def test_render_add_sections(renderer, tmp_path):
"""Test adding figures/images to section."""
tempdir = str(tmp_path)
report = Report(subjects_dir=subjects_dir)
# Check add_figure functionality
fig = plt.plot([1, 2], [1, 2])[0].figure
report.add_figure(fig=fig, title='evoked response', image_format='svg')
assert 'caption' not in report._content[-1].html
report.add_figure(fig=fig, title='evoked with caption', caption='descr')
assert 'caption' in report._content[-1].html
# Check add_image with png
img_fname = op.join(tempdir, 'testimage.png')
fig.savefig(img_fname)
report.add_image(image=img_fname, title='evoked response')
with pytest.raises(FileNotFoundError, match='No such file or directory'):
report.add_image(image='foobar.xxx', title='H')
evoked = read_evokeds(evoked_fname,
condition='Left Auditory',
baseline=(-0.2, 0.0))
fig = plot_alignment(evoked.info,
trans_fname,
subject='sample',
subjects_dir=subjects_dir)
report.add_figure(fig=fig, title='random image')
assert (repr(report))
fname = op.join(str(tmp_path), 'test.html')
report.save(fname, open_browser=False)
assert len(report) == 4
def test_render_report_extra(renderer_pyvistaqt, tmp_path, invisible_fig):
"""Test SVG and projector rendering separately."""
# ... otherwise things are very slow
tempdir = str(tmp_path)
raw_fname_new = op.join(tempdir, 'temp_raw.fif')
shutil.copyfile(raw_fname, raw_fname_new)
report = Report(info_fname=raw_fname_new,
subjects_dir=subjects_dir,
projs=True,
image_format='svg')
with pytest.warns(RuntimeWarning, match='Cannot render MRI'):
report.parse_folder(data_path=tempdir,
on_error='raise',
n_time_points_evokeds=2,
raw_butterfly=False,
stc_plot_kwargs=stc_plot_kwargs,
topomap_kwargs=topomap_kwargs)
assert repr(report)
report.data_path = tempdir
fname = op.join(tempdir, 'report.html')
report.save(fname=fname, open_browser=False)
assert op.isfile(fname)
html = Path(fname).read_text(encoding='utf-8')
# Projectors in Raw.info
assert 'SSP Projectors' in html
def test_render_non_fiff(tmp_path):
"""Test rendering non-FIFF files for mne report."""
tempdir = str(tmp_path)
fnames_in = [bdf_fname, edf_fname]
fnames_out = []
for fname in fnames_in:
basename = op.basename(fname)
basename, ext = op.splitext(basename)
fname_out = f'{basename}_raw{ext}'
outpath = op.join(tempdir, fname_out)
shutil.copyfile(fname, outpath)
fnames_out.append(fname_out)
report = Report()
report.parse_folder(data_path=tempdir,
render_bem=False,
on_error='raise',
raw_butterfly=False)
# Check correct paths and filenames
content_names = [element.name for element in report._content]
for fname in fnames_out:
assert (op.basename(fname) in [op.basename(x) for x in content_names])
assert len(report._content) == len(fnames_out)
report.data_path = tempdir
fname = op.join(tempdir, 'report.html')
report.save(fname=fname, open_browser=False)
html = Path(fname).read_text(encoding='utf-8')
assert 'test_raw.bdf' in html
assert 'test_raw.edf' in html
def test_render_mri_without_bem(tmpdir):
"""Test rendering MRI without BEM for mne report."""
tempdir = str(tmpdir)
os.mkdir(op.join(tempdir, 'sample'))
os.mkdir(op.join(tempdir, 'sample', 'mri'))
shutil.copyfile(mri_fname, op.join(tempdir, 'sample', 'mri', 'T1.mgz'))
report = Report(info_fname=raw_fname,
subject='sample', subjects_dir=tempdir)
with pytest.raises(RuntimeError, match='No matching files found'):
report.parse_folder(tempdir, render_bem=False)
with pytest.warns(RuntimeWarning, match='No BEM surfaces found'):
report.parse_folder(tempdir, render_bem=True, mri_decim=20)
assert 'BEM surfaces' in [element.name for element in report._content]
report.save(op.join(tempdir, 'report.html'), open_browser=False)
def test_survive_pickle(tmp_path):
"""Testing functionality of Report-Object after pickling."""
tempdir = str(tmp_path)
raw_fname_new = op.join(tempdir, 'temp_raw.fif')
shutil.copyfile(raw_fname, raw_fname_new)
# Pickle report object to simulate multiprocessing with joblib
report = Report(info_fname=raw_fname_new)
pickled_report = pickle.dumps(report)
report = pickle.loads(pickled_report)
# Just test if no errors occur
report.parse_folder(tempdir, render_bem=False)
save_name = op.join(tempdir, 'report.html')
report.save(fname=save_name, open_browser=False)
def test_add_custom_js(tmp_path):
"""Test adding custom JavaScript to the report."""
tempdir = str(tmp_path)
fname = op.join(tempdir, 'report.html')
fig = plt.figure() # Empty figure
report = Report()
report.add_figure(fig=fig, title='Test section')
custom_js = ('function hello() {\n' ' alert("Hello, report!");\n' '}')
report.add_custom_js(js=custom_js)
assert custom_js in report.include
report.save(fname, open_browser=False)
html = Path(fname).read_text(encoding='utf-8')
assert custom_js in html
def test_add_custom_css(tmp_path):
"""Test adding custom CSS rules to the report."""
tempdir = str(tmp_path)
fname = op.join(tempdir, 'report.html')
fig = plt.figure() # Empty figure
report = Report()
report.add_figure(fig=fig, title='Test section')
custom_css = '.report_custom { color: red; }'
report.add_custom_css(css=custom_css)
assert custom_css in report.include
report.save(fname, open_browser=False)
html = Path(fname).read_text(encoding='utf-8')
assert custom_css in html
def test_render_mri(renderer, tmpdir):
"""Test rendering MRI for mne report."""
tempdir = str(tmpdir)
trans_fname_new = op.join(tempdir, 'temp-trans.fif')
for a, b in [[trans_fname, trans_fname_new]]:
shutil.copyfile(a, b)
report = Report(info_fname=raw_fname,
subject='sample', subjects_dir=subjects_dir)
report.parse_folder(data_path=tempdir, mri_decim=30, pattern='*')
fname = op.join(tempdir, 'report.html')
report.save(fname, open_browser=False)
html = Path(fname).read_text(encoding='utf-8')
assert 'data-mne-tags=" bem "' in html
assert repr(report)
report.add_bem(subject='sample', title='extra', tags=('foo',),
subjects_dir=subjects_dir, decim=30)
report.save(fname, open_browser=False, overwrite=True)
html = Path(fname).read_text(encoding='utf-8')
assert 'data-mne-tags=" bem "' in html
assert 'data-mne-tags=" foo "' in html
def test_multiple_figs(tmpdir):
"""Test adding a slider with a series of figures to a Report."""
tempdir = str(tmpdir)
report = Report(info_fname=raw_fname,
subject='sample', subjects_dir=subjects_dir)
figs = _get_example_figures()
report.add_figure(fig=figs, title='my title')
assert report._content[0].name == 'my title'
report.save(op.join(tempdir, 'report.html'), open_browser=False)
with pytest.raises(ValueError):
report.add_figure(fig=figs, title='title', caption=['wug'])
with pytest.raises(ValueError,
match='Number of captions.*must be equal to.*figures'):
report.add_figure(fig=figs, title='title', caption='wug')
# Smoke test that SVG with unicode can be added
report = Report()
fig, ax = plt.subplots()
ax.set_xlabel('µ')
report.add_figure(fig=[fig] * 2, title='title', image_format='svg')
def test_render_report(renderer_pyvistaqt, tmp_path, invisible_fig):
"""Test rendering *.fif files for mne report."""
tempdir = str(tmp_path)
raw_fname_new = op.join(tempdir, 'temp_raw.fif')
raw_fname_new_bids = op.join(tempdir, 'temp_meg.fif')
ms_fname_new = op.join(tempdir, 'temp_ms_raw.fif')
event_fname_new = op.join(tempdir, 'temp_raw-eve.fif')
cov_fname_new = op.join(tempdir, 'temp_raw-cov.fif')
proj_fname_new = op.join(tempdir, 'temp_ecg-proj.fif')
fwd_fname_new = op.join(tempdir, 'temp_raw-fwd.fif')
inv_fname_new = op.join(tempdir, 'temp_raw-inv.fif')
nirs_fname_new = op.join(tempdir, 'temp_raw-nirs.snirf')
for a, b in [[raw_fname, raw_fname_new], [raw_fname, raw_fname_new_bids],
[ms_fname, ms_fname_new], [events_fname, event_fname_new],
[cov_fname, cov_fname_new], [ecg_proj_fname, proj_fname_new],
[fwd_fname, fwd_fname_new], [inv_fname, inv_fname_new],
[nirs_fname, nirs_fname_new]]:
shutil.copyfile(a, b)
# create and add -epo.fif and -ave.fif files
epochs_fname = op.join(tempdir, 'temp-epo.fif')
evoked_fname = op.join(tempdir, 'temp-ave.fif')
# Speed it up by picking channels
raw = read_raw_fif(raw_fname_new)
raw.pick_channels(['MEG 0111', 'MEG 0121', 'EEG 001', 'EEG 002'])
raw.del_proj()
raw.set_eeg_reference(projection=True).load_data()
epochs = Epochs(raw, read_events(events_fname), 1, -0.2, 0.2)
epochs.save(epochs_fname, overwrite=True)
# This can take forever, so let's make it fast
# Also, make sure crop range is wide enough to avoid rendering bug
evoked = epochs.average()
with pytest.warns(RuntimeWarning, match='tmax is not in Evoked'):
evoked.crop(0.1, 0.2)
evoked.save(evoked_fname)
report = Report(info_fname=raw_fname_new,
subjects_dir=subjects_dir,
projs=False,
image_format='png')
with pytest.warns(RuntimeWarning, match='Cannot render MRI'):
report.parse_folder(data_path=tempdir,
on_error='raise',
n_time_points_evokeds=2,
raw_butterfly=False,
stc_plot_kwargs=stc_plot_kwargs,
topomap_kwargs=topomap_kwargs)
assert repr(report)
# Check correct paths and filenames
fnames = glob.glob(op.join(tempdir, '*.fif'))
fnames.extend(glob.glob(op.join(tempdir, '*.snirf')))
titles = [op.basename(x) for x in fnames if not x.endswith('-ave.fif')]
titles.append(f'{op.basename(evoked_fname)}: {evoked.comment}')
content_names = [element.name for element in report._content]
for title in titles:
assert title in content_names
assert (''.join(report.html).find(title) != -1)
assert len(report._content) == len(fnames)
# Check saving functionality
report.data_path = tempdir
fname = op.join(tempdir, 'report.html')
report.save(fname=fname, open_browser=False)
assert (op.isfile(fname))
html = Path(fname).read_text(encoding='utf-8')
# Evoked in `evoked_fname`
assert f'{op.basename(evoked_fname)}: {evoked.comment}' in html
assert 'Topographies' in html
assert 'Global field power' in html
assert len(report._content) == len(fnames)
# Check saving same report to new filename
report.save(fname=op.join(tempdir, 'report2.html'), open_browser=False)
assert (op.isfile(op.join(tempdir, 'report2.html')))
# Check overwriting file
report.save(fname=op.join(tempdir, 'report.html'),
open_browser=False,
overwrite=True)
assert (op.isfile(op.join(tempdir, 'report.html')))
# Check pattern matching with multiple patterns
pattern = ['*proj.fif', '*eve.fif']
with pytest.warns(RuntimeWarning, match='Cannot render MRI'):
report.parse_folder(data_path=tempdir,
pattern=pattern,
raw_butterfly=False)
assert (repr(report))
fnames = glob.glob(op.join(tempdir, '*.raw')) + \
glob.glob(op.join(tempdir, '*.raw'))
content_names = [element.name for element in report._content]
for fname in fnames:
assert (op.basename(fname) in [op.basename(x) for x in content_names])
assert (''.join(report.html).find(op.basename(fname)) != -1)
with pytest.raises(ValueError, match='Invalid value'):
Report(image_format='foo')
with pytest.raises(ValueError, match='Invalid value'):
Report(image_format=None)
# ndarray support smoke test
report.add_figure(fig=np.zeros((2, 3, 3)), title='title')
with pytest.raises(TypeError, match='It seems you passed a path'):
report.add_figure(fig='foo', title='title')