defacing with template automated, need to add mni & average pet flags/options next

Author: bendhouseart

data/participants.tsv

@@ -1,2 +1,3 @@
 participant_id	height	weight	age	gender
-sub-01	178	58	28	male
+sub-01	178	58	28	male
+sub-mni305	200	65	10	n/a

data/sub-mni305/anat/sub-mni305_T1w.nii.gz

@@ -10,39 +10,41 @@
 
 def get_data_path(filename: str) -> Path:
     """Get the path to a data file included in the package.
-    
+
     Parameters
     ----------
     filename : str
         Name of the file to get the path for. This should be relative to the data directory.
         For example: "sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.nii"
-    
+
     Returns
     -------
     Path
         Path to the requested data file
-        
+
     Raises
     ------
     FileNotFoundError
         If the requested file is not found in the package data
     """
     # Get the path to the data directory
     data_dir = Path(__file__).parent.parent / "data"
-    
+
     # Construct the full path
     full_path = data_dir / filename
-    
+
     # Check if the file exists
     if not full_path.exists():
-        raise FileNotFoundError(f"Could not find data file {filename} in data directory")
-    
+        raise FileNotFoundError(
+            f"Could not find data file {filename} in data directory"
+        )
+
     return full_path
 
 
 def get_default_anat() -> Path:
     """Get the path to the default anatomical image.
-    
+
     Returns
     -------
     Path
@@ -54,7 +56,7 @@ def get_default_anat() -> Path:
 
 def get_default_anat_data() -> nibabel.Nifti1Image:
     """Get the default anatomical image as a nibabel image object.
-    
+
     Returns
     -------
     nibabel.Nifti1Image
@@ -65,56 +67,58 @@ def get_default_anat_data() -> nibabel.Nifti1Image:
 
 def extract_subject_id(input_str: str) -> str:
     """Extract subject ID from various input formats.
-    
+
     This function can handle:
     - Full paths (e.g., "/path/to/sub-123/anat/file.nii")
     - Subject IDs with prefix (e.g., "sub-123")
     - Raw subject IDs (e.g., "123")
-    
+
     Parameters
     ----------
     input_str : str
         Input string containing a subject ID in any format
-        
+
     Returns
     -------
     str
         Extracted subject ID without the 'sub-' prefix
-        
+
     Raises
     ------
     ValueError
         If no valid subject ID can be extracted
     """
     # Pattern to match 'sub-XXXX' in various contexts
     # The pattern captures everything after 'sub-' until it hits a non-alphanumeric character or the end of the string
-    pattern = r'sub-([a-zA-Z0-9]+)(?:_|$)'
-    
+    pattern = r"sub-([a-zA-Z0-9]+)(?:_|$)"
+
     # Try to find a match
     match = re.search(pattern, input_str)
-    
+
     if match:
         # Return the captured group (the subject ID without 'sub-' prefix)
         return match.group(1)
     else:
         # If no 'sub-' prefix is found, check if the input is a valid subject ID
-        if re.match(r'^[a-zA-Z0-9]+$', input_str):
+        if re.match(r"^[a-zA-Z0-9]+$", input_str):
             return input_str
         else:
             # Try a more flexible approach for paths
-            path_match = re.search(r'sub-([a-zA-Z0-9]+)', input_str)
+            path_match = re.search(r"sub-([a-zA-Z0-9]+)", input_str)
             if path_match:
                 return path_match.group(1)
             else:
-                raise ValueError(f"Could not extract a valid subject ID from '{input_str}'")
+                raise ValueError(
+                    f"Could not extract a valid subject ID from '{input_str}'"
+                )
 
 
 def copy_default_anat_to_subject(bids_dir: Union[str, Path], subject_id: str) -> dict:
     """Copy the default anatomical image to a PET subject's folder in a BIDS dataset.
-    
+
     This function extracts the subject ID from the provided string using regex,
     then copies the default anatomical image and its JSON metadata to the subject's folder in the BIDS dataset.
-    
+
     Parameters
     ----------
     bids_dir : Union[str, Path]
@@ -124,7 +128,7 @@ def copy_default_anat_to_subject(bids_dir: Union[str, Path], subject_id: str) ->
         - Full path (e.g., "/path/to/sub-123/anat/file.nii")
         - Subject ID with prefix (e.g., "sub-123")
         - Raw subject ID (e.g., "123")
-        
+
     Returns
     -------
     dict
@@ -135,7 +139,7 @@ def copy_default_anat_to_subject(bids_dir: Union[str, Path], subject_id: str) ->
             'created_dirs': List of paths to newly created directories,
             'created_files': List of paths to newly created files
         }
-        
+
     Raises
     ------
     FileNotFoundError
@@ -145,71 +149,71 @@ def copy_default_anat_to_subject(bids_dir: Union[str, Path], subject_id: str) ->
     """
     # Convert bids_dir to Path if it's a string
     bids_dir = Path(bids_dir)
-    
+
     # Check if the BIDS directory exists
     if not bids_dir.exists():
         raise FileNotFoundError(f"BIDS directory {bids_dir} does not exist")
-    
+
     # Extract subject ID using regex
     try:
         extracted_id = extract_subject_id(subject_id)
     except ValueError as e:
         raise ValueError(f"Invalid subject ID: {e}")
-    
+
     # Create the subject directory structure
     subject_dir = bids_dir / f"sub-{extracted_id}"
-    
+
     # Check if the subject directory exists
     if not subject_dir.exists():
         raise FileNotFoundError(f"Subject directory {subject_dir} does not exist")
-    
+
     anat_dir = subject_dir / "anat"
-    
+
     # Create the anatomical directory if it doesn't exist
     created_dirs = []
     if not anat_dir.exists():
         anat_dir.mkdir(parents=True, exist_ok=True)
         created_dirs.append(anat_dir)
-    
+
     # Define the target file paths
     target_nii = anat_dir / f"sub-{extracted_id}_T1w.nii"
     target_json = anat_dir / f"sub-{extracted_id}_T1w.json"
-    
+
     # Get the source file paths
     source_nii = get_default_anat()
     source_json = get_data_path("sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.json")
-    
+
     # Copy the files
     created_files = []
     shutil.copy2(source_nii, target_nii)
     created_files.append(target_nii)
-    
+
     shutil.copy2(source_json, target_json)
     created_files.append(target_json)
-    
+
     print(f"Copied default anatomical image to {target_nii}")
     print(f"Copied default anatomical metadata to {target_json}")
-    
+
     # Return information about created files and directories
     return {
-        'subject_dir': subject_dir,
-        'anat_dir': anat_dir,
-        'created_dirs': created_dirs,
-        'created_files': created_files
+        "subject_dir": subject_dir,
+        "anat_dir": anat_dir,
+        "created_dirs": created_dirs,
+        "created_files": created_files,
     }
 
 
 def remove_default_anat(
-    bids_dir: Union[str, Path], 
-    subject_id: Optional[str] = None, 
-    created_items: Optional[Dict] = None
+    bids_dir: Union[str, Path],
+    subject_id: Optional[str] = None,
+    created_items: Optional[Dict] = None,
 ) -> None:
     """Remove the default anatomical image and directory created for a subject.
-    
+
     This function can be used in two ways:
     1. With the bids_dir and subject_id to identify what to remove
     2. With the bids_dir and the dictionary returned by copy_default_anat_to_subject
-    
+
     Parameters
     ----------
     bids_dir : Union[str, Path]
@@ -218,11 +222,11 @@ def remove_default_anat(
         Subject ID in any format (if created_items is not provided)
     created_items : Optional[Dict]
         Dictionary returned by copy_default_anat_to_subject (if subject_id is not provided)
-        
+
     Returns
     -------
     None
-        
+
     Raises
     ------
     ValueError
@@ -232,68 +236,67 @@ def remove_default_anat(
     """
     # Convert bids_dir to Path if it's a string
     bids_dir = Path(bids_dir)
-    
+
     # Check if the BIDS directory exists
     if not bids_dir.exists():
         raise FileNotFoundError(f"BIDS directory {bids_dir} does not exist")
-    
+
     # Determine which approach to use
     if subject_id is not None and created_items is not None:
         raise ValueError("Cannot provide both subject_id and created_items")
     elif subject_id is None and created_items is None:
         raise ValueError("Must provide either subject_id or created_items")
-    
+
     if created_items is not None:
         # Use the dictionary returned by copy_default_anat_to_subject
-        anat_dir = created_items['anat_dir']
-        created_files = created_items['created_files']
-        created_dirs = created_items['created_dirs']
+        anat_dir = created_items["anat_dir"]
+        created_files = created_items["created_files"]
+        created_dirs = created_items["created_dirs"]
     else:
         # Extract subject ID using regex
         try:
             extracted_id = extract_subject_id(subject_id)
         except ValueError as e:
             raise ValueError(f"Invalid subject ID: {e}")
-        
+
         # Create the subject directory structure
         subject_dir = bids_dir / f"sub-{extracted_id}"
-        
+
         # Check if the subject directory exists
         if not subject_dir.exists():
             raise FileNotFoundError(f"Subject directory {subject_dir} does not exist")
-        
+
         anat_dir = subject_dir / "anat"
-        
+
         # Define the file paths
         target_nii = anat_dir / f"sub-{extracted_id}_T1w.nii"
         target_json = anat_dir / f"sub-{extracted_id}_T1w.json"
-        
+
         # Check if the files exist
         created_files = []
         if target_nii.exists():
             created_files.append(target_nii)
         if target_json.exists():
             created_files.append(target_json)
-        
+
         # Check if the directory exists and is empty
         created_dirs = []
         if anat_dir.exists():
             # Only add to created_dirs if it's empty or only contains our files
             remaining_files = set(anat_dir.iterdir()) - set(created_files)
             if not remaining_files:
                 created_dirs.append(anat_dir)
-    
+
     # Remove the files
     for file_path in created_files:
         if file_path.exists():
             file_path.unlink()
             print(f"Removed file: {file_path}")
-    
+
     # Remove the directories (only if they're empty)
     for dir_path in created_dirs:
         if dir_path.exists() and not any(dir_path.iterdir()):
             dir_path.rmdir()
             print(f"Removed directory: {dir_path}")
-    
-    print("Cleanup completed successfully")
 
+    print("Cleanup completed successfully")