1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725
|
"""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
import warnings
from itertools import cycle
from functools import partial
import numpy as np
from scipy import ndimage
# XXX : don't import pyplot here or you will break the doc
from ..baseline import rescale
from ..utils import deprecated
from ..io.pick import channel_type, pick_types
from ..fixes import normalize_colors
from ..utils import _clean_names
from .utils import _mutable_defaults, _check_delayed_ssp, COLORS
from .utils import _draw_proj_checkbox
def iter_topography(info, layout=None, on_pick=None, fig=None,
fig_facecolor='k', axis_facecolor='k',
axis_spinecolor='k', layout_scale=None,
colorbar=False):
""" 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 mne.io.meas_info.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.
"""
import matplotlib.pyplot as plt
if fig is None:
fig = plt.figure()
fig.set_facecolor(fig_facecolor)
if layout is None:
from ..layouts import find_layout
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]
for idx, name in iter_ch:
ax = plt.axes(pos[idx])
ax.patch.set_facecolor(axis_facecolor)
plt.setp(list(ax.spines.values()), color=axis_spinecolor)
ax.set_xticklabels([])
ax.set_yticklabels([])
plt.setp(ax.get_xticklines(), visible=False)
plt.setp(ax.get_yticklines(), visible=False)
ch_idx = ch_names.index(name)
vars(ax)['_mne_ch_name'] = name
vars(ax)['_mne_ch_idx'] = ch_idx
vars(ax)['_mne_ax_face_color'] = axis_facecolor
yield ax, ch_idx
def _plot_topo(info=None, times=None, show_func=None, layout=None,
decim=None, vmin=None, vmax=None, ylim=None, colorbar=None,
border='none', cmap=None, layout_scale=None, title=None,
x_label=None, y_label=None, vline=None):
"""Helper function to plot on sensor layout"""
import matplotlib.pyplot as plt
# prepare callbacks
tmin, tmax = times[[0, -1]]
on_pick = partial(show_func, tmin=tmin, tmax=tmax, vmin=vmin,
vmax=vmax, ylim=ylim, x_label=x_label,
y_label=y_label, colorbar=colorbar)
fig = plt.figure()
if colorbar:
norm = normalize_colors(vmin=vmin, vmax=vmax)
sm = plt.cm.ScalarMappable(cmap=cmap, norm=norm)
sm.set_array(np.linspace(vmin, vmax))
ax = plt.axes([0.015, 0.025, 1.05, .8], axisbg='k')
cb = fig.colorbar(sm, ax=ax)
cb_yticks = plt.getp(cb.ax.axes, 'yticklabels')
plt.setp(cb_yticks, color='w')
my_topo_plot = iter_topography(info, layout=layout, on_pick=on_pick,
fig=fig, layout_scale=layout_scale,
axis_spinecolor=border,
colorbar=colorbar)
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 ylim_ and not any(v is None for v in ylim_):
plt.ylim(*ylim_)
if title is not None:
plt.figtext(0.03, 0.9, title, color='w', fontsize=19)
return fig
def _plot_topo_onpick(event, show_func=None, colorbar=False):
"""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
if event.inaxes is None:
return
import matplotlib.pyplot as plt
try:
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)
ax.set_axis_bgcolor(face_color)
# allow custom function to override parameters
show_func(plt, 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 err
def _imshow_tfr(ax, ch_idx, tmin, tmax, vmin, vmax, ylim=None, tfr=None,
freq=None, vline=None, x_label=None, y_label=None,
colorbar=False, picker=True, cmap=None):
""" Aux function to show time-freq map on topo """
import matplotlib.pyplot as plt
if cmap is None:
cmap = plt.cm.jet
extent = (tmin, tmax, freq[0], freq[-1])
ax.imshow(tfr[ch_idx], extent=extent, aspect="auto", origin="lower",
vmin=vmin, vmax=vmax, picker=picker, cmap=cmap)
if x_label is not None:
plt.xlabel(x_label)
if y_label is not None:
plt.ylabel(y_label)
if colorbar:
plt.colorbar()
def _plot_timeseries(ax, ch_idx, tmin, tmax, vmin, vmax, ylim, data, color,
times, vline=None, x_label=None, y_label=None,
colorbar=False):
""" Aux function to show time series on topo """
import matplotlib.pyplot as plt
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_, picker=1e9)
picker_flag = True
else:
ax.plot(times, data_[ch_idx], color_)
if vline:
[plt.axvline(x, color='w', linewidth=0.5) for x in vline]
if x_label is not None:
plt.xlabel(x_label)
if y_label is not None:
plt.ylabel(y_label)
if colorbar:
plt.colorbar()
def _check_vlim(vlim):
"""AUX function"""
return not np.isscalar(vlim) and not vlim is None
def plot_topo(evoked, layout=None, layout_scale=0.945, color=None,
border='none', ylim=None, scalings=None, title=None, proj=False,
vline=[0.0]):
"""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.
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)`.
ylim : dict | None
ylim for plots. The value determines the upper and lower subplot
limits. e.g. ylim = dict(eeg=[-200e-6, 200e6]). Valid keys are eeg,
mag, grad, misc. If None, the ylim parameter for each channel is
determined by the maximum absolute peak.
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.
title : str
Title of the figure.
vline : list of floats | None
The values at which to show a vertical line.
Returns
-------
fig : Instance of matplotlib.figure.Figure
Images of evoked responses at sensor locations
"""
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'] + COLORS
stop = (slice(len(evoked)) if len(evoked) < len(colors)
else slice(len(colors)))
color = cycle(colors[stop])
if len(evoked) > len(colors):
warnings.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')
info = evoked[0].info
ch_names = evoked[0].ch_names
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 layout is None:
from ..layouts.layout import find_layout
layout = find_layout(info)
# 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)
# one check for all vendors
meg_types = ['mag'], ['grad'], ['mag', 'grad'],
is_meg = any(types_used == set(k) for k in meg_types)
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, **types_used_kwargs)]
assert isinstance(picks, list) and len(types_used) == len(picks)
scalings = _mutable_defaults(('scalings', scalings))[0]
evoked = [e.copy() for e in evoked]
for e in evoked:
for pick, t in zip(picks, types_used):
e.data[pick] = e.data[pick] * scalings[t]
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)
if ylim is None:
set_ylim = lambda x: 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_ = _mutable_defaults(('ylim', ylim))[0]
ylim_ = [ylim_[kk] for kk in types_used]
ylim_ = zip(*[np.array(yl) for yl in ylim_])
else:
raise ValueError('ylim must be None ore a dict')
plot_fun = partial(_plot_timeseries, data=[e.data for e in evoked],
color=color, times=times, vline=vline)
fig = _plot_topo(info=info, times=times, show_func=plot_fun, layout=layout,
decim=1, colorbar=False, ylim=ylim_, cmap=None,
layout_scale=layout_scale, border=border, title=title,
x_label='Time (s)', vline=vline)
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,
projs=evoked[0].info['projs'], fig=fig)
_draw_proj_checkbox(None, params)
return fig
def _plot_update_evoked_topo(params, bools):
"""Helper function to update topo sensor plots"""
evokeds, times, fig = [params[k] for k in ('evokeds', 'times', 'fig')]
projs = [proj for ii, proj in enumerate(params['projs'])
if ii in np.where(bools)[0]]
params['proj_bools'] = bools
evokeds = [e.copy() for e in evokeds]
for e in evokeds:
e.info['projs'] = []
e.add_proj(projs)
e.apply_proj()
# make sure to only modify the time courses, not the ticks
axes = fig.get_axes()
n_lines = len(axes[0].lines)
n_diff = len(evokeds) - n_lines
ax_slice = slice(abs(n_diff)) if n_diff < 0 else slice(n_lines)
for ax in axes:
lines = ax.lines[ax_slice]
for line, evoked in zip(lines, evokeds):
line.set_data(times, evoked.data[ax._mne_ch_idx])
fig.canvas.draw()
@deprecated('`plot_topo_tfr` is deprecated and will be removed in '
'MNE 0.9. Use `plot_topo` method on TFR objects.')
def plot_topo_tfr(epochs, tfr, freq, layout=None, colorbar=True, vmin=None,
vmax=None, cmap='RdBu_r', layout_scale=0.945, title=None):
"""Plot time-frequency data on sensor layout
Clicking on the time-frequency map of an individual sensor opens a
new figure showing the time-frequency map of the selected sensor.
Parameters
----------
epochs : instance of Epochs
The epochs used to generate the power
tfr : 3D-array shape=(n_sensors, n_freqs, n_times)
The time-frequency data. Must have the same channels as Epochs.
freq : array-like
Frequencies of interest as passed to induced_power
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.
colorbar : bool
If true, colorbar will be added to the plot
vmin : float
Minimum value mapped to lowermost color
vmax : float
Minimum value mapped to upppermost color
cmap : instance of matplotlib.pyplot.colormap | str
Colors to be mapped to the values. Default 'RdBu_r'.
layout_scale : float
Scaling factor for adjusting the relative size of the layout
on the canvas
title : str
Title of the figure.
Returns
-------
fig : Instance of matplotlib.figure.Figure
Images of time-frequency data at sensor locations
"""
if vmin is None:
vmin = tfr.min()
if vmax is None:
vmax = tfr.max()
if layout is None:
from ..layouts.layout import find_layout
layout = find_layout(epochs.info)
tfr_imshow = partial(_imshow_tfr, tfr=tfr.copy(), freq=freq, cmap=cmap)
fig = _plot_topo(info=epochs.info, times=epochs.times,
show_func=tfr_imshow, layout=layout, border='w',
colorbar=colorbar, vmin=vmin, vmax=vmax, cmap=cmap,
layout_scale=layout_scale, title=title,
x_label='Time (s)', y_label='Frequency (Hz)')
return fig
@deprecated('`plot_topo_power` is deprecated and will be removed in '
'MNE 0.9. Use `plot_topo` method on TFR objects.')
def plot_topo_power(epochs, power, freq, layout=None, baseline=None,
mode='mean', decim=1, colorbar=True, vmin=None, vmax=None,
cmap=None, layout_scale=0.945, dB=True, title=None):
"""Plot induced power on sensor layout
Clicking on the induced power map of an individual sensor opens a
new figure showing the induced power map of the selected sensor.
Parameters
----------
epochs : instance of Epochs
The epochs used to generate the power
power : 3D-array
First return value from mne.time_frequency.induced_power
freq : array-like
Frequencies of interest as passed to induced_power
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.
baseline : tuple or list of length 2
The time interval to apply rescaling / baseline correction.
If None do not apply it. If baseline is (a, b)
the interval is between "a (s)" and "b (s)".
If a is None the beginning of the data is used
and if b is None then b is set to the end of the interval.
If baseline is equal to (None, None) all the time
interval is used.
mode : 'logratio' | 'ratio' | 'zscore' | 'mean' | 'percent'
Do baseline correction with ratio (power is divided by mean
power during baseline) or z-score (power is divided by standard
deviation of power during baseline after subtracting the mean,
power = [power - mean(power_baseline)] / std(power_baseline))
If None, baseline no correction will be performed.
decim : integer
Increment for selecting each nth time slice
colorbar : bool
If true, colorbar will be added to the plot
vmin : float
Minimum value mapped to lowermost color
vmax : float
Minimum value mapped to upppermost color
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
dB : bool
If True, log10 will be applied to the data.
title : str
Title of the figure.
Returns
-------
fig : Instance of matplotlib.figure.Figure
Images of induced power at sensor locations
"""
times = epochs.times[::decim].copy()
if mode is not None:
if baseline is None:
baseline = epochs.baseline
power = rescale(power.copy(), times, baseline, mode)
times *= 1e3
if dB:
power = 20 * np.log10(power)
if vmin is None:
vmin = power.min()
if vmax is None:
vmax = power.max()
if layout is None:
from ..layouts.layout import find_layout
layout = find_layout(epochs.info)
power_imshow = partial(_imshow_tfr, tfr=power.copy(), freq=freq)
fig = _plot_topo(info=epochs.info, times=times,
show_func=power_imshow, layout=layout, decim=decim,
colorbar=colorbar, vmin=vmin, vmax=vmax, cmap=cmap,
layout_scale=layout_scale, title=title, border='w',
x_label='Time (s)', y_label='Frequency (Hz)')
return fig
@deprecated('`plot_topo_phase_lock` is deprecated and will be removed in '
'MNE 0.9. Use `plot_topo` method on TFR objects.')
def plot_topo_phase_lock(epochs, phase, freq, layout=None, baseline=None,
mode='mean', decim=1, colorbar=True, vmin=None,
vmax=None, cmap=None, layout_scale=0.945,
title=None):
"""Plot phase locking values (PLV) on sensor layout
Clicking on the PLV map of an individual sensor opens a new figure
showing the PLV map of the selected sensor.
Parameters
----------
epochs : instance of Epochs
The epochs used to generate the phase locking value
phase_lock : 3D-array
Phase locking value, second return value from
mne.time_frequency.induced_power.
freq : array-like
Frequencies of interest as passed to induced_power
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.
baseline : tuple or list of length 2
The time interval to apply rescaling / baseline correction.
If None do not apply it. If baseline is (a, b)
the interval is between "a (s)" and "b (s)".
If a is None the beginning of the data is used
and if b is None then b is set to the end of the interval.
If baseline is equal to (None, None) all the time
interval is used.
mode : 'logratio' | 'ratio' | 'zscore' | 'mean' | 'percent' | None
Do baseline correction with ratio (phase is divided by mean
phase during baseline) or z-score (phase is divided by standard
deviation of phase during baseline after subtracting the mean,
phase = [phase - mean(phase_baseline)] / std(phase_baseline)).
If None, baseline no correction will be performed.
decim : integer
Increment for selecting each nth time slice
colorbar : bool
If true, colorbar will be added to the plot
vmin : float
Minimum value mapped to lowermost color
vmax : float
Minimum value mapped to upppermost color
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.
Returns
-------
fig : Instance of matplotlib.figure.Figrue
Phase lock images at sensor locations
"""
times = epochs.times[::decim] * 1e3
if mode is not None:
if baseline is None:
baseline = epochs.baseline
phase = rescale(phase.copy(), times, baseline, mode)
if vmin is None:
vmin = phase.min()
if vmax is None:
vmax = phase.max()
if layout is None:
from ..layouts.layout import find_layout
layout = find_layout(epochs.info)
phase_imshow = partial(_imshow_tfr, tfr=phase.copy(), freq=freq)
fig = _plot_topo(info=epochs.info, times=times,
show_func=phase_imshow, layout=layout, decim=decim,
colorbar=colorbar, vmin=vmin, vmax=vmax, cmap=cmap,
layout_scale=layout_scale, title=title, border='w',
x_label='Time (s)', y_label='Frequency (Hz)')
return fig
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):
"""Aux function to plot erfimage on sensor topography"""
import matplotlib.pyplot as plt
this_data = data[:, ch_idx, :].copy()
ch_type = channel_type(epochs.info, ch_idx)
if not ch_type in scalings:
raise KeyError('%s channel type not in scalings' % ch_type)
this_data *= scalings[ch_type]
if callable(order):
order = order(epochs.times, this_data)
if order is not None:
this_data = this_data[order]
this_data = ndimage.gaussian_filter1d(this_data, sigma=sigma, axis=0)
ax.imshow(this_data, extent=[tmin, tmax, 0, len(data)], aspect='auto',
origin='lower', vmin=vmin, vmax=vmax, picker=True)
if x_label is not None:
plt.xlabel(x_label)
if y_label is not None:
plt.ylabel(y_label)
if colorbar:
plt.colorbar()
def plot_topo_image_epochs(epochs, layout=None, sigma=0.3, vmin=None,
vmax=None, colorbar=True, order=None, cmap=None,
layout_scale=.95, title=None, scalings=None):
"""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.
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)`.
Returns
-------
fig : instance of matplotlib figure
Figure distributing one image per channel across sensor topography.
"""
scalings = _mutable_defaults(('scalings', scalings))[0]
data = epochs.get_data()
if vmin is None:
vmin = data.min()
if vmax is None:
vmax = data.max()
if layout is None:
from ..layouts.layout import find_layout
layout = find_layout(epochs.info)
erf_imshow = partial(_erfimage_imshow, scalings=scalings, order=order,
data=data, epochs=epochs, sigma=sigma)
fig = _plot_topo(info=epochs.info, times=epochs.times,
show_func=erf_imshow, layout=layout, decim=1,
colorbar=colorbar, vmin=vmin, vmax=vmax, cmap=cmap,
layout_scale=layout_scale, title=title,
border='w', x_label='Time (s)', y_label='Epoch')
return fig
|