def test_update_sidecar_jsons(_get_bids_test_dir, _bids_validate,
_get_sidecar_json_update_file):
"""Test updating sidecar JSON files."""
bids_path = BIDSPath(subject=subject_id,
session=session_id,
run=run,
acquisition=acq,
task=task,
suffix='meg',
root=_get_bids_test_dir)
# expected key, original value, and expected value after update
# Fields that are not `None` already are expected to exist
# in this sidecar file. Fields that are `None` will get
# written with the sidecar json value when update is called.
expected_checks = [('InstitutionName', None, 'mne-bids'),
('InstitutionAddress', None, 'Internet'),
('MEGChannelCount', 306, 300),
('MEGREFChannelCount', 0, 6), ('ECGChannelCount', 0, 0),
('SEEGChannelCount', None, 0)]
# get the sidecar json
sidecar_path = bids_path.copy().update(extension='.json')
sidecar_fpath = sidecar_path.fpath
with open(sidecar_fpath, 'r', encoding='utf-8') as fin:
sidecar_json = json.load(fin)
for key, val, _ in expected_checks:
assert sidecar_json.get(key) == val
_bids_validate(bids_path.root)
# update sidecars
update_sidecar_json(sidecar_path, _get_sidecar_json_update_file)
with open(sidecar_fpath, 'r', encoding='utf-8') as fin:
sidecar_json = json.load(fin)
for key, _, val in expected_checks:
assert sidecar_json.get(key) == val
_bids_validate(bids_path.root)
# should result in error if you don't explicitly say
# its a json file
with pytest.raises(RuntimeError, match='Only works for ".json"'):
update_sidecar_json(sidecar_path.copy().update(extension=None),
_get_sidecar_json_update_file)
# error should raise if the file path doesn't exist
error_bids_path = sidecar_path.copy().update(subject='02')
with pytest.raises(RuntimeError, match='Sidecar file ' 'does not exist.'):
update_sidecar_json(error_bids_path, _get_sidecar_json_update_file)
# Define a sidecar update as a dictionary
entries = {
'PowerLineFrequency': 60,
'Manufacturer': "MEGIN",
'InstitutionName': "Martinos Center"
}
# Note: ``update_sidecar_json`` will perform essentially a
# dictionary update to your sidecar json file, so be absolutely sure
# that the ``entries`` are defined with the proper fields specified
# by BIDS. For example, if you are updating the ``coordsystem.json``
# file, then you don't want to include ``PowerLineFrequency`` in
# ``entries``.
#
# Now update all sidecar fields according to our updating dictionary
update_sidecar_json(bids_path=sidecar_path, entries=entries)
###############################################################################
# Read the updated dataset
# ------------------------
# new line frequency is now 60 Hz
raw = read_raw_bids(bids_path=bids_path)
print(raw.info['line_freq'])
###############################################################################
# Generate a new report based on the updated metadata.
# The manufacturer was changed to ``MEGIN``
print(make_report(bids_root))