def run_createmergefile(
input_dir: PathLike, output_dir: PathLike, ref_dir: PathLike
) -> None:
import shutil
from filecmp import cmp
from os import remove
from os.path import abspath, dirname, join
import pandas as pd
from clinica.iotools.utils import data_handling as dt
# Arrange
out_tsv = output_dir / "output_file.tsv"
subject_session_tsv = input_dir / "subjects_sessions.tsv"
caps_directory = output_dir / "caps"
shutil.copytree(input_dir / "caps", caps_directory, copy_function=shutil.copy)
# Act
dt.create_merge_file(
input_dir / "bids",
out_tsv,
caps_dir=caps_directory,
tsv_file=subject_session_tsv,
pipelines=None,
atlas_selection=None,
pvc_restriction=None,
group_selection=None,
)
# Assert
ref_tsv = fspath(ref_dir / "output_file.tsv")
out_df = pd.read_csv(out_tsv, sep="/")
ref_df = pd.read_csv(ref_tsv, sep="/")
assert out_df.equals(ref_df)
assert cmp(out_tsv, ref_tsv)
def merge_tsv(
bids_directory: str,
output_tsv: str,
caps_directory: Optional[str] = None,
pipelines: Optional[List[str]] = None,
volume_atlas_selection: Optional[List[str]] = None,
freesurfer_atlas_selection: Optional[List[str]] = None,
pvc_restriction: Optional[int] = None,
pet_tracers_selection: Optional[List[str]] = None,
group_selection: Optional[List[str]] = None,
subjects_sessions_tsv: Optional[str] = None,
ignore_scan_files: bool = False,
ignore_session_scan_files: bool = False,
) -> None:
"""Merge clinical data into a single TSV file."""
from clinica.iotools.utils.data_handling import create_merge_file
from clinica.utils.inputs import check_bids_folder
check_bids_folder(bids_directory)
create_merge_file(
bids_directory,
output_tsv,
caps_dir=caps_directory,
pipelines=pipelines,
ignore_scan_files=ignore_scan_files,
ignore_sessions_files=ignore_session_scan_files,
volume_atlas_selection=volume_atlas_selection,
freesurfer_atlas_selection=freesurfer_atlas_selection,
pvc_restriction=pvc_restriction,
tsv_file=subjects_sessions_tsv,
group_selection=group_selection,
tracers_selection=pet_tracers_selection,
)
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_CreateMergeFile(cmdopt):
import shutil
from filecmp import cmp
from os import remove
from os.path import abspath, dirname, join
from clinica.iotools.utils import data_handling as dt
root = join(dirname(abspath(__file__)), pardir, 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,
tsv_file=subject_session_tsv,
pipelines=None,
atlas_selection=None,
pvc_restriction=None,
group_selection=None,
)
# Comparison step
ref_tsv = join(root, "ref", "output_file.tsv")
assert cmp(out_tsv, ref_tsv)
remove(out_tsv)
clean_folder(join(root, "out", "caps"), recreate=False)
def run_command(self, args):
from clinica.iotools.utils import data_handling as dt
from clinica.utils.inputs import check_bids_folder
check_bids_folder(args.bids_directory)
dt.create_merge_file(args.bids_directory,
args.out_tsv,
caps_dir=args.caps_directory,
pipelines=args.pipelines,
atlas_selection=args.atlas_selection,
pvc_restriction=args.pvc_restriction,
tsv_file=args.subjects_sessions_tsv,
group_selection=args.group_selection)
def run_command(self, args):
from clinica.iotools.utils import data_handling as dt
from clinica.utils.inputs import check_bids_folder
check_bids_folder(args.bids_directory)
dt.create_merge_file(
args.bids_directory,
args.out_tsv,
caps_dir=args.caps_directory,
pipelines=args.pipelines,
ignore_scan_files=args.ignore_scan_files,
ignore_sessions_files=args.ignore_session_scan_files,
volume_atlas_selection=args.volume_atlas_selection,
freesurfer_atlas_selection=args.freesurfer_atlas_selection,
pvc_restriction=args.pvc_restriction,
tsv_file=args.subjects_sessions_tsv,
group_selection=args.group_selection,
tracers_selection=args.pet_tracers_selection,
)
def run_command(self, args):
from clinica.iotools.utils import data_handling as dt
dt.create_merge_file(args.bids_directory, args.out_directory, args.true_false_mode)