def run_command(self, args):
from clinica.iotools.utils import data_handling as dt
from clinica.utils.inputs import check_bids_folder
check_bids_folder(args.bids_directory)
dt.compute_missing_mods(args.bids_directory, args.out_directory,
args.output_prefix)
def run_computemissingmodalities(
input_dir: PathLike, output_dir: PathLike, ref_dir: PathLike
) -> None:
from clinica.iotools.utils import data_handling as dt
output_name = "missing_modalities"
bids_dir = input_dir / "bids"
dt.compute_missing_mods(bids_dir, output_dir, output_name)
filenames = [
"missing_modalities_ses-M00.tsv",
"missing_modalities_ses-M03.tsv",
"missing_modalities_ses-M06.tsv",
"missing_modalities_ses-M12.tsv",
"missing_modalities_ses-M24.tsv",
"missing_modalities_ses-M48.tsv",
]
for i in range(len(filenames)):
outname = output_dir / filenames[i]
refname = ref_dir / filenames[i]
if not outname.exists():
raise FileNotFoundError(
"A file called "
+ outname
+ " should have been generated, but it does not exists"
)
assert same_missing_modality_tsv(outname, refname)
def test_run_ComputeMissingModalities(cmdopt):
from os.path import join, dirname, abspath, exists
from os import remove
from clinica.iotools.utils import data_handling as dt
root = join(dirname(abspath(__file__)), pardir, 'data',
'ComputeMissingMod')
bids_directory = join(root, 'in', 'bids')
output_directory = join(root, 'out')
output_name = 'missing_modalities'
dt.compute_missing_mods(bids_directory, output_directory, output_name)
filenames = [
'missing_modalities_ses-M00.tsv', 'missing_modalities_ses-M03.tsv',
'missing_modalities_ses-M06.tsv', 'missing_modalities_ses-M12.tsv',
'missing_modalities_ses-M24.tsv', 'missing_modalities_ses-M48.tsv'
]
for i in range(len(filenames)):
outname = join(root, 'out', filenames[i])
refname = join(root, 'ref', filenames[i])
if not exists(outname):
raise FileNotFoundError(
'A file called ' + outname +
' should have been generated, but it does not exists')
assert same_missing_modality_tsv(outname, refname)
remove(join(root, 'out', filenames[i]))
def test_run_ComputeMissingModalities(cmdopt):
from os import remove
from os.path import abspath, dirname, exists, join
from clinica.iotools.utils import data_handling as dt
root = join(dirname(abspath(__file__)), pardir, pardir, "data",
"ComputeMissingMod")
bids_directory = join(root, "in", "bids")
output_directory = join(root, "out")
output_name = "missing_modalities"
dt.compute_missing_mods(bids_directory, output_directory, output_name)
filenames = [
"missing_modalities_ses-M00.tsv",
"missing_modalities_ses-M03.tsv",
"missing_modalities_ses-M06.tsv",
"missing_modalities_ses-M12.tsv",
"missing_modalities_ses-M24.tsv",
"missing_modalities_ses-M48.tsv",
]
for i in range(len(filenames)):
outname = join(root, "out", filenames[i])
refname = join(root, "ref", filenames[i])
if not exists(outname):
raise FileNotFoundError(
"A file called " + outname +
" should have been generated, but it does not exists")
assert same_missing_modality_tsv(outname, refname)
remove(join(root, "out", filenames[i]))
def check_missing_modalities(
bids_directory: str,
output_directory: str,
output_prefix: str = "missing_mods",
) -> None:
"""Check missing modalities in a BIDS dataset."""
from clinica.iotools.utils.data_handling import compute_missing_mods
from clinica.utils.inputs import check_bids_folder
check_bids_folder(bids_directory)
compute_missing_mods(bids_directory, output_directory, output_prefix)
def run_command(self, args):
from clinica.iotools.utils import data_handling as dt
dt.compute_missing_mods(args.bids_directory, args.out_directory, args.output_prefix)
