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# -*- coding: utf-8 -*-
# Authors: Mainak Jas <mainak@neuro.hut.fi>
# Teon Brooks <teon.brooks@gmail.com>
#
# License: BSD (3-clause)
import copy
import glob
import os
import os.path as op
import shutil
import numpy as np
from numpy.testing import assert_equal
import pytest
from mne import Epochs, read_events, read_evokeds
from mne.io import read_raw_fif
from mne.datasets import testing
from mne.report import Report, open_report
from mne.utils import (_TempDir, requires_mayavi, requires_nibabel,
run_tests_if_main, traits_test, requires_h5py)
from mne.viz import plot_alignment
import matplotlib
matplotlib.use('Agg') # for testing don't use X server
data_dir = testing.data_path(download=False)
subjects_dir = op.join(data_dir, 'subjects')
report_dir = op.join(data_dir, 'MEG', 'sample')
raw_fname = op.join(report_dir, 'sample_audvis_trunc_raw.fif')
ms_fname = op.join(data_dir, 'SSS', 'test_move_anon_raw.fif')
event_fname = op.join(report_dir, 'sample_audvis_trunc_raw-eve.fif')
cov_fname = op.join(report_dir, 'sample_audvis_trunc-cov.fif')
fwd_fname = op.join(report_dir, 'sample_audvis_trunc-meg-eeg-oct-6-fwd.fif')
trans_fname = op.join(report_dir, 'sample_audvis_trunc-trans.fif')
inv_fname = op.join(report_dir,
'sample_audvis_trunc-meg-eeg-oct-6-meg-inv.fif')
mri_fname = op.join(subjects_dir, 'sample', 'mri', 'T1.mgz')
base_dir = op.realpath(op.join(op.dirname(__file__), '..', 'io', 'tests',
'data'))
evoked_fname = op.join(base_dir, 'test-ave.fif')
def _get_example_figures():
"""Create two example figures."""
from matplotlib import pyplot as plt
fig1 = plt.plot([1, 2], [1, 2])[0].figure
fig2 = plt.plot([3, 4], [3, 4])[0].figure
return [fig1, fig2]
@pytest.mark.slowtest
@testing.requires_testing_data
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')
@testing.requires_testing_data
def test_report_raw_psd_and_date():
"""Test report raw PSD and DATE_NONE functionality."""
with pytest.raises(TypeError, match='dict'):
Report(raw_psd='foo')
tempdir = _TempDir()
raw = read_raw_fif(raw_fname).crop(0, 1.).load_data()
raw_fname_new = op.join(tempdir, 'temp_raw.fif')
raw.save(raw_fname_new)
report = Report(raw_psd=True)
report.parse_folder(data_path=tempdir, render_bem=False,
on_error='raise')
assert isinstance(report.html, list)
assert 'PSD' in ''.join(report.html)
assert 'GMT' in ''.join(report.html)
# DATE_NONE functionality
report = Report()
raw.anonymize()
raw.save(raw_fname_new, overwrite=True)
report.parse_folder(data_path=tempdir, render_bem=False,
on_error='raise')
assert isinstance(report.html, list)
assert 'GMT' not in ''.join(report.html)
@testing.requires_testing_data
@requires_mayavi
@traits_test
def test_render_add_sections():
"""Test adding figures/images to section."""
tempdir = _TempDir()
import matplotlib.pyplot as plt
report = Report(subjects_dir=subjects_dir)
# Check add_figs_to_section functionality
fig = plt.plot([1, 2], [1, 2])[0].figure
report.add_figs_to_section(figs=fig, # test non-list input
captions=['evoked response'], scale=1.2,
image_format='svg')
pytest.raises(ValueError, report.add_figs_to_section, figs=[fig, fig],
captions='H')
pytest.raises(ValueError, report.add_figs_to_section, figs=fig,
captions=['foo'], scale=0, image_format='svg')
pytest.raises(ValueError, report.add_figs_to_section, figs=fig,
captions=['foo'], scale=1e-10, image_format='svg')
# need to recreate because calls above change size
fig = plt.plot([1, 2], [1, 2])[0].figure
# Check add_images_to_section with png
img_fname = op.join(tempdir, 'testimage.png')
fig.savefig(img_fname)
report.add_images_to_section(fnames=[img_fname],
captions=['evoked response'])
report.add_images_to_section(fnames=[img_fname],
captions=['evoked response'])
pytest.raises(ValueError, report.add_images_to_section,
fnames=[img_fname, img_fname], captions='H')
pytest.raises(ValueError, report.add_images_to_section,
fnames=['foobar.xxx'], captions='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_figs_to_section(figs=fig, # test non-list input
captions='random image', scale=1.2)
assert (repr(report))
@pytest.mark.slowtest
@testing.requires_testing_data
@requires_mayavi
@traits_test
@requires_nibabel()
def test_render_mri():
"""Test rendering MRI for mne report."""
tempdir = _TempDir()
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='*')
report.save(op.join(tempdir, 'report.html'), open_browser=False)
assert repr(report)
report.add_bem_to_section('sample', caption='extra', section='foo',
subjects_dir=subjects_dir, decim=30)
report.save(op.join(tempdir, 'report.html'), open_browser=False,
overwrite=True)
@testing.requires_testing_data
@requires_nibabel()
def test_render_mri_without_bem():
"""Test rendering MRI without BEM for mne report."""
tempdir = _TempDir()
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)
report.parse_folder(tempdir, render_bem=False)
report.save(op.join(tempdir, 'report.html'), open_browser=False)
@testing.requires_testing_data
@requires_nibabel()
def test_add_htmls_to_section():
"""Test adding html str to mne report."""
report = Report(info_fname=raw_fname,
subject='sample', subjects_dir=subjects_dir)
html = '<b>MNE-Python is AWESOME</b>'
caption, section = 'html', 'html_section'
report.add_htmls_to_section(html, caption, section)
idx = report._sectionlabels.index('report_' + section)
html_compare = report.html[idx]
assert (html in html_compare)
assert (repr(report))
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 = _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_validate_input():
"""Test Report input validation."""
report = Report()
items = ['a', 'b', 'c']
captions = ['Letter A', 'Letter B', 'Letter C']
section = 'ABCs'
comments = ['First letter of the alphabet.',
'Second letter of the alphabet',
'Third letter of the alphabet']
pytest.raises(ValueError, report._validate_input, items, captions[:-1],
section, comments=None)
pytest.raises(ValueError, report._validate_input, items, captions, section,
comments=comments[:-1])
values = report._validate_input(items, captions, section, comments=None)
items_new, captions_new, comments_new = values
assert_equal(len(comments_new), len(items))
@requires_h5py
def test_open_report():
"""Test the open_report function."""
tempdir = _TempDir()
hdf5 = op.join(tempdir, 'report.h5')
# Test creating a new report through the open_report function
fig1 = _get_example_figures()[0]
with open_report(hdf5, subjects_dir=subjects_dir) as report:
assert report.subjects_dir == subjects_dir
assert report._fname == hdf5
report.add_figs_to_section(figs=fig1, captions=['evoked response'])
# Exiting the context block should have triggered saving to HDF5
assert op.exists(hdf5)
# Load the HDF5 version of the report and check equivalency
report2 = open_report(hdf5)
assert report2._fname == hdf5
assert report2.subjects_dir == report.subjects_dir
assert report2.html == report.html
assert report2.__getstate__() == report.__getstate__()
assert '_fname' not in report2.__getstate__()
# Check parameters when loading a report
pytest.raises(ValueError, open_report, hdf5, foo='bar') # non-existing
pytest.raises(ValueError, open_report, hdf5, subjects_dir='foo')
open_report(hdf5, subjects_dir=subjects_dir) # This should work
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_figs_to_section(fig1, 'figure1', '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_or_replace():
"""Test replacing existing figures in a report."""
r = Report()
fig1, fig2 = _get_example_figures()
r.add_figs_to_section(fig1, 'duplicate', 'mysection')
r.add_figs_to_section(fig1, 'duplicate', 'mysection')
r.add_figs_to_section(fig1, 'duplicate', 'othersection')
r.add_figs_to_section(fig2, 'nonduplicate', 'mysection')
# By default, replace=False, so all figures should be there
assert len(r.html) == 4
old_r = copy.deepcopy(r)
# Re-add fig1 with replace=True, it should overwrite the last occurrence of
# fig1 in section 'mysection'.
r.add_figs_to_section(fig2, 'duplicate', 'mysection', replace=True)
assert len(r.html) == 4
assert r.html[1] != old_r.html[1] # This figure should have changed
# All other figures should be the same
assert r.html[0] == old_r.html[0]
assert r.html[2] == old_r.html[2]
assert r.html[3] == old_r.html[3]
run_tests_if_main()
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