def test_no_conversion():
""" Test bti no-conversion option """
for pdf, config, hs in zip(pdf_fnames, config_fnames, hs_fnames):
raw = read_raw_bti(pdf, config, hs, convert=False)
raw_con = read_raw_bti(pdf, config, hs, convert=True)
bti_info = _read_bti_header(pdf, config)
dev_ctf_t = _correct_trans(bti_info["bti_transform"][0])
assert_array_equal(dev_ctf_t, raw.info["dev_ctf_t"]["trans"])
assert_array_equal(raw.info["dev_head_t"]["trans"], np.eye(4))
assert_array_equal(raw.info["ctf_head_t"]["trans"], np.eye(4))
dig, t = _process_bti_headshape(hs, convert=False, use_hpi=False)
assert_array_equal(t["trans"], np.eye(4))
for ii, (old, new, con) in enumerate(zip(dig, raw.info["dig"], raw_con.info["dig"])):
assert_equal(old["ident"], new["ident"])
assert_array_equal(old["r"], new["r"])
assert_true(not np.allclose(old["r"], con["r"]))
if ii > 10:
break
ch_map = dict((ch["chan_label"], ch["coil_trans"]) for ch in bti_info["chs"])
for ii, ch_label in enumerate(raw.bti_ch_labels):
if not ch_label.startswith("A"):
continue
t1 = _correct_trans(ch_map[ch_label])
t2 = raw.info["chs"][ii]["coil_trans"]
t3 = raw_con.info["chs"][ii]["coil_trans"]
assert_array_equal(t1, t2)
assert_true(not np.allclose(t1, t3))
def test_no_conversion():
""" Test bti no-conversion option """
get_info = partial(_get_bti_info,
rotation_x=0.0,
translation=(0.0, 0.02, 0.11),
convert=False,
ecg_ch='E31',
eog_ch=('E63', 'E64'),
rename_channels=False,
sort_by_ch_name=False)
for pdf, config, hs in zip(pdf_fnames, config_fnames, hs_fnames):
raw_info, _ = get_info(pdf, config, hs, convert=False)
raw_info_con = read_raw_bti(pdf_fname=pdf,
config_fname=config,
head_shape_fname=hs,
convert=True,
preload=False).info
pick_info(raw_info_con,
pick_types(raw_info_con, meg=True, ref_meg=True),
copy=False)
pick_info(raw_info,
pick_types(raw_info, meg=True, ref_meg=True),
copy=False)
bti_info = _read_bti_header(pdf, config)
dev_ctf_t = _correct_trans(bti_info['bti_transform'][0])
assert_array_equal(dev_ctf_t, raw_info['dev_ctf_t']['trans'])
assert_array_equal(raw_info['dev_head_t']['trans'], np.eye(4))
assert_array_equal(raw_info['ctf_head_t']['trans'], np.eye(4))
dig, t = _process_bti_headshape(hs, convert=False, use_hpi=False)
assert_array_equal(t['trans'], np.eye(4))
for ii, (old, new, con) in enumerate(
zip(dig, raw_info['dig'], raw_info_con['dig'])):
assert_equal(old['ident'], new['ident'])
assert_array_equal(old['r'], new['r'])
assert_true(not np.allclose(old['r'], con['r']))
if ii > 10:
break
ch_map = dict((ch['chan_label'], ch['loc']) for ch in bti_info['chs'])
for ii, ch_label in enumerate(raw_info['ch_names']):
if not ch_label.startswith('A'):
continue
t1 = ch_map[ch_label] # correction already performed in bti_info
t2 = raw_info['chs'][ii]['loc']
t3 = raw_info_con['chs'][ii]['loc']
assert_allclose(t1, t2, atol=1e-15)
assert_true(not np.allclose(t1, t3))
idx_a = raw_info_con['ch_names'].index('MEG 001')
idx_b = raw_info['ch_names'].index('A22')
assert_equal(raw_info_con['chs'][idx_a]['coord_frame'],
FIFF.FIFFV_COORD_DEVICE)
assert_equal(raw_info['chs'][idx_b]['coord_frame'],
FIFF.FIFFV_MNE_COORD_4D_HEAD)
def test_no_conversion():
""" Test bti no-conversion option """
get_info = partial(
_get_bti_info,
rotation_x=0.0, translation=(0.0, 0.02, 0.11), convert=False,
ecg_ch='E31', eog_ch=('E63', 'E64'),
rename_channels=False, sort_by_ch_name=False)
for pdf, config, hs in zip(pdf_fnames, config_fnames, hs_fnames):
with warnings.catch_warnings(record=True): # weight tables
raw_info, _ = get_info(pdf, config, hs, convert=False)
with warnings.catch_warnings(record=True): # weight tables
raw_info_con = read_raw_bti(
pdf_fname=pdf, config_fname=config, head_shape_fname=hs,
convert=True, preload=False).info
pick_info(raw_info_con,
pick_types(raw_info_con, meg=True, ref_meg=True),
copy=False)
pick_info(raw_info,
pick_types(raw_info, meg=True, ref_meg=True), copy=False)
bti_info = _read_bti_header(pdf, config)
dev_ctf_t = _correct_trans(bti_info['bti_transform'][0])
assert_array_equal(dev_ctf_t, raw_info['dev_ctf_t']['trans'])
assert_array_equal(raw_info['dev_head_t']['trans'], np.eye(4))
assert_array_equal(raw_info['ctf_head_t']['trans'], np.eye(4))
dig, t = _process_bti_headshape(hs, convert=False, use_hpi=False)
assert_array_equal(t['trans'], np.eye(4))
for ii, (old, new, con) in enumerate(zip(
dig, raw_info['dig'], raw_info_con['dig'])):
assert_equal(old['ident'], new['ident'])
assert_array_equal(old['r'], new['r'])
assert_true(not np.allclose(old['r'], con['r']))
if ii > 10:
break
ch_map = dict((ch['chan_label'],
ch['loc']) for ch in bti_info['chs'])
for ii, ch_label in enumerate(raw_info['ch_names']):
if not ch_label.startswith('A'):
continue
t1 = ch_map[ch_label] # correction already performed in bti_info
t2 = raw_info['chs'][ii]['loc']
t3 = raw_info_con['chs'][ii]['loc']
assert_allclose(t1, t2, atol=1e-15)
assert_true(not np.allclose(t1, t3))
idx_a = raw_info_con['ch_names'].index('MEG 001')
idx_b = raw_info['ch_names'].index('A22')
assert_equal(
raw_info_con['chs'][idx_a]['coord_frame'],
FIFF.FIFFV_COORD_DEVICE)
assert_equal(
raw_info['chs'][idx_b]['coord_frame'],
FIFF.FIFFV_MNE_COORD_4D_HEAD)
def test_nan_trans():
"""Test unlikely case that the device to head transform is empty."""
for ii, pdf_fname in enumerate(pdf_fnames):
bti_info = _read_bti_header(pdf_fname,
config_fnames[ii],
sort_by_ch_name=True)
dev_ctf_t = Transform('ctf_meg', 'ctf_head',
_correct_trans(bti_info['bti_transform'][0]))
# reading params
convert = True
rotation_x = 0.
translation = (0.0, 0.02, 0.11)
bti_dev_t = _get_bti_dev_t(rotation_x, translation)
bti_dev_t = Transform('ctf_meg', 'meg', bti_dev_t)
ecg_ch = 'E31'
eog_ch = ('E63', 'E64')
# read parts of info to get trans
bti_ch_names = list()
for ch in bti_info['chs']:
ch_name = ch['name']
if not ch_name.startswith('A'):
ch_name = ch.get('chan_label', ch_name)
bti_ch_names.append(ch_name)
neuromag_ch_names = _rename_channels(bti_ch_names,
ecg_ch=ecg_ch,
eog_ch=eog_ch)
ch_mapping = zip(bti_ch_names, neuromag_ch_names)
# add some nan in some locations!
dev_ctf_t['trans'][:, 3] = np.nan
_check_nan_dev_head_t(dev_ctf_t)
for idx, (chan_4d, chan_neuromag) in enumerate(ch_mapping):
loc = bti_info['chs'][idx]['loc']
if loc is not None:
if convert:
t = _loc_to_coil_trans(bti_info['chs'][idx]['loc'])
t = _convert_coil_trans(t, dev_ctf_t, bti_dev_t)
def test_nan_trans():
"""Test unlikely case that the device to head transform is empty."""
for ii, pdf_fname in enumerate(pdf_fnames):
bti_info = _read_bti_header(
pdf_fname, config_fnames[ii], sort_by_ch_name=True)
dev_ctf_t = Transform('ctf_meg', 'ctf_head',
_correct_trans(bti_info['bti_transform'][0]))
# reading params
convert = True
rotation_x = 0.
translation = (0.0, 0.02, 0.11)
bti_dev_t = _get_bti_dev_t(rotation_x, translation)
bti_dev_t = Transform('ctf_meg', 'meg', bti_dev_t)
ecg_ch = 'E31'
eog_ch = ('E63', 'E64')
# read parts of info to get trans
bti_ch_names = list()
for ch in bti_info['chs']:
ch_name = ch['name']
if not ch_name.startswith('A'):
ch_name = ch.get('chan_label', ch_name)
bti_ch_names.append(ch_name)
neuromag_ch_names = _rename_channels(
bti_ch_names, ecg_ch=ecg_ch, eog_ch=eog_ch)
ch_mapping = zip(bti_ch_names, neuromag_ch_names)
# add some nan in some locations!
dev_ctf_t['trans'][:, 3] = np.nan
_check_nan_dev_head_t(dev_ctf_t)
for idx, (chan_4d, chan_neuromag) in enumerate(ch_mapping):
loc = bti_info['chs'][idx]['loc']
if loc is not None:
if convert:
t = _loc_to_coil_trans(bti_info['chs'][idx]['loc'])
t = _convert_coil_trans(t, dev_ctf_t, bti_dev_t)
