontal line.
units : dict | None
The units of the channel types used for axes labels. If None,
defaults to `dict(eeg='uV', grad='fT/cm', mag='fT')`.
scalings : dict | None
The scalings of the channel types to be applied for plotting. If None,
defaults to ``dict(eeg=1e6, grad=1e13, mag=1e15)``.
titles : dict | None
The titles associated with the channels. If None, defaults to
`dict(eeg='EEG', grad='Gradiometers', mag='Magnetometers')`.
axes : instance of Axis | list | None
The axes to plot to. If list, the list must be a list of Axes of
the same length as the number of channel types. If instance of
Axes, there must be only one channel type plotted.
gfp : bool | 'only'
Plot GFP in green if True or "only". If "only", then the individual
channel traces will not be shown.
window_title : str | None
The title to put at the top of the figure.
spatial_colors : bool
If True, the lines are color coded by mapping physical sensor
coordinates into color values. Spatially similar channels will have
similar colors. Bad channels will be dotted. If False, the good
channels are plotted black and bad channels red. Defaults to False.
zorder : str | callable
Which channels to put in the front or back. Only matters if
`spatial_colors` is used.
If str, must be `std` or `unsorted` (defaults to `unsorted`). If
`std`, data with the lowest standard deviation (weakest effects) will
be put in front so that they are not obscured by those with stronger
effects. If `unsorted`, channels are z-sorted as in the evoked
instance.
If callable, must take one argument: a numpy array of the same
dimensionality as the evoked raw data; and return a list of
unique integers corresponding to the number of channels.
.. versionadded:: 0.13.0
selectable : bool
Whether to use interactive features. If True (default), it is possible
to paint an area to draw topomaps. When False, the interactive features
are disabled. Disabling interactive features reduces memory consumption
and is useful when using ``axes`` parameter to draw multiaxes figures.
.. versionadded:: 0.13.0
noise_cov : instance of Covariance | str | None
Noise covariance used to whiten the data while plotting.
Whitened data channel names are shown in italic.
Can be a string to load a covariance from disk.
See also :meth:`mne.Evoked.plot_white` for additional inspection
of noise covariance properties when whitening evoked data.
For data processed with SSS, the effective dependence between
magnetometers and gradiometers may introduce differences in scaling,
consider using :meth:`mne.Evoked.plot_white`.
.. versionadded:: 0.16.0
time_unit : str
The units for the time axis, can be "ms" or "s" (default).
.. versionadded:: 0.16
verbose : bool, str, int, or None
If not None, override default verbose level (see :func:`mne.verbose`
and :ref:`Logging documentation <tut_logging>` for more).
Returns
-------
fig : instance of matplotlib.figure.Figure
Figure containing the butterfly plots.
See Also
--------
mne.viz.plot_evoked_white
"""
return _plot_evoked(
evoked=evoked, picks=picks, exclude=exclude, unit=unit, show=show,
ylim=ylim, proj=proj, xlim=xlim, hline=hline, units=units,
scalings=scalings, titles=titles, axes=axes, plot_type="butterfly",
gfp=gfp, window_title=window_title, spatial_colors=spatial_colors,
selectable=selectable, zorder=zorder, noise_cov=noise_cov,
time_unit=time_unit)
def plot_evoked_topo(evoked, layout=None, layout_scale=0.945, color=None,
border='none', ylim=None, scalings=None, title=None,
proj=False, vline=[0.0], fig_background=None,
merge_grads=False, legend=True, axes=None,
background_color='w', noise_cov=None, show=True):
"""Plot 2D topography of evoked responses.
Clicking on the plot of an individual sensor opens a new figure showing
the evoked response for the selected sensor.
Parameters
----------
evoked : list of Evoked | Evoked
The evoked response to plot.
layout : instance of Layout | None
Layout instance specifying sensor positions (does not need to
be specified for Neuromag data). If possible, the correct layout is
inferred from the data.
layout_scale: float
Scaling factor for adjusting the relative size of the layout
on the canvas
color : list of color objects | color object | None
Everything matplotlib accepts to specify colors. If not list-like,
the color specified will be repeated. If None, colors are
automatically drawn.
border : str
matplotlib borders style to be used for each sensor plot.
ylim : dict | None
ylim for plots (after scaling has been applied). The value
determines the upper and lower subplot limits. e.g.
ylim = dict(eeg=[-20, 20]). Valid keys are eeg, mag, grad, misc.
If None, the ylim parameter for each channel is determined by
the maximum absolute peak.
scalings : dict | None
The scalings of the channel types to be applied for plotting. If None,`
defaults to `dict(eeg=1e6, grad=1e13, mag=1e15)`.
title : str
Title of the figure.
proj : bool | 'interactive'
If true SSP projections are applied before display. If 'interactive',
a check box for reversible selection of SSP projection vectors will
be shown.
vline : list of floats | None
The values at which to show a vertical line.
fig_background : None | numpy ndarray
A background image for the figure. This must work with a call to
plt.imshow. Defaults to None.
merge_grads : bool
Whether to use RMS value of gradiometer pairs. Only works for Neuromag
data. Defaults to False.
legend : bool | int | string | tuple
If True, create a legend based on evoked.comment. If False, disable the
legend. Otherwise, the legend is created and the parameter value is
passed as the location parameter to the matplotlib legend call. It can
be an integer (e.g. 0 corresponds to upper right corner of the plot),
a string (e.g. 'upper right'), or a tuple (x, y coordinates of the
lower left corner of the legend in the axes coordinate system).
See matplotlib documentation for more details.
axes : instance of matplotlib Axes | None
Axes to plot into. If None, axes will be created.
background_color : str | obj
Background color. Typically 'k' (black) or 'w' (white; default).
.. versionadded:: 0.15.0
noise_cov : instance of Covariance | str | None
Noise covariance used to whiten the data while plotting.
Whitened data channel names are shown in italic.
Can be a string to load a covariance from disk.
.. versionadded:: 0.16.0
show : bool
Show figure if True.
Returns
-------
fig : instance of matplotlib.figure.Figure
Images of evoked responses at sensor locations
"""
from matplotlib.colors import colorConverter
if not type(evoked) in (tuple, list):
evoked = [evoked]
dark_background = \
np.mean(colorConverter.to_rgb(background_color)) < 0.5
if dark_background:
fig_facecolor = background_color
axis_facecolor = background_color
font_color = 'w'
else:
fig_facecolor = background_color
axis_facecolor = background_color
font_color = 'k'
if color is None:
if dark_background:
color = ['w'] + _get_color_list()
else:
color = _get_color_list()
color = color * ((len(evoked) % len(color)) + 1)
color = color[:len(evoked)]
return _plot_evoked_topo(evoked=evoked, layout=layout,
layout_scale=layout_scale, color=color,
border=border, ylim=ylim, scalings=scalings,
title=title, proj=proj, vline=vline,
fig_facecolor=fig_facecolor,
fig_background=fig_background,
axis_facecolor=axis_facecolor,
font_color=font_color, merge_grads=merge_grads,
legend=legend, axes=axes, show=show,
noise_cov=noise_cov)
def plot_evoked_image(evoked, picks=None, exclude='bads', unit=True,
show=True, clim=None, xlim='tight', proj=False,
units=None, scalings=None, titles=None, axes=None,
cmap='RdBu_r', colorbar=True, mask=None,
mask_style=None, mask_cmap="Greys", mask_alpha=.25,
time_unit='s', show_names="auto", group_by=None):
"""Plot evoked data as images.
Parameters
----------
evoked : instance of Evoked
The evoked data
picks : array-like of int | None
The indices of channels to plot. If None show all.
This parameter can also be used to set the order the channels
are shown in, as the channel image is sorted by the order of picks.
exclude : list of str | 'bads'
Channels names to exclude from being shown. If 'bads', the
bad channels are excluded.
unit : bool
Scale plot with channel (SI) unit.
show : bool
Show figure if True.
clim : dict | None
clim for plots (after scaling has been applied). e.g.
clim = dict(eeg=[-20, 20])
Valid keys are eeg, mag, grad, misc. If None, the clim parameter
for each channel equals the pyplot default.
xlim : 'tight' | tuple | None
xlim for plots.
proj : bool | 'interactive'
If true SSP projections are applied before display. If 'interactive',
a check box for reversible selection of SSP projection vectors will
be shown.
units : dict | None
The units of the channel types used for axes labels. If None,
defaults to ``dict(eeg='uV', grad='fT/cm', mag='fT')``.
scalings : dict | None
The scalings of the channel types to be applied for plotting. If None,`
defaults to ``dict(eeg=1e6, grad=1e13, mag=1e15)``.
titles : dict | None
The titles associated with the channels. If None, defaults to
``dict(eeg='EEG', grad='Gradiometers', mag='Magnetometers')``.
axes : instance of Axis | list | dict | None
The axes to plot to. If list, the list must be a list of Axes of
the same length as the number of channel types. If instance of
Axes, there must be only one channel type plotted.
If `group_by` is a dict, this cannot be a list, but it can be a dict
of lists of axes, with the keys matching those of `group_by`. In that
case, the provided axes will be used for the corresponding groups.
Defaults to `None`.
cmap : matplotlib colormap | (colormap, bool) | 'interactive'
Colormap. If tuple, the first value indicates the colormap to use and
the second value is a boolean defining interactivity. In interactive
mode the colors are adjustable by clicking and dragging the colorbar
with left and right mouse button. Left mouse button moves the scale up
and down and right mouse button adjusts the range. Hitting space bar
resets the scale. Up and down arrows can be used to change the
colormap. If 'interactive', translates to ``('RdBu_r', True)``.
Defaults to ``'RdBu_r'``.
colorbar : bool
If True, plot a colorbar. Defaults to True.
.. versionadded:: 0.16
mask : ndarray | None
An array of booleans of the same shape as the data. Entries of the
data that correspond to ```False`` in the mask are masked (see
`do_mask` below). Useful for, e.g., masking for statistical
significance.
.. versionadded:: 0.16
mask_style: None | 'both' | 'contour' | 'mask'
If `mask` is not None: if 'contour', a contour line is drawn around
the masked areas (``True`` in `mask`). If 'mask', entries not
``True`` in `mask` are shown transparently. If 'both', both a contour
and transparency are used.
If ``None``, defaults to 'both' if `mask` is not None, and is ignored
otherwise.
.. versionadded:: 0.16
mask_cmap : matplotlib colormap | (colormap, bool) | 'interactive'
The colormap chosen for masked parts of the image (see below), if
`mask` is not ``None``. If None, `cmap` is reused. Defaults to
``Greys``. Not interactive. Otherwise, as `cmap`.
mask_alpha : float
A float between 0 and 1. If `mask` is not None, this sets the
alpha level (degree of transparency) for the masked-out segments.
I.e., if 0, masked-out segments are not visible at all.
Defaults to .25.
.. versionadded:: 0.16
time_unit : str
The units for the time axis, can be "ms" or "s" (default).
.. versionadded:: 0.16
show_names : bool | str
Determines if channel names should be plotted on the y axis. If False,
no names are shown. If True, ticks are set automatically and the
corresponding channel names are shown. If str, must be "auto" or "all".
If "all", all channel names are shown.
If "auto", is set to False if `picks` is ``None``; to ``True`` if
`picks` is not ``None`` and fewer than 25 picks are shown; to "all"
if `picks` is not ``None`` and contains fewer than 25 entries.
group_by : None | dict
If a dict, the values must be picks, and `axes` must also be a dict
with matching keys, or None. If `axes` is None, one figure and one axis
will be created for each entry in `group_by`.
Then, for each entry, the picked channels will be plotted
to the corresponding axis. If `titles` are None, keys will become plot
titles. This is useful for e.g. ROIs. Each entry must contain only
one channel type. For example::
group_by=dict(Left_ROI=[1, 2, 3, 4], Right_ROI=[5, 6, 7, 8])
If None, all picked channels are plotted to the same axis.
Returns
-------
fig : instance of matplotlib.figure.Figure
Figure containing the images.
"""
return _plot_evoked(evoked=evoked, picks=picks, exclude=exclude, unit=unit,
show=show, ylim=clim, proj=proj, xlim=xlim, hline=None,
units=units, scalings=scalings, titles=titles,
axes=axes, plot_type="image", cmap=cmap,
colorbar=colorbar, mask=mask, mask_style=mask_style,
mask_cmap=mask_cmap, mask_alpha=mask_alpha,
time_unit=time_unit, show_names=show_names,
group_by=group_by)
def _plot_update_evoked(params, bools):
"""Update the plot evoked lines."""
picks, evoked = [params[k] for k in ('picks', 'evoked')]
projs = [proj for ii, proj in enumerate(params['projs'])
if ii in np.where(bools)[0]]
params['proj_bools'] = bools
new_evoked = evoked.copy()
new_evoked.info['projs'] = []
new_evoked.add_proj(projs)
new_evoked.apply_proj()
for ax, t in zip(params['axes'], params['ch_types_used']):
this_scaling = params['scalings'][t]
idx = [picks[i] for i in range(len(picks)) if params['types'][i] == t]
D = this_scaling * new_evoked.data[idx, :]
if params['plot_type'] == 'butterfly':
for line, di in zip(ax.lines, D):
line.set_ydata(di)
else:
ax.images[0].set_data(D)
params['fig'].canvas.draw()
@verbose
def plot_evoked_white(evoked, noise_cov, show=True, rank=None, time_unit='s',
verbose=None):
u"""Plot whitened evoked response.
Plots the whitened evoked response and the whitened GFP as described in
[1]_. This function is especially useful for investigating noise
covariance properties to determine if data are properly whitened (e.g.,
achieving expected values in line with model assumptions, see Notes below).
Parameters
----------
evoked : instance of mne.Evoked
The evoked response.
noise_cov : list | instance of Covariance | str
The noise covariance. Can be a string to load a covariance from disk.
show : bool
Show figure if True.
rank : dict of int | None
Dict of ints where keys are 'eeg', 'meg', mag' or 'grad'. If None,
the rank is detected automatically. Defaults to None. 'mag' or
'grad' cannot be specified jointly with 'meg'. For SSS'd data,
only 'meg' is valid. For non-SSS'd data, 'mag' and/or 'grad' must be
specified separately. If only one is specified, the other one gets
estimated. Note. The rank estimation will be printed by the logger for
each noise covariance estimator that is passed.
time_unit : str
The units for the time axis, can be "ms" or "s" (default).
.. versionadded:: 0.16
verbose : bool, str, int, or None
If not None, override default verbose level (see :func:`mne.verbose`
and :ref:`Logging documentation <tut_logging>` for more).
Returns
-------
fig : instance of matplotlib.figure.Figure
The figure object containing the plot.
See Also
--------
mne.Evoked.plot
Notes
-----
If baseline signals match the assumption of Gaussian white noise,
values should be centered at 0, and be within 2 standard deviations
(±1.96) for 95% of the time points. For the global field power (GFP),
we expect it to fluctuate around a value of 1.
If one single covariance object is passed, the GFP panel (bottom)
will depict different sensor types. If multiple covariance objects are
passed as a list, the left column will display the whitened evoked
responses for each channel based on the whitener from the noise covariance
that has the highest log-likelihood. The left column will depict the
whitened GFPs based on each estimator separately for each sensor type.
Instead of numbers of channels the GFP display shows the estimated rank.
Note. The rank estimation will be printed by the logger
(if ``verbose=True``) for each noise covariance estimator that is passed.
References
----------
.. [1] Engemann D. and Gramfort A. (2015) Automated model selection in
covariance estimation and spatial whitening of MEG and EEG
signals, vol. 108, 328-342, NeuroImage.
"""
return _plot_evoked_white(evoked=evoked, noise_cov=noise_cov,
scalings=None, rank=rank, show=show,
time_unit=time_unit)
def _plot_evoked_white(evoked, noise_cov, scalings=None, rank=None, show=True,
time_unit='s'):
"""Help plot_evoked_white.
Additional Parameters
---------------------
scalings : dict | None
The rescaling method to be applied to improve the accuracy of rank
estimaiton. If dict, it will override the following default values
(used if None)::
dict(mag=1e12, grad=1e11, eeg=1e5)
Note. Theses values were tested on different datests across various
conditions. You should not need to update them.
"""
from ..cov import whiten_evoked, read_cov # recursive import
import matplotlib.pyplot as plt
time_unit, times = _check_time_unit(time_unit, evoked.times)
if isinstance(noise_cov, string_types):
noise_cov = read_cov(noise_cov)
if not isinstance(noise_cov, (list, tuple)):
noise_cov = [noise_cov]
evoked = evoked.copy() # handle ref meg
passive_idx = [idx for idx, proj in enumerate(evoked.info['projs'])
if not proj['active']]
# either applied already or not-- else issue
for idx in passive_idx[::-1]: # reverse order so idx does not change
evoked.del_proj(idx)
evoked.pick_types(ref_meg=False, exclude='bads', **_PICK_TYPES_DATA_DICT)
n_ch_used, rank_list, picks_list, has_sss = _triage_rank_sss(
evoked.info, noise_cov, rank, scalings)
del rank, scalings
if has_sss:
logger.info('SSS has been applied to data. Showing mag and grad '
'whitening jointly.')
# get one whitened evoked per cov
evokeds_white = [whiten_evoked(evoked, cov, picks=None, rank=r)
for cov, r in zip(noise_cov, rank_list)]
def whitened_gfp(x, rank=None):
"""Whitened Global Field Power.
The MNE inverse solver assumes zero mean whitened data as input.
Therefore, a chi^2 statistic will be best to detect model violations.
"""
return np.sum(x ** 2, axis=0) / (len(x) if rank is None else rank)
# prepare plot
if len(noise_cov) > 1:
n_columns = 2
n_extra_row = 0
else:
n_columns = 1
n_extra_row = 1
n_rows = n_ch_used + n_extra_row
fig, axes = plt.subplots(n_rows,
n_columns, sharex=True, sharey=False,
figsize=(8.8, 2.2 * n_rows))
if n_columns > 1:
suptitle = ('Whitened evoked (left, best estimator = "%s")\n'
'and global field power '
'(right, comparison of estimators)' %
noise_cov[0].get('method', 'empirical'))
fig.suptitle(suptitle)
if any(((n_columns == 1 and n_ch_used >= 1),
(n_columns == 2 and n_ch_used == 1))):
axes_evoked = axes[:n_ch_used]
ax_gfp = axes[-1:]
elif n_columns == 2 and n_ch_used > 1:
axes_evoked = axes[:n_ch_used, 0]
ax_gfp = axes[:, 1]
else:
raise RuntimeError('Wrong axes inputs')
titles_ = _handle_default('titles')
if has_sss:
titles_['meg'] = 'MEG (combined)'
colors = [plt.cm.Set1(i) for i in np.linspace(0, 0.5, len(noise_cov))]
ch_colors = _handle_default('color', None)
iter_gfp = zip(evokeds_white, noise_cov, rank_list, colors)
# the first is by law the best noise cov, on the left we plot that one.
if not has_sss:
evokeds_white[0].plot(unit=False, axes=axes_evoked,
hline=[-1.96, 1.96], show=False,
time_unit=time_unit)
else:
for ((ch_type, picks), ax) in zip(picks_list, axes_evoked):
ax.plot(times, evokeds_white[0].data[picks].T, color='k',
lw=0.5)
for hline in [-1.96, 1.96]:
ax.axhline(hline, color='red', linestyle='--', lw=2)
ax.set(title='%s (%d channel%s)'
% (titles_[ch_type], len(picks), _pl(len(picks))))
# Now plot the GFP for all covs if indicated.
for evoked_white, noise_cov, rank_, color in iter_gfp:
i = 0
for ch, sub_picks in picks_list:
this_rank = rank_[ch]
title = '{0} ({2}{1})'.format(
titles_[ch] if n_columns > 1 else ch,
this_rank, 'rank ' if n_columns > 1 else '')
label = noise_cov.get('method', 'empirical')
ax = ax_gfp[i]
ax.set_title(title if n_columns > 1 else
'Whitened GFP, method = "%s"' % label)
data = evoked_white.data[sub_picks]
gfp = whitened_gfp(data, rank=this_rank)
# Wrap SSS-processed data (MEG) to the mag color
color_ch = 'mag' if ch == 'meg' else ch
ax.plot(times, gfp,
label=label if n_columns > 1 else title,
color=color if n_columns > 1 else ch_colors[color_ch],
lw=0.5)
ax.set(xlabel='Time (%s)' % (time_unit,), ylabel=r'GFP ($\chi^2$)',
xlim=[times[0], times[-1]], ylim=(0, 10))
ax.axhline(1, color='red', linestyle='--', lw=2.)
if n_columns > 1:
i += 1
ax = ax_gfp[0]
if n_columns == 1:
ax.legend( # mpl < 1.2.1 compatibility: use prop instead of fontsize
loc='upper right', bbox_to_anchor=(0.98, 0.9), prop=dict(size=12))
else:
ax.legend(loc='upper right', prop=dict(size=10))
params = dict(top=[0.69, 0.82, 0.87][n_rows - 1],
bottom=[0.22, 0.13, 0.09][n_rows - 1])
if has_sss:
params['hspace'] = 0.49
fig.subplots_adjust(**params)
fig.canvas.draw()
plt_show(show)
return fig
@verbose
def plot_snr_estimate(evoked, inv, show=True, verbose=None):
"""Plot a data SNR estimate.
Parameters
----------
evoked : instance of Evoked
The evoked instance. This should probably be baseline-corrected.
inv : instance of InverseOperator
The minimum-norm inverse operator.
show : bool
Show figure if True.
verbose : bool, str, int, or None
If not None, override default verbose level (see :func:`mne.verbose`
and :ref:`Logging documentation <tut_logging>` for more).
Returns
-------
fig : instance of matplotlib.figure.Figure
The figure object containing the plot.
Notes
-----
The bluish green line is the SNR determined by the GFP of the whitened
evoked data. The orange line is the SNR estimated based on the mismatch
between the data and the data re-estimated from the regularized inverse.
.. versionadded:: 0.9.0
"""
import matplotlib.pyplot as plt
from ..minimum_norm import estimate_snr
snr, snr_est = estimate_snr(evoked, inv)
fig, ax = plt.subplots(1, 1)
lims = np.concatenate([evoked.times[[0, -1]], [-1, snr_est.max()]])
ax.axvline(0, color='k', ls=':', lw=1)
ax.axhline(0, color='k', ls=':', lw=1)
# Colors are "bluish green" and "vermilion" taken from:
# http://bconnelly.net/2013/10/creating-colorblind-friendly-figures/
ax.plot(evoked.times, snr_est, color=[0.0, 0.6, 0.5])
ax.plot(evoked.times, snr - 1, color=[0.8, 0.4, 0.0])
ax.set(xlim=lims[:2], ylim=lims[2:], ylabel='SNR', xlabel='Time (s)')
if evoked.comment is not None:
ax.set_title(evoked.comment)
plt_show(show)
return fig
def plot_evoked_joint(evoked, times="peaks", title='', picks=None,
exclude=None, show=True, ts_args=None,
topomap_args=None):
"""Plot evoked data as butterfly plot and add topomaps for time points.
Parameters
----------
evoked : instance of Evoked
The evoked instance.
times : float | array of floats | "auto" | "peaks"
The time point(s) to plot. If "auto", 5 evenly spaced topographies
between the first and last time instant will be shown. If "peaks",
finds time points automatically by checking for 3 local maxima in
Global Field Power. Defaults to "peaks".
title : str | None
The title. If `None`, suppress printing channel type. If an empty
string, a default title is created. Defaults to ''.
picks : array-like of int | None
The indices of channels to plot. If None show all. Defaults to None.
exclude : None | list of str | 'bads'
Channels names to exclude from being shown. If 'bads', the
bad channels are excluded. Defaults to None.
show : bool
Show figure if True. Defaults to True.
ts_args : None | dict
A dict of `kwargs` that are forwarded to :meth:`mne.Evoked.plot` to
style the butterfly plot. If they are not in this dict, the following
defaults are passed: ``spatial_colors=True``, ``zorder='std'``.
``show`` and ``exclude`` are illegal.
If None, no customizable arguments will be passed.
Defaults to `None`.
topomap_args : None | dict
A dict of `kwargs` that are forwarded to
:meth:`mne.Evoked.plot_topomap` to style the topomaps.
If it is not in this dict, ``outlines='skirt'``
will be passed. `show`, `times`, `colorbar` are illegal`
If None, no customizable arguments will be passed.
Defaults to `None`.
Returns
-------
fig : instance of matplotlib.figure.Figure | list
The figure object containing the plot. If `evoked` has multiple
channel types, a list of figures, one for each channel type, is
returned.
Notes
-----
.. versionadded:: 0.12.0
"""
import matplotlib.pyplot as plt
if ts_args is not None and not isinstance(ts_args, dict):
raise TypeError('ts_args must be dict or None, got type %s'
% (type(ts_args),))
ts_args = dict() if ts_args is None else ts_args.copy()
ts_args['time_unit'], evoked_times = _check_time_unit(
ts_args.get('time_unit', 's'), evoked.times)
if topomap_args is None:
topomap_args = dict()
illegal_args = {"show", 'times', 'exclude'}
for args in (ts_args, topomap_args):
if any((x in args for x in illegal_args)):
raise ValueError("Don't pass any of {} as *_args.".format(
", ".join(list(illegal_args))))
if ("axes" in ts_args) or ("axes" in topomap_args):
if not ("axes" in ts_args) and ("axes" in topomap_args):
raise ValueError("If one of `ts_args` and `topomap_args` contains "
"'axes', the other must, too.")
if "axes" in ts_args:
_validate_if_list_of_axes([ts_args["axes"]], 1)
n_topomaps = (3 if times is None else len(times)) + 1
if "axes" in topomap_args:
_validate_if_list_of_axes(list(topomap_args["axes"]), n_topomaps)
# channel selection
# simply create a new evoked object with the desired channel selection
evoked = _pick_inst(evoked, picks, exclude, copy=True)
info = evoked.info
ch_types = _get_channel_types(info, restrict_data_types=True)
# if multiple sensor types: one plot per channel type, recursive call
if len(ch_types) > 1:
if "axes" in ts_args or "axes" in topomap_args:
raise NotImplementedError(
"Currently, passing axes manually (via `ts_args` or "
"`topomap_args`) is not supported for multiple channel types.")
figs = list()
for this_type in ch_types: # pick only the corresponding channel type
ev_ = evoked.copy().pick_channels(
[info['ch_names'][idx] for idx in range(info['nchan'])
if channel_type(info, idx) == this_type])
if len(_get_channel_types(ev_.info)) > 1:
raise RuntimeError('Possibly infinite loop due to channel '
'selection problem. This should never '
'happen! Please check your channel types.')
figs.append(
plot_evoked_joint(
ev_, times=times, title=title, show=show, ts_args=ts_args,
exclude=list(), topomap_args=topomap_args))
return figs
# set up time points to show topomaps for
times_sec = _process_times(evoked, times, few=True)
del times
_, times_ts = _check_time_unit(ts_args['time_unit'], times_sec)
# prepare axes for topomap
if ("axes" not in topomap_args) or ("axes" not in ts_args):
fig, ts_ax, map_ax, cbar_ax = _prepare_joint_axes(len(times_sec),
figsize=(8.0, 4.2))
else:
ts_ax = ts_args["axes"]
del ts_args["axes"]
map_ax = topomap_args["axes"][:-1]
cbar_ax = topomap_args["axes"][-1]
del topomap_args["axes"]
fig = cbar_ax.figure
# butterfly/time series plot
# most of this code is about passing defaults on demand
ts_args_def = dict(picks=None, unit=True, ylim=None, xlim='tight',
proj=False, hline=None, units=None, scalings=None,
titles=None, gfp=False, window_title=None,
spatial_colors=True, zorder='std')
ts_args_def.update(ts_args)
_plot_evoked(evoked, axes=ts_ax, show=False, plot_type='butterfly',
exclude=[], set_tight_layout=False, **ts_args_def)
# handle title
# we use a new axis for the title to handle scaling of plots
old_title = ts_ax.get_title()
ts_ax.set_title('')
if title is not None:
title_ax = plt.subplot(4, 3, 2)
if title == '':
title = old_title
title_ax.text(.5, .5, title, transform=title_ax.transAxes,
horizontalalignment='center',
verticalalignment='center')
title_ax.axis('off')
# topomap
contours = topomap_args.get('contours', 6)
ch_type = ch_types.pop() # set should only contain one element
# Since the data has all the ch_types, we get the limits from the plot.
vmin, vmax = ts_ax.get_ylim()
norm = ch_type == 'grad'
vmin = 0 if norm else vmin
vmin, vmax = _setup_vmin_vmax(evoked.data, vmin, vmax, norm)
if not isinstance(contours, (list, np.ndarray)):
locator, contours = _set_contour_locator(vmin, vmax, contours)
else:
locator = None
topomap_args_pass = topomap_args.copy()
topomap_args_pass['outlines'] = topomap_args.get('outlines', 'skirt')
topomap_args_pass['contours'] = contours
evoked.plot_topomap(times=times_sec, axes=map_ax, show=False,
colorbar=False, **topomap_args_pass)
if topomap_args.get('colorbar', True):
from matplotlib import ticker
cbar = plt.colorbar(map_ax[0].images[0], cax=cbar_ax)
if isinstance(contours, (list, np.ndarray)):
cbar.set_ticks(contours)
else:
if locator is None:
locator = ticker.MaxNLocator(nbins=5)
cbar.locator = locator
cbar.update_ticks()
plt.subplots_adjust(left=.1, right=.93, bottom=.14,
top=1. if title is not None else 1.2)
# connection lines
# draw the connection lines between time series and topoplots
lines = [_connection_line(timepoint, fig, ts_ax, map_ax_)
for timepoint, map_ax_ in zip(times_ts, map_ax)]
for line in lines:
fig.lines.append(line)
# mark times in time series plot
for timepoint in times_ts:
ts_ax.axvline(timepoint, color='grey', linestyle='-',
linewidth=1.5, alpha=.66, zorder=0)
# show and return it
plt_show(show)
return fig
def _aux_setup_styles(conditions, style_dict, style, default):
"""Set linestyles and colors for plot_compare_evokeds."""
# check user-supplied style to condition matching
tags = set([tag for cond in conditions for tag in cond.split("/")])
msg = ("Can't map between conditions and the provided {0}. Make sure "
"you have provided keys in the format of '/'-separated tags, "
"and that these correspond to '/'-separated tags for the condition "
"names (e.g., conditions like 'Visual/Right', and styles like "
"'colors=dict(Visual='red'))'. The offending tag was '{1}'.")
for key in style_dict:
for tag in key.split("/"):
if tag not in tags:
raise ValueError(msg.format(style, tag))
# check condition to style matching, and fill in defaults
condition_warning = "Condition {0} could not be mapped to a " + style
style_warning = ". Using the default of {0}.".format(default)
for condition in conditions:
if condition not in style_dict:
if "/" not in condition:
warn(condition_warning.format(condition) + style_warning)
style_dict[condition] = default
for style_ in style_dict:
if style_ in condition.split("/"):
style_dict[condition] = style_dict[style_]
break
return style_dict
def _truncate_yaxis(axes, ymin, ymax, orig_ymin, orig_ymax, fraction,
any_positive, any_negative, truncation_style):
"""Truncate the y axis in plot_compare_evokeds."""
if truncation_style != "max_ticks":
abs_lims = (orig_ymax if orig_ymax > np.abs(orig_ymin)
else np.abs(orig_ymin))
ymin_, ymax_ = (-(abs_lims // fraction), abs_lims // fraction)
# user supplied ymin and ymax overwrite everything
if ymin is not None and ymin > ymin_:
ymin_ = ymin
if ymax is not None and ymax < ymax_:
ymax_ = ymax
yticks = (ymin_ if any_negative else 0, ymax_ if any_positive else 0)
axes.set_yticks(yticks)
ymin_bound, ymax_bound = (-(abs_lims // fraction),
abs_lims // fraction)
# user supplied ymin and ymax still overwrite everything
if ymin is not None and ymin > ymin_bound:
ymin_bound = ymin
if ymax is not None and ymax < ymax_bound:
ymax_bound = ymax
precision = 0.25 # round to .25
if ymin is None:
ymin_bound = round(ymin_bound / precision) * precision
if ymin is None:
ymax_bound = round(ymax_bound / precision) * precision
axes.spines['left'].set_bounds(ymin_bound, ymax_bound)
else: # code stolen from seaborn
yticks = axes.get_yticks()
firsttick = np.compress(yticks >= min(axes.get_ylim()),
yticks)[0]
lasttick = np.compress(yticks <= max(axes.get_ylim()),
yticks)[-1]
axes.spines['left'].set_bounds(firsttick, lasttick)
newticks = yticks.compress(yticks <= lasttick)
newticks = newticks.compress(newticks >= firsttick)
axes.set_yticks(newticks)
ymin_bound, ymax_bound = newticks[[0, -1]]
return ymin_bound, ymax_bound
def _combine_grad(evoked, picks):
"""Create a new instance of Evoked with combined gradiometers (RMSE)."""
def pair_and_combine(data):
data = data ** 2
data = (data[::2, :] + data[1::2, :]) / 2
return np.sqrt(data)
picks, ch_names = _grad_pair_pick_and_name(evoked.info, picks)
this_data = pair_and_combine(evoked.data[picks, :])
ch_names = ch_names[::2]
evoked = evoked.copy().pick_channels(ch_names)
combined_ch_names = [ch_name[:-1] + "X" for ch_name in ch_names]
evoked.rename_channels({c_old: c_new for c_old, c_new
in zip(evoked.ch_names, combined_ch_names)})
evoked.data = this_data
return evoked
def _check_loc_legal(loc, what='your choice', default=1):
"""Check if loc is a legal location for MPL subordinate axes."""
true_default = {"show_legend": 3, "show_sensors": 4}.get(what, default)
if isinstance(loc, bool) and loc:
loc = true_default
loc_dict = {'upper right': 1, 'upper left': 2, 'lower left': 3,
'lower right': 4, 'right': 5, 'center left': 6,
'center right': 7, 'lower center': 8, 'upper center': 9,
'center': 10}
loc_ = loc_dict.get(loc, loc)
if loc_ not in range(11):
raise ValueError(str(loc) + " is not a legal MPL loc, please supply"
"another value for " + what + ".")
return loc_
def _format_evokeds_colors(evokeds, cmap, colors):
"""Set up to have evokeds as a dict as well as colors."""
from ..evoked import Evoked, _check_evokeds_ch_names_times
if isinstance(evokeds, Evoked):
evokeds = dict(Evoked=evokeds) # title becomes 'Evoked'
elif not isinstance(evokeds, dict): # it's assumed to be a list
if (cmap is not None) and (colors is None):
colors = dict((str(ii + 1), ii) for ii, _ in enumerate(evokeds))
evokeds = dict((str(ii + 1), evoked)
for ii, evoked in enumerate(evokeds))
else:
assert isinstance(evokeds, dict)
if (colors is None) and cmap is not None:
raise ValueError('If evokeds is a dict and a cmap is passed, '
'you must specify the colors.')
for cond in evokeds.keys():
_validate_type(cond, 'str', "Conditions")
# Now make sure all values are list of Evoked objects
evokeds = {condition: [v] if isinstance(v, Evoked) else v
for condition, v in evokeds.items()}
# Check that all elements are of type evoked
for this_evoked in evokeds.values():
for ev in this_evoked:
_validate_type(ev, Evoked, "All evokeds entries ", "Evoked")
# Check that all evoked objects have the same time axis and channels
all_evoked = sum(evokeds.values(), [])
_check_evokeds_ch_names_times(all_evoked)
return evokeds, colors
def _setup_styles(conditions, styles, cmap, colors, linestyles):
"""Set up plotting styles for each condition."""
import matplotlib.pyplot as plt
# continuous colors
the_colors, color_conds, color_order = None, None, None
colors_are_float = False
if cmap is not None:
for color_value in colors.values():
try:
float(color_value)
except ValueError:
raise TypeError("If ``cmap`` is not None, the values of "
"``colors`` must be numeric. Got %s" %
type(color_value))
cmapper = getattr(plt.cm, cmap, cmap)
color_conds = list(colors.keys())
all_colors = [colors[cond] for cond in color_conds]
color_order = np.array(all_colors).argsort()
color_indices = color_order.argsort()
if all([isinstance(color, Integral) for color in all_colors]):
msg = "Integer colors detected, mapping to rank positions ..."
n_colors = len(all_colors)
colors_ = {cond: ind for cond, ind in
zip(color_conds, color_indices)}
def convert_colors(color):
return colors_[color]
else:
for color in all_colors:
if not 0 <= color <= 1:
raise ValueError("Values of colors must be all-integer or "
"floats between 0 and 1, got %s." % color)
msg = "Float colors detected, mapping to percentiles ..."
n_colors = 101 # percentiles plus 1 if we have 1.0s
colors_old = colors.copy()
def convert_colors(color):
return int(colors_old[color] * 100)
colors_are_float = True
logger.info(msg)
the_colors = cmapper(np.linspace(0, 1, n_colors))
colors = dict()
for cond in conditions:
cond_ = cond.split("/")
for color in color_conds:
if color in cond_:
colors[cond] = the_colors[convert_colors(color)]
continue
# categorical colors
if not isinstance(colors, dict):
colors_ = _get_color_list()
if len(conditions) > len(colors_):
msg = ("Trying to plot more than {0} conditions. We provide"
"only {0} default colors. Please supply colors manually.")
raise ValueError(msg.format(len(colors_)))
colors = dict((condition, color) for condition, color
in zip(conditions, colors_))
else:
colors = _aux_setup_styles(conditions, colors, "color", "grey")
# linestyles
if not isinstance(linestyles, dict):
linestyles = dict((condition, linestyle) for condition, linestyle in
zip(conditions, ['-'] * len(conditions)))
else:
linestyles = _aux_setup_styles(conditions, linestyles,
"linestyle", "-")
# finally, put it all together
if styles is None:
styles = dict()
for condition, color, linestyle in zip(conditions, colors, linestyles):
styles[condition] = styles.get(condition, dict())
styles[condition]['c'] = styles[condition].get('c', colors[condition])
styles[condition]['linestyle'] = styles[condition].get(
'linestyle', linestyles[condition])
return styles, the_colors, color_conds, color_order, colors_are_float
def plot_compare_evokeds(evokeds, picks=None, gfp=False, colors=None,
linestyles=['-'], styles=None, cmap=None,
vlines="auto", ci=0.95, truncate_yaxis="max_ticks",
truncate_xaxis=True, ylim=dict(), invert_y=False,
show_sensors=None, show_legend=True,
split_legend=False, axes=None, title=None, show=True):
"""Plot evoked time courses for one or more conditions and/or channels.
Parameters
----------
evokeds : instance of mne.Evoked | list | dict
If a single Evoked instance, it is plotted as a time series.
If a dict whose values are Evoked objects, the contents are plotted as
single time series each and the keys are used as condition labels.
If a list of Evokeds, the contents are plotted with indices as labels.
If a [dict/list] of lists, the unweighted mean is plotted as a time
series and the parametric confidence interval is plotted as a shaded
area. All instances must have the same shape - channel numbers, time
points etc.
If dict, keys must be of type str.
picks : None | int | list of int
If int or list of int, the indices of the sensors to average and plot.
If multiple channel types are selected, one figure will be returned for
each channel type.
If the selected channels are gradiometers, the signal from
corresponding (gradiometer) pairs will be combined.
If None, it defaults to all data channels, in which case the global
field power will be plotted for all channel type available.
gfp : bool
If True, the channel type wise GFP is plotted.
If `picks` is an empty list (default), this is set to True.
colors : list | dict | None
If a list, will be sequentially used for line colors.
If a dict, can map evoked keys or '/'-separated (HED) tags to
conditions.
For example, if `evokeds` is a dict with the keys "Aud/L", "Aud/R",
"Vis/L", "Vis/R", `colors` can be `dict(Aud='r', Vis='b')` to map both
Aud/L and Aud/R to the color red and both Visual conditions to blue.
If None (default), a sequence of desaturated colors is used.
If `cmap` is None, `colors` will indicate how each condition is
colored with reference to its position on the colormap - see `cmap`
below. In that case, the values of colors must be either integers,
in which case they will be mapped to colors in rank order; or floats
between 0 and 1, in which case they will be mapped to percentiles of
the colormap.
linestyles : list | dict
If a list, will be sequentially and repeatedly used for evoked plot
linestyles.
If a dict, can map the `evoked` keys or '/'-separated (HED) tags to
conditions.
For example, if evokeds is a dict with the keys "Aud/L", "Aud/R",
"Vis/L", "Vis/R", `linestyles` can be `dict(L='--', R='-')` to map both
Aud/L and Vis/L to dashed lines and both Right-side conditions to
straight lines.
styles : dict | None
If a dict, keys must map to evoked keys or conditions, and values must
be a dict of legal inputs to `matplotlib.pyplot.plot`. These
parameters will be passed to the line plot call of the corresponding
condition, overriding defaults.
E.g., if evokeds is a dict with the keys "Aud/L", "Aud/R",
"Vis/L", "Vis/R", `styles` can be `{"Aud/L": {"linewidth": 1}}` to set
the linewidth for "Aud/L" to 1. Note that HED ('/'-separated) tags are
not supported.
cmap : None | str | tuple
If not None, plot evoked activity with colors from a color gradient
(indicated by a str referencing a matplotlib colormap - e.g., "viridis"
or "Reds").
If ``evokeds`` is a list and ``colors`` is `None`, the color will
depend on the list position. If ``colors`` is a list, it must contain
integers where the list positions correspond to ``evokeds``, and the
value corresponds to the position on the colorbar.
If ``evokeds`` is a dict, ``colors`` should be a dict mapping from
(potentially HED-style) condition tags to numbers corresponding to
positions on the colorbar - rank order for integers, or floats for
percentiles. E.g., ::
evokeds={"cond1/A": ev1, "cond2/A": ev2, "cond3/A": ev3, "B": ev4},
cmap='viridis', colors=dict(cond1=1 cond2=2, cond3=3),
linestyles={"A": "-", "B": ":"}
If ``cmap`` is a tuple of length 2, the first item must be
a string which will become the colorbar label, and the second one
must indicate a colormap, e.g. ::
cmap=('conds', 'viridis'), colors=dict(cond1=1 cond2=2, cond3=3),
vlines : "auto" | list of float
A list in seconds at which to plot dashed vertical lines.
If "auto" and the supplied data includes 0, it is set to [0.]
and a vertical bar is plotted at time 0. If an empty list is passed,
no vertical lines are plotted.
ci : float | callable | None | bool
If not None and ``evokeds`` is a [list/dict] of lists, a shaded
confidence interval is drawn around the individual time series. If
float, a percentile bootstrap method is used to estimate the confidence
interval and this value determines the CI width. E.g., if this value is
.95 (the default), the 95% confidence interval is drawn. If a callable,
it must take as its single argument an array (observations x times) and
return the upper and lower confidence bands.
If None or False, no confidence band is plotted.
If True, a 95% bootstrapped confidence interval is drawn.
truncate_yaxis : bool | str
If not False, the left y axis spine is truncated to reduce visual
clutter. If 'max_ticks', the spine is truncated at the minimum and
maximum ticks. Else, it is truncated to half the max absolute value,
rounded to .25. Defaults to "max_ticks".
truncate_xaxis : bool
If True, the x axis is truncated to span from the first to the last.
xtick. Defaults to True.
ylim : dict | None
ylim for plots (after scaling has been applied). e.g.
ylim = dict(eeg=[-20, 20])
Valid keys are eeg, mag, grad, misc. If None, the ylim parameter
for each channel equals the pyplot default.
invert_y : bool
If True, negative values are plotted up (as is sometimes done
for ERPs out of tradition). Defaults to False.
show_sensors: bool | int | str | None
If not False, channel locations are plotted on a small head circle.
If int or str, the position of the axes (forwarded to
``mpl_toolkits.axes_grid1.inset_locator.inset_axes``).
If None, defaults to True if ``gfp`` is False, else to False.
show_legend : bool | str | int
If not False, show a legend. If int or str, it is the position of the
legend axes (forwarded to
``mpl_toolkits.axes_grid1.inset_locator.inset_axes``).
split_legend : bool
If True, the legend shows color and linestyle separately; `colors` must
not be None. Defaults to True if ``cmap`` is not None, else defaults to
False.
axes : None | `matplotlib.axes.Axes` instance | list of `axes`
What axes to plot to. If None, a new axes is created.
When plotting multiple channel types, can also be a list of axes, one
per channel type.
title : None | str
If str, will be plotted as figure title. If None, the channel names
will be shown.
show : bool
If True, show the figure.
Returns
-------
fig : Figure | list of Figures
The figure(s) in which the plot is drawn. When plotting multiple
channel types, a list of figures, one for each channel type is
returned.
Notes
-----
When multiple channels are passed, this function combines them all, to
get one time course for each condition. If gfp is True it combines
channels using global field power (GFP) computation, else it is taking
a plain mean.
This function is useful for comparing multiple ER[P/F]s - e.g., for
multiple conditions - at a specific location.
It can plot:
- a simple :class:`mne.Evoked` object,
- a list or dict of :class:`mne.Evoked` objects (e.g., for multiple
conditions),
- a list or dict of lists of :class:`mne.Evoked` (e.g., for multiple
subjects in multiple conditions).
In the last case, it can show a confidence interval (across e.g. subjects)
using parametric or bootstrap estimation.
When ``picks`` includes more than one planar gradiometer, the planar
gradiometers are combined with RMSE. For example data from a
VectorView system with 204 gradiometers will be transformed to
102 channels.
"""
import matplotlib.pyplot as plt
import matplotlib.lines as mlines
evokeds, colors = _format_evokeds_colors(evokeds, cmap, colors)
conditions = sorted(list(evokeds.keys()))
# check ci parameter
if ci is None:
ci = False
if ci is True:
ci = .95
elif ci is not False and not (isinstance(ci, np.float) or callable(ci)):
raise TypeError('ci must be None, bool, float or callable, got %s' %
type(ci))
# get and set a few limits and variables (times, channels, units)
one_evoked = evokeds[conditions[0]][0]
times = one_evoked.times
info = one_evoked.info
tmin, tmax = times[0], times[-1]
if vlines == "auto" and (tmin < 0 and tmax > 0):
vlines = [0.]
_validate_type(vlines, (list, tuple), "vlines", "list or tuple")
if isinstance(picks, Integral):
picks = [picks]
elif picks is None:
logger.info("No picks, plotting the GFP ...")
gfp = True
picks = _pick_data_channels(info, with_ref_meg=False)
_validate_type(picks, (list, np.ndarray), "picks",
"list or np.array of integers")
for entry in picks:
_validate_type(entry, 'int', "entries of picks", "integers")
if len(picks) == 0:
raise ValueError("No valid channels were found to plot the GFP. " +
"Use 'picks' instead to select them manually.")
if ylim is None:
ylim = dict()
# deal with picks: infer indices and names
if gfp is True:
if show_sensors is None:
show_sensors = False # don't show sensors for GFP
ch_names = ['Global Field Power']
if len(picks) < 2:
raise ValueError("Cannot compute GFP for fewer than 2 channels, "
"please pick more than %d channels." % len(picks))
else:
if show_sensors is None:
show_sensors = True # show sensors when not doing GFP
ch_names = [one_evoked.ch_names[pick] for pick in picks]
picks_by_types = channel_indices_by_type(info, picks)
# keep only channel types for which there is a channel:
ch_types = [t for t in picks_by_types if len(picks_by_types[t]) > 0]
# let's take care of axis and figs
if axes is not None:
if not isinstance(axes, list):
axes = [axes]
_validate_if_list_of_axes(axes, obligatory_len=len(ch_types))
else:
axes = [plt.subplots(figsize=(8, 6))[1] for _ in range(len(ch_types))]
if len(ch_types) > 1:
logger.info("Multiple channel types selected, returning one figure "
"per type.")
figs = list()
for ii, t in enumerate(ch_types):
picks_ = picks_by_types[t]
title_ = "GFP, " + t if (title is None and gfp is True) else title
figs.append(plot_compare_evokeds(
evokeds, picks=picks_, gfp=gfp, colors=colors,
linestyles=linestyles, styles=styles, vlines=vlines, ci=ci,
truncate_yaxis=truncate_yaxis, ylim=ylim, invert_y=invert_y,
axes=axes[ii], title=title_, show=show))
return figs
# From now on there is only 1 channel type
assert len(ch_types) == 1
ch_type = ch_types[0]
all_positive = gfp # True if not gfp, False if gfp
pos_picks = picks # keep locations to pick for plotting
if ch_type == "grad" and len(picks) > 1:
logger.info('Combining all planar gradiometers with RMSE.')
pos_picks, _ = _grad_pair_pick_and_name(one_evoked.info, picks)
pos_picks = pos_picks[::2]
all_positive = True
for cond, this_evokeds in evokeds.items():
evokeds[cond] = [_combine_grad(e, picks) for e in this_evokeds]
ch_names = evokeds[cond][0].ch_names
picks = range(len(ch_names))
del info
ymin, ymax = ylim.get(ch_type, [None, None])
scaling = _handle_default("scalings")[ch_type]
unit = _handle_default("units")[ch_type]
if (ymin is None) and all_positive:
ymin = 0. # 'grad' and GFP are plotted as all-positive
# if we have a dict/list of lists, we compute the grand average and the CI
_ci_fun = None
if ci is not False:
if callable(ci):
_ci_fun = ci
else:
from ..stats import _ci
_ci_fun = partial(_ci, ci=ci, method="bootstrap")
# calculate the CI
ci_dict, data_dict = dict(), dict()
for cond in conditions:
this_evokeds = evokeds[cond]
# this will fail if evokeds do not have the same structure
# (e.g. channel count)
data = [e.data[picks, :] * scaling for e in this_evokeds]
data = np.array(data)
if gfp:
data = np.sqrt(np.mean(data * data, axis=1))
else:
data = np.mean(data, axis=1) # average across channels
if _ci_fun is not None: # compute CI if requested:
ci_dict[cond] = _ci_fun(data)
# average across conditions:
data_dict[cond] = data = np.mean(data, axis=0)
_check_if_nan(data)
del evokeds
# we now have dicts for data ('evokeds' - grand averaged Evoked's)
# and the CI ('ci_array') with cond name labels
# style the individual condition time series
# Styles (especially color and linestyle) are pulled from a dict 'styles'.
# This dict has one entry per condition. Its color and linestyle entries
# are pulled from the 'colors' and 'linestyles' dicts via '/'-tag matching
# unless they are overwritten by entries from a user-provided 'styles'.
# first, copy to avoid overwriting
styles = deepcopy(styles)
colors = deepcopy(colors)
linestyles = deepcopy(linestyles)
# second, check if input is valid
if isinstance(styles, dict):
for style_ in styles:
if style_ not in conditions:
raise ValueError("Could not map between 'styles' and "
"conditions. Condition " + style_ +
" was not found in the supplied data.")
# third, color
# check: is color a list?
if (colors is not None and not isinstance(colors, string_types) and
not isinstance(colors, dict) and len(colors) > 1):
colors = dict((condition, color) for condition, color
in zip(conditions, colors))
if cmap is not None:
if not isinstance(cmap, string_types) and len(cmap) == 2:
cmap_label, cmap = cmap
else:
cmap_label = ""
# dealing with a split legend
if split_legend is None:
split_legend = cmap is not None # default to True iff cmap is given
if split_legend is True:
if colors is None:
raise ValueError(
"If `split_legend` is True, `colors` must not be None.")
# mpl 1.3 requires us to split it like this. with recent mpl,
# we could use the label parameter of the Line2D
legend_lines, legend_labels = list(), list()
if cmap is None: # ... one set of lines for the colors
for color in sorted(colors.keys()):
line = mlines.Line2D([], [], linestyle="-",
color=colors[color])
legend_lines.append(line)
legend_labels.append(color)
if len(list(linestyles)) > 1: # ... one set for the linestyle
for style, s in linestyles.items():
line = mlines.Line2D([], [], color='k', linestyle=s)
legend_lines.append(line)
legend_labels.append(style)
styles, the_colors, color_conds, color_order, colors_are_float =\
_setup_styles(data_dict.keys(), styles, cmap, colors, linestyles)
# We now have a 'styles' dict with one entry per condition, specifying at
# least color and linestyles.
ax, = axes
del axes
# the actual plot
any_negative, any_positive = False, False
for condition in conditions:
# plot the actual data ('d') as a line
d = data_dict[condition].T
ax.plot(times, d, zorder=1000, label=condition, clip_on=False,
**styles[condition])
if np.any(d > 0) or all_positive:
any_positive = True
if np.any(d < 0):
any_negative = True
# plot the confidence interval if available
if _ci_fun is not None:
ci_ = ci_dict[condition]
ax.fill_between(times, ci_[0].flatten(), ci_[1].flatten(),
zorder=9, color=styles[condition]['c'], alpha=.3,
clip_on=False)
# truncate the y axis
orig_ymin, orig_ymax = ax.get_ylim()
if not any_positive:
orig_ymax = 0
if not any_negative:
orig_ymin = 0
ax.set_ylim(orig_ymin if ymin is None else ymin,
orig_ymax if ymax is None else ymax)
fraction = 2 if ax.get_ylim()[0] >= 0 else 3
if truncate_yaxis is not False:
_, ymax_bound = _truncate_yaxis(
ax, ymin, ymax, orig_ymin, orig_ymax, fraction,
any_positive, any_negative, truncate_yaxis)
else:
if truncate_yaxis is True and ymin is not None and ymin > 0:
warn("ymin is all-positive, not truncating yaxis")
ymax_bound = ax.get_ylim()[-1]
title = _set_title_multiple_electrodes(
title, "average" if gfp is False else "gfp", ch_names, ch_type=ch_type)
ax.set_title(title)
current_ymin = ax.get_ylim()[0]
# plot v lines
if invert_y is True and current_ymin < 0:
upper_v, lower_v = -ymax_bound, ax.get_ylim()[-1]
else:
upper_v, lower_v = ax.get_ylim()[0], ymax_bound
if vlines:
ax.vlines(vlines, upper_v, lower_v, linestyles='--', colors='k',
linewidth=1., zorder=1)
_setup_ax_spines(ax, vlines, tmin, tmax, invert_y, ymax_bound, unit,
truncate_xaxis)
# and now for 3 "legends" ..
# a head plot showing the sensors that are being plotted
if show_sensors:
_validate_type(show_sensors, (np.int, bool, str, type(None)),
"show_sensors", "numeric, str, None or bool")
if not _check_ch_locs(np.array(one_evoked.info['chs'])[pos_picks]):
warn("Cannot find channel coordinates in the supplied Evokeds. "
"Not showing channel locations.")
else:
if show_sensors is True:
ymin, ymax = np.abs(ax.get_ylim())
show_sensors = "lower right" if ymin > ymax else "upper right"
pos = _auto_topomap_coords(one_evoked.info, pos_picks,
ignore_overlap=True, to_sphere=True)
head_pos = {'center': (0, 0), 'scale': (0.5, 0.5)}
pos, outlines = _check_outlines(pos, np.array([1, 1]), head_pos)
show_sensors = _check_loc_legal(show_sensors, "show_sensors")
_plot_legend(pos, ["k"] * len(picks), ax, list(), outlines,
show_sensors, size=25)
# the condition legend
if len(conditions) > 1 and show_legend is not False:
show_legend = _check_loc_legal(show_legend, "show_legend")
legend_params = dict(loc=show_legend, frameon=True)
if split_legend:
if len(legend_lines) > 1:
ax.legend(legend_lines, legend_labels, # see above: mpl 1.3
ncol=1 + (len(legend_lines) // 4), **legend_params)
else:
ax.legend(ncol=1 + (len(conditions) // 5), **legend_params)
# the colormap, if `cmap` is provided
if split_legend and cmap is not None:
# plot the colorbar ... complicated cause we don't have a heatmap
from mpl_toolkits.axes_grid1 import make_axes_locatable
divider = make_axes_locatable(ax)
ax_cb = divider.append_axes("right", size="5%", pad=0.05)
if colors_are_float:
ax_cb.imshow(the_colors[:, np.newaxis, :], interpolation='none',
aspect=.05)
color_ticks = np.array(list(set(colors.values()))) * 100
ax_cb.set_yticks(color_ticks)
ax_cb.set_yticklabels(color_ticks)
else:
ax_cb.imshow(the_colors[:, np.newaxis, :], interpolation='none')
ax_cb.set_yticks(np.arange(len(the_colors)))
ax_cb.set_yticklabels(np.array(color_conds)[color_order])
ax_cb.yaxis.tick_right()
ax_cb.set(xticks=(), ylabel=cmap_label)
plt_show(show)
return ax.figure
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