# Authors: Mainak Jas # Teon Brooks # # License: BSD (3-clause) import glob import os import os.path as op import shutil import sys import warnings from nose.tools import assert_true, assert_equal, assert_raises from nose.plugins.skip import SkipTest from mne import Epochs, read_events, pick_types, read_evokeds from mne.io import read_raw_fif from mne.datasets import testing from mne.report import Report from mne.utils import (_TempDir, requires_mayavi, requires_nibabel, requires_PIL, run_tests_if_main, slow_test) from mne.viz import plot_trans 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') 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') # Set our plotters to test mode warnings.simplefilter('always') # enable b/c these tests throw warnings @slow_test @testing.requires_testing_data @requires_PIL 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) @testing.requires_testing_data @requires_mayavi @requires_PIL def test_render_add_sections(): """Test adding figures/images to section.""" from PIL import Image 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') assert_raises(ValueError, report.add_figs_to_section, figs=[fig, fig], captions='H') assert_raises(ValueError, report.add_figs_to_section, figs=fig, captions=['foo'], scale=0, image_format='svg') assert_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 and then gif img_fname = op.join(tempdir, 'testimage.png') fig.savefig(img_fname) report.add_images_to_section(fnames=[img_fname], captions=['evoked response']) im = Image.open(img_fname) op.join(tempdir, 'testimage.gif') im.save(img_fname) # matplotlib does not support gif report.add_images_to_section(fnames=[img_fname], captions=['evoked response']) assert_raises(ValueError, report.add_images_to_section, fnames=[img_fname, img_fname], captions='H') assert_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_trans(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_true(repr(report)) @slow_test @testing.requires_testing_data @requires_mayavi @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) with warnings.catch_warnings(record=True): warnings.simplefilter('always') report.parse_folder(data_path=tempdir, mri_decim=30, pattern='*', n_jobs=2) report.save(op.join(tempdir, 'report.html'), open_browser=False) assert_true(repr(report)) @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) with warnings.catch_warnings(record=True) as w: warnings.simplefilter('always') report.parse_folder(tempdir) assert_true(len(w) >= 1) 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 = 'MNE-Python is AWESOME' 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_true(html in html_compare) assert_true(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 = 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_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'] assert_raises(ValueError, report._validate_input, items, captions[:-1], section, comments=None) assert_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)) run_tests_if_main()