def visualise(exp_num,main_title,*args):
layout = find_layout(info, ch_type='grad')
number_of_heads = len(args)
tmp = [list(l) for l in zip(*args)]
titles = tmp[0]
data = tmp[1]
max_row_lenght = 5 #depends from monitor length (:
fig,axes=plt.subplots(-(-number_of_heads//max_row_lenght),min(max_row_lenght,number_of_heads),figsize=(20, 20))
fig.suptitle(main_title, fontsize=14)
min_value = np.array(map(lambda x:x.min(),data)).min()
max_value = np.array(map(lambda x:x.max(),data)).max()
for i in range(number_of_heads):
axes[np.unravel_index(i,axes.shape)].set_title(titles[i])
if data[i].any():
im,_ = plot_topomap(data[i],layout.pos,axes=axes[np.unravel_index(i,axes.shape)],
vmin=min_value,vmax=max_value,show=False)
fig.colorbar(im,ax=axes.ravel().tolist(),shrink=0.3,fraction=0.025)
save_fig(exp_num,main_title,fig)
def __init__(self, sensor_type='mag'):
# @sensor_type "mag" or "grad"
sensor_type = sensor_type
code_dir = os.path.dirname(os.path.realpath(__file__))
info_path = os.path.join(code_dir, 'neuromag_info')
if (sensor_type == 'mag'):
neighboring_filename = os.path.join(info_path,
'neuromag306mag_neighb.mat')
if (sensor_type == 'grad'):
neighboring_filename = os.path.join(
info_path, 'neuromag306planar_neighb.mat')
neuromag = read_raw_fif(sample.data_path() +
'/MEG/sample/sample_audvis_raw.fif')
self.topography_2D = find_layout(neuromag.info,
ch_type=sensor_type).pos
topography_3D = np.array([
ch['loc'][:3] for ch in neuromag.info['chs']
if (ch['ch_name'][-1] == '1') & (ch['ch_name'][0:3] == 'MEG')
])
neighboring, ch_names = read_ch_connectivity(
neighboring_filename,
picks=None) #ch. names written in 'MEG1111' format
neighboring = neighboring.toarray()
num_channels = len(ch_names)
Convolutions.__init__(self, neighboring, topography_3D, ch_names,
num_channels)
def __init__(self,sensor_type = 'mag'):
# sensor_type - mag or grad. Grad not yet implemented
code_dir = os.path.dirname(os.path.realpath(__file__))
info_path = os.path.join(code_dir, 'neuromag_info')
neuromag = read_raw_fif(sample.data_path() +
'/MEG/sample/sample_audvis_raw.fif')
topography_2D = find_layout(neuromag.info, ch_type=sensor_type).pos[:,:2]
if (sensor_type == 'mag'):
topography_3D = np.array([ch['loc'][:3] for ch in neuromag.info['chs'] if
(ch['ch_name'][-1] == '1') &
(ch['ch_name'][0:3] == 'MEG')]) #Numbers of mag sensors ended by '1'
neighboring_filename = os.path.join(info_path, 'neuromag306mag_neighb.mat')
if (sensor_type == 'grad'):
topography_3D = np.array([ch['loc'][:3] for ch in neuromag.info['chs'] if
((ch['ch_name'][-1] == '2') | (ch['ch_name'][-1] == '3')) &
(ch['ch_name'][0:3] == 'MEG')]) # Numbers of grad sensors ended by '2' or '3'
neighboring_filename = os.path.join(info_path, 'neuromag306planar_neighb.mat')
neighboring, ch_names = read_ch_connectivity(neighboring_filename,
picks=None) # ch. names written in 'MEG1111' format
neighboring = neighboring.toarray()
num_channels = len(ch_names)
self.sensor_type = sensor_type
Device.__init__(self,ch_names, topography_3D, topography_2D, neighboring, num_channels)
def visualise(t_data, p_data, sensor_type, freq):
#reseives t-values (and optionaly p-values) as vectors [channel x 1]
layout = find_layout(info, ch_type=sensor_type.lower())
im, _ = plot_topomap(data=t_data,
pos=layout.pos,
show=False,
vmin=-4.5,
vmax=4.5)
plt.colorbar(im)
title = 'fq=%d_min_p=%0.4f' % (freq, p_data.min())
plt.title(title)
return title
def test_find_layout():
"""Test finding layout."""
pytest.raises(ValueError, find_layout, _get_test_info(), ch_type='meep')
sample_info = read_info(fif_fname)
grads = pick_types(sample_info, meg='grad')
sample_info2 = pick_info(sample_info, grads)
mags = pick_types(sample_info, meg='mag')
sample_info3 = pick_info(sample_info, mags)
# mock new convention
sample_info4 = copy.deepcopy(sample_info)
for ii, name in enumerate(sample_info4['ch_names']):
new = name.replace(' ', '')
sample_info4['chs'][ii]['ch_name'] = new
eegs = pick_types(sample_info, meg=False, eeg=True)
sample_info5 = pick_info(sample_info, eegs)
lout = find_layout(sample_info, ch_type=None)
assert lout.kind == 'Vectorview-all'
assert all(' ' in k for k in lout.names)
lout = find_layout(sample_info2, ch_type='meg')
assert_equal(lout.kind, 'Vectorview-all')
# test new vector-view
lout = find_layout(sample_info4, ch_type=None)
assert_equal(lout.kind, 'Vectorview-all')
assert all(' ' not in k for k in lout.names)
lout = find_layout(sample_info, ch_type='grad')
assert_equal(lout.kind, 'Vectorview-grad')
lout = find_layout(sample_info2)
assert_equal(lout.kind, 'Vectorview-grad')
lout = find_layout(sample_info2, ch_type='grad')
assert_equal(lout.kind, 'Vectorview-grad')
lout = find_layout(sample_info2, ch_type='meg')
assert_equal(lout.kind, 'Vectorview-all')
lout = find_layout(sample_info, ch_type='mag')
assert_equal(lout.kind, 'Vectorview-mag')
lout = find_layout(sample_info3)
assert_equal(lout.kind, 'Vectorview-mag')
lout = find_layout(sample_info3, ch_type='mag')
assert_equal(lout.kind, 'Vectorview-mag')
lout = find_layout(sample_info3, ch_type='meg')
assert_equal(lout.kind, 'Vectorview-all')
lout = find_layout(sample_info, ch_type='eeg')
assert_equal(lout.kind, 'EEG')
lout = find_layout(sample_info5)
assert_equal(lout.kind, 'EEG')
lout = find_layout(sample_info5, ch_type='eeg')
assert_equal(lout.kind, 'EEG')
# no common layout, 'meg' option not supported
lout = find_layout(read_info(fname_ctf_raw))
assert_equal(lout.kind, 'CTF-275')
fname_bti_raw = op.join(bti_dir, 'exported4D_linux_raw.fif')
lout = find_layout(read_info(fname_bti_raw))
assert_equal(lout.kind, 'magnesWH3600')
raw_kit = read_raw_kit(fname_kit_157)
lout = find_layout(raw_kit.info)
assert_equal(lout.kind, 'KIT-157')
raw_kit.info['bads'] = ['MEG 013', 'MEG 014', 'MEG 015', 'MEG 016']
raw_kit.info._check_consistency()
lout = find_layout(raw_kit.info)
assert_equal(lout.kind, 'KIT-157')
# fallback for missing IDs
for val in (35, 52, 54, 1001):
raw_kit.info['kit_system_id'] = val
lout = find_layout(raw_kit.info)
assert lout.kind == 'custom'
raw_umd = read_raw_kit(fname_kit_umd)
lout = find_layout(raw_umd.info)
assert_equal(lout.kind, 'KIT-UMD-3')
# Test plotting
lout.plot()
lout.plot(picks=np.arange(10))
plt.close('all')
def test_find_layout():
"""Test finding layout"""
assert_raises(ValueError, find_layout, test_info, ch_type='meep')
sample_info = Raw(fif_fname).info
grads = pick_types(sample_info, meg='grad')
sample_info2 = pick_info(sample_info, grads)
mags = pick_types(sample_info, meg='mag')
sample_info3 = pick_info(sample_info, mags)
# mock new convention
sample_info4 = copy.deepcopy(sample_info)
for ii, name in enumerate(sample_info4['ch_names']):
new = name.replace(' ', '')
sample_info4['ch_names'][ii] = new
sample_info4['chs'][ii]['ch_name'] = new
eegs = pick_types(sample_info, meg=False, eeg=True)
sample_info5 = pick_info(sample_info, eegs)
lout = find_layout(sample_info, ch_type=None)
assert_true(lout.kind == 'Vectorview-all')
assert_true(all(' ' in k for k in lout.names))
lout = find_layout(sample_info2, ch_type='meg')
assert_true(lout.kind == 'Vectorview-all')
# test new vector-view
lout = find_layout(sample_info4, ch_type=None)
assert_true(lout.kind == 'Vectorview-all')
assert_true(all(' ' not in k for k in lout.names))
lout = find_layout(sample_info, ch_type='grad')
assert_true(lout.kind == 'Vectorview-grad')
lout = find_layout(sample_info2)
assert_true(lout.kind == 'Vectorview-grad')
lout = find_layout(sample_info2, ch_type='grad')
assert_true(lout.kind == 'Vectorview-grad')
lout = find_layout(sample_info2, ch_type='meg')
assert_true(lout.kind == 'Vectorview-all')
lout = find_layout(sample_info, ch_type='mag')
assert_true(lout.kind == 'Vectorview-mag')
lout = find_layout(sample_info3)
assert_true(lout.kind == 'Vectorview-mag')
lout = find_layout(sample_info3, ch_type='mag')
assert_true(lout.kind == 'Vectorview-mag')
lout = find_layout(sample_info3, ch_type='meg')
assert_true(lout.kind == 'Vectorview-all')
lout = find_layout(sample_info, ch_type='eeg')
assert_true(lout.kind == 'EEG')
lout = find_layout(sample_info5)
assert_true(lout.kind == 'EEG')
lout = find_layout(sample_info5, ch_type='eeg')
assert_true(lout.kind == 'EEG')
# no common layout, 'meg' option not supported
fname_bti_raw = op.join(bti_dir, 'exported4D_linux_raw.fif')
lout = find_layout(Raw(fname_bti_raw).info)
assert_true(lout.kind == 'magnesWH3600')
lout = find_layout(Raw(fname_ctf_raw).info)
assert_true(lout.kind == 'CTF-275')
lout = find_layout(read_raw_kit(fname_kit_157).info)
assert_true(lout.kind == 'KIT-157')
def test_find_layout():
"""Test finding layout"""
import matplotlib.pyplot as plt
assert_raises(ValueError, find_layout, _get_test_info(), ch_type='meep')
sample_info = read_info(fif_fname)
grads = pick_types(sample_info, meg='grad')
sample_info2 = pick_info(sample_info, grads)
mags = pick_types(sample_info, meg='mag')
sample_info3 = pick_info(sample_info, mags)
# mock new convention
sample_info4 = copy.deepcopy(sample_info)
for ii, name in enumerate(sample_info4['ch_names']):
new = name.replace(' ', '')
sample_info4['chs'][ii]['ch_name'] = new
eegs = pick_types(sample_info, meg=False, eeg=True)
sample_info5 = pick_info(sample_info, eegs)
lout = find_layout(sample_info, ch_type=None)
assert_equal(lout.kind, 'Vectorview-all')
assert_true(all(' ' in k for k in lout.names))
lout = find_layout(sample_info2, ch_type='meg')
assert_equal(lout.kind, 'Vectorview-all')
# test new vector-view
lout = find_layout(sample_info4, ch_type=None)
assert_equal(lout.kind, 'Vectorview-all')
assert_true(all(' ' not in k for k in lout.names))
lout = find_layout(sample_info, ch_type='grad')
assert_equal(lout.kind, 'Vectorview-grad')
lout = find_layout(sample_info2)
assert_equal(lout.kind, 'Vectorview-grad')
lout = find_layout(sample_info2, ch_type='grad')
assert_equal(lout.kind, 'Vectorview-grad')
lout = find_layout(sample_info2, ch_type='meg')
assert_equal(lout.kind, 'Vectorview-all')
lout = find_layout(sample_info, ch_type='mag')
assert_equal(lout.kind, 'Vectorview-mag')
lout = find_layout(sample_info3)
assert_equal(lout.kind, 'Vectorview-mag')
lout = find_layout(sample_info3, ch_type='mag')
assert_equal(lout.kind, 'Vectorview-mag')
lout = find_layout(sample_info3, ch_type='meg')
assert_equal(lout.kind, 'Vectorview-all')
lout = find_layout(sample_info, ch_type='eeg')
assert_equal(lout.kind, 'EEG')
lout = find_layout(sample_info5)
assert_equal(lout.kind, 'EEG')
lout = find_layout(sample_info5, ch_type='eeg')
assert_equal(lout.kind, 'EEG')
# no common layout, 'meg' option not supported
lout = find_layout(read_info(fname_ctf_raw))
assert_equal(lout.kind, 'CTF-275')
fname_bti_raw = op.join(bti_dir, 'exported4D_linux_raw.fif')
lout = find_layout(read_info(fname_bti_raw))
assert_equal(lout.kind, 'magnesWH3600')
raw_kit = read_raw_kit(fname_kit_157)
lout = find_layout(raw_kit.info)
assert_equal(lout.kind, 'KIT-157')
raw_kit.info['bads'] = ['MEG 13', 'MEG 14', 'MEG 15', 'MEG 16']
lout = find_layout(raw_kit.info)
assert_equal(lout.kind, 'KIT-157')
raw_umd = read_raw_kit(fname_kit_umd)
lout = find_layout(raw_umd.info)
assert_equal(lout.kind, 'KIT-UMD-3')
# Test plotting
lout.plot()
lout.plot(picks=np.arange(10))
plt.close('all')
def test_find_layout():
"""Test finding layout"""
import matplotlib.pyplot as plt
assert_raises(ValueError, find_layout, _get_test_info(), ch_type='meep')
sample_info = Raw(fif_fname).info
grads = pick_types(sample_info, meg='grad')
sample_info2 = pick_info(sample_info, grads)
mags = pick_types(sample_info, meg='mag')
sample_info3 = pick_info(sample_info, mags)
# mock new convention
sample_info4 = copy.deepcopy(sample_info)
for ii, name in enumerate(sample_info4['ch_names']):
new = name.replace(' ', '')
sample_info4['chs'][ii]['ch_name'] = new
eegs = pick_types(sample_info, meg=False, eeg=True)
sample_info5 = pick_info(sample_info, eegs)
lout = find_layout(sample_info, ch_type=None)
assert_equal(lout.kind, 'Vectorview-all')
assert_true(all(' ' in k for k in lout.names))
lout = find_layout(sample_info2, ch_type='meg')
assert_equal(lout.kind, 'Vectorview-all')
# test new vector-view
lout = find_layout(sample_info4, ch_type=None)
assert_equal(lout.kind, 'Vectorview-all')
assert_true(all(' ' not in k for k in lout.names))
lout = find_layout(sample_info, ch_type='grad')
assert_equal(lout.kind, 'Vectorview-grad')
lout = find_layout(sample_info2)
assert_equal(lout.kind, 'Vectorview-grad')
lout = find_layout(sample_info2, ch_type='grad')
assert_equal(lout.kind, 'Vectorview-grad')
lout = find_layout(sample_info2, ch_type='meg')
assert_equal(lout.kind, 'Vectorview-all')
lout = find_layout(sample_info, ch_type='mag')
assert_equal(lout.kind, 'Vectorview-mag')
lout = find_layout(sample_info3)
assert_equal(lout.kind, 'Vectorview-mag')
lout = find_layout(sample_info3, ch_type='mag')
assert_equal(lout.kind, 'Vectorview-mag')
lout = find_layout(sample_info3, ch_type='meg')
assert_equal(lout.kind, 'Vectorview-all')
lout = find_layout(sample_info, ch_type='eeg')
assert_equal(lout.kind, 'EEG')
lout = find_layout(sample_info5)
assert_equal(lout.kind, 'EEG')
lout = find_layout(sample_info5, ch_type='eeg')
assert_equal(lout.kind, 'EEG')
# no common layout, 'meg' option not supported
lout = find_layout(Raw(fname_ctf_raw).info)
assert_equal(lout.kind, 'CTF-275')
fname_bti_raw = op.join(bti_dir, 'exported4D_linux_raw.fif')
lout = find_layout(Raw(fname_bti_raw).info)
assert_equal(lout.kind, 'magnesWH3600')
raw_kit = read_raw_kit(fname_kit_157)
lout = find_layout(raw_kit.info)
assert_equal(lout.kind, 'KIT-157')
raw_kit.info['bads'] = ['MEG 13', 'MEG 14', 'MEG 15', 'MEG 16']
lout = find_layout(raw_kit.info)
assert_equal(lout.kind, 'KIT-157')
raw_umd = read_raw_kit(fname_kit_umd)
lout = find_layout(raw_umd.info)
assert_equal(lout.kind, 'KIT-UMD-3')
# Test plotting
lout.plot()
plt.close('all')
##############################################################################
# The results of these mass univariate analyses can be visualised by plotting
# :class:`mne.Evoked` objects as images (via :class:`mne.Evoked.plot_image`)
# and masking points for significance.
# Here, we group channels by Regions of Interest to facilitate localising
# effects on the head.
# We need an evoked object to plot the image to be masked
evoked = mne.combine_evoked([long.average(), -short.average()],
weights='equal') # calculate difference wave
time_unit = dict(time_unit="s")
evoked.plot_joint(title="Long vs. short words", ts_args=time_unit,
topomap_args=time_unit) # show difference wave
# Create ROIs by checking channel labels
pos = find_layout(epochs.info).pos
rois = dict()
for pick, channel in enumerate(epochs.ch_names):
last_char = channel[-1] # for 10/20, last letter codes the hemisphere
roi = ("Midline" if last_char in "z12" else
("Left" if int(last_char) % 2 else "Right"))
rois[roi] = rois.get(roi, list()) + [pick]
# sort channels from front to center
# (y-coordinate of the position info in the layout)
rois = {roi: np.array(picks)[pos[picks, 1].argsort()]
for roi, picks in rois.items()}
# Visualize the results
fig, axes = plt.subplots(nrows=3, figsize=(8, 8))
vmax = np.abs(evoked.data).max() * 1e6
def test_find_layout():
"""Test finding layout"""
import matplotlib.pyplot as plt
assert_raises(ValueError, find_layout, _get_test_info(), ch_type="meep")
sample_info = Raw(fif_fname).info
grads = pick_types(sample_info, meg="grad")
sample_info2 = pick_info(sample_info, grads)
mags = pick_types(sample_info, meg="mag")
sample_info3 = pick_info(sample_info, mags)
# mock new convention
sample_info4 = copy.deepcopy(sample_info)
for ii, name in enumerate(sample_info4["ch_names"]):
new = name.replace(" ", "")
sample_info4["chs"][ii]["ch_name"] = new
eegs = pick_types(sample_info, meg=False, eeg=True)
sample_info5 = pick_info(sample_info, eegs)
lout = find_layout(sample_info, ch_type=None)
assert_true(lout.kind == "Vectorview-all")
assert_true(all(" " in k for k in lout.names))
lout = find_layout(sample_info2, ch_type="meg")
assert_true(lout.kind == "Vectorview-all")
# test new vector-view
lout = find_layout(sample_info4, ch_type=None)
assert_true(lout.kind == "Vectorview-all")
assert_true(all(" " not in k for k in lout.names))
lout = find_layout(sample_info, ch_type="grad")
assert_true(lout.kind == "Vectorview-grad")
lout = find_layout(sample_info2)
assert_true(lout.kind == "Vectorview-grad")
lout = find_layout(sample_info2, ch_type="grad")
assert_true(lout.kind == "Vectorview-grad")
lout = find_layout(sample_info2, ch_type="meg")
assert_true(lout.kind == "Vectorview-all")
lout = find_layout(sample_info, ch_type="mag")
assert_true(lout.kind == "Vectorview-mag")
lout = find_layout(sample_info3)
assert_true(lout.kind == "Vectorview-mag")
lout = find_layout(sample_info3, ch_type="mag")
assert_true(lout.kind == "Vectorview-mag")
lout = find_layout(sample_info3, ch_type="meg")
assert_true(lout.kind == "Vectorview-all")
lout = find_layout(sample_info, ch_type="eeg")
assert_true(lout.kind == "EEG")
lout = find_layout(sample_info5)
assert_true(lout.kind == "EEG")
lout = find_layout(sample_info5, ch_type="eeg")
assert_true(lout.kind == "EEG")
# no common layout, 'meg' option not supported
fname_bti_raw = op.join(bti_dir, "exported4D_linux_raw.fif")
lout = find_layout(Raw(fname_bti_raw).info)
assert_true(lout.kind == "magnesWH3600")
lout = find_layout(Raw(fname_ctf_raw).info)
assert_true(lout.kind == "CTF-275")
lout = find_layout(read_raw_kit(fname_kit_157).info)
assert_true(lout.kind == "KIT-157")
# Test plotting
lout.plot()
plt.close("all")
