def test_run_Adni2Bids(cmdopt):
from clinica.iotools.converters.adni_to_bids.adni_to_bids import AdniToBids
from os.path import dirname, join, abspath
root = join(dirname(abspath(__file__)), 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_25-04-19')
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 test_run_CenterNifti(cmdopt):
from clinica.iotools.utils.data_handling import center_all_nifti
from os.path import dirname, join, abspath
root = dirname(abspath(join(abspath(__file__), pardir)))
root = join(root, 'data', 'CenterNifti')
clean_folder(join(root, 'out', 'bids_centered'), recreate=True)
bids_dir = join(root, 'in', 'bids')
output_dir = join(root, 'out', 'bids_centered')
all_modalities = [
't1w', 'pet', 'dwi', 'magnitude', 'bold', 'flair', 't2', 'phasediff'
]
center_all_nifti(bids_dir,
output_dir,
all_modalities,
center_all_files=True)
hashes_out = create_list_hashes(output_dir,
extensions_to_keep=('.nii.gz', '.nii'))
hashes_ref = create_list_hashes(join(root, 'ref', 'bids_centered'),
extensions_to_keep=('.nii.gz', '.nii'))
if hashes_out != hashes_ref:
raise RuntimeError(
'Hashes of nii* files are different between out and ref')
clean_folder(join(root, 'out', 'bids_centered'), recreate=False)
def test_run_CreateMergeFile(cmdopt):
from os.path import join, dirname, abspath
from os import remove
from filecmp import cmp
import shutil
from clinica.iotools.utils import data_handling as dt
root = join(dirname(abspath(__file__)), pardir, 'data', 'CreateMergeFile')
bids_directory = join(root, 'in', 'bids')
out_tsv = join(root, 'out', 'output_file.tsv')
subject_session_tsv = join(root, 'in', 'subjects_sessions.tsv')
clean_folder(join(root, 'out', 'caps'), recreate=False)
shutil.copytree(join(root, 'in', 'caps'), join(root, 'out', 'caps'))
caps_directory = join(root, 'out', 'caps')
dt.create_merge_file(bids_directory,
out_tsv,
caps_dir=caps_directory,
pipelines=None,
atlas_selection=None,
pvc_restriction=None,
tsv_file=subject_session_tsv,
group_selection=None)
# Comparison step
ref_tsv = join(root, 'ref', 'output_file.tsv')
assert cmp(out_tsv, ref_tsv)
remove(out_tsv)
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 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)
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)
