def test_calculate_chpi_positions():
"""Test calculation of cHPI positions."""
trans, rot, t = head_pos_to_trans_rot_t(read_head_pos(pos_fname))
raw = read_raw_fif(chpi_fif_fname, allow_maxshield='yes', preload=True,
add_eeg_ref=False)
t -= raw.first_samp / raw.info['sfreq']
quats = _calculate_chpi_positions(raw, verbose='debug')
trans_est, rot_est, t_est = head_pos_to_trans_rot_t(quats)
_compare_positions((trans, rot, t), (trans_est, rot_est, t_est), 0.003)
# degenerate conditions
raw_no_chpi = read_raw_fif(test_fif_fname, add_eeg_ref=False)
assert_raises(RuntimeError, _calculate_chpi_positions, raw_no_chpi)
raw_bad = raw.copy()
for d in raw_bad.info['dig']:
if d['kind'] == FIFF.FIFFV_POINT_HPI:
d['coord_frame'] = 999
break
assert_raises(RuntimeError, _calculate_chpi_positions, raw_bad)
raw_bad = raw.copy()
for d in raw_bad.info['dig']:
if d['kind'] == FIFF.FIFFV_POINT_HPI:
d['r'] = np.ones(3)
raw_bad.crop(0, 1., copy=False)
with warnings.catch_warnings(record=True): # bad pos
with catch_logging() as log_file:
_calculate_chpi_positions(raw_bad, verbose=True)
# ignore HPI info header and [done] footer
assert_true('0/5 good' in log_file.getvalue().strip().split('\n')[-2])
# half the rate cuts off cHPI coils
with warnings.catch_warnings(record=True): # uint cast suggestion
raw.resample(300., npad='auto')
assert_raises_regex(RuntimeError, 'above the',
_calculate_chpi_positions, raw)
def test_calculate_chpi_positions():
"""Test calculation of cHPI positions
"""
trans, rot, t = head_pos_to_trans_rot_t(read_head_pos(pos_fname))
raw = Raw(chpi_fif_fname, allow_maxshield='yes', preload=True)
t -= raw.first_samp / raw.info['sfreq']
quats = _calculate_chpi_positions(raw, verbose='debug')
trans_est, rot_est, t_est = head_pos_to_trans_rot_t(quats)
_compare_positions((trans, rot, t), (trans_est, rot_est, t_est), 0.003)
# degenerate conditions
raw_no_chpi = Raw(test_fif_fname)
assert_raises(RuntimeError, _calculate_chpi_positions, raw_no_chpi)
raw_bad = raw.copy()
for d in raw_bad.info['dig']:
if d['kind'] == FIFF.FIFFV_POINT_HPI:
d['coord_frame'] = 999
break
assert_raises(RuntimeError, _calculate_chpi_positions, raw_bad)
raw_bad = raw.copy()
for d in raw_bad.info['dig']:
if d['kind'] == FIFF.FIFFV_POINT_HPI:
d['r'] = np.ones(3)
raw_bad.crop(0, 1., copy=False)
with warnings.catch_warnings(record=True): # bad pos
with catch_logging() as log_file:
_calculate_chpi_positions(raw_bad, verbose=True)
# ignore HPI info header and [done] footer
for line in log_file.getvalue().strip().split('\n')[4:-1]:
assert_true('0/5 good' in line)
# half the rate cuts off cHPI coils
raw.resample(300., npad='auto')
assert_raises_regex(RuntimeError, 'above the', _calculate_chpi_positions,
raw)
def test_calculate_chpi_positions():
"""Test calculation of cHPI positions
"""
trans, rot, t = head_pos_to_trans_rot_t(read_head_pos(pos_fname))
raw = Raw(chpi_fif_fname, allow_maxshield="yes", preload=True)
t -= raw.first_samp / raw.info["sfreq"]
quats = _calculate_chpi_positions(raw, verbose="debug")
trans_est, rot_est, t_est = head_pos_to_trans_rot_t(quats)
_compare_positions((trans, rot, t), (trans_est, rot_est, t_est), 0.003)
# degenerate conditions
raw_no_chpi = Raw(test_fif_fname)
assert_raises(RuntimeError, _calculate_chpi_positions, raw_no_chpi)
raw_bad = raw.copy()
for d in raw_bad.info["dig"]:
if d["kind"] == FIFF.FIFFV_POINT_HPI:
d["coord_frame"] = 999
break
assert_raises(RuntimeError, _calculate_chpi_positions, raw_bad)
raw_bad = raw.copy()
for d in raw_bad.info["dig"]:
if d["kind"] == FIFF.FIFFV_POINT_HPI:
d["r"] = np.ones(3)
raw_bad.crop(0, 1.0, copy=False)
with warnings.catch_warnings(record=True): # bad pos
with catch_logging() as log_file:
_calculate_chpi_positions(raw_bad, verbose=True)
# ignore HPI info header and [done] footer
for line in log_file.getvalue().strip().split("\n")[4:-1]:
assert_true("0/5 good" in line)
# half the rate cuts off cHPI coils
with warnings.catch_warnings(record=True): # uint cast suggestion
raw.resample(300.0, npad="auto")
assert_raises_regex(RuntimeError, "above the", _calculate_chpi_positions, raw)
def test_calculate_chpi_positions():
"""Test calculation of cHPI positions."""
# Check to make sure our fits match MF decently
mf_quats = read_head_pos(pos_fname)
raw = read_raw_fif(chpi_fif_fname, allow_maxshield='yes', preload=True)
# This is a little hack (aliasing while decimating) to make it much faster
# for testing purposes only. We can relax this later if we find it breaks
# something.
raw_dec = _decimate_chpi(raw, 15)
with catch_logging() as log:
py_quats = _calculate_chpi_positions(raw_dec,
t_step_max=1.,
verbose='debug')
assert_true(log.getvalue().startswith('HPIFIT'))
_assert_quats(py_quats, mf_quats, dist_tol=0.004, angle_tol=2.5)
# degenerate conditions
raw_no_chpi = read_raw_fif(test_fif_fname)
assert_raises(RuntimeError, _calculate_chpi_positions, raw_no_chpi)
raw_bad = raw.copy()
del raw_bad.info['hpi_meas'][0]['hpi_coils'][0]['coil_freq']
assert_raises(RuntimeError, _calculate_chpi_positions, raw_bad)
raw_bad = raw.copy()
for d in raw_bad.info['dig']:
if d['kind'] == FIFF.FIFFV_POINT_HPI:
d['coord_frame'] = FIFF.FIFFV_COORD_UNKNOWN
break
assert_raises(RuntimeError, _calculate_chpi_positions, raw_bad)
for d in raw_bad.info['dig']:
if d['kind'] == FIFF.FIFFV_POINT_HPI:
d['coord_frame'] = FIFF.FIFFV_COORD_HEAD
d['r'] = np.ones(3)
raw_bad.crop(0, 1.)
picks = np.concatenate([
np.arange(306, len(raw_bad.ch_names)),
pick_types(raw_bad.info, meg=True)[::16]
])
raw_bad.pick_channels([raw_bad.ch_names[pick] for pick in picks])
with warnings.catch_warnings(record=True): # bad pos
with catch_logging() as log_file:
_calculate_chpi_positions(raw_bad, t_step_min=1., verbose=True)
# ignore HPI info header and [done] footer
assert_true('0/5 good' in log_file.getvalue().strip().split('\n')[-2])
# half the rate cuts off cHPI coils
raw.info['lowpass'] /= 2.
assert_raises_regex(RuntimeError, 'above the', _calculate_chpi_positions,
raw)
# test on 5k artemis data
raw = read_raw_artemis123(art_fname, preload=True)
mf_quats = read_head_pos(art_mc_fname)
with catch_logging() as log:
py_quats = _calculate_chpi_positions(raw,
t_step_min=2.,
verbose='debug')
_assert_quats(py_quats, mf_quats, dist_tol=0.004, angle_tol=2.5)
def test_calculate_chpi_positions():
"""Test calculation of cHPI positions."""
# Check to make sure our fits match MF decently
mf_quats = read_head_pos(pos_fname)
raw = read_raw_fif(chpi_fif_fname, allow_maxshield='yes', preload=True)
# This is a little hack (aliasing while decimating) to make it much faster
# for testing purposes only. We can relax this later if we find it breaks
# something.
raw_dec = _decimate_chpi(raw, 15)
with catch_logging() as log:
py_quats = _calculate_chpi_positions(raw_dec, t_step_max=1.,
verbose='debug')
assert_true(log.getvalue().startswith('HPIFIT'))
_assert_quats(py_quats, mf_quats, dist_tol=0.004, angle_tol=2.5)
# degenerate conditions
raw_no_chpi = read_raw_fif(test_fif_fname)
assert_raises(RuntimeError, _calculate_chpi_positions, raw_no_chpi)
raw_bad = raw.copy()
del raw_bad.info['hpi_meas'][0]['hpi_coils'][0]['coil_freq']
assert_raises(RuntimeError, _calculate_chpi_positions, raw_bad)
raw_bad = raw.copy()
for d in raw_bad.info['dig']:
if d['kind'] == FIFF.FIFFV_POINT_HPI:
d['coord_frame'] = FIFF.FIFFV_COORD_UNKNOWN
break
assert_raises(RuntimeError, _calculate_chpi_positions, raw_bad)
for d in raw_bad.info['dig']:
if d['kind'] == FIFF.FIFFV_POINT_HPI:
d['coord_frame'] = FIFF.FIFFV_COORD_HEAD
d['r'] = np.ones(3)
raw_bad.crop(0, 1.)
picks = np.concatenate([np.arange(306, len(raw_bad.ch_names)),
pick_types(raw_bad.info, meg=True)[::16]])
raw_bad.pick_channels([raw_bad.ch_names[pick] for pick in picks])
with warnings.catch_warnings(record=True): # bad pos
with catch_logging() as log_file:
_calculate_chpi_positions(raw_bad, t_step_min=1., verbose=True)
# ignore HPI info header and [done] footer
assert_true('0/5 good' in log_file.getvalue().strip().split('\n')[-2])
# half the rate cuts off cHPI coils
raw.info['lowpass'] /= 2.
assert_raises_regex(RuntimeError, 'above the',
_calculate_chpi_positions, raw)
# test on 5k artemis data
raw = read_raw_artemis123(art_fname, preload=True)
mf_quats = read_head_pos(art_mc_fname)
with catch_logging() as log:
py_quats = _calculate_chpi_positions(raw, t_step_min=2.,
verbose='debug')
_assert_quats(py_quats, mf_quats, dist_tol=0.004, angle_tol=2.5)
def test_calculate_chpi_positions():
"""Test calculation of cHPI positions."""
# Check to make sure our fits match MF decently
mf_quats = read_head_pos(pos_fname)
raw = read_raw_fif(chpi_fif_fname, allow_maxshield='yes', preload=True)
# This is a little hack (aliasing while decimating) to make it much faster
# for testing purposes only. We can relax this later if we find it breaks
# something.
raw_dec = _decimate_chpi(raw, 15)
with catch_logging() as log:
py_quats = _calculate_chpi_positions(raw_dec, verbose='debug')
assert_true(log.getvalue().startswith('HPIFIT'))
_assert_quats(py_quats, mf_quats, dist_tol=0.004, angle_tol=2.5)
# degenerate conditions
raw_no_chpi = read_raw_fif(test_fif_fname)
assert_raises(RuntimeError, _calculate_chpi_positions, raw_no_chpi)
raw_bad = raw.copy()
for d in raw_bad.info['dig']:
if d['kind'] == FIFF.FIFFV_POINT_HPI:
d['coord_frame'] = 999
break
assert_raises(RuntimeError, _calculate_chpi_positions, raw_bad)
raw_bad = raw.copy()
for d in raw_bad.info['dig']:
if d['kind'] == FIFF.FIFFV_POINT_HPI:
d['r'] = np.ones(3)
raw_bad.crop(0, 1.)
with warnings.catch_warnings(record=True): # bad pos
with catch_logging() as log_file:
_calculate_chpi_positions(raw_bad, t_step_min=5., verbose=True)
# ignore HPI info header and [done] footer
assert_true('0/5 good' in log_file.getvalue().strip().split('\n')[-2])
# half the rate cuts off cHPI coils
raw.info['lowpass'] /= 2.
assert_raises_regex(RuntimeError, 'above the', _calculate_chpi_positions,
raw)
def test_calculate_chpi_positions():
"""Test calculation of cHPI positions."""
# Check to make sure our fits match MF decently
mf_quats = read_head_pos(pos_fname)
raw = read_raw_fif(chpi_fif_fname, allow_maxshield='yes', preload=True)
# This is a little hack (aliasing while decimating) to make it much faster
# for testing purposes only. We can relax this later if we find it breaks
# something.
raw_dec = _decimate_chpi(raw, 15)
with catch_logging() as log:
py_quats = _calculate_chpi_positions(raw_dec, verbose='debug')
assert_true(log.getvalue().startswith('HPIFIT'))
_assert_quats(py_quats, mf_quats, dist_tol=0.004, angle_tol=2.5)
# degenerate conditions
raw_no_chpi = read_raw_fif(test_fif_fname)
assert_raises(RuntimeError, _calculate_chpi_positions, raw_no_chpi)
raw_bad = raw.copy()
for d in raw_bad.info['dig']:
if d['kind'] == FIFF.FIFFV_POINT_HPI:
d['coord_frame'] = 999
break
assert_raises(RuntimeError, _calculate_chpi_positions, raw_bad)
raw_bad = raw.copy()
for d in raw_bad.info['dig']:
if d['kind'] == FIFF.FIFFV_POINT_HPI:
d['r'] = np.ones(3)
raw_bad.crop(0, 1.)
with warnings.catch_warnings(record=True): # bad pos
with catch_logging() as log_file:
_calculate_chpi_positions(raw_bad, t_step_min=5., verbose=True)
# ignore HPI info header and [done] footer
assert_true('0/5 good' in log_file.getvalue().strip().split('\n')[-2])
# half the rate cuts off cHPI coils
raw.info['lowpass'] /= 2.
assert_raises_regex(RuntimeError, 'above the',
_calculate_chpi_positions, raw)