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_report():
"""Test rendering -*.fif files for mne report.
"""
report = Report(info_fname=raw_fname)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
report.parse_folder(data_path=base_dir)
assert_true(len(w) == 1)
# Check correct paths and filenames
assert_true(raw_fname in report.fnames)
assert_true(event_name in report.fnames)
assert_true(report.data_path == base_dir)
# Check if all files were rendered in the report
fnames = glob.glob(op.join(base_dir, '*.fif'))
bad_name = 'test_ctf_comp_raw-eve.fif'
decrement = any(fname.endswith(bad_name) for fname in fnames)
fnames = [fname for fname in fnames if
fname.endswith(('-eve.fif', '-ave.fif', '-cov.fif',
'-sol.fif', '-fwd.fif', '-inv.fif',
'-src.fif', '-trans.fif', 'raw.fif',
'sss.fif', '-epo.fif')) and
not fname.endswith(bad_name)]
# last file above gets created by another test, and it shouldn't be there
for fname in fnames:
assert_true(''.join(report.html).find(op.basename(fname)) != -1)
assert_equal(len(report.fnames), len(fnames))
assert_equal(len(report.html), len(report.fnames))
evoked1 = read_evokeds(evoked1_fname)
evoked2 = read_evokeds(evoked2_fname)
assert_equal(len(report.fnames) + len(evoked1) + len(evoked2) - 2,
report.initial_id - decrement)
# Check saving functionality
report.data_path = tempdir
report.save(fname=op.join(tempdir, 'report.html'), open_browser=False)
assert_true(op.isfile(op.join(tempdir, 'report.html')))
# Check add_section functionality
fig = evoked1[0].plot(show=False)
report.add_section(figs=fig, # test non-list input
captions=['evoked response'])
assert_equal(len(report.html), len(fnames) + 1)
assert_equal(len(report.html), len(report.fnames))
assert_raises(ValueError, report.add_section, figs=[fig, fig],
captions='H')
# Check saving same report to new filename
report.save(fname=op.join(tempdir, 'report2.html'), open_browser=False)
assert_true(op.isfile(op.join(tempdir, 'report2.html')))
# Check overwriting file
report.save(fname=op.join(tempdir, 'report.html'), open_browser=False,
overwrite=True)
assert_true(op.isfile(op.join(tempdir, 'report.html')))
def test_render_non_fiff(tmpdir):
"""Test rendering non-FIFF files for mne report."""
tempdir = str(tmpdir)
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')
# Check correct paths and filenames
for fname in fnames_out:
assert (op.basename(fname) in [op.basename(x) for x in report.fnames])
assert len(report.fnames) == len(fnames_out)
assert len(report.html) == len(report.fnames)
assert len(report.fnames) == len(report)
report.data_path = tempdir
fname = op.join(tempdir, 'report.html')
report.save(fname=fname, open_browser=False)
with open(fname, 'rb') as fid:
html = fid.read().decode('utf-8')
assert '<h4>Raw: test_raw.bdf</h4>' in html
assert '<h4>Raw: test_raw.edf</h4>' in html
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_report():
"""Test rendering -*.fif files for mne report.
"""
tempdir = _TempDir()
raw_fname_new = op.join(tempdir, 'temp_raw.fif')
event_fname_new = op.join(tempdir, 'temp_raw-eve.fif')
cov_fname_new = op.join(tempdir, 'temp_raw-cov.fif')
fwd_fname_new = op.join(tempdir, 'temp_raw-fwd.fif')
inv_fname_new = op.join(tempdir, 'temp_raw-inv.fif')
for a, b in [[raw_fname, raw_fname_new],
[event_fname, event_fname_new],
[cov_fname, cov_fname_new],
[fwd_fname, fwd_fname_new],
[inv_fname, inv_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')
raw = Raw(raw_fname_new)
picks = pick_types(raw.info, meg='mag', eeg=False) # faster with one type
epochs = Epochs(raw, read_events(event_fname), 1, -0.2, 0.2, picks=picks)
epochs.save(epochs_fname)
epochs.average().save(evoked_fname)
report = Report(info_fname=raw_fname_new, subjects_dir=subjects_dir)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
report.parse_folder(data_path=tempdir)
assert_true(len(w) >= 1)
# Check correct paths and filenames
fnames = glob.glob(op.join(tempdir, '*.fif'))
for fname in fnames:
assert_true(op.basename(fname) in
[op.basename(x) for x in report.fnames])
assert_true(''.join(report.html).find(op.basename(fname)) != -1)
assert_equal(len(report.fnames), len(fnames))
assert_equal(len(report.html), len(report.fnames))
# Check saving functionality
report.data_path = tempdir
report.save(fname=op.join(tempdir, 'report.html'), open_browser=False)
assert_true(op.isfile(op.join(tempdir, 'report.html')))
assert_equal(len(report.html), len(fnames))
assert_equal(len(report.html), len(report.fnames))
# Check saving same report to new filename
report.save(fname=op.join(tempdir, 'report2.html'), open_browser=False)
assert_true(op.isfile(op.join(tempdir, 'report2.html')))
# Check overwriting file
report.save(fname=op.join(tempdir, 'report.html'), open_browser=False,
overwrite=True)
assert_true(op.isfile(op.join(tempdir, 'report.html')))
def test_render_report():
"""Test rendering -*.fif files for mne report.
"""
tempdir = _TempDir()
raw_fname_new = op.join(tempdir, 'temp_raw.fif')
event_fname_new = op.join(tempdir, 'temp_raw-eve.fif')
cov_fname_new = op.join(tempdir, 'temp_raw-cov.fif')
fwd_fname_new = op.join(tempdir, 'temp_raw-fwd.fif')
inv_fname_new = op.join(tempdir, 'temp_raw-inv.fif')
for a, b in [[raw_fname, raw_fname_new], [event_fname, event_fname_new],
[cov_fname, cov_fname_new], [fwd_fname, fwd_fname_new],
[inv_fname, inv_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')
raw = Raw(raw_fname_new)
picks = pick_types(raw.info, meg='mag', eeg=False) # faster with one type
epochs = Epochs(raw, read_events(event_fname), 1, -0.2, 0.2, picks=picks)
epochs.save(epochs_fname)
epochs.average().save(evoked_fname)
report = Report(info_fname=raw_fname_new, subjects_dir=subjects_dir)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
report.parse_folder(data_path=tempdir)
assert_true(len(w) >= 1)
# Check correct paths and filenames
fnames = glob.glob(op.join(tempdir, '*.fif'))
for fname in fnames:
assert_true(
op.basename(fname) in [op.basename(x) for x in report.fnames])
assert_true(''.join(report.html).find(op.basename(fname)) != -1)
assert_equal(len(report.fnames), len(fnames))
assert_equal(len(report.html), len(report.fnames))
# Check saving functionality
report.data_path = tempdir
report.save(fname=op.join(tempdir, 'report.html'), open_browser=False)
assert_true(op.isfile(op.join(tempdir, 'report.html')))
assert_equal(len(report.html), len(fnames))
assert_equal(len(report.html), len(report.fnames))
# Check saving same report to new filename
report.save(fname=op.join(tempdir, 'report2.html'), open_browser=False)
assert_true(op.isfile(op.join(tempdir, 'report2.html')))
# Check overwriting file
report.save(fname=op.join(tempdir, 'report.html'),
open_browser=False,
overwrite=True)
assert_true(op.isfile(op.join(tempdir, 'report.html')))
def setup_provenance(script,
results_dir,
config=None,
use_agg=True,
run_id=None):
"""Setup provenance tracking
Parameters
----------
script : str
The script that was executed.
results_dir : str
The results directory.
config : None | str
The name of the config file. By default, the function expects the
config to be under `__script__/' named `config.py`. It can also
be another kind of textfile, e.g. .json.
use_agg : bool
Whether to use the 'Agg' backend for matplotlib or not.
Returns
-------
report : mne.report.Report
The mne report.
Side-effects
------------
- make results dir if it does not exists
- sets log file for sterr output
- writes log file with runtime information
"""
if use_agg is True:
import matplotlib
matplotlib.use('Agg')
if not op.isfile(script):
raise ValueError('sorry, this is not a script!')
if not op.isdir(results_dir):
results_dir = op.join(op.dirname(op.dirname(script)), results_dir)
step = op.splitext(op.split(script)[1])[0]
if not op.isabs(results_dir):
results_dir = op.abspath(results_dir)
start_path = op.dirname(results_dir)
results_dir = op.join(results_dir, step)
if not op.exists(results_dir):
logger.info('generating results dir')
_forec_create_dir(results_dir, start=start_path)
if run_id is None:
run_id = create_run_id()
logger.info('generated run id: %s' % run_id)
else:
logger.info('using existing run id: %s' % run_id)
logger.info('preparing logging:')
logging_dir = op.join(results_dir, run_id)
if not op.exists(logging_dir):
logger.info('... making logging directory: %s' % logging_dir)
os.mkdir(logging_dir)
else:
logger.info('... using logging directory: %s' % logging_dir)
modules = get_versions(sys)
runtime_log = op.join(logging_dir, 'run_time.json')
with open(runtime_log, 'w') as fid:
json.dump(modules, fid)
logger.info('... writing runtime info to: %s' % runtime_log)
script_code = op.join(logging_dir, 'script.py')
if not op.isfile(script_code):
with open(script_code, 'w') as fid:
with open(script) as script_fid:
source_code = script_fid.read()
fid.write(source_code)
logger.info('... logging source code of calling script')
if config is None:
config = 'config.py'
if op.isabs(config):
config_fname = config
else:
config_fname = op.join(op.dirname(script), config)
config_code = op.join( # weird behavior of join if last arg is path
results_dir, run_id,
op.split(config_fname)[-1])
if not op.isfile(config_fname):
logger.info('... No config found. Logging nothing.')
elif op.isfile(config_code):
logger.info('... Config already written. I assume that you are using'
' the same run_id for different runs of your script.')
else:
with open(config_code, 'w') as fid:
with open(config_fname) as config_fid:
source_code = config_fid.read()
fid.write(source_code)
logger.info('... logging source code of "%s".' % config_fname)
logger.info('... preparing Report')
report = Report(title=step)
report.data_path = logging_dir
std_logfile = op.join(logging_dir, 'run_output.log')
logger.info('... setting logfile: %s' % std_logfile)
set_log_file(std_logfile)
return report, run_id, results_dir, logger
def setup_provenance(script, results_dir, config=None, use_agg=True,
run_id=None):
"""Setup provenance tracking
Parameters
----------
script : str
The script that was executed.
results_dir : str
The results directory.
config : None | str
The name of the config file. By default, the function expects the
config to be under `__script__/' named `config.py`. It can also
be another kind of textfile, e.g. .json.
use_agg : bool
Whether to use the 'Agg' backend for matplotlib or not.
Returns
-------
report : mne.report.Report
The mne report.
Side-effects
------------
- make results dir if it does not exists
- sets log file for sterr output
- writes log file with runtime information
"""
if use_agg is True:
import matplotlib
matplotlib.use('Agg')
if not callable(script):
if not op.isfile(script):
raise ValueError('sorry, this is not a script!')
if not op.isdir(results_dir) and not callable(script):
results_dir = op.join(op.dirname(op.dirname(script)), results_dir)
else:
results_dir = op.join(op.curdir, results_dir)
if not callable(script):
step = op.splitext(op.split(script)[1])[0]
else:
step = script.__name__
if not op.isabs(results_dir):
results_dir = op.abspath(results_dir)
start_path = op.dirname(results_dir)
results_dir = op.join(results_dir, step)
if not op.exists(results_dir):
logger.info('generating results dir')
_forec_create_dir(results_dir, start=start_path)
if run_id is None:
run_id = create_run_id()
logger.info('generated run id: %s' % run_id)
else:
logger.info('using existing run id: %s' % run_id)
logger.info('preparing logging:')
logging_dir = op.join(results_dir, run_id)
if not op.exists(logging_dir):
logger.info('... making logging directory: %s' % logging_dir)
os.mkdir(logging_dir)
else:
logger.info('... using logging directory: %s' % logging_dir)
modules = get_versions(sys)
runtime_log = op.join(logging_dir, 'run_time.json')
with open(runtime_log, 'w') as fid:
json.dump(modules, fid)
logger.info('... writing runtime info to: %s' % runtime_log)
script_code_out = op.join(logging_dir, 'script.py')
if callable(script):
script_code_in = inspect.getsourcefile(script)
else:
script_code_in = script
if not op.isfile(script_code_out):
with open(script_code_out, 'w') as fid:
with open(script_code_in) as script_fid:
source_code = script_fid.read()
fid.write(source_code)
logger.info('... logging source code of calling script')
if config is None:
config = 'config.py'
if op.isabs(config):
config_fname = config
else:
config_fname = ''
config_code = op.join( # weird behavior of join if last arg is path
results_dir, run_id, op.split(config_fname)[-1])
if not op.isfile(config_fname):
logger.info('... No config found. Logging nothing.')
elif op.isfile(config_code):
logger.info('... Config already written. I assume that you are using'
' the same run_id for different runs of your script.')
else:
with open(config_code, 'w') as fid:
with open(config_fname) as config_fid:
source_code = config_fid.read()
fid.write(source_code)
logger.info('... logging source code of "%s".' % config_fname)
logger.info('... preparing Report')
report = Report(title=step)
report.data_path = logging_dir
std_logfile = op.join(logging_dir, 'run_output.log')
logger.info('... setting logfile: %s' % std_logfile)
set_log_file(std_logfile)
return report, run_id, results_dir, logger
def test_render_report():
"""Test rendering -*.fif files for mne report."""
tempdir = _TempDir()
raw_fname_new = op.join(tempdir, 'temp_raw.fif')
event_fname_new = op.join(tempdir, 'temp_raw-eve.fif')
cov_fname_new = op.join(tempdir, 'temp_raw-cov.fif')
fwd_fname_new = op.join(tempdir, 'temp_raw-fwd.fif')
inv_fname_new = op.join(tempdir, 'temp_raw-inv.fif')
for a, b in [[raw_fname, raw_fname_new],
[event_fname, event_fname_new],
[cov_fname, cov_fname_new],
[fwd_fname, fwd_fname_new],
[inv_fname, inv_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, preload=True)
raw.pick_channels(['MEG 0111', 'MEG 0121'])
epochs = Epochs(raw, read_events(event_fname), 1, -0.2, 0.2)
epochs.save(epochs_fname)
# This can take forever (stall Travis), so let's make it fast
# Also, make sure crop range is wide enough to avoid rendering bug
epochs.average().crop(0.1, 0.2).save(evoked_fname)
report = Report(info_fname=raw_fname_new, subjects_dir=subjects_dir)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
report.parse_folder(data_path=tempdir, on_error='raise')
assert_true(len(w) >= 1)
assert_true(repr(report))
# Check correct paths and filenames
fnames = glob.glob(op.join(tempdir, '*.fif'))
for fname in fnames:
assert_true(op.basename(fname) in
[op.basename(x) for x in report.fnames])
assert_true(''.join(report.html).find(op.basename(fname)) != -1)
assert_equal(len(report.fnames), len(fnames))
assert_equal(len(report.html), len(report.fnames))
assert_equal(len(report.fnames), len(report))
# Check saving functionality
report.data_path = tempdir
report.save(fname=op.join(tempdir, 'report.html'), open_browser=False)
assert_true(op.isfile(op.join(tempdir, 'report.html')))
assert_equal(len(report.html), len(fnames))
assert_equal(len(report.html), len(report.fnames))
# Check saving same report to new filename
report.save(fname=op.join(tempdir, 'report2.html'), open_browser=False)
assert_true(op.isfile(op.join(tempdir, 'report2.html')))
# Check overwriting file
report.save(fname=op.join(tempdir, 'report.html'), open_browser=False,
overwrite=True)
assert_true(op.isfile(op.join(tempdir, 'report.html')))
# Check pattern matching with multiple patterns
pattern = ['*raw.fif', '*eve.fif']
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
report.parse_folder(data_path=tempdir, pattern=pattern)
assert_true(len(w) >= 1)
assert_true(repr(report))
fnames = glob.glob(op.join(tempdir, '*.raw')) + \
glob.glob(op.join(tempdir, '*.raw'))
for fname in fnames:
assert_true(op.basename(fname) in
[op.basename(x) for x in report.fnames])
assert_true(''.join(report.html).find(op.basename(fname)) != -1)
assert_raises(ValueError, Report, image_format='foo')
assert_raises(ValueError, Report, image_format=None)
# SVG rendering
report = Report(info_fname=raw_fname_new, subjects_dir=subjects_dir,
image_format='svg')
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
report.parse_folder(data_path=tempdir, on_error='raise')
def test_render_report():
"""Test rendering -*.fif files for mne report."""
tempdir = _TempDir()
raw_fname_new = op.join(tempdir, 'temp_raw.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')
fwd_fname_new = op.join(tempdir, 'temp_raw-fwd.fif')
inv_fname_new = op.join(tempdir, 'temp_raw-inv.fif')
for a, b in [[raw_fname, raw_fname_new], [ms_fname, ms_fname_new],
[event_fname, event_fname_new], [cov_fname, cov_fname_new],
[fwd_fname, fwd_fname_new], [inv_fname, inv_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, preload=True)
raw.pick_channels(['MEG 0111', 'MEG 0121'])
raw.del_proj()
epochs = Epochs(raw, read_events(event_fname), 1, -0.2, 0.2)
epochs.save(epochs_fname, overwrite=True)
# This can take forever (stall Travis), so let's make it fast
# Also, make sure crop range is wide enough to avoid rendering bug
epochs.average().crop(0.1, 0.2).save(evoked_fname)
report = Report(info_fname=raw_fname_new, subjects_dir=subjects_dir)
with pytest.warns(RuntimeWarning, match='Cannot render MRI'):
report.parse_folder(data_path=tempdir, on_error='raise')
assert repr(report)
# Check correct paths and filenames
fnames = glob.glob(op.join(tempdir, '*.fif'))
for fname in fnames:
assert (op.basename(fname) in [op.basename(x) for x in report.fnames])
assert (''.join(report.html).find(op.basename(fname)) != -1)
assert_equal(len(report.fnames), len(fnames))
assert_equal(len(report.html), len(report.fnames))
assert_equal(len(report.fnames), len(report))
# Check saving functionality
report.data_path = tempdir
fname = op.join(tempdir, 'report.html')
report.save(fname=fname, open_browser=False)
assert (op.isfile(fname))
with open(fname, 'rb') as fid:
html = fid.read().decode('utf-8')
assert '(MaxShield on)' in html
assert_equal(len(report.html), len(fnames))
assert_equal(len(report.html), len(report.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 = ['*raw.fif', '*eve.fif']
with pytest.warns(RuntimeWarning, match='Cannot render MRI'):
report.parse_folder(data_path=tempdir, pattern=pattern)
assert (repr(report))
fnames = glob.glob(op.join(tempdir, '*.raw')) + \
glob.glob(op.join(tempdir, '*.raw'))
for fname in fnames:
assert (op.basename(fname) in [op.basename(x) for x in report.fnames])
assert (''.join(report.html).find(op.basename(fname)) != -1)
pytest.raises(ValueError, Report, image_format='foo')
pytest.raises(ValueError, Report, image_format=None)
# SVG rendering
report = Report(info_fname=raw_fname_new,
subjects_dir=subjects_dir,
image_format='svg')
with pytest.warns(RuntimeWarning, match='Cannot render MRI'):
report.parse_folder(data_path=tempdir, on_error='raise')
# ndarray support smoke test
report.add_figs_to_section(np.zeros((2, 3, 3)), 'caption', 'section')
with pytest.raises(TypeError, match='Each fig must be a'):
report.add_figs_to_section('foo', 'caption', 'section')
with pytest.raises(TypeError, match='Each fig must be a'):
report.add_figs_to_section(['foo'], 'caption', 'section')
def test_render_report():
"""Test rendering -*.fif files for mne report."""
tempdir = _TempDir()
raw_fname_new = op.join(tempdir, 'temp_raw.fif')
event_fname_new = op.join(tempdir, 'temp_raw-eve.fif')
cov_fname_new = op.join(tempdir, 'temp_raw-cov.fif')
fwd_fname_new = op.join(tempdir, 'temp_raw-fwd.fif')
inv_fname_new = op.join(tempdir, 'temp_raw-inv.fif')
for a, b in [[raw_fname, raw_fname_new], [event_fname, event_fname_new],
[cov_fname, cov_fname_new], [fwd_fname, fwd_fname_new],
[inv_fname, inv_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')
raw = read_raw_fif(raw_fname_new, add_eeg_ref=False)
picks = pick_types(raw.info, meg='mag', eeg=False) # faster with one type
epochs = Epochs(raw,
read_events(event_fname),
1,
-0.2,
0.2,
picks=picks,
add_eeg_ref=False)
epochs.save(epochs_fname)
epochs.average().save(evoked_fname)
report = Report(info_fname=raw_fname_new, subjects_dir=subjects_dir)
if sys.version.startswith('3.5'): # XXX Some strange MPL/3.5 error...
raise SkipTest('Python 3.5 and mpl have unresolved issues')
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
report.parse_folder(data_path=tempdir, on_error='raise')
assert_true(len(w) >= 1)
assert_true(repr(report))
# Check correct paths and filenames
fnames = glob.glob(op.join(tempdir, '*.fif'))
for fname in fnames:
assert_true(
op.basename(fname) in [op.basename(x) for x in report.fnames])
assert_true(''.join(report.html).find(op.basename(fname)) != -1)
assert_equal(len(report.fnames), len(fnames))
assert_equal(len(report.html), len(report.fnames))
assert_equal(len(report.fnames), len(report))
# Check saving functionality
report.data_path = tempdir
report.save(fname=op.join(tempdir, 'report.html'), open_browser=False)
assert_true(op.isfile(op.join(tempdir, 'report.html')))
assert_equal(len(report.html), len(fnames))
assert_equal(len(report.html), len(report.fnames))
# Check saving same report to new filename
report.save(fname=op.join(tempdir, 'report2.html'), open_browser=False)
assert_true(op.isfile(op.join(tempdir, 'report2.html')))
# Check overwriting file
report.save(fname=op.join(tempdir, 'report.html'),
open_browser=False,
overwrite=True)
assert_true(op.isfile(op.join(tempdir, 'report.html')))
# Check pattern matching with multiple patterns
pattern = ['*raw.fif', '*eve.fif']
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
report.parse_folder(data_path=tempdir, pattern=pattern)
assert_true(len(w) >= 1)
assert_true(repr(report))
fnames = glob.glob(op.join(tempdir, '*.raw')) + \
glob.glob(op.join(tempdir, '*.raw'))
for fname in fnames:
assert_true(
op.basename(fname) in [op.basename(x) for x in report.fnames])
assert_true(''.join(report.html).find(op.basename(fname)) != -1)
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')
def test_render_report(renderer, tmpdir):
"""Test rendering *.fif files for mne report."""
tempdir = str(tmpdir)
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], [event_fname, event_fname_new],
[cov_fname, cov_fname_new], [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, preload=True)
raw.pick_channels(['MEG 0111', 'MEG 0121', 'EEG 001', 'EEG 002'])
raw.del_proj()
raw.set_eeg_reference(projection=True)
epochs = Epochs(raw, read_events(event_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=True)
with pytest.warns(RuntimeWarning, match='Cannot render MRI'):
report.parse_folder(data_path=tempdir, on_error='raise')
assert repr(report)
# Check correct paths and filenames
fnames = glob.glob(op.join(tempdir, '*.fif'))
fnames.extend(glob.glob(op.join(tempdir, '*.snirf')))
for fname in fnames:
assert (op.basename(fname) in [op.basename(x) for x in report.fnames])
assert (''.join(report.html).find(op.basename(fname)) != -1)
assert len(report.fnames) == len(fnames)
assert len(report.html) == len(report.fnames)
assert len(report.fnames) == len(report)
# Check saving functionality
report.data_path = tempdir
fname = op.join(tempdir, 'report.html')
report.save(fname=fname, open_browser=False)
assert (op.isfile(fname))
with open(fname, 'rb') as fid:
html = fid.read().decode('utf-8')
assert '(MaxShield on)' in html
# Projectors in Raw.info
assert '<h4>SSP Projectors</h4>' in html
# Projectors in `proj_fname_new`
assert f'SSP Projectors: {op.basename(proj_fname_new)}' in html
# Evoked in `evoked_fname`
assert f'Evoked: {op.basename(evoked_fname)} ({evoked.comment})' in html
assert 'Topomap (ch_type =' in html
assert f'Evoked: {op.basename(evoked_fname)} (GFPs)' in html
assert len(report.html) == len(fnames)
assert len(report.html) == len(report.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 = ['*raw.fif', '*eve.fif']
with pytest.warns(RuntimeWarning, match='Cannot render MRI'):
report.parse_folder(data_path=tempdir, pattern=pattern)
assert (repr(report))
fnames = glob.glob(op.join(tempdir, '*.raw')) + \
glob.glob(op.join(tempdir, '*.raw'))
for fname in fnames:
assert (op.basename(fname) in [op.basename(x) for x in report.fnames])
assert (''.join(report.html).find(op.basename(fname)) != -1)
pytest.raises(ValueError, Report, image_format='foo')
pytest.raises(ValueError, Report, image_format=None)
# SVG rendering
report = Report(info_fname=raw_fname_new,
subjects_dir=subjects_dir,
image_format='svg')
tempdir = pathlib.Path(tempdir) # test using pathlib.Path
with pytest.warns(RuntimeWarning, match='Cannot render MRI'):
report.parse_folder(data_path=tempdir, on_error='raise')
# ndarray support smoke test
report.add_figs_to_section(np.zeros((2, 3, 3)), 'caption', 'section')
with pytest.raises(TypeError, match='figure must be a'):
report.add_figs_to_section('foo', 'caption', 'section')
with pytest.raises(TypeError, match='figure must be a'):
report.add_figs_to_section(['foo'], 'caption', 'section')
def test_render_report():
"""Test rendering -*.fif files for mne report."""
tempdir = _TempDir()
raw_fname_new = op.join(tempdir, 'temp_raw.fif')
event_fname_new = op.join(tempdir, 'temp_raw-eve.fif')
cov_fname_new = op.join(tempdir, 'temp_raw-cov.fif')
fwd_fname_new = op.join(tempdir, 'temp_raw-fwd.fif')
inv_fname_new = op.join(tempdir, 'temp_raw-inv.fif')
for a, b in [[raw_fname, raw_fname_new],
[event_fname, event_fname_new],
[cov_fname, cov_fname_new],
[fwd_fname, fwd_fname_new],
[inv_fname, inv_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')
raw = read_raw_fif(raw_fname_new)
picks = pick_types(raw.info, meg='mag', eeg=False) # faster with one type
epochs = Epochs(raw, read_events(event_fname), 1, -0.2, 0.2, picks=picks)
epochs.save(epochs_fname)
epochs.average().save(evoked_fname)
report = Report(info_fname=raw_fname_new, subjects_dir=subjects_dir)
if sys.version.startswith('3.5'): # XXX Some strange MPL/3.5 error...
raise SkipTest('Python 3.5 and mpl have unresolved issues')
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
report.parse_folder(data_path=tempdir, on_error='raise')
assert_true(len(w) >= 1)
assert_true(repr(report))
# Check correct paths and filenames
fnames = glob.glob(op.join(tempdir, '*.fif'))
for fname in fnames:
assert_true(op.basename(fname) in
[op.basename(x) for x in report.fnames])
assert_true(''.join(report.html).find(op.basename(fname)) != -1)
assert_equal(len(report.fnames), len(fnames))
assert_equal(len(report.html), len(report.fnames))
assert_equal(len(report.fnames), len(report))
# Check saving functionality
report.data_path = tempdir
report.save(fname=op.join(tempdir, 'report.html'), open_browser=False)
assert_true(op.isfile(op.join(tempdir, 'report.html')))
assert_equal(len(report.html), len(fnames))
assert_equal(len(report.html), len(report.fnames))
# Check saving same report to new filename
report.save(fname=op.join(tempdir, 'report2.html'), open_browser=False)
assert_true(op.isfile(op.join(tempdir, 'report2.html')))
# Check overwriting file
report.save(fname=op.join(tempdir, 'report.html'), open_browser=False,
overwrite=True)
assert_true(op.isfile(op.join(tempdir, 'report.html')))
# Check pattern matching with multiple patterns
pattern = ['*raw.fif', '*eve.fif']
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
report.parse_folder(data_path=tempdir, pattern=pattern)
assert_true(len(w) >= 1)
assert_true(repr(report))
fnames = glob.glob(op.join(tempdir, '*.raw')) + \
glob.glob(op.join(tempdir, '*.raw'))
for fname in fnames:
assert_true(op.basename(fname) in
[op.basename(x) for x in report.fnames])
assert_true(''.join(report.html).find(op.basename(fname)) != -1)
def test_render_report():
"""Test rendering -*.fif files for mne report."""
tempdir = _TempDir()
raw_fname_new = op.join(tempdir, 'temp_raw.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')
fwd_fname_new = op.join(tempdir, 'temp_raw-fwd.fif')
inv_fname_new = op.join(tempdir, 'temp_raw-inv.fif')
for a, b in [[raw_fname, raw_fname_new],
[ms_fname, ms_fname_new],
[event_fname, event_fname_new],
[cov_fname, cov_fname_new],
[fwd_fname, fwd_fname_new],
[inv_fname, inv_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, preload=True)
raw.pick_channels(['MEG 0111', 'MEG 0121'])
raw.del_proj()
epochs = Epochs(raw, read_events(event_fname), 1, -0.2, 0.2)
epochs.save(epochs_fname)
# This can take forever (stall Travis), so let's make it fast
# Also, make sure crop range is wide enough to avoid rendering bug
epochs.average().crop(0.1, 0.2).save(evoked_fname)
report = Report(info_fname=raw_fname_new, subjects_dir=subjects_dir)
with pytest.warns(RuntimeWarning, match='Cannot render MRI'):
report.parse_folder(data_path=tempdir, on_error='raise')
assert repr(report)
# Check correct paths and filenames
fnames = glob.glob(op.join(tempdir, '*.fif'))
for fname in fnames:
assert (op.basename(fname) in
[op.basename(x) for x in report.fnames])
assert (''.join(report.html).find(op.basename(fname)) != -1)
assert_equal(len(report.fnames), len(fnames))
assert_equal(len(report.html), len(report.fnames))
assert_equal(len(report.fnames), len(report))
# Check saving functionality
report.data_path = tempdir
fname = op.join(tempdir, 'report.html')
report.save(fname=fname, open_browser=False)
assert (op.isfile(fname))
with open(fname, 'rb') as fid:
html = fid.read().decode('utf-8')
assert '(MaxShield on)' in html
assert_equal(len(report.html), len(fnames))
assert_equal(len(report.html), len(report.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 = ['*raw.fif', '*eve.fif']
with pytest.warns(RuntimeWarning, match='Cannot render MRI'):
report.parse_folder(data_path=tempdir, pattern=pattern)
assert (repr(report))
fnames = glob.glob(op.join(tempdir, '*.raw')) + \
glob.glob(op.join(tempdir, '*.raw'))
for fname in fnames:
assert (op.basename(fname) in
[op.basename(x) for x in report.fnames])
assert (''.join(report.html).find(op.basename(fname)) != -1)
pytest.raises(ValueError, Report, image_format='foo')
pytest.raises(ValueError, Report, image_format=None)
# SVG rendering
report = Report(info_fname=raw_fname_new, subjects_dir=subjects_dir,
image_format='svg')
with pytest.warns(RuntimeWarning, match='Cannot render MRI'):
report.parse_folder(data_path=tempdir, on_error='raise')
# ndarray support smoke test
report.add_figs_to_section(np.zeros((2, 3, 3)), 'caption', 'section')
def setup_provenance(script, results_dir, use_agg=True):
"""Setup provenance tracking
Parameters
----------
script : str
The script that was executed.
results_dir : str
The results directory.
use_agg : bool
Whether to use the 'Agg' backend for matplotlib or not.
Returns
-------
report : mne.report.Report
The mne report.
Side-effects
------------
- make results dir if it does not exists
- sets log file for sterr output
- writes log file with runtime information
"""
if use_agg is True:
import matplotlib
matplotlib.use('Agg')
if not op.isfile(script):
raise ValueError('sorry, this is not a script!')
step = op.splitext(op.split(script)[1])[0]
results_dir = op.join(results_dir, step)
if not op.exists(results_dir):
logger.info('generating results dir')
os.mkdir(results_dir)
run_id = create_run_id()
logger.info('generated run id: %s' % run_id)
logger.info('preparing logging:')
logging_dir = op.join(results_dir, run_id)
logger.info('... making logging directory: %s' % logging_dir)
os.mkdir(logging_dir)
modules = get_versions(sys)
runtime_log = op.join(logging_dir, 'run_time.json')
with open(runtime_log, 'w') as fid:
json.dump(modules, fid)
logger.info('... writing runtime info to: %s' % runtime_log)
std_logfile = op.join(logging_dir, 'run_output.log')
script_code = op.join(logging_dir, 'script.py')
with open(script_code, 'w') as fid:
with open(script) as script_fid:
source_code = script_fid.read()
fid.write(source_code)
logger.info('... logging source code')
logger.info('... preparing Report')
report = Report(title=step)
report.data_path = logging_dir
logger.info('... setting logfile: %s' % std_logfile)
set_log_file(std_logfile)
return report, run_id, results_dir, logger
