Reformatted code using black to fix linting issues

brainles_preprocessing/brain_extraction/brain_extractor.py

@@ -1,5 +1,5 @@
 # TODO add typing and docs
-import shutil 
+import shutil
 from abc import ABC, abstractmethod
 from pathlib import Path
 from typing import Optional, Union
@@ -10,8 +10,9 @@
 
 
 class Mode(Enum):
-    FAST = 'fast'
-    ACCURATE = 'accurate'
+    FAST = "fast"
+    ACCURATE = "accurate"
+
 
 class BrainExtractor:
     @abstractmethod
@@ -51,7 +52,6 @@ def apply_mask(
             mask_path (str or Path): Path to the brain mask image (NIfTI format).
             bet_image_path (str or Path): Path to save the resulting masked image (NIfTI format).
         """
-
 
         try:
             # Read data
@@ -105,11 +105,11 @@ def extract(
             device (str or int): Device to use for computation (e.g., 0 for GPU 0, 'cpu' for CPU).
             do_tta (bool): whether to do test time data augmentation by mirroring along all axes.
         """
-        
+
         # Ensure mode is a Mode enum instance
         if isinstance(mode, str):
             try:
-                mode_enum =  Mode(mode.lower())
+                mode_enum = Mode(mode.lower())
             except ValueError:
                 raise ValueError(f"'{mode}' is not a valid Mode.")
         elif isinstance(mode, Mode):
@@ -132,7 +132,9 @@ def extract(
 
         # Construct the path to the generated mask
         masked_image_path = Path(masked_image_path)
-        hdbet_mask_path = masked_image_path.with_name(masked_image_path.name.replace('.nii.gz', '_mask.nii.gz'))
+        hdbet_mask_path = masked_image_path.with_name(
+            masked_image_path.name.replace(".nii.gz", "_mask.nii.gz")
+        )
 
         if hdbet_mask_path.resolve() != Path(brain_mask_path).resolve():
             try:
@@ -142,4 +144,3 @@ def extract(
                 )
             except Exception as e:
                 raise RuntimeError(f"Error copying mask file: {e}") from e
-

brainles_preprocessing/defacing/defacer.py

@@ -12,6 +12,7 @@ class Defacer(ABC):
     Subclasses should implement the `deface` method to generate a defaced image
     based on the provided input image and mask.
     """
+
     @abstractmethod
     def deface(
         self,
@@ -41,23 +42,27 @@ def apply_mask(
             mask_path (str or Path): Path to the brain mask image (NIfTI format).
             defaced_image_path (str or Path): Path to save the resulting defaced image (NIfTI format).
         """
-        
+
         if not input_image_path.is_file():
-            raise FileNotFoundError(f"Input image file does not exist: {input_image_path}")
+            raise FileNotFoundError(
+                f"Input image file does not exist: {input_image_path}"
+            )
         if not mask_path.is_file():
             raise FileNotFoundError(f"Mask file does not exist: {mask_path}")
-        
+
         try:
             # Read data
             input_data = read_nifti(str(input_image_path))
             mask_data = read_nifti(str(mask_path))
         except Exception as e:
-            raise RuntimeError(f"An error occurred while reading input files: {e}") from e
-
+            raise RuntimeError(
+                f"An error occurred while reading input files: {e}"
+            ) from e
+
         # Check that the input and mask have the same shape
         if input_data.shape != mask_data.shape:
             raise ValueError("Input image and mask must have the same dimensions.")
-        
+
         # Apply mask (element-wise multiplication)
         masked_data = input_data * mask_data
 

brainles_preprocessing/modality.py

@@ -58,12 +58,12 @@ def __init__(
         modality_name: str,
         input_path: Union[str, Path],
         normalizer: Optional[Normalizer] = None,
-        raw_bet_output_path: Optional[Union[str, Path]]  = None,
-        raw_skull_output_path: Optional[Union[str, Path]]  = None,
-        raw_defaced_output_path: Optional[Union[str, Path]]  = None,
-        normalized_bet_output_path: Optional[Union[str, Path]]  = None,
-        normalized_skull_output_path: Optional[Union[str, Path]]  = None,
-        normalized_defaced_output_path: Optional[Union[str, Path]]  = None,
+        raw_bet_output_path: Optional[Union[str, Path]] = None,
+        raw_skull_output_path: Optional[Union[str, Path]] = None,
+        raw_defaced_output_path: Optional[Union[str, Path]] = None,
+        normalized_bet_output_path: Optional[Union[str, Path]] = None,
+        normalized_skull_output_path: Optional[Union[str, Path]] = None,
+        normalized_defaced_output_path: Optional[Union[str, Path]] = None,
         atlas_correction: bool = True,
     ) -> None:
         # Basics
@@ -89,9 +89,15 @@ def __init__(
             )
 
         # handle input paths
-        self.raw_bet_output_path = Path(raw_bet_output_path) if raw_bet_output_path else None
-        self.raw_skull_output_path = Path(raw_skull_output_path) if raw_skull_output_path else None
-        self.raw_defaced_output_path = Path(raw_defaced_output_path) if raw_defaced_output_path else None
+        self.raw_bet_output_path = (
+            Path(raw_bet_output_path) if raw_bet_output_path else None
+        )
+        self.raw_skull_output_path = (
+            Path(raw_skull_output_path) if raw_skull_output_path else None
+        )
+        self.raw_defaced_output_path = (
+            Path(raw_defaced_output_path) if raw_defaced_output_path else None
+        )
 
         if normalized_bet_output_path:
             if normalizer is None:
@@ -163,15 +169,19 @@ def normalize(
             store_unnormalized.mkdir(parents=True, exist_ok=True)
             shutil.copyfile(
                 src=str(self.current),
-                dst=str(store_unnormalized / f"unnormalized__{self.modality_name}.nii.gz"),
+                dst=str(
+                    store_unnormalized / f"unnormalized__{self.modality_name}.nii.gz"
+                ),
             )
 
         if temporary_directory:
             unnormalized_dir = Path(temporary_directory) / "unnormalized"
             unnormalized_dir.mkdir(parents=True, exist_ok=True)
             shutil.copyfile(
                 src=str(self.current),
-                dst=str(unnormalized_dir / f"unnormalized__{self.modality_name}.nii.gz"),
+                dst=str(
+                    unnormalized_dir / f"unnormalized__{self.modality_name}.nii.gz"
+                ),
             )
 
         # Normalize the image
@@ -208,13 +218,13 @@ def register(
         """
         fixed_image_path = Path(fixed_image_path)
         registration_dir = Path(registration_dir)
-        
+
         registered = registration_dir / f"{moving_image_name}.nii.gz"
         registered_log = registration_dir / f"{moving_image_name}.log"
-        
+
         # Note, add file ending depending on registration backend!
         registered_matrix = registration_dir / f"{moving_image_name}"
-        
+
         registrator.register(
             fixed_image_path=fixed_image_path,
             moving_image_path=self.current,
@@ -277,9 +287,11 @@ def apply_deface_mask(
             deface_dir = Path(deface_dir)
             defaced_img = deface_dir / f"atlas__{self.modality_name}_defaced.nii.gz"
             input_img = self.steps[
-                PreprocessorSteps.ATLAS_CORRECTED
-                if self.atlas_correction
-                else PreprocessorSteps.ATLAS_REGISTERED
+                (
+                    PreprocessorSteps.ATLAS_CORRECTED
+                    if self.atlas_correction
+                    else PreprocessorSteps.ATLAS_REGISTERED
+                )
             ]
             defacer.apply_mask(
                 input_image_path=input_img,
@@ -381,7 +393,7 @@ def deface(
         """
 
         if isinstance(defacer, QuickshearDefacer):
-            
+
             defaced_dir_path = Path(defaced_dir_path)
             atlas_mask_path = (
                 defaced_dir_path / f"atlas__{self.modality_name}_deface_mask.nii.gz"
@@ -430,4 +442,4 @@ def save_current_image(
             shutil.copyfile(
                 src=str(self.current),
                 dst=str(output_path),
-            )
+            )

brainles_preprocessing/preprocessor.py

@@ -55,12 +55,14 @@ def __init__(
 
         self.center_modality = center_modality
         self.moving_modalities = moving_modalities
-        
+
         if atlas_image_path is None:
-            self.atlas_image_path = Path(__file__).parent / "registration" / "atlas" / "t1_brats_space.nii"
+            self.atlas_image_path = (
+                Path(__file__).parent / "registration" / "atlas" / "t1_brats_space.nii"
+            )
         else:
             self.atlas_image_path = Path(atlas_image_path)
-  
+
         self.registrator = registrator
         if self.registrator is None:
             logger.warning(
@@ -86,7 +88,7 @@ def __init__(
 
         self.atlas_dir = self.temp_folder / "atlas-space"
         self.atlas_dir.mkdir(exist_ok=True, parents=True)
-        
+
     def _configure_gpu(
         self, use_gpu: Optional[bool], limit_cuda_visible_devices: Optional[str] = None
     ) -> None:
@@ -249,7 +251,9 @@ def run(
         self._set_log_file(log_file=log_file)
         logger.info(f"{' Starting preprocessing ':=^80}")
         logger.info(f"Logs are saved to {self.log_file_handler.baseFilename}")
-        modality_names = ', '.join([modality.modality_name for modality in self.moving_modalities])
+        modality_names = ", ".join(
+            [modality.modality_name for modality in self.moving_modalities]
+        )
         logger.info(
             f"Received center modality: {self.center_modality.modality_name} "
             f"and moving modalities: {modality_names}"
@@ -298,17 +302,19 @@ def run(
         self.run_brain_extraction(
             save_dir_brain_extraction=save_dir_brain_extraction,
         )
-        
+
         # Defacing
         logger.info(f"{' Checking optional defacing ':-^80}")
         self.run_defacing(
             save_dir_defacing=save_dir_defacing,
         )
-        
+
         # End
         logger.info(f"{' Preprocessing complete ':=^80}")
 
-    def run_coregistration(self, save_dir_coregistration: Optional[Union[str, Path]] = None) -> None:
+    def run_coregistration(
+        self, save_dir_coregistration: Optional[Union[str, Path]] = None
+    ) -> None:
         """
         Coregister moving modalities to center modality.
 
@@ -336,8 +342,10 @@ def run_coregistration(self, save_dir_coregistration: Optional[Union[str, Path]]
 
         shutil.copyfile(
             src=str(self.center_modality.input_path),
-            dst=str(coregistration_dir / 
-                f"native__{self.center_modality.modality_name}.nii.gz"),
+            dst=str(
+                coregistration_dir
+                / f"native__{self.center_modality.modality_name}.nii.gz"
+            ),
         )
 
         self._save_output(
@@ -417,8 +425,11 @@ def run_atlas_correction(
                 )
 
         if self.center_modality.atlas_correction:
-            center_atlas_corrected_path = atlas_correction_dir / f"atlas_corrected__{self.center_modality.modality_name}.nii.gz"
-
+            center_atlas_corrected_path = (
+                atlas_correction_dir
+                / f"atlas_corrected__{self.center_modality.modality_name}.nii.gz"
+            )
+
             shutil.copyfile(
                 src=str(self.center_modality.current),
                 dst=str(center_atlas_corrected_path),
@@ -503,7 +514,9 @@ def run_brain_extraction(
                     normalization=True,
                 )
 
-    def run_defacing(self, save_dir_defacing: Optional[Union[str, Path]] = None) -> None:
+    def run_defacing(
+        self, save_dir_defacing: Optional[Union[str, Path]] = None
+    ) -> None:
         """Deface images to remove facial features using specified Defacer.
 
         Args:
@@ -563,7 +576,7 @@ def run_defacing(self, save_dir_defacing: Optional[Union[str, Path]] = None) ->
 
     def _save_output(
         self,
-        src:  Union[str, Path],
+        src: Union[str, Path],
         save_dir: Optional[Union[str, Path]],
     ):
         """

brainles_preprocessing/registration/ANTs/ANTs.py

@@ -60,11 +60,11 @@ def register(
             **kwargs: Additional registration parameters to update the instantiated defaults.
         """
         start_time = datetime.datetime.now()
-        
+
         # TODO - self.registration_params
         # We update the registration parameters with the provided kwargs
         registration_kwargs = {**self.registration_params, **kwargs}
-        
+
         # Convert all paths to Path objects
         fixed_image_path = Path(fixed_image_path)
         moving_image_path = Path(moving_image_path)
@@ -76,7 +76,7 @@ def register(
             raise FileNotFoundError(f"Fixed image not found: {fixed_image_path}")
         if not moving_image_path.is_file():
             raise FileNotFoundError(f"Moving image not found: {moving_image_path}")
-        
+
         # Ensure matrix_path has .mat suffix
         if matrix_path.suffix != ".mat":
             matrix_path = matrix_path.with_suffix(".mat")
@@ -89,17 +89,17 @@ def register(
             **registration_kwargs,
         )
         transformed_image = registration_result["warpedmovout"]
-        
+
         # Ensure output directories exist
         transformed_image_path.parent.mkdir(parents=True, exist_ok=True)
         matrix_path.parent.mkdir(parents=True, exist_ok=True)
-        
+
         ants.image_write(transformed_image, str(transformed_image_path))
 
         shutil.copyfile(
-                src=registration_result["fwdtransforms"][0],
-                dst=str(matrix_path),
-            )
+            src=registration_result["fwdtransforms"][0],
+            dst=str(matrix_path),
+        )
 
         end_time = datetime.datetime.now()
 
@@ -142,7 +142,7 @@ def transform(
         # TODO - self.transformation_params
         # we update the transformation parameters with the provided kwargs
         transform_kwargs = {**self.transformation_params, **kwargs}
-        
+
         # Convert all paths to Path objects
         fixed_image_path = Path(fixed_image_path)
         moving_image_path = Path(moving_image_path)
@@ -155,10 +155,9 @@ def transform(
         if not moving_image_path.is_file():
             raise FileNotFoundError(f"Moving image not found: {moving_image_path}")
 
-
         fixed_image = ants.image_read(str(fixed_image_path))
         moving_image = ants.image_read(str(moving_image_path))
-        
+
         # Ensure output directory exist
         transformed_image_path.parent.mkdir(parents=True, exist_ok=True)