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from __future__ import print_function
import os
import os.path as op
from subprocess import CalledProcessError
import warnings
from nose.tools import assert_raises, assert_true
from numpy.testing import (assert_equal, assert_allclose)
from mne.datasets import sample
from mne.io import Raw
from mne.io import read_raw_kit
from mne.io import read_raw_bti
from mne import (read_forward_solution, make_forward_solution,
do_forward_solution, setup_source_space, read_trans,
convert_forward_solution)
from mne.utils import requires_mne, _TempDir
from mne.tests.test_source_space import _compare_source_spaces
from mne.forward import Forward
data_path = sample.data_path(download=False)
fname = op.join(data_path, 'MEG', 'sample', 'sample_audvis-meg-oct-6-fwd.fif')
fname_meeg = op.join(data_path, 'MEG', 'sample',
'sample_audvis-meg-eeg-oct-6-fwd.fif')
fname_raw = op.join(op.dirname(__file__), '..', '..', 'io', 'tests', 'data',
'test_raw.fif')
fname_evoked = op.join(op.dirname(__file__), '..', '..', 'io', 'tests',
'data', 'test-ave.fif')
fname_mri = op.join(data_path, 'MEG', 'sample', 'sample_audvis_raw-trans.fif')
subjects_dir = os.path.join(data_path, 'subjects')
temp_dir = _TempDir()
# make a file that exists with some data in it
existing_file = op.join(temp_dir, 'test.fif')
with open(existing_file, 'w') as fid:
fid.write('aoeu')
def _compare_forwards(fwd, fwd_py, n_sensors, n_src,
meg_rtol=1e-4, meg_atol=1e-9):
"""Helper to test forwards"""
# check source spaces
assert_equal(len(fwd['src']), len(fwd_py['src']))
_compare_source_spaces(fwd['src'], fwd_py['src'], mode='approx')
for surf_ori in [False, True]:
if surf_ori:
# use copy here to leave our originals unmodified
fwd = convert_forward_solution(fwd, surf_ori, copy=True)
fwd_py = convert_forward_solution(fwd, surf_ori, copy=True)
for key in ['nchan', 'source_nn', 'source_rr', 'source_ori',
'surf_ori', 'coord_frame', 'nsource']:
print(key)
assert_allclose(fwd_py[key], fwd[key], rtol=1e-4, atol=1e-7)
assert_allclose(fwd_py['mri_head_t']['trans'],
fwd['mri_head_t']['trans'], rtol=1e-5, atol=1e-8)
assert_equal(fwd_py['sol']['data'].shape, (n_sensors, n_src))
assert_equal(len(fwd['sol']['row_names']), n_sensors)
assert_equal(len(fwd_py['sol']['row_names']), n_sensors)
# check MEG
print('check MEG')
assert_allclose(fwd['sol']['data'][:306],
fwd_py['sol']['data'][:306],
rtol=meg_rtol, atol=meg_atol)
# check EEG
if fwd['sol']['data'].shape[0] > 306:
print('check EEG')
assert_allclose(fwd['sol']['data'][306:],
fwd_py['sol']['data'][306:],
rtol=1e-3, atol=1e-3)
@sample.requires_sample_data
@requires_mne
def test_make_forward_solution_kit():
"""Test making fwd using KIT, BTI, and CTF (compensated) files
"""
fname_bem = op.join(subjects_dir, 'sample', 'bem',
'sample-5120-bem-sol.fif')
kit_dir = op.join(op.dirname(__file__), '..', '..', 'io', 'kit',
'tests', 'data')
sqd_path = op.join(kit_dir, 'test.sqd')
mrk_path = op.join(kit_dir, 'test_mrk.sqd')
elp_path = op.join(kit_dir, 'test_elp.txt')
hsp_path = op.join(kit_dir, 'test_hsp.txt')
mri_path = op.join(kit_dir, 'trans-sample.fif')
fname_kit_raw = op.join(kit_dir, 'test_bin_raw.fif')
bti_dir = op.join(op.dirname(__file__), '..', '..', 'io', 'bti',
'tests', 'data')
bti_pdf = op.join(bti_dir, 'test_pdf_linux')
bti_config = op.join(bti_dir, 'test_config_linux')
bti_hs = op.join(bti_dir, 'test_hs_linux')
fname_bti_raw = op.join(bti_dir, 'exported4D_linux_raw.fif')
fname_ctf_raw = op.join(op.dirname(__file__), '..', '..', 'io', 'tests',
'data', 'test_ctf_comp_raw.fif')
# first set up a testing source space
fname_src = op.join(temp_dir, 'oct2-src.fif')
src = setup_source_space('sample', fname_src, 'oct2',
subjects_dir=subjects_dir)
# first use mne-C: convert file, make forward solution
fwd = do_forward_solution('sample', fname_kit_raw, src=fname_src,
mindist=0.0, bem=fname_bem, mri=mri_path,
eeg=False, meg=True, subjects_dir=subjects_dir)
assert_true(isinstance(fwd, Forward))
# now let's use python with the same raw file
fwd_py = make_forward_solution(fname_kit_raw, mindist=0.0,
src=src, eeg=False, meg=True,
bem=fname_bem, mri=mri_path)
_compare_forwards(fwd, fwd_py, 157, 108)
assert_true(isinstance(fwd_py, Forward))
# now let's use mne-python all the way
raw_py = read_raw_kit(sqd_path, mrk_path, elp_path, hsp_path)
# without ignore_ref=True, this should throw an error:
assert_raises(NotImplementedError, make_forward_solution, raw_py.info,
mindist=0.0, src=src, eeg=False, meg=True,
bem=fname_bem, mri=mri_path)
fwd_py = make_forward_solution(raw_py.info, mindist=0.0,
src=src, eeg=False, meg=True,
bem=fname_bem, mri=mri_path,
ignore_ref=True)
_compare_forwards(fwd, fwd_py, 157, 108,
meg_rtol=1e-3, meg_atol=1e-7)
# BTI python end-to-end versus C
fwd = do_forward_solution('sample', fname_bti_raw, src=fname_src,
mindist=0.0, bem=fname_bem, mri=mri_path,
eeg=False, meg=True, subjects_dir=subjects_dir)
raw_py = read_raw_bti(bti_pdf, bti_config, bti_hs)
fwd_py = make_forward_solution(raw_py.info, mindist=0.0,
src=src, eeg=False, meg=True,
bem=fname_bem, mri=mri_path)
_compare_forwards(fwd, fwd_py, 248, 108)
# now let's test CTF w/compensation
fwd_py = make_forward_solution(fname_ctf_raw, mindist=0.0,
src=src, eeg=False, meg=True,
bem=fname_bem, mri=fname_mri)
fwd = do_forward_solution('sample', fname_ctf_raw, src=fname_src,
mindist=0.0, bem=fname_bem, mri=fname_mri,
eeg=False, meg=True, subjects_dir=subjects_dir)
_compare_forwards(fwd, fwd_py, 274, 108)
# CTF with compensation changed in python
ctf_raw = Raw(fname_ctf_raw, compensation=2)
fwd_py = make_forward_solution(ctf_raw.info, mindist=0.0,
src=src, eeg=False, meg=True,
bem=fname_bem, mri=fname_mri)
with warnings.catch_warnings(record=True):
fwd = do_forward_solution('sample', ctf_raw, src=fname_src,
mindist=0.0, bem=fname_bem, mri=fname_mri,
eeg=False, meg=True,
subjects_dir=subjects_dir)
_compare_forwards(fwd, fwd_py, 274, 108)
@sample.requires_sample_data
def test_make_forward_solution():
"""Test making M-EEG forward solution from python
"""
fname_src = op.join(subjects_dir, 'sample', 'bem', 'sample-oct-6-src.fif')
fname_bem = op.join(subjects_dir, 'sample', 'bem',
'sample-5120-5120-5120-bem-sol.fif')
fwd_py = make_forward_solution(fname_raw, mindist=5.0,
src=fname_src, eeg=True, meg=True,
bem=fname_bem, mri=fname_mri)
assert_true(isinstance(fwd_py, Forward))
fwd = read_forward_solution(fname_meeg)
assert_true(isinstance(fwd, Forward))
_compare_forwards(fwd, fwd_py, 366, 22494)
@sample.requires_sample_data
@requires_mne
def test_do_forward_solution():
"""Test wrapping forward solution from python
"""
mri = read_trans(fname_mri)
fname_fake = op.join(temp_dir, 'no_have.fif')
# ## Error checks
# bad subject
assert_raises(ValueError, do_forward_solution, 1, fname_raw,
subjects_dir=subjects_dir)
# bad meas
assert_raises(ValueError, do_forward_solution, 'sample', 1,
subjects_dir=subjects_dir)
# meas doesn't exist
assert_raises(IOError, do_forward_solution, 'sample', fname_fake,
subjects_dir=subjects_dir)
# don't specify trans and meas
assert_raises(ValueError, do_forward_solution, 'sample', fname_raw,
subjects_dir=subjects_dir)
# specify both trans and meas
assert_raises(ValueError, do_forward_solution, 'sample', fname_raw,
trans='me', mri='you', subjects_dir=subjects_dir)
# specify non-existent trans
assert_raises(IOError, do_forward_solution, 'sample', fname_raw,
trans=fname_fake, subjects_dir=subjects_dir)
# specify non-existent mri
assert_raises(IOError, do_forward_solution, 'sample', fname_raw,
mri=fname_fake, subjects_dir=subjects_dir)
# specify non-string mri
assert_raises(ValueError, do_forward_solution, 'sample', fname_raw,
mri=1, subjects_dir=subjects_dir)
# specify non-string trans
assert_raises(ValueError, do_forward_solution, 'sample', fname_raw,
trans=1, subjects_dir=subjects_dir)
# test specifying an actual trans in python space -- this should work but
# the transform I/O reduces our accuracy -- so we'll just hack a test here
# by making it bomb with eeg=False and meg=False
assert_raises(ValueError, do_forward_solution, 'sample', fname_raw,
mri=mri, eeg=False, meg=False, subjects_dir=subjects_dir)
# mindist as non-integer
assert_raises(TypeError, do_forward_solution, 'sample', fname_raw,
mri=fname_mri, mindist=dict(), subjects_dir=subjects_dir)
# mindist as string but not 'all'
assert_raises(ValueError, do_forward_solution, 'sample', fname_raw,
mri=fname_mri, eeg=False, mindist='yall',
subjects_dir=subjects_dir)
# src, spacing, and bem as non-str
assert_raises(ValueError, do_forward_solution, 'sample', fname_raw,
mri=fname_mri, src=1, subjects_dir=subjects_dir)
assert_raises(ValueError, do_forward_solution, 'sample', fname_raw,
mri=fname_mri, spacing=1, subjects_dir=subjects_dir)
assert_raises(ValueError, do_forward_solution, 'sample', fname_raw,
mri=fname_mri, bem=1, subjects_dir=subjects_dir)
# no overwrite flag
assert_raises(IOError, do_forward_solution, 'sample', fname_raw,
existing_file, mri=fname_mri, subjects_dir=subjects_dir)
# let's catch an MNE error, this time about trans being wrong
assert_raises(CalledProcessError, do_forward_solution, 'sample',
fname_raw, existing_file, trans=fname_mri, overwrite=True,
spacing='oct6', subjects_dir=subjects_dir)
# No need to actually calculate and check here, since it's effectively
# done in previous tests.
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