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"""Functions to plot M/EEG data e.g. 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>
#
# License: Simplified BSD
import math
import copy
from functools import partial
import itertools
from numbers import Integral
import warnings
import numpy as np
from ..baseline import rescale
from ..io.pick import (pick_types, _picks_by_type, channel_type, pick_info,
_pick_data_channels, pick_channels)
from ..utils import _clean_names, _time_mask, verbose, logger, warn
from .utils import (tight_layout, _setup_vmin_vmax, _prepare_trellis,
_check_delayed_ssp, _draw_proj_checkbox, figure_nobar,
plt_show, _process_times, DraggableColorbar,
_validate_if_list_of_axes, _setup_cmap, _check_time_unit)
from ..time_frequency import psd_multitaper
from ..defaults import _handle_default
from ..channels.layout import _find_topomap_coords
from ..io.meas_info import Info
from ..externals.six import string_types
def _prepare_topo_plot(inst, ch_type, layout):
"""Prepare topo plot."""
info = copy.deepcopy(inst if isinstance(inst, Info) else inst.info)
if layout is None and ch_type is not 'eeg':
from ..channels import find_layout
layout = find_layout(info) # XXX : why not passing ch_type???
elif layout == 'auto':
layout = None
clean_ch_names = _clean_names(info['ch_names'])
for ii, this_ch in enumerate(info['chs']):
this_ch['ch_name'] = clean_ch_names[ii]
info['bads'] = _clean_names(info['bads'])
for comp in info['comps']:
comp['data']['col_names'] = _clean_names(comp['data']['col_names'])
info._update_redundant()
info._check_consistency()
# special case for merging grad channels
if (ch_type == 'grad' and layout is not None and
(layout.kind.startswith('Vectorview') or
layout.kind.startswith('Neuromag_122'))):
from ..channels.layout import _pair_grad_sensors
picks, pos = _pair_grad_sensors(info, layout)
merge_grads = True
else:
merge_grads = False
if ch_type == 'eeg':
picks = pick_types(info, meg=False, eeg=True, ref_meg=False,
exclude='bads')
else:
picks = pick_types(info, meg=ch_type, ref_meg=False,
exclude='bads')
if len(picks) == 0:
raise ValueError("No channels of type %r" % ch_type)
if layout is None:
pos = _find_topomap_coords(info, picks)
else:
names = [n.upper() for n in layout.names]
pos = list()
for pick in picks:
this_name = info['ch_names'][pick].upper()
if this_name in names:
pos.append(layout.pos[names.index(this_name)])
else:
warn('Failed to locate %s channel positions from layout. '
'Inferring channel positions from data.' % ch_type)
pos = _find_topomap_coords(info, picks)
break
ch_names = [info['ch_names'][k] for k in picks]
if merge_grads:
# change names so that vectorview combined grads appear as MEG014x
# instead of MEG0142 or MEG0143 which are the 2 planar grads.
ch_names = [ch_names[k][:-1] + 'x' for k in range(0, len(ch_names), 2)]
pos = np.array(pos)[:, :2] # 2D plot, otherwise interpolation bugs
return picks, pos, merge_grads, ch_names, ch_type
def _plot_update_evoked_topomap(params, bools):
"""Update topomaps."""
from ..channels.layout import _merge_grad_data
projs = [proj for ii, proj in enumerate(params['projs'])
if ii in np.where(bools)[0]]
params['proj_bools'] = bools
new_evoked = params['evoked'].copy()
new_evoked.info['projs'] = []
new_evoked.add_proj(projs)
new_evoked.apply_proj()
data = new_evoked.data[:, params['time_idx']] * params['scale']
if params['merge_grads']:
data = _merge_grad_data(data)
interp = params['interp']
new_contours = list()
for cont, ax, im, d in zip(params['contours_'], params['axes'],
params['images'], data.T):
Zi = interp.set_values(d)()
im.set_data(Zi)
# must be removed and re-added
if len(cont.collections) > 0:
tp = cont.collections[0]
visible = tp.get_visible()
patch_ = tp.get_clip_path()
color = tp.get_color()
lw = tp.get_linewidth()
for tp in cont.collections:
tp.remove()
cont = ax.contour(interp.Xi, interp.Yi, Zi, params['contours'],
colors=color, linewidths=lw)
for tp in cont.collections:
tp.set_visible(visible)
tp.set_clip_path(patch_)
new_contours.append(cont)
params['contours_'] = new_contours
params['fig'].canvas.draw()
def _add_colorbar(ax, im, cmap, side="right", pad=.05, title=None,
format=None, size="5%"):
"""Add a colorbar to an axis."""
import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid1 import make_axes_locatable # noqa: F401
divider = make_axes_locatable(ax)
cax = divider.append_axes(side, size=size, pad=pad)
cbar = plt.colorbar(im, cax=cax, cmap=cmap, format=format)
if cmap is not None and cmap[1]:
ax.CB = DraggableColorbar(cbar, im)
if title is not None:
cax.set_title(title, y=1.05, fontsize=10)
return cbar, cax
def _eliminate_zeros(proj):
"""Remove grad or mag data if only contains 0s (gh 5641)."""
GRAD_ENDING = ('2', '3')
MAG_ENDING = '1'
proj = copy.deepcopy(proj)
proj['data']['data'] = np.atleast_2d(proj['data']['data'])
for ending in (GRAD_ENDING, MAG_ENDING):
names = proj['data']['col_names']
idx = [i for i, name in enumerate(names) if name.endswith(ending)]
# if all 0, remove the 0s an their labels
if not proj['data']['data'][0][idx].any():
new_col_names = np.delete(np.array(names), idx).tolist()
new_data = np.delete(np.array(proj['data']['data'][0]), idx)
proj['data']['col_names'] = new_col_names
proj['data']['data'] = np.array([new_data])
proj['data']['ncol'] = len(proj['data']['col_names'])
return proj
def plot_projs_topomap(projs, layout=None, cmap=None, sensors=True,
colorbar=False, res=64, size=1, show=True,
outlines='head', contours=6, image_interp='bilinear',
axes=None, info=None):
"""Plot topographic maps of SSP projections.
Parameters
----------
projs : list of Projection
The projections
layout : None | Layout | list of Layout
Layout instance specifying sensor positions (does not need to be
specified for Neuromag data). Or a list of Layout if projections
are from different sensor types.
cmap : matplotlib colormap | (colormap, bool) | 'interactive' | None
Colormap to use. If tuple, the first value indicates the colormap to
use and the second value is a boolean defining interactivity. In
interactive mode (only works if ``colorbar=True``) 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 range. Up
and down arrows can be used to change the colormap. If None (default),
'Reds' is used for all positive data, otherwise defaults to 'RdBu_r'.
If 'interactive', translates to (None, True).
sensors : bool | str
Add markers for sensor locations to the plot. Accepts matplotlib plot
format string (e.g., 'r+' for red plusses). If True, a circle will be
used (via .add_artist). Defaults to True.
colorbar : bool
Plot a colorbar.
res : int
The resolution of the topomap image (n pixels along each side).
size : scalar
Side length of the topomaps in inches (only applies when plotting
multiple topomaps at a time).
show : bool
Show figure if True.
outlines : 'head' | 'skirt' | dict | None
The outlines to be drawn. If 'head', the default head scheme will be
drawn. If 'skirt' the head scheme will be drawn, but sensors are
allowed to be plotted outside of the head circle. If dict, each key
refers to a tuple of x and y positions, the values in 'mask_pos' will
serve as image mask, and the 'autoshrink' (bool) field will trigger
automated shrinking of the positions due to points outside the outline.
Alternatively, a matplotlib patch object can be passed for advanced
masking options, either directly or as a function that returns patches
(required for multi-axis plots). If None, nothing will be drawn.
Defaults to 'head'.
contours : int | array of float
The number of contour lines to draw. If 0, no contours will be drawn.
When an integer, matplotlib ticker locator is used to find suitable
values for the contour thresholds (may sometimes be inaccurate, use
array for accuracy). If an array, the values represent the levels for
the contours. Defaults to 6.
image_interp : str
The image interpolation to be used. All matplotlib options are
accepted.
axes : instance of Axes | 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 projectors. If instance of Axes,
there must be only one projector. Defaults to None.
info : instance of Info | None
The measurement information to use to determine the layout.
If not None, ``layout`` must be None.
Returns
-------
fig : instance of matplotlib figure
Figure distributing one image per channel across sensor topography.
Notes
-----
.. versionadded:: 0.9.0
"""
import matplotlib.pyplot as plt
from ..channels.layout import (_pair_grad_sensors_ch_names_vectorview,
_pair_grad_sensors_ch_names_neuromag122,
Layout, _merge_grad_data)
from ..channels import _get_ch_type
is_layout_parameter_none = layout is None
is_info_parameter_none = info is None
if info is not None:
if not isinstance(info, Info):
raise TypeError('info must be an instance of Info, got %s'
% (type(info),))
if layout is not None:
raise ValueError('layout must be None if info is provided')
else:
if layout is None:
from ..channels import read_layout
layout = read_layout('Vectorview-all')
if not isinstance(layout, (list, tuple)):
layout = [layout]
if not isinstance(layout, (list, tuple)):
raise TypeError('layout must be an instance of Layout, list, '
'or None, got %s' % (type(layout),))
for l in layout:
if not isinstance(l, Layout):
raise TypeError('All entries in layout list must be of type '
'Layout, got type %s' % (type(l),))
n_projs = len(projs)
nrows = math.floor(math.sqrt(n_projs))
ncols = math.ceil(n_projs / nrows)
if axes is None:
plt.figure()
axes = list()
for idx in range(len(projs)):
ax = plt.subplot(nrows, ncols, idx + 1)
axes.append(ax)
elif isinstance(axes, plt.Axes):
axes = [axes]
if len(axes) != len(projs):
raise RuntimeError('There must be an axes for each picked projector.')
for proj_idx, proj in enumerate(projs):
title = proj['desc']
title = '\n'.join(title[ii:ii + 22] for ii in range(0, len(title), 22))
axes[proj_idx].set_title(title, fontsize=10)
proj = _eliminate_zeros(proj) # gh 5641
ch_names = _clean_names(proj['data']['col_names'],
remove_whitespace=True)
data = proj['data']['data'].ravel()
if info is not None:
info_names = _clean_names(info['ch_names'],
remove_whitespace=True)
use_info = pick_info(info, pick_channels(info_names, ch_names))
data_picks, pos, merge_grads, names, _ = _prepare_topo_plot(
use_info, _get_ch_type(use_info, None), None)
data = data[data_picks]
if merge_grads:
data = _merge_grad_data(data).ravel()
else: # list of layouts
idx = []
for l in layout:
is_vv = l.kind.startswith('Vectorview')
grad_pairs = None
if is_vv:
grad_pairs = \
_pair_grad_sensors_ch_names_vectorview(ch_names)
if grad_pairs:
ch_names = [ch_names[i] for i in grad_pairs]
is_neuromag122 = l.kind.startswith('Neuromag_122')
if is_neuromag122:
grad_pairs = \
_pair_grad_sensors_ch_names_neuromag122(ch_names)
if grad_pairs:
ch_names = [ch_names[i] for i in grad_pairs]
l_names = _clean_names(l.names, remove_whitespace=True)
idx = [l_names.index(c) for c in ch_names if c in l_names]
if len(idx) == 0:
continue
pos = l.pos[idx]
if grad_pairs:
shape = (len(idx) // 2, 2, -1)
pos = pos.reshape(shape).mean(axis=1)
data = _merge_grad_data(data[grad_pairs]).ravel()
break
if len(idx) == 0:
if ch_names[0].startswith('EEG'):
msg = ('Cannot find a proper layout for projection {0}.'
' The proper layout of an EEG topomap cannot be'
' inferred from the data. '.format(proj['desc']))
if is_layout_parameter_none and is_info_parameter_none:
msg += (' For EEG data, valid `layout` or `info` is'
' required. None was provided, please consider'
' passing one of them.')
elif not is_layout_parameter_none:
msg += (' A `layout` was provided but could not be'
' used for display. Please review the `layout`'
' parameter.')
else: # layout is none, but we have info
msg += (' The `info` parameter was provided but could'
' not be for display. Please review the `info`'
' parameter.')
raise RuntimeError(msg)
else:
raise RuntimeError('Cannot find a proper layout for '
'projection %s, consider explicitly '
'passing a Layout or Info as the layout'
' parameter.' % proj['desc'])
im = plot_topomap(data, pos[:, :2], vmax=None, cmap=cmap,
sensors=sensors, res=res, axes=axes[proj_idx],
outlines=outlines, contours=contours,
image_interp=image_interp, show=False)[0]
if colorbar:
_add_colorbar(axes[proj_idx], im, cmap)
tight_layout(fig=axes[0].get_figure())
plt_show(show)
return axes[0].get_figure()
def _check_outlines(pos, outlines, head_pos=None):
"""Check or create outlines for topoplot."""
pos = np.array(pos, float)[:, :2] # ensure we have a copy
head_pos = dict() if head_pos is None else head_pos
if not isinstance(head_pos, dict):
raise TypeError('head_pos must be dict or None')
head_pos = copy.deepcopy(head_pos)
for key in head_pos.keys():
if key not in ('center', 'scale'):
raise KeyError('head_pos must only contain "center" and '
'"scale"')
head_pos[key] = np.array(head_pos[key], float)
if head_pos[key].shape != (2,):
raise ValueError('head_pos["%s"] must have shape (2,), not '
'%s' % (key, head_pos[key].shape))
if isinstance(outlines, np.ndarray) or outlines in ('head', 'skirt', None):
radius = 0.5
ll = np.linspace(0, 2 * np.pi, 101)
head_x = np.cos(ll) * radius
head_y = np.sin(ll) * radius
nose_x = np.array([0.18, 0, -0.18]) * radius
nose_y = np.array([radius - .004, radius * 1.15, radius - .004])
ear_x = np.array([.497, .510, .518, .5299, .5419, .54, .547,
.532, .510, .489])
ear_y = np.array([.0555, .0775, .0783, .0746, .0555, -.0055, -.0932,
-.1313, -.1384, -.1199])
# shift and scale the electrode positions
if 'center' not in head_pos:
head_pos['center'] = 0.5 * (pos.max(axis=0) + pos.min(axis=0))
pos -= head_pos['center']
if outlines is not None:
# Define the outline of the head, ears and nose
outlines_dict = dict(head=(head_x, head_y), nose=(nose_x, nose_y),
ear_left=(ear_x, ear_y),
ear_right=(-ear_x, ear_y))
else:
outlines_dict = dict()
if isinstance(outlines, string_types) and outlines == 'skirt':
if 'scale' not in head_pos:
# By default, fit electrodes inside the head circle
head_pos['scale'] = 1.0 / (pos.max(axis=0) - pos.min(axis=0))
pos *= head_pos['scale']
# Make the figure encompass slightly more than all points
mask_scale = 1.25 * (pos.max(axis=0) - pos.min(axis=0))
outlines_dict['autoshrink'] = False
outlines_dict['mask_pos'] = (mask_scale[0] * head_x,
mask_scale[1] * head_y)
outlines_dict['clip_radius'] = (mask_scale / 2.)
else:
if 'scale' not in head_pos:
# The default is to make the points occupy a slightly smaller
# proportion (0.85) of the total width and height
# this number was empirically determined (seems to work well)
head_pos['scale'] = 0.85 / (pos.max(axis=0) - pos.min(axis=0))
pos *= head_pos['scale']
outlines_dict['mask_pos'] = head_x, head_y
if isinstance(outlines, np.ndarray):
outlines_dict['autoshrink'] = False
outlines_dict['clip_radius'] = outlines
x_scale = np.max(outlines_dict['head'][0]) / outlines[0]
y_scale = np.max(outlines_dict['head'][1]) / outlines[1]
for key in ['head', 'nose', 'ear_left', 'ear_right']:
value = outlines_dict[key]
value = (value[0] / x_scale, value[1] / y_scale)
outlines_dict[key] = value
else:
outlines_dict['autoshrink'] = True
outlines_dict['clip_radius'] = (0.5, 0.5)
outlines = outlines_dict
elif isinstance(outlines, dict):
if 'mask_pos' not in outlines:
raise ValueError('You must specify the coordinates of the image '
'mask.')
else:
raise ValueError('Invalid value for `outlines`.')
return pos, outlines
def _draw_outlines(ax, outlines):
"""Draw the outlines for a topomap."""
outlines_ = dict([(k, v) for k, v in outlines.items() if k not in
['patch', 'autoshrink']])
for key, (x_coord, y_coord) in outlines_.items():
if 'mask' in key:
continue
ax.plot(x_coord, y_coord, color='k', linewidth=1, clip_on=False)
return outlines_
class _GridData(object):
"""Unstructured (x,y) data interpolator.
This class allows optimized interpolation by computing parameters
for a fixed set of true points, and allowing the values at those points
to be set independently.
"""
def __init__(self, pos):
from scipy.spatial.qhull import Delaunay
# in principle this works in N dimensions, not just 2
assert pos.ndim == 2 and pos.shape[1] == 2
# Adding points outside the extremes helps the interpolators
extremes = np.array([pos.min(axis=0), pos.max(axis=0)])
diffs = extremes[1] - extremes[0]
extremes[0] -= diffs
extremes[1] += diffs
eidx = np.array(list(itertools.product(
*([[0] * (pos.shape[1] - 1) + [1]] * pos.shape[1]))))
pidx = np.tile(np.arange(pos.shape[1])[np.newaxis], (len(eidx), 1))
self.n_extra = pidx.shape[0]
outer_pts = extremes[eidx, pidx]
pos = np.concatenate((pos, outer_pts))
self.tri = Delaunay(pos)
def set_values(self, v):
"""Set the values at interpolation points."""
# Rbf with thin-plate is what we used to use, but it's slower and
# looks about the same:
#
# zi = Rbf(x, y, v, function='multiquadric', smooth=0)(xi, yi)
#
# Eventually we could also do set_values with this class if we want,
# see scipy/interpolate/rbf.py, especially the self.nodes one-liner.
from scipy.interpolate import CloughTocher2DInterpolator
v = np.concatenate((v, np.zeros(self.n_extra)))
self.interpolator = CloughTocher2DInterpolator(self.tri, v)
return self
def set_locations(self, Xi, Yi):
"""Set locations for easier (delayed) calling."""
self.Xi = Xi
self.Yi = Yi
return self
def __call__(self, *args):
"""Evaluate the interpolator."""
if len(args) == 0:
args = [self.Xi, self.Yi]
return self.interpolator(*args)
def _plot_sensors(pos_x, pos_y, sensors, ax):
"""Plot sensors."""
if sensors is True:
ax.scatter(pos_x, pos_y, s=0.25, marker='o',
edgecolor=['k'] * len(pos_x), facecolor='none')
else:
ax.plot(pos_x, pos_y, sensors)
def plot_topomap(data, pos, vmin=None, vmax=None, cmap=None, sensors=True,
res=64, axes=None, names=None, show_names=False, mask=None,
mask_params=None, outlines='head',
contours=6, image_interp='bilinear', show=True,
head_pos=None, onselect=None):
"""Plot a topographic map as image.
Parameters
----------
data : array, shape (n_chan,)
The data values to plot.
pos : array, shape (n_chan, 2) | instance of Info
Location information for the data points(/channels).
If an array, for each data point, the x and y coordinates.
If an Info object, it must contain only one data type and
exactly `len(data)` data channels, and the x/y coordinates will
be inferred from this Info object.
vmin : float | callable | None
The value specifying the lower bound of the color range.
If None, and vmax is None, -vmax is used. Else np.min(data).
If callable, the output equals vmin(data). Defaults to None.
vmax : float | callable | None
The value specifying the upper bound of the color range.
If None, the maximum absolute value is used. If callable, the output
equals vmax(data). Defaults to None.
cmap : matplotlib colormap | None
Colormap to use. If None, 'Reds' is used for all positive data,
otherwise defaults to 'RdBu_r'.
sensors : bool | str
Add markers for sensor locations to the plot. Accepts matplotlib plot
format string (e.g., 'r+' for red plusses). If True (default), circles
will be used.
res : int
The resolution of the topomap image (n pixels along each side).
axes : instance of Axes | None
The axes to plot to. If None, the current axes will be used.
names : list | None
List of channel names. If None, channel names are not plotted.
show_names : bool | callable
If True, show channel names on top of the map. If a callable is
passed, channel names will be formatted using the callable; e.g., to
delete the prefix 'MEG ' from all channel names, pass the function
lambda x: x.replace('MEG ', ''). If `mask` is not None, only
significant sensors will be shown.
If `True`, a list of names must be provided (see `names` keyword).
mask : ndarray of bool, shape (n_channels, n_times) | None
The channels to be marked as significant at a given time point.
Indices set to `True` will be considered. Defaults to None.
mask_params : dict | None
Additional plotting parameters for plotting significant sensors.
Default (None) equals::
dict(marker='o', markerfacecolor='w', markeredgecolor='k',
linewidth=0, markersize=4)
outlines : 'head' | 'skirt' | dict | None
The outlines to be drawn. If 'head', the default head scheme will be
drawn. If 'skirt' the head scheme will be drawn, but sensors are
allowed to be plotted outside of the head circle. If dict, each key
refers to a tuple of x and y positions, the values in 'mask_pos' will
serve as image mask, and the 'autoshrink' (bool) field will trigger
automated shrinking of the positions due to points outside the outline.
Alternatively, a matplotlib patch object can be passed for advanced
masking options, either directly or as a function that returns patches
(required for multi-axes plots). If None, nothing will be drawn.
Defaults to 'head'.
contours : int | array of float
The number of contour lines to draw. If 0, no contours will be drawn.
If an array, the values represent the levels for the contours. The
values are in uV for EEG, fT for magnetometers and fT/m for
gradiometers. Defaults to 6.
image_interp : str
The image interpolation to be used. All matplotlib options are
accepted.
show : bool
Show figure if True.
head_pos : dict | None
If None (default), the sensors are positioned such that they span
the head circle. If dict, can have entries 'center' (tuple) and
'scale' (tuple) for what the center and scale of the head should be
relative to the electrode locations.
onselect : callable | None
Handle for a function that is called when the user selects a set of
channels by rectangle selection (matplotlib ``RectangleSelector``). If
None interactive selection is disabled. Defaults to None.
Returns
-------
im : matplotlib.image.AxesImage
The interpolated data.
cn : matplotlib.contour.ContourSet
The fieldlines.
"""
return _plot_topomap(data, pos, vmin, vmax, cmap, sensors, res, axes,
names, show_names, mask, mask_params, outlines,
contours, image_interp, show,
head_pos, onselect)[:2]
def _plot_topomap(data, pos, vmin=None, vmax=None, cmap=None, sensors=True,
res=64, axes=None, names=None, show_names=False, mask=None,
mask_params=None, outlines='head',
contours=6, image_interp='bilinear', show=True,
head_pos=None, onselect=None):
import matplotlib.pyplot as plt
from matplotlib.widgets import RectangleSelector
data = np.asarray(data)
logger.debug('Plotting topomap for data shape %s' % (data.shape,))
if isinstance(pos, Info): # infer pos from Info object
picks = _pick_data_channels(pos) # pick only data channels
pos = pick_info(pos, picks)
# check if there is only 1 channel type, and n_chans matches the data
ch_type = set(channel_type(pos, idx)
for idx, _ in enumerate(pos["chs"]))
info_help = ("Pick Info with e.g. mne.pick_info and "
"mne.io.pick.channel_indices_by_type.")
if len(ch_type) > 1:
raise ValueError("Multiple channel types in Info structure. " +
info_help)
elif len(pos["chs"]) != data.shape[0]:
raise ValueError("Number of channels in the Info object and "
"the data array does not match. " + info_help)
else:
ch_type = ch_type.pop()
if any(type_ in ch_type for type_ in ('planar', 'grad')):
# deal with grad pairs
from ..channels.layout import (_merge_grad_data, find_layout,
_pair_grad_sensors)
picks, pos = _pair_grad_sensors(pos, find_layout(pos))
data = _merge_grad_data(data[picks]).reshape(-1)
else:
picks = list(range(data.shape[0]))
pos = _find_topomap_coords(pos, picks=picks)
if data.ndim > 1:
raise ValueError("Data needs to be array of shape (n_sensors,); got "
"shape %s." % str(data.shape))
# Give a helpful error message for common mistakes regarding the position
# matrix.
pos_help = ("Electrode positions should be specified as a 2D array with "
"shape (n_channels, 2). Each row in this matrix contains the "
"(x, y) position of an electrode.")
if pos.ndim != 2:
error = ("{ndim}D array supplied as electrode positions, where a 2D "
"array was expected").format(ndim=pos.ndim)
raise ValueError(error + " " + pos_help)
elif pos.shape[1] == 3:
error = ("The supplied electrode positions matrix contains 3 columns. "
"Are you trying to specify XYZ coordinates? Perhaps the "
"mne.channels.create_eeg_layout function is useful for you.")
raise ValueError(error + " " + pos_help)
# No error is raised in case of pos.shape[1] == 4. In this case, it is
# assumed the position matrix contains both (x, y) and (width, height)
# values, such as Layout.pos.
elif pos.shape[1] == 1 or pos.shape[1] > 4:
raise ValueError(pos_help)
if len(data) != len(pos):
raise ValueError("Data and pos need to be of same length. Got data of "
"length %s, pos of length %s" % (len(data), len(pos)))
norm = min(data) >= 0
vmin, vmax = _setup_vmin_vmax(data, vmin, vmax, norm)
if cmap is None:
cmap = 'Reds' if norm else 'RdBu_r'
pos, outlines = _check_outlines(pos, outlines, head_pos)
assert isinstance(outlines, dict)
ax = axes if axes else plt.gca()
pos_x, pos_y = _prepare_topomap(pos, ax)
xlim = np.inf, -np.inf,
ylim = np.inf, -np.inf,
mask_ = np.c_[outlines['mask_pos']]
xmin, xmax = (np.min(np.r_[xlim[0], mask_[:, 0]]),
np.max(np.r_[xlim[1], mask_[:, 0]]))
ymin, ymax = (np.min(np.r_[ylim[0], mask_[:, 1]]),
np.max(np.r_[ylim[1], mask_[:, 1]]))
# interpolate data
xi = np.linspace(xmin, xmax, res)
yi = np.linspace(ymin, ymax, res)
Xi, Yi = np.meshgrid(xi, yi)
interp = _GridData(np.array((pos_x, pos_y)).T).set_values(data)
Zi = interp.set_locations(Xi, Yi)()
_use_default_outlines = any(k.startswith('head') for k in outlines)
if _use_default_outlines:
# prepare masking
pos = _autoshrink(outlines, pos, res)
mask_params = _handle_default('mask_params', mask_params)
# plot outline
patch_ = None
if 'patch' in outlines:
patch_ = outlines['patch']
patch_ = patch_() if callable(patch_) else patch_
patch_.set_clip_on(False)
ax.add_patch(patch_)
ax.set_transform(ax.transAxes)
ax.set_clip_path(patch_)
if _use_default_outlines:
from matplotlib import patches
patch_ = patches.Ellipse((0, 0),
2 * outlines['clip_radius'][0],
2 * outlines['clip_radius'][1],
clip_on=True,
transform=ax.transData)
# plot map and contour
im = ax.imshow(Zi, cmap=cmap, vmin=vmin, vmax=vmax, origin='lower',
aspect='equal', extent=(xmin, xmax, ymin, ymax),
interpolation=image_interp)
# This tackles an incomprehensible matplotlib bug if no contours are
# drawn. To avoid rescalings, we will always draw contours.
# But if no contours are desired we only draw one and make it invisible .
linewidth = mask_params['markeredgewidth']
no_contours = False
if isinstance(contours, (np.ndarray, list)):
pass # contours precomputed
elif contours == 0:
contours, no_contours = 1, True
if (Zi == Zi[0, 0]).all():
cont = None # can't make contours for constant-valued functions
else:
with warnings.catch_warnings(record=True):
warnings.simplefilter('ignore')
cont = ax.contour(Xi, Yi, Zi, contours, colors='k',
linewidths=linewidth / 2.)
if no_contours and cont is not None:
for col in cont.collections:
col.set_visible(False)
if patch_ is not None:
im.set_clip_path(patch_)
if cont is not None:
for col in cont.collections:
col.set_clip_path(patch_)
if sensors is not False and mask is None:
_plot_sensors(pos_x, pos_y, sensors=sensors, ax=ax)
elif sensors and mask is not None:
idx = np.where(mask)[0]
ax.plot(pos_x[idx], pos_y[idx], **mask_params)
idx = np.where(~mask)[0]
_plot_sensors(pos_x[idx], pos_y[idx], sensors=sensors, ax=ax)
elif not sensors and mask is not None:
idx = np.where(mask)[0]
ax.plot(pos_x[idx], pos_y[idx], **mask_params)
if isinstance(outlines, dict):
_draw_outlines(ax, outlines)
if show_names:
if names is None:
raise ValueError("To show names, a list of names must be provided"
" (see `names` keyword).")
if show_names is True:
def _show_names(x):
return x
else:
_show_names = show_names
show_idx = np.arange(len(names)) if mask is None else np.where(mask)[0]
for ii, (p, ch_id) in enumerate(zip(pos, names)):
if ii not in show_idx:
continue
ch_id = _show_names(ch_id)
ax.text(p[0], p[1], ch_id, horizontalalignment='center',
verticalalignment='center', size='x-small')
plt.subplots_adjust(top=.95)
if onselect is not None:
ax.RS = RectangleSelector(ax, onselect=onselect)
plt_show(show)
return im, cont, interp
def _autoshrink(outlines, pos, res):
"""Make an image mask."""
if outlines.get('autoshrink', False):
mask_ = np.c_[outlines['mask_pos']]
inside = _inside_contour(pos, mask_)
outside = np.invert(inside)
outlier_points = pos[outside]
while np.any(outlier_points): # auto shrink
pos *= 0.99
inside = _inside_contour(pos, mask_)
outside = np.invert(inside)
outlier_points = pos[outside]
return pos
def _inside_contour(pos, contour):
"""Check if points are inside a contour."""
npos = len(pos)
x, y = pos[:, :2].T
check_mask = np.ones((npos), dtype=bool)
check_mask[((x < np.min(x)) | (y < np.min(y)) |
(x > np.max(x)) | (y > np.max(y)))] = False
critval = 0.1
contourx = contour[:, 0] - pos[check_mask, 0][:, np.newaxis]
contoury = contour[:, 1] - pos[check_mask, 1][:, np.newaxis]
angle = np.arctan2(contoury, contourx)
angle = np.unwrap(angle)
check_mask[check_mask] = (np.abs(np.sum(np.diff(angle, axis=1), axis=1)) >
critval)
return check_mask
def _plot_ica_topomap(ica, idx=0, ch_type=None, res=64, layout=None,
vmin=None, vmax=None, cmap='RdBu_r', colorbar=False,
title=None, show=True, outlines='head', contours=6,
image_interp='bilinear', head_pos=None, axes=None,
sensors=True):
"""Plot single ica map to axes."""
import matplotlib as mpl
from ..channels import _get_ch_type
if ica.info is None:
raise RuntimeError('The ICA\'s measurement info is missing. Please '
'fit the ICA or add the corresponding info object.')
if not isinstance(axes, mpl.axes.Axes):
raise ValueError('axis has to be an instance of matplotlib Axes, '
'got %s instead.' % type(axes))
ch_type = _get_ch_type(ica, ch_type)
data = ica.get_components()[:, idx]
data_picks, pos, merge_grads, names, _ = _prepare_topo_plot(
ica, ch_type, layout)
pos, outlines = _check_outlines(pos, outlines, head_pos)
assert outlines is not None
if outlines != 'head':
pos = _autoshrink(outlines, pos, res)
data = data[data_picks]
if merge_grads:
from ..channels.layout import _merge_grad_data
data = _merge_grad_data(data)
axes.set_title(ica._ica_names[idx], fontsize=12)
vmin_, vmax_ = _setup_vmin_vmax(data, vmin, vmax)
im = plot_topomap(
data.ravel(), pos, vmin=vmin_, vmax=vmax_, res=res, axes=axes,
cmap=cmap, outlines=outlines, contours=contours, sensors=sensors,
image_interp=image_interp, show=show)[0]
if colorbar:
cbar, cax = _add_colorbar(axes, im, cmap, pad=.05, title="AU",
format='%3.2f')
cbar.ax.tick_params(labelsize=12)
cbar.set_ticks((vmin_, vmax_))
_hide_frame(axes)
def plot_ica_components(ica, picks=None, ch_type=None, res=64,
layout=None, vmin=None, vmax=None, cmap='RdBu_r',
sensors=True, colorbar=False, title=None,
show=True, outlines='head', contours=6,
image_interp='bilinear', head_pos=None,
inst=None):
"""Project unmixing matrix on interpolated sensor topography.
Parameters
----------
ica : instance of mne.preprocessing.ICA
The ICA solution.
picks : int | array-like | None
The indices of the sources to be plotted.
If None all are plotted in batches of 20.
ch_type : 'mag' | 'grad' | 'planar1' | 'planar2' | 'eeg' | None
The channel type to plot. For 'grad', the gradiometers are
collected in pairs and the RMS for each pair is plotted.
If None, then channels are chosen in the order given above.
res : int
The resolution of the topomap image (n pixels along each side).
layout : None | Layout
Layout instance specifying sensor positions (does not need to
be specified for Neuromag data). If possible, the correct layout is
inferred from the data.
vmin : float | callable | None
The value specifying the lower bound of the color range.
If None, and vmax is None, -vmax is used. Else np.min(data).
If callable, the output equals vmin(data). Defaults to None.
vmax : float | callable | None
The value specifying the upper bound of the color range.
If None, the maximum absolute value is used. If callable, the output
equals vmax(data). Defaults to None.
cmap : matplotlib colormap | (colormap, bool) | 'interactive' | None
Colormap to use. 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 range. Up and down arrows can be used to change
the colormap. If None, 'Reds' is used for all positive data,
otherwise defaults to 'RdBu_r'. If 'interactive', translates to
(None, True). Defaults to 'RdBu_r'.
.. warning:: Interactive mode works smoothly only for a small amount
of topomaps.
sensors : bool | str
Add markers for sensor locations to the plot. Accepts matplotlib
plot format string (e.g., 'r+' for red plusses). If True (default),
circles will be used.
colorbar : bool
Plot a colorbar.
title : str | None
Title to use.
show : bool
Show figure if True.
outlines : 'head' | 'skirt' | dict | None
The outlines to be drawn. If 'head', the default head scheme will be
drawn. If 'skirt' the head scheme will be drawn, but sensors are
allowed to be plotted outside of the head circle. If dict, each key
refers to a tuple of x and y positions, the values in 'mask_pos' will
serve as image mask, and the 'autoshrink' (bool) field will trigger
automated shrinking of the positions due to points outside the outline.
Alternatively, a matplotlib patch object can be passed for advanced
masking options, either directly or as a function that returns patches
(required for multi-axis plots). If None, nothing will be drawn.
Defaults to 'head'.
contours : int | array of float
The number of contour lines to draw. If 0, no contours will be drawn.
When an integer, matplotlib ticker locator is used to find suitable
values for the contour thresholds (may sometimes be inaccurate, use
array for accuracy). If an array, the values represent the levels for
the contours. Defaults to 6.
image_interp : str
The image interpolation to be used. All matplotlib options are
accepted.
head_pos : dict | None
If None (default), the sensors are positioned such that they span
the head circle. If dict, can have entries 'center' (tuple) and
'scale' (tuple) for what the center and scale of the head should be
relative to the electrode locations.
inst : Raw | Epochs | None
To be able to see component properties after clicking on component
topomap you need to pass relevant data - instances of Raw or Epochs
(for example the data that ICA was trained on). This takes effect
only when running matplotlib in interactive mode.
Returns
-------
fig : instance of matplotlib.pyplot.Figure or list
The figure object(s).
Notes
-----
When run in interactive mode, ``plot_ica_components`` allows to reject
components by clicking on their title label. The state of each component
is indicated by its label color (gray: rejected; black: retained). It is
also possible to open component properties by clicking on the component
topomap (this option is only available when the ``inst`` argument is
supplied).
"""
from ..io import BaseRaw
from ..epochs import BaseEpochs
from ..channels import _get_ch_type
if picks is None: # plot components by sets of 20
ch_type = _get_ch_type(ica, ch_type)
n_components = ica.mixing_matrix_.shape[1]
p = 20
figs = []
for k in range(0, n_components, p):
picks = range(k, min(k + p, n_components))
fig = plot_ica_components(ica, picks=picks, ch_type=ch_type,
res=res, layout=layout, vmax=vmax,
cmap=cmap, sensors=sensors,
colorbar=colorbar, title=title,
show=show, outlines=outlines,
contours=contours,
image_interp=image_interp,
head_pos=head_pos, inst=inst)
figs.append(fig)
return figs
elif np.isscalar(picks):
picks = [picks]
ch_type = _get_ch_type(ica, ch_type)
cmap = _setup_cmap(cmap, n_axes=len(picks))
data = np.dot(ica.mixing_matrix_[:, picks].T,
ica.pca_components_[:ica.n_components_])
if ica.info is None:
raise RuntimeError('The ICA\'s measurement info is missing. Please '
'fit the ICA or add the corresponding info object.')
data_picks, pos, merge_grads, names, _ = _prepare_topo_plot(ica, ch_type,
layout)
pos, outlines = _check_outlines(pos, outlines, head_pos)
if outlines == 'head':
pos = _autoshrink(outlines, pos, res)
data = np.atleast_2d(data)
data = data[:, data_picks]
# prepare data for iteration
fig, axes = _prepare_trellis(len(data), max_col=5)
if title is None:
title = 'ICA components'
fig.suptitle(title)
if merge_grads:
from ..channels.layout import _merge_grad_data
titles = list()
for ii, data_, ax in zip(picks, data, axes):
kwargs = dict(color='gray') if ii in ica.exclude else dict()
titles.append(ax.set_title(ica._ica_names[ii], fontsize=12, **kwargs))
data_ = _merge_grad_data(data_) if merge_grads else data_
vmin_, vmax_ = _setup_vmin_vmax(data_, vmin, vmax)
im = plot_topomap(
data_.flatten(), pos, vmin=vmin_, vmax=vmax_, res=res, axes=ax,
cmap=cmap[0], outlines=outlines, contours=contours,
image_interp=image_interp, show=False, sensors=sensors)[0]
im.axes.set_label(ica._ica_names[ii])
if colorbar:
cbar, cax = _add_colorbar(ax, im, cmap, title="AU",
side="right", pad=.05, format='%3.2f')
cbar.ax.tick_params(labelsize=12)
cbar.set_ticks((vmin_, vmax_))
_hide_frame(ax)
tight_layout(fig=fig)
fig.subplots_adjust(top=0.88, bottom=0.)
fig.canvas.draw()
# add title selection interactivity
def onclick_title(event, ica=ica, titles=titles):
# check if any title was pressed
title_pressed = None
for title in titles:
if title.contains(event)[0]:
title_pressed = title
break
# title was pressed -> identify the IC
if title_pressed is not None:
label = title_pressed.get_text()
ic = int(label[-3:])
# add or remove IC from exclude depending on current state
if ic in ica.exclude:
ica.exclude.remove(ic)
title_pressed.set_color('k')
else:
ica.exclude.append(ic)
title_pressed.set_color('gray')
fig.canvas.draw()
fig.canvas.mpl_connect('button_press_event', onclick_title)
# add plot_properties interactivity only if inst was passed
if isinstance(inst, (BaseRaw, BaseEpochs)):
def onclick_topo(event, ica=ica, inst=inst):
# check which component to plot
if event.inaxes is not None:
label = event.inaxes.get_label()
if label.startswith('ICA'):
ic = int(label[-3:])
ica.plot_properties(inst, picks=ic, show=True)
fig.canvas.mpl_connect('button_press_event', onclick_topo)
plt_show(show)
return fig
def plot_tfr_topomap(tfr, tmin=None, tmax=None, fmin=None, fmax=None,
ch_type=None, baseline=None, mode='mean', layout=None,
vmin=None, vmax=None, cmap=None, sensors=True,
colorbar=True, unit=None, res=64, size=2,
cbar_fmt='%1.1e', show_names=False, title=None,
axes=None, show=True, outlines='head', head_pos=None,
contours=6):
"""Plot topographic maps of specific time-frequency intervals of TFR data.
Parameters
----------
tfr : AverageTFR
The AverageTFR object.
tmin : None | float
The first time instant to display. If None the first time point
available is used.
tmax : None | float
The last time instant to display. If None the last time point available
is used.
fmin : None | float
The first frequency to display. If None the first frequency available
is used.
fmax : None | float
The last frequency to display. If None the last frequency available is
used.
ch_type : 'mag' | 'grad' | 'planar1' | 'planar2' | 'eeg' | None
The channel type to plot. For 'grad', the gradiometers are collected in
pairs and the RMS for each pair is plotted. If None, then channels are
chosen in the order given above.
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) the whole time interval is used.
mode : 'mean' | 'ratio' | 'logratio' | 'percent' | 'zscore' | 'zlogratio' | None
Perform baseline correction by
- subtracting the mean baseline power ('mean')
- dividing by the mean baseline power ('ratio')
- dividing by the mean baseline power and taking the log ('logratio')
- subtracting the mean baseline power followed by dividing by the
mean baseline power ('percent')
- subtracting the mean baseline power and dividing by the standard
deviation of the baseline power ('zscore')
- dividing by the mean baseline power, taking the log, and dividing
by the standard deviation of the baseline power ('zlogratio')
If None no baseline correction is applied.
layout : None | Layout
Layout instance specifying sensor positions (does not need to be
specified for Neuromag data). If possible, the correct layout file is
inferred from the data; if no appropriate layout file was found, the
layout is automatically generated from the sensor locations.
vmin : float | callable | None
The value specifying the lower bound of the color range.
If None, and vmax is None, -vmax is used. Else np.min(data) or in case
data contains only positive values 0. If callable, the output equals
vmin(data). Defaults to None.
vmax : float | callable | None
The value specifying the upper bound of the color range. If None, the
maximum value is used. If callable, the output equals vmax(data).
Defaults to None.
cmap : matplotlib colormap | (colormap, bool) | 'interactive' | None
Colormap to use. 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 range. Up and down arrows can be used to change
the colormap. If None (default), 'Reds' is used for all positive data,
otherwise defaults to 'RdBu_r'. If 'interactive', translates to
(None, True).
sensors : bool | str
Add markers for sensor locations to the plot. Accepts matplotlib plot
format string (e.g., 'r+'). If True (default), circles will be used.
colorbar : bool
Plot a colorbar.
unit : str | None
The unit of the channel type used for colorbar labels.
res : int
The resolution of the topomap image (n pixels along each side).
size : float
Side length per topomap in inches (only applies when plotting multiple
topomaps at a time).
cbar_fmt : str
String format for colorbar values.
show_names : bool | callable
If True, show channel names on top of the map. If a callable is passed,
channel names will be formatted using the callable; e.g., to delete the
prefix 'MEG ' from all channel names, pass the function
``lambda x: x.replace('MEG ', '')``. If `mask` is not None, only
significant sensors will be shown.
title : str | None
Plot title. If None (default), no title is displayed.
axes : instance of Axis | None
The axes to plot to. If None the axes is defined automatically.
show : bool
Show figure if True.
outlines : 'head' | 'skirt' | dict | None
The outlines to be drawn. If 'head', the default head scheme will be
drawn. If 'skirt' the head scheme will be drawn, but sensors are
allowed to be plotted outside of the head circle. If dict, each key
refers to a tuple of x and y positions, the values in 'mask_pos' will
serve as image mask, and the 'autoshrink' (bool) field will trigger
automated shrinking of the positions due to points outside the outline.
Alternatively, a matplotlib patch object can be passed for advanced
masking options, either directly or as a function that returns patches
(required for multi-axis plots). If None, nothing will be drawn.
Defaults to 'head'.
head_pos : dict | None
If None (default), the sensors are positioned such that they span the
head circle. If dict, can have entries 'center' (tuple) and 'scale'
(tuple) for what the center and scale of the head should be relative to
the electrode locations.
contours : int | array of float
The number of contour lines to draw. If 0, no contours will be drawn.
When an integer, matplotlib ticker locator is used to find suitable
values for the contour thresholds (may sometimes be inaccurate, use
array for accuracy). If an array, the values represent the levels for
the contours. If colorbar=True, the ticks in colorbar correspond to the
contour levels. Defaults to 6.
Returns
-------
fig : matplotlib.figure.Figure
The figure containing the topography.
""" # noqa: E501
from ..channels import _get_ch_type
ch_type = _get_ch_type(tfr, ch_type)
import matplotlib.pyplot as plt
picks, pos, merge_grads, names, _ = _prepare_topo_plot(tfr, ch_type,
layout)
if not show_names:
names = None
data = tfr.data[picks, :, :]
# merging grads before rescaling makes ERDs visible
if merge_grads:
from ..channels.layout import _merge_grad_data
data = _merge_grad_data(data)
data = rescale(data, tfr.times, baseline, mode, copy=True)
# crop time
itmin, itmax = None, None
idx = np.where(_time_mask(tfr.times, tmin, tmax))[0]
if tmin is not None:
itmin = idx[0]
if tmax is not None:
itmax = idx[-1] + 1
# crop freqs
ifmin, ifmax = None, None
idx = np.where(_time_mask(tfr.freqs, fmin, fmax))[0]
if fmin is not None:
ifmin = idx[0]
if fmax is not None:
ifmax = idx[-1] + 1
data = data[:, ifmin:ifmax, itmin:itmax]
data = np.mean(np.mean(data, axis=2), axis=1)[:, np.newaxis]
norm = False if np.min(data) < 0 else True
vmin, vmax = _setup_vmin_vmax(data, vmin, vmax, norm)
cmap = _setup_cmap(cmap, norm=norm)
if axes is None:
fig = plt.figure(figsize=(size, size))
ax = fig.gca()
else:
fig = axes.figure
ax = axes
_hide_frame(ax)
locator = None
if not isinstance(contours, (list, np.ndarray)):
locator, contours = _set_contour_locator(vmin, vmax, contours)
if title is not None:
ax.set_title(title)
fig_wrapper = list()
selection_callback = partial(_onselect, tfr=tfr, pos=pos, ch_type=ch_type,
itmin=itmin, itmax=itmax, ifmin=ifmin,
ifmax=ifmax, cmap=cmap[0], fig=fig_wrapper,
layout=layout)
if not isinstance(contours, (list, np.ndarray)):
_, contours = _set_contour_locator(vmin, vmax, contours)
im, _ = plot_topomap(data[:, 0], pos, vmin=vmin, vmax=vmax,
axes=ax, cmap=cmap[0], image_interp='bilinear',
contours=contours, names=names, show_names=show_names,
show=False, onselect=selection_callback,
sensors=sensors, res=res, head_pos=head_pos,
outlines=outlines)
if colorbar:
from matplotlib import ticker
unit = _handle_default('units', unit)['misc']
cbar, cax = _add_colorbar(ax, im, cmap, title=unit, format=cbar_fmt)
if locator is None:
locator = ticker.MaxNLocator(nbins=5)
cbar.locator = locator
cbar.update_ticks()
cbar.ax.tick_params(labelsize=12)
plt_show(show)
return fig
def plot_evoked_topomap(evoked, times="auto", ch_type=None, layout=None,
vmin=None, vmax=None, cmap=None, sensors=True,
colorbar=None, scalings=None,
units=None, res=64, size=1, cbar_fmt='%3.1f',
time_unit='s', time_format=None, proj=False,
show=True, show_names=False, title=None, mask=None,
mask_params=None, outlines='head', contours=6,
image_interp='bilinear', average=None, head_pos=None,
axes=None):
"""Plot topographic maps of specific time points of evoked data.
Parameters
----------
evoked : Evoked
The Evoked object.
times : float | array of floats | "auto" | "peaks" | "interactive"
The time point(s) to plot. If "auto", the number of ``axes`` determines
the amount of time point(s). If ``axes`` is also None, at most 10
topographies will be shown with a regular time spacing between the
first and last time instant. If "peaks", finds time points
automatically by checking for local maxima in global field power. If
"interactive", the time can be set interactively at run-time by using a
slider.
ch_type : 'mag' | 'grad' | 'planar1' | 'planar2' | 'eeg' | None
The channel type to plot. For 'grad', the gradiometers are collected in
pairs and the RMS for each pair is plotted.
If None, then channels are chosen in the order given above.
layout : None | Layout
Layout instance specifying sensor positions (does not need to
be specified for Neuromag data). If possible, the correct layout file
is inferred from the data; if no appropriate layout file was found, the
layout is automatically generated from the sensor locations.
vmin : float | callable | None
The value specifying the lower bound of the color range.
If None, and vmax is None, -vmax is used. Else np.min(data).
If callable, the output equals vmin(data). Defaults to None.
vmax : float | callable | None
The value specifying the upper bound of the color range.
If None, the maximum absolute value is used. If callable, the output
equals vmax(data). Defaults to None.
cmap : matplotlib colormap | (colormap, bool) | 'interactive' | None
Colormap to use. 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 (zoom).
The mouse scroll can also be used to adjust the range. Hitting space
bar resets the range. Up and down arrows can be used to change the
colormap. If None (default), 'Reds' is used for all positive data,
otherwise defaults to 'RdBu_r'. If 'interactive', translates to
(None, True).
.. warning:: Interactive mode works smoothly only for a small amount
of topomaps. Interactive mode is disabled by default for more than
2 topomaps.
sensors : bool | str
Add markers for sensor locations to the plot. Accepts matplotlib plot
format string (e.g., 'r+' for red plusses). If True (default),
circles will be used.
colorbar : bool | None
Plot a colorbar in the rightmost column of the figure.
None (default) is the same as True, but emits a warning if custom
``axes`` are provided to remind the user that the colorbar will
occupy the last :class:`matplotlib.axes.Axes` instance.
scalings : dict | float | None
The scalings of the channel types to be applied for plotting.
If None, defaults to ``dict(eeg=1e6, grad=1e13, mag=1e15)``.
units : dict | str | None
The unit of the channel type used for colorbar label. If
scale is None the unit is automatically determined.
res : int
The resolution of the topomap image (n pixels along each side).
size : float
Side length per topomap in inches.
cbar_fmt : str
String format for colorbar values.
time_unit : str
The units for the time axis, can be "ms" or "s" (default).
.. versionadded:: 0.16
time_format : str | None
String format for topomap values. Defaults (None) to "%01d ms" if
``time_unit='ms'``, "%0.3f s" if ``time_unit='s'``, and
"%g" otherwise.
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 show.
show : bool
Show figure if True.
show_names : bool | callable
If True, show channel names on top of the map. If a callable is
passed, channel names will be formatted using the callable; e.g., to
delete the prefix 'MEG ' from all channel names, pass the function
lambda x: x.replace('MEG ', ''). If `mask` is not None, only
significant sensors will be shown.
title : str | None
Title. If None (default), no title is displayed.
mask : ndarray of bool, shape (n_channels, n_times) | None
The channels to be marked as significant at a given time point.
Indices set to `True` will be considered. Defaults to None.
mask_params : dict | None
Additional plotting parameters for plotting significant sensors.
Default (None) equals::
dict(marker='o', markerfacecolor='w', markeredgecolor='k',
linewidth=0, markersize=4)
outlines : 'head' | 'skirt' | dict | None
The outlines to be drawn. If 'head', the default head scheme will be
drawn. If 'skirt' the head scheme will be drawn, but sensors are
allowed to be plotted outside of the head circle. If dict, each key
refers to a tuple of x and y positions, the values in 'mask_pos' will
serve as image mask, and the 'autoshrink' (bool) field will trigger
automated shrinking of the positions due to points outside the outline.
Alternatively, a matplotlib patch object can be passed for advanced
masking options, either directly or as a function that returns patches
(required for multi-axis plots). If None, nothing will be drawn.
Defaults to 'head'.
contours : int | array of float
The number of contour lines to draw. If 0, no contours will be drawn.
When an integer, matplotlib ticker locator is used to find suitable
values for the contour thresholds (may sometimes be inaccurate, use
array for accuracy). If an array, the values represent the levels for
the contours. The values are in uV for EEG, fT for magnetometers and
fT/m for gradiometers. If colorbar=True, the ticks in colorbar
correspond to the contour levels. Defaults to 6.
image_interp : str
The image interpolation to be used. All matplotlib options are
accepted.
average : float | None
The time window around a given time to be used for averaging (seconds).
For example, 0.01 would translate into window that starts 5 ms before
and ends 5 ms after a given time point. Defaults to None, which means
no averaging.
head_pos : dict | None
If None (default), the sensors are positioned such that they span
the head circle. If dict, can have entries 'center' (tuple) and
'scale' (tuple) for what the center and scale of the head should be
relative to the electrode locations.
axes : instance of Axes | list | None
The axes to plot to. If list, the list must be a list of Axes of the
same length as ``times`` (unless ``times`` is None). If instance of
Axes, ``times`` must be a float or a list of one float.
Defaults to None.
Returns
-------
fig : instance of matplotlib.figure.Figure
The figure.
"""
from ..channels import _get_ch_type
from ..channels.layout import _merge_grad_data
import matplotlib.pyplot as plt
from matplotlib import gridspec
from matplotlib.widgets import Slider
ch_type = _get_ch_type(evoked, ch_type)
time_unit, _ = _check_time_unit(time_unit, evoked.times)
scaling_time = 1. if time_unit == 's' else 1e3
if time_format is None:
time_format = '%0.3f s' if time_unit == 's' else '%01d ms'
del time_unit
if colorbar is None:
colorbar = True
colorbar_warn = True
else:
colorbar_warn = False
mask_params = _handle_default('mask_params', mask_params)
mask_params['markersize'] *= size / 2.
mask_params['markeredgewidth'] *= size / 2.
picks, pos, merge_grads, names, ch_type = _prepare_topo_plot(
evoked, ch_type, layout)
# project before picks
if proj is True and evoked.proj is not True:
data = evoked.copy().apply_proj().data
else:
data = evoked.data
# because we are only plotting we can safely remove compensation matrices
# regardless of compensation status.
evoked = evoked.copy()
evoked.info['comps'] = []
evoked = evoked._pick_drop_channels(picks)
interactive = isinstance(times, string_types) and times == 'interactive'
if axes is not None:
if isinstance(axes, plt.Axes):
axes = [axes]
times = _process_times(evoked, times, n_peaks=len(axes))
else:
times = _process_times(evoked, times, n_peaks=None)
space = 1 / (2. * evoked.info['sfreq'])
if (max(times) > max(evoked.times) + space or
min(times) < min(evoked.times) - space):
raise ValueError('Times should be between {0:0.3f} and '
'{1:0.3f}.'.format(evoked.times[0], evoked.times[-1]))
n_times = len(times)
nax = n_times + bool(colorbar)
width = size * nax
height = size + max(0, 0.1 * (4 - size)) + bool(title) * 0.5
cols = n_times + 1 if colorbar else n_times # room for the colorbar
if interactive:
if axes is not None:
raise ValueError("User provided axes not allowed when "
"times='interactive'.")
height_ratios = [5, 1]
rows = 2
g_kwargs = {'left': 0.2, 'right': 1., 'bottom': 0.05, 'top': 0.95}
else:
rows, height_ratios, g_kwargs = 1, None, {}
gs = gridspec.GridSpec(rows, cols, height_ratios=height_ratios, **g_kwargs)
if axes is None:
figure_nobar(figsize=(width * 1.5, height * 1.5))
axes = list()
for ax_idx in range(len(times)):
axes.append(plt.subplot(gs[ax_idx]))
elif colorbar and colorbar_warn:
warn('Colorbar is drawn to the rightmost column of the figure. Be '
'sure to provide enough space for it or turn it off with '
'colorbar=False.')
if len(axes) != n_times:
raise RuntimeError('Axes and times must be equal in sizes.')
if ch_type.startswith('planar'):
key = 'grad'
else:
key = ch_type
scaling = _handle_default('scalings', scalings)[key]
unit = _handle_default('units', units)[key]
if not show_names:
names = None
w_frame = plt.rcParams['figure.subplot.wspace'] / (2 * nax)
top_frame = max((0.05 if title is None else 0.25), .2 / size)
fig = axes[0].get_figure()
fig.subplots_adjust(left=w_frame, right=1 - w_frame, bottom=0,
top=1 - top_frame)
# find first index that's >= (to rounding error) to each time point
time_idx = [np.where(_time_mask(evoked.times, tmin=t,
tmax=None,
sfreq=evoked.info['sfreq']))[0][0]
for t in times]
if average is None:
data = data[np.ix_(picks, time_idx)]
elif isinstance(average, float):
if not average > 0:
raise ValueError('The average parameter must be positive. You '
'passed a negative value')
data_ = np.zeros((len(picks), len(time_idx)))
ave_time = float(average) / 2.
iter_times = evoked.times[time_idx]
for ii, (idx, tmin_, tmax_) in enumerate(zip(time_idx,
iter_times - ave_time,
iter_times + ave_time)):
my_range = (tmin_ < evoked.times) & (evoked.times < tmax_)
data_[:, ii] = data[picks][:, my_range].mean(-1)
data = data_
else:
raise ValueError('The average parameter must be None or a float.'
'Check your input.')
data *= scaling
if merge_grads:
data = _merge_grad_data(data)
images, contours_ = [], []
if mask is not None:
if ch_type == 'grad':
mask_ = (mask[np.ix_(picks[::2], time_idx)] |
mask[np.ix_(picks[1::2], time_idx)])
else: # mag, eeg, planar1, planar2
mask_ = mask[np.ix_(picks, time_idx)]
pos, outlines = _check_outlines(pos, outlines, head_pos)
assert outlines is not None
pos = _autoshrink(outlines, pos, res)
vlims = [_setup_vmin_vmax(data[:, i], vmin, vmax, norm=merge_grads)
for i in range(len(times))]
vmin = np.min(vlims)
vmax = np.max(vlims)
cmap = _setup_cmap(cmap, n_axes=len(times), norm=vmin >= 0)
if not isinstance(contours, (list, np.ndarray)):
_, contours = _set_contour_locator(vmin, vmax, contours)
kwargs = dict(vmin=vmin, vmax=vmax, sensors=sensors, res=res, names=names,
show_names=show_names, cmap=cmap[0], mask_params=mask_params,
outlines=outlines, contours=contours,
image_interp=image_interp, show=False)
for idx, time in enumerate(times):
tp, cn, interp = _plot_topomap(
data[:, idx], pos, axes=axes[idx],
mask=mask_[:, idx] if mask is not None else None, **kwargs)
images.append(tp)
if cn is not None:
contours_.append(cn)
if time_format is not None:
axes[idx].set_title(time_format % (time * scaling_time))
if interactive:
axes.append(plt.subplot(gs[2]))
slider = Slider(axes[-1], 'Time', evoked.times[0], evoked.times[-1],
times[0], valfmt='%1.2fs')
slider.vline.remove() # remove initial point indicator
func = _merge_grad_data if merge_grads else lambda x: x
changed_callback = partial(_slider_changed, ax=axes[0],
data=evoked.data, times=evoked.times,
pos=pos, scaling=scaling, func=func,
time_format=time_format,
scaling_time=scaling_time, kwargs=kwargs)
slider.on_changed(changed_callback)
ts = np.tile(evoked.times, len(evoked.data)).reshape(evoked.data.shape)
axes[-1].plot(ts, evoked.data, color='k')
axes[-1].slider = slider
if title is not None:
plt.suptitle(title, verticalalignment='top', size='x-large')
if colorbar:
# works both when fig axes pre-defined and when not
n_fig_axes = max(nax, len(fig.get_axes()))
cax = plt.subplot(1, n_fig_axes + 1, n_fig_axes + 1)
# resize the colorbar (by default the color fills the whole axes)
_resize_cbar(cax, n_fig_axes, size)
if unit is not None:
cax.set_title(unit)
cbar = fig.colorbar(images[-1], ax=cax, cax=cax, format=cbar_fmt)
cbar.set_ticks(cn.levels)
cbar.ax.tick_params(labelsize=7)
if cmap[1]:
for im in images:
im.axes.CB = DraggableColorbar(cbar, im)
if proj == 'interactive':
_check_delayed_ssp(evoked)
params = dict(
evoked=evoked, fig=fig, projs=evoked.info['projs'], picks=picks,
images=images, contours_=contours_, pos=pos, time_idx=time_idx,
res=res, plot_update_proj_callback=_plot_update_evoked_topomap,
merge_grads=merge_grads, scale=scaling, axes=axes,
contours=contours, interp=interp)
_draw_proj_checkbox(None, params)
plt_show(show)
return fig
def _resize_cbar(cax, n_fig_axes, size=1):
"""Resize colorbar."""
cpos = cax.get_position()
if size <= 1:
cpos.x0 = 1 - (.7 + .1 / size) / n_fig_axes
cpos.x1 = cpos.x0 + .1 / n_fig_axes
cpos.y0 = .2
cpos.y1 = .7
cax.set_position(cpos)
def _slider_changed(val, ax, data, times, pos, scaling, func, time_format,
scaling_time, kwargs):
"""Handle selection in interactive topomap."""
idx = np.argmin(np.abs(times - val))
data = func(data[:, idx]).ravel() * scaling
ax.clear()
im, _ = plot_topomap(data, pos, axes=ax, **kwargs)
if hasattr(ax, 'CB'):
ax.CB.mappable = im
_resize_cbar(ax.CB.cbar.ax, 2)
if time_format is not None:
ax.set_title(time_format % (val * scaling_time))
def _plot_topomap_multi_cbar(data, pos, ax, title=None, unit=None, vmin=None,
vmax=None, cmap=None, outlines='head',
colorbar=False, cbar_fmt='%3.3f'):
"""Plot topomap multi cbar."""
_hide_frame(ax)
vmin = np.min(data) if vmin is None else vmin
vmax = np.max(data) if vmax is None else vmax
cmap = _setup_cmap(cmap)
if title is not None:
ax.set_title(title, fontsize=10)
im, _ = plot_topomap(data, pos, vmin=vmin, vmax=vmax, axes=ax,
cmap=cmap[0], image_interp='bilinear', contours=0,
outlines=outlines, show=False)
if colorbar is True:
cbar, cax = _add_colorbar(ax, im, cmap, pad=.25, title=None,
size="10%", format=cbar_fmt)
cbar.set_ticks((vmin, vmax))
if unit is not None:
cbar.ax.set_title(unit, fontsize=8)
cbar.ax.tick_params(labelsize=8)
@verbose
def plot_epochs_psd_topomap(epochs, bands=None, vmin=None, vmax=None,
tmin=None, tmax=None, proj=False,
bandwidth=None, adaptive=False, low_bias=True,
normalization='length', ch_type=None, layout=None,
cmap='RdBu_r', agg_fun=None, dB=False, n_jobs=1,
normalize=False, cbar_fmt='%0.3f',
outlines='head', axes=None, show=True,
verbose=None):
"""Plot the topomap of the power spectral density across epochs.
Parameters
----------
epochs : instance of Epochs
The epochs object
bands : list of tuple | None
The lower and upper frequency and the name for that band. If None,
(default) expands to:
bands = [(0, 4, 'Delta'), (4, 8, 'Theta'), (8, 12, 'Alpha'),
(12, 30, 'Beta'), (30, 45, 'Gamma')]
vmin : float | callable | None
The value specifying the lower bound of the color range.
If None np.min(data) is used. If callable, the output equals
vmin(data).
vmax : float | callable | None
The value specifying the upper bound of the color range.
If None, the maximum absolute value is used. If callable, the output
equals vmax(data). Defaults to None.
tmin : float | None
Start time to consider.
tmax : float | None
End time to consider.
proj : bool
Apply projection.
bandwidth : float
The bandwidth of the multi taper windowing function in Hz. The default
value is a window half-bandwidth of 4 Hz.
adaptive : bool
Use adaptive weights to combine the tapered spectra into PSD
(slow, use n_jobs >> 1 to speed up computation).
low_bias : bool
Only use tapers with more than 90% spectral concentration within
bandwidth.
normalization : str
Either "full" or "length" (default). If "full", the PSD will
be normalized by the sampling rate as well as the length of
the signal (as in nitime).
ch_type : 'mag' | 'grad' | 'planar1' | 'planar2' | 'eeg' | None
The channel type to plot. For 'grad', the gradiometers are collected in
pairs and the RMS for each pair is plotted. If None, then first
available channel type from order given above is used. Defaults to
None.
layout : None | Layout
Layout instance specifying sensor positions (does not need to
be specified for Neuromag data). If possible, the correct layout
file is inferred from the data; if no appropriate layout file was
found, the layout is automatically generated from the sensor
locations.
cmap : matplotlib colormap | (colormap, bool) | 'interactive' | None
Colormap to use. 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 range. Up and down arrows can be used to change
the colormap. If None (default), 'Reds' is used for all positive data,
otherwise defaults to 'RdBu_r'. If 'interactive', translates to
(None, True).
agg_fun : callable
The function used to aggregate over frequencies.
Defaults to np.sum. if normalize is True, else np.mean.
dB : bool
If True, transform data to decibels (with ``10 * np.log10(data)``)
following the application of `agg_fun`. Only valid if normalize is
False.
n_jobs : int
Number of jobs to run in parallel.
normalize : bool
If True, each band will be divided by the total power. Defaults to
False.
cbar_fmt : str
The colorbar format. Defaults to '%0.3f'.
outlines : 'head' | 'skirt' | dict | None
The outlines to be drawn. If 'head', the default head scheme will be
drawn. If 'skirt' the head scheme will be drawn, but sensors are
allowed to be plotted outside of the head circle. If dict, each key
refers to a tuple of x and y positions, the values in 'mask_pos' will
serve as image mask, and the 'autoshrink' (bool) field will trigger
automated shrinking of the positions due to points outside the outline.
Alternatively, a matplotlib patch object can be passed for advanced
masking options, either directly or as a function that returns patches
(required for multi-axis plots). If None, nothing will be drawn.
Defaults to 'head'.
axes : list of axes | None
List of axes to plot consecutive topographies to. If None the axes
will be created automatically. Defaults to None.
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 distributing one image per channel across sensor topography.
"""
from ..channels import _get_ch_type
ch_type = _get_ch_type(epochs, ch_type)
picks, pos, merge_grads, names, ch_type = _prepare_topo_plot(
epochs, ch_type, layout)
psds, freqs = psd_multitaper(epochs, tmin=tmin, tmax=tmax,
bandwidth=bandwidth, adaptive=adaptive,
low_bias=low_bias,
normalization=normalization, picks=picks,
proj=proj, n_jobs=n_jobs)
psds = np.mean(psds, axis=0)
if merge_grads:
from ..channels.layout import _merge_grad_data
psds = _merge_grad_data(psds)
return plot_psds_topomap(
psds=psds, freqs=freqs, pos=pos, agg_fun=agg_fun, vmin=vmin,
vmax=vmax, bands=bands, cmap=cmap, dB=dB, normalize=normalize,
cbar_fmt=cbar_fmt, outlines=outlines, axes=axes, show=show)
def plot_psds_topomap(
psds, freqs, pos, agg_fun=None, vmin=None, vmax=None, bands=None,
cmap=None, dB=True, normalize=False, cbar_fmt='%0.3f', outlines='head',
axes=None, show=True):
"""Plot spatial maps of PSDs.
Parameters
----------
psds : np.ndarray of float, shape (n_channels, n_freqs)
Power spectral densities
freqs : np.ndarray of float, shape (n_freqs)
Frequencies used to compute psds.
pos : numpy.ndarray of float, shape (n_sensors, 2)
The positions of the sensors.
agg_fun : callable
The function used to aggregate over frequencies.
Defaults to np.sum. if normalize is True, else np.mean.
vmin : float | callable | None
The value specifying the lower bound of the color range.
If None np.min(data) is used. If callable, the output equals
vmin(data).
vmax : float | callable | None
The value specifying the upper bound of the color range.
If None, the maximum absolute value is used. If callable, the output
equals vmax(data). Defaults to None.
bands : list of tuple | None
The lower and upper frequency and the name for that band. If None,
(default) expands to:
bands = [(0, 4, 'Delta'), (4, 8, 'Theta'), (8, 12, 'Alpha'),
(12, 30, 'Beta'), (30, 45, 'Gamma')]
cmap : matplotlib colormap | (colormap, bool) | 'interactive' | None
Colormap to use. 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 range. Up and down arrows can be used to change
the colormap. If None (default), 'Reds' is used for all positive data,
otherwise defaults to 'RdBu_r'. If 'interactive', translates to
(None, True).
dB : bool
If True, transform data to decibels (with ``10 * np.log10(data)``)
following the application of `agg_fun`. Only valid if normalize is
False.
normalize : bool
If True, each band will be divided by the total power. Defaults to
False.
cbar_fmt : str
The colorbar format. Defaults to '%0.3f'.
outlines : 'head' | 'skirt' | dict | None
The outlines to be drawn. If 'head', the default head scheme will be
drawn. If 'skirt' the head scheme will be drawn, but sensors are
allowed to be plotted outside of the head circle. If dict, each key
refers to a tuple of x and y positions, the values in 'mask_pos' will
serve as image mask, and the 'autoshrink' (bool) field will trigger
automated shrinking of the positions due to points outside the outline.
Alternatively, a matplotlib patch object can be passed for advanced
masking options, either directly or as a function that returns patches
(required for multi-axis plots). If None, nothing will be drawn.
Defaults to 'head'.
axes : list of axes | None
List of axes to plot consecutive topographies to. If None the axes
will be created automatically. Defaults to None.
show : bool
Show figure if True.
Returns
-------
fig : instance of matplotlib figure
Figure distributing one image per channel across sensor topography.
"""
import matplotlib.pyplot as plt
if bands is None:
bands = [(0, 4, 'Delta'), (4, 8, 'Theta'), (8, 12, 'Alpha'),
(12, 30, 'Beta'), (30, 45, 'Gamma')]
if agg_fun is None:
agg_fun = np.sum if normalize is True else np.mean
if normalize is True:
psds /= psds.sum(axis=-1)[..., None]
assert np.allclose(psds.sum(axis=-1), 1.)
n_axes = len(bands)
if axes is not None:
_validate_if_list_of_axes(axes, n_axes)
fig = axes[0].figure
else:
fig, axes = plt.subplots(1, n_axes, figsize=(2 * n_axes, 1.5))
if n_axes == 1:
axes = [axes]
for ax, (fmin, fmax, title) in zip(axes, bands):
freq_mask = (fmin < freqs) & (freqs < fmax)
if freq_mask.sum() == 0:
raise RuntimeError('No frequencies in band "%s" (%s, %s)'
% (title, fmin, fmax))
data = agg_fun(psds[:, freq_mask], axis=1)
if dB is True and normalize is False:
data = 10 * np.log10(data)
unit = 'dB'
else:
unit = 'power'
_plot_topomap_multi_cbar(data, pos, ax, title=title, vmin=vmin,
vmax=vmax, cmap=cmap, outlines=outlines,
colorbar=True, unit=unit, cbar_fmt=cbar_fmt)
tight_layout(fig=fig)
fig.canvas.draw()
plt_show(show)
return fig
def plot_layout(layout, picks=None, show=True):
"""Plot the sensor positions.
Parameters
----------
layout : None | Layout
Layout instance specifying sensor positions.
picks : array-like
Indices of the channels to show. If None (default), all the channels
are shown.
show : bool
Show figure if True. Defaults to True.
Returns
-------
fig : instance of matplotlib figure
Figure containing the sensor topography.
Notes
-----
.. versionadded:: 0.12.0
"""
import matplotlib.pyplot as plt
fig = plt.figure(figsize=(max(plt.rcParams['figure.figsize']),) * 2)
ax = fig.add_subplot(111)
fig.subplots_adjust(left=0, bottom=0, right=1, top=1, wspace=None,
hspace=None)
ax.set(xticks=[], yticks=[], aspect='equal')
pos = [(p[0] + p[2] / 2., p[1] + p[3] / 2.) for p in layout.pos]
pos, outlines = _check_outlines(pos, 'head')
_draw_outlines(ax, outlines)
if picks is None:
names = layout.names
else:
pos = pos[picks]
names = np.array(layout.names)[picks]
for ii, (this_pos, ch_id) in enumerate(zip(pos, names)):
ax.annotate(ch_id, xy=this_pos[:2], horizontalalignment='center',
verticalalignment='center', size='x-small')
tight_layout(fig=fig, pad=0, w_pad=0, h_pad=0)
plt_show(show)
return fig
def _onselect(eclick, erelease, tfr, pos, ch_type, itmin, itmax, ifmin, ifmax,
cmap, fig, layout=None):
"""Handle drawing average tfr over channels called from topomap."""
import matplotlib.pyplot as plt
from matplotlib.collections import PathCollection
pos, _ = _check_outlines(pos, outlines='head', head_pos=None)
ax = eclick.inaxes
xmin = min(eclick.xdata, erelease.xdata)
xmax = max(eclick.xdata, erelease.xdata)
ymin = min(eclick.ydata, erelease.ydata)
ymax = max(eclick.ydata, erelease.ydata)
indices = ((pos[:, 0] < xmax) & (pos[:, 0] > xmin) &
(pos[:, 1] < ymax) & (pos[:, 1] > ymin))
colors = ['r' if ii else 'k' for ii in indices]
indices = np.where(indices)[0]
for collection in ax.collections:
if isinstance(collection, PathCollection): # this is our "scatter"
collection.set_color(colors)
ax.figure.canvas.draw()
if len(indices) == 0:
return
data = tfr.data
if ch_type == 'mag':
picks = pick_types(tfr.info, meg=ch_type, ref_meg=False)
data = np.mean(data[indices, ifmin:ifmax, itmin:itmax], axis=0)
chs = [tfr.ch_names[picks[x]] for x in indices]
elif ch_type == 'grad':
from ..channels.layout import _pair_grad_sensors
grads = _pair_grad_sensors(tfr.info, layout=layout,
topomap_coords=False)
idxs = list()
for idx in indices:
idxs.append(grads[idx * 2])
idxs.append(grads[idx * 2 + 1]) # pair of grads
data = np.mean(data[idxs, ifmin:ifmax, itmin:itmax], axis=0)
chs = [tfr.ch_names[x] for x in idxs]
elif ch_type == 'eeg':
picks = pick_types(tfr.info, meg=False, eeg=True, ref_meg=False)
data = np.mean(data[indices, ifmin:ifmax, itmin:itmax], axis=0)
chs = [tfr.ch_names[picks[x]] for x in indices]
logger.info('Averaging TFR over channels ' + str(chs))
if len(fig) == 0:
fig.append(figure_nobar())
if not plt.fignum_exists(fig[0].number):
fig[0] = figure_nobar()
ax = fig[0].add_subplot(111)
itmax = len(tfr.times) - 1 if itmax is None else min(itmax,
len(tfr.times) - 1)
ifmax = len(tfr.freqs) - 1 if ifmax is None else min(ifmax,
len(tfr.freqs) - 1)
if itmin is None:
itmin = 0
if ifmin is None:
ifmin = 0
extent = (tfr.times[itmin] * 1e3, tfr.times[itmax] * 1e3, tfr.freqs[ifmin],
tfr.freqs[ifmax])
title = 'Average over %d %s channels.' % (len(chs), ch_type)
ax.set_title(title)
ax.set_xlabel('Time (ms)')
ax.set_ylabel('Frequency (Hz)')
img = ax.imshow(data, extent=extent, aspect="auto", origin="lower",
cmap=cmap)
if len(fig[0].get_axes()) < 2:
fig[0].get_axes()[1].cbar = fig[0].colorbar(mappable=img)
else:
fig[0].get_axes()[1].cbar.on_mappable_changed(mappable=img)
fig[0].canvas.draw()
plt.figure(fig[0].number)
plt_show(True)
def _prepare_topomap(pos, ax, check_nonzero=True):
"""Prepare the topomap."""
pos_x = pos[:, 0]
pos_y = pos[:, 1]
_hide_frame(ax)
if check_nonzero and any([not pos_y.any(), not pos_x.any()]):
raise RuntimeError('No position information found, cannot compute '
'geometries for topomap.')
return pos_x, pos_y
def _hide_frame(ax):
"""Hide axis frame for topomaps."""
ax.get_yticks()
ax.xaxis.set_ticks([])
ax.yaxis.set_ticks([])
ax.set_frame_on(False)
def _init_anim(ax, ax_line, ax_cbar, params, merge_grads):
"""Initialize animated topomap."""
from matplotlib import pyplot as plt, patches
logger.info('Initializing animation...')
data = params['data']
items = list()
if params['butterfly']:
all_times = params['all_times']
for idx in range(len(data)):
ax_line.plot(all_times, data[idx], color='k')
vmin, vmax = _setup_vmin_vmax(data, None, None)
ax_line.set_yticks(np.around(np.linspace(vmin, vmax, 5), -1))
params['line'], = ax_line.plot([all_times[0], all_times[0]],
ax_line.get_ylim(), color='r')
items.append(params['line'])
if merge_grads:
from mne.channels.layout import _merge_grad_data
data = _merge_grad_data(data)
norm = True if np.min(data) > 0 else False
cmap = 'Reds' if norm else 'RdBu_r'
vmin, vmax = _setup_vmin_vmax(data, None, None, norm)
pos, outlines = _check_outlines(params['pos'], 'head', None)
_hide_frame(ax)
xlim = np.inf, -np.inf,
ylim = np.inf, -np.inf,
mask_ = np.c_[outlines['mask_pos']]
xmin, xmax = (np.min(np.r_[xlim[0], mask_[:, 0]]),
np.max(np.r_[xlim[1], mask_[:, 0]]))
ymin, ymax = (np.min(np.r_[ylim[0], mask_[:, 1]]),
np.max(np.r_[ylim[1], mask_[:, 1]]))
res = 64
xi = np.linspace(xmin, xmax, res)
yi = np.linspace(ymin, ymax, res)
Xi, Yi = np.meshgrid(xi, yi)
params['Zis'] = list()
interp = _GridData(pos)
for frame in params['frames']:
params['Zis'].append(interp.set_values(data[:, frame])(Xi, Yi))
Zi = params['Zis'][0]
zi_min = np.min(params['Zis'])
zi_max = np.max(params['Zis'])
cont_lims = np.linspace(zi_min, zi_max, 7, endpoint=False)[1:]
pos = _autoshrink(outlines, pos, res)
params.update({'vmin': vmin, 'vmax': vmax, 'Xi': Xi, 'Yi': Yi, 'Zi': Zi,
'extent': (xmin, xmax, ymin, ymax), 'cmap': cmap,
'cont_lims': cont_lims})
# plot map and contour
im = ax.imshow(Zi, cmap=cmap, vmin=vmin, vmax=vmax, origin='lower',
aspect='equal', extent=(xmin, xmax, ymin, ymax),
interpolation='bilinear')
plt.colorbar(im, cax=ax_cbar, cmap=cmap)
cont = ax.contour(Xi, Yi, Zi, levels=cont_lims, colors='k', linewidths=1)
patch_ = patches.Ellipse((0, 0),
2 * outlines['clip_radius'][0],
2 * outlines['clip_radius'][1],
clip_on=True,
transform=ax.transData)
im.set_clip_path(patch_)
text = ax.text(0.55, 0.95, '', transform=ax.transAxes, va='center',
ha='right')
params['text'] = text
items.append(im)
items.append(text)
for col in cont.collections:
col.set_clip_path(patch_)
outlines_ = _draw_outlines(ax, outlines)
params.update({'patch': patch_, 'outlines': outlines_})
return tuple(items) + tuple(cont.collections)
def _animate(frame, ax, ax_line, params):
"""Update animated topomap."""
if params['pause']:
frame = params['frame']
time_idx = params['frames'][frame]
if params['time_unit'] == 'ms':
title = '%6.0f ms' % (params['times'][frame] * 1e3,)
else:
title = '%6.3f s' % (params['times'][frame],)
if params['blit']:
text = params['text']
else:
ax.cla() # Clear old contours.
text = ax.text(0.45, 1.15, '', transform=ax.transAxes)
for k, (x, y) in params['outlines'].items():
if 'mask' in k:
continue
ax.plot(x, y, color='k', linewidth=1, clip_on=False)
_hide_frame(ax)
text.set_text(title)
vmin = params['vmin']
vmax = params['vmax']
Xi = params['Xi']
Yi = params['Yi']
Zi = params['Zis'][frame]
extent = params['extent']
cmap = params['cmap']
patch = params['patch']
im = ax.imshow(Zi, cmap=cmap, vmin=vmin, vmax=vmax, origin='lower',
aspect='equal', extent=extent, interpolation='bilinear')
cont_lims = params['cont_lims']
cont = ax.contour(Xi, Yi, Zi, levels=cont_lims, colors='k', linewidths=1)
im.set_clip_path(patch)
items = [im, text]
for col in cont.collections:
col.set_clip_path(patch)
if params['butterfly']:
all_times = params['all_times']
line = params['line']
line.remove()
params['line'] = ax_line.plot([all_times[time_idx],
all_times[time_idx]],
ax_line.get_ylim(), color='r')[0]
items.append(params['line'])
params['frame'] = frame
return tuple(items) + tuple(cont.collections)
def _pause_anim(event, params):
"""Pause or continue the animation on mouse click."""
params['pause'] = not params['pause']
def _key_press(event, params):
"""Handle key presses for the animation."""
if event.key == 'left':
params['pause'] = True
params['frame'] = max(params['frame'] - 1, 0)
elif event.key == 'right':
params['pause'] = True
params['frame'] = min(params['frame'] + 1, len(params['frames']) - 1)
def _topomap_animation(evoked, ch_type='mag', times=None, frame_rate=None,
butterfly=False, blit=True, show=True, time_unit='s'):
"""Make animation of evoked data as topomap timeseries.
Animation can be paused/resumed with left mouse button.
Left and right arrow keys can be used to move backward or forward in
time.
Parameters
----------
evoked : instance of Evoked
The evoked data.
ch_type : str | None
Channel type to plot. Accepted data types: 'mag', 'grad', 'eeg'.
If None, first available channel type from ('mag', 'grad', 'eeg') is
used. Defaults to None.
times : array of floats | None
The time points to plot. If None, 10 evenly spaced samples are
calculated over the evoked time series. Defaults to None.
frame_rate : int | None
Frame rate for the animation in Hz. If None, frame rate = sfreq / 10.
Defaults to None.
butterfly : bool
Whether to plot the data as butterfly plot under the topomap.
Defaults to False.
blit : bool
Whether to use blit to optimize drawing. In general, it is recommended
to use blit in combination with ``show=True``. If you intend to save
the animation it is better to disable blit. For MacOSX blit is always
disabled. Defaults to True.
show : bool
Whether to show the animation. Defaults to True.
time_unit : str
The units for the time axis, can be "ms" or "s" (default).
Returns
-------
fig : instance of matplotlib figure
The figure.
anim : instance of matplotlib FuncAnimation
Animation of the topomap.
Notes
-----
.. versionadded:: 0.12.0
"""
from matplotlib import pyplot as plt, animation
if ch_type is None:
ch_type = _picks_by_type(evoked.info)[0][0]
if ch_type not in ('mag', 'grad', 'eeg'):
raise ValueError("Channel type not supported. Supported channel "
"types include 'mag', 'grad' and 'eeg'.")
time_unit, _ = _check_time_unit(time_unit, evoked.times)
if times is None:
times = np.linspace(evoked.times[0], evoked.times[-1], 10)
times = np.array(times)
if times.ndim != 1:
raise ValueError('times must be 1D, got %d dimensions' % times.ndim)
if max(times) > evoked.times[-1] or min(times) < evoked.times[0]:
raise ValueError('All times must be inside the evoked time series.')
frames = [np.abs(evoked.times - time).argmin() for time in times]
blit = False if plt.get_backend() == 'MacOSX' else blit
picks, pos, merge_grads, _, ch_type = _prepare_topo_plot(
evoked, ch_type=ch_type, layout=None)
data = evoked.data[picks, :]
data *= _handle_default('scalings')[ch_type]
fig = plt.figure()
offset = 0. if blit else 0.4 # XXX: blit changes the sizes for some reason
ax = plt.axes([0. + offset / 2., 0. + offset / 2., 1. - offset,
1. - offset], xlim=(-1, 1), ylim=(-1, 1))
if butterfly:
ax_line = plt.axes([0.2, 0.05, 0.6, 0.1], xlim=(evoked.times[0],
evoked.times[-1]))
else:
ax_line = None
if isinstance(frames, Integral):
frames = np.linspace(0, len(evoked.times) - 1, frames).astype(int)
ax_cbar = plt.axes([0.85, 0.1, 0.05, 0.8])
ax_cbar.set_title(_handle_default('units')[ch_type], fontsize=10)
params = dict(data=data, pos=pos, all_times=evoked.times, frame=0,
frames=frames, butterfly=butterfly, blit=blit,
pause=False, times=times, time_unit=time_unit)
init_func = partial(_init_anim, ax=ax, ax_cbar=ax_cbar, ax_line=ax_line,
params=params, merge_grads=merge_grads)
animate_func = partial(_animate, ax=ax, ax_line=ax_line, params=params)
pause_func = partial(_pause_anim, params=params)
fig.canvas.mpl_connect('button_press_event', pause_func)
key_press_func = partial(_key_press, params=params)
fig.canvas.mpl_connect('key_press_event', key_press_func)
if frame_rate is None:
frame_rate = evoked.info['sfreq'] / 10.
interval = 1000 / frame_rate # interval is in ms
anim = animation.FuncAnimation(fig, animate_func, init_func=init_func,
frames=len(frames), interval=interval,
blit=blit)
fig.mne_animation = anim # to make sure anim is not garbage collected
plt_show(show, block=False)
if 'line' in params:
# Finally remove the vertical line so it does not appear in saved fig.
params['line'].remove()
return fig, anim
def _set_contour_locator(vmin, vmax, contours):
"""Set correct contour levels."""
locator = None
if isinstance(contours, Integral) and contours > 0:
from matplotlib import ticker
# nbins = ticks - 1, since 2 of the ticks are vmin and vmax, the
# correct number of bins is equal to contours + 1.
locator = ticker.MaxNLocator(nbins=contours + 1)
contours = locator.tick_values(vmin, vmax)
return locator, contours
def _plot_corrmap(data, subjs, indices, ch_type, ica, label, show, outlines,
layout, cmap, contours, template=False):
"""Customize ica.plot_components for corrmap."""
if not template:
title = 'Detected components'
if label is not None:
title += ' of type ' + label
else:
title = "Supplied template"
picks = list(range(len(data)))
p = 20
if len(picks) > p: # plot components by sets of 20
n_components = len(picks)
figs = [_plot_corrmap(data[k:k + p], subjs[k:k + p],
indices[k:k + p], ch_type, ica, label, show,
outlines=outlines, layout=layout, cmap=cmap,
contours=contours)
for k in range(0, n_components, p)]
return figs
elif np.isscalar(picks):
picks = [picks]
data_picks, pos, merge_grads, names, _ = _prepare_topo_plot(
ica, ch_type, layout)
pos, outlines = _check_outlines(pos, outlines)
data = np.atleast_2d(data)
data = data[:, data_picks]
# prepare data for iteration
fig, axes = _prepare_trellis(len(picks), max_col=5)
fig.suptitle(title)
if merge_grads:
from ..channels.layout import _merge_grad_data
for ii, data_, ax, subject, idx in zip(picks, data, axes, subjs, indices):
if template:
ttl = 'Subj. {0}, {1}'.format(subject, ica._ica_names[idx])
ax.set_title(ttl, fontsize=12)
data_ = _merge_grad_data(data_) if merge_grads else data_
vmin_, vmax_ = _setup_vmin_vmax(data_, None, None)
plot_topomap(data_.flatten(), pos, vmin=vmin_, vmax=vmax_,
res=64, axes=ax, cmap=cmap, outlines=outlines,
contours=contours, show=False, image_interp='bilinear')[0]
_hide_frame(ax)
tight_layout(fig=fig)
fig.subplots_adjust(top=0.8)
fig.canvas.draw()
plt_show(show)
return fig
def _trigradient(x, y, z):
"""Take gradients of z on a mesh."""
from matplotlib.tri import CubicTriInterpolator, Triangulation
with warnings.catch_warnings(): # catch matplotlib warnings
warnings.filterwarnings("ignore", category=DeprecationWarning)
tri = Triangulation(x, y)
tci = CubicTriInterpolator(tri, z)
dx, dy = tci.gradient(tri.x, tri.y)
return dx, dy
def plot_arrowmap(data, info_from, info_to=None, scale=1e-10, vmin=None,
vmax=None, cmap=None, sensors=True, res=64, axes=None,
names=None, show_names=False, mask=None, mask_params=None,
outlines='head', contours=6, image_interp='bilinear',
show=True, head_pos=None, onselect=None):
"""Plot arrow map.
Compute arrowmaps, based upon the Hosaka-Cohen transformation [1]_,
these arrows represents an estimation of the current flow underneath
the MEG sensors. They are a poor man's MNE.
Since planar gradiometers takes gradients along latitude and longitude,
they need to be projected to the flatten manifold span by magnetometer
or radial gradiometers before taking the gradients in the 2D Cartesian
coordinate system for visualization on the 2D topoplot. You can use the
``info_from`` and ``info_to`` parameters to interpolate from
gradiometer data to magnetometer data.
Parameters
----------
data : array, shape (n_channels,)
The data values to plot.
info_from : instance of Info
The measurement info from data to interpolate from.
info_to : instance of Info | None
The measurement info to interpolate to. If None, it is assumed
to be the same as info_from.
scale : float, default 1e-10
To scale the arrows
vmin : float | callable | None
The value specifying the lower bound of the color range.
If None, and vmax is None, -vmax is used. Else np.min(data).
If callable, the output equals vmin(data). Defaults to None.
vmax : float | callable | None
The value specifying the upper bound of the color range.
If None, the maximum absolute value is used. If callable, the output
equals vmax(data). Defaults to None.
cmap : matplotlib colormap | None
Colormap to use. If None, 'Reds' is used for all positive data,
otherwise defaults to 'RdBu_r'.
sensors : bool | str
Add markers for sensor locations to the plot. Accepts matplotlib plot
format string (e.g., 'r+' for red plusses). If True (default), circles
will be used.
res : int
The resolution of the topomap image (n pixels along each side).
axes : instance of Axes | None
The axes to plot to. If None, a new figure will be created.
names : list | None
List of channel names. If None, channel names are not plotted.
show_names : bool | callable
If True, show channel names on top of the map. If a callable is
passed, channel names will be formatted using the callable; e.g., to
delete the prefix 'MEG ' from all channel names, pass the function
lambda x: x.replace('MEG ', ''). If `mask` is not None, only
significant sensors will be shown.
If `True`, a list of names must be provided (see `names` keyword).
mask : ndarray of bool, shape (n_channels, n_times) | None
The channels to be marked as significant at a given time point.
Indices set to `True` will be considered. Defaults to None.
mask_params : dict | None
Additional plotting parameters for plotting significant sensors.
Default (None) equals::
dict(marker='o', markerfacecolor='w', markeredgecolor='k',
linewidth=0, markersize=4)
outlines : 'head' | 'skirt' | dict | None
The outlines to be drawn. If 'head', the default head scheme will be
drawn. If 'skirt' the head scheme will be drawn, but sensors are
allowed to be plotted outside of the head circle. If dict, each key
refers to a tuple of x and y positions, the values in 'mask_pos' will
serve as image mask, and the 'autoshrink' (bool) field will trigger
automated shrinking of the positions due to points outside the outline.
Alternatively, a matplotlib patch object can be passed for advanced
masking options, either directly or as a function that returns patches
(required for multi-axes plots). If None, nothing will be drawn.
Defaults to 'head'.
contours : int | array of float
The number of contour lines to draw. If 0, no contours will be drawn.
If an array, the values represent the levels for the contours. The
values are in uV for EEG, fT for magnetometers and fT/m for
gradiometers. Defaults to 6.
image_interp : str
The image interpolation to be used. All matplotlib options are
accepted.
show : bool
Show figure if True.
head_pos : dict | None
If None (default), the sensors are positioned such that they span
the head circle. If dict, can have entries 'center' (tuple) and
'scale' (tuple) for what the center and scale of the head should be
relative to the electrode locations.
onselect : callable | None
Handle for a function that is called when the user selects a set of
channels by rectangle selection (matplotlib ``RectangleSelector``). If
None interactive selection is disabled. Defaults to None.
Returns
-------
fig : matplotlib.figure.Figure
The Figure of the plot
Notes
-----
.. versionadded:: 0.17
References
----------
.. [1] D. Cohen, H. Hosaka
"Part II magnetic field produced by a current dipole",
Journal of electrocardiology, Volume 9, Number 4, pp. 409-417, 1976.
DOI: 10.1016/S0022-0736(76)80041-6
"""
from matplotlib import pyplot as plt
from ..forward import _map_meg_channels
ch_type = _picks_by_type(info_from)
if len(ch_type) > 1:
raise ValueError('Multiple channel types are not supported.'
'All channels must either be of type \'grad\' '
'or \'mag\'.')
else:
ch_type = ch_type[0][0]
if ch_type not in ('mag', 'grad'):
raise ValueError("Channel type '%s' not supported. Supported channel "
"types are 'mag' and 'grad'." % ch_type)
if info_to is None and ch_type == 'mag':
info_to = info_from
else:
ch_type = _picks_by_type(info_to)
if len(ch_type) > 1:
raise ValueError("Multiple channel types are not supported.")
else:
ch_type = ch_type[0][0]
if ch_type != 'mag':
raise ValueError("only 'mag' channel type is supported. "
"Got %s" % ch_type)
if info_to is not info_from:
mapping = _map_meg_channels(info_from, info_to, mode='accurate')
data = np.dot(mapping, data)
pos = _prepare_topo_plot(info_to, ch_type='mag', layout=None)[1]
pos = _check_outlines(pos, 'head', None)[0]
if axes is None:
fig, axes = plt.subplots()
else:
fig = axes.figure
plot_topomap(data, pos, axes=axes, vmin=vmin, vmax=vmax, cmap=cmap,
sensors=sensors, res=res, names=names, show_names=show_names,
mask=mask, mask_params=mask_params, outlines=outlines,
contours=contours, image_interp=image_interp, show=show,
head_pos=head_pos, onselect=onselect)
x, y = tuple(pos.T)
dx, dy = _trigradient(x, y, data)
dxx = dy.data
dyy = -dx.data
axes.quiver(x, y, dxx, dyy, scale=scale, color='k', lw=1)
tight_layout(fig=fig)
return fig
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