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# -*- coding: utf-8 -*-
import os
from os import path as op
import shutil
import glob
import warnings
from nose.tools import assert_true, assert_raises
from mne import concatenate_raws
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_PIL,
requires_mayavi, requires_tvtk, requires_freesurfer,
ArgvSetter, slow_test, ultra_slow_test)
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')
warnings.simplefilter('always')
def check_usage(module, force_help=False):
"""Helper to ensure we print usage"""
args = ('--help',) if force_help else ()
with ArgvSetter(args) as out:
try:
module.run()
except SystemExit:
pass
assert_true('Usage: ' in out.stdout.getvalue())
@slow_test
def test_browse_raw():
"""Test mne browse_raw."""
check_usage(mne_browse_raw)
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()
@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, add_eeg_ref=False)
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_true(len(fnames) == 2) # two projs
fnames = glob.glob(op.join(tempdir, '*-eve.fif'))
assert_true(len(fnames) == 3) # raw plus two projs
@slow_test
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')):
fun.run()
fnames = glob.glob(op.join(tempdir, '*proj.fif'))
assert_true(len(fnames) == 1)
fnames = glob.glob(op.join(tempdir, '*-eve.fif'))
assert_true(len(fnames) == 1)
def test_coreg():
"""Test mne coreg."""
assert_true(hasattr(mne_coreg, 'run'))
def test_kit2fiff():
"""Test mne kit2fiff."""
# Can't check
check_usage(mne_kit2fiff, force_help=True)
@requires_tvtk
@requires_mne
@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)
orig_mne = os.getenv('MNE_ROOT')
if orig_fs is not None:
del os.environ['FREESURFER_HOME']
cmd = ('-s', 'sample', '--subjects-dir', tempdir)
os.environ['_MNE_TESTING_SCALP'] = 'true'
try:
with ArgvSetter(cmd, disable_stdout=False, disable_stderr=False):
assert_raises(RuntimeError, mne_make_scalp_surfaces.run)
os.environ['FREESURFER_HOME'] = tempdir # don't need it
del os.environ['MNE_ROOT']
assert_raises(RuntimeError, mne_make_scalp_surfaces.run)
os.environ['MNE_ROOT'] = orig_mne
mne_make_scalp_surfaces.run()
assert_true(op.isfile(op.join(subj_dir, 'sample-head-dense.fif')))
assert_true(op.isfile(op.join(subj_dir, 'sample-head-medium.fif')))
assert_raises(IOError, mne_make_scalp_surfaces.run) # no overwrite
finally:
if orig_fs is not None:
os.environ['FREESURFER_HOME'] = orig_fs
os.environ['MNE_ROOT'] = orig_mne
del os.environ['_MNE_TESTING_SCALP']
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 warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
os.environ['_MNE_MAXFILTER_TEST'] = 'true'
try:
mne_maxfilter.run()
finally:
del os.environ['_MNE_MAXFILTER_TEST']
assert_true(len(w) == 1)
for check in ('maxfilter', '-trans', '-movecomp'):
assert_true(check in out.stdout.getvalue(), check)
@slow_test
@requires_mayavi
@requires_PIL
@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')):
mne_report.run()
fnames = glob.glob(op.join(tempdir, '*.html'))
assert_true(len(fnames) == 1)
def test_surf2bem():
"""Test mne surf2bem."""
check_usage(mne_surf2bem)
@ultra_slow_test
@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()
@ultra_slow_test
@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()
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