brainles-preprocessing 0.6.8__tar.gz → 0.6.10__tar.gz

{brainles_preprocessing-0.6.8 → brainles_preprocessing-0.6.10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: brainles_preprocessing
-Version: 0.6.8
+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-0.6.8 → brainles_preprocessing-0.6.10}/brainles_preprocessing/defacing/defacer.py

@@ -1,17 +1,26 @@
 from abc import ABC, abstractmethod
 from pathlib import Path
-from typing import Union
-
+from typing import Union, Optional
+import numpy as np
 from auxiliary.io import read_image, write_image
 
 
 class Defacer(ABC):
-    """
-    Base class for defacing medical images using brain masks.
+    def __init__(
+        self,
+        masking_value: Optional[Union[int, float]] = None,
+    ):
+        """
+        Base class for defacing medical images using brain masks.
 
-    Subclasses should implement the `deface` method to generate a defaced image
-    based on the provided input image and mask.
-    """
+        Subclasses should implement the `deface` method to generate a defaced image
+        based on the provided input image and mask.
+        """
+        # Here, masking value functions as a global value across all images and modalities
+        # If no value is passed, the minimum of a given input image is chosen
+        # TODO: Consider extending this to modality-specific masking values in the future, this should
+        # probably be implemented as a property of the the specific modality
+        self.masking_value = masking_value
 
     @abstractmethod
     def deface(
@@ -24,7 +33,7 @@ class Defacer(ABC):
 
         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).
+            mask_image_path (str or Path): Path to save the output mask image (NIfTI format).
         """
         pass
 
@@ -43,6 +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}"
@@ -63,8 +75,17 @@ class Defacer(ABC):
         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
+        # 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:
+            current_masking_value = (
+                np.array(self.masking_value).astype(input_data.dtype).item()
+            )
+        # Apply mask (element-wise either input or masking value)
+        masked_data = np.where(
+            mask_data.astype(bool), input_data, current_masking_value
+        )
 
         # Save the defaced image
         write_image(

{brainles_preprocessing-0.6.8 → 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-0.6.8 → brainles_preprocessing-0.6.10}/brainles_preprocessing/defacing/quickshear/quickshear.py

@@ -1,5 +1,5 @@
 from pathlib import Path
-from typing import Union
+from typing import Union, Optional
 
 import nibabel as nib
 from auxiliary.io import read_image, write_image
@@ -35,6 +35,7 @@ class QuickshearDefacer(Defacer):
         buffer: float = 10.0,
         force_atlas_registration: bool = True,
         atlas_image_path: Union[str, Path, Atlas] = Atlas.SRI24,
+        masking_value: Optional[Union[int, float]] = None,
     ):
         """Initialize Quickshear defacer
 
@@ -42,8 +43,9 @@ class QuickshearDefacer(Defacer):
             buffer (float, optional): buffer parameter from quickshear algorithm. Defaults to 10.0.
             force_atlas_registration (bool, optional): If True, forces atlas registration of the BET mask before defacing to potentially boost quickshear performance. Defaults to True.
             atlas_image_path (Union[str, Path, Atlas], optional): Path to the atlas image or an Atlas enum value that will be used for the optional atlas registrations. Defaults to Atlas.SRI24.
+            masking_value (Optional[Union[int, float]], optional): global value to be inserted in the masked areas. Default is None which leads to the minimum of each respective image.
         """
-        super().__init__()
+        super().__init__(masking_value=masking_value)
         self.buffer = buffer
         self.force_atlas_registration = force_atlas_registration
         self.atlas_image_path = atlas_image_path

{brainles_preprocessing-0.6.8 → 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-0.6.8 → brainles_preprocessing-0.6.10}/pyproject.toml

@@ -14,7 +14,7 @@ exclude = [
 ]
 
 name = "brainles_preprocessing"
-version = "0.6.8"                                                                                                              # 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"