def test_read_raw():
"""Test the raw reading."""
# Use a file ending that does not exist
f = 'file.bogus'
with pytest.raises(ValueError, match='file name extension must be one of'):
_read_raw(f)
def interpolate(self):
"""
Interpolates bad channels to create new data and updates info
Parameters
----------
none
Returns
-------
none
"""
result_filename = self.unique_name + "_results.json"
result_file_overall = os.path.join(self.result_path, result_filename)
processed_filename = self.unique_name + "_raw.fif"
processed_file_overall = os.path.join(self.result_path,
processed_filename)
if os.path.isfile(result_file_overall) and os.path.isfile(
processed_file_overall):
eeg = _read_raw(processed_file_overall)
with open(result_file_overall) as json_file:
automagic = json.load(json_file)
else:
raise (ValueError, "The block has not been preprocessed yet.")
return
interpolate_chans = self.to_be_interpolated
if interpolate_chans == []:
raise (
ValueError,
"The block is rated to be interpolated but no channels chosen",
)
return
if (self.params == [] or not "interpolation_params" in self.params
or self.params["interpolation_params"] == []):
default_params = self.config["default_params"]
interpolation_params = default_params["interpolation_params"]
else:
interpolation_params = self.params["interpolation_params"]
eeg.load_data()
eeg.info["dig"] = mne.channels.make_standard_montage(self.montage)
interpolated = eeg.interpolate_bads(
) # (origin=interpolation_params['origin'])
overall_thresh = self.project.quality_thresholds["overall_thresh"]
time_thresh = self.project.quality_thresholds["time_thresh"]
chan_thresh = self.project.quality_thresholds["chan_thresh"]
apply_common_avg = self.project.quality_thresholds["apply_common_avg"]
quality_scores = calcQuality(
interpolated.get_data(),
interpolate_chans,
overall_thresh,
time_thresh,
chan_thresh,
apply_common_avg,
)
update_to_be_stored = {
"rate": "not rated",
"is_manually_rated": False,
"to_be_interpolated": [],
"final_bad_chans": interpolate_chans,
"is_interpolated": True,
"quality_scores": quality_scores,
}
self.update_rating(update_to_be_stored)
automagic.update({
"interpolation": {
"channels": interpolate_chans,
"params": interpolation_params,
},
"quality_scores": self.quality_scores,
"rate": self.rate,
})
results = {"preprocessed": interpolated, "automagic": automagic}
self.write_log(automagic)
automagic.update({
"to_be_interpolated": self.to_be_interpolated,
"rate": self.rate,
"quality_scores": self.quality_scores,
"is_manually_rated": self.is_manually_rated,
"is_interpolated": self.is_interpolated,
})
main_result_file = results["automagic"]
result_filename = self.unique_name + "_results.json"
result_file_overall = os.path.join(self.result_path, result_filename)
_write_json(result_file_overall,
main_result_file,
overwrite=True,
verbose=True)
processed = results["preprocessed"]
processed.info["dig"] = None
processed_filename = self.unique_name + "_raw.fif"
processed_file_overall = os.path.join(self.result_path,
processed_filename)
processed.save(processed_file_overall, overwrite=True)
return results
def run():
"""Run the raw_to_bids command."""
from mne.commands.utils import get_optparser
parser = get_optparser(__file__, usage="usage: %prog options args",
prog_prefix='mne_bids',
version=mne_bids.__version__)
parser.add_option('--subject_id', dest='subject_id',
help=('subject name in BIDS compatible format '
'(01, 02, etc.)'))
parser.add_option('--task', dest='task',
help='name of the task the data is based on')
parser.add_option('--raw', dest='raw_fname',
help='path to the raw MEG file')
parser.add_option('--bids_root', dest='bids_root',
help='The path of the BIDS compatible folder.')
parser.add_option('--session_id', dest='session_id',
help='session name in BIDS compatible format')
parser.add_option('--run', dest='run',
help='run number for this dataset')
parser.add_option('--acq', dest='acq',
help='acquisition parameter for this dataset')
parser.add_option('--events_data', dest='events_data',
help='events file (events.tsv)')
parser.add_option('--event_id', dest='event_id',
help='event id dict', metavar='eid')
parser.add_option('--hpi', dest='hpi',
help='path to the MEG marker points')
parser.add_option('--electrode', dest='electrode',
help='path to head-native digitizer points')
parser.add_option('--hsp', dest='hsp',
help='path to headshape points')
parser.add_option('--config', dest='config',
help='path to the configuration file')
parser.add_option('--overwrite', dest='overwrite',
help="whether to overwrite existing data (BOOLEAN)")
parser.add_option('--line_freq', dest='line_freq',
help="The frequency of the line noise in Hz "
"(e.g. 50 or 60). If unknown, pass None")
opt, args = parser.parse_args()
if len(args) > 0:
parser.print_help()
parser.error('Do not specify arguments without flags. Found: "{}".\n'
.format(args))
if not all([opt.subject_id, opt.task, opt.raw_fname, opt.bids_root]):
parser.print_help()
parser.error('Arguments missing. You need to specify at least the'
'following: --subject_id, --task, --raw, --bids_root.')
bids_path = BIDSPath(
subject=opt.subject_id, session=opt.session_id, run=opt.run,
acquisition=opt.acq, task=opt.task, root=opt.bids_root)
allow_maxshield = False
if opt.raw_fname.endswith('.fif'):
allow_maxshield = 'yes'
raw = _read_raw(opt.raw_fname, hpi=opt.hpi, electrode=opt.electrode,
hsp=opt.hsp, config_path=opt.config,
allow_maxshield=allow_maxshield)
if opt.line_freq is not None:
line_freq = None if opt.line_freq == "None" else opt.line_freq
raw.info['line_freq'] = line_freq
write_raw_bids(raw, bids_path, event_id=opt.event_id,
events_data=opt.events_data, overwrite=opt.overwrite,
verbose=True)
def run():
"""Run the raw_to_bids command."""
from mne.commands.utils import get_optparser
parser = get_optparser(__file__,
usage="usage: %prog options args",
prog_prefix='mne_bids',
version=mne_bids.__version__)
parser.add_option('--subject_id',
dest='subject_id',
help=('subject name in BIDS compatible format '
'(01, 02, etc.)'))
parser.add_option('--task',
dest='task',
help='name of the task the data is based on')
parser.add_option('--raw',
dest='raw_fname',
help='path to the raw MEEG file')
parser.add_option('--output_path',
dest='output_path',
help='path to the BIDS compatible folder')
parser.add_option('--session_id',
dest='session_id',
help='session name in BIDS compatible format')
parser.add_option('--run', dest='run', help='run number for this dataset')
parser.add_option('--acq',
dest='acq',
help='acquisition parameter for this dataset')
parser.add_option('--events_data',
dest='events_data',
help='events file (events.tsv)')
parser.add_option('--event_id',
dest='event_id',
help='event id dict',
metavar='eid')
parser.add_option('--hpi',
dest='hpi',
help='path to the MEG marker points')
parser.add_option('--electrode',
dest='electrode',
help='path to head-native digitizer points')
parser.add_option('--hsp', dest='hsp', help='path to headshape points')
parser.add_option('--config',
dest='config',
help='path to the configuration file')
parser.add_option('--overwrite',
dest='overwrite',
help="whether to overwrite existing data (BOOLEAN)")
parser.add_option('--allow_maxshield',
dest='allow_maxshield',
help="whether to allow non maxfiltered data (BOOLEAN)",
action='store_true')
opt, args = parser.parse_args()
if len(args) > 0:
parser.print_help()
parser.error(
'Do not specify arguments without flags. Found: "{}".\n'.format(
args))
if not all([opt.subject_id, opt.task, opt.raw_fname, opt.output_path]):
parser.print_help()
parser.error('Arguments missing. You need to specify at least the'
'following: --subject_id, --task, --raw, --output_path.')
bids_basename = make_bids_basename(subject=opt.subject_id,
session=opt.session_id,
run=opt.run,
acquisition=opt.acq,
task=opt.task)
raw = _read_raw(opt.raw_fname,
hpi=opt.hpi,
electrode=opt.electrode,
hsp=opt.hsp,
config=opt.config,
allow_maxshield=opt.allow_maxshield)
write_raw_bids(raw,
bids_basename,
opt.output_path,
event_id=opt.event_id,
events_data=opt.events_data,
overwrite=opt.overwrite,
verbose=True)
