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fixing indents in defacer base class #173

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Merged
nicmuenster merged 3 commits into from
Jan 29, 2026
Merged

fixing indents in defacer base class #173

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f8d5a86
fix all
neuronflow Jan 28, 2026
f2956f6
mewp
neuronflow Jan 28, 2026
07e982b
Autoformat with black
brainless-bot[bot] Jan 28, 2026
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31 changes: 17 additions & 14 deletions brainles_preprocessing/defacing/defacer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,20 +22,20 @@ def __init__(
# 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,
Expand All @@ -52,6 +52,9 @@ def apply_mask(
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)
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Copilot AI Jan 28, 2026

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For consistency with the handling of input_image_path and mask_path, consider also converting defaced_image_path to a Path object at the beginning of the method. While not strictly necessary (since it's only used with str() on line 93), this would ensure uniform type handling for all path parameters.

Suggested change
mask_path = Path(mask_path)
mask_path = Path(mask_path)
defaced_image_path = Path(defaced_image_path)

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@neuronflow neuronflow Jan 28, 2026

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consistency with what?


if not input_image_path.is_file():
raise FileNotFoundError(
f"Input image file does not exist: {input_image_path}"
Expand All @@ -72,7 +75,7 @@ def apply_mask(
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:
Expand Down
2 changes: 0 additions & 2 deletions brainles_preprocessing/registration/__init__.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,5 @@
import warnings


try:
from .ANTs.ANTs import ANTsRegistrator
except ImportError:
Expand All @@ -11,7 +10,6 @@

from .niftyreg.niftyreg import NiftyRegRegistrator


try:
from .elastix.elastix import ElastixRegistrator
except ImportError:
Expand Down
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