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"""Functions to plot M/EEG data on topo (one axes per channel)."""
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>
#
# License: Simplified BSD
from copy import deepcopy
from functools import partial
from itertools import cycle
import numpy as np
from ..io.constants import Bunch
from ..io.pick import channel_type, pick_types
from ..utils import _clean_names, warn
from ..channels.layout import _merge_grad_data, _pair_grad_sensors, find_layout
from ..defaults import _handle_default
from .utils import (_check_delayed_ssp, _get_color_list, _draw_proj_checkbox,
add_background_image, plt_show, _setup_vmin_vmax,
DraggableColorbar, _set_ax_facecolor, _setup_ax_spines,
_check_cov, _plot_masked_image)
def iter_topography(info, layout=None, on_pick=None, fig=None,
fig_facecolor='k', axis_facecolor='k',
axis_spinecolor='k', layout_scale=None):
"""Create iterator over channel positions.
This function returns a generator that unpacks into
a series of matplotlib axis objects and data / channel
indices, both corresponding to the sensor positions
of the related layout passed or inferred from the channel info.
`iter_topography`, hence, allows to conveniently realize custom
topography plots.
Parameters
----------
info : instance of Info
The measurement info.
layout : instance of mne.layout.Layout | None
The layout to use. If None, layout will be guessed
on_pick : callable | None
The callback function to be invoked on clicking one
of the axes. Is supposed to instantiate the following
API: `function(axis, channel_index)`
fig : matplotlib.figure.Figure | None
The figure object to be considered. If None, a new
figure will be created.
fig_facecolor : str | obj
The figure face color. Defaults to black.
axis_facecolor : str | obj
The axis face color. Defaults to black.
axis_spinecolor : str | obj
The axis spine color. Defaults to black. In other words,
the color of the axis' edge lines.
layout_scale: float | None
Scaling factor for adjusting the relative size of the layout
on the canvas. If None, nothing will be scaled.
Returns
-------
A generator that can be unpacked into:
ax : matplotlib.axis.Axis
The current axis of the topo plot.
ch_dx : int
The related channel index.
"""
return _iter_topography(info, layout, on_pick, fig, fig_facecolor,
axis_facecolor, axis_spinecolor, layout_scale)
def _iter_topography(info, layout, on_pick, fig, fig_facecolor='k',
axis_facecolor='k', axis_spinecolor='k',
layout_scale=None, unified=False, img=False, axes=None):
"""Iterate over topography.
Has the same parameters as iter_topography, plus:
unified : bool
If False (default), multiple matplotlib axes will be used.
If True, a single axis will be constructed. The former is
useful for custom plotting, the latter for speed.
"""
from matplotlib import pyplot as plt, collections
if fig is None:
fig = plt.figure()
def format_coord_unified(x, y, pos=None, ch_names=None):
"""Update status bar with channel name under cursor."""
# find candidate channels (ones that are down and left from cursor)
pdist = np.array([x, y]) - pos[:, :2]
pind = np.where((pdist >= 0).all(axis=1))[0]
if len(pind) > 0:
# find the closest channel
closest = pind[np.sum(pdist[pind, :]**2, axis=1).argmin()]
# check whether we are inside its box
in_box = (pdist[closest, :] < pos[closest, 2:]).all()
else:
in_box = False
return (('%s (click to magnify)' % ch_names[closest]) if
in_box else 'No channel here')
def format_coord_multiaxis(x, y, ch_name=None):
"""Update status bar with channel name under cursor."""
return '%s (click to magnify)' % ch_name
fig.set_facecolor(fig_facecolor)
if layout is None:
layout = find_layout(info)
if on_pick is not None:
callback = partial(_plot_topo_onpick, show_func=on_pick)
fig.canvas.mpl_connect('button_press_event', callback)
pos = layout.pos.copy()
if layout_scale:
pos[:, :2] *= layout_scale
ch_names = _clean_names(info['ch_names'])
iter_ch = [(x, y) for x, y in enumerate(layout.names) if y in ch_names]
if unified:
if axes is None:
under_ax = plt.axes([0, 0, 1, 1])
under_ax.axis('off')
else:
under_ax = axes
under_ax.format_coord = partial(format_coord_unified, pos=pos,
ch_names=layout.names)
under_ax.set(xlim=[0, 1], ylim=[0, 1])
axs = list()
for idx, name in iter_ch:
ch_idx = ch_names.index(name)
if not unified: # old, slow way
ax = plt.axes(pos[idx])
ax.patch.set_facecolor(axis_facecolor)
plt.setp(list(ax.spines.values()), color=axis_spinecolor)
ax.set(xticklabels=[], yticklabels=[])
plt.setp(ax.get_xticklines(), visible=False)
plt.setp(ax.get_yticklines(), visible=False)
ax._mne_ch_name = name
ax._mne_ch_idx = ch_idx
ax._mne_ax_face_color = axis_facecolor
ax.format_coord = partial(format_coord_multiaxis, ch_name=name)
yield ax, ch_idx
else:
ax = Bunch(ax=under_ax, pos=pos[idx], data_lines=list(),
_mne_ch_name=name, _mne_ch_idx=ch_idx,
_mne_ax_face_color=axis_facecolor)
axs.append(ax)
if unified:
under_ax._mne_axs = axs
# Create a PolyCollection for the axis backgrounds
verts = np.transpose([pos[:, :2],
pos[:, :2] + pos[:, 2:] * [1, 0],
pos[:, :2] + pos[:, 2:],
pos[:, :2] + pos[:, 2:] * [0, 1],
], [1, 0, 2])
if not img:
under_ax.add_collection(collections.PolyCollection(
verts, facecolor=axis_facecolor, edgecolor=axis_spinecolor,
linewidth=1.)) # Not needed for image plots.
for ax in axs:
yield ax, ax._mne_ch_idx
def _plot_topo(info, times, show_func, click_func=None, layout=None,
vmin=None, vmax=None, ylim=None, colorbar=None, border='none',
axis_facecolor='k', fig_facecolor='k', cmap='RdBu_r',
layout_scale=None, title=None, x_label=None, y_label=None,
font_color='w', unified=False, img=False, axes=None):
"""Plot on sensor layout."""
import matplotlib.pyplot as plt
if layout.kind == 'custom':
layout = deepcopy(layout)
layout.pos[:, :2] -= layout.pos[:, :2].min(0)
layout.pos[:, :2] /= layout.pos[:, :2].max(0)
# prepare callbacks
tmin, tmax = times[[0, -1]]
click_func = show_func if click_func is None else click_func
on_pick = partial(click_func, tmin=tmin, tmax=tmax, vmin=vmin,
vmax=vmax, ylim=ylim, x_label=x_label,
y_label=y_label, colorbar=colorbar)
if axes is None:
fig = plt.figure()
axes = plt.axes([0.015, 0.025, 0.97, 0.95])
_set_ax_facecolor(axes, fig_facecolor)
else:
fig = axes.figure
if colorbar:
sm = plt.cm.ScalarMappable(cmap=cmap, norm=plt.Normalize(vmin, vmax))
sm.set_array(np.linspace(vmin, vmax))
cb = fig.colorbar(sm, ax=axes, pad=0.025, fraction=0.075, shrink=0.5,
anchor=(-1, 0.5))
cb_yticks = plt.getp(cb.ax.axes, 'yticklabels')
plt.setp(cb_yticks, color=font_color)
axes.axis('off')
my_topo_plot = _iter_topography(info, layout=layout, on_pick=on_pick,
fig=fig, layout_scale=layout_scale,
axis_spinecolor=border,
axis_facecolor=axis_facecolor,
fig_facecolor=fig_facecolor,
unified=unified, img=img, axes=axes)
for ax, ch_idx in my_topo_plot:
if layout.kind == 'Vectorview-all' and ylim is not None:
this_type = {'mag': 0, 'grad': 1}[channel_type(info, ch_idx)]
ylim_ = [v[this_type] if _check_vlim(v) else v for v in ylim]
else:
ylim_ = ylim
show_func(ax, ch_idx, tmin=tmin, tmax=tmax, vmin=vmin,
vmax=vmax, ylim=ylim_)
if title is not None:
plt.figtext(0.03, 0.95, title, color=font_color, fontsize=15, va='top')
return fig
def _plot_topo_onpick(event, show_func):
"""Onpick callback that shows a single channel in a new figure."""
# make sure that the swipe gesture in OS-X doesn't open many figures
orig_ax = event.inaxes
import matplotlib.pyplot as plt
try:
if hasattr(orig_ax, '_mne_axs'): # in unified, single-axes mode
x, y = event.xdata, event.ydata
for ax in orig_ax._mne_axs:
if x >= ax.pos[0] and y >= ax.pos[1] and \
x <= ax.pos[0] + ax.pos[2] and \
y <= ax.pos[1] + ax.pos[3]:
orig_ax = ax
break
else:
# no axis found
return
elif not hasattr(orig_ax, '_mne_ch_idx'):
# neither old nor new mode
return
ch_idx = orig_ax._mne_ch_idx
face_color = orig_ax._mne_ax_face_color
fig, ax = plt.subplots(1)
plt.title(orig_ax._mne_ch_name)
_set_ax_facecolor(ax, face_color)
# allow custom function to override parameters
show_func(ax, ch_idx)
except Exception as err:
# matplotlib silently ignores exceptions in event handlers,
# so we print
# it here to know what went wrong
print(err)
raise
def _compute_scalings(bn, xlim, ylim):
"""Compute scale factors for a unified plot."""
if isinstance(ylim[0], (tuple, list, np.ndarray)):
ylim = (ylim[0][0], ylim[1][0])
pos = bn.pos
bn.x_s = pos[2] / (xlim[1] - xlim[0])
bn.x_t = pos[0] - bn.x_s * xlim[0]
bn.y_s = pos[3] / (ylim[1] - ylim[0])
bn.y_t = pos[1] - bn.y_s * ylim[0]
def _check_vlim(vlim):
"""Check the vlim."""
return not np.isscalar(vlim) and vlim is not None
def _imshow_tfr(ax, ch_idx, tmin, tmax, vmin, vmax, onselect, ylim=None,
tfr=None, freq=None, x_label=None, y_label=None,
colorbar=False, cmap=('RdBu_r', True), yscale='auto',
mask=None, mask_style="both", mask_cmap="Greys",
mask_alpha=0.1, is_jointplot=False):
"""Show time-frequency map as two-dimensional image."""
from matplotlib import pyplot as plt
from matplotlib.widgets import RectangleSelector
if yscale not in ['auto', 'linear', 'log']:
raise ValueError("yscale should be either 'auto', 'linear', or 'log'"
", got {}".format(yscale))
cmap, interactive_cmap = cmap
times = np.linspace(tmin, tmax, num=tfr[ch_idx].shape[1])
img, t_end = _plot_masked_image(
ax, tfr[ch_idx], times, mask, picks=None, yvals=freq, cmap=cmap,
vmin=vmin, vmax=vmax, mask_style=mask_style, mask_alpha=mask_alpha,
mask_cmap=mask_cmap, yscale=yscale)
if x_label is not None:
ax.set_xlabel(x_label)
if y_label is not None:
ax.set_ylabel(y_label)
if colorbar:
if isinstance(colorbar, DraggableColorbar):
cbar = colorbar.cbar # this happens with multiaxes case
else:
cbar = plt.colorbar(mappable=img)
if interactive_cmap:
ax.CB = DraggableColorbar(cbar, img)
ax.RS = RectangleSelector(ax, onselect=onselect) # reference must be kept
return t_end
def _imshow_tfr_unified(bn, ch_idx, tmin, tmax, vmin, vmax, onselect,
ylim=None, tfr=None, freq=None, vline=None,
x_label=None, y_label=None, colorbar=False,
picker=True, cmap='RdBu_r', title=None, hline=None):
"""Show multiple tfrs on topo using a single axes."""
_compute_scalings(bn, (tmin, tmax), (freq[0], freq[-1]))
ax = bn.ax
data_lines = bn.data_lines
extent = (bn.x_t + bn.x_s * tmin, bn.x_t + bn.x_s * tmax,
bn.y_t + bn.y_s * freq[0], bn.y_t + bn.y_s * freq[-1])
data_lines.append(ax.imshow(tfr[ch_idx], clip_on=True, clip_box=bn.pos,
extent=extent, aspect="auto", origin="lower",
vmin=vmin, vmax=vmax, cmap=cmap))
def _plot_timeseries(ax, ch_idx, tmin, tmax, vmin, vmax, ylim, data, color,
times, vline=None, x_label=None, y_label=None,
colorbar=False, hline=None, hvline_color='w',
labels=None):
"""Show time series on topo split across multiple axes."""
import matplotlib.pyplot as plt
from matplotlib.colors import colorConverter
picker_flag = False
for data_, color_ in zip(data, color):
if not picker_flag:
# use large tol for picker so we can click anywhere in the axes
ax.plot(times, data_[ch_idx], color=color_, picker=1e9)
picker_flag = True
else:
ax.plot(times, data_[ch_idx], color=color_)
if x_label is not None:
ax.set(xlabel=x_label)
if y_label is not None:
if isinstance(y_label, list):
ax.set_ylabel(y_label[ch_idx])
else:
ax.set_ylabel(y_label)
def _format_coord(x, y, labels, ax):
"""Create status string based on cursor coordinates."""
idx = np.abs(times - x).argmin()
ylabel = ax.get_ylabel()
unit = (ylabel[ylabel.find('(') + 1:ylabel.find(')')]
if '(' in ylabel and ')' in ylabel else '')
labels = [''] * len(data) if labels is None else labels
# try to estimate whether to truncate condition labels
slen = 10 + sum([12 + len(unit) + len(label) for label in labels])
bar_width = (ax.figure.get_size_inches() * ax.figure.dpi)[0] / 5.5
trunc_labels = bar_width < slen
s = '%6.3f s: ' % times[idx]
for data_, label in zip(data, labels):
s += '%7.2f %s' % (data_[ch_idx, idx], unit)
if trunc_labels:
label = (label if len(label) <= 10 else
'%s..%s' % (label[:6], label[-2:]))
s += ' [%s] ' % label if label else ' '
return s
ax.format_coord = lambda x, y: _format_coord(x, y, labels=labels, ax=ax)
def _cursor_vline(event):
"""Draw cursor (vertical line)."""
ax = event.inaxes
if not ax:
return
if ax._cursorline is not None:
ax._cursorline.remove()
ax._cursorline = ax.axvline(event.xdata, color=ax._cursorcolor)
ax.figure.canvas.draw()
def _rm_cursor(event):
ax = event.inaxes
if ax._cursorline is not None:
ax._cursorline.remove()
ax._cursorline = None
ax.figure.canvas.draw()
ax._cursorline = None
# choose cursor color based on perceived brightness of background
try:
facecol = colorConverter.to_rgb(ax.get_facecolor())
except AttributeError: # older MPL
facecol = colorConverter.to_rgb(ax.get_axis_bgcolor())
face_brightness = np.dot(facecol, np.array([299, 587, 114]))
ax._cursorcolor = 'white' if face_brightness < 150 else 'black'
plt.connect('motion_notify_event', _cursor_vline)
plt.connect('axes_leave_event', _rm_cursor)
_setup_ax_spines(ax, vline, tmin, tmax)
ax.figure.set_facecolor('k' if hvline_color is 'w' else 'w')
ax.spines['bottom'].set_color(hvline_color)
ax.spines['left'].set_color(hvline_color)
ax.tick_params(axis='x', colors=hvline_color, which='both')
ax.tick_params(axis='y', colors=hvline_color, which='both')
ax.title.set_color(hvline_color)
ax.xaxis.label.set_color(hvline_color)
ax.yaxis.label.set_color(hvline_color)
if vline:
plt.axvline(vline, color=hvline_color, linewidth=1.0,
linestyle='--')
if hline:
plt.axhline(hline, color=hvline_color, linewidth=1.0, zorder=10)
if colorbar:
plt.colorbar()
def _plot_timeseries_unified(bn, ch_idx, tmin, tmax, vmin, vmax, ylim, data,
color, times, vline=None, x_label=None,
y_label=None, colorbar=False, hline=None,
hvline_color='w'):
"""Show multiple time series on topo using a single axes."""
import matplotlib.pyplot as plt
if not (ylim and not any(v is None for v in ylim)):
ylim = np.array([np.min(data), np.max(data)])
# Translation and scale parameters to take data->under_ax normalized coords
_compute_scalings(bn, (tmin, tmax), ylim)
pos = bn.pos
data_lines = bn.data_lines
ax = bn.ax
# XXX These calls could probably be made faster by using collections
for data_, color_ in zip(data, color):
data_lines.append(ax.plot(
bn.x_t + bn.x_s * times, bn.y_t + bn.y_s * data_[ch_idx],
linewidth=0.5, color=color_, clip_on=True, clip_box=pos)[0])
if vline:
vline = np.array(vline) * bn.x_s + bn.x_t
ax.vlines(vline, pos[1], pos[1] + pos[3], color=hvline_color,
linewidth=0.5, linestyle='--')
if hline:
hline = np.array(hline) * bn.y_s + bn.y_t
ax.hlines(hline, pos[0], pos[0] + pos[2], color=hvline_color,
linewidth=0.5)
if x_label is not None:
ax.text(pos[0] + pos[2] / 2., pos[1], x_label,
horizontalalignment='center', verticalalignment='top')
if y_label is not None:
y_label = y_label[ch_idx] if isinstance(y_label, list) else y_label
ax.text(pos[0], pos[1] + pos[3] / 2., y_label,
horizontalignment='right', verticalalignment='middle',
rotation=90)
if colorbar:
plt.colorbar()
def _erfimage_imshow(ax, ch_idx, tmin, tmax, vmin, vmax, ylim=None, data=None,
epochs=None, sigma=None, order=None, scalings=None,
vline=None, x_label=None, y_label=None, colorbar=False,
cmap='RdBu_r'):
"""Plot erfimage on sensor topography."""
from scipy import ndimage
import matplotlib.pyplot as plt
this_data = data[:, ch_idx, :].copy() * scalings[ch_idx]
if callable(order):
order = order(epochs.times, this_data)
if order is not None:
this_data = this_data[order]
if sigma > 0.:
this_data = ndimage.gaussian_filter1d(this_data, sigma=sigma, axis=0)
img = ax.imshow(this_data, extent=[tmin, tmax, 0, len(data)],
aspect='auto', origin='lower', vmin=vmin, vmax=vmax,
picker=True, cmap=cmap, interpolation='nearest')
ax = plt.gca()
if x_label is not None:
ax.set_xlabel(x_label)
if y_label is not None:
ax.set_ylabel(y_label)
if colorbar:
plt.colorbar(mappable=img)
def _erfimage_imshow_unified(bn, ch_idx, tmin, tmax, vmin, vmax, ylim=None,
data=None, epochs=None, sigma=None, order=None,
scalings=None, vline=None, x_label=None,
y_label=None, colorbar=False, cmap='RdBu_r'):
"""Plot erfimage topography using a single axis."""
from scipy import ndimage
_compute_scalings(bn, (tmin, tmax), (0, len(epochs.events)))
ax = bn.ax
data_lines = bn.data_lines
extent = (bn.x_t + bn.x_s * tmin, bn.x_t + bn.x_s * tmax, bn.y_t,
bn.y_t + bn.y_s * len(epochs.events))
this_data = data[:, ch_idx, :].copy() * scalings[ch_idx]
if callable(order):
order = order(epochs.times, this_data)
if order is not None:
this_data = this_data[order]
if sigma > 0.:
this_data = ndimage.gaussian_filter1d(this_data, sigma=sigma, axis=0)
data_lines.append(ax.imshow(this_data, extent=extent, aspect='auto',
origin='lower', vmin=vmin, vmax=vmax,
picker=True, cmap=cmap,
interpolation='nearest'))
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.,), hline=(0.,), fig_facecolor='k',
fig_background=None, axis_facecolor='k', font_color='w',
merge_grads=False, legend=True, axes=None, show=True,
noise_cov=None):
"""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. 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.
hline : list of floats | None
The values at which to show a horizontal line.
fig_facecolor : str | obj
The figure face color. Defaults to black.
fig_background : None | array
A background image for the figure. This must be a valid input to
`matplotlib.pyplot.imshow`. Defaults to None.
axis_facecolor : str | obj
The face color to be used for each sensor plot. Defaults to black.
font_color : str | obj
The color of text in the colorbar and title. Defaults to white.
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.
show : bool
Show figure if True.
noise_cov : instance of Covariance | str | None
Noise covariance used to whiten the data while plotting.
Whitened data channels names are shown in italic.
Can be a string to load a covariance from disk.
.. versionadded:: 0.16.0
Returns
-------
fig : Instance of matplotlib.figure.Figure
Images of evoked responses at sensor locations
"""
import matplotlib.pyplot as plt
from ..cov import whiten_evoked
if not type(evoked) in (tuple, list):
evoked = [evoked]
if type(color) in (tuple, list):
if len(color) != len(evoked):
raise ValueError('Lists of evoked objects and colors'
' must have the same length')
elif color is None:
colors = ['w'] + _get_color_list
stop = (slice(len(evoked)) if len(evoked) < len(colors)
else slice(len(colors)))
color = cycle(colors[stop])
if len(evoked) > len(colors):
warn('More evoked objects than colors available. You should pass '
'a list of unique colors.')
else:
color = cycle([color])
times = evoked[0].times
if not all((e.times == times).all() for e in evoked):
raise ValueError('All evoked.times must be the same')
noise_cov = _check_cov(noise_cov, evoked[0].info)
if noise_cov is not None:
evoked = [whiten_evoked(e, noise_cov) for e in evoked]
else:
evoked = [e.copy() for e in evoked]
info = evoked[0].info
ch_names = evoked[0].ch_names
scalings = _handle_default('scalings', scalings)
if not all(e.ch_names == ch_names for e in evoked):
raise ValueError('All evoked.picks must be the same')
ch_names = _clean_names(ch_names)
if merge_grads:
picks = _pair_grad_sensors(info, topomap_coords=False)
chs = list()
for pick in picks[::2]:
ch = info['chs'][pick]
ch['ch_name'] = ch['ch_name'][:-1] + 'X'
chs.append(ch)
info['chs'] = chs
info['bads'] = list() # bads dropped on pair_grad_sensors
info._update_redundant()
info._check_consistency()
new_picks = list()
for e in evoked:
data = _merge_grad_data(e.data[picks])
if noise_cov is None:
data *= scalings['grad']
e.data = data
new_picks.append(range(len(data)))
picks = new_picks
types_used = ['grad']
unit = _handle_default('units')['grad'] if noise_cov is None else 'NA'
y_label = 'RMS amplitude (%s)' % unit
if layout is None:
layout = find_layout(info)
if not merge_grads:
# XXX. at the moment we are committed to 1- / 2-sensor-types layouts
chs_in_layout = set(layout.names) & set(ch_names)
types_used = set(channel_type(info, ch_names.index(ch))
for ch in chs_in_layout)
# remove possible reference meg channels
types_used = set.difference(types_used, set('ref_meg'))
# one check for all vendors
meg_types = set(('mag', 'grad'))
is_meg = len(set.intersection(types_used, meg_types)) > 0
if is_meg:
types_used = list(types_used)[::-1] # -> restore kwarg order
picks = [pick_types(info, meg=kk, ref_meg=False, exclude=[])
for kk in types_used]
else:
types_used_kwargs = dict((t, True) for t in types_used)
picks = [pick_types(info, meg=False, exclude=[],
**types_used_kwargs)]
assert isinstance(picks, list) and len(types_used) == len(picks)
if noise_cov is None:
for e in evoked:
for pick, ch_type in zip(picks, types_used):
e.data[pick] *= scalings[ch_type]
if proj is True and all(e.proj is not True for e in evoked):
evoked = [e.apply_proj() for e in evoked]
elif proj == 'interactive': # let it fail early.
for e in evoked:
_check_delayed_ssp(e)
# Y labels for picked plots must be reconstructed
y_label = list()
for ch_idx in range(len(chs_in_layout)):
if noise_cov is None:
unit = _handle_default('units')[channel_type(info, ch_idx)]
else:
unit = 'NA'
y_label.append('Amplitude (%s)' % unit)
if ylim is None:
def set_ylim(x):
return np.abs(x).max()
ylim_ = [set_ylim([e.data[t] for e in evoked]) for t in picks]
ymax = np.array(ylim_)
ylim_ = (-ymax, ymax)
elif isinstance(ylim, dict):
ylim_ = _handle_default('ylim', ylim)
ylim_ = [ylim_[kk] for kk in types_used]
# extra unpack to avoid bug #1700
if len(ylim_) == 1:
ylim_ = ylim_[0]
else:
ylim_ = zip(*[np.array(yl) for yl in ylim_])
else:
raise TypeError('ylim must be None or a dict. Got %s.' % type(ylim))
data = [e.data for e in evoked]
comments = [e.comment for e in evoked]
show_func = partial(_plot_timeseries_unified, data=data, color=color,
times=times, vline=vline, hline=hline,
hvline_color=font_color)
click_func = partial(_plot_timeseries, data=data, color=color, times=times,
vline=vline, hline=hline, hvline_color=font_color,
labels=comments)
fig = _plot_topo(info=info, times=times, show_func=show_func,
click_func=click_func, layout=layout, colorbar=False,
ylim=ylim_, cmap=None, layout_scale=layout_scale,
border=border, fig_facecolor=fig_facecolor,
font_color=font_color, axis_facecolor=axis_facecolor,
title=title, x_label='Time (s)', y_label=y_label,
unified=True, axes=axes)
add_background_image(fig, fig_background)
if legend is not False:
legend_loc = 0 if legend is True else legend
labels = [e.comment if e.comment else 'Unknown' for e in evoked]
legend = plt.legend(labels, loc=legend_loc,
prop={'size': 10})
legend.get_frame().set_facecolor(axis_facecolor)
txts = legend.get_texts()
for txt, col in zip(txts, color):
txt.set_color(col)
if proj == 'interactive':
for e in evoked:
_check_delayed_ssp(e)
params = dict(evokeds=evoked, times=times,
plot_update_proj_callback=_plot_update_evoked_topo_proj,
projs=evoked[0].info['projs'], fig=fig)
_draw_proj_checkbox(None, params)
plt_show(show)
return fig
def _plot_update_evoked_topo_proj(params, bools):
"""Update topo sensor plots."""
evokeds = [e.copy() for e in params['evokeds']]
fig = params['fig']
projs = [proj for proj, b in zip(params['projs'], bools) if b]
params['proj_bools'] = bools
for e in evokeds:
e.add_proj(projs, remove_existing=True)
e.apply_proj()
# make sure to only modify the time courses, not the ticks
for ax in fig.axes[0]._mne_axs:
for line, evoked in zip(ax.data_lines, evokeds):
line.set_ydata(ax.y_t + ax.y_s * evoked.data[ax._mne_ch_idx])
fig.canvas.draw()
def plot_topo_image_epochs(epochs, layout=None, sigma=0., vmin=None,
vmax=None, colorbar=True, order=None, cmap='RdBu_r',
layout_scale=.95, title=None, scalings=None,
border='none', fig_facecolor='k',
fig_background=None, font_color='w', show=True):
"""Plot Event Related Potential / Fields image on topographies.
Parameters
----------
epochs : instance of Epochs
The epochs.
layout: instance of Layout
System specific sensor positions.
sigma : float
The standard deviation of the Gaussian smoothing to apply along
the epoch axis to apply in the image. If 0., no smoothing is applied.
vmin : float
The min value in the image. The unit is uV for EEG channels,
fT for magnetometers and fT/cm for gradiometers.
vmax : float
The max value in the image. The unit is uV for EEG channels,
fT for magnetometers and fT/cm for gradiometers.
colorbar : bool
Display or not a colorbar.
order : None | array of int | callable
If not None, order is used to reorder the epochs on the y-axis
of the image. If it's an array of int it should be of length
the number of good epochs. If it's a callable the arguments
passed are the times vector and the data as 2d array
(data.shape[1] == len(times)).
cmap : instance of matplotlib.pyplot.colormap
Colors to be mapped to the values.
layout_scale: float
scaling factor for adjusting the relative size of the layout
on the canvas.
title : str
Title of the figure.
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)`.
border : str
matplotlib borders style to be used for each sensor plot.
fig_facecolor : str | obj
The figure face color. Defaults to black.
fig_background : None | array
A background image for the figure. This must be a valid input to
`matplotlib.pyplot.imshow`. Defaults to None.
font_color : str | obj
The color of tick labels in the colorbar. Defaults to white.
show : bool
Show figure if True.
Returns
-------
fig : instance of matplotlib figure
Figure distributing one image per channel across sensor topography.
"""
scalings = _handle_default('scalings', scalings)
data = epochs.get_data()
scale_coeffs = list()
for idx in range(epochs.info['nchan']):
ch_type = channel_type(epochs.info, idx)
scale_coeffs.append(scalings.get(ch_type, 1))
vmin, vmax = _setup_vmin_vmax(data, vmin, vmax)
if layout is None:
layout = find_layout(epochs.info)
show_func = partial(_erfimage_imshow_unified, scalings=scale_coeffs,
order=order, data=data, epochs=epochs, sigma=sigma,
cmap=cmap)
erf_imshow = partial(_erfimage_imshow, scalings=scale_coeffs, order=order,
data=data, epochs=epochs, sigma=sigma, cmap=cmap)
fig = _plot_topo(info=epochs.info, times=epochs.times,
click_func=erf_imshow, show_func=show_func, layout=layout,
colorbar=colorbar, vmin=vmin, vmax=vmax, cmap=cmap,
layout_scale=layout_scale, title=title,
fig_facecolor=fig_facecolor, font_color=font_color,
border=border, x_label='Time (s)', y_label='Epoch',
unified=True, img=True)
add_background_image(fig, fig_background)
plt_show(show)
return fig
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