# -*- 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 import matplotlib from mne import concatenate_raws, read_bem_surfaces 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) from mne.datasets import testing, sample from mne.io import read_raw_fif from mne.utils import (run_tests_if_main, _TempDir, requires_mne, requires_mayavi, requires_tvtk, requires_freesurfer, traits_test, ArgvSetter) matplotlib.use('Agg') 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_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(): """Test mne clean_eog_ecg.""" check_usage(mne_clean_eog_ecg) tempdir = _TempDir() 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() fnames = glob.glob(op.join(tempdir, '*proj.fif')) assert len(fnames) == 2 # two projs fnames = glob.glob(op.join(tempdir, '*-eve.fif')) assert len(fnames) == 3 # raw plus two projs @pytest.mark.slowtest def test_compute_proj_ecg_eog(): """Test mne compute_proj_ecg/eog.""" for fun in (mne_compute_proj_ecg, mne_compute_proj_eog): check_usage(fun) tempdir = _TempDir() 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) @requires_tvtk @testing.requires_testing_data def test_make_scalp_surfaces(): """Test mne make_scalp_surfaces.""" check_usage(mne_make_scalp_surfaces) # Copy necessary files to avoid FreeSurfer call tempdir = _TempDir() 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) orig_fs = os.getenv('FREESURFER_HOME', None) if orig_fs is not None: del os.environ['FREESURFER_HOME'] cmd = ('-s', 'sample', '--subjects-dir', tempdir) os.environ['_MNE_TESTING_SCALP'] = 'true' dense_fname = op.join(subj_dir, 'sample-head-dense.fif') medium_fname = op.join(subj_dir, 'sample-head-medium.fif') try: with ArgvSetter(cmd, disable_stdout=False, disable_stderr=False): pytest.raises(RuntimeError, mne_make_scalp_surfaces.run) os.environ['FREESURFER_HOME'] = tempdir # don't actually use it mne_make_scalp_surfaces.run() assert op.isfile(dense_fname) assert op.isfile(medium_fname) pytest.raises(IOError, mne_make_scalp_surfaces.run) # no overwrite finally: if orig_fs is not None: os.environ['FREESURFER_HOME'] = orig_fs else: del os.environ['FREESURFER_HOME'] del os.environ['_MNE_TESTING_SCALP'] # 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']) 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(): """Test mne report.""" check_usage(mne_report) tempdir = _TempDir() 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.slowtest @pytest.mark.ultraslowtest @requires_freesurfer @testing.requires_testing_data def test_watershed_bem(): """Test mne watershed bem.""" check_usage(mne_watershed_bem) # Copy necessary files to tempdir tempdir = _TempDir() mridata_path = op.join(subjects_dir, 'sample', 'mri') mridata_path_new = op.join(tempdir, 'sample', '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')) with ArgvSetter(('-d', tempdir, '-s', 'sample', '-o'), disable_stdout=False, disable_stderr=False): mne_watershed_bem.run() @pytest.mark.slowtest @pytest.mark.ultraslowtest @requires_freesurfer @sample.requires_sample_data def test_flash_bem(): """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 = _TempDir() mridata_path = op.join(subjects_dir, 'sample', 'mri') mridata_path_new = op.join(tempdir, 'sample', 'mri') os.makedirs(op.join(mridata_path_new, 'flash')) os.makedirs(op.join(tempdir, 'sample', '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 files = glob.glob(op.join(mridata_path, 'flash', 'mef*.mgz')) for infile in files: shutil.copyfile(infile, op.join(mridata_path_new, 'flash', op.basename(infile))) # Test mne flash_bem with --noconvert option # (since there are no DICOM Flash images in dataset) currdir = os.getcwd() with ArgvSetter(('-d', tempdir, '-s', 'sample', '-n'), disable_stdout=False, disable_stderr=False): mne_flash_bem.run() os.chdir(currdir) 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()