Add clinical preprocessing utilities for CT and MRI modalities.

monai/tests/test_clinical_preprocessing.py

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+import pytest
+from monai.transforms import LoadImage, EnsureChannelFirst, ScaleIntensityRange, NormalizeIntensity
+from monai.transforms.clinical_preprocessing import (
+    get_ct_preprocessing_pipeline,
+    get_mri_preprocessing_pipeline,
+    preprocess_dicom_series,
+    UnsupportedModalityError,
+    ModalityTypeError,
+)
+
+
+def test_ct_preprocessing_pipeline():
+    """Test CT preprocessing pipeline returns expected transform composition."""
+    pipeline = get_ct_preprocessing_pipeline()
+    assert hasattr(pipeline, 'transforms')
+    assert len(pipeline.transforms) == 3
+    assert isinstance(pipeline.transforms[0], LoadImage)
+    assert isinstance(pipeline.transforms[1], EnsureChannelFirst)
+    assert isinstance(pipeline.transforms[2], ScaleIntensityRange)
+
+
+def test_mri_preprocessing_pipeline():
+    """Test MRI preprocessing pipeline returns expected transform composition."""
+    pipeline = get_mri_preprocessing_pipeline()
+    assert hasattr(pipeline, 'transforms')
+    assert len(pipeline.transforms) == 3
+    assert isinstance(pipeline.transforms[0], LoadImage)
+    assert isinstance(pipeline.transforms[1], EnsureChannelFirst)
+    assert isinstance(pipeline.transforms[2], NormalizeIntensity)
+
+
+def test_preprocess_dicom_series_invalid_modality():
+    """Test preprocess_dicom_series raises UnsupportedModalityError for unsupported modality."""
+    with pytest.raises(UnsupportedModalityError, match=r"Unsupported modality.*PET.*CT, MR, MRI"):
+        preprocess_dicom_series("dummy_path.dcm", "PET")
+
+
+def test_preprocess_dicom_series_invalid_type():
+    """Test preprocess_dicom_series raises ModalityTypeError for non-string modality."""
+    with pytest.raises(ModalityTypeError, match=r"modality must be a string, got int"):
+        preprocess_dicom_series("dummy_path.dcm", 123)

monai/transforms/clinical_preprocessing.py

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+"""Clinical DICOM preprocessing utilities for CT and MRI modalities."""
+
+from typing import Union
+from os import PathLike
+
+from monai.data import MetaTensor
+from monai.transforms import (
+    Compose,
+    LoadImage,
+    EnsureChannelFirst,
+    ScaleIntensityRange,
+    NormalizeIntensity,
+)
+
+SUPPORTED_MODALITIES = ("CT", "MR", "MRI")
+
+
+class UnsupportedModalityError(ValueError):
+    """Raised when an unsupported modality is provided."""
+    pass
+
+
+class ModalityTypeError(TypeError):
+    """Raised when modality is not a string."""
+    pass
+
+
+def get_ct_preprocessing_pipeline() -> Compose:
+    """Return a CT preprocessing pipeline."""
+    return Compose([
+        LoadImage(image_only=True),
+        EnsureChannelFirst(),
+        ScaleIntensityRange(a_min=-1000, a_max=400, b_min=0.0, b_max=1.0, clip=True),
+    ])
+
+
+def get_mri_preprocessing_pipeline() -> Compose:
+    """Return an MRI preprocessing pipeline."""
+    return Compose([
+        LoadImage(image_only=True),
+        EnsureChannelFirst(),
+        NormalizeIntensity(nonzero=True),
+    ])
+
+
+def preprocess_dicom_series(
+    dicom_path: Union[str, bytes, PathLike],
+    modality: str,
+) -> MetaTensor:
+    """Preprocess a DICOM series according to modality (CT or MRI).
+
+    Args:
+        dicom_path (Union[str, bytes, PathLike]): Path to DICOM series.
+        modality (str): Modality type, must be one of 'CT', 'MR', 'MRI'.
+
+    Returns:
+        MetaTensor: Preprocessed image tensor.
+
+    Raises:
+        ModalityTypeError: If modality is not a string.
+        UnsupportedModalityError: If modality is not supported.
+    """
+    if not isinstance(modality, str):
+        raise ModalityTypeError(f"modality must be a string, got {type(modality).__name__}")
+
+    modality = modality.strip().upper()
+
+    if modality == "CT":
+        transform = get_ct_preprocessing_pipeline()
+    elif modality in ("MR", "MRI"):
+        transform = get_mri_preprocessing_pipeline()
+    else:
+        raise UnsupportedModalityError(
+            f"Unsupported modality: {modality}. Supported values: {', '.join(SUPPORTED_MODALITIES)}"
+        )
+
+    return transform(dicom_path)