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FIX: construct mgh image only when vox2ras_tkr is needed
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@jasmainak
jasmainak committed Jul 20, 2019
1 parent a978e83 commit 64e976e
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Showing 3 changed files with 52 additions and 57 deletions.
3 changes: 3 additions & 0 deletions examples/convert_mri_and_trans.py
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Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,9 @@

import numpy as np
import matplotlib.pyplot as plt

from nilearn.plotting import plot_anat

import mne
from mne.datasets import sample
from mne.source_space import head_to_mri
Expand Down Expand Up @@ -148,6 +150,7 @@
plot_anat(t1_mgh_fname, axes=axs[point_idx],
cut_coords=mri_pos[point_idx, :],
title=label)
plt.show()


###############################################################################
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100 changes: 46 additions & 54 deletions mne_bids/tests/test_write.py
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Original file line number Diff line number Diff line change
Expand Up @@ -48,6 +48,7 @@
task=task)
bids_basename_minimal = make_bids_basename(subject=subject_id, task=task)


# WINDOWS issues:
# the bids-validator development version does not work properly on Windows as
# of 2019-06-25 --> https://github.com/bids-standard/bids-validator/issues/790
Expand All @@ -56,16 +57,29 @@
# using the stable bids-validator and make a direct call of bids-validator
# also: for windows, shell = True is needed to call npm, bids-validator etc.
# see: https://stackoverflow.com/q/28891053/5201771
shell = False
bids_validator_exe = ['bids-validator']
if platform.system() == 'Windows':
shell = True
exe = os.getenv('VALIDATOR_EXECUTABLE', 'n/a')
if 'VALIDATOR_EXECUTABLE' != 'n/a':
bids_validator_exe = ['node', exe]
@pytest.fixture(scope="session")
def _bids_validate():
shell = False
config_path = _TempDir()
config_fname = op.join(config_path, 'validator_config.json')
with open(config_fname, 'w') as f:
json.dump(dict(error=["NIFTI_UNIT"]), f)

bids_validator_exe = ['bids-validator', '--config', config_fname]
if platform.system() == 'Windows':
shell = True
exe = os.getenv('VALIDATOR_EXECUTABLE', 'n/a')
if 'VALIDATOR_EXECUTABLE' != 'n/a':
bids_validator_exe = ['node', exe]

def _validate(output_path):
cmd = bids_validator_exe + [output_path]
run_subprocess(cmd, shell=shell)

return _validate


def test_fif():
def test_fif(_bids_validate):
"""Test functionality of the write_raw_bids conversion for fif."""
output_path = _TempDir()
data_path = testing.data_path()
Expand All @@ -89,8 +103,7 @@ def test_fif():
with pytest.warns(UserWarning, match='No events found or provided.'):
write_raw_bids(raw, bids_basename, output_path, overwrite=False)

cmd = bids_validator_exe + [output_path]
run_subprocess(cmd, shell=shell)
_bids_validate(output_path)

# write the same data but pretend it is empty room data:
raw = mne.io.read_raw_fif(raw_fname)
Expand Down Expand Up @@ -170,8 +183,7 @@ def test_fif():
with pytest.raises(ValueError, match='raw.filenames is missing'):
write_raw_bids(raw, bids_basename2, output_path)

cmd = bids_validator_exe + [output_path]
run_subprocess(cmd, shell=shell)
_bids_validate(output_path)

assert op.exists(op.join(output_path, 'participants.tsv'))

Expand Down Expand Up @@ -199,7 +211,7 @@ def test_fif():
assert 'part' in FILE


def test_kit():
def test_kit(_bids_validate):
"""Test functionality of the write_raw_bids conversion for KIT data."""
output_path = _TempDir()
data_path = op.join(base_path, 'kit', 'tests', 'data')
Expand All @@ -220,8 +232,8 @@ def test_kit():
write_raw_bids(raw, kit_bids_basename, output_path,
events_data=events_fname,
event_id=event_id, overwrite=False)
cmd = bids_validator_exe + [output_path]
run_subprocess(cmd, shell=shell)

_bids_validate(output_path)
assert op.exists(op.join(output_path, 'participants.tsv'))

read_raw_bids(kit_bids_basename + '_meg.sqd', output_path)
Expand Down Expand Up @@ -264,8 +276,8 @@ def test_kit():
kit_bids_basename.replace('sub-01', 'sub-%s' % subject_id2),
output_path, events_data=events_fname, event_id=event_id,
overwrite=False)
cmd = bids_validator_exe + [output_path]
run_subprocess(cmd, shell=shell)

_bids_validate(output_path)
# ensure the marker files are renamed correctly
marker_fname = make_bids_basename(
subject=subject_id2, session=session_id, task=task, run=run,
Expand All @@ -291,7 +303,7 @@ def test_kit():
overwrite=True)


def test_ctf():
def test_ctf(_bids_validate):
"""Test functionality of the write_raw_bids conversion for CTF data."""
output_path = _TempDir()
data_path = op.join(testing.data_path(download=False), 'CTF')
Expand All @@ -301,8 +313,7 @@ def test_ctf():
with pytest.warns(UserWarning, match='No line frequency'):
write_raw_bids(raw, bids_basename, output_path=output_path)

cmd = bids_validator_exe + [output_path]
run_subprocess(cmd, shell=shell)
_bids_validate(output_path)
with pytest.warns(UserWarning, match='Expected to find a single events'):
raw = read_raw_bids(bids_basename + '_meg.ds', output_path)

Expand All @@ -313,7 +324,7 @@ def test_ctf():
assert op.exists(op.join(output_path, 'participants.tsv'))


def test_bti():
def test_bti(_bids_validate):
"""Test functionality of the write_raw_bids conversion for BTi data."""
output_path = _TempDir()
data_path = op.join(base_path, 'bti', 'tests', 'data')
Expand All @@ -327,9 +338,7 @@ def test_bti():
write_raw_bids(raw, bids_basename, output_path, verbose=True)

assert op.exists(op.join(output_path, 'participants.tsv'))

cmd = bids_validator_exe + [output_path]
run_subprocess(cmd, shell=shell)
_bids_validate(output_path)

raw = read_raw_bids(bids_basename + '_meg', output_path)

Expand All @@ -338,7 +347,7 @@ def test_bti():
# see: https://github.com/mne-tools/mne-python/pull/6558
@pytest.mark.skipif(LooseVersion(mne.__version__) < LooseVersion('0.19'),
reason="requires mne 0.19.dev0 or higher")
def test_vhdr():
def test_vhdr(_bids_validate):
"""Test write_raw_bids conversion for BrainVision data."""
output_path = _TempDir()
data_path = op.join(base_path, 'brainvision', 'tests', 'data')
Expand All @@ -353,9 +362,7 @@ def test_vhdr():

# write with injected bad channels
write_raw_bids(raw, bids_basename_minimal, output_path, overwrite=False)

cmd = bids_validator_exe + [output_path]
run_subprocess(cmd, shell=shell)
_bids_validate(output_path)

# read and also get the bad channels
raw = read_raw_bids(bids_basename_minimal + '_eeg.vhdr', output_path)
Expand Down Expand Up @@ -390,12 +397,10 @@ def test_vhdr():
for i in mne.pick_types(raw.info, eeg=True)})
output_path = _TempDir()
write_raw_bids(raw, bids_basename, output_path, overwrite=False)
_bids_validate(output_path)

cmd = bids_validator_exe + [output_path]
run_subprocess(cmd, shell=shell)


def test_edf():
def test_edf(_bids_validate):
"""Test write_raw_bids conversion for European Data Format data."""
output_path = _TempDir()
data_path = op.join(testing.data_path(), 'EDF')
Expand All @@ -422,9 +427,7 @@ def test_edf():

bids_fname = bids_basename.replace('run-01', 'run-%s' % run2)
write_raw_bids(raw, bids_fname, output_path, overwrite=True)

cmd = bids_validator_exe + [output_path]
run_subprocess(cmd, shell=shell)
_bids_validate(output_path)

# ensure there is an EMG channel in the channels.tsv:
channels_tsv = make_bids_basename(
Expand All @@ -447,12 +450,10 @@ def test_edf():
for i in mne.pick_types(raw.info, eeg=True)})
output_path = _TempDir()
write_raw_bids(raw, bids_basename, output_path)
_bids_validate(output_path)

cmd = bids_validator_exe + [output_path]
run_subprocess(cmd, shell=shell)


def test_bdf():
def test_bdf(_bids_validate):
"""Test write_raw_bids conversion for Biosemi data."""
output_path = _TempDir()
data_path = op.join(base_path, 'edf', 'tests', 'data')
Expand All @@ -461,9 +462,7 @@ def test_bdf():
raw = mne.io.read_raw_bdf(raw_fname)
with pytest.warns(UserWarning, match='No line frequency found'):
write_raw_bids(raw, bids_basename, output_path, overwrite=False)

cmd = bids_validator_exe + [output_path]
run_subprocess(cmd, shell=shell)
_bids_validate(output_path)

# Test also the reading of channel types from channels.tsv
# the first channel in the raw data is not MISC right now
Expand Down Expand Up @@ -491,7 +490,7 @@ def test_bdf():
write_raw_bids(raw, bids_basename, output_path)


def test_set():
def test_set(_bids_validate):
"""Test write_raw_bids conversion for EEGLAB data."""
# standalone .set file
output_path = _TempDir()
Expand All @@ -518,9 +517,7 @@ def test_set():
with pytest.raises(FileExistsError, match="already exists"): # noqa: F821
write_raw_bids(raw, bids_basename, output_path=output_path,
overwrite=False)

cmd = bids_validator_exe + [output_path]
run_subprocess(cmd, shell=shell)
_bids_validate(output_path)

# check events.tsv is written
# XXX: only from 0.18 onwards because events_from_annotations
Expand All @@ -537,13 +534,11 @@ def test_set():
for i in mne.pick_types(raw.info, eeg=True)})
output_path = _TempDir()
write_raw_bids(raw, bids_basename, output_path)

cmd = bids_validator_exe + [output_path]
run_subprocess(cmd, shell=shell)
_bids_validate(output_path)


@requires_nibabel()
def test_write_anat():
def test_write_anat(_bids_validate):
"""Test writing anatomical data."""
# Get the MNE testing sample data
output_path = _TempDir()
Expand All @@ -570,10 +565,7 @@ def test_write_anat():

anat_dir = write_anat(output_path, subject_id, t1w_mgh, session_id, acq,
raw=raw, trans=trans, verbose=True)

# Validate BIDS
cmd = bids_validator_exe + [output_path]
run_subprocess(cmd, shell=shell)
_bids_validate(output_path)

# Validate that files are as expected
t1w_json_path = op.join(anat_dir, 'sub-01_ses-01_acq-01_T1w.json')
Expand Down
6 changes: 3 additions & 3 deletions mne_bids/write.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1015,17 +1015,16 @@ def write_anat(bids_root, subject, t1w, session=None, acquisition=None,
raise ValueError('`t1w` must be a path to a T1 weighted MRI data file '
', or a nibabel image object, but it is of type '
'"{}"'.format(type(t1w)))
t1_mgh = nib.MGHImage(t1w.dataobj, t1w.affine)

# Now give the NIfTI file a BIDS name and write it to the BIDS location
t1w_basename = make_bids_basename(subject=subject, session=session,
acquisition=acquisition, prefix=anat_dir,
suffix='T1w.nii.gz')
if not op.exists(t1w_basename):
nib.save(t1_mgh, t1w_basename)
nib.save(t1w, t1w_basename)
elif overwrite:
os.remove(t1w_basename)
nib.save(t1_mgh, t1w_basename)
nib.save(t1w, t1w_basename)
else:
raise IOError('Wanted to write a file but it already exists and '
'`overwrite` is set to False. File: "{}"'
Expand All @@ -1051,6 +1050,7 @@ def write_anat(bids_root, subject, t1w, session=None, acquisition=None,
mri_landmarks = apply_trans(trans, meg_landmarks, move=True) * 1e3

# Get landmarks in voxel space, using the mgh version of our T1 data
t1_mgh = nib.MGHImage(t1w.dataobj, t1w.affine)
vox2ras_tkr = t1_mgh.header.get_vox2ras_tkr()
ras2vox_tkr = np.linalg.inv(vox2ras_tkr)
mri_landmarks = apply_trans(ras2vox_tkr, mri_landmarks) # in vox
Expand Down

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