def test_read_correct_inputs():
"""Test that inputs of read functions are correct."""
bids_path = 'sub-01_ses-01_meg.fif'
with pytest.raises(RuntimeError, match='"bids_path" must be a '
'BIDSPath object'):
read_raw_bids(bids_path)
with pytest.raises(RuntimeError, match='"bids_path" must be a '
'BIDSPath object'):
get_head_mri_trans(bids_path)
def test_get_head_mri_trans():
"""Test getting a trans object from BIDS data."""
import nibabel as nib
event_id = {'Auditory/Left': 1, 'Auditory/Right': 2, 'Visual/Left': 3,
'Visual/Right': 4, 'Smiley': 5, 'Button': 32}
events_fname = op.join(data_path, 'MEG', 'sample',
'sample_audvis_trunc_raw-eve.fif')
# Drop unknown events.
events = mne.read_events(events_fname)
events = events[events[:, 2] != 0]
# Write it to BIDS
raw = _read_raw_fif(raw_fname)
bids_root = _TempDir()
bids_path = _bids_path.copy().update(root=bids_root)
write_raw_bids(raw, bids_path, events_data=events, event_id=event_id,
overwrite=False)
# We cannot recover trans, if no MRI has yet been written
with pytest.raises(RuntimeError):
estimated_trans = get_head_mri_trans(bids_path=bids_path)
# Write some MRI data and supply a `trans` so that a sidecar gets written
trans = mne.read_trans(raw_fname.replace('_raw.fif', '-trans.fif'))
# Get the T1 weighted MRI data file ... test write_anat with a nibabel
# image instead of a file path
t1w_mgh = op.join(data_path, 'subjects', 'sample', 'mri', 'T1.mgz')
t1w_mgh = nib.load(t1w_mgh)
t1w_bidspath = BIDSPath(subject=subject_id, session=session_id,
acquisition=acq, root=bids_root)
t1w_bidspath = write_anat(t1w_mgh, bids_path=t1w_bidspath,
raw=raw, trans=trans, verbose=True)
anat_dir = t1w_bidspath.directory
# Try to get trans back through fitting points
estimated_trans = get_head_mri_trans(bids_path=bids_path)
assert trans['from'] == estimated_trans['from']
assert trans['to'] == estimated_trans['to']
assert_almost_equal(trans['trans'], estimated_trans['trans'])
print(trans)
print(estimated_trans)
# provoke an error by introducing NaNs into MEG coords
with pytest.raises(RuntimeError, match='AnatomicalLandmarkCoordinates'):
raw.info['dig'][0]['r'] = np.ones(3) * np.nan
sh.rmtree(anat_dir)
bids_path = write_anat(t1w_mgh, bids_path=t1w_bidspath,
raw=raw, trans=trans, verbose=True)
estimated_trans = get_head_mri_trans(bids_path=bids_path)
def test_get_head_mri_trans_ctf():
"""Test getting a trans object from BIDS data in CTF."""
import nibabel as nib
ctf_data_path = op.join(testing.data_path(), 'CTF')
raw_ctf_fname = op.join(ctf_data_path, 'testdata_ctf.ds')
raw_ctf = mne.io.read_raw_ctf(raw_ctf_fname)
bids_root = _TempDir()
write_raw_bids(raw_ctf, bids_basename, bids_root, overwrite=False)
# Take a fake trans
trans = mne.read_trans(raw_fname.replace('_raw.fif', '-trans.fif'))
# Get the T1 weighted MRI data file ... test write_anat with a nibabel
# image instead of a file path
t1w_mgh = op.join(data_path, 'subjects', 'sample', 'mri', 'T1.mgz')
t1w_mgh = nib.load(t1w_mgh)
write_anat(bids_root,
subject_id,
t1w_mgh,
session_id,
acq,
raw=raw_ctf,
trans=trans)
# Try to get trans back through fitting points
estimated_trans = get_head_mri_trans(bids_basename=bids_basename,
bids_root=bids_root)
assert_almost_equal(trans['trans'], estimated_trans['trans'])
def test_get_head_mri_trans_ctf(fname):
"""Test getting a trans object from BIDS data in CTF."""
import nibabel as nib
ctf_data_path = op.join(testing.data_path(), 'CTF')
raw_ctf_fname = op.join(ctf_data_path, fname)
raw_ctf = _read_raw_ctf(raw_ctf_fname, clean_names=True)
bids_root = _TempDir()
bids_path = _bids_path.copy().update(root=bids_root)
write_raw_bids(raw_ctf, bids_path, overwrite=False)
# Take a fake trans
trans = mne.read_trans(raw_fname.replace('_raw.fif', '-trans.fif'))
# Get the T1 weighted MRI data file ... test write_anat with a nibabel
# image instead of a file path
t1w_mgh = op.join(data_path, 'subjects', 'sample', 'mri', 'T1.mgz')
t1w_mgh = nib.load(t1w_mgh)
t1w_bids_path = BIDSPath(subject=subject_id,
session=session_id,
acquisition=acq,
root=bids_root)
write_anat(t1w_mgh, bids_path=t1w_bids_path, raw=raw_ctf, trans=trans)
# Try to get trans back through fitting points
estimated_trans = get_head_mri_trans(bids_path=bids_path,
extra_params=dict(clean_names=True))
assert_almost_equal(trans['trans'], estimated_trans['trans'])
def test_get_head_mri_trans(tmpdir):
"""Test getting a trans object from BIDS data."""
import nibabel as nib
event_id = {
'Auditory/Left': 1,
'Auditory/Right': 2,
'Visual/Left': 3,
'Visual/Right': 4,
'Smiley': 5,
'Button': 32
}
events_fname = op.join(data_path, 'MEG', 'sample',
'sample_audvis_trunc_raw-eve.fif')
subjects_dir = op.join(data_path, 'subjects')
# Drop unknown events.
events = mne.read_events(events_fname)
events = events[events[:, 2] != 0]
# Write it to BIDS
raw = _read_raw_fif(raw_fname)
bids_path = _bids_path.copy().update(root=tmpdir)
write_raw_bids(raw,
bids_path,
events_data=events,
event_id=event_id,
overwrite=False)
# We cannot recover trans if no MRI has yet been written
with pytest.raises(RuntimeError, match='Did not find any T1w'):
estimated_trans = get_head_mri_trans(bids_path=bids_path,
fs_subject='sample',
fs_subjects_dir=subjects_dir)
# Write some MRI data and supply a `trans` so that a sidecar gets written
trans = mne.read_trans(raw_fname.replace('_raw.fif', '-trans.fif'))
# Get the T1 weighted MRI data file ... test write_anat with a nibabel
# image instead of a file path
t1w_mgh = op.join(data_path, 'subjects', 'sample', 'mri', 'T1.mgz')
t1w_mgh = nib.load(t1w_mgh)
landmarks = get_anat_landmarks(t1w_mgh,
raw.info,
trans,
fs_subject='sample',
fs_subjects_dir=subjects_dir)
t1w_bids_path = write_anat(t1w_mgh,
bids_path=bids_path,
landmarks=landmarks,
verbose=True)
anat_dir = bids_path.directory
# Try to get trans back through fitting points
estimated_trans = get_head_mri_trans(bids_path=bids_path,
fs_subject='sample',
fs_subjects_dir=subjects_dir)
assert trans['from'] == estimated_trans['from']
assert trans['to'] == estimated_trans['to']
assert_almost_equal(trans['trans'], estimated_trans['trans'])
# provoke an error by introducing NaNs into MEG coords
raw.info['dig'][0]['r'] = np.full(3, np.nan)
sh.rmtree(anat_dir)
bad_landmarks = get_anat_landmarks(t1w_mgh, raw.info, trans, 'sample',
op.join(data_path, 'subjects'))
write_anat(t1w_mgh, bids_path=t1w_bids_path, landmarks=bad_landmarks)
with pytest.raises(RuntimeError, match='AnatomicalLandmarkCoordinates'):
estimated_trans = get_head_mri_trans(bids_path=t1w_bids_path,
fs_subject='sample',
fs_subjects_dir=subjects_dir)
# test we are permissive for different casings of landmark names in the
# sidecar, and also accept "nasion" instead of just "NAS"
raw = _read_raw_fif(raw_fname)
write_raw_bids(raw,
bids_path,
events_data=events,
event_id=event_id,
overwrite=True) # overwrite with new acq
t1w_bids_path = write_anat(t1w_mgh,
bids_path=bids_path,
landmarks=landmarks,
overwrite=True)
t1w_json_fpath = t1w_bids_path.copy().update(extension='.json').fpath
with t1w_json_fpath.open('r', encoding='utf-8') as f:
t1w_json = json.load(f)
coords = t1w_json['AnatomicalLandmarkCoordinates']
coords['lpa'] = coords['LPA']
coords['Rpa'] = coords['RPA']
coords['Nasion'] = coords['NAS']
del coords['LPA'], coords['RPA'], coords['NAS']
_write_json(t1w_json_fpath, t1w_json, overwrite=True)
estimated_trans = get_head_mri_trans(bids_path=bids_path,
fs_subject='sample',
fs_subjects_dir=subjects_dir)
assert_almost_equal(trans['trans'], estimated_trans['trans'])
# Test t1_bids_path parameter
#
# Case 1: different BIDS roots
meg_bids_path = _bids_path.copy().update(root=tmpdir / 'meg_root')
t1_bids_path = _bids_path.copy().update(root=tmpdir / 'mri_root')
raw = _read_raw_fif(raw_fname)
write_raw_bids(raw, bids_path=meg_bids_path)
landmarks = get_anat_landmarks(t1w_mgh,
raw.info,
trans,
fs_subject='sample',
fs_subjects_dir=subjects_dir)
write_anat(t1w_mgh, bids_path=t1_bids_path, landmarks=landmarks)
read_trans = get_head_mri_trans(bids_path=meg_bids_path,
t1_bids_path=t1_bids_path,
fs_subject='sample',
fs_subjects_dir=subjects_dir)
assert np.allclose(trans['trans'], read_trans['trans'])
# Case 2: different sessions
raw = _read_raw_fif(raw_fname)
meg_bids_path = _bids_path.copy().update(root=tmpdir / 'session_test',
session='01')
t1_bids_path = meg_bids_path.copy().update(session='02')
write_raw_bids(raw, bids_path=meg_bids_path)
write_anat(t1w_mgh, bids_path=t1_bids_path, landmarks=landmarks)
read_trans = get_head_mri_trans(bids_path=meg_bids_path,
t1_bids_path=t1_bids_path,
fs_subject='sample',
fs_subjects_dir=subjects_dir)
assert np.allclose(trans['trans'], read_trans['trans'])
# Test that incorrect subject directory throws error
with pytest.raises(ValueError, match='Could not find'):
estimated_trans = get_head_mri_trans(bids_path=bids_path,
fs_subject='bad',
fs_subjects_dir=subjects_dir)
def test_get_head_mri_trans():
"""Test getting a trans object from BIDS data."""
import nibabel as nib
event_id = {
'Auditory/Left': 1,
'Auditory/Right': 2,
'Visual/Left': 3,
'Visual/Right': 4,
'Smiley': 5,
'Button': 32
}
events_fname = op.join(data_path, 'MEG', 'sample',
'sample_audvis_trunc_raw-eve.fif')
# Write it to BIDS
raw = mne.io.read_raw_fif(raw_fname)
bids_root = _TempDir()
with pytest.warns(UserWarning, match='No line frequency'):
write_raw_bids(raw,
bids_basename,
bids_root,
events_data=events_fname,
event_id=event_id,
overwrite=False)
# We cannot recover trans, if no MRI has yet been written
with pytest.raises(RuntimeError):
bids_fname = bids_basename + '_meg.fif'
estimated_trans = get_head_mri_trans(bids_fname, bids_root)
# Write some MRI data and supply a `trans` so that a sidecar gets written
trans = mne.read_trans(raw_fname.replace('_raw.fif', '-trans.fif'))
# Get the T1 weighted MRI data file ... test write_anat with a nibabel
# image instead of a file path
t1w_mgh = op.join(data_path, 'subjects', 'sample', 'mri', 'T1.mgz')
t1w_mgh = nib.load(t1w_mgh)
anat_dir = write_anat(bids_root,
subject_id,
t1w_mgh,
session_id,
acq,
raw=raw,
trans=trans,
verbose=True)
# Try to get trans back through fitting points
estimated_trans = get_head_mri_trans(bids_fname, bids_root)
assert trans['from'] == estimated_trans['from']
assert trans['to'] == estimated_trans['to']
assert_almost_equal(trans['trans'], estimated_trans['trans'])
print(trans)
print(estimated_trans)
# Passing a path instead of a name works well
bids_fpath = op.join(bids_root, 'sub-{}'.format(subject_id),
'ses-{}'.format(session_id), 'meg',
bids_basename + '_meg.fif')
estimated_trans = get_head_mri_trans(bids_fpath, bids_root)
# provoke an error by pointing introducing NaNs into MEG coords
with pytest.raises(RuntimeError, match='AnatomicalLandmarkCoordinates'):
raw.info['dig'][0]['r'] = np.ones(3) * np.nan
sh.rmtree(anat_dir)
write_anat(bids_root,
subject_id,
t1w_mgh,
session_id,
acq,
raw=raw,
trans=trans,
verbose=True)
estimated_trans = get_head_mri_trans(bids_fname, bids_root)
def test_get_head_mri_trans(tmp_path):
"""Test getting a trans object from BIDS data."""
import nibabel as nib
event_id = {'Auditory/Left': 1, 'Auditory/Right': 2, 'Visual/Left': 3,
'Visual/Right': 4, 'Smiley': 5, 'Button': 32}
events_fname = op.join(data_path, 'MEG', 'sample',
'sample_audvis_trunc_raw-eve.fif')
subjects_dir = op.join(data_path, 'subjects')
# Drop unknown events.
events = mne.read_events(events_fname)
events = events[events[:, 2] != 0]
# Write it to BIDS
raw = _read_raw_fif(raw_fname)
bids_path = _bids_path.copy().update(
root=tmp_path, datatype='meg', suffix='meg'
)
write_raw_bids(raw, bids_path, events_data=events, event_id=event_id,
overwrite=False)
# We cannot recover trans if no MRI has yet been written
with pytest.raises(FileNotFoundError, match='Did not find'):
estimated_trans = get_head_mri_trans(
bids_path=bids_path, fs_subject='sample',
fs_subjects_dir=subjects_dir)
# Write some MRI data and supply a `trans` so that a sidecar gets written
trans = mne.read_trans(raw_fname.replace('_raw.fif', '-trans.fif'))
# Get the T1 weighted MRI data file ... test write_anat with a nibabel
# image instead of a file path
t1w_mgh = op.join(data_path, 'subjects', 'sample', 'mri', 'T1.mgz')
t1w_mgh = nib.load(t1w_mgh)
landmarks = get_anat_landmarks(
t1w_mgh, raw.info, trans, fs_subject='sample',
fs_subjects_dir=subjects_dir)
t1w_bids_path = bids_path.copy().update(
datatype='anat', suffix='T1w'
)
t1w_bids_path = write_anat(
t1w_mgh, bids_path=t1w_bids_path, landmarks=landmarks, verbose=True
)
anat_dir = t1w_bids_path.directory
# Try to get trans back through fitting points
estimated_trans = get_head_mri_trans(
bids_path=bids_path, fs_subject='sample', fs_subjects_dir=subjects_dir)
assert trans['from'] == estimated_trans['from']
assert trans['to'] == estimated_trans['to']
assert_almost_equal(trans['trans'], estimated_trans['trans'])
# provoke an error by introducing NaNs into MEG coords
raw.info['dig'][0]['r'] = np.full(3, np.nan)
sh.rmtree(anat_dir)
bad_landmarks = get_anat_landmarks(t1w_mgh, raw.info, trans, 'sample',
op.join(data_path, 'subjects'))
write_anat(t1w_mgh, bids_path=t1w_bids_path, landmarks=bad_landmarks)
with pytest.raises(RuntimeError, match='AnatomicalLandmarkCoordinates'):
estimated_trans = get_head_mri_trans(bids_path=t1w_bids_path,
fs_subject='sample',
fs_subjects_dir=subjects_dir)
# test raw with no fiducials to provoke error
t1w_bids_path = write_anat( # put back
t1w_mgh, bids_path=t1w_bids_path, landmarks=landmarks, overwrite=True
)
montage = raw.get_montage()
montage.remove_fiducials()
raw_test = raw.copy()
raw_test.set_montage(montage)
raw_test.save(bids_path.fpath, overwrite=True)
with pytest.raises(RuntimeError, match='Could not extract fiducial'):
get_head_mri_trans(bids_path=bids_path, fs_subject='sample',
fs_subjects_dir=subjects_dir)
# test we are permissive for different casings of landmark names in the
# sidecar, and also accept "nasion" instead of just "NAS"
raw = _read_raw_fif(raw_fname)
write_raw_bids(raw, bids_path, events_data=events, event_id=event_id,
overwrite=True) # overwrite with new acq
t1w_bids_path = write_anat(
t1w_mgh, bids_path=t1w_bids_path, landmarks=landmarks, overwrite=True
)
t1w_json_fpath = t1w_bids_path.copy().update(extension='.json').fpath
with t1w_json_fpath.open('r', encoding='utf-8') as f:
t1w_json = json.load(f)
coords = t1w_json['AnatomicalLandmarkCoordinates']
coords['lpa'] = coords['LPA']
coords['Rpa'] = coords['RPA']
coords['Nasion'] = coords['NAS']
del coords['LPA'], coords['RPA'], coords['NAS']
_write_json(t1w_json_fpath, t1w_json, overwrite=True)
estimated_trans = get_head_mri_trans(
bids_path=bids_path,
fs_subject='sample', fs_subjects_dir=subjects_dir)
assert_almost_equal(trans['trans'], estimated_trans['trans'])
# Test t1_bids_path parameter
#
# Case 1: different BIDS roots
meg_bids_path = _bids_path.copy().update(
root=tmp_path / 'meg_root', datatype='meg', suffix='meg'
)
t1_bids_path = _bids_path.copy().update(
root=tmp_path / 'mri_root', task=None, run=None
)
raw = _read_raw_fif(raw_fname)
write_raw_bids(raw, bids_path=meg_bids_path)
landmarks = get_anat_landmarks(
t1w_mgh, raw.info, trans, fs_subject='sample',
fs_subjects_dir=subjects_dir)
write_anat(t1w_mgh, bids_path=t1_bids_path, landmarks=landmarks)
read_trans = get_head_mri_trans(
bids_path=meg_bids_path, t1_bids_path=t1_bids_path,
fs_subject='sample', fs_subjects_dir=subjects_dir)
assert np.allclose(trans['trans'], read_trans['trans'])
# Case 2: different sessions
raw = _read_raw_fif(raw_fname)
meg_bids_path = _bids_path.copy().update(
root=tmp_path / 'session_test', session='01', datatype='meg',
suffix='meg'
)
t1_bids_path = meg_bids_path.copy().update(
session='02', task=None, run=None, datatype='anat', suffix='T1w'
)
write_raw_bids(raw, bids_path=meg_bids_path)
write_anat(t1w_mgh, bids_path=t1_bids_path, landmarks=landmarks)
read_trans = get_head_mri_trans(
bids_path=meg_bids_path, t1_bids_path=t1_bids_path,
fs_subject='sample', fs_subjects_dir=subjects_dir)
assert np.allclose(trans['trans'], read_trans['trans'])
# Test that incorrect subject directory throws error
with pytest.raises(ValueError, match='Could not find'):
estimated_trans = get_head_mri_trans(
bids_path=bids_path, fs_subject='bad',
fs_subjects_dir=subjects_dir)
# Case 3: write with suffix for kind
landmarks2 = landmarks.copy()
landmarks2.dig[0]['r'] *= -1
landmarks2.save(tmp_path / 'landmarks2.fif')
landmarks2 = tmp_path / 'landmarks2.fif'
write_anat(t1w_mgh, bids_path=t1_bids_path, overwrite=True,
deface=True,
landmarks={"coreg": landmarks, "deface": landmarks2})
read_trans1 = get_head_mri_trans(
bids_path=meg_bids_path, t1_bids_path=t1_bids_path,
fs_subject='sample', fs_subjects_dir=subjects_dir,
kind="coreg")
assert np.allclose(trans['trans'], read_trans1['trans'])
read_trans2 = get_head_mri_trans(
bids_path=meg_bids_path, t1_bids_path=t1_bids_path,
fs_subject='sample', fs_subjects_dir=subjects_dir,
kind="deface")
assert not np.allclose(trans['trans'], read_trans2['trans'])
# Test we're respecting existing suffix & data type
# The following path is supposed to mimic a derivative generated by the
# MNE-BIDS-Pipeline.
#
# XXX We MAY want to revise this once the BIDS-Pipeline produces more
# BIDS-compatible output, e.g. including `channels.tsv` files for written
# Raw data etc.
raw = _read_raw_fif(raw_fname)
deriv_root = tmp_path / 'derivatives' / 'mne-bids-pipeline'
electrophys_path = (
deriv_root / 'sub-01' / 'eeg' / 'sub-01_task-av_proc-filt_raw.fif'
)
electrophys_path.parent.mkdir(parents=True)
raw.save(electrophys_path)
electrophys_bids_path = BIDSPath(
subject='01', task='av', datatype='eeg', processing='filt',
suffix='raw', extension='.fif', root=deriv_root,
check=False
)
t1_bids_path = _bids_path.copy().update(
root=tmp_path / 'mri_root', task=None, run=None
)
with pytest.warns(RuntimeWarning, match='Did not find any channels.tsv'):
get_head_mri_trans(
bids_path=electrophys_bids_path,
t1_bids_path=t1_bids_path,
fs_subject='sample',
fs_subjects_dir=subjects_dir
)
# bids_path without datatype is deprecated
bids_path = electrophys_bids_path.copy().update(datatype=None)
with pytest.raises(FileNotFoundError): # defaut location is all wrong!
with pytest.warns(DeprecationWarning, match='no datatype'):
get_head_mri_trans(
bids_path=bids_path,
t1_bids_path=t1_bids_path,
fs_subject='sample',
fs_subjects_dir=subjects_dir
)
# bids_path without suffix is deprecated
bids_path = electrophys_bids_path.copy().update(suffix=None)
with pytest.raises(FileNotFoundError): # defaut location is all wrong!
with pytest.warns(DeprecationWarning, match='no datatype'):
get_head_mri_trans(
bids_path=bids_path,
t1_bids_path=t1_bids_path,
fs_subject='sample',
fs_subjects_dir=subjects_dir
)
# Should fail for an unsupported coordinate frame
raw = _read_raw_fif(raw_fname)
bids_root = tmp_path / 'unsupported_coord_frame'
bids_path = BIDSPath(
subject='01', task='av', datatype='meg', suffix='meg',
extension='.fif', root=bids_root
)
t1_bids_path = _bids_path.copy().update(
root=tmp_path / 'mri_root', task=None, run=None
)
write_raw_bids(raw=raw, bids_path=bids_path, verbose=False)
