def test_read_write_head_pos(tmpdir):
"""Test reading and writing head position quaternion parameters."""
temp_name = op.join(str(tmpdir), 'temp.pos')
# This isn't a 100% valid quat matrix but it should be okay for tests
head_pos_rand = np.random.RandomState(0).randn(20, 10)
# This one is valid
head_pos_read = read_head_pos(pos_fname)
for head_pos_orig in (head_pos_rand, head_pos_read):
write_head_pos(temp_name, head_pos_orig)
head_pos = read_head_pos(temp_name)
assert_allclose(head_pos_orig, head_pos, atol=1e-3)
# Degenerate cases
pytest.raises(TypeError, write_head_pos, 0, head_pos_read) # not filename
pytest.raises(ValueError, write_head_pos, temp_name, 'foo') # not array
pytest.raises(ValueError, write_head_pos, temp_name, head_pos_read[:, :9])
pytest.raises(TypeError, read_head_pos, 0)
pytest.raises(IOError, read_head_pos, temp_name + 'foo')
def test_read_write_head_pos(tmpdir):
"""Test reading and writing head position quaternion parameters."""
temp_name = op.join(str(tmpdir), 'temp.pos')
# This isn't a 100% valid quat matrix but it should be okay for tests
head_pos_rand = np.random.RandomState(0).randn(20, 10)
# This one is valid
head_pos_read = read_head_pos(pos_fname)
for head_pos_orig in (head_pos_rand, head_pos_read):
write_head_pos(temp_name, head_pos_orig)
head_pos = read_head_pos(temp_name)
assert_allclose(head_pos_orig, head_pos, atol=1e-3)
# Degenerate cases
pytest.raises(TypeError, write_head_pos, 0, head_pos_read) # not filename
pytest.raises(ValueError, write_head_pos, temp_name, 'foo') # not array
pytest.raises(ValueError, write_head_pos, temp_name, head_pos_read[:, :9])
pytest.raises(TypeError, read_head_pos, 0)
pytest.raises(IOError, read_head_pos, temp_name + 'foo')
from mne.io import read_raw_fif
from metacog import bp
from metacog.utils import setup_logging
from metacog.dataset_specific_utils import parse_args
logger = setup_logging(__file__)
def compute_head_position(src: Path) -> np.ndarray:
raw = read_raw_fif(src)
chpi_ampl = compute_chpi_amplitudes(raw)
chpi_locs = compute_chpi_locs(raw.info, chpi_ampl)
return compute_head_pos(raw.info, chpi_locs)
if __name__ == "__main__":
args = parse_args(description=__doc__, args=sys.argv[1:], emptyroom=False)
subj, task, run = args.subject, args.task, args.run
# input
raw = bp.root.fpath(subject=subj, task=task, run=run, session=None)
# output
headpos = bp.headpos.fpath(subject=subj, task=task, run=run)
headpos.parent.mkdir(exist_ok=True)
logger.info(f"Processing {raw.name} --> {headpos}")
head_pos = compute_head_position(raw)
write_head_pos(headpos, head_pos)
