def test_make_eeg_layout():
"""Test creation of EEG layout."""
tempdir = _TempDir()
tmp_name = 'foo'
lout_name = 'test_raw'
lout_orig = read_layout(kind=lout_name, path=lout_path)
info = read_info(fif_fname)
info['bads'].append(info['ch_names'][360])
layout = make_eeg_layout(info, exclude=[])
assert_array_equal(
len(layout.names),
len([ch for ch in info['ch_names'] if ch.startswith('EE')]))
layout.save(op.join(tempdir, tmp_name + '.lout'))
lout_new = read_layout(kind=tmp_name, path=tempdir, scale=False)
assert_array_equal(lout_new.kind, tmp_name)
assert_allclose(layout.pos, lout_new.pos, atol=0.1)
assert_array_equal(lout_orig.names, lout_new.names)
# Test input validation
pytest.raises(ValueError, make_eeg_layout, info, radius=-0.1)
pytest.raises(ValueError, make_eeg_layout, info, radius=0.6)
pytest.raises(ValueError, make_eeg_layout, info, width=-0.1)
pytest.raises(ValueError, make_eeg_layout, info, width=1.1)
pytest.raises(ValueError, make_eeg_layout, info, height=-0.1)
pytest.raises(ValueError, make_eeg_layout, info, height=1.1)
def test_make_eeg_layout():
"""Test creation of EEG layout"""
tempdir = _TempDir()
tmp_name = 'foo'
lout_name = 'test_raw'
lout_orig = read_layout(kind=lout_name, path=lout_path)
info = Raw(fif_fname).info
layout = make_eeg_layout(info)
layout.save(op.join(tempdir, tmp_name + '.lout'))
lout_new = read_layout(kind=tmp_name, path=tempdir, scale=False)
assert_array_equal(lout_new.kind, tmp_name)
assert_allclose(layout.pos, lout_new.pos, atol=0.1)
assert_array_equal(lout_orig.names, lout_new.names)
# Test input validation
assert_raises(ValueError, make_eeg_layout, info, radius=-0.1)
assert_raises(ValueError, make_eeg_layout, info, radius=0.6)
assert_raises(ValueError, make_eeg_layout, info, width=-0.1)
assert_raises(ValueError, make_eeg_layout, info, width=1.1)
assert_raises(ValueError, make_eeg_layout, info, height=-0.1)
assert_raises(ValueError, make_eeg_layout, info, height=1.1)
def test_make_eeg_layout():
"""Test creation of EEG layout"""
tempdir = _TempDir()
tmp_name = "foo"
lout_name = "test_raw"
lout_orig = read_layout(kind=lout_name, path=lout_path)
info = Raw(fif_fname).info
info["bads"].append(info["ch_names"][360])
layout = make_eeg_layout(info, exclude=[])
assert_array_equal(len(layout.names), len([ch for ch in info["ch_names"] if ch.startswith("EE")]))
layout.save(op.join(tempdir, tmp_name + ".lout"))
lout_new = read_layout(kind=tmp_name, path=tempdir, scale=False)
assert_array_equal(lout_new.kind, tmp_name)
assert_allclose(layout.pos, lout_new.pos, atol=0.1)
assert_array_equal(lout_orig.names, lout_new.names)
# Test input validation
assert_raises(ValueError, make_eeg_layout, info, radius=-0.1)
assert_raises(ValueError, make_eeg_layout, info, radius=0.6)
assert_raises(ValueError, make_eeg_layout, info, width=-0.1)
assert_raises(ValueError, make_eeg_layout, info, width=1.1)
assert_raises(ValueError, make_eeg_layout, info, height=-0.1)
assert_raises(ValueError, make_eeg_layout, info, height=1.1)
def test_make_eeg_layout():
"""Test creation of EEG layout."""
tempdir = _TempDir()
tmp_name = 'foo'
lout_name = 'test_raw'
lout_orig = read_layout(kind=lout_name, path=lout_path)
info = read_info(fif_fname)
info['bads'].append(info['ch_names'][360])
layout = make_eeg_layout(info, exclude=[])
assert_array_equal(len(layout.names), len([ch for ch in info['ch_names']
if ch.startswith('EE')]))
layout.save(op.join(tempdir, tmp_name + '.lout'))
lout_new = read_layout(kind=tmp_name, path=tempdir, scale=False)
assert_array_equal(lout_new.kind, tmp_name)
assert_allclose(layout.pos, lout_new.pos, atol=0.1)
assert_array_equal(lout_orig.names, lout_new.names)
# Test input validation
pytest.raises(ValueError, make_eeg_layout, info, radius=-0.1)
pytest.raises(ValueError, make_eeg_layout, info, radius=0.6)
pytest.raises(ValueError, make_eeg_layout, info, width=-0.1)
pytest.raises(ValueError, make_eeg_layout, info, width=1.1)
pytest.raises(ValueError, make_eeg_layout, info, height=-0.1)
pytest.raises(ValueError, make_eeg_layout, info, height=1.1)
def test_plot_topomap():
"""Test topomap plotting."""
import matplotlib.pyplot as plt
from matplotlib.patches import Circle
# evoked
warnings.simplefilter('always')
res = 8
fast_test = {"res": res, "contours": 0, "sensors": False}
evoked = read_evokeds(evoked_fname, 'Left Auditory', baseline=(None, 0))
# Test animation
_, anim = evoked.animate_topomap(ch_type='grad',
times=[0, 0.1],
butterfly=False)
anim._func(1) # _animate has to be tested separately on 'Agg' backend.
plt.close('all')
ev_bad = evoked.copy().pick_types(meg=False, eeg=True)
ev_bad.pick_channels(ev_bad.ch_names[:2])
plt_topomap = partial(ev_bad.plot_topomap, **fast_test)
plt_topomap(times=ev_bad.times[:2] - 1e-6) # auto, plots EEG
assert_raises(ValueError, plt_topomap, ch_type='mag')
assert_raises(TypeError, plt_topomap, head_pos='foo')
assert_raises(KeyError, plt_topomap, head_pos=dict(foo='bar'))
assert_raises(ValueError, plt_topomap, head_pos=dict(center=0))
assert_raises(ValueError, plt_topomap, times=[-100]) # bad time
assert_raises(ValueError, plt_topomap, times=[[0]]) # bad time
evoked.plot_topomap([0.1],
ch_type='eeg',
scalings=1,
res=res,
contours=[-100, 0, 100])
plt_topomap = partial(evoked.plot_topomap, **fast_test)
plt_topomap(0.1, layout=layout, scalings=dict(mag=0.1))
plt.close('all')
axes = [plt.subplot(221), plt.subplot(222)]
plt_topomap(axes=axes, colorbar=False)
plt.close('all')
plt_topomap(times=[-0.1, 0.2])
plt.close('all')
evoked_grad = evoked.copy().crop(0, 0).pick_types(meg='grad')
mask = np.zeros((204, 1), bool)
mask[[0, 3, 5, 6]] = True
names = []
def proc_names(x):
names.append(x)
return x[4:]
evoked_grad.plot_topomap(ch_type='grad',
times=[0],
mask=mask,
show_names=proc_names,
**fast_test)
assert_equal(sorted(names),
['MEG 011x', 'MEG 012x', 'MEG 013x', 'MEG 014x'])
mask = np.zeros_like(evoked.data, dtype=bool)
mask[[1, 5], :] = True
plt_topomap(ch_type='mag', outlines=None)
times = [0.1]
plt_topomap(times, ch_type='grad', mask=mask)
plt_topomap(times, ch_type='planar1')
plt_topomap(times, ch_type='planar2')
plt_topomap(times,
ch_type='grad',
mask=mask,
show_names=True,
mask_params={'marker': 'x'})
plt.close('all')
assert_raises(ValueError, plt_topomap, times, ch_type='eeg', average=-1e3)
assert_raises(ValueError, plt_topomap, times, ch_type='eeg', average='x')
p = plt_topomap(times,
ch_type='grad',
image_interp='bilinear',
show_names=lambda x: x.replace('MEG', ''))
subplot = [
x for x in p.get_children() if isinstance(x, matplotlib.axes.Subplot)
][0]
assert_true(
all('MEG' not in x.get_text() for x in subplot.get_children()
if isinstance(x, matplotlib.text.Text)))
# Plot array
for ch_type in ('mag', 'grad'):
evoked_ = evoked.copy().pick_types(eeg=False, meg=ch_type)
plot_topomap(evoked_.data[:, 0], evoked_.info, **fast_test)
# fail with multiple channel types
assert_raises(ValueError, plot_topomap, evoked.data[0, :], evoked.info)
# Test title
def get_texts(p):
return [
x.get_text() for x in p.get_children()
if isinstance(x, matplotlib.text.Text)
]
p = plt_topomap(times, ch_type='eeg', average=0.01)
assert_equal(len(get_texts(p)), 0)
p = plt_topomap(times, ch_type='eeg', title='Custom')
texts = get_texts(p)
assert_equal(len(texts), 1)
assert_equal(texts[0], 'Custom')
plt.close('all')
# delaunay triangulation warning
with warnings.catch_warnings(record=True): # can't show
warnings.simplefilter('always')
plt_topomap(times, ch_type='mag', layout=None)
assert_raises(RuntimeError,
plot_evoked_topomap,
evoked,
0.1,
'mag',
proj='interactive') # projs have already been applied
# change to no-proj mode
evoked = read_evokeds(evoked_fname,
'Left Auditory',
baseline=(None, 0),
proj=False)
with warnings.catch_warnings(record=True):
warnings.simplefilter('always')
fig1 = evoked.plot_topomap('interactive',
'mag',
proj='interactive',
**fast_test)
_fake_click(fig1, fig1.axes[1], (0.5, 0.5)) # click slider
data_max = np.max(fig1.axes[0].images[0]._A)
fig2 = plt.gcf()
_fake_click(fig2, fig2.axes[0], (0.075, 0.775)) # toggle projector
# make sure projector gets toggled
assert_true(np.max(fig1.axes[0].images[0]._A) != data_max)
assert_raises(RuntimeError, plot_evoked_topomap, evoked, np.repeat(.1, 50))
assert_raises(ValueError, plot_evoked_topomap, evoked, [-3e12, 15e6])
for ch in evoked.info['chs']:
if ch['coil_type'] == FIFF.FIFFV_COIL_EEG:
ch['loc'].fill(0)
# Remove extra digitization point, so EEG digitization points
# correspond with the EEG electrodes
del evoked.info['dig'][85]
pos = make_eeg_layout(evoked.info).pos[:, :2]
pos, outlines = _check_outlines(pos, 'head')
assert_true('head' in outlines.keys())
assert_true('nose' in outlines.keys())
assert_true('ear_left' in outlines.keys())
assert_true('ear_right' in outlines.keys())
assert_true('autoshrink' in outlines.keys())
assert_true(outlines['autoshrink'])
assert_true('clip_radius' in outlines.keys())
assert_array_equal(outlines['clip_radius'], 0.5)
pos, outlines = _check_outlines(pos, 'skirt')
assert_true('head' in outlines.keys())
assert_true('nose' in outlines.keys())
assert_true('ear_left' in outlines.keys())
assert_true('ear_right' in outlines.keys())
assert_true('autoshrink' in outlines.keys())
assert_true(not outlines['autoshrink'])
assert_true('clip_radius' in outlines.keys())
assert_array_equal(outlines['clip_radius'], 0.625)
pos, outlines = _check_outlines(pos,
'skirt',
head_pos={'scale': [1.2, 1.2]})
assert_array_equal(outlines['clip_radius'], 0.75)
# Plot skirt
evoked.plot_topomap(times, ch_type='eeg', outlines='skirt', **fast_test)
# Pass custom outlines without patch
evoked.plot_topomap(times, ch_type='eeg', outlines=outlines, **fast_test)
plt.close('all')
# Test interactive cmap
fig = plot_evoked_topomap(evoked,
times=[0., 0.1],
ch_type='eeg',
cmap=('Reds', True),
title='title',
**fast_test)
fig.canvas.key_press_event('up')
fig.canvas.key_press_event(' ')
fig.canvas.key_press_event('down')
cbar = fig.get_axes()[0].CB # Fake dragging with mouse.
ax = cbar.cbar.ax
_fake_click(fig, ax, (0.1, 0.1))
_fake_click(fig, ax, (0.1, 0.2), kind='motion')
_fake_click(fig, ax, (0.1, 0.3), kind='release')
_fake_click(fig, ax, (0.1, 0.1), button=3)
_fake_click(fig, ax, (0.1, 0.2), button=3, kind='motion')
_fake_click(fig, ax, (0.1, 0.3), kind='release')
fig.canvas.scroll_event(0.5, 0.5, -0.5) # scroll down
fig.canvas.scroll_event(0.5, 0.5, 0.5) # scroll up
plt.close('all')
# Pass custom outlines with patch callable
def patch():
return Circle((0.5, 0.4687),
radius=.46,
clip_on=True,
transform=plt.gca().transAxes)
outlines['patch'] = patch
plot_evoked_topomap(evoked,
times,
ch_type='eeg',
outlines=outlines,
**fast_test)
# Remove digitization points. Now topomap should fail
evoked.info['dig'] = None
assert_raises(RuntimeError,
plot_evoked_topomap,
evoked,
times,
ch_type='eeg')
plt.close('all')
# Error for missing names
n_channels = len(pos)
data = np.ones(n_channels)
assert_raises(ValueError, plot_topomap, data, pos, show_names=True)
# Test error messages for invalid pos parameter
pos_1d = np.zeros(n_channels)
pos_3d = np.zeros((n_channels, 2, 2))
assert_raises(ValueError, plot_topomap, data, pos_1d)
assert_raises(ValueError, plot_topomap, data, pos_3d)
assert_raises(ValueError, plot_topomap, data, pos[:3, :])
pos_x = pos[:, :1]
pos_xyz = np.c_[pos, np.zeros(n_channels)[:, np.newaxis]]
assert_raises(ValueError, plot_topomap, data, pos_x)
assert_raises(ValueError, plot_topomap, data, pos_xyz)
# An #channels x 4 matrix should work though. In this case (x, y, width,
# height) is assumed.
pos_xywh = np.c_[pos, np.zeros((n_channels, 2))]
plot_topomap(data, pos_xywh)
plt.close('all')
# Test peak finder
axes = [plt.subplot(131), plt.subplot(132)]
with warnings.catch_warnings(record=True): # rightmost column
evoked.plot_topomap(times='peaks', axes=axes, **fast_test)
plt.close('all')
evoked.data = np.zeros(evoked.data.shape)
evoked.data[50][1] = 1
assert_array_equal(_find_peaks(evoked, 10), evoked.times[1])
evoked.data[80][100] = 1
assert_array_equal(_find_peaks(evoked, 10), evoked.times[[1, 100]])
evoked.data[2][95] = 2
assert_array_equal(_find_peaks(evoked, 10), evoked.times[[1, 95]])
assert_array_equal(_find_peaks(evoked, 1), evoked.times[95])
# Test excluding bads channels
evoked_grad.info['bads'] += [evoked_grad.info['ch_names'][0]]
orig_bads = evoked_grad.info['bads']
evoked_grad.plot_topomap(ch_type='grad', times=[0])
assert_array_equal(evoked_grad.info['bads'], orig_bads)
plt.close('all')
def test_plot_topomap():
"""Test topomap plotting
"""
import matplotlib.pyplot as plt
from matplotlib.patches import Circle
# evoked
warnings.simplefilter("always")
res = 16
evoked = read_evokeds(evoked_fname, "Left Auditory", baseline=(None, 0))
# Test animation
_, anim = evoked.animate_topomap(ch_type="grad", times=[0, 0.1], butterfly=False)
anim._func(1) # _animate has to be tested separately on 'Agg' backend.
plt.close("all")
ev_bad = evoked.pick_types(meg=False, eeg=True, copy=True)
ev_bad.pick_channels(ev_bad.ch_names[:2])
ev_bad.plot_topomap(times=ev_bad.times[:2] - 1e-6) # auto, plots EEG
assert_raises(ValueError, ev_bad.plot_topomap, ch_type="mag")
assert_raises(TypeError, ev_bad.plot_topomap, head_pos="foo")
assert_raises(KeyError, ev_bad.plot_topomap, head_pos=dict(foo="bar"))
assert_raises(ValueError, ev_bad.plot_topomap, head_pos=dict(center=0))
assert_raises(ValueError, ev_bad.plot_topomap, times=[-100]) # bad time
assert_raises(ValueError, ev_bad.plot_topomap, times=[[0]]) # bad time
assert_raises(ValueError, ev_bad.plot_topomap, times=[[0]]) # bad time
evoked.plot_topomap(0.1, layout=layout, scale=dict(mag=0.1))
plt.close("all")
axes = [plt.subplot(221), plt.subplot(222)]
evoked.plot_topomap(axes=axes, colorbar=False)
plt.close("all")
evoked.plot_topomap(times=[-0.1, 0.2])
plt.close("all")
mask = np.zeros_like(evoked.data, dtype=bool)
mask[[1, 5], :] = True
evoked.plot_topomap(ch_type="mag", outlines=None)
times = [0.1]
evoked.plot_topomap(times, ch_type="eeg", res=res, scale=1)
evoked.plot_topomap(times, ch_type="grad", mask=mask, res=res)
evoked.plot_topomap(times, ch_type="planar1", res=res)
evoked.plot_topomap(times, ch_type="planar2", res=res)
evoked.plot_topomap(times, ch_type="grad", mask=mask, res=res, show_names=True, mask_params={"marker": "x"})
plt.close("all")
assert_raises(ValueError, evoked.plot_topomap, times, ch_type="eeg", res=res, average=-1000)
assert_raises(ValueError, evoked.plot_topomap, times, ch_type="eeg", res=res, average="hahahahah")
p = evoked.plot_topomap(
times, ch_type="grad", res=res, show_names=lambda x: x.replace("MEG", ""), image_interp="bilinear"
)
subplot = [x for x in p.get_children() if isinstance(x, matplotlib.axes.Subplot)][0]
assert_true(all("MEG" not in x.get_text() for x in subplot.get_children() if isinstance(x, matplotlib.text.Text)))
# Test title
def get_texts(p):
return [x.get_text() for x in p.get_children() if isinstance(x, matplotlib.text.Text)]
p = evoked.plot_topomap(times, ch_type="eeg", res=res, average=0.01)
assert_equal(len(get_texts(p)), 0)
p = evoked.plot_topomap(times, ch_type="eeg", title="Custom", res=res)
texts = get_texts(p)
assert_equal(len(texts), 1)
assert_equal(texts[0], "Custom")
plt.close("all")
# delaunay triangulation warning
with warnings.catch_warnings(record=True): # can't show
warnings.simplefilter("always")
evoked.plot_topomap(times, ch_type="mag", layout=None, res=res)
assert_raises(
RuntimeError, plot_evoked_topomap, evoked, 0.1, "mag", proj="interactive"
) # projs have already been applied
# change to no-proj mode
evoked = read_evokeds(evoked_fname, "Left Auditory", baseline=(None, 0), proj=False)
with warnings.catch_warnings(record=True):
warnings.simplefilter("always")
evoked.plot_topomap(0.1, "mag", proj="interactive", res=res)
assert_raises(RuntimeError, plot_evoked_topomap, evoked, np.repeat(0.1, 50))
assert_raises(ValueError, plot_evoked_topomap, evoked, [-3e12, 15e6])
with warnings.catch_warnings(record=True): # file conventions
warnings.simplefilter("always")
projs = read_proj(ecg_fname)
projs = [pp for pp in projs if pp["desc"].lower().find("eeg") < 0]
plot_projs_topomap(projs, res=res)
plt.close("all")
ax = plt.subplot(111)
plot_projs_topomap([projs[0]], res=res, axes=ax) # test axes param
plt.close("all")
for ch in evoked.info["chs"]:
if ch["coil_type"] == FIFF.FIFFV_COIL_EEG:
ch["loc"].fill(0)
# Remove extra digitization point, so EEG digitization points
# correspond with the EEG electrodes
del evoked.info["dig"][85]
pos = make_eeg_layout(evoked.info).pos[:, :2]
pos, outlines = _check_outlines(pos, "head")
assert_true("head" in outlines.keys())
assert_true("nose" in outlines.keys())
assert_true("ear_left" in outlines.keys())
assert_true("ear_right" in outlines.keys())
assert_true("autoshrink" in outlines.keys())
assert_true(outlines["autoshrink"])
assert_true("clip_radius" in outlines.keys())
assert_array_equal(outlines["clip_radius"], 0.5)
pos, outlines = _check_outlines(pos, "skirt")
assert_true("head" in outlines.keys())
assert_true("nose" in outlines.keys())
assert_true("ear_left" in outlines.keys())
assert_true("ear_right" in outlines.keys())
assert_true("autoshrink" in outlines.keys())
assert_true(not outlines["autoshrink"])
assert_true("clip_radius" in outlines.keys())
assert_array_equal(outlines["clip_radius"], 0.625)
pos, outlines = _check_outlines(pos, "skirt", head_pos={"scale": [1.2, 1.2]})
assert_array_equal(outlines["clip_radius"], 0.75)
# Plot skirt
evoked.plot_topomap(times, ch_type="eeg", outlines="skirt")
# Pass custom outlines without patch
evoked.plot_topomap(times, ch_type="eeg", outlines=outlines)
plt.close("all")
# Pass custom outlines with patch callable
def patch():
return Circle((0.5, 0.4687), radius=0.46, clip_on=True, transform=plt.gca().transAxes)
outlines["patch"] = patch
plot_evoked_topomap(evoked, times, ch_type="eeg", outlines=outlines)
# Remove digitization points. Now topomap should fail
evoked.info["dig"] = None
assert_raises(RuntimeError, plot_evoked_topomap, evoked, times, ch_type="eeg")
plt.close("all")
# Error for missing names
n_channels = len(pos)
data = np.ones(n_channels)
assert_raises(ValueError, plot_topomap, data, pos, show_names=True)
# Test error messages for invalid pos parameter
pos_1d = np.zeros(n_channels)
pos_3d = np.zeros((n_channels, 2, 2))
assert_raises(ValueError, plot_topomap, data, pos_1d)
assert_raises(ValueError, plot_topomap, data, pos_3d)
assert_raises(ValueError, plot_topomap, data, pos[:3, :])
pos_x = pos[:, :1]
pos_xyz = np.c_[pos, np.zeros(n_channels)[:, np.newaxis]]
assert_raises(ValueError, plot_topomap, data, pos_x)
assert_raises(ValueError, plot_topomap, data, pos_xyz)
# An #channels x 4 matrix should work though. In this case (x, y, width,
# height) is assumed.
pos_xywh = np.c_[pos, np.zeros((n_channels, 2))]
plot_topomap(data, pos_xywh)
plt.close("all")
# Test peak finder
axes = [plt.subplot(131), plt.subplot(132)]
with warnings.catch_warnings(record=True): # rightmost column
evoked.plot_topomap(times="peaks", axes=axes)
plt.close("all")
evoked.data = np.zeros(evoked.data.shape)
evoked.data[50][1] = 1
assert_array_equal(_find_peaks(evoked, 10), evoked.times[1])
evoked.data[80][100] = 1
assert_array_equal(_find_peaks(evoked, 10), evoked.times[[1, 100]])
evoked.data[2][95] = 2
assert_array_equal(_find_peaks(evoked, 10), evoked.times[[1, 95]])
assert_array_equal(_find_peaks(evoked, 1), evoked.times[95])
def test_plot_topomap():
"""Test topomap plotting
"""
import matplotlib.pyplot as plt
from matplotlib.patches import Circle
# evoked
warnings.simplefilter('always')
res = 16
evoked = read_evokeds(evoked_fname, 'Left Auditory',
baseline=(None, 0))
ev_bad = evoked.pick_types(meg=False, eeg=True, copy=True)
ev_bad.pick_channels(ev_bad.ch_names[:2])
ev_bad.plot_topomap(times=ev_bad.times[:2] - 1e-6) # auto, should plot EEG
assert_raises(ValueError, ev_bad.plot_topomap, ch_type='mag')
assert_raises(TypeError, ev_bad.plot_topomap, head_pos='foo')
assert_raises(KeyError, ev_bad.plot_topomap, head_pos=dict(foo='bar'))
assert_raises(ValueError, ev_bad.plot_topomap, head_pos=dict(center=0))
assert_raises(ValueError, ev_bad.plot_topomap, times=[-100]) # bad time
assert_raises(ValueError, ev_bad.plot_topomap, times=[[0]]) # bad time
evoked.plot_topomap(0.1, layout=layout, scale=dict(mag=0.1))
plt.close('all')
mask = np.zeros_like(evoked.data, dtype=bool)
mask[[1, 5], :] = True
evoked.plot_topomap(None, ch_type='mag', outlines=None)
times = [0.1]
evoked.plot_topomap(times, ch_type='eeg', res=res, scale=1)
evoked.plot_topomap(times, ch_type='grad', mask=mask, res=res)
evoked.plot_topomap(times, ch_type='planar1', res=res)
evoked.plot_topomap(times, ch_type='planar2', res=res)
evoked.plot_topomap(times, ch_type='grad', mask=mask, res=res,
show_names=True, mask_params={'marker': 'x'})
plt.close('all')
assert_raises(ValueError, evoked.plot_topomap, times, ch_type='eeg',
res=res, average=-1000)
assert_raises(ValueError, evoked.plot_topomap, times, ch_type='eeg',
res=res, average='hahahahah')
p = evoked.plot_topomap(times, ch_type='grad', res=res,
show_names=lambda x: x.replace('MEG', ''),
image_interp='bilinear')
subplot = [x for x in p.get_children() if
isinstance(x, matplotlib.axes.Subplot)][0]
assert_true(all('MEG' not in x.get_text()
for x in subplot.get_children()
if isinstance(x, matplotlib.text.Text)))
# Test title
def get_texts(p):
return [x.get_text() for x in p.get_children() if
isinstance(x, matplotlib.text.Text)]
p = evoked.plot_topomap(times, ch_type='eeg', res=res, average=0.01)
assert_equal(len(get_texts(p)), 0)
p = evoked.plot_topomap(times, ch_type='eeg', title='Custom', res=res)
texts = get_texts(p)
assert_equal(len(texts), 1)
assert_equal(texts[0], 'Custom')
plt.close('all')
# delaunay triangulation warning
with warnings.catch_warnings(record=True): # can't show
warnings.simplefilter('always')
evoked.plot_topomap(times, ch_type='mag', layout=None, res=res)
assert_raises(RuntimeError, plot_evoked_topomap, evoked, 0.1, 'mag',
proj='interactive') # projs have already been applied
# change to no-proj mode
evoked = read_evokeds(evoked_fname, 'Left Auditory',
baseline=(None, 0), proj=False)
with warnings.catch_warnings(record=True):
warnings.simplefilter('always')
evoked.plot_topomap(0.1, 'mag', proj='interactive', res=res)
assert_raises(RuntimeError, plot_evoked_topomap, evoked,
np.repeat(.1, 50))
assert_raises(ValueError, plot_evoked_topomap, evoked, [-3e12, 15e6])
with warnings.catch_warnings(record=True): # file conventions
warnings.simplefilter('always')
projs = read_proj(ecg_fname)
projs = [pp for pp in projs if pp['desc'].lower().find('eeg') < 0]
plot_projs_topomap(projs, res=res)
plt.close('all')
for ch in evoked.info['chs']:
if ch['coil_type'] == FIFF.FIFFV_COIL_EEG:
if ch['eeg_loc'] is not None:
ch['eeg_loc'].fill(0)
ch['loc'].fill(0)
# Remove extra digitization point, so EEG digitization points
# correspond with the EEG electrodes
del evoked.info['dig'][85]
pos = make_eeg_layout(evoked.info).pos
pos, outlines = _check_outlines(pos, 'head')
# test 1: pass custom outlines without patch
def patch():
return Circle((0.5, 0.4687), radius=.46,
clip_on=True, transform=plt.gca().transAxes)
# test 2: pass custom outlines with patch callable
outlines['patch'] = patch
plot_evoked_topomap(evoked, times, ch_type='eeg', outlines='head')
# Remove digitization points. Now topomap should fail
evoked.info['dig'] = None
assert_raises(RuntimeError, plot_evoked_topomap, evoked,
times, ch_type='eeg')
plt.close('all')
def test_plot_topomap():
"""Test topomap plotting."""
import matplotlib.pyplot as plt
from matplotlib.patches import Circle
# evoked
res = 8
fast_test = dict(res=res, contours=0, sensors=False, time_unit='s')
fast_test_noscale = dict(res=res, contours=0, sensors=False)
evoked = read_evokeds(evoked_fname, 'Left Auditory',
baseline=(None, 0))
# Test animation
_, anim = evoked.animate_topomap(ch_type='grad', times=[0, 0.1],
butterfly=False, time_unit='s')
anim._func(1) # _animate has to be tested separately on 'Agg' backend.
plt.close('all')
ev_bad = evoked.copy().pick_types(meg=False, eeg=True)
ev_bad.pick_channels(ev_bad.ch_names[:2])
plt_topomap = partial(ev_bad.plot_topomap, **fast_test)
plt_topomap(times=ev_bad.times[:2] - 1e-6) # auto, plots EEG
pytest.raises(ValueError, plt_topomap, ch_type='mag')
pytest.raises(TypeError, plt_topomap, head_pos='foo')
pytest.raises(KeyError, plt_topomap, head_pos=dict(foo='bar'))
pytest.raises(ValueError, plt_topomap, head_pos=dict(center=0))
pytest.raises(ValueError, plt_topomap, times=[-100]) # bad time
pytest.raises(ValueError, plt_topomap, times=[[0]]) # bad time
evoked.plot_topomap([0.1], ch_type='eeg', scalings=1, res=res,
contours=[-100, 0, 100], time_unit='ms')
plt_topomap = partial(evoked.plot_topomap, **fast_test)
plt_topomap(0.1, layout=layout, scalings=dict(mag=0.1))
plt.close('all')
axes = [plt.subplot(221), plt.subplot(222)]
plt_topomap(axes=axes, colorbar=False)
plt.close('all')
plt_topomap(times=[-0.1, 0.2])
plt.close('all')
evoked_grad = evoked.copy().crop(0, 0).pick_types(meg='grad')
mask = np.zeros((204, 1), bool)
mask[[0, 3, 5, 6]] = True
names = []
def proc_names(x):
names.append(x)
return x[4:]
evoked_grad.plot_topomap(ch_type='grad', times=[0], mask=mask,
show_names=proc_names, **fast_test)
assert_equal(sorted(names),
['MEG 011x', 'MEG 012x', 'MEG 013x', 'MEG 014x'])
mask = np.zeros_like(evoked.data, dtype=bool)
mask[[1, 5], :] = True
plt_topomap(ch_type='mag', outlines=None)
times = [0.1]
plt_topomap(times, ch_type='grad', mask=mask)
plt_topomap(times, ch_type='planar1')
plt_topomap(times, ch_type='planar2')
plt_topomap(times, ch_type='grad', mask=mask, show_names=True,
mask_params={'marker': 'x'})
plt.close('all')
pytest.raises(ValueError, plt_topomap, times, ch_type='eeg', average=-1e3)
pytest.raises(ValueError, plt_topomap, times, ch_type='eeg', average='x')
p = plt_topomap(times, ch_type='grad', image_interp='bilinear',
show_names=lambda x: x.replace('MEG', ''))
subplot = [x for x in p.get_children() if 'Subplot' in str(type(x))]
assert len(subplot) >= 1, [type(x) for x in p.get_children()]
subplot = subplot[0]
assert (all('MEG' not in x.get_text()
for x in subplot.get_children()
if isinstance(x, matplotlib.text.Text)))
# Plot array
for ch_type in ('mag', 'grad'):
evoked_ = evoked.copy().pick_types(eeg=False, meg=ch_type)
plot_topomap(evoked_.data[:, 0], evoked_.info, **fast_test_noscale)
# fail with multiple channel types
pytest.raises(ValueError, plot_topomap, evoked.data[0, :], evoked.info)
# Test title
def get_texts(p):
return [x.get_text() for x in p.get_children() if
isinstance(x, matplotlib.text.Text)]
p = plt_topomap(times, ch_type='eeg', average=0.01)
assert_equal(len(get_texts(p)), 0)
p = plt_topomap(times, ch_type='eeg', title='Custom')
texts = get_texts(p)
assert_equal(len(texts), 1)
assert_equal(texts[0], 'Custom')
plt.close('all')
# delaunay triangulation warning
plt_topomap(times, ch_type='mag', layout=None)
# projs have already been applied
pytest.raises(RuntimeError, plot_evoked_topomap, evoked, 0.1, 'mag',
proj='interactive', time_unit='s')
# change to no-proj mode
evoked = read_evokeds(evoked_fname, 'Left Auditory',
baseline=(None, 0), proj=False)
fig1 = evoked.plot_topomap('interactive', 'mag', proj='interactive',
**fast_test)
_fake_click(fig1, fig1.axes[1], (0.5, 0.5)) # click slider
data_max = np.max(fig1.axes[0].images[0]._A)
fig2 = plt.gcf()
_fake_click(fig2, fig2.axes[0], (0.075, 0.775)) # toggle projector
# make sure projector gets toggled
assert (np.max(fig1.axes[0].images[0]._A) != data_max)
pytest.raises(RuntimeError, plot_evoked_topomap, evoked,
np.repeat(.1, 50), time_unit='s')
pytest.raises(ValueError, plot_evoked_topomap, evoked, [-3e12, 15e6],
time_unit='s')
for ch in evoked.info['chs']:
if ch['coil_type'] == FIFF.FIFFV_COIL_EEG:
ch['loc'].fill(0)
# Remove extra digitization point, so EEG digitization points
# correspond with the EEG electrodes
del evoked.info['dig'][85]
pos = make_eeg_layout(evoked.info).pos[:, :2]
pos, outlines = _check_outlines(pos, 'head')
assert ('head' in outlines.keys())
assert ('nose' in outlines.keys())
assert ('ear_left' in outlines.keys())
assert ('ear_right' in outlines.keys())
assert ('autoshrink' in outlines.keys())
assert (outlines['autoshrink'])
assert ('clip_radius' in outlines.keys())
assert_array_equal(outlines['clip_radius'], 0.5)
pos, outlines = _check_outlines(pos, 'skirt')
assert ('head' in outlines.keys())
assert ('nose' in outlines.keys())
assert ('ear_left' in outlines.keys())
assert ('ear_right' in outlines.keys())
assert ('autoshrink' in outlines.keys())
assert (not outlines['autoshrink'])
assert ('clip_radius' in outlines.keys())
assert_array_equal(outlines['clip_radius'], 0.625)
pos, outlines = _check_outlines(pos, 'skirt',
head_pos={'scale': [1.2, 1.2]})
assert_array_equal(outlines['clip_radius'], 0.75)
# Plot skirt
evoked.plot_topomap(times, ch_type='eeg', outlines='skirt', **fast_test)
# Pass custom outlines without patch
evoked.plot_topomap(times, ch_type='eeg', outlines=outlines, **fast_test)
plt.close('all')
# Test interactive cmap
fig = plot_evoked_topomap(evoked, times=[0., 0.1], ch_type='eeg',
cmap=('Reds', True), title='title', **fast_test)
fig.canvas.key_press_event('up')
fig.canvas.key_press_event(' ')
fig.canvas.key_press_event('down')
cbar = fig.get_axes()[0].CB # Fake dragging with mouse.
ax = cbar.cbar.ax
_fake_click(fig, ax, (0.1, 0.1))
_fake_click(fig, ax, (0.1, 0.2), kind='motion')
_fake_click(fig, ax, (0.1, 0.3), kind='release')
_fake_click(fig, ax, (0.1, 0.1), button=3)
_fake_click(fig, ax, (0.1, 0.2), button=3, kind='motion')
_fake_click(fig, ax, (0.1, 0.3), kind='release')
fig.canvas.scroll_event(0.5, 0.5, -0.5) # scroll down
fig.canvas.scroll_event(0.5, 0.5, 0.5) # scroll up
plt.close('all')
# Pass custom outlines with patch callable
def patch():
return Circle((0.5, 0.4687), radius=.46,
clip_on=True, transform=plt.gca().transAxes)
outlines['patch'] = patch
plot_evoked_topomap(evoked, times, ch_type='eeg', outlines=outlines,
**fast_test)
# Remove digitization points. Now topomap should fail
evoked.info['dig'] = None
pytest.raises(RuntimeError, plot_evoked_topomap, evoked,
times, ch_type='eeg', time_unit='s')
plt.close('all')
# Error for missing names
n_channels = len(pos)
data = np.ones(n_channels)
pytest.raises(ValueError, plot_topomap, data, pos, show_names=True)
# Test error messages for invalid pos parameter
pos_1d = np.zeros(n_channels)
pos_3d = np.zeros((n_channels, 2, 2))
pytest.raises(ValueError, plot_topomap, data, pos_1d)
pytest.raises(ValueError, plot_topomap, data, pos_3d)
pytest.raises(ValueError, plot_topomap, data, pos[:3, :])
pos_x = pos[:, :1]
pos_xyz = np.c_[pos, np.zeros(n_channels)[:, np.newaxis]]
pytest.raises(ValueError, plot_topomap, data, pos_x)
pytest.raises(ValueError, plot_topomap, data, pos_xyz)
# An #channels x 4 matrix should work though. In this case (x, y, width,
# height) is assumed.
pos_xywh = np.c_[pos, np.zeros((n_channels, 2))]
plot_topomap(data, pos_xywh)
plt.close('all')
# Test peak finder
axes = [plt.subplot(131), plt.subplot(132)]
evoked.plot_topomap(times='peaks', axes=axes, **fast_test)
plt.close('all')
evoked.data = np.zeros(evoked.data.shape)
evoked.data[50][1] = 1
assert_array_equal(_find_peaks(evoked, 10), evoked.times[1])
evoked.data[80][100] = 1
assert_array_equal(_find_peaks(evoked, 10), evoked.times[[1, 100]])
evoked.data[2][95] = 2
assert_array_equal(_find_peaks(evoked, 10), evoked.times[[1, 95]])
assert_array_equal(_find_peaks(evoked, 1), evoked.times[95])
# Test excluding bads channels
evoked_grad.info['bads'] += [evoked_grad.info['ch_names'][0]]
orig_bads = evoked_grad.info['bads']
evoked_grad.plot_topomap(ch_type='grad', times=[0], time_unit='ms')
assert_array_equal(evoked_grad.info['bads'], orig_bads)
plt.close('all')
from udgan.io import convert_mat_structure
data_path = 'data/2010-02-16_0009'
# Events management
raw, events, event_id = convert_mat_structure(data_path)
mne.viz.plot_events(events=events, event_id=event_id,
sfreq=raw.info['sfreq'])
event_id = {'Boop': 1, 'Beep': 2, 'Motor response': 6}
# Check raw signals
raw.plot()
# Generate topographic layout
from mne.channels import make_eeg_layout
layout = make_eeg_layout(raw.info, exclude=['MOh','MOb'])
# Generate evoked potentials
tmin, tmax = -0.2, 0.5
include = []
picks = mne.pick_types(raw.info, meg=True, eeg=True, stim=False, eog=True,
include=include, exclude='bads')
epochs = mne.Epochs(raw, events, event_id, tmin, tmax, picks=picks,
baseline=(None, 0), preload=True)
epochs.plot(trellis=False, title='Auditory odd ball')
# Visualization of neural repsonses for differ
import matplotlib.pyplot as plt
from mne.viz import plot_topomap
import numpy as np
res=16
def test_plot_topomap():
"""Test topomap plotting
"""
import matplotlib.pyplot as plt
from matplotlib.patches import Circle
# evoked
warnings.simplefilter('always')
res = 16
evoked = read_evokeds(evoked_fname, 'Left Auditory', baseline=(None, 0))
# Test animation
_, anim = evoked.animate_topomap(ch_type='grad',
times=[0, 0.1],
butterfly=False)
anim._func(1) # _animate has to be tested separately on 'Agg' backend.
plt.close('all')
ev_bad = evoked.copy().pick_types(meg=False, eeg=True)
ev_bad.pick_channels(ev_bad.ch_names[:2])
ev_bad.plot_topomap(times=ev_bad.times[:2] - 1e-6) # auto, plots EEG
assert_raises(ValueError, ev_bad.plot_topomap, ch_type='mag')
assert_raises(TypeError, ev_bad.plot_topomap, head_pos='foo')
assert_raises(KeyError, ev_bad.plot_topomap, head_pos=dict(foo='bar'))
assert_raises(ValueError, ev_bad.plot_topomap, head_pos=dict(center=0))
assert_raises(ValueError, ev_bad.plot_topomap, times=[-100]) # bad time
assert_raises(ValueError, ev_bad.plot_topomap, times=[[0]]) # bad time
assert_raises(ValueError, ev_bad.plot_topomap, times=[[0]]) # bad time
evoked.plot_topomap(0.1, layout=layout, scale=dict(mag=0.1))
plt.close('all')
axes = [plt.subplot(221), plt.subplot(222)]
evoked.plot_topomap(axes=axes, colorbar=False)
plt.close('all')
evoked.plot_topomap(times=[-0.1, 0.2])
plt.close('all')
mask = np.zeros_like(evoked.data, dtype=bool)
mask[[1, 5], :] = True
evoked.plot_topomap(ch_type='mag', outlines=None)
times = [0.1]
evoked.plot_topomap(times, ch_type='eeg', res=res, scale=1)
evoked.plot_topomap(times, ch_type='grad', mask=mask, res=res)
evoked.plot_topomap(times, ch_type='planar1', res=res)
evoked.plot_topomap(times, ch_type='planar2', res=res)
evoked.plot_topomap(times,
ch_type='grad',
mask=mask,
res=res,
show_names=True,
mask_params={'marker': 'x'})
plt.close('all')
assert_raises(ValueError,
evoked.plot_topomap,
times,
ch_type='eeg',
res=res,
average=-1000)
assert_raises(ValueError,
evoked.plot_topomap,
times,
ch_type='eeg',
res=res,
average='hahahahah')
p = evoked.plot_topomap(times,
ch_type='grad',
res=res,
show_names=lambda x: x.replace('MEG', ''),
image_interp='bilinear')
subplot = [
x for x in p.get_children() if isinstance(x, matplotlib.axes.Subplot)
][0]
assert_true(
all('MEG' not in x.get_text() for x in subplot.get_children()
if isinstance(x, matplotlib.text.Text)))
# Plot array
for ch_type in ('mag', 'grad'):
evoked_ = evoked.copy().pick_types(eeg=False, meg=ch_type)
plot_topomap(evoked_.data[:, 0], evoked_.info)
# fail with multiple channel types
assert_raises(ValueError, plot_topomap, evoked.data[0, :], evoked.info)
# Test title
def get_texts(p):
return [
x.get_text() for x in p.get_children()
if isinstance(x, matplotlib.text.Text)
]
p = evoked.plot_topomap(times, ch_type='eeg', res=res, average=0.01)
assert_equal(len(get_texts(p)), 0)
p = evoked.plot_topomap(times, ch_type='eeg', title='Custom', res=res)
texts = get_texts(p)
assert_equal(len(texts), 1)
assert_equal(texts[0], 'Custom')
plt.close('all')
# delaunay triangulation warning
with warnings.catch_warnings(record=True): # can't show
warnings.simplefilter('always')
evoked.plot_topomap(times, ch_type='mag', layout=None, res=res)
assert_raises(RuntimeError,
plot_evoked_topomap,
evoked,
0.1,
'mag',
proj='interactive') # projs have already been applied
# change to no-proj mode
evoked = read_evokeds(evoked_fname,
'Left Auditory',
baseline=(None, 0),
proj=False)
with warnings.catch_warnings(record=True):
warnings.simplefilter('always')
evoked.plot_topomap(0.1, 'mag', proj='interactive', res=res)
assert_raises(RuntimeError, plot_evoked_topomap, evoked, np.repeat(.1, 50))
assert_raises(ValueError, plot_evoked_topomap, evoked, [-3e12, 15e6])
with warnings.catch_warnings(record=True): # file conventions
warnings.simplefilter('always')
projs = read_proj(ecg_fname)
projs = [pp for pp in projs if pp['desc'].lower().find('eeg') < 0]
plot_projs_topomap(projs, res=res)
plt.close('all')
ax = plt.subplot(111)
plot_projs_topomap([projs[0]], res=res, axes=ax) # test axes param
plt.close('all')
for ch in evoked.info['chs']:
if ch['coil_type'] == FIFF.FIFFV_COIL_EEG:
ch['loc'].fill(0)
# Remove extra digitization point, so EEG digitization points
# correspond with the EEG electrodes
del evoked.info['dig'][85]
pos = make_eeg_layout(evoked.info).pos[:, :2]
pos, outlines = _check_outlines(pos, 'head')
assert_true('head' in outlines.keys())
assert_true('nose' in outlines.keys())
assert_true('ear_left' in outlines.keys())
assert_true('ear_right' in outlines.keys())
assert_true('autoshrink' in outlines.keys())
assert_true(outlines['autoshrink'])
assert_true('clip_radius' in outlines.keys())
assert_array_equal(outlines['clip_radius'], 0.5)
pos, outlines = _check_outlines(pos, 'skirt')
assert_true('head' in outlines.keys())
assert_true('nose' in outlines.keys())
assert_true('ear_left' in outlines.keys())
assert_true('ear_right' in outlines.keys())
assert_true('autoshrink' in outlines.keys())
assert_true(not outlines['autoshrink'])
assert_true('clip_radius' in outlines.keys())
assert_array_equal(outlines['clip_radius'], 0.625)
pos, outlines = _check_outlines(pos,
'skirt',
head_pos={'scale': [1.2, 1.2]})
assert_array_equal(outlines['clip_radius'], 0.75)
# Plot skirt
evoked.plot_topomap(times, ch_type='eeg', outlines='skirt')
# Pass custom outlines without patch
evoked.plot_topomap(times, ch_type='eeg', outlines=outlines)
plt.close('all')
# Pass custom outlines with patch callable
def patch():
return Circle((0.5, 0.4687),
radius=.46,
clip_on=True,
transform=plt.gca().transAxes)
outlines['patch'] = patch
plot_evoked_topomap(evoked, times, ch_type='eeg', outlines=outlines)
# Remove digitization points. Now topomap should fail
evoked.info['dig'] = None
assert_raises(RuntimeError,
plot_evoked_topomap,
evoked,
times,
ch_type='eeg')
plt.close('all')
# Error for missing names
n_channels = len(pos)
data = np.ones(n_channels)
assert_raises(ValueError, plot_topomap, data, pos, show_names=True)
# Test error messages for invalid pos parameter
pos_1d = np.zeros(n_channels)
pos_3d = np.zeros((n_channels, 2, 2))
assert_raises(ValueError, plot_topomap, data, pos_1d)
assert_raises(ValueError, plot_topomap, data, pos_3d)
assert_raises(ValueError, plot_topomap, data, pos[:3, :])
pos_x = pos[:, :1]
pos_xyz = np.c_[pos, np.zeros(n_channels)[:, np.newaxis]]
assert_raises(ValueError, plot_topomap, data, pos_x)
assert_raises(ValueError, plot_topomap, data, pos_xyz)
# An #channels x 4 matrix should work though. In this case (x, y, width,
# height) is assumed.
pos_xywh = np.c_[pos, np.zeros((n_channels, 2))]
plot_topomap(data, pos_xywh)
plt.close('all')
# Test peak finder
axes = [plt.subplot(131), plt.subplot(132)]
with warnings.catch_warnings(record=True): # rightmost column
evoked.plot_topomap(times='peaks', axes=axes)
plt.close('all')
evoked.data = np.zeros(evoked.data.shape)
evoked.data[50][1] = 1
assert_array_equal(_find_peaks(evoked, 10), evoked.times[1])
evoked.data[80][100] = 1
assert_array_equal(_find_peaks(evoked, 10), evoked.times[[1, 100]])
evoked.data[2][95] = 2
assert_array_equal(_find_peaks(evoked, 10), evoked.times[[1, 95]])
assert_array_equal(_find_peaks(evoked, 1), evoked.times[95])
def test_plot_topomap():
"""Test topomap plotting
"""
import matplotlib.pyplot as plt
from matplotlib.patches import Circle
# evoked
warnings.simplefilter('always')
res = 16
evoked = read_evokeds(evoked_fname, 'Left Auditory',
baseline=(None, 0))
ev_bad = evoked.pick_types(meg=False, eeg=True, copy=True)
ev_bad.pick_channels(ev_bad.ch_names[:2])
ev_bad.plot_topomap(times=ev_bad.times[:2] - 1e-6) # auto, should plot EEG
assert_raises(ValueError, ev_bad.plot_topomap, ch_type='mag')
assert_raises(TypeError, ev_bad.plot_topomap, head_pos='foo')
assert_raises(KeyError, ev_bad.plot_topomap, head_pos=dict(foo='bar'))
assert_raises(ValueError, ev_bad.plot_topomap, head_pos=dict(center=0))
assert_raises(ValueError, ev_bad.plot_topomap, times=[-100]) # bad time
assert_raises(ValueError, ev_bad.plot_topomap, times=[[0]]) # bad time
assert_raises(ValueError, ev_bad.plot_topomap, times=[[0]]) # bad time
evoked.plot_topomap(0.1, layout=layout, scale=dict(mag=0.1))
plt.close('all')
axes = [plt.subplot(221), plt.subplot(222)]
evoked.plot_topomap(axes=axes, colorbar=False)
plt.close('all')
evoked.plot_topomap(times=[-0.1, 0.2])
plt.close('all')
mask = np.zeros_like(evoked.data, dtype=bool)
mask[[1, 5], :] = True
evoked.plot_topomap(ch_type='mag', outlines=None)
times = [0.1]
evoked.plot_topomap(times, ch_type='eeg', res=res, scale=1)
evoked.plot_topomap(times, ch_type='grad', mask=mask, res=res)
evoked.plot_topomap(times, ch_type='planar1', res=res)
evoked.plot_topomap(times, ch_type='planar2', res=res)
evoked.plot_topomap(times, ch_type='grad', mask=mask, res=res,
show_names=True, mask_params={'marker': 'x'})
plt.close('all')
assert_raises(ValueError, evoked.plot_topomap, times, ch_type='eeg',
res=res, average=-1000)
assert_raises(ValueError, evoked.plot_topomap, times, ch_type='eeg',
res=res, average='hahahahah')
p = evoked.plot_topomap(times, ch_type='grad', res=res,
show_names=lambda x: x.replace('MEG', ''),
image_interp='bilinear')
subplot = [x for x in p.get_children() if
isinstance(x, matplotlib.axes.Subplot)][0]
assert_true(all('MEG' not in x.get_text()
for x in subplot.get_children()
if isinstance(x, matplotlib.text.Text)))
# Test title
def get_texts(p):
return [x.get_text() for x in p.get_children() if
isinstance(x, matplotlib.text.Text)]
p = evoked.plot_topomap(times, ch_type='eeg', res=res, average=0.01)
assert_equal(len(get_texts(p)), 0)
p = evoked.plot_topomap(times, ch_type='eeg', title='Custom', res=res)
texts = get_texts(p)
assert_equal(len(texts), 1)
assert_equal(texts[0], 'Custom')
plt.close('all')
# delaunay triangulation warning
with warnings.catch_warnings(record=True): # can't show
warnings.simplefilter('always')
evoked.plot_topomap(times, ch_type='mag', layout=None, res=res)
assert_raises(RuntimeError, plot_evoked_topomap, evoked, 0.1, 'mag',
proj='interactive') # projs have already been applied
# change to no-proj mode
evoked = read_evokeds(evoked_fname, 'Left Auditory',
baseline=(None, 0), proj=False)
with warnings.catch_warnings(record=True):
warnings.simplefilter('always')
evoked.plot_topomap(0.1, 'mag', proj='interactive', res=res)
assert_raises(RuntimeError, plot_evoked_topomap, evoked,
np.repeat(.1, 50))
assert_raises(ValueError, plot_evoked_topomap, evoked, [-3e12, 15e6])
with warnings.catch_warnings(record=True): # file conventions
warnings.simplefilter('always')
projs = read_proj(ecg_fname)
projs = [pp for pp in projs if pp['desc'].lower().find('eeg') < 0]
plot_projs_topomap(projs, res=res)
plt.close('all')
ax = plt.subplot(111)
plot_projs_topomap([projs[0]], res=res, axes=ax) # test axes param
plt.close('all')
for ch in evoked.info['chs']:
if ch['coil_type'] == FIFF.FIFFV_COIL_EEG:
ch['loc'].fill(0)
# Remove extra digitization point, so EEG digitization points
# correspond with the EEG electrodes
del evoked.info['dig'][85]
pos = make_eeg_layout(evoked.info).pos[:, :2]
pos, outlines = _check_outlines(pos, 'head')
assert_true('head' in outlines.keys())
assert_true('nose' in outlines.keys())
assert_true('ear_left' in outlines.keys())
assert_true('ear_right' in outlines.keys())
assert_true('autoshrink' in outlines.keys())
assert_true(outlines['autoshrink'])
assert_true('clip_radius' in outlines.keys())
assert_array_equal(outlines['clip_radius'], 0.5)
pos, outlines = _check_outlines(pos, 'skirt')
assert_true('head' in outlines.keys())
assert_true('nose' in outlines.keys())
assert_true('ear_left' in outlines.keys())
assert_true('ear_right' in outlines.keys())
assert_true('autoshrink' in outlines.keys())
assert_true(not outlines['autoshrink'])
assert_true('clip_radius' in outlines.keys())
assert_array_equal(outlines['clip_radius'], 0.625)
pos, outlines = _check_outlines(pos, 'skirt',
head_pos={'scale': [1.2, 1.2]})
assert_array_equal(outlines['clip_radius'], 0.75)
# Plot skirt
evoked.plot_topomap(times, ch_type='eeg', outlines='skirt')
# Pass custom outlines without patch
evoked.plot_topomap(times, ch_type='eeg', outlines=outlines)
plt.close('all')
# Pass custom outlines with patch callable
def patch():
return Circle((0.5, 0.4687), radius=.46,
clip_on=True, transform=plt.gca().transAxes)
outlines['patch'] = patch
plot_evoked_topomap(evoked, times, ch_type='eeg', outlines=outlines)
# Remove digitization points. Now topomap should fail
evoked.info['dig'] = None
assert_raises(RuntimeError, plot_evoked_topomap, evoked,
times, ch_type='eeg')
plt.close('all')
# Error for missing names
n_channels = len(pos)
data = np.ones(n_channels)
assert_raises(ValueError, plot_topomap, data, pos, show_names=True)
# Test error messages for invalid pos parameter
pos_1d = np.zeros(n_channels)
pos_3d = np.zeros((n_channels, 2, 2))
assert_raises(ValueError, plot_topomap, data, pos_1d)
assert_raises(ValueError, plot_topomap, data, pos_3d)
assert_raises(ValueError, plot_topomap, data, pos[:3, :])
pos_x = pos[:, :1]
pos_xyz = np.c_[pos, np.zeros(n_channels)[:, np.newaxis]]
assert_raises(ValueError, plot_topomap, data, pos_x)
assert_raises(ValueError, plot_topomap, data, pos_xyz)
# An #channels x 4 matrix should work though. In this case (x, y, width,
# height) is assumed.
pos_xywh = np.c_[pos, np.zeros((n_channels, 2))]
plot_topomap(data, pos_xywh)
plt.close('all')
# Test peak finder
axes = [plt.subplot(131), plt.subplot(132)]
evoked.plot_topomap(times='peaks', axes=axes)
plt.close('all')
evoked.data = np.zeros(evoked.data.shape)
evoked.data[50][1] = 1
assert_array_equal(_find_peaks(evoked, 10), evoked.times[1])
evoked.data[80][100] = 1
assert_array_equal(_find_peaks(evoked, 10), evoked.times[[1, 100]])
evoked.data[2][95] = 2
assert_array_equal(_find_peaks(evoked, 10), evoked.times[[1, 95]])
assert_array_equal(_find_peaks(evoked, 1), evoked.times[95])
def test_plot_topomap():
"""Test topomap plotting
"""
import matplotlib.pyplot as plt
from matplotlib.patches import Circle
# evoked
warnings.simplefilter('always')
res = 16
evoked = read_evokeds(evoked_fname, 'Left Auditory',
baseline=(None, 0))
ev_bad = evoked.pick_types(meg=False, eeg=True, copy=True)
ev_bad.pick_channels(ev_bad.ch_names[:2])
ev_bad.plot_topomap(times=ev_bad.times[:2] - 1e-6) # auto, should plot EEG
assert_raises(ValueError, ev_bad.plot_topomap, ch_type='mag')
assert_raises(TypeError, ev_bad.plot_topomap, head_pos='foo')
assert_raises(KeyError, ev_bad.plot_topomap, head_pos=dict(foo='bar'))
assert_raises(ValueError, ev_bad.plot_topomap, head_pos=dict(center=0))
assert_raises(ValueError, ev_bad.plot_topomap, times=[-100]) # bad time
assert_raises(ValueError, ev_bad.plot_topomap, times=[[0]]) # bad time
evoked.plot_topomap(0.1, layout=layout, scale=dict(mag=0.1))
plt.close('all')
axes = [plt.subplot(221), plt.subplot(222)]
evoked.plot_topomap(axes=axes, colorbar=False)
plt.close('all')
evoked.plot_topomap(times=[-0.1, 0.2])
plt.close('all')
mask = np.zeros_like(evoked.data, dtype=bool)
mask[[1, 5], :] = True
evoked.plot_topomap(None, ch_type='mag', outlines=None)
times = [0.1]
evoked.plot_topomap(times, ch_type='eeg', res=res, scale=1)
evoked.plot_topomap(times, ch_type='grad', mask=mask, res=res)
evoked.plot_topomap(times, ch_type='planar1', res=res)
evoked.plot_topomap(times, ch_type='planar2', res=res)
evoked.plot_topomap(times, ch_type='grad', mask=mask, res=res,
show_names=True, mask_params={'marker': 'x'})
plt.close('all')
assert_raises(ValueError, evoked.plot_topomap, times, ch_type='eeg',
res=res, average=-1000)
assert_raises(ValueError, evoked.plot_topomap, times, ch_type='eeg',
res=res, average='hahahahah')
p = evoked.plot_topomap(times, ch_type='grad', res=res,
show_names=lambda x: x.replace('MEG', ''),
image_interp='bilinear')
subplot = [x for x in p.get_children() if
isinstance(x, matplotlib.axes.Subplot)][0]
assert_true(all('MEG' not in x.get_text()
for x in subplot.get_children()
if isinstance(x, matplotlib.text.Text)))
# Test title
def get_texts(p):
return [x.get_text() for x in p.get_children() if
isinstance(x, matplotlib.text.Text)]
p = evoked.plot_topomap(times, ch_type='eeg', res=res, average=0.01)
assert_equal(len(get_texts(p)), 0)
p = evoked.plot_topomap(times, ch_type='eeg', title='Custom', res=res)
texts = get_texts(p)
assert_equal(len(texts), 1)
assert_equal(texts[0], 'Custom')
plt.close('all')
# delaunay triangulation warning
with warnings.catch_warnings(record=True): # can't show
warnings.simplefilter('always')
evoked.plot_topomap(times, ch_type='mag', layout=None, res=res)
assert_raises(RuntimeError, plot_evoked_topomap, evoked, 0.1, 'mag',
proj='interactive') # projs have already been applied
# change to no-proj mode
evoked = read_evokeds(evoked_fname, 'Left Auditory',
baseline=(None, 0), proj=False)
with warnings.catch_warnings(record=True):
warnings.simplefilter('always')
evoked.plot_topomap(0.1, 'mag', proj='interactive', res=res)
assert_raises(RuntimeError, plot_evoked_topomap, evoked,
np.repeat(.1, 50))
assert_raises(ValueError, plot_evoked_topomap, evoked, [-3e12, 15e6])
with warnings.catch_warnings(record=True): # file conventions
warnings.simplefilter('always')
projs = read_proj(ecg_fname)
projs = [pp for pp in projs if pp['desc'].lower().find('eeg') < 0]
plot_projs_topomap(projs, res=res)
plt.close('all')
ax = plt.subplot(111)
plot_projs_topomap([projs[0]], res=res, axes=ax) # test axes param
plt.close('all')
for ch in evoked.info['chs']:
if ch['coil_type'] == FIFF.FIFFV_COIL_EEG:
if ch['eeg_loc'] is not None:
ch['eeg_loc'].fill(0)
ch['loc'].fill(0)
# Remove extra digitization point, so EEG digitization points
# correspond with the EEG electrodes
del evoked.info['dig'][85]
pos = make_eeg_layout(evoked.info).pos
pos, outlines = _check_outlines(pos, 'head')
assert_true('head' in outlines.keys())
assert_true('nose' in outlines.keys())
assert_true('ear_left' in outlines.keys())
assert_true('ear_right' in outlines.keys())
assert_true('autoshrink' in outlines.keys())
assert_true(outlines['autoshrink'])
assert_true('clip_radius' in outlines.keys())
assert_array_equal(outlines['clip_radius'], 0.5)
pos, outlines = _check_outlines(pos, 'skirt')
assert_true('head' in outlines.keys())
assert_true('nose' in outlines.keys())
assert_true('ear_left' in outlines.keys())
assert_true('ear_right' in outlines.keys())
assert_true('autoshrink' in outlines.keys())
assert_true(not outlines['autoshrink'])
assert_true('clip_radius' in outlines.keys())
assert_array_equal(outlines['clip_radius'], 0.625)
pos, outlines = _check_outlines(pos, 'skirt',
head_pos={'scale': [1.2, 1.2]})
assert_array_equal(outlines['clip_radius'], 0.75)
# Plot skirt
evoked.plot_topomap(times, ch_type='eeg', outlines='skirt')
# Pass custom outlines without patch
evoked.plot_topomap(times, ch_type='eeg', outlines=outlines)
plt.close('all')
# Pass custom outlines with patch callable
def patch():
return Circle((0.5, 0.4687), radius=.46,
clip_on=True, transform=plt.gca().transAxes)
outlines['patch'] = patch
plot_evoked_topomap(evoked, times, ch_type='eeg', outlines=outlines)
# Remove digitization points. Now topomap should fail
evoked.info['dig'] = None
assert_raises(RuntimeError, plot_evoked_topomap, evoked,
times, ch_type='eeg')
plt.close('all')