code stringlengths 3 6.57k |
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logger.debug('globbing for %s', expr) |
glob.glob(expr) |
convert(dicom_dir, fullfile) |
os.path.join(args.bids, scan['type'], fbase + '.json') |
logger.debug('adding provenance to %s', sidecar_file) |
open(sidecar_file) |
json.load(fo) |
commons.atomic_write(sidecar_file, json.dumps(sidecarjs, indent=2) |
proc_dwi(config, args) |
dict() |
iterconfig(config, 'dwi') |
scan.get('id', None) |
string.Template(templ) |
legal.sub('', args.subject) |
legal.sub('', args.session) |
scan.get('acquisition', None) |
scan.get('direction', None) |
scan.get('run', None) |
scan.get('modality', None) |
os.path.join(args.sourcedata, scan['type']) |
os.path.exists(sourcedata_dir) |
os.makedirs(sourcedata_dir) |
os.path.join(sourcedata_dir, '{0}.dicom'.format(fbase) |
logger.info('downloading session=%s, scan=%s, loc=%s', args.session, scan['scan'], dicom_dir) |
args.xnat.download(args.session, [scan['scan']], out_dir=dicom_dir) |
format(fbase) |
os.path.join(scan['type'], fname) |
os.path.join(args.bids, scan['type'], fname) |
logger.info('converting %s to %s', dicom_dir, fullfile) |
scan.get('modality', None) |
convert(dicom_dir, fullfile) |
os.path.join(args.bids, scan['type'], fbase + '.json') |
logger.debug('adding provenance to %s', sidecar_file) |
open(sidecar_file) |
json.load(fo) |
commons.atomic_write(sidecar_file, json.dumps(sidecarjs, indent=2) |
proc_fmap(config, args, func_refs=None) |
dict() |
iterconfig(config, 'fmap') |
scan.get('id', None) |
string.Template(templ) |
legal.sub('', args.subject) |
legal.sub('', args.session) |
scan.get('acquisition', None) |
scan.get('run', None) |
scan.get('direction', None) |
scan.get('modality', None) |
os.path.join(args.sourcedata, scan['type']) |
os.path.exists(sourcedata_dir) |
os.makedirs(sourcedata_dir) |
os.path.join(sourcedata_dir, '{0}.dicom'.format(fbase) |
logger.info('downloading session=%s, scan=%s, loc=%s', args.session, scan['scan'], dicom_dir) |
args.xnat.download(args.session, [scan['scan']], out_dir=dicom_dir) |
format(fbase) |
os.path.join(scan['type'], fname) |
os.path.join(args.bids, scan['type'], fname) |
logger.info('converting %s to %s', dicom_dir, fullfile) |
convert(dicom_dir, fullfile) |
scan.get('modality', None) |
rename_fmapm(args.bids, fbase) |
scan.get('modality', None) |
rename_fmapp(args.bids, fbase) |
os.path.join(args.bids, scan['type'], fbase + '.json') |
open(sidecar_file, 'r') |
json.load(fo) |
logger.info('adding IntendedFor %s to %s', func_refs[intended], sidecar_file) |
list() |
append(func_refs[intended]) |
logger.info('writing file %s', sidecar_file) |
commons.atomic_write(sidecar_file, json.dumps(sidecarjs, indent=2) |
iterconfig(config, scan_type) |
iter(config[scan_type].items() |
rename_fmapm(bids_base, basename) |
dict() |
format(basename, echo, ext) |
os.path.join(bids_base, 'fmap', fname) |
os.path.exists(src) |
format(echo) |
format(echo) |
logger.debug('renaming %s to %s', src, dst) |
os.rename(src, dst) |
rename_fmapp(bids_base, basename) |
dict() |
format(basename, ext) |
os.path.join(bids_base, 'fmap', fname) |
os.path.exists(src) |
logger.debug('renaming %s to %s', src, dst) |
os.rename(src, dst) |
convert(input, output, single_file=False) |
os.path.dirname(output) |
os.path.exists(dirname) |
os.makedirs(dirname) |
os.path.basename(output) |
re.sub('.nii(.gz) |
commons.which('dcm2niix') |
logger.debug(cmd) |
sp.check_output(cmd) |
build_url(ticker, start_date = None, end_date = None, interval = "1d") |
int(pd.Timestamp("now") |
timestamp() |
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