def test_load_heuristics():
test_heuristic = 'heur_test_acq'
heuristic_output_filename = utils.load_heuristic(test_heuristic).filename
assert test_heuristic in heuristic_output_filename
with raises(Exception) as errorinfo:
utils.load_heuristic('')
assert 'Failed to import heuristic' in str(errorinfo.value)
def use_heuristic(heur_file, sub, ses, filename, outdir, record_label=''):
utils.check_file_exists(heur_file)
"""
Import the heuristic file specified by the user and uses its output
to rename the file.
Input
-----
heur_file: path
Fullpath to heuristic file.
sub: str or int
Name of subject.
ses: str or int or None
Name of session.
filename: path
Name of the input of phys2bids.
outdir: str or path
Path to the directory that will become the "site" folder
("root" folder of BIDS database).
record_label: str
Optional label for the "record" entry of BIDS.
Output
-------
heurpath: str or path
Returned fullpath to tsv.gz new file (post BIDS formatting).
"""
if sub[:4] != 'sub-':
name = 'sub-' + sub
else:
name = sub
fldr = outdir + '/' + name
if ses:
if ses[:4] != 'ses-':
fldr = fldr + '/ses-' + ses
name = name + '_ses-' + ses
else:
fldr = fldr + '/' + ses
name = name + ses
fldr = fldr + '/func'
utils.path_exists_or_make_it(fldr)
cwd = os.getcwd()
os.chdir(outdir)
heur = utils.load_heuristic(heur_file)
name = heur.heur(Path(filename).stem, name)
recording = ''
if record_label:
recording = f'_recording-{record_label}'
heurpath = fldr + '/' + name + recording + '_physio'
# for ext in ['.tsv.gz', '.json', '.log']:
# move_file(outfile, heurpath, ext)
os.chdir(cwd)
return heurpath
def use_heuristic(heur_file, sub, ses, filename, outdir, run='', record_label=''):
"""
Import and use the heuristic specified by the user to rename the file.
Parameters
----------
heur_file: path
Fullpath to heuristic file.
sub: str or int
Name of subject.
ses: str or int or None
Name of session.
filename: path
Name of the input of phys2bids.
outdir: str or path
Path to the directory that will become the "site" folder
("root" folder of BIDS database).
record_label: str
Optional label for the "record" entry of BIDS.
Returns
-------
heurpath: str or path
Returned fullpath to tsv.gz new file (post BIDS formatting).
Raises
------
KeyError
if `bids_keys['task']` is empty
"""
utils.check_file_exists(heur_file)
# Initialise a dictionary of bids_keys that has already "recording"
bids_keys = {'sub': '', 'ses': '', 'task': '', 'acq': '', 'ce': '',
'dir': '', 'rec': '', 'run': run, 'recording': record_label}
# Start filling bids_keys dictionary and path with subject and session
if sub.startswith('sub-'):
bids_keys['sub'] = sub[4:]
fldr = os.path.join(outdir, sub)
else:
bids_keys['sub'] = sub
fldr = os.path.join(outdir, f'sub-{sub}')
if ses:
if ses.startswith('ses-'):
bids_keys['ses'] = ses[4:]
fldr = os.path.join(fldr, ses)
else:
bids_keys['ses'] = ses
fldr = os.path.join(fldr, f'ses-{ses}')
# Load heuristic and use it to fill dictionary
heur = utils.load_heuristic(heur_file)
bids_keys.update(heur.heur(Path(filename).stem, run))
# If bids_keys['task'] is still empty, stop the program
if not bids_keys['task']:
LGR.warning(f'The heuristic {heur_file} could not deal with'
f'{Path(filename).stem}')
raise KeyError('No "task" attribute found')
# Compose name by looping in the bids_keys dictionary
# and adding nonempty keys
name = ''
for key in bids_keys:
if bids_keys[key] != '':
name = f'{name}{key}-{bids_keys[key]}_'
# Finish path, create it, add filename, export
fldr = os.path.join(fldr, 'func')
os.makedirs(fldr, exist_ok=True)
heurpath = os.path.join(fldr, f'{name}physio')
return heurpath
def test_load_heuristics():
test_heuristic = 'heur_test_acq'
heuristic_output_filename = utils.load_heuristic(test_heuristic).filename
assert test_heuristic in heuristic_output_filename
