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Change to use new AtlasCentricPreprocessor #160

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Merged
merged 4 commits into from
Sep 4, 2025
Merged

Change to use new AtlasCentricPreprocessor #160

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d5508de
Change to use new AtlasCentricPreprocessor
MarcelRosier Sep 4, 2025
9c08579
Merge branch 'main' into 156-feature-cli-uses-outdated-preprocessor
MarcelRosier Sep 4, 2025
756f4de
Fix eval security issue
MarcelRosier Sep 4, 2025
52d6fda
Merge branch '156-feature-cli-uses-outdated-preprocessor' of github.c…
MarcelRosier Sep 4, 2025
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25 changes: 14 additions & 11 deletions brainles_preprocessing/cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@
from brainles_preprocessing.normalization.percentile_normalizer import (
PercentileNormalizer,
)
from brainles_preprocessing.preprocessor import Preprocessor
from brainles_preprocessing.preprocessor import AtlasCentricPreprocessor


def version_callback(value: bool):
Expand Down Expand Up @@ -59,7 +59,7 @@ def main(
),
],
output_dir: Annotated[
str,
str | Path,
typer.Option(
"-o",
"--output_dir",
Expand Down Expand Up @@ -117,11 +117,14 @@ def main(
defacing_mask_output_path=output_dir / "t1c_defacing_mask.nii.gz",
)

for modality in ["t1", "t2", "fla"]:
moving_modalities = [
moving_modalities = []
for input_path, modality in zip(
[input_t1, input_t2, input_fla], ["t1", "t2", "fla"]
):
moving_modalities.append(
Modality(
modality_name=modality,
input_path=eval(f"input_{modality}"),
input_path=input_path,
normalizer=percentile_normalizer,
# specify the output paths for the raw and normalized images of each step - here only for atlas registered and brain extraction
raw_skull_output_path=output_dir / f"{modality}_skull_raw.nii.gz",
Expand All @@ -134,18 +137,18 @@ def main(
normalized_defaced_output_path=output_dir
/ f"{modality}_defaced_normalized.nii.gz",
)
]
)

# if the input atlas is the SRI24 BraTS atlas, set it to None, because it will be picked up through the package
if input_atlas == "SRI24 BraTS atlas":
input_atlas = None
optional_kwargs = {}
if input_atlas is not None:
optional_kwargs["atlas_image_path"] = input_atlas

# instantiate and run the preprocessor using defaults for registration/ brain extraction/ defacing backends
preprocessor = Preprocessor(
preprocessor = AtlasCentricPreprocessor(
center_modality=center,
moving_modalities=moving_modalities,
temp_folder=output_dir / "temp",
input_atlas=input_atlas,
**optional_kwargs,
)

preprocessor.run()
Expand Down