def run_command(self, args): from clinica.iotools.converters.oasis_to_bids.oasis_to_bids import OasisToBids oasis_to_bids = OasisToBids() oasis_to_bids.convert_images(args.dataset_directory, args.bids_directory) oasis_to_bids.convert_clinical_data(args.clinical_data_directory, args.bids_directory)
def run_oasis2bids(input_dir: PathLike, output_dir: PathLike, ref_dir: PathLike) -> None: from clinica.iotools.converters.oasis_to_bids.oasis_to_bids import OasisToBids # Arrange clinical_data_directory = input_dir / "clinical_data" # Act oasis_to_bids = OasisToBids() oasis_to_bids.convert_images(input_dir / "unorganized", output_dir / "bids") oasis_to_bids.convert_clinical_data(clinical_data_directory, output_dir / "bids") # Assert compare_folders(output_dir / "bids", ref_dir / "bids", output_dir)
def cli( dataset_directory: str, clinical_data_directory: str, bids_directory: str, ) -> None: """OASIS to BIDS converter. Convert the imaging and clinical data of OASIS (http://oasis-brains.org/), located in DATASET_DIRECTORY and CLINICAL_DATA_DIRECTORY respectively, to a BIDS dataset in the target BIDS_DIRECTORY. """ from clinica.iotools.converters.oasis_to_bids.oasis_to_bids import OasisToBids oasis_to_bids = OasisToBids() oasis_to_bids.convert_images(dataset_directory, bids_directory) oasis_to_bids.convert_clinical_data(clinical_data_directory, bids_directory)
def run_command(self, args): from clinica.iotools.converters.oasis_to_bids.oasis_to_bids import OasisToBids from clinica.iotools.converter_utils import check_bin from clinica.utils.stream import cprint from colorama import Fore import sys missing_bin = check_bin('mri_convert') if missing_bin: cprint(Fore.RED + 'mri_convert from FreeSurfer is required.' + ' Install it and re-run the converter.' + Fore.RESET) cprint('Exiting clinica...') sys.exit() oasis_to_bids = OasisToBids() oasis_to_bids.convert_images(args.dataset_directory, args.bids_directory) oasis_to_bids.convert_clinical_data(args.clinical_data_directory, args.bids_directory)
def test_run_Oasis2Bids(cmdopt): from os.path import abspath, dirname, join from clinica.iotools.converters.oasis_to_bids.oasis_to_bids import OasisToBids root = join(dirname(abspath(__file__)), pardir, pardir, "data", "Oasis2Bids") clean_folder(join(root, "out", "bids"), recreate=True) # Data location dataset_directory = join(root, "in", "unorganized") bids_directory = join(root, "out", "bids") clinical_data_directory = join(root, "in", "clinical_data") oasis_to_bids = OasisToBids() oasis_to_bids.convert_images(dataset_directory, bids_directory) oasis_to_bids.convert_clinical_data(clinical_data_directory, bids_directory) compare_folders(join(root, "out"), join(root, "ref"), shared_folder_name="bids") clean_folder(join(root, "out", "bids"), recreate=True)
def test_run_Oasis2Bids(cmdopt): from clinica.iotools.converters.oasis_to_bids.oasis_to_bids import OasisToBids from os.path import dirname, join, abspath root = join(dirname(abspath(__file__)), pardir, 'data', 'Oasis2Bids') clean_folder(join(root, 'out', 'bids'), recreate=True) # Data location dataset_directory = join(root, 'in', 'unorganized') bids_directory = join(root, 'out', 'bids') clinical_data_directory = join(root, 'in', 'clinical_data') oasis_to_bids = OasisToBids() oasis_to_bids.convert_images(dataset_directory, bids_directory) oasis_to_bids.convert_clinical_data(clinical_data_directory, bids_directory) compare_folders(join(root, 'out'), join(root, 'ref'), shared_folder_name='bids') clean_folder(join(root, 'out', 'bids'), recreate=True)