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28 changes: 28 additions & 0 deletions src/imgtools/transforms/intensity_transforms.py
Original file line number Diff line number Diff line change
@@ -1,12 +1,14 @@
from dataclasses import dataclass

from SimpleITK import Image
from SimpleITK import N4BiasFieldCorrectionImageFilter

from .base_transform import BaseTransform
from .functional import (
clip_intensity,
window_intensity,
)
from .lambda_transforms import SimpleITKFilter

__all__ = [
"IntensityTransform",
Expand Down Expand Up @@ -150,3 +152,29 @@ def __call__(self, image: Image) -> Image:
"""

return window_intensity(image, self.window, self.level)

@dataclass
class N4BiasFieldCorrection(IntensityTransform):
"""
N4 bias-field correction.
- Corrects smooth intensity inhomogeneity (bias field) in the image.
- Does NOT change image geometry (no rotation, translation, or scaling).
"""

def __post_init__(self) -> None:
self.filter = SimpleITKFilter(N4BiasFieldCorrectionImageFilter())

def __call__(self, image: Image) -> Image:
"""Apply N4 bias-field intensity correction to an image.

Parameters
----------
image : Image
The input intensity image (e.g., MRI).
Returns
-------
Image
Image with corrected intensities and unchanged geometry.
"""
return self.filter(image)

6 changes: 6 additions & 0 deletions src/imgtools/transforms/transformer.py
Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,7 @@
IntensityTransform,
SpatialTransform,
)
from imgtools.transforms.intensity_transforms import N4BiasFieldCorrection

# Define TypeVars for the different image types
T_MedImage = TypeVar("T_MedImage", bound=MedImage)
Expand Down Expand Up @@ -68,6 +69,11 @@ def _apply_transforms(
and transform.supports_reference()
):
transformed_image = transform(transformed_image, ref)
elif (
isinstance(transform, N4BiasFieldCorrection)
and transformed_image.metadata.get("Modality", "Unknown") == "MR"
):
transformed_image = transform(transformed_image)
elif isinstance(
transform, (IntensityTransform, SpatialTransform)
):
Expand Down
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