def test_run_PETVolume(cmdopt):
from clinica.pipelines.pet_volume.pet_volume_pipeline import PETVolume
from os.path import dirname, join, abspath, exists
import shutil
working_dir = cmdopt
root = dirname(abspath(join(abspath(__file__), pardir)))
root = join(root, 'data', 'PETVolume')
clean_folder(join(root, 'out', 'caps'), recreate=False)
clean_folder(join(working_dir, 'PETVolume'))
shutil.copytree(join(root, 'in', 'caps'), join(root, 'out', 'caps'))
pipeline = PETVolume(bids_directory=join(root, 'in', 'bids'),
caps_directory=join(root, 'out', 'caps'),
tsv_file=join(root, 'in', 'subjects.tsv'),
group_id='UnitTest',
fwhm_tsv=None)
pipeline.base_dir = join(working_dir, 'PETVolume')
pipeline.build()
pipeline.run(plugin='MultiProc',
plugin_args={'n_procs': 4},
bypass_check=True)
subjects = [
'sub-ADNI011S4105', 'sub-ADNI023S4020', 'sub-ADNI035S4082',
'sub-ADNI128S4832'
]
out_files = [
join(
root, 'out/caps/subjects/' + sub +
'/ses-M00/pet/preprocessing/group-UnitTest', sub +
'_ses-M00_task-rest_acq-fdg_pet_space-Ixi549Space_suvr-pons_mask-brain_fwhm-8mm_pet.nii.gz'
) for sub in subjects
]
ref_files = [
join(
root, 'ref', sub +
'_ses-M00_task-rest_acq-fdg_pet_space-Ixi549Space_suvr-pons_mask-brain_fwhm-8mm_pet.nii.gz'
) for sub in subjects
]
for i in range(len(out_files)):
assert likeliness_measure(out_files[i], ref_files[i], (1e-2, 0.25),
(1e-1, 0.001))
clean_folder(join(root, 'out', 'caps'), recreate=False)
def run_command(self, args):
"""
"""
from tempfile import mkdtemp
from clinica.utils.stream import cprint
from clinica.pipelines.pet_volume.pet_volume_pipeline import PETVolume
pipeline = PETVolume(
bids_directory=self.absolute_path(args.bids_directory),
caps_directory=self.absolute_path(args.caps_directory),
tsv_file=self.absolute_path(args.subjects_sessions_tsv),
group_id=args.group_id,
fwhm_tsv=self.absolute_path(args.psf_tsv))
pipeline.parameters.update({
'pet_type': args.pet_tracer,
'mask_tissues': args.mask_tissues,
'mask_threshold': args.mask_threshold,
'pvc_mask_tissues': args.pvc_mask_tissues,
'smooth': args.smooth,
'atlas_list': args.atlases
})
if args.working_directory is None:
args.working_directory = mkdtemp()
pipeline.base_dir = self.absolute_path(args.working_directory)
if args.n_procs:
pipeline.run(plugin='MultiProc',
plugin_args={'n_procs': args.n_procs})
else:
pipeline.run()
cprint(
"The " + self._name +
" pipeline has completed. You can now delete the working directory ("
+ args.working_directory + ").")