parser.add_option('--eog_ch', dest='eog_ch', type='str',
help='4D EOG channel names',
default='E63,E64')
options, args = parser.parse_args()
pdf_fname = options.pdf_fname
if pdf_fname is None:
parser.print_help()
sys.exit(1)
config_fname = options.config_fname
head_shape_fname = options.head_shape_fname
out_fname = options.out_fname
rotation_x = options.rotation_x
translation = options.translation
ecg_ch = options.ecg_ch
eog_ch = options.ecg_ch.split(',')
if out_fname == 'as_data_fname':
out_fname = pdf_fname + '_raw.fif'
raw = read_raw_bti(pdf_fname=pdf_fname, config_fname=config_fname,
head_shape_fname=head_shape_fname,
rotation_x=rotation_x, translation=translation,
ecg_ch=ecg_ch, eog_ch=eog_ch)
raw.save(out_fname)
raw.close()
sys.exit(0)
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__), '..', '..', 'fiff', '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.fif')
bti_dir = op.join(op.dirname(__file__), '..', '..', 'fiff', '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.fif')
fname_ctf_raw = op.join(op.dirname(__file__), '..', '..', 'fiff', '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)
# 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)
# 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)
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)
options, args = parser.parse_args()
pdf_fname = options.pdf_fname
if pdf_fname is None:
parser.print_help()
sys.exit(1)
config_fname = options.config_fname
head_shape_fname = options.head_shape_fname
out_fname = options.out_fname
rotation_x = options.rotation_x
translation = options.translation
ecg_ch = options.ecg_ch
eog_ch = options.ecg_ch.split(',')
if out_fname == 'as_data_fname':
out_fname = pdf_fname + '_raw.fif'
raw = read_raw_bti(pdf_fname=pdf_fname,
config_fname=config_fname,
head_shape_fname=head_shape_fname,
rotation_x=rotation_x,
translation=translation,
ecg_ch=ecg_ch,
eog_ch=eog_ch)
raw.save(out_fname)
raw.close()
sys.exit(0)
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__), '..', '..', 'fiff', '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.fif')
bti_dir = op.join(op.dirname(__file__), '..', '..', 'fiff', '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.fif')
fname_ctf_raw = op.join(op.dirname(__file__), '..', '..', 'fiff', '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)
# 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)
# 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)
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)
