Merge branch 'no-anatomical' of github.com:openneuropet/petdeface into no-anatomical

Author: bendhouseart

README.md

@@ -36,9 +36,9 @@ This software can be installed via source or via pip from PyPi with `pip install
 
 ```bash
 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]
+                    [--skip_bids_validator] [--version] [--placement PLACEMENT] [--remove_existing]
                     [--participant_label_exclude participant_label_exclude [participant_label_exclude ...]] [--session_label SESSION [SESSION ...]]
-                    [--session_label_exclude session_label_exclude [session_label_exclude ...]]
+                    [--session_label_exclude session_label_exclude [session_label_exclude ...]] [--open_browser]
                     bids_dir [output_dir] [analysis_level]
 
 PetDeface
@@ -63,15 +63,15 @@ options:
                         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.
+  --remove_existing, -r Remove existing output files in output_dir.
   --preview_pics        Create preview pictures of defacing, defaults to false for docker
   --participant_label_exclude participant_label_exclude [participant_label_exclude ...]
                         Exclude a subject(s) from the defacing workflow. e.g. --participant_label_exclude sub-01 sub-02
   --session_label SESSION [SESSION ...]
                         Select only a specific session(s) to include in the defacing workflow
   --session_label_exclude session_label_exclude [session_label_exclude ...]
                         Select a specific session(s) to exclude from the defacing workflow
+  --open_browser        Open browser to show QA reports after completion
 ```
 
 Working example usage:

docs/usage.rst

@@ -123,6 +123,7 @@ options:
                         Select only a specific session(s) to include in the defacing workflow
   --session_label_exclude session_label_exclude [session_label_exclude ...]
                         Select a specific session(s) to exclude from the defacing workflow
+  --open_browser        Following defacing this flag will open the browser to view the defacing results
 
 Docker Based
 ------------

petdeface/petdeface.py

@@ -8,11 +8,9 @@
 from bids import BIDSLayout, BIDSLayoutIndexer
 import glob
 from platform import system
-
-# import shutil
+from pathlib import Path
 import subprocess
 from typing import Union
-
 from nipype.interfaces.freesurfer import MRICoreg
 from nipype.interfaces.io import DataSink
 from nipype.interfaces.base.traits_extension import File as traits_extensionFile
@@ -21,16 +19,9 @@
 from niworkflows.utils.bids import collect_data
 from niworkflows.utils.bids import collect_participants
 from niworkflows.utils.misc import check_valid_fs_license
-
 from petutils.petutils import collect_anat_and_pet
 from importlib.metadata import version
 
-
-# Import local modules - handle both script and module execution
-import sys
-import os
-from pathlib import Path
-
 # Determine if we're running as a script (including through debugger)
 is_script = (
     __name__ == "__main__"
@@ -346,7 +337,7 @@ def init_single_subject_wf(
     :type bids_data: pathlib.Path, BIDSLayout]
     :param output_dir: _description_, defaults to None
     :type output_dir: pathlib.Path, optional
-    :param preview_pics: _description_, defaults to False
+    :param preview_pics: _description_, defaults to False (soon to be deprecated)
     :type preview_pics: bool, optional
     :param anat_only: _description_, defaults to False
     :type anat_only: bool, optional
@@ -872,7 +863,7 @@ def __init__(
         skip_bids_validator=False,
         remove_existing=True,
         placement="adjacent",
-        preview_pics=True,
+        preview_pics=False,
         participant_label_exclude=[],
         session_label=[],
         session_label_exclude=[],