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added session inclusion/exclusion
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@bendhouseart
bendhouseart committed Nov 15, 2024
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24 changes: 15 additions & 9 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -35,37 +35,43 @@ This software can be installed via source or via pip from PyPi with `pip install
**_NOTE:_** This project is currently in beta release, some features listed below may not be available for version numbers < 1.0.0

```bash
usage: petdeface.py [-h] [--anat_only] [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]] [--session SESSION] [--docker] [--singularity] [--n_procs N_PROCS] [--skip_bids_validator] [--version] [--placement PLACEMENT] [--remove_existing] [--preview_pics]
[--excludeparticipant EXCLUDEPARTICIPANT [EXCLUDEPARTICIPANT ...]]
usage: petdeface.py [-h] [--anat_only] [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]] [--docker] [--singularity] [--n_procs N_PROCS]
[--skip_bids_validator] [--version] [--placement PLACEMENT] [--remove_existing] [--preview_pics]
[--exclude_participant EXCLUDE_PARTICIPANT [EXCLUDE_PARTICIPANT ...]] [--session SESSION [SESSION ...]]
[--exclude_session EXCLUDE_SESSION [EXCLUDE_SESSION ...]]
bids_dir [output_dir] [analysis_level]

PetDeface

positional arguments:
bids_dir The directory with the input dataset
output_dir The directory where the output files should be stored, if not supplied will default to <bids_dir>/derivatives/petdeface
analysis_level This BIDS app always operates at the participant level, if this argument is changed it will be ignored and run as a participant level analysis
analysis_level This BIDS app always operates at the participant level, if this argument is changed it will be ignored and run as a participant level
analysis

options:
-h, --help show this help message and exit
--anat_only, -a Only deface anatomical images
--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...], -pl PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]
The label(s) of the participant/subject to be processed. When specifying multiple subjects separate them with spaces.
--session SESSION, -ses SESSION
The label of the session to be processed.
--docker, -d Run in docker container
--singularity, -si Run in singularity container
--n_procs N_PROCS Number of processors to use when running the workflow
--skip_bids_validator
--version, -v show program's version number and exit
--placement PLACEMENT, -p PLACEMENT
Where to place the defaced images. Options are 'adjacent': next to the bids_dir (default) in a folder appended with _defaced'inplace': defaces the dataset in place, e.g. replaces faced PET and T1w images w/ defaced at bids_dir'derivatives': does all of the
defacing within the derivatives folder in bids_dir.
Where to place the defaced images. Options are 'adjacent': next to the bids_dir (default) in a folder appended with _defaced'inplace':
defaces the dataset in place, e.g. replaces faced PET and T1w images w/ defaced at bids_dir'derivatives': does all of the defacing within
the derivatives folder in bids_dir.
--remove_existing, -r
Remove existing output files in output_dir.
--preview_pics Create preview pictures of defacing, defaults to false for docker
--excludeparticipant EXCLUDEPARTICIPANT [EXCLUDEPARTICIPANT ...]
Exclude a subject(s) from the defacing workflow. e.g. --excludeparticipant sub-01 sub-02
--exclude_participant EXCLUDE_PARTICIPANT [EXCLUDE_PARTICIPANT ...]
Exclude a subject(s) from the defacing workflow. e.g. --exclude_participant sub-01 sub-02
--session SESSION [SESSION ...]
Select only a specific session(s) to include in the defacing workflow
--exclude_session EXCLUDE_SESSION [EXCLUDE_SESSION ...]
Select a specific session(s) to exclude from the defacing workflow
```
Working example usage:
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64 changes: 35 additions & 29 deletions docs/usage.rst
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Expand Up @@ -86,37 +86,43 @@ The number of processors made available to PETdeface can be set by the `--n_proc
Additional options can be found in the help menu::

petdeface -h
usage: petdeface.py [-h] [--anat_only] [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]] [--session SESSION] [--docker] [--singularity] [--n_procs N_PROCS] [--skip_bids_validator] [--version] [--placement PLACEMENT] [--remove_existing] [--preview_pics]
[--excludeparticipant EXCLUDEPARTICIPANT [EXCLUDEPARTICIPANT ...]]
usage: petdeface.py [-h] [--anat_only] [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]] [--docker] [--singularity] [--n_procs N_PROCS]
[--skip_bids_validator] [--version] [--placement PLACEMENT] [--remove_existing] [--preview_pics]
[--exclude_participant EXCLUDE_PARTICIPANT [EXCLUDE_PARTICIPANT ...]] [--session SESSION [SESSION ...]]
[--exclude_session EXCLUDE_SESSION [EXCLUDE_SESSION ...]]
bids_dir [output_dir] [analysis_level]

PetDeface

positional arguments:
bids_dir The directory with the input dataset
output_dir The directory where the output files should be stored, if not supplied will default to <bids_dir>/derivatives/petdeface
analysis_level This BIDS app always operates at the participant level, if this argument is changed it will be ignored and run as a participant level analysis

options:
-h, --help show this help message and exit
--anat_only, -a Only deface anatomical images
--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...], -pl PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]
The label(s) of the participant/subject to be processed. When specifying multiple subjects separate them with spaces.
--session SESSION, -ses SESSION
The label of the session to be processed.
--docker, -d Run in docker container
--singularity, -si Run in singularity container
--n_procs N_PROCS Number of processors to use when running the workflow
--skip_bids_validator
--version, -v show program's version number and exit
--placement PLACEMENT, -p PLACEMENT
Where to place the defaced images. Options are 'adjacent': next to the bids_dir (default) in a folder appended with _defaced'inplace': defaces the dataset in place, e.g. replaces faced PET and T1w images w/ defaced at bids_dir'derivatives': does all of the
defacing within the derivatives folder in bids_dir.
--remove_existing, -r
Remove existing output files in output_dir.
--preview_pics Create preview pictures of defacing, defaults to false for docker
--excludeparticipant EXCLUDEPARTICIPANT [EXCLUDEPARTICIPANT ...]
Exclude a subject(s) from the defacing workflow. e.g. --excludeparticipant sub-01 sub-02
PetDeface

positional arguments:
bids_dir The directory with the input dataset
output_dir The directory where the output files should be stored, if not supplied will default to <bids_dir>/derivatives/petdeface
analysis_level This BIDS app always operates at the participant level, if this argument is changed it will be ignored and run as a participant level
analysis

options:
-h, --help show this help message and exit
--anat_only, -a Only deface anatomical images
--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...], -pl PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]
The label(s) of the participant/subject to be processed. When specifying multiple subjects separate them with spaces.
--docker, -d Run in docker container
--singularity, -si Run in singularity container
--n_procs N_PROCS Number of processors to use when running the workflow
--skip_bids_validator
--version, -v show program's version number and exit
--placement PLACEMENT, -p PLACEMENT
Where to place the defaced images. Options are 'adjacent': next to the bids_dir (default) in a folder appended with _defaced'inplace':
defaces the dataset in place, e.g. replaces faced PET and T1w images w/ defaced at bids_dir'derivatives': does all of the defacing within
the derivatives folder in bids_dir.
--remove_existing, -r
Remove existing output files in output_dir.
--preview_pics Create preview pictures of defacing, defaults to false for docker
--exclude_participant EXCLUDE_PARTICIPANT [EXCLUDE_PARTICIPANT ...]
Exclude a subject(s) from the defacing workflow. e.g. --exclude_participant sub-01 sub-02
--session SESSION [SESSION ...]
Select only a specific session(s) to include in the defacing workflow
--exclude_session EXCLUDE_SESSION [EXCLUDE_SESSION ...]
Select a specific session(s) to exclude from the defacing workflow

Docker Based
------------
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51 changes: 40 additions & 11 deletions petdeface/petdeface.py
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Original file line number Diff line number Diff line change
Expand Up @@ -249,15 +249,15 @@ def deface(args: Union[dict, argparse.Namespace]) -> None:
)

# check to see if any subjects are excluded from the defacing workflow
if args.excludeparticipant != []:
if args.exclude_participant != []:
print(
f"Removing the following subjects {args.excludeparticipant} from the defacing workflow"
f"Removing the following subjects {args.exclude_participant} from the defacing workflow"
)
args.excludeparticipant = [
subject.replace("sub-", "") for subject in args.excludeparticipant
args.exclude_participant = [
subject.replace("sub-", "") for subject in args.exclude_participant
]
subjects = [
subject for subject in subjects if subject not in args.excludeparticipant
subject for subject in subjects if subject not in args.exclude_participant
]

print(f"Subjects remaining in the defacing workflow: {subjects}")
Expand All @@ -277,6 +277,8 @@ def deface(args: Union[dict, argparse.Namespace]) -> None:
args.bids_dir,
preview_pics=args.preview_pics,
anat_only=args.anat_only,
session=args.session,
exclude_session=args.exclude_session,
)
except FileNotFoundError:
single_subject_wf = None
Expand All @@ -303,6 +305,8 @@ def init_single_subject_wf(
output_dir: pathlib.Path = None,
preview_pics=False,
anat_only=False,
session=[],
exclude_session=[],
) -> Workflow:
"""
Organize the preprocessing pipeline for a single subject.
Expand All @@ -317,6 +321,10 @@ def init_single_subject_wf(
:type preview_pics: bool, optional
:param anat_only: _description_, defaults to False
:type anat_only: bool, optional
:param session: _description_, will default to only selecting session(s) supplied to this argument, defaults to []
:type session: list, optional
:param exclude_session: _description_, will exclude any session(s) supplied to this argument, defaults to []
:type exclude_session: list, optional
:raises FileNotFoundError: _description_
:return: _description_
:rtype: Workflow
Expand All @@ -333,6 +341,13 @@ def init_single_subject_wf(
if subject_data is None:
raise FileNotFoundError(f"Could not find data for subject sub-{subject_id}")

# we combine the sessions to include and exclude into a single set of sessions to exclude from
# the set of all sessions
if session:
sessions_to_exclude = list(set(bids_data.get_sessions()) - (set(bids_data.get_sessions()) & set(session)) | set(exclude_session))
else:
sessions_to_exclude = exclude_session

# check if any t1w images exist for the pet images
for pet_image, t1w_image in subject_data.items():
if t1w_image == "":
Expand Down Expand Up @@ -426,6 +441,10 @@ def init_single_subject_wf(
ses_id = ""
pet_string = f"sub-{subject_id}"

# skip anything in the exclude list
if ses_id.replace("ses-", "") in sessions_to_exclude:
continue

# collect run info from pet file
try:
run_id = "_" + re.search("run-[^_|\/]*", str(pet_file)).group(0)
Expand Down Expand Up @@ -744,7 +763,9 @@ def __init__(
remove_existing=True,
placement="adjacent",
preview_pics=True,
excludeparticipant=[],
exclude_participant=[],
session=[],
exclude_session=[],
):
self.bids_dir = bids_dir
self.remove_existing = remove_existing
Expand All @@ -755,7 +776,9 @@ def __init__(
self.n_procs = n_procs
self.skip_bids_validator = skip_bids_validator
self.preview_pics = preview_pics
self.excludeparticipant = excludeparticipant
self.exclude_participant = exclude_participant
self.session = session
self.exclude_session = exclude_session

# check if freesurfer license is valid
self.fs_license = check_valid_fs_license()
Expand Down Expand Up @@ -785,7 +808,9 @@ def run(self):
"placement": self.placement,
"remove_existing": self.remove_existing,
"preview_pics": self.preview_pics,
"excludeparticipant": self.excludeparticipant,
"exclude_participant": self.exclude_participant,
"session": self.session,
"exclude_session": self.exclude_session,
}
)
wrap_up_defacing(
Expand Down Expand Up @@ -886,13 +911,15 @@ def cli():
default=False,
)
parser.add_argument(
"--excludeparticipant",
help="Exclude a subject(s) from the defacing workflow. e.g. --excludeparticipant sub-01 sub-02",
"--exclude_participant",
help="Exclude a subject(s) from the defacing workflow. e.g. --exclude_participant sub-01 sub-02",
type=str,
nargs="+",
required=False,
default=[],
)
parser.add_argument("--session", help="Select only a specific session(s) to include in the defacing workflow", type=str, nargs="+", required=False, default=[])
parser.add_argument("--exclude_session", help="Select a specific session(s) to exclude from the defacing workflow", type=str, nargs="+", required=False, default=[])

arguments = parser.parse_args()
return arguments
Expand Down Expand Up @@ -1087,7 +1114,9 @@ def main(): # noqa: max-complexity: 12
remove_existing=args.remove_existing,
placement=args.placement,
preview_pics=args.preview_pics,
excludeparticipant=args.excludeparticipant,
exclude_participant=args.exclude_participant,
session=args.session,
exclude_session=args.exclude_session,
)
petdeface.run()

Expand Down

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