1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270
|
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.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 os.path as op
from collections import namedtuple
import numpy as np
import pytest
import matplotlib
import matplotlib.pyplot as plt
from mne import read_events, Epochs, pick_channels_evoked, read_cov
from mne.channels import read_layout
from mne.io import read_raw_fif
from mne.time_frequency.tfr import AverageTFR
from mne.utils import run_tests_if_main
from mne.viz import (plot_topo_image_epochs, _get_presser,
mne_analyze_colormap, plot_evoked_topo)
from mne.viz.evoked import _line_plot_onselect
from mne.viz.utils import _fake_click
from mne.viz.topo import (_plot_update_evoked_topo_proj, iter_topography,
_imshow_tfr)
base_dir = op.join(op.dirname(__file__), '..', '..', 'io', 'tests', 'data')
evoked_fname = op.join(base_dir, 'test-ave.fif')
raw_fname = op.join(base_dir, 'test_raw.fif')
event_name = op.join(base_dir, 'test-eve.fif')
cov_fname = op.join(base_dir, 'test-cov.fif')
event_id, tmin, tmax = 1, -0.2, 0.2
layout = read_layout('Vectorview-all')
def _get_events():
"""Get events."""
return read_events(event_name)
def _get_picks(raw):
"""Get picks."""
return [0, 1, 2, 6, 7, 8, 306, 340, 341, 342] # take a only few channels
def _get_epochs():
"""Get epochs."""
raw = read_raw_fif(raw_fname)
raw.add_proj([], remove_existing=True)
events = _get_events()
picks = _get_picks(raw)
# bad proj warning
epochs = Epochs(raw, events[:10], event_id, tmin, tmax, picks=picks)
return epochs
def _get_epochs_delayed_ssp():
"""Get epochs with delayed SSP."""
raw = read_raw_fif(raw_fname)
events = _get_events()
picks = _get_picks(raw)
reject = dict(mag=4e-12)
with pytest.warns(RuntimeWarning, match='projection'):
epochs_delayed_ssp = Epochs(
raw, events[:10], event_id, tmin, tmax, picks=picks,
proj='delayed', reject=reject)
return epochs_delayed_ssp
def test_plot_joint():
"""Test joint plot."""
evoked = _get_epochs().average()
evoked.plot_joint(ts_args=dict(time_unit='s'),
topomap_args=dict(time_unit='s'))
def return_inds(d): # to test function kwarg to zorder arg of evoked.plot
return list(range(d.shape[0]))
evoked.plot_joint(title='test', topomap_args=dict(contours=0, res=8,
time_unit='ms'),
ts_args=dict(spatial_colors=True, zorder=return_inds,
time_unit='s'))
pytest.raises(ValueError, evoked.plot_joint, ts_args=dict(axes=True,
time_unit='s'))
axes = plt.subplots(nrows=3)[-1].flatten().tolist()
evoked.plot_joint(times=[0], picks=[6, 7, 8], ts_args=dict(axes=axes[0]),
topomap_args={"axes": axes[1:], "time_unit": "s"})
with pytest.raises(ValueError, match='array of length 6'):
evoked.plot_joint(picks=[6, 7, 8], ts_args=dict(axes=axes[0]),
topomap_args=dict(axes=axes[2:]))
plt.close('all')
def test_plot_topo():
"""Test plotting of ERP topography."""
# Show topography
evoked = _get_epochs().average()
# should auto-find layout
plot_evoked_topo([evoked, evoked], merge_grads=True, background_color='w')
picked_evoked = evoked.copy().pick_channels(evoked.ch_names[:3])
picked_evoked_eeg = evoked.copy().pick_types(meg=False, eeg=True)
picked_evoked_eeg.pick_channels(picked_evoked_eeg.ch_names[:3])
# test scaling
for ylim in [dict(mag=[-600, 600]), None]:
plot_evoked_topo([picked_evoked] * 2, layout, ylim=ylim)
for evo in [evoked, [evoked, picked_evoked]]:
pytest.raises(ValueError, plot_evoked_topo, evo, layout,
color=['y', 'b'])
evoked_delayed_ssp = _get_epochs_delayed_ssp().average()
ch_names = evoked_delayed_ssp.ch_names[:3] # make it faster
picked_evoked_delayed_ssp = pick_channels_evoked(evoked_delayed_ssp,
ch_names)
fig = plot_evoked_topo(picked_evoked_delayed_ssp, layout,
proj='interactive')
func = _get_presser(fig)
event = namedtuple('Event', ['inaxes', 'xdata', 'ydata'])
func(event(inaxes=fig.axes[0], xdata=fig.axes[0]._mne_axs[0].pos[0],
ydata=fig.axes[0]._mne_axs[0].pos[1]))
func(event(inaxes=fig.axes[0], xdata=0, ydata=0))
params = dict(evokeds=[picked_evoked_delayed_ssp],
times=picked_evoked_delayed_ssp.times,
fig=fig, projs=picked_evoked_delayed_ssp.info['projs'])
bools = [True] * len(params['projs'])
with pytest.warns(RuntimeWarning, match='projection'):
_plot_update_evoked_topo_proj(params, bools)
# should auto-generate layout
plot_evoked_topo(picked_evoked_eeg.copy(),
fig_background=np.zeros((4, 3, 3)), proj=True,
background_color='k')
# Test RMS plot of grad pairs
picked_evoked.plot_topo(merge_grads=True, background_color='w')
plt.close('all')
for ax, idx in iter_topography(evoked.info, legend=True):
ax.plot(evoked.data[idx], color='red')
# test status bar message
if idx != -1:
assert (evoked.ch_names[idx] in ax.format_coord(.5, .5))
assert idx == -1
plt.close('all')
cov = read_cov(cov_fname)
cov['projs'] = []
evoked.pick_types(meg=True).plot_topo(noise_cov=cov)
plt.close('all')
# test plot_topo
evoked.plot_topo() # should auto-find layout
_line_plot_onselect(0, 200, ['mag', 'grad'], evoked.info, evoked.data,
evoked.times)
plt.close('all')
for ax, idx in iter_topography(evoked.info): # brief test with false
ax.plot([0, 1, 2])
break
plt.close('all')
def test_plot_topo_single_ch():
"""Test single channel topoplot with time cursor."""
evoked = _get_epochs().average()
evoked2 = evoked.copy()
# test plotting several evokeds on different time grids
evoked.crop(-.19, 0)
evoked2.crop(.05, .19)
fig = plot_evoked_topo([evoked, evoked2], background_color='w')
# test status bar message
ax = plt.gca()
assert ('MEG 0113' in ax.format_coord(.065, .63))
num_figures_before = len(plt.get_fignums())
_fake_click(fig, fig.axes[0], (0.08, 0.65))
assert num_figures_before + 1 == len(plt.get_fignums())
fig = plt.gcf()
ax = plt.gca()
_fake_click(fig, ax, (.5, .5), kind='motion') # cursor should appear
assert (isinstance(ax._cursorline, matplotlib.lines.Line2D))
_fake_click(fig, ax, (1.5, 1.5), kind='motion') # cursor should disappear
assert ax._cursorline is None
plt.close('all')
def test_plot_topo_image_epochs():
"""Test plotting of epochs image topography."""
title = 'ERF images - MNE sample data'
epochs = _get_epochs()
epochs.load_data()
cmap = mne_analyze_colormap(format='matplotlib')
data_min = epochs._data.min()
plt.close('all')
fig = plot_topo_image_epochs(epochs, sigma=0.5, vmin=-200, vmax=200,
colorbar=True, title=title, cmap=cmap)
assert epochs._data.min() == data_min
num_figures_before = len(plt.get_fignums())
_fake_click(fig, fig.axes[0], (0.08, 0.64))
assert num_figures_before + 1 == len(plt.get_fignums())
# test for auto-showing a colorbar when only 1 sensor type
ep = epochs.copy().pick_types(meg=False, eeg=True)
fig = plot_topo_image_epochs(ep, vmin=None, vmax=None, colorbar=None,
cmap=cmap)
ax = [x for x in fig.get_children() if isinstance(x, matplotlib.axes.Axes)]
qm_cmap = [y.cmap for x in ax for y in x.get_children()
if isinstance(y, matplotlib.collections.QuadMesh)]
assert qm_cmap[0] is cmap
plt.close('all')
def test_plot_tfr_topo():
"""Test plotting of TFR data."""
epochs = _get_epochs()
n_freqs = 3
nave = 1
data = np.random.RandomState(0).randn(len(epochs.ch_names),
n_freqs, len(epochs.times))
tfr = AverageTFR(epochs.info, data, epochs.times, np.arange(n_freqs), nave)
plt.close('all')
fig = tfr.plot_topo(baseline=(None, 0), mode='ratio',
title='Average power', vmin=0., vmax=14.)
# test opening tfr by clicking
num_figures_before = len(plt.get_fignums())
# could use np.reshape(fig.axes[-1].images[0].get_extent(), (2, 2)).mean(1)
with pytest.warns(None): # on old mpl (at least 2.0) there is a warning
_fake_click(fig, fig.axes[0], (0.08, 0.65))
assert num_figures_before + 1 == len(plt.get_fignums())
plt.close('all')
tfr.plot([4], baseline=(None, 0), mode='ratio', show=False, title='foo')
pytest.raises(ValueError, tfr.plot, [4], yscale='lin', show=False)
# nonuniform freqs
freqs = np.logspace(*np.log10([3, 10]), num=3)
tfr = AverageTFR(epochs.info, data, epochs.times, freqs, nave)
fig = tfr.plot([4], baseline=(None, 0), mode='mean', vmax=14., show=False)
assert fig.axes[0].get_yaxis().get_scale() == 'log'
# one timesample
tfr = AverageTFR(epochs.info, data[:, :, [0]], epochs.times[[1]],
freqs, nave)
with pytest.warns(None): # matplotlib equal left/right
tfr.plot([4], baseline=None, vmax=14., show=False, yscale='linear')
# one frequency bin, log scale required: as it doesn't make sense
# to plot log scale for one value, we test whether yscale is set to linear
vmin, vmax = 0., 2.
fig, ax = plt.subplots()
tmin, tmax = epochs.times[0], epochs.times[-1]
with pytest.warns(RuntimeWarning, match='not masking'):
_imshow_tfr(ax, 3, tmin, tmax, vmin, vmax, None, tfr=data[:, [0], :],
freq=freqs[[-1]], x_label=None, y_label=None,
colorbar=False, cmap=('RdBu_r', True), yscale='log')
fig = plt.gcf()
assert fig.axes[0].get_yaxis().get_scale() == 'linear'
# ValueError when freq[0] == 0 and yscale == 'log'
these_freqs = freqs[:3].copy()
these_freqs[0] = 0
with pytest.warns(RuntimeWarning, match='not masking'):
pytest.raises(ValueError, _imshow_tfr, ax, 3, tmin, tmax, vmin, vmax,
None, tfr=data[:, :3, :], freq=these_freqs, x_label=None,
y_label=None, colorbar=False, cmap=('RdBu_r', True),
yscale='log')
run_tests_if_main()
|