# -*- coding: utf-8 -*- import os from os import path as op import shutil import glob import pytest from numpy.testing import assert_equal, assert_allclose from mne import concatenate_raws, read_bem_surfaces, read_surface from mne.commands import (mne_browse_raw, mne_bti2fiff, mne_clean_eog_ecg, mne_compute_proj_ecg, mne_compute_proj_eog, mne_coreg, mne_kit2fiff, mne_make_scalp_surfaces, mne_maxfilter, mne_report, mne_surf2bem, mne_watershed_bem, mne_compare_fiff, mne_flash_bem, mne_show_fiff, mne_show_info, mne_what) from mne.datasets import testing, sample from mne.io import read_raw_fif from mne.utils import (run_tests_if_main, requires_mne, requires_mayavi, requires_tvtk, requires_freesurfer, traits_test, ArgvSetter, modified_env) base_dir = op.join(op.dirname(__file__), '..', '..', 'io', 'tests', 'data') raw_fname = op.join(base_dir, 'test_raw.fif') subjects_dir = op.join(testing.data_path(download=False), 'subjects') def check_usage(module, force_help=False): """Ensure we print usage.""" args = ('--help',) if force_help else () with ArgvSetter(args) as out: try: module.run() except SystemExit: pass assert 'Usage: ' in out.stdout.getvalue() @pytest.mark.slowtest def test_browse_raw(): """Test mne browse_raw.""" check_usage(mne_browse_raw) with ArgvSetter(('--raw', raw_fname)): with pytest.warns(None): # mpl show warning sometimes mne_browse_raw.run() def test_what(): """Test mne browse_raw.""" check_usage(mne_browse_raw) with ArgvSetter((raw_fname,)) as out: mne_what.run() assert 'raw' == out.stdout.getvalue().strip() def test_bti2fiff(): """Test mne bti2fiff.""" check_usage(mne_bti2fiff) def test_compare_fiff(): """Test mne compare_fiff.""" check_usage(mne_compare_fiff) def test_show_fiff(): """Test mne compare_fiff.""" check_usage(mne_show_fiff) with ArgvSetter((raw_fname,)): mne_show_fiff.run() with ArgvSetter((raw_fname, '--tag=102')): mne_show_fiff.run() @requires_mne def test_clean_eog_ecg(tmpdir): """Test mne clean_eog_ecg.""" check_usage(mne_clean_eog_ecg) tempdir = str(tmpdir) raw = concatenate_raws([read_raw_fif(f) for f in [raw_fname, raw_fname, raw_fname]]) raw.info['bads'] = ['MEG 2443'] use_fname = op.join(tempdir, op.basename(raw_fname)) raw.save(use_fname) with ArgvSetter(('-i', use_fname, '--quiet')): mne_clean_eog_ecg.run() for key, count in (('proj', 2), ('-eve', 3)): fnames = glob.glob(op.join(tempdir, '*%s.fif' % key)) assert len(fnames) == count @pytest.mark.slowtest @pytest.mark.parametrize('fun', (mne_compute_proj_ecg, mne_compute_proj_eog)) def test_compute_proj_exg(tmpdir, fun): """Test mne compute_proj_ecg/eog.""" check_usage(fun) tempdir = str(tmpdir) use_fname = op.join(tempdir, op.basename(raw_fname)) bad_fname = op.join(tempdir, 'bads.txt') with open(bad_fname, 'w') as fid: fid.write('MEG 2443\n') shutil.copyfile(raw_fname, use_fname) with ArgvSetter(('-i', use_fname, '--bad=' + bad_fname, '--rej-eeg', '150')): with pytest.warns(None): # samples, sometimes fun.run() fnames = glob.glob(op.join(tempdir, '*proj.fif')) assert len(fnames) == 1 fnames = glob.glob(op.join(tempdir, '*-eve.fif')) assert len(fnames) == 1 def test_coreg(): """Test mne coreg.""" assert hasattr(mne_coreg, 'run') def test_kit2fiff(): """Test mne kit2fiff.""" # Can't check check_usage(mne_kit2fiff, force_help=True) @pytest.mark.slowtest # slow on Travis OSX @requires_tvtk @testing.requires_testing_data def test_make_scalp_surfaces(tmpdir): """Test mne make_scalp_surfaces.""" check_usage(mne_make_scalp_surfaces) has = 'SUBJECTS_DIR' in os.environ # Copy necessary files to avoid FreeSurfer call tempdir = str(tmpdir) surf_path = op.join(subjects_dir, 'sample', 'surf') surf_path_new = op.join(tempdir, 'sample', 'surf') os.mkdir(op.join(tempdir, 'sample')) os.mkdir(surf_path_new) subj_dir = op.join(tempdir, 'sample', 'bem') os.mkdir(subj_dir) shutil.copy(op.join(surf_path, 'lh.seghead'), surf_path_new) cmd = ('-s', 'sample', '--subjects-dir', tempdir) with modified_env(**{'_MNE_TESTING_SCALP': 'true'}): dense_fname = op.join(subj_dir, 'sample-head-dense.fif') medium_fname = op.join(subj_dir, 'sample-head-medium.fif') with ArgvSetter(cmd, disable_stdout=False, disable_stderr=False): with modified_env(FREESURFER_HOME=None): pytest.raises(RuntimeError, mne_make_scalp_surfaces.run) with modified_env(FREESURFER_HOME=tempdir): mne_make_scalp_surfaces.run() assert op.isfile(dense_fname) assert op.isfile(medium_fname) with pytest.raises(IOError, match='overwrite'): mne_make_scalp_surfaces.run() # actually check the outputs head_py = read_bem_surfaces(dense_fname) assert_equal(len(head_py), 1) head_py = head_py[0] head_c = read_bem_surfaces(op.join(subjects_dir, 'sample', 'bem', 'sample-head-dense.fif'))[0] assert_allclose(head_py['rr'], head_c['rr']) if not has: assert 'SUBJECTS_DIR' not in os.environ def test_maxfilter(): """Test mne maxfilter.""" check_usage(mne_maxfilter) with ArgvSetter(('-i', raw_fname, '--st', '--movecomp', '--linefreq', '60', '--trans', raw_fname)) as out: with pytest.warns(RuntimeWarning, match="Don't use"): os.environ['_MNE_MAXFILTER_TEST'] = 'true' try: mne_maxfilter.run() finally: del os.environ['_MNE_MAXFILTER_TEST'] for check in ('maxfilter', '-trans', '-movecomp'): assert check in out.stdout.getvalue(), check @pytest.mark.slowtest @requires_mayavi @traits_test @testing.requires_testing_data def test_report(tmpdir): """Test mne report.""" check_usage(mne_report) tempdir = str(tmpdir) use_fname = op.join(tempdir, op.basename(raw_fname)) shutil.copyfile(raw_fname, use_fname) with ArgvSetter(('-p', tempdir, '-i', use_fname, '-d', subjects_dir, '-s', 'sample', '--no-browser', '-m', '30')): with pytest.warns(None): # contour levels mne_report.run() fnames = glob.glob(op.join(tempdir, '*.html')) assert len(fnames) == 1 def test_surf2bem(): """Test mne surf2bem.""" check_usage(mne_surf2bem) @pytest.mark.timeout(600) # took ~400 sec on a local test @pytest.mark.slowtest @pytest.mark.ultraslowtest @requires_freesurfer @testing.requires_testing_data def test_watershed_bem(tmpdir): """Test mne watershed bem.""" check_usage(mne_watershed_bem) # Copy necessary files to tempdir tempdir = str(tmpdir) mridata_path = op.join(subjects_dir, 'sample', 'mri') subject_path_new = op.join(tempdir, 'sample') mridata_path_new = op.join(subject_path_new, 'mri') os.mkdir(op.join(tempdir, 'sample')) os.mkdir(mridata_path_new) if op.exists(op.join(mridata_path, 'T1')): shutil.copytree(op.join(mridata_path, 'T1'), op.join(mridata_path_new, 'T1')) if op.exists(op.join(mridata_path, 'T1.mgz')): shutil.copyfile(op.join(mridata_path, 'T1.mgz'), op.join(mridata_path_new, 'T1.mgz')) out_fnames = list() for kind in ('outer_skin', 'outer_skull', 'inner_skull'): out_fnames.append(op.join(subject_path_new, 'bem', 'inner_skull.surf')) assert not any(op.isfile(out_fname) for out_fname in out_fnames) with ArgvSetter(('-d', tempdir, '-s', 'sample', '-o'), disable_stdout=False, disable_stderr=False): mne_watershed_bem.run() for out_fname in out_fnames: _, tris = read_surface(out_fname) assert len(tris) == 20480 @pytest.mark.timeout(300) # took 200 sec locally @pytest.mark.slowtest @pytest.mark.ultraslowtest @requires_freesurfer @sample.requires_sample_data def test_flash_bem(tmpdir): """Test mne flash_bem.""" check_usage(mne_flash_bem, force_help=True) # Using the sample dataset subjects_dir = op.join(sample.data_path(download=False), 'subjects') # Copy necessary files to tempdir tempdir = str(tmpdir) mridata_path = op.join(subjects_dir, 'sample', 'mri') subject_path_new = op.join(tempdir, 'sample') mridata_path_new = op.join(subject_path_new, 'mri') os.makedirs(op.join(mridata_path_new, 'flash')) os.makedirs(op.join(subject_path_new, 'bem')) shutil.copyfile(op.join(mridata_path, 'T1.mgz'), op.join(mridata_path_new, 'T1.mgz')) shutil.copyfile(op.join(mridata_path, 'brain.mgz'), op.join(mridata_path_new, 'brain.mgz')) # Copy the available mri/flash/mef*.mgz files from the dataset flash_path = op.join(mridata_path_new, 'flash') for kind in (5, 30): in_fname = op.join(mridata_path, 'flash', 'mef%02d.mgz' % kind) shutil.copyfile(in_fname, op.join(flash_path, op.basename(in_fname))) # Test mne flash_bem with --noconvert option # (since there are no DICOM Flash images in dataset) out_fnames = list() for kind in ('outer_skin', 'outer_skull', 'inner_skull'): out_fnames.append(op.join(subject_path_new, 'bem', 'outer_skin.surf')) assert not any(op.isfile(out_fname) for out_fname in out_fnames) with ArgvSetter(('-d', tempdir, '-s', 'sample', '-n'), disable_stdout=False, disable_stderr=False): mne_flash_bem.run() # do they exist and are expected size for out_fname in out_fnames: _, tris = read_surface(out_fname) assert len(tris) == 5120 def test_show_info(): """Test mne show_info.""" check_usage(mne_show_info) with ArgvSetter((raw_fname,)): mne_show_info.run() run_tests_if_main()