def cli(
dataset_directory: str,
clinical_data_directory: str,
bids_directory: str,
clinical_data_only: bool = False,
overwrite: bool = False,
) -> None:
"""AIBL to BIDS converter.
Convert the imaging and clinical data of AIBL (https://aibl.csiro.au/adni/index.html), located in DATASET_DIRECTORY
and CLINICAL_DATA_DIRECTORY respectively, to a BIDS dataset in the target BIDS_DIRECTORY.
"""
from os import makedirs
from clinica.iotools.converters.aibl_to_bids.aibl_to_bids import (
convert_clinical_data,
convert_images,
)
from clinica.utils.check_dependency import check_dcm2niix
check_dcm2niix()
makedirs(bids_directory, exist_ok=True)
if not clinical_data_only:
convert_images(
dataset_directory,
clinical_data_directory,
bids_directory,
overwrite,
)
convert_clinical_data(bids_directory, clinical_data_directory)
def run_command(self, args):
"""Run the converter with defined args."""
from os import makedirs
from os.path import exists
from clinica.iotools.converters.aibl_to_bids.aibl_to_bids import (
convert_clinical_data,
convert_images,
)
from clinica.utils.check_dependency import (
check_dcm2nii,
check_dcm2niix,
check_freesurfer,
)
check_dcm2nii()
check_dcm2niix()
check_freesurfer()
if not exists(args.bids_directory):
makedirs(args.bids_directory)
convert_images(args.dataset_directory, args.clinical_data_directory,
args.bids_directory)
convert_clinical_data(args.bids_directory,
args.clinical_data_directory)
def run_aibl2bids(input_dir: PathLike, output_dir: PathLike,
ref_dir: PathLike) -> None:
from clinica.iotools.converters.aibl_to_bids.aibl_to_bids import (
convert_clinical_data,
convert_images,
)
# Arrange
clinical_data_directory = input_dir / "Data_extract_3.2.5"
dataset_directory = input_dir / "unorganized_data"
# Act
convert_images(
dataset_directory,
clinical_data_directory,
output_dir / "bids",
)
convert_clinical_data(output_dir / "bids", clinical_data_directory)
# Assert
compare_folders(output_dir / "bids", ref_dir / "bids", output_dir)
def test_run_Aibl2Bids(cmdopt):
from clinica.iotools.converters.aibl_to_bids.aibl_to_bids import convert_clinical_data, convert_images
from os.path import dirname, join, abspath
from .comparison_functions import compare_folders
root = join(dirname(abspath(__file__)), 'data', 'Aibl2Bids')
dataset_directory = join(root, 'in', 'unorganized_data')
clinical_data_directory = join(root, 'in', 'Data_extract_3.2.5')
bids_directory = join(root, 'out', 'bids')
clean_folder(join(root, 'out', 'bids'), recreate=True)
# Perform conversion of dataset
convert_images(dataset_directory, clinical_data_directory, bids_directory)
convert_clinical_data(bids_directory, clinical_data_directory)
# Evaluate difference between ref and out
compare_folders(join(root, 'out'),
join(root, 'ref'),
shared_folder_name='bids')
clean_folder(join(root, 'out', 'bids'), recreate=True)
def run_command(self, args):
from os.path import exists
from os import makedirs
from colorama import Fore
from clinica.iotools.converters.aibl_to_bids.aibl_to_bids import convert_clinical_data, convert_images
from clinica.utils.check_dependency import is_binary_present, check_freesurfer
from clinica.utils.exceptions import ClinicaMissingDependencyError
list_binaries = ['dcm2niix', 'dcm2nii']
for binary in list_binaries:
if not is_binary_present(binary):
raise ClinicaMissingDependencyError(
'%s\n[Error] Clinica could not find %s software: it is not present in your '
'PATH environment.%s' % (Fore.RED, binary, Fore.RESET))
check_freesurfer()
if not exists(args.bids_directory):
makedirs(args.bids_directory)
convert_images(args.dataset_directory, args.clinical_data_directory,
args.bids_directory)
convert_clinical_data(args.bids_directory,
args.clinical_data_directory)
def run_command(self, args):
from clinica.iotools.converters.aibl_to_bids.aibl_to_bids import convert_clinical_data, convert_images
convert_images(args.dataset_directory, args.clinical_data_directory, args.bids_directory)
convert_clinical_data(args.bids_directory, args.clinical_data_directory)