def test_chpi_adjust():
"""Test cHPI logging and adjustment."""
raw = read_raw_fif(chpi_fif_fname, allow_maxshield='yes')
with catch_logging() as log:
_get_hpi_initial_fit(raw.info, adjust=True, verbose='debug')
_get_hpi_info(raw.info, verbose='debug')
# Ran MaxFilter (with -list, -v, -movecomp, etc.), and got:
msg = [
'HPIFIT: 5 coils digitized in order 5 1 4 3 2',
'HPIFIT: 3 coils accepted: 1 2 4',
'Hpi coil moments (3 5):',
'2.08542e-15 -1.52486e-15 -1.53484e-15',
'2.14516e-15 2.09608e-15 7.30303e-16',
'-3.2318e-16 -4.25666e-16 2.69997e-15',
'5.21717e-16 1.28406e-15 1.95335e-15',
'1.21199e-15 -1.25801e-19 1.18321e-15',
'HPIFIT errors: 0.3, 0.3, 5.3, 0.4, 3.2 mm.',
'HPI consistency of isotrak and hpifit is OK.',
'HP fitting limits: err = 5.0 mm, gval = 0.980.',
'Using 5 HPI coils: 83 143 203 263 323 Hz', # actually came earlier
]
log = log.getvalue().splitlines()
assert set(log) == set(msg), '\n' + '\n'.join(set(msg) - set(log))
# Then took the raw file, did this:
raw.info['dig'][5]['r'][2] += 1.
# And checked the result in MaxFilter, which changed the logging as:
msg = msg[:8] + [
'HPIFIT errors: 0.3, 0.3, 5.3, 999.7, 3.2 mm.',
'Note: HPI coil 3 isotrak is adjusted by 5.3 mm!',
'Note: HPI coil 5 isotrak is adjusted by 3.2 mm!'
] + msg[-2:]
with catch_logging() as log:
_get_hpi_initial_fit(raw.info, adjust=True, verbose='debug')
_get_hpi_info(raw.info, verbose='debug')
log = log.getvalue().splitlines()
assert set(log) == set(msg), '\n' + '\n'.join(set(msg) - set(log))
def test_chpi_adjust():
"""Test cHPI logging and adjustment."""
raw = read_raw_fif(chpi_fif_fname, allow_maxshield='yes')
with catch_logging() as log:
_get_hpi_initial_fit(raw.info, adjust=True, verbose='debug')
_get_hpi_info(raw.info, verbose='debug')
# Ran MaxFilter (with -list, -v, -movecomp, etc.), and got:
msg = ['HPIFIT: 5 coils digitized in order 5 1 4 3 2',
'HPIFIT: 3 coils accepted: 1 2 4',
'Hpi coil moments (3 5):',
'2.08542e-15 -1.52486e-15 -1.53484e-15',
'2.14516e-15 2.09608e-15 7.30303e-16',
'-3.2318e-16 -4.25666e-16 2.69997e-15',
'5.21717e-16 1.28406e-15 1.95335e-15',
'1.21199e-15 -1.25801e-19 1.18321e-15',
'HPIFIT errors: 0.3, 0.3, 5.3, 0.4, 3.2 mm.',
'HPI consistency of isotrak and hpifit is OK.',
'HP fitting limits: err = 5.0 mm, gval = 0.980.',
'Using 5 HPI coils: 83 143 203 263 323 Hz', # actually came earlier
]
log = log.getvalue().splitlines()
assert_true(set(log) == set(msg), '\n' + '\n'.join(set(msg) - set(log)))
# Then took the raw file, did this:
raw.info['dig'][5]['r'][2] += 1.
# And checked the result in MaxFilter, which changed the logging as:
msg = msg[:8] + [
'HPIFIT errors: 0.3, 0.3, 5.3, 999.7, 3.2 mm.',
'Note: HPI coil 3 isotrak is adjusted by 5.3 mm!',
'Note: HPI coil 5 isotrak is adjusted by 3.2 mm!'] + msg[-2:]
with catch_logging() as log:
_get_hpi_initial_fit(raw.info, adjust=True, verbose='debug')
_get_hpi_info(raw.info, verbose='debug')
log = log.getvalue().splitlines()
assert_true(set(log) == set(msg), '\n' + '\n'.join(set(msg) - set(log)))
def _check_dists(info, cHPI_digs, n_bad=0, bad_low=0.02, bad_high=0.04):
__tracebackhide__ = True
orig = _get_hpi_initial_fit(info)
hpi_coil_distances = cdist(orig, orig)
new_pos = np.array([d['r'] for d in cHPI_digs])
mask, distances = _compute_good_distances(hpi_coil_distances, new_pos)
good_idx = np.where(mask)[0]
assert len(good_idx) >= 3
meds = np.empty(len(orig))
for ii in range(len(orig)):
idx = np.setdiff1d(good_idx, ii)
meds[ii] = np.median(distances[ii][idx])
meds = np.array(meds)
assert_array_less(meds[good_idx], 0.003)
bad_idx = np.where(~mask)[0]
if len(bad_idx):
bads = meds[bad_idx]
assert_array_less(bad_low, bads)
assert_array_less(bads, bad_high)
