Disable preview pics by default (#40)

* turned off preview pics, disabled in docker entirely
* reformat file
* bump version

petdeface/petdeface.py

@@ -218,7 +218,9 @@ def deface(args: Union[dict, argparse.Namespace]) -> None:
 
     for subject_id in participants:
         try:
-            single_subject_wf = init_single_subject_wf(subject_id, args.bids_dir)
+            single_subject_wf = init_single_subject_wf(
+                subject_id, args.bids_dir, preview_pics=args.preview_pics
+            )
         except FileNotFoundError:
             single_subject_wf = None
 
@@ -242,6 +244,7 @@ def init_single_subject_wf(
     subject_id: str,
     bids_data: [pathlib.Path, BIDSLayout],
     output_dir: pathlib.Path = None,
+    preview_pics=False,
 ) -> Workflow:
     """
     Organize the preprocessing pipeline for a single subject.
@@ -308,11 +311,9 @@ def init_single_subject_wf(
 
         t1w_wf = Workflow(name=workflow_name)
 
-        # create preview pics
+        # always set preview pics to false if running in docker
         if determine_in_docker():
             preview_pics = False
-        else:
-            preview_pics = True
 
         deface_t1w = Node(
             Mideface(
@@ -670,6 +671,7 @@ def __init__(
         skip_bids_validator=True,
         remove_existing=True,  # TODO: currently not implemented
         placement="adjacent",  # TODO: currently not implemented
+        preview_pics=True,
     ):
         self.bids_dir = bids_dir
         self.remove_existing = remove_existing
@@ -680,6 +682,7 @@ def __init__(
         self.session = session
         self.n_procs = n_procs
         self.skip_bids_validator = skip_bids_validator
+        self.preview_pics = preview_pics
 
         # check if freesurfer license is valid
         self.fs_license = check_valid_fs_license()
@@ -703,6 +706,7 @@ def run(self):
                 "participant_label": self.subject,
                 "placement": self.placement,
                 "remove_existing": self.remove_existing,
+                "preview_pics": self.preview_pics,
             }
         )
         wrap_up_defacing(
@@ -790,9 +794,14 @@ def cli():
         action="store_true",
         default=False,
     )
+    parser.add_argument(
+        "--preview_pics",
+        help="Create preview pictures of defacing, defaults to false for docker",
+        action="store_true",
+        default=False,
+    )
 
     arguments = parser.parse_args()
-
     return arguments
 
 
@@ -918,6 +927,7 @@ def main():  # noqa: max-complexity: 12
             skip_bids_validator=args.skip_bids_validator,
             remove_existing=args.remove_existing,
             placement=args.placement,
+            preview_pics=args.preview_pics,
         )
         petdeface.run()
 

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "petdeface"
-version = "0.1.0"
+version = "0.1.1"
 description = "A nipype PET and MR defacing pipeline for BIDS datasets utilizing FreeSurfer's MiDeFace."
 authors = ["Martin Nørgaard <martin.noergaard@nru.dk>", "Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>", "Murat Bilgel <bilgelm@gmail.com>"]
 license = "MIT"