def run_oasis3tobids(input_dir: PathLike, output_dir: PathLike,
ref_dir: PathLike) -> None:
from clinica.iotools.converters.oasis3_to_bids.oasis3_to_bids import convert_images
# Arrange
clinical_data_directory = input_dir / "clinical_data"
# Act
convert_images(input_dir / "unorganized", output_dir / "bids",
clinical_data_directory)
# Assert
compare_folders(output_dir / "bids", ref_dir / "bids", output_dir)
def test_run_Nifd2Bids(cmdopt):
import shutil
from os.path import abspath, dirname, join
from clinica.iotools.converters.nifd_to_bids.nifd_to_bids import (
convert_clinical_data,
convert_images,
)
root = join(dirname(abspath(__file__)), pardir, pardir, "data", "Nifd2Bids")
clean_folder(join(root, "out", "bids"), recreate=True)
clean_folder(join(root, "out", "clinical_data"), recreate=False)
shutil.copytree(
join(root, "in", "clinical_data"), join(root, "out", "clinical_data")
)
# Data location
dataset_directory = join(root, "in", "unorganized")
bids_directory = join(root, "out", "bids")
clinical_data_directory = join(root, "out", "clinical_data")
# Conversion
to_convert = convert_images(
dataset_directory, bids_directory, clinical_data_directory
)
convert_clinical_data(bids_directory, clinical_data_directory, to_convert)
compare_folders_structures(bids_directory, join(root, "ref", "hashes_nifd.p"))
clean_folder(join(root, "out", "bids"), recreate=True)
clean_folder(join(root, "out", "clinical_data"), recreate=False)
def run_command(self, args):
from clinica.iotools.converters.nifd_to_bids.nifd_to_bids import convert_images, convert_clinical_data
from clinica.iotools.converter_utils import check_bin
from clinica.utils.stream import cprint
from colorama import Fore
import sys
missing_bin = check_bin('dcm2niix')
if missing_bin:
cprint(
Fore.RED + 'dcm2niix is required.' +
' Install it and re-run the converter. You can use the following link :'
+ Fore.BLUE + '\nhttps://github.com/rordenlab/dcm2niix' +
Fore.RESET)
cprint('Exiting clinica...')
sys.exit()
# to_convert = convert_images(args.dataset_directory, args.ida_file, args.bids_directory)
# convert_clinical_data(args.bids_directory, args.ida_file, args.clinical_data_file, to_convert)
to_convert = convert_images(args.dataset_directory,
args.bids_directory,
args.clinical_data_directory)
convert_clinical_data(args.bids_directory,
args.clinical_data_directory, to_convert)
cprint(Fore.GREEN + 'Conversion to BIDS succeeded' + Fore.RESET)
def test_run_Nifd2Bids(cmdopt):
from clinica.iotools.converters.nifd_to_bids.nifd_to_bids import convert_clinical_data, convert_images
from os.path import dirname, join, abspath
import shutil
root = join(dirname(abspath(__file__)), pardir, 'data', 'Nifd2Bids')
clean_folder(join(root, 'out', 'bids'), recreate=True)
clean_folder(join(root, 'out', 'clinical_data'), recreate=False)
shutil.copytree(join(root, 'in', 'clinical_data'),
join(root, 'out', 'clinical_data'))
# Data location
dataset_directory = join(root, 'in', 'unorganized')
bids_directory = join(root, 'out', 'bids')
clinical_data_directory = join(root, 'out', 'clinical_data')
# Conversion
to_convert = convert_images(dataset_directory, bids_directory,
clinical_data_directory)
convert_clinical_data(bids_directory, clinical_data_directory, to_convert)
compare_folders_structures(bids_directory,
join(root, 'ref', 'hashes_nifd.p'))
clean_folder(join(root, 'out', 'bids'), recreate=True)
clean_folder(join(root, 'out', 'clinical_data'), recreate=False)
def cli(
dataset_directory: str,
clinical_data_directory: str,
bids_directory: str,
) -> None:
"""NIFD to BIDS converter.
Convert the imaging and clinical data of NIFD (http://4rtni-ftldni.ini.usc.edu/), located in DATASET_DIRECTORY and
CLINICAL_DATA_DIRECTORY respectively, to a BIDS dataset in the target BIDS_DIRECTORY.
"""
from clinica.iotools.converters.nifd_to_bids.nifd_to_bids import convert_images
from clinica.utils.check_dependency import check_dcm2niix
from clinica.utils.stream import cprint
check_dcm2niix()
convert_images(dataset_directory, bids_directory, clinical_data_directory)
cprint("Conversion to BIDS succeeded.")
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
root = dirname(abspath(join(abspath(__file__), pardir)))
root = join(root, '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):
"""Run the converter with defined args."""
from colorama import Fore
from clinica.iotools.converters.nifd_to_bids.nifd_to_bids import convert_images, convert_clinical_data
from clinica.utils.stream import cprint
from clinica.utils.check_dependency import check_dcm2niix
check_dcm2niix()
# to_convert = convert_images(args.dataset_directory, args.ida_file, args.bids_directory)
# convert_clinical_data(args.bids_directory, args.ida_file, args.clinical_data_file, to_convert)
to_convert = convert_images(args.dataset_directory, args.bids_directory, args.clinical_data_directory)
convert_clinical_data(args.bids_directory, args.clinical_data_directory, to_convert)
cprint(Fore.GREEN + 'Conversion to BIDS succeeded' + Fore.RESET)
def test_run_Aibl2Bids(cmdopt):
from os.path import abspath, dirname, join
from clinica.iotools.converters.aibl_to_bids.aibl_to_bids import (
convert_clinical_data,
convert_images,
)
root = dirname(abspath(join(abspath(__file__), pardir, pardir)))
root = join(root, "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_nifd2bids(input_dir: PathLike, output_dir: PathLike,
ref_dir: PathLike) -> None:
import shutil
from clinica.iotools.converters.nifd_to_bids.nifd_to_bids import convert_images
# Arrange
shutil.copytree(
input_dir / "clinical_data",
output_dir / "clinical_data",
copy_function=shutil.copy,
)
# Arrange - Data location
clinical_data_directory = output_dir / "clinical_data"
# Acte - Conversion
to_convert = convert_images(input_dir / "unorganized", output_dir / "bids",
clinical_data_directory)
# Assert
compare_folders_structures(fspath(output_dir / "bids"),
fspath(ref_dir / "hashes_nifd.p"))