brainles-preprocessing 0.6.9__tar.gz → 0.6.10__tar.gz

{brainles_preprocessing-0.6.9 → brainles_preprocessing-0.6.10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: brainles_preprocessing
-Version: 0.6.9
+Version: 0.6.10
 Summary: Tool for preprocessing tasks in biomedical imaging, with a focus on (but not limited to) multi-modal brain MRI
 License: Apache-2.0
 License-File: LICENSE

{brainles_preprocessing-0.6.9 → brainles_preprocessing-0.6.10}/brainles_preprocessing/defacing/defacer.py

@@ -22,20 +22,20 @@ class Defacer(ABC):
         # probably be implemented as a property of the the specific modality
         self.masking_value = masking_value
 
-        @abstractmethod
-        def deface(
-            self,
-            input_image_path: Union[str, Path],
-            mask_image_path: Union[str, Path],
-        ) -> None:
-            """
-            Generate a defacing mask provided an input image.
+    @abstractmethod
+    def deface(
+        self,
+        input_image_path: Union[str, Path],
+        mask_image_path: Union[str, Path],
+    ) -> None:
+        """
+        Generate a defacing mask provided an input image.
 
-            Args:
-                input_image_path (str or Path): Path to the input image (NIfTI format).
-                mask_image_path (str or Path): Path to the output mask image (NIfTI format).
-            """
-            pass
+        Args:
+            input_image_path (str or Path): Path to the input image (NIfTI format).
+            mask_image_path (str or Path): Path to save the output mask image (NIfTI format).
+        """
+        pass
 
     def apply_mask(
         self,
@@ -52,6 +52,9 @@ class Defacer(ABC):
             defaced_image_path (str or Path): Path to save the resulting defaced image (NIfTI format).
         """
 
+        input_image_path = Path(input_image_path)
+        mask_path = Path(mask_path)
+
         if not input_image_path.is_file():
             raise FileNotFoundError(
                 f"Input image file does not exist: {input_image_path}"
@@ -72,7 +75,7 @@ class Defacer(ABC):
         if input_data.shape != mask_data.shape:
             raise ValueError("Input image and mask must have the same dimensions.")
 
-        # check whether a global masking value was passed, otherwise choose minimum
+        # Check whether a global masking value was passed, otherwise choose minimum
         if self.masking_value is None:
             current_masking_value = np.min(input_data)
         else:

{brainles_preprocessing-0.6.9 → brainles_preprocessing-0.6.10}/brainles_preprocessing/defacing/quickshear/nipy_quickshear.py

@@ -11,6 +11,7 @@ import sys
 import nibabel as nb
 import numpy as np
 from numpy.typing import NDArray
+from scipy.ndimage import convolve
 
 try:
     from duecredit import BibTeX, due
@@ -83,14 +84,9 @@ def edge_mask(mask):
     brain = mask.any(axis=0)
 
     # Simple edge detection
-    edgemask = (
-        4 * brain
-        - np.roll(brain, 1, 0)
-        - np.roll(brain, -1, 0)
-        - np.roll(brain, 1, 1)
-        - np.roll(brain, -1, 1)
-        != 0
-    )
+    kernel = np.array([[0, -1, 0], [-1, 4, -1], [0, -1, 0]])
+    edgemask = convolve(brain, kernel, mode="constant", cval=0.0) != 0
+
     return edgemask.astype("uint8")
 
 

{brainles_preprocessing-0.6.9 → brainles_preprocessing-0.6.10}/brainles_preprocessing/registration/__init__.py

@@ -1,6 +1,5 @@
 import warnings
 
-
 try:
     from .ANTs.ANTs import ANTsRegistrator
 except ImportError:
@@ -11,7 +10,6 @@ except ImportError:
 
 from .niftyreg.niftyreg import NiftyRegRegistrator
 
-
 try:
     from .elastix.elastix import ElastixRegistrator
 except ImportError:

{brainles_preprocessing-0.6.9 → brainles_preprocessing-0.6.10}/pyproject.toml

@@ -14,7 +14,7 @@ exclude = [
 ]
 
 name = "brainles_preprocessing"
-version = "0.6.9"                                                                                                              # will be overwritten by poetry-dynamic-versioning but needs to be set
+version = "0.6.10"                                                                                                              # will be overwritten by poetry-dynamic-versioning but needs to be set
 description = "Tool for preprocessing tasks in biomedical imaging, with a focus on (but not limited to) multi-modal brain MRI"
 license = "Apache-2.0"