157 bug bet deface masks are not saved

brainles_preprocessing/modality.py

@@ -139,7 +139,9 @@ def __init__(
         else:
             self.normalized_defaced_output_path = None
 
-        self.steps = {k: None for k in PreprocessorSteps}
+        self.steps: Dict[PreprocessorSteps, Path | None] = {
+            k: None for k in PreprocessorSteps
+        }
         self.steps[PreprocessorSteps.INPUT] = self.input_path
 
     @property
@@ -265,7 +267,7 @@ def register(
             moving_image_path=self.current,
             transformed_image_path=registered,
             matrix_path=registered_matrix,
-            log_file_path=registered_log,
+            log_file_path=str(registered_log),
         )
         self.current = registered
         self.steps[step] = registered
@@ -394,24 +396,24 @@ def transform(
             ), "Coregistration must be performed before applying atlas registration."
 
             registrator.transform(
-                fixed_image_path=fixed_image_path,
-                moving_image_path=self.steps[PreprocessorSteps.INPUT],
-                transformed_image_path=transformed,
+                fixed_image_path=str(fixed_image_path),
+                moving_image_path=str(self.steps[PreprocessorSteps.INPUT]),
+                transformed_image_path=str(transformed),
                 matrix_path=[
                     self.transformation_paths[
                         PreprocessorSteps.COREGISTERED
                     ],  # coregistration matrix
                     transformation_matrix_path,  # atlas registration matrix
                 ],
-                log_file_path=transformed_log,
+                log_file_path=str(transformed_log),
             )
         else:
             registrator.transform(
-                fixed_image_path=fixed_image_path,
-                moving_image_path=self.current,
-                transformed_image_path=transformed,
-                matrix_path=transformation_matrix_path,
-                log_file_path=transformed_log,
+                fixed_image_path=str(fixed_image_path),
+                moving_image_path=str(self.current),
+                transformed_image_path=str(transformed),
+                matrix_path=str(transformation_matrix_path),
+                log_file_path=str(transformed_log),
             )
 
         self.current = transformed
@@ -638,6 +640,12 @@ def extract_brain_region(
 
         if self.bet:
             self.current = bet
+
+        if self.bet_mask_output_path:
+            self.save_mask(
+                mask_path=mask_path,
+                output_path=self.bet_mask_output_path,
+            )
         return mask_path
 
     def deface(
@@ -684,7 +692,7 @@ def deface(
                     moving_image_path=self.steps[PreprocessorSteps.BET],
                     transformed_image_path=atlas_bet,
                     matrix_path=atlas_bet_M,
-                    log_file_path=defaced_dir_path / "atlas_bet.log",
+                    log_file_path=str(defaced_dir_path / "atlas_bet.log"),
                 )
 
                 deface_mask_atlas = defaced_dir_path / "deface_mask_atlas.nii.gz"
@@ -706,6 +714,12 @@ def deface(
                     mask_image_path=mask_path,
                 )
 
+            if self.defacing_mask_output_path:
+                self.save_mask(
+                    mask_path=mask_path,
+                    output_path=self.defacing_mask_output_path,
+                )
+
             return mask_path
         else:
             logger.warning(

brainles_preprocessing/normalization/normalizer_base.py

@@ -1,4 +1,5 @@
 from abc import ABC, abstractmethod
+from numpy.typing import NDArray
 
 
 class Normalizer(ABC):
@@ -10,7 +11,7 @@ def __init__(self):
         super().__init__()
 
     @abstractmethod
-    def normalize(self, image):
+    def normalize(self, image) -> NDArray:
         """
         Normalize the input image based on the chosen method.
 

brainles_preprocessing/normalization/percentile_normalizer.py

@@ -1,5 +1,6 @@
 import numpy as np
 from .normalizer_base import Normalizer
+from numpy.typing import NDArray
 
 
 class PercentileNormalizer(Normalizer):
@@ -29,7 +30,7 @@ def __init__(
         self.lower_limit = lower_limit
         self.upper_limit = upper_limit
 
-    def normalize(self, image: np.ndarray):
+    def normalize(self, image: np.ndarray) -> NDArray:
         """
         Normalize the input image using percentile-based mapping.
 

brainles_preprocessing/normalization/windowing_normalizer.py

@@ -1,5 +1,6 @@
 import numpy as np
 from .normalizer_base import Normalizer
+from numpy.typing import NDArray
 
 
 class WindowingNormalizer(Normalizer):
@@ -19,7 +20,7 @@ def __init__(self, center, width):
         self.center = center
         self.width = width
 
-    def normalize(self, image):
+    def normalize(self, image) -> NDArray:
         """
         Normalize the input image using windowing.
 

brainles_preprocessing/preprocessor/atlas_centric_preprocessor.py

@@ -323,29 +323,34 @@ def run_defacing(
         atlas_mask = self.center_modality.deface(
             defacer=self.defacer, defaced_dir_path=deface_dir
         )
-        # looping over _all_ modalities since .deface is no applying the computed mask
-        for moving_modality in self.all_modalities:
-            logger.info(f"Applying deface mask to {moving_modality.modality_name}...")
-            moving_modality.apply_deface_mask(
-                defacer=self.defacer,
-                mask_path=atlas_mask,
-                deface_dir=deface_dir,
-            )
-
-        self._save_output(
-            src=deface_dir,
-            save_dir=save_dir_defacing,
-        )
-        # now we save images that are skull-stripped
-        logger.info("Saving defaced images...")
-        for modality in self.all_modalities:
-            if modality.raw_defaced_output_path:
-                modality.save_current_image(
-                    modality.raw_defaced_output_path,
-                    normalization=False,
+        if atlas_mask is not None:
+            # looping over _all_ modalities since .deface is no applying the computed mask
+            for moving_modality in self.all_modalities:
+                logger.info(
+                    f"Applying deface mask to {moving_modality.modality_name}..."
                 )
-            if modality.normalized_defaced_output_path:
-                modality.save_current_image(
-                    modality.normalized_defaced_output_path,
-                    normalization=True,
+                moving_modality.apply_deface_mask(
+                    defacer=self.defacer,
+                    mask_path=atlas_mask,
+                    deface_dir=deface_dir,
                 )
+
+            self._save_output(
+                src=deface_dir,
+                save_dir=save_dir_defacing,
+            )
+            # now we save images that are skull-stripped
+            logger.info("Saving defaced images...")
+            for modality in self.all_modalities:
+                if modality.raw_defaced_output_path:
+                    modality.save_current_image(
+                        modality.raw_defaced_output_path,
+                        normalization=False,
+                    )
+                if modality.normalized_defaced_output_path:
+                    modality.save_current_image(
+                        modality.normalized_defaced_output_path,
+                        normalization=True,
+                    )
+        else:
+            logger.warning("Defacing was requested but no defacing mask was created.")

brainles_preprocessing/registration/registrator.py

@@ -36,7 +36,7 @@ def transform(
         transformed_image_path: Any,
         matrix_path: Any,
         log_file_path: str,
-        interpolator: str,
+        interpolator: str = "default",
         **kwargs
     ):
         """
@@ -61,7 +61,7 @@ def inverse_transform(
         transformed_image_path: Any,
         matrix_path: Any,
         log_file_path: str,
-        interpolator: str,
+        interpolator: str = "default",
     ):
         """
         Abstract method for inverse transforming images.

example/example_atlas_centric_preprocessor.py

@@ -45,6 +45,8 @@ def preprocess(input_dir: Path, output_dir: Path):
         raw_defaced_output_path=raw_deface_dir / f"t1c_defaced_raw.nii.gz",
         normalizer=percentile_normalizer,
         atlas_correction=True,
+        bet_mask_output_path=output_dir / f"bet_mask.nii.gz",
+        defacing_mask_output_path=output_dir / f"defacing_mask.nii.gz",
     )
     moving_modalities = [
         Modality(
@@ -92,6 +94,7 @@ def preprocess(input_dir: Path, output_dir: Path):
         save_dir_n4_bias_correction=output_dir / "n4_bias_correction",
         save_dir_brain_extraction=output_dir / "brain_extraction",
         save_dir_defacing=output_dir / "defacing",
+        save_dir_transformations=output_dir / "transformations",
     )
 
 

example/example_native_space_preprocessor.py

@@ -38,6 +38,8 @@ def preprocess(input_dir: Path, output_dir: Path):
         normalized_skull_output_path=norm_skull_dir / f"t1c_skull_normalized.nii.gz",
         raw_defaced_output_path=raw_deface_dir / f"t1c_defaced_raw.nii.gz",
         normalizer=percentile_normalizer,
+        bet_mask_output_path=output_dir / f"bet_mask.nii.gz",
+        defacing_mask_output_path=output_dir / f"defacing_mask.nii.gz",
     )
     moving_modalities = [
         Modality(