def test_remove():
"""Test removing figures from a report."""
r = Report()
fig1, fig2 = _get_example_figures()
r.add_figs_to_section(fig1, 'figure1', 'mysection')
r.add_slider_to_section([fig1, fig2],
title='figure1',
section='othersection')
r.add_figs_to_section(fig2, 'figure1', 'mysection')
r.add_figs_to_section(fig2, 'figure2', 'mysection')
# Test removal by caption
r2 = copy.deepcopy(r)
removed_index = r2.remove(caption='figure1')
assert removed_index == 2
assert len(r2.html) == 3
assert r2.html[0] == r.html[0]
assert r2.html[1] == r.html[1]
assert r2.html[2] == r.html[3]
# Test restricting to section
r2 = copy.deepcopy(r)
removed_index = r2.remove(caption='figure1', section='othersection')
assert removed_index == 1
assert len(r2.html) == 3
assert r2.html[0] == r.html[0]
assert r2.html[1] == r.html[2]
assert r2.html[2] == r.html[3]
# Test removal of empty sections
r2 = copy.deepcopy(r)
r2.remove(caption='figure1', section='othersection')
assert r2.sections == ['mysection']
assert r2._sectionvars == {'mysection': 'report_mysection'}
def test_remove():
"""Test removing figures from a report."""
r = Report()
fig1, fig2 = _get_example_figures()
r.add_figs_to_section(fig1, 'figure1', 'mysection')
r.add_slider_to_section([fig1, fig2], title='figure1',
section='othersection')
r.add_figs_to_section(fig2, 'figure1', 'mysection')
r.add_figs_to_section(fig2, 'figure2', 'mysection')
# Test removal by caption
r2 = copy.deepcopy(r)
removed_index = r2.remove(caption='figure1')
assert removed_index == 2
assert len(r2.html) == 3
assert r2.html[0] == r.html[0]
assert r2.html[1] == r.html[1]
assert r2.html[2] == r.html[3]
# Test restricting to section
r2 = copy.deepcopy(r)
removed_index = r2.remove(caption='figure1', section='othersection')
assert removed_index == 1
assert len(r2.html) == 3
assert r2.html[0] == r.html[0]
assert r2.html[1] == r.html[2]
assert r2.html[2] == r.html[3]
# Test removal of empty sections
r2 = copy.deepcopy(r)
r2.remove(caption='figure1', section='othersection')
assert r2.sections == ['mysection']
assert r2._sectionvars == {'mysection': 'report_mysection'}
def test_add_slider_to_section():
"""Test adding a slider with a series of images to mne report."""
tempdir = _TempDir()
from matplotlib import pyplot as plt
report = Report(info_fname=raw_fname,
subject='sample', subjects_dir=subjects_dir)
section = 'slider_section'
figs = list()
figs.append(plt.figure())
plt.plot([1, 2, 3])
plt.close('all')
figs.append(plt.figure())
plt.plot([3, 2, 1])
plt.close('all')
report.add_slider_to_section(figs, section=section)
report.save(op.join(tempdir, 'report.html'), open_browser=False)
assert_raises(NotImplementedError, report.add_slider_to_section,
[figs, figs])
assert_raises(ValueError, report.add_slider_to_section, figs, ['wug'])
assert_raises(TypeError, report.add_slider_to_section, figs, 'wug')
# need at least 2
assert_raises(ValueError, report.add_slider_to_section, figs[:1], 'wug')
# Smoke test that SVG w/unicode can be added
report = Report()
fig, ax = plt.subplots()
ax.set_xlabel(u'μ')
report.add_slider_to_section([fig] * 2, image_format='svg')
def test_add_slider_to_section():
"""Test adding a slider with a series of images to mne report."""
tempdir = _TempDir()
from matplotlib import pyplot as plt
report = Report(info_fname=raw_fname,
subject='sample',
subjects_dir=subjects_dir)
section = 'slider_section'
figs = list()
figs.append(plt.figure())
plt.plot([1, 2, 3])
plt.close('all')
figs.append(plt.figure())
plt.plot([3, 2, 1])
plt.close('all')
report.add_slider_to_section(figs, section=section)
report.save(op.join(tempdir, 'report.html'), open_browser=False)
pytest.raises(NotImplementedError, report.add_slider_to_section,
[figs, figs])
pytest.raises(ValueError, report.add_slider_to_section, figs, ['wug'])
pytest.raises(TypeError, report.add_slider_to_section, figs, 'wug')
# need at least 2
pytest.raises(ValueError, report.add_slider_to_section, figs[:1], 'wug')
# Smoke test that SVG w/unicode can be added
report = Report()
fig, ax = plt.subplots()
ax.set_xlabel(u'μ')
report.add_slider_to_section([fig] * 2, image_format='svg')
def test_add_slider_to_section():
"""Test adding a slider with a series of images to mne report."""
tempdir = _TempDir()
from matplotlib import pyplot as plt
report = Report(info_fname=raw_fname,
subject='sample', subjects_dir=subjects_dir)
section = 'slider_section'
figs = list()
figs.append(plt.figure())
plt.plot([1, 2, 3])
plt.close('all')
figs.append(plt.figure())
plt.plot([3, 2, 1])
plt.close('all')
report.add_slider_to_section(figs, section=section)
report.save(op.join(tempdir, 'report.html'), open_browser=False)
assert_raises(NotImplementedError, report.add_slider_to_section,
[figs, figs])
assert_raises(ValueError, report.add_slider_to_section, figs, ['wug'])
assert_raises(TypeError, report.add_slider_to_section, figs, 'wug')
def test_add_slider_to_section():
"""Test adding a slider with a series of images to mne report."""
tempdir = _TempDir()
report = Report(info_fname=raw_fname,
subject='sample', subjects_dir=subjects_dir)
section = 'slider_section'
figs = _get_example_figures()
report.add_slider_to_section(figs, section=section)
report.save(op.join(tempdir, 'report.html'), open_browser=False)
pytest.raises(NotImplementedError, report.add_slider_to_section,
[figs, figs])
pytest.raises(ValueError, report.add_slider_to_section, figs, ['wug'])
pytest.raises(TypeError, report.add_slider_to_section, figs, 'wug')
# need at least 2
pytest.raises(ValueError, report.add_slider_to_section, figs[:1], 'wug')
# Smoke test that SVG w/unicode can be added
report = Report()
fig, ax = plt.subplots()
ax.set_xlabel(u'μ')
report.add_slider_to_section([fig] * 2, image_format='svg')
def test_add_slider_to_section():
"""Test adding a slider with a series of images to mne report."""
tempdir = _TempDir()
report = Report(info_fname=raw_fname,
subject='sample', subjects_dir=subjects_dir)
section = 'slider_section'
figs = _get_example_figures()
report.add_slider_to_section(figs, section=section, title='my title')
assert report.fnames[0] == 'my title-#-report_slider_section-#-custom'
report.save(op.join(tempdir, 'report.html'), open_browser=False)
pytest.raises(NotImplementedError, report.add_slider_to_section,
[figs, figs])
pytest.raises(ValueError, report.add_slider_to_section, figs, ['wug'])
pytest.raises(TypeError, report.add_slider_to_section, figs, 'wug')
# need at least 2
pytest.raises(ValueError, report.add_slider_to_section, figs[:1], 'wug')
# Smoke test that SVG w/unicode can be added
report = Report()
fig, ax = plt.subplots()
ax.set_xlabel(u'μ')
report.add_slider_to_section([fig] * 2, image_format='svg')
reject_log.plot_epochs(this_epoch, scalings='auto')
epochs_ar.plot(scalings='auto')
epochs_ar.plot_drop_log() #dropp epochs
#---------------------Report-------------------------------#
###################################################################
name = 'Subject1_report'
report = Report(image_format='png', raw_psd=False, title=name, subject=name)
#generate ICA
fig = ica.plot_components(inst=raw)
report.add_htmls_to_section(
"Filter parameters: 0.1-50 Hz, fir_design='firwin'; ICA parameters: n_components=40, random_state=97, max_iter=800, method = 'fastica'",
captions="Description")
report.add_slider_to_section(fig,
title="ICA",
section="ICA_components",
image_format='png')
# generate images with properties
n = list(range(0, 40))
fig_2 = ica.plot_properties(raw, picks=n, psd_args={'fmax': 50})
report.add_slider_to_section(fig_2,
title="ICA",
section="ICA_components_properties",
image_format='png')
report.save('/Users/n/PycharmProjects/application/' + name + '.html',
overwrite=True)
# Authors: Teon Brooks <[email protected] # # License: BSD (3-clause) from mne.report import Report from mne.datasets import sample from mne import read_evokeds from matplotlib import pyplot as plt report = Report() path = sample.data_path() fname = path + '/MEG/sample/sample_audvis-ave.fif' # Load the evoked data evoked = read_evokeds(fname, condition='Left Auditory', baseline=(None, 0), verbose=False) evoked.crop(0, .2) times = evoked.times[::4] # Create a list of figs for the slider figs = list() for time in times: figs.append(evoked.plot_topomap(time, vmin=-300, vmax=300, res=100, show=False)) plt.close(figs[-1]) report.add_slider_to_section(figs, times, 'Evoked Response') # # to save report # report.save('foobar.html', True)
def gen_html_report(p, subjects, structurals, run_indices=None):
"""Generates HTML reports"""
import matplotlib.pyplot as plt
from ._mnefun import (_load_trans_to, plot_good_coils, _head_pos_annot,
_get_bem_src_trans, safe_inserter, _prebad,
_load_meg_bads, mlab_offscreen, _fix_raw_eog_cals,
_handle_dict, _get_t_window, plot_chpi_snr_raw)
if run_indices is None:
run_indices = [None] * len(subjects)
style = {'axes.spines.right': 'off', 'axes.spines.top': 'off',
'axes.grid': True}
time_kwargs = dict()
if 'time_unit' in mne.fixes._get_args(mne.viz.plot_evoked):
time_kwargs['time_unit'] = 's'
for si, subj in enumerate(subjects):
struc = structurals[si]
report = Report(verbose=False)
print(' Processing subject %s/%s (%s)'
% (si + 1, len(subjects), subj))
# raw
fnames = get_raw_fnames(p, subj, 'raw', erm=False, add_splits=False,
run_indices=run_indices[si])
for fname in fnames:
if not op.isfile(fname):
raise RuntimeError('Cannot create reports until raw data '
'exist, missing:\n%s' % fname)
raw = [read_raw_fif(fname, allow_maxshield='yes')
for fname in fnames]
_fix_raw_eog_cals(raw)
prebad_file = _prebad(p, subj)
for r in raw:
_load_meg_bads(r, prebad_file, disp=False)
raw = mne.concatenate_raws(raw)
# sss
sss_fnames = get_raw_fnames(p, subj, 'sss', False, False,
run_indices[si])
has_sss = all(op.isfile(fname) for fname in sss_fnames)
sss_info = mne.io.read_raw_fif(sss_fnames[0]) if has_sss else None
bad_file = get_bad_fname(p, subj)
if bad_file is not None:
sss_info.load_bad_channels(bad_file)
sss_info = sss_info.info
# pca
pca_fnames = get_raw_fnames(p, subj, 'pca', False, False,
run_indices[si])
has_pca = all(op.isfile(fname) for fname in pca_fnames)
# whitening and source localization
inv_dir = op.join(p.work_dir, subj, p.inverse_dir)
has_fwd = op.isfile(op.join(p.work_dir, subj, p.forward_dir,
subj + p.inv_tag + '-fwd.fif'))
with plt.style.context(style):
ljust = 25
#
# Head coils
#
section = 'Good HPI count'
if p.report_params.get('good_hpi_count', True) and p.movecomp:
t0 = time.time()
print((' %s ... ' % section).ljust(ljust), end='')
figs = list()
captions = list()
for fname in fnames:
_, _, fit_data = _head_pos_annot(p, fname, prefix=' ')
assert fit_data is not None
fig = plot_good_coils(fit_data, show=False)
fig.set_size_inches(10, 2)
fig.tight_layout()
figs.append(fig)
captions.append('%s: %s' % (section, op.split(fname)[-1]))
report.add_figs_to_section(figs, captions, section,
image_format='svg')
print('%5.1f sec' % ((time.time() - t0),))
else:
print(' %s skipped' % section)
#
# cHPI SNR
#
section = 'cHPI SNR'
if p.report_params.get('chpi_snr', True) and p.movecomp:
t0 = time.time()
print((' %s ... ' % section).ljust(ljust), end='')
figs = list()
captions = list()
for fname in fnames:
raw = mne.io.read_raw_fif(fname, allow_maxshield='yes')
t_window = _get_t_window(p, raw)
fig = plot_chpi_snr_raw(raw, t_window, show=False,
verbose=False)
fig.set_size_inches(10, 5)
fig.subplots_adjust(0.1, 0.1, 0.8, 0.95,
wspace=0, hspace=0.5)
figs.append(fig)
captions.append('%s: %s' % (section, op.split(fname)[-1]))
report.add_figs_to_section(figs, captions, section,
image_format='png') # svd too slow
print('%5.1f sec' % ((time.time() - t0),))
else:
print(' %s skipped' % section)
#
# Head movement
#
section = 'Head movement'
if p.report_params.get('head_movement', True) and p.movecomp:
print((' %s ... ' % section).ljust(ljust), end='')
t0 = time.time()
trans_to = _load_trans_to(p, subj, run_indices[si], raw)
figs = list()
captions = list()
for fname in fnames:
pos, _, _ = _head_pos_annot(p, fname, prefix=' ')
fig = plot_head_positions(pos=pos, destination=trans_to,
info=raw.info, show=False)
for ax in fig.axes[::2]:
"""
# tighten to the sensor limits
assert ax.lines[0].get_color() == (0., 0., 0., 1.)
mn, mx = np.inf, -np.inf
for line in ax.lines:
ydata = line.get_ydata()
if np.isfinite(ydata).any():
mn = min(np.nanmin(ydata), mn)
mx = max(np.nanmax(line.get_ydata()), mx)
"""
# always show at least 10cm span, and use tight limits
# if greater than that
coord = ax.lines[0].get_ydata()
for line in ax.lines:
if line.get_color() == 'r':
extra = line.get_ydata()[0]
mn, mx = coord.min(), coord.max()
md = (mn + mx) / 2.
mn = min([mn, md - 50., extra])
mx = max([mx, md + 50., extra])
assert (mn <= coord).all()
assert (mx >= coord).all()
ax.set_ylim(mn, mx)
fig.set_size_inches(10, 6)
fig.tight_layout()
figs.append(fig)
captions.append('%s: %s' % (section, op.split(fname)[-1]))
del trans_to
report.add_figs_to_section(figs, captions, section,
image_format='svg')
print('%5.1f sec' % ((time.time() - t0),))
else:
print(' %s skipped' % section)
#
# Raw segments
#
if op.isfile(pca_fnames[0]):
raw_pca = mne.concatenate_raws(
[mne.io.read_raw_fif(fname) for fname in pca_fnames])
section = 'Raw segments'
if p.report_params.get('raw_segments', True) and has_pca:
times = np.linspace(raw.times[0], raw.times[-1], 12)[1:-1]
raw_plot = list()
for t in times:
this_raw = raw_pca.copy().crop(t - 0.5, t + 0.5)
this_raw.load_data()
this_raw._data[:] -= np.mean(this_raw._data, axis=-1,
keepdims=True)
raw_plot.append(this_raw)
raw_plot = mne.concatenate_raws(raw_plot)
for key in ('BAD boundary', 'EDGE boundary'):
raw_plot.annotations.delete(
np.where(raw_plot.annotations.description == key)[0])
new_events = np.linspace(
0, int(round(10 * raw.info['sfreq'])) - 1, 11).astype(int)
new_events += raw_plot.first_samp
new_events = np.array([new_events,
np.zeros_like(new_events),
np.ones_like(new_events)]).T
fig = raw_plot.plot(group_by='selection', butterfly=True,
events=new_events)
fig.axes[0].lines[-1].set_zorder(10) # events
fig.axes[0].set(xticks=np.arange(0, len(times)) + 0.5)
xticklabels = ['%0.1f' % t for t in times]
fig.axes[0].set(xticklabels=xticklabels)
fig.axes[0].set(xlabel='Center of 1-second segments')
fig.axes[0].grid(False)
for _ in range(len(fig.axes) - 1):
fig.delaxes(fig.axes[-1])
fig.set(figheight=(fig.axes[0].get_yticks() != 0).sum(),
figwidth=12)
fig.subplots_adjust(0.0, 0.0, 1, 1, 0, 0)
report.add_figs_to_section(fig, 'Processed', section,
image_format='png') # svg too slow
#
# PSD
#
section = 'PSD'
if p.report_params.get('psd', True) and has_pca:
t0 = time.time()
print((' %s ... ' % section).ljust(ljust), end='')
if p.lp_trans == 'auto':
lp_trans = 0.25 * p.lp_cut
else:
lp_trans = p.lp_trans
n_fft = 8192
fmax = raw.info['lowpass']
figs = [raw.plot_psd(fmax=fmax, n_fft=n_fft, show=False)]
captions = ['%s: Raw' % section]
fmax = p.lp_cut + 2 * lp_trans
figs.append(raw.plot_psd(fmax=fmax, n_fft=n_fft, show=False))
captions.append('%s: Raw (zoomed)' % section)
if op.isfile(pca_fnames[0]):
figs.append(raw_pca.plot_psd(fmax=fmax, n_fft=n_fft,
show=False))
captions.append('%s: Processed' % section)
# shared y limits
n = len(figs[0].axes) // 2
for ai, axes in enumerate(list(zip(
*[f.axes for f in figs]))[:n]):
ylims = np.array([ax.get_ylim() for ax in axes])
ylims = [np.min(ylims[:, 0]), np.max(ylims[:, 1])]
for ax in axes:
ax.set_ylim(ylims)
ax.set(title='')
for fig in figs:
fig.set_size_inches(8, 8)
with warnings.catch_warnings(record=True):
fig.tight_layout()
report.add_figs_to_section(figs, captions, section,
image_format='svg')
print('%5.1f sec' % ((time.time() - t0),))
else:
print(' %s skipped' % section)
#
# SSP
#
section = 'SSP topomaps'
proj_nums = _handle_dict(p.proj_nums, subj)
if p.report_params.get('ssp_topomaps', True) and has_pca and \
np.sum(proj_nums) > 0:
assert sss_info is not None
t0 = time.time()
print((' %s ... ' % section).ljust(ljust), end='')
figs = []
comments = []
proj_files = get_proj_fnames(p, subj)
if p.proj_extra is not None:
comments.append('Custom')
projs = read_proj(op.join(p.work_dir, subj, p.pca_dir,
p.proj_extra))
figs.append(plot_projs_topomap(projs, info=sss_info,
show=False))
if any(proj_nums[0]): # ECG
if 'preproc_ecg-proj.fif' in proj_files:
comments.append('ECG')
figs.append(_proj_fig(op.join(
p.work_dir, subj, p.pca_dir,
'preproc_ecg-proj.fif'), sss_info,
proj_nums[0], p.proj_meg, 'ECG'))
if any(proj_nums[1]): # EOG
if 'preproc_blink-proj.fif' in proj_files:
comments.append('Blink')
figs.append(_proj_fig(op.join(
p.work_dir, subj, p.pca_dir,
'preproc_blink-proj.fif'), sss_info,
proj_nums[1], p.proj_meg, 'EOG'))
if any(proj_nums[2]): # ERM
if 'preproc_cont-proj.fif' in proj_files:
comments.append('Continuous')
figs.append(_proj_fig(op.join(
p.work_dir, subj, p.pca_dir,
'preproc_cont-proj.fif'), sss_info,
proj_nums[2], p.proj_meg, 'ERM'))
captions = [section] + [None] * (len(comments) - 1)
report.add_figs_to_section(
figs, captions, section, image_format='svg',
comments=comments)
print('%5.1f sec' % ((time.time() - t0),))
else:
print(' %s skipped' % section)
#
# Source alignment
#
section = 'Source alignment'
source_alignment = p.report_params.get('source_alignment', True)
if source_alignment is True or isinstance(source_alignment, dict) \
and has_sss and has_fwd:
assert sss_info is not None
kwargs = source_alignment
if isinstance(source_alignment, dict):
kwargs = dict(**source_alignment)
else:
assert source_alignment is True
kwargs = dict()
t0 = time.time()
print((' %s ... ' % section).ljust(ljust), end='')
captions = [section]
try:
from mayavi import mlab
except ImportError:
warnings.warn('Cannot plot alignment in Report, mayavi '
'could not be imported')
else:
subjects_dir = mne.utils.get_subjects_dir(
p.subjects_dir, raise_error=True)
bem, src, trans, _ = _get_bem_src_trans(
p, sss_info, subj, struc)
if len(mne.pick_types(sss_info)):
coord_frame = 'meg'
else:
coord_frame = 'head'
with mlab_offscreen():
fig = mlab.figure(bgcolor=(0., 0., 0.),
size=(1000, 1000))
for key, val in (
('info', sss_info),
('subjects_dir', subjects_dir), ('bem', bem),
('dig', True), ('coord_frame', coord_frame),
('show_axes', True), ('fig', fig),
('trans', trans), ('src', src)):
kwargs[key] = kwargs.get(key, val)
try_surfs = ['head-dense', 'head', 'inner_skull']
for surf in try_surfs:
try:
mne.viz.plot_alignment(surfaces=surf, **kwargs)
except Exception:
pass
else:
break
else:
raise RuntimeError('Could not plot any surface '
'for alignment:\n%s'
% (try_surfs,))
fig.scene.parallel_projection = True
view = list()
for ai, angle in enumerate([180, 90, 0]):
mlab.view(angle, 90, focalpoint=(0., 0., 0.),
distance=0.6, figure=fig)
view.append(mlab.screenshot(figure=fig))
mlab.close(fig)
view = trim_bg(np.concatenate(view, axis=1), 0)
report.add_figs_to_section(view, captions, section)
print('%5.1f sec' % ((time.time() - t0),))
else:
print(' %s skipped' % section)
#
# SNR
#
section = 'SNR'
if p.report_params.get('snr', None) is not None:
t0 = time.time()
print((' %s ... ' % section).ljust(ljust), end='')
snrs = p.report_params['snr']
if not isinstance(snrs, (list, tuple)):
snrs = [snrs]
for snr in snrs:
assert isinstance(snr, dict)
analysis = snr['analysis']
name = snr['name']
times = snr.get('times', [0.1])
inv_dir = op.join(p.work_dir, subj, p.inverse_dir)
fname_inv = op.join(inv_dir,
safe_inserter(snr['inv'], subj))
fname_evoked = op.join(inv_dir, '%s_%d%s_%s_%s-ave.fif'
% (analysis, p.lp_cut, p.inv_tag,
p.eq_tag, subj))
if not op.isfile(fname_inv):
print(' Missing inv: %s'
% op.basename(fname_inv), end='')
elif not op.isfile(fname_evoked):
print(' Missing evoked: %s'
% op.basename(fname_evoked), end='')
else:
inv = mne.minimum_norm.read_inverse_operator(fname_inv)
this_evoked = mne.read_evokeds(fname_evoked, name)
title = ('%s<br>%s["%s"] (N=%d)'
% (section, analysis, name, this_evoked.nave))
figs = plot_snr_estimate(this_evoked, inv,
verbose=False)
figs.axes[0].set_ylim(auto=True)
captions = ('%s<br>%s["%s"] (N=%d)'
% (section, analysis, name,
this_evoked.nave))
report.add_figs_to_section(
figs, captions, section=section,
image_format='svg')
print('%5.1f sec' % ((time.time() - t0),))
#
# BEM
#
section = 'BEM'
if p.report_params.get('bem', True) and has_fwd:
caption = '%s<br>%s' % (section, struc)
bem, src, trans, _ = _get_bem_src_trans(
p, raw.info, subj, struc)
if not bem['is_sphere']:
subjects_dir = mne.utils.get_subjects_dir(
p.subjects_dir, raise_error=True)
mri_fname = op.join(subjects_dir, struc, 'mri', 'T1.mgz')
if not op.isfile(mri_fname):
warnings.warn(
'Could not find MRI:\n%s\nIf using surrogate '
'subjects, use '
'params.report_params["bem"] = False to avoid '
'this warning', stacklevel=2)
else:
t0 = time.time()
print((' %s ... ' % section).ljust(ljust), end='')
report.add_bem_to_section(struc, caption, section,
decim=10, n_jobs=1,
subjects_dir=subjects_dir)
print('%5.1f sec' % ((time.time() - t0),))
else:
print(' %s skipped (sphere)' % section)
else:
print(' %s skipped' % section)
#
# Whitening
#
section = 'Whitening'
if p.report_params.get('whitening', False):
t0 = time.time()
print((' %s ... ' % section).ljust(ljust), end='')
whitenings = p.report_params['whitening']
if not isinstance(whitenings, (list, tuple)):
whitenings = [whitenings]
for whitening in whitenings:
assert isinstance(whitening, dict)
analysis = whitening['analysis']
name = whitening['name']
cov_name = op.join(p.work_dir, subj, p.cov_dir,
safe_inserter(whitening['cov'], subj))
# Load the inverse
fname_evoked = op.join(inv_dir, '%s_%d%s_%s_%s-ave.fif'
% (analysis, p.lp_cut, p.inv_tag,
p.eq_tag, subj))
if not op.isfile(cov_name):
print(' Missing cov: %s'
% op.basename(cov_name), end='')
elif not op.isfile(fname_evoked):
print(' Missing evoked: %s'
% op.basename(fname_evoked), end='')
else:
noise_cov = mne.read_cov(cov_name)
evo = mne.read_evokeds(fname_evoked, name)
captions = ('%s<br>%s["%s"] (N=%d)'
% (section, analysis, name, evo.nave))
fig = evo.plot_white(noise_cov, **time_kwargs)
report.add_figs_to_section(
fig, captions, section=section, image_format='png')
print('%5.1f sec' % ((time.time() - t0),))
else:
print(' %s skipped' % section)
#
# Sensor space plots
#
section = 'Responses'
if p.report_params.get('sensor', False):
t0 = time.time()
print((' %s ... ' % section).ljust(ljust), end='')
sensors = p.report_params['sensor']
if not isinstance(sensors, (list, tuple)):
sensors = [sensors]
for sensor in sensors:
assert isinstance(sensor, dict)
analysis = sensor['analysis']
name = sensor['name']
times = sensor.get('times', [0.1, 0.2])
fname_evoked = op.join(inv_dir, '%s_%d%s_%s_%s-ave.fif'
% (analysis, p.lp_cut, p.inv_tag,
p.eq_tag, subj))
if not op.isfile(fname_evoked):
print(' Missing evoked: %s'
% op.basename(fname_evoked), end='')
else:
this_evoked = mne.read_evokeds(fname_evoked, name)
figs = this_evoked.plot_joint(
times, show=False, ts_args=dict(**time_kwargs),
topomap_args=dict(outlines='head', **time_kwargs))
if not isinstance(figs, (list, tuple)):
figs = [figs]
captions = ('%s<br>%s["%s"] (N=%d)'
% (section, analysis, name,
this_evoked.nave))
captions = [captions] + [None] * (len(figs) - 1)
report.add_figs_to_section(
figs, captions, section=section,
image_format='png')
print('%5.1f sec' % ((time.time() - t0),))
#
# Source estimation
#
section = 'Source estimation'
if p.report_params.get('source', False):
t0 = time.time()
print((' %s ... ' % section).ljust(ljust), end='')
sources = p.report_params['source']
if not isinstance(sources, (list, tuple)):
sources = [sources]
for source in sources:
assert isinstance(source, dict)
analysis = source['analysis']
name = source['name']
times = source.get('times', [0.1, 0.2])
# Load the inverse
inv_dir = op.join(p.work_dir, subj, p.inverse_dir)
fname_inv = op.join(inv_dir,
safe_inserter(source['inv'], subj))
fname_evoked = op.join(inv_dir, '%s_%d%s_%s_%s-ave.fif'
% (analysis, p.lp_cut, p.inv_tag,
p.eq_tag, subj))
if not op.isfile(fname_inv):
print(' Missing inv: %s'
% op.basename(fname_inv), end='')
elif not op.isfile(fname_evoked):
print(' Missing evoked: %s'
% op.basename(fname_evoked), end='')
else:
inv = mne.minimum_norm.read_inverse_operator(fname_inv)
this_evoked = mne.read_evokeds(fname_evoked, name)
title = ('%s<br>%s["%s"] (N=%d)'
% (section, analysis, name, this_evoked.nave))
stc = mne.minimum_norm.apply_inverse(
this_evoked, inv,
lambda2=source.get('lambda2', 1. / 9.),
method=source.get('method', 'dSPM'))
stc = abs(stc)
# get clim using the reject_tmin <->reject_tmax
stc_crop = stc.copy().crop(
p.reject_tmin, p.reject_tmax)
clim = source.get('clim', dict(kind='percent',
lims=[82, 90, 98]))
out = mne.viz._3d._limits_to_control_points(
clim, stc_crop.data, 'viridis',
transparent=True) # dummy cmap
if isinstance(out[0], (list, tuple, np.ndarray)):
clim = out[0] # old MNE
else:
clim = out[1] # new MNE (0.17+)
clim = dict(kind='value', lims=clim)
if not isinstance(stc, mne.SourceEstimate):
print('Only surface source estimates currently '
'supported')
else:
subjects_dir = mne.utils.get_subjects_dir(
p.subjects_dir, raise_error=True)
with mlab_offscreen():
brain = stc.plot(
hemi=source.get('hemi', 'split'),
views=source.get('views', ['lat', 'med']),
size=source.get('size', (800, 600)),
colormap=source.get('colormap', 'viridis'),
transparent=source.get('transparent',
True),
foreground='k', background='w',
clim=clim, subjects_dir=subjects_dir,
)
imgs = list()
for t in times:
brain.set_time(t)
imgs.append(
trim_bg(brain.screenshot(), 255))
brain.close()
captions = ['%2.3f sec' % t for t in times]
report.add_slider_to_section(
imgs, captions=captions, section=section,
title=title, image_format='png')
print('%5.1f sec' % ((time.time() - t0),))
else:
print(' %s skipped' % section)
report_fname = get_report_fnames(p, subj)[0]
report.save(report_fname, open_browser=False, overwrite=True)
report = Report(image_format='png',
subjects_dir=subjects_dir,
info_fname=evoked_fname,
subject='sample',
raw_psd=False) # use False for speed here
report.parse_folder(meg_path, on_error='ignore', mri_decim=10)
###############################################################################
# Add a custom section with an evoked slider:
# Load the evoked data
evoked = read_evokeds(evoked_fname,
condition='Left Auditory',
baseline=(None, 0),
verbose=False)
evoked.crop(0, .2)
times = evoked.times[::4]
# Create a list of figs for the slider
figs = list()
for t in times:
figs.append(
evoked.plot_topomap(t, vmin=-300, vmax=300, res=100, show=False))
plt.close(figs[-1])
report.add_slider_to_section(figs,
times,
'Evoked Response',
image_format='png') # can also use 'svg'
# Save the report
report.save('my_report.html', overwrite=True)
baseline=param['tfr_baseline_time'])
# Plot in report
chans_to_plot = ['Cz', 'Pz', 'CPz', 'Oz', 'Fz', 'FCz']
figs_tfr = []
for c in chans_to_plot:
pick = induced.ch_names.index(c)
figs_tfr.append(
induced.plot(
picks=[pick],
tmin=param['erpbaseline'],
tmax=param['erpepochend'],
show=False,
))
report.add_slider_to_section(figs_tfr,
captions=chans_to_plot,
section='TFR',
title='Zscored TFR')
# # same thing for shocks
events_s = events[events.trigger_info == 'shock']
events_s['cue_num'] = 255
events_s['empty'] = 0
events_shocks = np.asarray(events_s[['sample', 'empty', 'cue_num']])
events_id = {
'shock': 255,
}
#
# # Reject very bad trials
tf_shocks = mne.Epochs(raw,
events=events_shocks,
event_id=events_id,
figs_butter = []
evokeds = dict()
for cond in events_id.keys():
evokeds[cond] = erp_cues[cond].average()
figs_butter.append(
pej(evokeds[cond],
title=cond,
show=False,
ts_args={'time_unit': 'ms'},
topomap_args={'time_unit': 'ms'}))
evokeds[cond].save(
opj(outdir, p + '_task-fearcond_' + cond + '_ave.fif'))
report.add_slider_to_section(figs_butter,
captions=list(events_id.keys()),
section='ERPs for cues',
title='Butterfly plots for cues')
# # Plot some channels and add to report
chans_to_plot = ['Cz', 'Pz', 'CPz', 'Oz', 'Fz', 'FCz']
figs_chan = []
for c in chans_to_plot:
pick = erp_cues.ch_names.index(c)
figs_chan.append(
mne.viz.plot_compare_evokeds(evokeds, picks=pick, show=False)[0])
report.add_slider_to_section(figs_chan,
captions=chans_to_plot,
section='ERPs for cues',
title='Cues/chans')
# Authors: Teon Brooks <[email protected] # # License: BSD (3-clause) from mne.report import Report from mne.datasets import sample from mne import read_evokeds from matplotlib import pyplot as plt report = Report() path = sample.data_path() fname = path + '/MEG/sample/sample_audvis-ave.fif' # Load the evoked data evoked = read_evokeds(fname, condition='Left Auditory', baseline=(None, 0), verbose=False) evoked.crop(0, .2) times = evoked.times[::4] # Create a list of figs for the slider figs = list() for time in times: figs.append( evoked.plot_topomap(time, vmin=-300, vmax=300, res=100, show=False)) plt.close(figs[-1]) report.add_slider_to_section(figs, times, 'Evoked Response') # # to save report # report.save('foobar.html', True)
report = Report(image_format='png',
subjects_dir=subjects_dir,
info_fname=evoked_fname,
subject='sample')
report.parse_folder(meg_path)
###############################################################################
# Add a custom section with an evoked slider:
# Load the evoked data
evoked = read_evokeds(evoked_fname,
condition='Left Auditory',
baseline=(None, 0),
verbose=False)
evoked.crop(0, .2)
times = evoked.times[::4]
# Create a list of figs for the slider
figs = list()
for t in times:
figs.append(
evoked.plot_topomap(t, vmin=-300, vmax=300, res=100, show=False))
plt.close(figs[-1])
report.add_slider_to_section(figs,
times,
'Evoked Response',
image_format='svg')
# to save report
# report.save('foobar.html', True)
meg_path = data_path + '/MEG/sample'
subjects_dir = data_path + '/subjects'
evoked_fname = meg_path + '/sample_audvis-ave.fif'
###############################################################################
# Do standard folder parsing (this can take a couple of minutes):
report = Report(image_format='png', subjects_dir=subjects_dir,
info_fname=evoked_fname, subject='sample', raw_psd=True)
report.parse_folder(meg_path)
###############################################################################
# Add a custom section with an evoked slider:
# Load the evoked data
evoked = read_evokeds(evoked_fname, condition='Left Auditory',
baseline=(None, 0), verbose=False)
evoked.crop(0, .2)
times = evoked.times[::4]
# Create a list of figs for the slider
figs = list()
for t in times:
figs.append(evoked.plot_topomap(t, vmin=-300, vmax=300, res=100,
show=False))
plt.close(figs[-1])
report.add_slider_to_section(figs, times, 'Evoked Response',
image_format='svg')
# to save report
# report.save('foobar.html', True)
picks='all',
psd_args={'fmax': 35.},
show=False)
for ical in range(len(ica._ica_names)):
figs.append(f[ical])
capts.append(ica._ica_names[ical])
ica.exclude = [ical]
figs.append(ica.plot_sources(eog_averagev,
show=False))
plt.close("all")
f = None
report.add_slider_to_section(figs, captions=None,
section='ICA-FULL')
# Remove components manually identified
ica.exclude = icatoremove
# Apply ICA
ica.apply(raw)
# ______________________________________________________________________
# Re-reference data
raw, _ = mne.set_eeg_reference(raw, param['ref'], projection=False)
# Interpolate channels
if raw.info['bads']:
raw.interpolate_bads(reset_bads=True)
# ______________________________________________________________________