def run_adni2bids(input_dir: PathLike, output_dir: PathLike,
ref_dir: PathLike) -> None:
from clinica.iotools.converters.adni_to_bids.adni_to_bids import AdniToBids
# Arrange
clinical_data_directory = input_dir / "clinical_data"
dataset_directory = input_dir / "unorganized_data"
subjects_list = input_dir / "subjects.txt"
modalities = [
"T1", "PET_FDG", "PET_AMYLOID", "PET_TAU", "DWI", "FLAIR", "fMRI"
]
# Act
adni_to_bids = AdniToBids()
adni_to_bids.check_adni_dependencies()
adni_to_bids.convert_images(
dataset_directory,
clinical_data_directory,
output_dir / "bids",
subjects_list,
modalities,
)
adni_to_bids.convert_clinical_data(clinical_data_directory,
output_dir / "bids")
# Assert
compare_folders(output_dir / "bids", ref_dir / "bids", output_dir)
def test_run_Adni2Bids(cmdopt):
from os.path import abspath, dirname, join
from clinica.iotools.converters.adni_to_bids.adni_to_bids import AdniToBids
root = join(dirname(abspath(__file__)), pardir, pardir, "data", "Adni2Bids")
clean_folder(join(root, "out", "bids"), recreate=True)
adni_to_bids = AdniToBids()
adni_to_bids.check_adni_dependencies()
dataset_directory = join(root, "in", "unorganized_data")
clinical_data_directory = join(root, "in", "clinical_data")
bids_directory = join(root, "out", "bids")
subjects_list = join(root, "in", "subjects.txt")
modalities = ["T1", "PET_FDG", "PET_AMYLOID", "PET_TAU", "DWI", "FLAIR", "fMRI"]
adni_to_bids.convert_images(
dataset_directory,
clinical_data_directory,
bids_directory,
subjects_list,
modalities,
)
adni_to_bids.convert_clinical_data(clinical_data_directory, bids_directory)
# Generate tree of output files
compare_folders(join(root, "out"), join(root, "ref"), shared_folder_name="bids")
clean_folder(join(root, "out", "bids"), recreate=True)
def run_habs_to_bids(input_dir: Path, output_dir: Path, ref_dir: Path):
from click.testing import CliRunner
from clinica.iotools.converters.habs_to_bids.habs_to_bids_cli import cli
runner = CliRunner()
result = runner.invoke(cli, [str(input_dir), str(output_dir)])
assert result.exit_code == 0
compare_folders(output_dir, ref_dir, output_dir)
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 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_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_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)