def map_ch_coords_to_mne(inst):
"""Transform sensors to MNE coordinates
.. note::
operates in place
.. warning::
For several reasons we do not use the MNE coordinates for the inverse
modeling. This however won't always play nicely with visualization.
Parameters
----------
inst : MNE data containers
Raw, Epochs, Evoked.
"""
bti_dev_t = Transform('ctf_meg', 'meg', _get_bti_dev_t())
dev_ctf_t = inst.info['dev_ctf_t']
for ch in inst.info['chs']:
loc = ch['loc'][:]
if loc is not None:
logger.debug('converting %s' % ch['ch_name'])
t = _loc_to_coil_trans(loc)
t = _convert_coil_trans(t, dev_ctf_t, bti_dev_t)
loc = _coil_trans_to_loc(t)
ch['loc'] = loc
def test_transforms():
""" Test transformations """
bti_trans = (0.0, 0.02, 0.11)
bti_dev_t = Transform("ctf_meg", "meg", _get_bti_dev_t(0.0, bti_trans))
for pdf, config, hs in zip(pdf_fnames, config_fnames, hs_fnames):
raw = read_raw_bti(pdf, config, hs)
dev_ctf_t = raw.info["dev_ctf_t"]
dev_head_t_old = raw.info["dev_head_t"]
ctf_head_t = raw.info["ctf_head_t"]
# 1) get BTI->Neuromag
bti_dev_t = Transform("ctf_meg", "meg", _get_bti_dev_t(0.0, bti_trans))
# 2) get Neuromag->BTI head
t = combine_transforms(invert_transform(bti_dev_t), dev_ctf_t, "meg", "ctf_head")
# 3) get Neuromag->head
dev_head_t_new = combine_transforms(t, ctf_head_t, "meg", "head")
assert_array_equal(dev_head_t_new["trans"], dev_head_t_old["trans"])
def test_transforms():
"""Test transformations."""
bti_trans = (0.0, 0.02, 0.11)
bti_dev_t = Transform('ctf_meg', 'meg', _get_bti_dev_t(0.0, bti_trans))
for pdf, config, hs, in zip(pdf_fnames, config_fnames, hs_fnames):
raw = read_raw_bti(pdf, config, hs, preload=False)
dev_ctf_t = raw.info['dev_ctf_t']
dev_head_t_old = raw.info['dev_head_t']
ctf_head_t = raw.info['ctf_head_t']
# 1) get BTI->Neuromag
bti_dev_t = Transform('ctf_meg', 'meg', _get_bti_dev_t(0.0, bti_trans))
# 2) get Neuromag->BTI head
t = combine_transforms(invert_transform(bti_dev_t), dev_ctf_t, 'meg',
'ctf_head')
# 3) get Neuromag->head
dev_head_t_new = combine_transforms(t, ctf_head_t, 'meg', 'head')
assert_array_equal(dev_head_t_new['trans'], dev_head_t_old['trans'])
def test_transforms():
"""Test transformations."""
bti_trans = (0.0, 0.02, 0.11)
bti_dev_t = Transform('ctf_meg', 'meg', _get_bti_dev_t(0.0, bti_trans))
for pdf, config, hs, in zip(pdf_fnames, config_fnames, hs_fnames):
raw = read_raw_bti(pdf, config, hs, preload=False)
dev_ctf_t = raw.info['dev_ctf_t']
dev_head_t_old = raw.info['dev_head_t']
ctf_head_t = raw.info['ctf_head_t']
# 1) get BTI->Neuromag
bti_dev_t = Transform('ctf_meg', 'meg', _get_bti_dev_t(0.0, bti_trans))
# 2) get Neuromag->BTI head
t = combine_transforms(invert_transform(bti_dev_t), dev_ctf_t,
'meg', 'ctf_head')
# 3) get Neuromag->head
dev_head_t_new = combine_transforms(t, ctf_head_t, 'meg', 'head')
assert_array_equal(dev_head_t_new['trans'], dev_head_t_old['trans'])
def transform_sensors_to_mne(inst):
""" Transform sensors to MNE coordinates
For several reasons we do not use the MNE coordinates for the inverse
modeling. This however won't always play nicely with visualization.
"""
bti_dev_t = Transform('ctf_meg', 'meg', _get_bti_dev_t())
dev_ctf_t = inst.info['dev_ctf_t']
for ch in inst.info['chs']:
loc = ch['loc'][:]
if loc is not None:
logger.debug('converting %s' % ch['ch_name'])
t = _loc_to_coil_trans(loc)
t = _convert_coil_trans(t, dev_ctf_t, bti_dev_t)
loc = _coil_trans_to_loc(t)
ch['loc'] = loc
def transform_sensors_to_mne(inst):
""" Transform sensors to MNE coordinates
For several reasons we do not use the MNE coordinates for the inverse
modeling. This however won't always play nicely with visualization.
"""
bti_dev_t = Transform('ctf_meg', 'meg', _get_bti_dev_t())
dev_ctf_t = inst.info['dev_ctf_t']
for ch in inst.info['chs']:
loc = ch['loc'][:]
if loc is not None:
print('converting %s' % ch['ch_name'])
t = _loc_to_coil_trans(loc)
t = _convert_coil_trans(t, dev_ctf_t, bti_dev_t)
loc = _coil_trans_to_loc(t)
ch['loc'] = loc
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)