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"""Utility functions for plotting M/EEG data
"""
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>
# Mainak Jas <mainak@neuro.hut.fi>
#
# License: Simplified BSD
import math
from copy import deepcopy
from functools import partial
import difflib
import webbrowser
from warnings import warn
import tempfile
import numpy as np
from ..io import show_fiff
from ..utils import verbose
COLORS = ['b', 'g', 'r', 'c', 'm', 'y', 'k', '#473C8B', '#458B74',
'#CD7F32', '#FF4040', '#ADFF2F', '#8E2323', '#FF1493']
DEFAULTS = dict(color=dict(mag='darkblue', grad='b', eeg='k', eog='k', ecg='r',
emg='k', ref_meg='steelblue', misc='k', stim='k',
resp='k', chpi='k', exci='k', ias='k', syst='k'),
units=dict(eeg='uV', grad='fT/cm', mag='fT', misc='AU'),
scalings=dict(eeg=1e6, grad=1e13, mag=1e15, misc=1.0),
scalings_plot_raw=dict(mag=1e-12, grad=4e-11, eeg=20e-6,
eog=150e-6, ecg=5e-4, emg=1e-3,
ref_meg=1e-12, misc=1e-3,
stim=1, resp=1, chpi=1e-4, exci=1,
ias=1, syst=1),
ylim=dict(mag=(-600., 600.), grad=(-200., 200.),
eeg=(-200., 200.), misc=(-5., 5.)),
titles=dict(eeg='EEG', grad='Gradiometers',
mag='Magnetometers', misc='misc'),
mask_params=dict(marker='o',
markerfacecolor='w',
markeredgecolor='k',
linewidth=0,
markeredgewidth=1,
markersize=4))
def _mutable_defaults(*mappings):
""" To avoid dicts as default keyword arguments
Use this function instead to resolve default dict values.
Example usage:
scalings, units = _mutable_defaults(('scalings', scalings,
'units', units))
"""
out = []
for k, v in mappings:
this_mapping = DEFAULTS[k]
if v is not None:
this_mapping = deepcopy(DEFAULTS[k])
this_mapping.update(v)
out += [this_mapping]
return out
def _setup_vmin_vmax(data, vmin, vmax):
"""Aux function to handle vmin and vamx parameters"""
if vmax is None and vmin is None:
vmax = np.abs(data).max()
vmin = -vmax
else:
if callable(vmin):
vmin = vmin(data)
elif vmin is None:
vmin = np.min(data)
if callable(vmax):
vmax = vmax(data)
elif vmin is None:
vmax = np.max(data)
return vmin, vmax
def tight_layout(pad=1.2, h_pad=None, w_pad=None, fig=None):
""" Adjust subplot parameters to give specified padding.
Note. For plotting please use this function instead of plt.tight_layout
Parameters
----------
pad : float
padding between the figure edge and the edges of subplots, as a
fraction of the font-size.
h_pad, w_pad : float
padding (height/width) between edges of adjacent subplots.
Defaults to `pad_inches`.
"""
import matplotlib.pyplot as plt
if fig is None:
fig = plt.gcf()
try: # see https://github.com/matplotlib/matplotlib/issues/2654
fig.canvas.draw()
fig.tight_layout(pad=pad, h_pad=h_pad, w_pad=w_pad)
except:
msg = ('Matplotlib function \'tight_layout\'%s.'
' Skipping subpplot adjusment.')
if not hasattr(plt, 'tight_layout'):
case = ' is not available'
else:
case = (' is not supported by your backend: `%s`'
% plt.get_backend())
warn(msg % case)
def _check_delayed_ssp(container):
""" Aux function to be used for interactive SSP selection
"""
if container.proj is True or\
all([p['active'] for p in container.info['projs']]):
raise RuntimeError('Projs are already applied. Please initialize'
' the data with proj set to False.')
elif len(container.info['projs']) < 1:
raise RuntimeError('No projs found in evoked.')
def mne_analyze_colormap(limits=[5, 10, 15], format='mayavi'):
"""Return a colormap similar to that used by mne_analyze
Parameters
----------
limits : list (or array) of length 3
Bounds for the colormap.
format : str
Type of colormap to return. If 'matplotlib', will return a
matplotlib.colors.LinearSegmentedColormap. If 'mayavi', will
return an RGBA array of shape (256, 4).
Returns
-------
cmap : instance of matplotlib.pyplot.colormap | array
A teal->blue->gray->red->yellow colormap.
Notes
-----
For this will return a colormap that will display correctly for data
that are scaled by the plotting function to span [-fmax, fmax].
Examples
--------
The following code will plot a STC using standard MNE limits:
colormap = mne.viz.mne_analyze_colormap(limits=[5, 10, 15])
brain = stc.plot('fsaverage', 'inflated', 'rh', colormap)
brain.scale_data_colormap(fmin=-15, fmid=0, fmax=15, transparent=False)
"""
l = np.asarray(limits, dtype='float')
if len(l) != 3:
raise ValueError('limits must have 3 elements')
if any(l < 0):
raise ValueError('limits must all be positive')
if any(np.diff(l) <= 0):
raise ValueError('limits must be monotonically increasing')
if format == 'matplotlib':
from matplotlib import colors
l = (np.concatenate((-np.flipud(l), l)) + l[-1]) / (2 * l[-1])
cdict = {'red': ((l[0], 0.0, 0.0),
(l[1], 0.0, 0.0),
(l[2], 0.5, 0.5),
(l[3], 0.5, 0.5),
(l[4], 1.0, 1.0),
(l[5], 1.0, 1.0)),
'green': ((l[0], 1.0, 1.0),
(l[1], 0.0, 0.0),
(l[2], 0.5, 0.5),
(l[3], 0.5, 0.5),
(l[4], 0.0, 0.0),
(l[5], 1.0, 1.0)),
'blue': ((l[0], 1.0, 1.0),
(l[1], 1.0, 1.0),
(l[2], 0.5, 0.5),
(l[3], 0.5, 0.5),
(l[4], 0.0, 0.0),
(l[5], 0.0, 0.0))}
return colors.LinearSegmentedColormap('mne_analyze', cdict)
elif format == 'mayavi':
l = np.concatenate((-np.flipud(l), [0], l)) / l[-1]
r = np.array([0, 0, 0, 0, 1, 1, 1])
g = np.array([1, 0, 0, 0, 0, 0, 1])
b = np.array([1, 1, 1, 0, 0, 0, 0])
a = np.array([1, 1, 0, 0, 0, 1, 1])
xp = (np.arange(256) - 128) / 128.0
colormap = np.r_[[np.interp(xp, l, 255 * c) for c in [r, g, b, a]]].T
return colormap
else:
raise ValueError('format must be either matplotlib or mayavi')
def _toggle_options(event, params):
"""Toggle options (projectors) dialog"""
import matplotlib.pyplot as plt
if len(params['projs']) > 0:
if params['fig_opts'] is None:
_draw_proj_checkbox(event, params, draw_current_state=False)
else:
# turn off options dialog
plt.close(params['fig_opts'])
del params['proj_checks']
params['fig_opts'] = None
def _toggle_proj(event, params):
"""Operation to perform when proj boxes clicked"""
# read options if possible
if 'proj_checks' in params:
bools = [x[0].get_visible() for x in params['proj_checks'].lines]
for bi, (b, p) in enumerate(zip(bools, params['projs'])):
# see if they tried to deactivate an active one
if not b and p['active']:
bools[bi] = True
else:
bools = [True] * len(params['projs'])
compute_proj = False
if not 'proj_bools' in params:
compute_proj = True
elif not np.array_equal(bools, params['proj_bools']):
compute_proj = True
# if projectors changed, update plots
if compute_proj is True:
params['plot_update_proj_callback'](params, bools)
def _prepare_trellis(n_cells, max_col):
"""Aux function
"""
import matplotlib.pyplot as plt
if n_cells == 1:
nrow = ncol = 1
elif n_cells <= max_col:
nrow, ncol = 1, n_cells
else:
nrow, ncol = int(math.ceil(n_cells / float(max_col))), max_col
fig, axes = plt.subplots(nrow, ncol, figsize=(7.4, 1.5 * nrow + 1))
axes = [axes] if ncol == nrow == 1 else axes.flatten()
for ax in axes[n_cells:]: # hide unused axes
ax.set_visible(False)
return fig, axes
def _draw_proj_checkbox(event, params, draw_current_state=True):
"""Toggle options (projectors) dialog"""
import matplotlib.pyplot as plt
import matplotlib as mpl
projs = params['projs']
# turn on options dialog
labels = [p['desc'] for p in projs]
actives = ([p['active'] for p in projs] if draw_current_state else
[True] * len(params['projs']))
width = max([len(p['desc']) for p in projs]) / 6.0 + 0.5
height = len(projs) / 6.0 + 0.5
fig_proj = figure_nobar(figsize=(width, height))
fig_proj.canvas.set_window_title('SSP projection vectors')
ax_temp = plt.axes((0, 0, 1, 1))
ax_temp.get_yaxis().set_visible(False)
ax_temp.get_xaxis().set_visible(False)
fig_proj.add_axes(ax_temp)
proj_checks = mpl.widgets.CheckButtons(ax_temp, labels=labels,
actives=actives)
# change already-applied projectors to red
for ii, p in enumerate(projs):
if p['active'] is True:
for x in proj_checks.lines[ii]:
x.set_color('r')
# make minimal size
# pass key presses from option dialog over
proj_checks.on_clicked(partial(_toggle_proj, params=params))
params['proj_checks'] = proj_checks
# this should work for non-test cases
try:
fig_proj.canvas.draw()
fig_proj.show()
except Exception:
pass
@verbose
def compare_fiff(fname_1, fname_2, fname_out=None, show=True, indent=' ',
read_limit=np.inf, max_str=30, verbose=None):
"""Compare the contents of two fiff files using diff and show_fiff
Parameters
----------
fname_1 : str
First file to compare.
fname_2 : str
Second file to compare.
fname_out : str | None
Filename to store the resulting diff. If None, a temporary
file will be created.
show : bool
If True, show the resulting diff in a new tab in a web browser.
indent : str
How to indent the lines.
read_limit : int
Max number of bytes of data to read from a tag. Can be np.inf
to always read all data (helps test read completion).
max_str : int
Max number of characters of string representation to print for
each tag's data.
verbose : bool, str, int, or None
If not None, override default verbose level (see mne.verbose).
Returns
-------
fname_out : str
The filename used for storing the diff. Could be useful for
when a temporary file is used.
"""
file_1 = show_fiff(fname_1, output=list, indent=indent,
read_limit=read_limit, max_str=max_str)
file_2 = show_fiff(fname_2, output=list, indent=indent,
read_limit=read_limit, max_str=max_str)
diff = difflib.HtmlDiff().make_file(file_1, file_2, fname_1, fname_2)
if fname_out is not None:
f = open(fname_out, 'w')
else:
f = tempfile.NamedTemporaryFile('w', delete=False)
fname_out = f.name
with f as fid:
fid.write(diff)
if show is True:
webbrowser.open_new_tab(fname_out)
return fname_out
def figure_nobar(*args, **kwargs):
"""Make matplotlib figure with no toolbar"""
import matplotlib.pyplot as plt
import matplotlib as mpl
old_val = mpl.rcParams['toolbar']
try:
mpl.rcParams['toolbar'] = 'none'
fig = plt.figure(*args, **kwargs)
# remove button press catchers (for toolbar)
cbs = list(fig.canvas.callbacks.callbacks['key_press_event'].keys())
for key in cbs:
fig.canvas.callbacks.disconnect(key)
except Exception as ex:
raise ex
finally:
mpl.rcParams['toolbar'] = old_val
return fig
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